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Sample records for chemical shift selective

  1. Chemical shift selective magnetic resonance imaging of the optic nerve in patients with acute optic neuritis

    DEFF Research Database (Denmark)

    Larsson, H B; Thomsen, C; Frederiksen, J;

    1988-01-01

    Optic neuritis is often the first manifestation of multiple sclerosis (MS). Sixteen patients with acute optic neuritis and one patient with benign intracranial hypertension (BIH) were investigated by magnetic resonance imaging, using a chemical shift selective double spin echo sequence. In 3...... were only shown in 3/16 (19%) of the patients with optic neuritis. Nevertheless, the presented chemical shift selective double spin echo sequence may be of great value for detection of retrobulbar lesions....

  2. Chemical shift selective magnetic resonance imaging of the optic nerve in patients with acute optic neuritis

    Energy Technology Data Exchange (ETDEWEB)

    Larsson, H.B.W.; Thomsen, C.; Frederiksen, J.; Henriksen, O.; Olesen, J.

    Optic neuritis is often the first manifestion of multiple sclerosis (MS). Sixteen patients with acute optic neuritis and one patient with benign intracranial hypertension (BIH) were investigated by magnetic resonance imaging, using a chemical shift selective double spin echo sequence. In 3 of the 16 patients, abnormalities were seen. In one patient with bilateral symptoms, signal hyperintensity and swelling of the right side of the chiasm were found. In another patient the optic nerve was found diffusely enlarged with only a marginally increased signal in the second echo. In the third patient an area of signal hyperintensity and swelling was seen in the left optic nerve. In the patient with BIH the subarachnoid space which surrounds the optic nerves was enlarged. Even using this refined pulse sequence, avoiding the major artefact in imaging the optic nerve, the chemical shift artefact, lesions were only shown in 3/16 (19%) of the patients with optic neuritis. Nevertheless, the presented chemical shift selective double spin echo sequence may be of great value for detection of retrobulbar lesions.

  3. Protein Chemical Shift Prediction

    CERN Document Server

    Larsen, Anders S

    2014-01-01

    The protein chemical shifts holds a large amount of information about the 3-dimensional structure of the protein. A number of chemical shift predictors based on the relationship between structures resolved with X-ray crystallography and the corresponding experimental chemical shifts have been developed. These empirical predictors are very accurate on X-ray structures but tends to be insensitive to small structural changes. To overcome this limitation it has been suggested to make chemical shift predictors based on quantum mechanical(QM) calculations. In this thesis the development of the QM derived chemical shift predictor Procs14 is presented. Procs14 is based on 2.35 million density functional theory(DFT) calculations on tripeptides and contains corrections for hydrogen bonding, ring current and the effect of the previous and following residue. Procs14 is capable at performing predictions for the 13CA, 13CB, 13CO, 15NH, 1HN and 1HA backbone atoms. In order to benchmark Procs14, a number of QM NMR calculatio...

  4. Conformationally selective multidimensional chemical shift ranges in proteins from a PACSY database purged using intrinsic quality criteria

    OpenAIRE

    2015-01-01

    We have determined refined multidimensional chemical shift ranges for intra-residue correlations ([superscript 13]C–[superscript 13]C, [superscript 15]N–[superscript 13]C, etc.) in proteins, which can be used to gain type-assignment and/or secondary-structure information from experimental NMR spectra. The chemical-shift ranges are the result of a statistical analysis of the PACSY database of >3000 proteins with 3D structures (1,200,207 [superscript 13]C chemical shifts and >3 million chemical...

  5. Conformationally selective multidimensional chemical shift ranges in proteins from a PACSY database purged using intrinsic quality criteria

    Energy Technology Data Exchange (ETDEWEB)

    Fritzsching, Keith J., E-mail: kfritzsc@brandeis.edu [Brandeis University, Department of Chemistry (United States); Hong, Mei [Massachusetts Institute of Technology, Department of Chemistry (United States); Schmidt-Rohr, Klaus, E-mail: srohr@brandeis.edu [Brandeis University, Department of Chemistry (United States)

    2016-02-15

    We have determined refined multidimensional chemical shift ranges for intra-residue correlations ({sup 13}C–{sup 13}C, {sup 15}N–{sup 13}C, etc.) in proteins, which can be used to gain type-assignment and/or secondary-structure information from experimental NMR spectra. The chemical-shift ranges are the result of a statistical analysis of the PACSY database of >3000 proteins with 3D structures (1,200,207 {sup 13}C chemical shifts and >3 million chemical shifts in total); these data were originally derived from the Biological Magnetic Resonance Data Bank. Using relatively simple non-parametric statistics to find peak maxima in the distributions of helix, sheet, coil and turn chemical shifts, and without the use of limited “hand-picked” data sets, we show that ∼94 % of the {sup 13}C NMR data and almost all {sup 15}N data are quite accurately referenced and assigned, with smaller standard deviations (0.2 and 0.8 ppm, respectively) than recognized previously. On the other hand, approximately 6 % of the {sup 13}C chemical shift data in the PACSY database are shown to be clearly misreferenced, mostly by ca. −2.4 ppm. The removal of the misreferenced data and other outliers by this purging by intrinsic quality criteria (PIQC) allows for reliable identification of secondary maxima in the two-dimensional chemical-shift distributions already pre-separated by secondary structure. We demonstrate that some of these correspond to specific regions in the Ramachandran plot, including left-handed helix dihedral angles, reflect unusual hydrogen bonding, or are due to the influence of a following proline residue. With appropriate smoothing, significantly more tightly defined chemical shift ranges are obtained for each amino acid type in the different secondary structures. These chemical shift ranges, which may be defined at any statistical threshold, can be used for amino-acid type assignment and secondary-structure analysis of chemical shifts from intra

  6. Conformationally selective multidimensional chemical shift ranges in proteins from a PACSY database purged using intrinsic quality criteria.

    Science.gov (United States)

    Fritzsching, Keith J; Hong, Mei; Schmidt-Rohr, Klaus

    2016-02-01

    We have determined refined multidimensional chemical shift ranges for intra-residue correlations ((13)C-(13)C, (15)N-(13)C, etc.) in proteins, which can be used to gain type-assignment and/or secondary-structure information from experimental NMR spectra. The chemical-shift ranges are the result of a statistical analysis of the PACSY database of >3000 proteins with 3D structures (1,200,207 (13)C chemical shifts and >3 million chemical shifts in total); these data were originally derived from the Biological Magnetic Resonance Data Bank. Using relatively simple non-parametric statistics to find peak maxima in the distributions of helix, sheet, coil and turn chemical shifts, and without the use of limited "hand-picked" data sets, we show that ~94% of the (13)C NMR data and almost all (15)N data are quite accurately referenced and assigned, with smaller standard deviations (0.2 and 0.8 ppm, respectively) than recognized previously. On the other hand, approximately 6% of the (13)C chemical shift data in the PACSY database are shown to be clearly misreferenced, mostly by ca. -2.4 ppm. The removal of the misreferenced data and other outliers by this purging by intrinsic quality criteria (PIQC) allows for reliable identification of secondary maxima in the two-dimensional chemical-shift distributions already pre-separated by secondary structure. We demonstrate that some of these correspond to specific regions in the Ramachandran plot, including left-handed helix dihedral angles, reflect unusual hydrogen bonding, or are due to the influence of a following proline residue. With appropriate smoothing, significantly more tightly defined chemical shift ranges are obtained for each amino acid type in the different secondary structures. These chemical shift ranges, which may be defined at any statistical threshold, can be used for amino-acid type assignment and secondary-structure analysis of chemical shifts from intra-residue cross peaks by inspection or by using a provided

  7. Improved chemical shift based fragment selection for CS-Rosetta using Rosetta3 fragment picker

    Energy Technology Data Exchange (ETDEWEB)

    Vernon, Robert [Hospital for Sick Children, Program in Molecular Structure and Function (Canada); Shen, Yang [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States); Baker, David [University of Washington, Department of Biochemistry (United States); Lange, Oliver F., E-mail: oliver.lange@tum.de [Technische Universitaet Muenchen, Department Chemie, Biomolecular NMR and Munich Center for Integrated Protein Science (Germany)

    2013-10-15

    A new fragment picker has been developed for CS-Rosetta that combines beneficial features of the original fragment picker, MFR, used with CS-Rosetta, and the fragment picker, NNMake, that was used for purely sequence based fragment selection in the context of ROSETTA de-novo structure prediction. Additionally, the new fragment picker has reduced sensitivity to outliers and other difficult to match data points rendering the protocol more robust and less likely to introduce bias towards wrong conformations in cases where data is bad, missing or inconclusive. The fragment picker protocol gives significant improvements on 6 of 23 CS-Rosetta targets. An independent benchmark on 39 protein targets, whose NMR data sets were published only after protocol optimization had been finished, also show significantly improved performance for the new fragment picker (van der Schot et al. in J Biomol NMR, 2013)

  8. Evaluation of a rabbit model for osteomyelitis by high field, high resolution imaging using the chemical-shift-specific-slice-selection technique.

    Science.gov (United States)

    Volk, A; Crémieux, A C; Belmatoug, N; Vallois, J M; Pocidalo, J J; Carbon, C

    1994-01-01

    The rabbit model of osteomyelitis introduced by C.W. Norden, based on injection of an infecting solution (Staphylococcus aureus, sodium morrhuate) into the tibia, was studied at 4.7 Tesla with a time-efficient chemical shift selective imaging technique, Chemical Shift Specific Slice Selection (C4S). The evolution of the disease over several weeks was followed on water-selective, fat-selective, and sum images obtained simultaneously with this imaging sequence. Experiments were performed either on different groups of rabbits at different times after infection with subsequent sacrifice of the animal and microbiological analysis of the infected tibia or on the same group of animals imaged several times after infection. Associated analysis of the water and fat selective images revealed marrow modifications very early (Day 5 after inoculation) demonstrating the high sensitivity of the employed imaging technique. Later on, bone modifications were best identified on the sum images. Additional experiments performed on animals injected with a noninfecting solution containing only sodium morrhuate showed however that the sclerosing agent alone can yield images similar to those produced by infection at early stages after inoculation. Therefore, the Norden model would not be suitable for monitoring quantitatively outcome of therapy by magnetic resonance imaging. It is however well adapted for the evaluation and optimization of MRI techniques or protocols intended to detect early changes of bone marrow produced by septic or aseptic infarct.

  9. Free variable selection QSPR study to predict (19)F chemical shifts of some fluorinated organic compounds using Random Forest and RBF-PLS methods.

    Science.gov (United States)

    Goudarzi, Nasser

    2016-04-05

    In this work, two new and powerful chemometrics methods are applied for the modeling and prediction of the (19)F chemical shift values of some fluorinated organic compounds. The radial basis function-partial least square (RBF-PLS) and random forest (RF) are employed to construct the models to predict the (19)F chemical shifts. In this study, we didn't used from any variable selection method and RF method can be used as variable selection and modeling technique. Effects of the important parameters affecting the ability of the RF prediction power such as the number of trees (nt) and the number of randomly selected variables to split each node (m) were investigated. The root-mean-square errors of prediction (RMSEP) for the training set and the prediction set for the RBF-PLS and RF models were 44.70, 23.86, 29.77, and 23.69, respectively. Also, the correlation coefficients of the prediction set for the RBF-PLS and RF models were 0.8684 and 0.9313, respectively. The results obtained reveal that the RF model can be used as a powerful chemometrics tool for the quantitative structure-property relationship (QSPR) studies.

  10. Empirical isotropic chemical shift surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Czinki, Eszter; Csaszar, Attila G. [Eoetvoes University, Laboratory of Molecular Spectroscopy, Institute of Chemistry (Hungary)], E-mail: csaszar@chem.elte.hu

    2007-08-15

    A list of proteins is given for which spatial structures, with a resolution better than 2.5 A, are known from entries in the Protein Data Bank (PDB) and isotropic chemical shift (ICS) values are known from the RefDB database related to the Biological Magnetic Resonance Bank (BMRB) database. The structures chosen provide, with unknown uncertainties, dihedral angles {phi} and {psi} characterizing the backbone structure of the residues. The joint use of experimental ICSs of the same residues within the proteins, again with mostly unknown uncertainties, and ab initio ICS({phi},{psi}) surfaces obtained for the model peptides For-(l-Ala){sub n}-NH{sub 2}, with n = 1, 3, and 5, resulted in so-called empirical ICS({phi},{psi}) surfaces for all major nuclei of the 20 naturally occurring {alpha}-amino acids. Out of the many empirical surfaces determined, it is the 13C{sup {alpha}} ICS({phi},{psi}) surface which seems to be most promising for identifying major secondary structure types, {alpha}-helix, {beta}-strand, left-handed helix ({alpha}{sub D}), and polyproline-II. Detailed tests suggest that Ala is a good model for many naturally occurring {alpha}-amino acids. Two-dimensional empirical 13C{sup {alpha}}-{sup 1}H{sup {alpha}} ICS({phi},{psi}) correlation plots, obtained so far only from computations on small peptide models, suggest the utility of the experimental information contained therein and thus they should provide useful constraints for structure determinations of proteins.

  11. Protein Structure Determination Using Chemical Shifts

    DEFF Research Database (Denmark)

    Christensen, Anders Steen

    In this thesis, a protein structure determination using chemical shifts is presented. The method is implemented in the open source PHAISTOS protein simulation framework. The method combines sampling from a generative model with a coarse-grained force field and an energy function that includes...... chemical shifts. The method is benchmarked on folding simulations of five small proteins. In four cases the resulting structures are in excellent agreement with experimental data, the fifth case fail likely due to inaccuracies in the energy function. For the Chymotrypsin Inhibitor protein, a structure...... is determined using only chemical shifts recorded and assigned through automated processes. The CARMSD to the experimental X-ray for this structure is 1.1. Å. Additionally, the method is combined with very sparse NOE-restraints and evolutionary distance restraints and tested on several protein structures >100...

  12. Chemical shift prediction for denatured proteins

    Energy Technology Data Exchange (ETDEWEB)

    Prestegard, James H., E-mail: jpresteg@ccrc.uga.edu; Sahu, Sarata C.; Nkari, Wendy K.; Morris, Laura C.; Live, David; Gruta, Christian

    2013-02-15

    While chemical shift prediction has played an important role in aspects of protein NMR that include identification of secondary structure, generation of torsion angle constraints for structure determination, and assignment of resonances in spectra of intrinsically disordered proteins, interest has arisen more recently in using it in alternate assignment strategies for crosspeaks in {sup 1}H-{sup 15}N HSQC spectra of sparsely labeled proteins. One such approach involves correlation of crosspeaks in the spectrum of the native protein with those observed in the spectrum of the denatured protein, followed by assignment of the peaks in the latter spectrum. As in the case of disordered proteins, predicted chemical shifts can aid in these assignments. Some previously developed empirical formulas for chemical shift prediction have depended on basis data sets of 20 pentapeptides. In each case the central residue was varied among the 20 amino common acids, with the flanking residues held constant throughout the given series. However, previous choices of solvent conditions and flanking residues make the parameters in these formulas less than ideal for general application to denatured proteins. Here, we report {sup 1}H and {sup 15}N shifts for a set of alanine based pentapeptides under the low pH urea denaturing conditions that are more appropriate for sparse label assignments. New parameters have been derived and a Perl script was created to facilitate comparison with other parameter sets. A small, but significant, improvement in shift predictions for denatured ubiquitin is demonstrated.

  13. Accessible surface area from NMR chemical shifts

    Energy Technology Data Exchange (ETDEWEB)

    Hafsa, Noor E.; Arndt, David; Wishart, David S., E-mail: david.wishart@ualberta.ca [University of Alberta, Department of Computing Science (Canada)

    2015-07-15

    Accessible surface area (ASA) is the surface area of an atom, amino acid or biomolecule that is exposed to solvent. The calculation of a molecule’s ASA requires three-dimensional coordinate data and the use of a “rolling ball” algorithm to both define and calculate the ASA. For polymers such as proteins, the ASA for individual amino acids is closely related to the hydrophobicity of the amino acid as well as its local secondary and tertiary structure. For proteins, ASA is a structural descriptor that can often be as informative as secondary structure. Consequently there has been considerable effort over the past two decades to try to predict ASA from protein sequence data and to use ASA information (derived from chemical modification studies) as a structure constraint. Recently it has become evident that protein chemical shifts are also sensitive to ASA. Given the potential utility of ASA estimates as structural constraints for NMR we decided to explore this relationship further. Using machine learning techniques (specifically a boosted tree regression model) we developed an algorithm called “ShiftASA” that combines chemical-shift and sequence derived features to accurately estimate per-residue fractional ASA values of water-soluble proteins. This method showed a correlation coefficient between predicted and experimental values of 0.79 when evaluated on a set of 65 independent test proteins, which was an 8.2 % improvement over the next best performing (sequence-only) method. On a separate test set of 92 proteins, ShiftASA reported a mean correlation coefficient of 0.82, which was 12.3 % better than the next best performing method. ShiftASA is available as a web server ( http://shiftasa.wishartlab.com http://shiftasa.wishartlab.com ) for submitting input queries for fractional ASA calculation.

  14. Random coil chemical shift for intrinsically disordered proteins

    DEFF Research Database (Denmark)

    Kjærgaard, Magnus; Brander, Søren; Poulsen, Flemming Martin

    2011-01-01

    . Temperature has a non-negligible effect on the (13)C random coil chemical shifts, so temperature coefficients are reported for the random coil chemical shifts to allow extrapolation to other temperatures. The pH dependence of the histidine random coil chemical shifts is investigated in a titration series......, which allows the accurate random coil chemical shifts to be obtained at any pH. By correcting the random coil chemical shifts for the effects of temperature and pH, systematic biases of the secondary chemical shifts are minimized, which will improve the reliability of detection of transient secondary...

  15. Bayesian inference of protein structure from chemical shift data

    DEFF Research Database (Denmark)

    Bratholm, Lars Andersen; Christensen, Anders Steen; Hamelryck, Thomas Wim;

    2015-01-01

    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...... 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......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...

  16. 外物干扰平衡移动中的自变量选择%Selection of Variable in Chemical Equilibrium Shift during Exterior Perturbation

    Institute of Scientific and Technical Information of China (English)

    张索林; 郑河; 张光宁

    2014-01-01

    It explained carefully the reasons and ways of selection of variable from reactant concentration (i) to reactant quantity ni (or inert gas). The deduced formulae are clear, regular and practical for use and understanding.%详细阐述了议题中选择ni(或惰)为自变量之后,各微积分表达式更简洁、整齐和实用,且不影响所用浓度(i)的内涵特点。

  17. Is the Lamb shift chemically significant?

    Science.gov (United States)

    Dyall, Kenneth G.; Bauschlicher, Charles W., Jr.; Schwenke, David W.; Pyykko, Pekka; Arnold, James (Technical Monitor)

    2001-01-01

    The contribution of the Lamb shift to the atomization energies of some prototype molecules, BF3, AlF3, and GaF3, is estimated by a perturbation procedure. It is found to be in the range of 3-5% of the one-electron scalar relativistic contribution to the atomization energy. The maximum absolute value is 0.2 kcal/mol for GaF3. These sample calculations indicate that the Lamb shift is probably small enough to be neglected for energetics of molecules containing light atoms if the target accuracy is 1 kcal/mol, but for higher accuracy calculations and for molecules containing heavy elements it must be considered.

  18. Improved chemical shift prediction by Rosetta conformational sampling

    Energy Technology Data Exchange (ETDEWEB)

    Tian Ye [Sanford Burnham Medical Research Institute (United States); Opella, Stanley J. [University of California San Diego, Department of Chemistry and Biochemistry (United States); Marassi, Francesca M., E-mail: fmarassi@sbmri.org [Sanford Burnham Medical Research Institute (United States)

    2012-11-15

    Chemical shift frequencies represent a time-average of all the conformational states populated by a protein. Thus, chemical shift prediction programs based on sequence and database analysis yield higher accuracy for rigid rather than flexible protein segments. Here we show that the prediction accuracy can be significantly improved by averaging over an ensemble of structures, predicted solely from amino acid sequence with the Rosetta program. This approach to chemical shift and structure prediction has the potential to be useful for guiding resonance assignments, especially in solid-state NMR structural studies of membrane proteins in proteoliposomes.

  19. Calculations of proton chemical shifts in olefins and aromatics

    CERN Document Server

    Escrihuela, M C

    2000-01-01

    induced reagents on alpha,beta unsaturated ketones has also been investigated in order to deduce molecular structures and to obtain the assignment of the spectra of these molecules. A semi-empirical calculation of the partial atomic charges in organic compounds based on molecular dipole moments (CHARGE3) was developed into a model capable of predicting proton chemical shifts in a wide variety of organic compounds to a reasonable degree of accuracy. The model has been modified to include condensed aromatic hydrocarbons and substituted benzenes, alkenes, halo-monosubstituted benzenes and halo-alkenes. Within the aromatic compounds the influence of the pi electron densities and the ring current have been investigated, along with the alpha, beta and gamma effects. The model gives the first accurate calculation of the proton chemical shifts of condensed aromatic compounds and the proton substituent chemical shifts (SCS) in the benzene ring. For the data set of 55 proton chemical shifts spanning 3 ppm the rms error...

  20. Bayesian inference of protein structure from chemical shift data

    DEFF Research Database (Denmark)

    Bratholm, Lars Andersen; Christensen, Anders Steen; Hamelryck, Thomas Wim;

    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...... 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......, 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....

  1. Counterion influence on chemical shifts in strychnine salts

    Energy Technology Data Exchange (ETDEWEB)

    Metaxas, Athena E.; Cort, John R.

    2013-05-01

    The highly toxic plant alkaloid strychnine is often isolated in the form of the anion salt of its protonated tertiary amine. Here we characterize the relative influence of different counterions on 1H and 13C chemical shifts in several strychnine salts in D2O, methanol-d4 (CD3OD) and chloroform-d (CDCl3) solvents. In organic solvents, but not in water, substantial variation in chemical shifts of protons near the tertiary amine was observed among different salts. These secondary shifts reveal differences in the way each anion influences electronic structure within the protonated amine. The distributions of secondary shifts allow salts to be easily distinguished from each other as well as from the free base form. The observed effects are much greater in organic solvents than in water. Slight concentration-dependence in chemical shifts of some protons near the amine was observed for two salts in CDCl3, but this effect is small compared to the influence of the counterion. Distinct chemical shifts in different salt forms of the same compound may be useful as chemical forensic signatures for source attribution and sample matching of alkaloids such as strychnine and possibly other organic acid and base salts.

  2. Selected readings in chemical kinetics

    CERN Document Server

    Back, Margaret H

    2013-01-01

    Selected Readings in Chemical Kinetics covers excerpts from 12 papers in the field of general and gas-phase kinetics. The book discusses papers on the laws of connexion between the conditions of a chemical change and its amount; on the reaction velocity of the inversion of the cane sugar by acids; and the calculation in absolute measure of velocity constants and equilibrium constants in gaseous systems. The text then tackles papers on simple gas reactions; on the absolute rate of reactions in condensed phases; on the radiation theory of chemical action; and on the theory of unimolecular reacti

  3. Comparison of brown and white adipose tissue fat fractions in ob, seipin, and Fsp27 gene knockout mice by chemical shift-selective imaging and (1)H-MR spectroscopy.

    Science.gov (United States)

    Peng, Xin-Gui; Ju, Shenghong; Fang, Fang; Wang, Yu; Fang, Ke; Cui, Xin; Liu, George; Li, Peng; Mao, Hui; Teng, Gao-Jun

    2013-01-15

    Brown adipose tissue (BAT) plays a key role in thermogenesis to protect the body from cold and obesity. White adipose tissue (WAT) stores excess energy in the form of triglycerides. To better understand the genetic effect on regulation of WAT and BAT, we investigated the fat fraction (FF) in two types of adipose tissues in ob/ob, human BSCL2/seipin gene knockout (SKO), Fsp27 gene knockout (Fsp27(-/-)), and wild-type (WT) mice in vivo using chemical shift selective imaging and (1)H-MR spectroscopy. We reported that the visceral fat volume in WAT was significantly larger in ob/ob mice, but visceral fat volumes were lower in SKO and Fsp27(-/-) mice compared with WT mice. BAT FF was significantly higher in ob/ob mice than the WT group and similar to that of WAT. In contrast, WAT FFs in SKO and Fsp27(-/-) mice were lower and similar to that of BAT. The adipocyte size of WAT in ob/ob mice and the BAT adipocyte size in ob/ob, SKO, and Fsp27 mice were significantly larger compared with WT mice. However, the WAT adipocyte size was significantly smaller in SKO mice than in WT mice. Positive correlations were observed between the adipocyte size and FFs of WAT and BAT. These results suggested that smaller adipocyte size correlates with lower FFs of WAT and BAT. In addition, the differences in FFs in WAT and BAT measured by MR methods in different mouse models were related to the different regulation effects of ob, seipin, or Fsp27 gene on developing WAT and BAT.

  4. SELECTION OF BRILLOUIN SHIFT DISCRIMINATOR FOR BRILLOUIN LIDAR

    Institute of Scientific and Technical Information of China (English)

    吴东; 刘智深

    2002-01-01

    For the measurement of vertical profiles of sound speed in the sea using laser excited Brillouin scattering, a high-resolution measurement of Brillouin frequency shift is required. In this work, a molecular absorption cell was selected as the frequency shift discriminator and several kinds of absorption gases were tried. It was found that the strong line ( # 1095) of 127 I2 at 18783. 3297 cm-1 and two absorption lines of 129 I2 located at the two sides of the # 1095 line of 127 I2 could be used as frequency shift discriminator to detect the changes of the Brillouin frequency shift. This selection is the best one within the range from 532.0131 run to 532.5154 nm. But it is not perfect and there is a lot of work to do before its practical application.

  5. Improving 3D structure prediction from chemical shift data

    Energy Technology Data Exchange (ETDEWEB)

    Schot, Gijs van der [Utrecht University, Computational Structural Biology, Bijvoet Center for Biomolecular Research, Faculty of Science-Chemistry (Netherlands); Zhang, Zaiyong [Technische Universitaet Muenchen, Biomolecular NMR and Munich Center for Integrated Protein Science, Department Chemie (Germany); Vernon, Robert [University of Washington, Department of Biochemistry (United States); Shen, Yang [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States); Vranken, Wim F. [VIB, Department of Structural Biology (Belgium); Baker, David [University of Washington, Department of Biochemistry (United States); Bonvin, Alexandre M. J. J., E-mail: a.m.j.j.bonvin@uu.nl [Utrecht University, Computational Structural Biology, Bijvoet Center for Biomolecular Research, Faculty of Science-Chemistry (Netherlands); Lange, Oliver F., E-mail: oliver.lange@tum.de [Technische Universitaet Muenchen, Biomolecular NMR and Munich Center for Integrated Protein Science, Department Chemie (Germany)

    2013-09-15

    We report advances in the calculation of protein structures from chemical shift nuclear magnetic resonance data alone. Our previously developed method, CS-Rosetta, assembles structures from a library of short protein fragments picked from a large library of protein structures using chemical shifts and sequence information. Here we demonstrate that combination of a new and improved fragment picker and the iterative sampling algorithm RASREC yield significant improvements in convergence and accuracy. Moreover, we introduce improved criteria for assessing the accuracy of the models produced by the method. The method was tested on 39 proteins in the 50-100 residue size range and yields reliable structures in 70 % of the cases. All structures that passed the reliability filter were accurate (<2 A RMSD from the reference)

  6. Magnetic shift of the chemical freezeout and electric charge fluctuations

    CERN Document Server

    Fukushima, Kenji

    2016-01-01

    We discuss the effect of a strong magnetic field on the chemical freezeout points in the ultra-relativistic heavy-ion collision. As a result of the inverse magnetic catalysis or the magnetic inhibition, the crossover onset to hot and dense matter out of quarks and gluons should be shifted to a lower temperature. To quantify this shift we employ the hadron resonance gas model and an empirical condition for the chemical freezeout. We point out that the charged particle abundances are significantly affected by the magnetic field so that the electric charge fluctuation is largely enhanced especially at high baryon density. The charge conservation partially cancels the enhancement but our calculation shows that the electric charge fluctuation could serve as a magnetometer.

  7. Protein secondary structure prediction using NMR chemical shift data.

    Science.gov (United States)

    Zhao, Yuzhong; Alipanahi, Babak; Li, Shuai Cheng; Li, Ming

    2010-10-01

    Accurate determination of protein secondary structure from the chemical shift information is a key step for NMR tertiary structure determination. Relatively few work has been done on this subject. There needs to be a systematic investigation of algorithms that are (a) robust for large datasets; (b) easily extendable to (the dynamic) new databases; and (c) approaching to the limit of accuracy. We introduce new approaches using k-nearest neighbor algorithm to do the basic prediction and use the BCJR algorithm to smooth the predictions and combine different predictions from chemical shifts and based on sequence information only. Our new system, SUCCES, improves the accuracy of all existing methods on a large dataset of 805 proteins (at 86% Q(3) accuracy and at 92.6% accuracy when the boundary residues are ignored), and it is easily extendable to any new dataset without requiring any new training. The software is publicly available at http://monod.uwaterloo.ca/nmr/succes.

  8. Estimation of optical chemical shift in nuclear spin optical rotation

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Fang [Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui 230026 (China); Yao, Guo-hua [Key Laboratory of Ion Beam Bio-engineering, Institute of Technical Biology and Agriculture Engineering, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031 (China); He, Tian-jing [Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui 230026 (China); Chen, Dong-ming, E-mail: dmchen@ustc.edu.cn [Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui 230026 (China); Liu, Fan-chen, E-mail: fcliu@ustc.edu.cn [Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui 230026 (China)

    2014-05-19

    Highlights: • Analytical theory of nuclear spin optical rotation (NSOR) is further developed. • Derive formula of NSOR ratio R between different nuclei in a same molecule. • Calculated results of R agree with the experiments. • Analyze influence factors on R and chemical distinction by NSOR. - Abstract: A recently proposed optical chemical shift in nuclear spin optical rotation (NSOR) is studied by theoretical comparison of NSOR magnitude between chemically non-equivalent or different element nuclei in the same molecule. Theoretical expressions of the ratio R between their NSOR magnitudes are derived by using a known semi-empirical formula of NSOR. Taking methanol, tri-ethyl-phosphite and 2-methyl-benzothiazole as examples, the ratios R are calculated and the results approximately agree with the experiments. Based on those, the important influence factors on R and chemical distinction by NSOR are discussed.

  9. 4D Non-uniformly sampled HCBCACON and {sup 1}J(NC{sup {alpha}})-selective HCBCANCO experiments for the sequential assignment and chemical shift analysis of intrinsically disordered proteins

    Energy Technology Data Exchange (ETDEWEB)

    Novacek, Jiri [Masaryk University, Faculty of Science, NCBR, and CEITEC (Czech Republic); Haba, Noam Y.; Chill, Jordan H. [Bar Ilan University, Department of Chemistry (Israel); Zidek, Lukas, E-mail: lzidek@chemi.muni.cz; Sklenar, Vladimir [Masaryk University, Faculty of Science, NCBR, and CEITEC (Czech Republic)

    2012-06-15

    A pair of 4D NMR experiments for the backbone assignment of disordered proteins is presented. The experiments exploit {sup 13}C direct detection and non-uniform sampling of the indirectly detected dimensions, and provide correlations of the aliphatic proton (H{sup {alpha}}, and H{sup {beta}}) and carbon (C{sup {alpha}}, C{sup {beta}}) resonance frequencies to the protein backbone. Thus, all the chemical shifts regularly used to map the transient secondary structure motifs in the intrinsically disordered proteins (H{sup {alpha}}, C{sup {alpha}}, C{sup {beta}}, C Prime , and N) can be extracted from each spectrum. Compared to the commonly used assignment strategy based on matching the C{sup {alpha}} and C{sup {beta}} chemical shifts, inclusion of the H{sup {alpha}} and H{sup {beta}} provides up to three extra resonance frequencies that decrease the chance of ambiguous assignment. The experiments were successfully applied to the original assignment of a 12.8 kDa intrinsically disordered protein having a high content of proline residues (26 %) in the sequence.

  10. SELECTION OF BRILLOUIN SHIFT DISCRIMINATOR FOR BRILLOUIN LIDAR

    Institute of Scientific and Technical Information of China (English)

    吴东; 刘智深

    2002-01-01

    For the measurement of vertical profiles of sound speed in the sea using laser excited Brillouin scattering, a high-resolution measurement of Brillouin frequency shift is required. In this work, a molecular absorption cell was selec ted as the frequency shift discriminator and several kinds of absorption gases were tri ed. It was found that the strong line (#1095) of 127I2 at 18783.3297 cm-1 and two absorption lines of 129I2 located at the two sides of the #1095 line of 127 I2 could be used as frequency shift discriminator to detect the changes of the Brillouin frequency s hift. This selection is the best one within the range from 532.0131 nm to 532.5154 nm. But it is not perfect and there is a lot of work to do before its practical application.

  11. A convergent mean shift algorithm to select targets for LAMOST

    Institute of Scientific and Technical Information of China (English)

    Guang-Wei Li; Gang Zhao

    2009-01-01

    This paper firstly finds that the Mean Shift Algorithm used by the Observation Control System (OCS) Research Group of the University of Science and Technology of China in Survey Strategy System 2.10 (SSS2.10) to select targets for the Large Sky Area Multi-Object Fiber Spectroscopic Telescope (LAMOST) is not convergent in theory. By carefully studying the mathematical formulation of the Mean Shift Algorithm, we find that it tries to find a point where some objective function achieves its maximum value; the Mean Shift Vector can be regarded as the ascension direction for the objective function. If we regard the objective function as the numerical description for the imaging quality of all targets covered by the focal panel, then the Mean Shift Algorithm can find the place where the imaging quality is the best. So, the problem of selecting targets is equal to the problem of finding the place where the imaging quality is the best. In addition, we also give some effective heuristics to improve computational speed and propose an effective method to assign point sources to the respective fibers. As a result, our program runs fast, and it costs only several seconds to generate an observation.

  12. Two-Dimensional Proton Chemical-Shift Imaging of Human Muscle Metabolites

    Science.gov (United States)

    Hu, Jiani; Willcott, M. Robert; Moore, Gregory J.

    1997-06-01

    Large lipid signals and strong susceptibility gradients introduced by muscle-bone interfaces represent major technical challenges forin vivoproton MRS of human muscle. Here, the demonstration of two-dimensional proton chemical-shift imaging of human muscle metabolites is presented. This technique utilizes a chemical-shift-selective method for water and lipid suppression and automatic shimming for optimal homogeneity of the magnetic field. The 2D1H CSI technique described facilitates the acquisition of high-spatial-resolution spectra, and allows one to acquire data from multiple muscle groups in a single experiment. A preliminary investigation utilizing this technique in healthy adult males (n= 4) revealed a highly significant difference in the ratio of the creatine to trimethylamine resonance between the fast and slow twitch muscle groups examined. The technique is robust, can be implemented on a commercial scanner with relative ease, and should prove to be a useful tool for both clinical and basic investigators.

  13. Theoretical Modeling of 99 Tc NMR Chemical Shifts

    Energy Technology Data Exchange (ETDEWEB)

    Hall, Gabriel B.; Andersen, Amity; Washton, Nancy M.; Chatterjee, Sayandev; Levitskaia, Tatiana G.

    2016-09-06

    Technetium (Tc) displays a rich chemistry due to the wide range of oxidation states (from -I to +VII) and ability to form coordination compounds. Determination of Tc speciation in complex mixtures is a major challenge, and 99Tc NMR spec-troscopy is widely used to probe chemical environments of Tc in odd oxidation states. However interpretation of the 99Tc NMR data is hindered by the lack of reference compounds. DFT computations can help fill this gap, but to date few com-putational studies have focused on 99Tc NMR of compounds and complexes. This work systematically evaluates the inclu-sion small percentages of Hartree-Fock exchange correlation and relativistic effects in DFT computations to support in-terpretation of the 99Tc NMR spectra. Hybrid functionals are found to perform better than their pure GGA counterparts, and non-relativistic calculations have been found to generally show a lower mean absolute deviation from experiment. Overall non-relativistic PBE0 and B3PW91 calculations are found to most accurately predict 99Tc NMR chemical shifts.

  14. Relationship between chemical shift value and accessible surface area for all amino acid atoms

    Directory of Open Access Journals (Sweden)

    Rieping Wolfgang

    2009-04-01

    Full Text Available Abstract Background Chemical shifts obtained from NMR experiments are an important tool in determining secondary, even tertiary, protein structure. The main repository for chemical shift data is the BioMagResBank, which provides NMR-STAR files with this type of information. However, it is not trivial to link this information to available coordinate data from the PDB for non-backbone atoms due to atom and chain naming differences, as well as sequence numbering changes. Results We here describe the analysis of a consistent set of chemical shift and coordinate data, in which we focus on the relationship between the per-atom solvent accessible surface area (ASA in the reported coordinates and their reported chemical shift value. The data is available online on http://www.ebi.ac.uk/pdbe/docs/NMR/shiftAnalysis/index.html. Conclusion Atoms with zero per-atom ASA have a significantly larger chemical shift dispersion and often have a different chemical shift distribution compared to those that are solvent accessible. With higher per-atom ASA, the chemical shift values also tend towards random coil values. The per-atom ASA, although not the determinant of the chemical shift, thus provides a way to directly correlate chemical shift information to the atomic coordinates.

  15. Applications of Chemical Shift Imaging to Marine Sciences

    Directory of Open Access Journals (Sweden)

    Haakil Lee

    2010-08-01

    Full Text Available The successful applications of magnetic resonance imaging (MRI in medicine are mostly due to the non-invasive and non-destructive nature of MRI techniques. Longitudinal studies of humans and animals are easily accomplished, taking advantage of the fact that MRI does not use harmful radiation that would be needed for plain film radiographic, computerized tomography (CT or positron emission (PET scans. Routine anatomic and functional studies using the strong signal from the most abundant magnetic nucleus, the proton, can also provide metabolic information when combined with in vivo magnetic resonance spectroscopy (MRS. MRS can be performed using either protons or hetero-nuclei (meaning any magnetic nuclei other than protons or 1H including carbon (13C or phosphorus (31P. In vivo MR spectra can be obtained from single region ofinterest (ROI or voxel or multiple ROIs simultaneously using the technique typically called chemical shift imaging (CSI. Here we report applications of CSI to marine samples and describe a technique to study in vivo glycine metabolism in oysters using 13C MRS 12 h after immersion in a sea water chamber dosed with [2-13C]-glycine. This is the first report of 13C CSI in a marine organism.

  16. MRI of intraosseous fistulous systems and sequesters in chronic osteomyelitis with standard spin echo sequences, highly selective chemical-shift imaging, diffusion weighted imaging, and magnetization-transfer; MRT-Darstellung intraossaerer Sequester und Fistelsysteme bei chronischer Osteomyelitis durch Standardsequenzen, hochselektive Chemical-Shift-Bildgebung, Diffusionsgewichtung und Magnetisierungstransfer

    Energy Technology Data Exchange (ETDEWEB)

    Bitzer, M.; Hartmann, J.; Geist-Barth, B.; Stern, W.; Seemann, M.; Pereira, P.; Claussen, C.D. [Abteilung fuer Radiologische Diagnostik, Klinikum der Eberhart-Karls-Universitaet Tuebingen (Germany); Schick, F. [Sektion fuer Experimentelle Radiologie, Klinikum der Eberhard-Karls-Universitaet Tuebingen (Germany); Krackhardt, T. [Berufsgenossenschaftliche Klinik, Tuebingen (Germany); Morgalla, M. [Chirurgische Klinik, Klinikum der Eberhard-Karls-Universitaet Tuebingen (Germany)

    2002-11-01

    Purpose: To study and test the impact of modern MRI techniques in diagnostic imaging in the evaluation of intra-osseous fistulous systems and sequesters. Materials and Methods: In a prospective study, nine patients with chronic osteomyelitis of the legs were examined by MRI. Patients with clinical signs of osteomyelitis requiring surgery were included in the study. T1-weighted spin echo (SE) sequences, proton density (PD) and T2-weighted fast spin echo (FSE) sequences, water- and fat-selective FSE sequences, and diffusion weighted (DW) PSIF sequences were used preoperatively. Furthermore, magnetizing transfer (MT) with gradient echo (GRE) sequences was evaluated. Results: Water selective sequences revealed the highest sensitivity for the detection of fistulas (100%), providing the best delineation of the extent of the entire fistulous systems. Fat-selective sequences (sensitivity 55.6%) and T1-weighted sequences (sensitivity 77.8%) displayed fistulas as hypointense bands, which, however, cannot be well differentiated from cortical bone in the transcortical areas. PD and T2-weighted images were found to have a poor sensitivity (55.6% and 66.7%) for fistulas in any location. The sensitivity of water-selective sequences to demonstrate intraosseous sequesters was 100%. The sensitivity was low for the other sequences. In 4 of 5 patients with surgically proven infection, DW and MT revealed an abnormal spatial distribution, with high diffusion in the central parts of the fistulas and high MT effect peripherally surrounding a weak MT effect centrally. (orig.) [German] Zielsetzung: Die vorliegende Arbeit soll die Moeglichkeiten des Einsatzes spezieller Sequenztechniken der MRT bei der Diagnostik von intraossaeren Fisteln und Sequestern pruefen und beschreiben. Material und Methode: In einer prospektiven Studie wurden 9 Patienten mit chronischen Osteomyelitiden der unteren Extremitaeten kernspintomographisch untersucht. Die MRT-Befunde wurden qualitativ anhand der Operations

  17. Deuterium isotope effects on 13C chemical shifts of 10-Hydroxybenzo[h]quinolines

    DEFF Research Database (Denmark)

    Hansen, Poul Erik; Kamounah, Fadhil S.; Gryko, Daniel T.

    2013-01-01

    Deuterium isotope effects on 13C-NMR chemical shifts are investigated in a series of 10-hydroxybenzo[h]quinolines (HBQ’s) The OH proton is deuteriated. The isotope effects on 13C chemical shifts in these hydrogen bonded systems are rather unusual. The formal four-bond effects are found to be nega......Deuterium isotope effects on 13C-NMR chemical shifts are investigated in a series of 10-hydroxybenzo[h]quinolines (HBQ’s) The OH proton is deuteriated. The isotope effects on 13C chemical shifts in these hydrogen bonded systems are rather unusual. The formal four-bond effects are found...

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

    Science.gov (United States)

    Mechelke, Martin; Habeck, Michael

    2013-06-01

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

  19. Inferential protein structure determination and refinement using fast, electronic structure based backbone amide chemical shift predictions

    CERN Document Server

    Christensen, Anders S

    2015-01-01

    This report covers the development of a new, fast method for calculating the backbone amide proton chemical shifts in proteins. Through quantum chemical calculations, structure-based forudsiglese the chemical shift for amidprotonen in protein has been parameterized. The parameters are then implemented in a computer program called Padawan. The program has since been implemented in protein folding program Phaistos, wherein the method andvendes to de novo folding of the protein structures and to refine the existing protein structures.

  20. Ab Initio Calculation of Nuclear Magnetic Resonance Chemical Shift Anisotropy Tensors 1. Influence of Basis Set on the Calculation of 31P Chemical Shifts

    Energy Technology Data Exchange (ETDEWEB)

    Alam, T.M.

    1998-09-01

    The influence of changes in the contracted Gaussian basis set used for ab initio calculations of nuclear magnetic resonance (NMR) phosphorous chemical shift anisotropy (CSA) tensors was investigated. The isotropic chemical shitl and chemical shift anisotropy were found to converge with increasing complexity of the basis set at the Hartree-Fock @IF) level. The addition of d polarization function on the phosphorous nucIei was found to have a major impact of the calculated chemical shi~ but diminished with increasing number of polarization fimctions. At least 2 d polarization fimctions are required for accurate calculations of the isotropic phosphorous chemical shift. The introduction of density fictional theory (DFT) techniques through tie use of hybrid B3LYP methods for the calculation of the phosphorous chemical shift tensor resulted in a poorer estimation of the NMR values, even though DFT techniques result in improved energy and force constant calculations. The convergence of the W parametem with increasing basis set complexity was also observed for the DFT calculations, but produced results with consistent large deviations from experiment. The use of a HF 6-31 l++G(242p) basis set represents a good compromise between accuracy of the simulation and the complexity of the calculation for future ab initio calculations of 31P NMR parameters in larger complexes.

  1. Correlation of chemical shifts predicted by molecular dynamics simulations for partially disordered proteins

    Energy Technology Data Exchange (ETDEWEB)

    Karp, Jerome M.; Erylimaz, Ertan; Cowburn, David, E-mail: cowburn@cowburnlab.org, E-mail: David.cowburn@einstein.yu.edu [Albert Einstein College of Medicine of Yeshiva University, Department of Biochemistry (United States)

    2015-01-15

    There has been a longstanding interest in being able to accurately predict NMR chemical shifts from structural data. Recent studies have focused on using molecular dynamics (MD) simulation data as input for improved prediction. Here we examine the accuracy of chemical shift prediction for intein systems, which have regions of intrinsic disorder. We find that using MD simulation data as input for chemical shift prediction does not consistently improve prediction accuracy over use of a static X-ray crystal structure. This appears to result from the complex conformational ensemble of the disordered protein segments. We show that using accelerated molecular dynamics (aMD) simulations improves chemical shift prediction, suggesting that methods which better sample the conformational ensemble like aMD are more appropriate tools for use in chemical shift prediction for proteins with disordered regions. Moreover, our study suggests that data accurately reflecting protein dynamics must be used as input for chemical shift prediction in order to correctly predict chemical shifts in systems with disorder.

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

    Science.gov (United States)

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

    2015-11-01

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

  3. Chemical shift assignments of two oleanane triterpenes from Euonymus hederaceus

    Institute of Scientific and Technical Information of China (English)

    HU He-jiao; WANG Kui-wu; WU Bin; SUN Cui-rong; PAN Yuan-jiang

    2005-01-01

    1H-NMR and 13C-NMR assignments of 12-oleanene-3,11-dione (compound 1) were completely described for the first time through conventional 1D NMR and 2D shift-correlated NMR experiments using 1H-1HCOSY, HMQC, HMBC techniques.Based on its NMR data, the assignments of 28-hydroxyolean-12-ene-3,11-dione (compound 2) were partially revised.

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

    DEFF Research Database (Denmark)

    Christensen, Anders Steen; Linnet, Troels Emtekær; Borg, Mikael;

    2013-01-01

    We present the ProCS method for the rapid and accurate prediction of protein backbone amide proton chemical shifts - sensitive probes of the geometry of key hydrogen bonds that determine protein structure. ProCS is parameterized against quantum mechanical (QM) calculations and reproduces high level...... QM results obtained for a small protein with an RMSD of 0.25 ppm (r = 0.94). ProCS is interfaced with the PHAISTOS protein simulation program and is used to infer statistical protein ensembles that reflect experimentally measured amide proton chemical shift values. Such chemical shift...

  5. Effects of structural differences on the NMR chemical shifts in isostructural dipeptides.

    Science.gov (United States)

    Altheimer, Benjamin D; Mehta, Manish A

    2014-04-10

    Porous crystalline dipeptides have gained recent attention for their potential as gas-storage materials. Within this large class is a group of dipeptides containing alanine, valine, and isoleucine with very similar crystal structures. We report the (13)C (carbonyl and Cα) and (15)N (amine and amide) solid-state NMR isotropic chemical shifts in a series of seven such isostructural porous dipeptides as well as shift tensor data for the carbonyl and amide sites. Using their known crystal structures and aided by ab initio quantum chemical calculations for the resonance assignments, we elucidate trends relating local structure, hydrogen-bonding patterns, and chemical shift. We find good correlation between the backbone dihedral angles and the Cα1 and Cα2 shifts. For the C1 shift tensor, the δ11 value shifts downfield as the hydrogen-bond distance increases, δ22 shifts upfield, and δ33 shows little variation. The C2 shift tensor shows no appreciable correlation with structural parameters. For the N2 tensor, δ11 shows little dependence on the hydrogen-bond length, whereas δ22 and δ33 both show a decrease in shielding as the hydrogen bond shortens. Our analysis teases apart some, but not all, structural contributors to the observed differences the solid-state NMR chemical shifts.

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

    Energy Technology Data Exchange (ETDEWEB)

    Li, Dawei; Brüschweiler, Rafael, E-mail: bruschweiler.1@osu.edu [The Ohio State University, Campus Chemical Instrument Center (United States)

    2015-07-15

    We mined the most recent editions of the BioMagResDataBank and the protein data bank to parametrize a new empirical knowledge-based chemical shift predictor of protein backbone atoms using either a linear or an artificial neural network model. The resulting chemical shift predictor PPM-One accepts a single static 3D structure as input and emulates the effect of local protein dynamics via interatomic steric contacts. Furthermore, the chemical shift prediction was extended to most side-chain protons and it is found that the prediction accuracy is at a level allowing an independent assessment of stereospecific assignments. For a previously established set of test proteins some overall improvement was achieved over current top-performing chemical shift prediction programs.

  7. Conversion of biomass to selected chemical products.

    Science.gov (United States)

    Gallezot, Pierre

    2012-02-21

    This critical review provides a survey illustrated by recent references of different strategies to achieve a sustainable conversion of biomass to bioproducts. Because of the huge number of chemical products that can be potentially manufactured, a selection of starting materials and targeted chemicals has been done. Also, thermochemical conversion processes such as biomass pyrolysis or gasification as well as the synthesis of biofuels were not considered. The synthesis of chemicals by conversion of platform molecules obtained by depolymerisation and fermentation of biopolymers is presently the most widely envisioned approach. Successful catalytic conversion of these building blocks into intermediates, specialties and fine chemicals will be examined. However, the platform molecule value chain is in competition with well-optimised, cost-effective synthesis routes from fossil resources to produce chemicals that have already a market. The literature covering alternative value chains whereby biopolymers are converted in one or few steps to functional materials will be analysed. This approach which does not require the use of isolated, pure chemicals is well adapted to produce high tonnage products, such as paper additives, paints, resins, foams, surfactants, lubricants, and plasticisers. Another objective of the review was to examine critically the green character of conversion processes because using renewables as raw materials does not exempt from abiding by green chemistry principles (368 references).

  8. Prediction of hydrogen and carbon chemical shifts from RNA using database mining and support vector regression

    Energy Technology Data Exchange (ETDEWEB)

    Brown, Joshua D.; Summers, Michael F. [University of Maryland Baltimore County, Howard Hughes Medical Institute (United States); Johnson, Bruce A., E-mail: bruce.johnson@asrc.cuny.edu [University of Maryland Baltimore County, Department of Chemistry and Biochemistry (United States)

    2015-09-15

    The Biological Magnetic Resonance Data Bank (BMRB) contains NMR chemical shift depositions for over 200 RNAs and RNA-containing complexes. We have analyzed the {sup 1}H NMR and {sup 13}C chemical shifts reported for non-exchangeable protons of 187 of these RNAs. Software was developed that downloads BMRB datasets and corresponding PDB structure files, and then generates residue-specific attributes based on the calculated secondary structure. Attributes represent properties present in each sequential stretch of five adjacent residues and include variables such as nucleotide type, base-pair presence and type, and tetraloop types. Attributes and {sup 1}H and {sup 13}C NMR chemical shifts of the central nucleotide are then used as input to train a predictive model using support vector regression. These models can then be used to predict shifts for new sequences. The new software tools, available as stand-alone scripts or integrated into the NMR visualization and analysis program NMRViewJ, should facilitate NMR assignment and/or validation of RNA {sup 1}H and {sup 13}C chemical shifts. In addition, our findings enabled the re-calibration a ring-current shift model using published NMR chemical shifts and high-resolution X-ray structural data as guides.

  9. Chemical shift MRI can aid in the diagnosis of indeterminate skeletal lesions of the spine

    Energy Technology Data Exchange (ETDEWEB)

    Douis, H. [University Hospital Birmingham, Department of Radiology, Birmingham (United Kingdom); Royal Orthopaedic Hospital, Department of Radiology, Birmingham (United Kingdom); Davies, A.M. [Royal Orthopaedic Hospital, Department of Radiology, Birmingham (United Kingdom); Jeys, L. [Royal Orthopaedic Hospital, Department of Orthopaedic Oncology, Birmingham (United Kingdom); Sian, P. [Royal Orthopaedic Hospital, Department of Spinal Surgery and Spinal Oncology, Birmingham (United Kingdom)

    2016-04-15

    To evaluate the role of chemical shift MRI in the characterisation of indeterminate skeletal lesions of the spine as benign or malignant. Fifty-five patients (mean age 54.7 years) with 57 indeterminate skeletal lesions of the spine were included in this retrospective study. In addition to conventional MRI at 3 T which included at least sagittal T1WI and T2WI/STIR sequences, patients underwent chemical shift MRI. A cut-off value with a signal drop-out of 20 % was used to differentiate benign lesions from malignant lesions (signal drop-out <20 % being malignant). There were 45 benign lesions and 12 malignant lesions. Chemical shift imaging correctly diagnosed 33 of 45 lesions as benign and 11 of 12 lesions as malignant. In contrast, there were 12 false positive cases and 1 false negative case based on chemical shift MRI. This yielded a sensitivity of 91.7 %, a specificity of 73.3 %, a negative predictive value of 97.1 %, a positive predictive value of 47.8 % and a diagnostic accuracy of 82.5 %. Chemical shift MRI can aid in the characterisation of indeterminate skeletal lesions of the spine in view of its high sensitivity in diagnosing malignant lesions. Chemical shift MRI can potentially avoid biopsy in a considerable percentage of patients with benign skeletal lesions of the spine. (orig.)

  10. Cardiovascular risk factors and primary selection into shift work

    DEFF Research Database (Denmark)

    Nabe-Nielsen, Kirsten; Garde, Anne Helene; Tüchsen, Finn

    2008-01-01

    : In the unadjusted analyses, baseline obesity was associated with fixed evening work at follow-up. Minimal or light-to-moderate leisure-time physical activity was associated with a decrease in the odds ratio (OR) for two or three shifts including night work. Smoking status was associated with fixed evening work......OBJECTIVES: This study examined differences between future shift workers and future day workers as regards cardiovascular risk factors before they began different work schedules and the differences that remained after control for sociodemographic factors and general self-efficacy. METHODS......: Altogether 2870 newly educated social and health care workers filled out a questionnaire a few weeks before finishing their formal training and again 1 year after graduation. They answered questions on diabetes, hypertension, lifestyle habits, sociodemographic factors, and general self-efficacy. RESULTS...

  11. Proton chemical shift tensors determined by 3D ultrafast MAS double-quantum NMR spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Rongchun; Mroue, Kamal H.; Ramamoorthy, Ayyalusamy, E-mail: ramamoor@umich.edu [Biophysics and Department of Chemistry, The University of Michigan, Ann Arbor, Michigan 48109-1055 (United States)

    2015-10-14

    Proton NMR spectroscopy in the solid state has recently attracted much attention owing to the significant enhancement in spectral resolution afforded by the remarkable advances in ultrafast magic angle spinning (MAS) capabilities. In particular, proton chemical shift anisotropy (CSA) has become an important tool for obtaining specific insights into inter/intra-molecular hydrogen bonding. However, even at the highest currently feasible spinning frequencies (110–120 kHz), {sup 1}H MAS NMR spectra of rigid solids still suffer from poor resolution and severe peak overlap caused by the strong {sup 1}H–{sup 1}H homonuclear dipolar couplings and narrow {sup 1}H chemical shift (CS) ranges, which render it difficult to determine the CSA of specific proton sites in the standard CSA/single-quantum (SQ) chemical shift correlation experiment. Herein, we propose a three-dimensional (3D) {sup 1}H double-quantum (DQ) chemical shift/CSA/SQ chemical shift correlation experiment to extract the CS tensors of proton sites whose signals are not well resolved along the single-quantum chemical shift dimension. As extracted from the 3D spectrum, the F1/F3 (DQ/SQ) projection provides valuable information about {sup 1}H–{sup 1}H proximities, which might also reveal the hydrogen-bonding connectivities. In addition, the F2/F3 (CSA/SQ) correlation spectrum, which is similar to the regular 2D CSA/SQ correlation experiment, yields chemical shift anisotropic line shapes at different isotropic chemical shifts. More importantly, since the F2/F1 (CSA/DQ) spectrum correlates the CSA with the DQ signal induced by two neighboring proton sites, the CSA spectrum sliced at a specific DQ chemical shift position contains the CSA information of two neighboring spins indicated by the DQ chemical shift. If these two spins have different CS tensors, both tensors can be extracted by numerical fitting. We believe that this robust and elegant single-channel proton-based 3D experiment provides useful atomistic

  12. Further conventions for NMR shielding and chemical shifts (IUPAC Recommendations 2008)

    Energy Technology Data Exchange (ETDEWEB)

    Harris, R.K. [University of Durham, Durham (United Kingdom). Dept. of Chemistry; Becker, E.D. [National Institutes of Health, Bethesda, MD (United States); Menezes, S.M. Cabral de [PETROBRAS, Rio de Janeiro, RJ (Brazil). Centro de Pesquisas (CENPES); Granger, P. [University Louis Pasteur, Strasbourg (France). Inst. of Chemistry; Hoffman, R.E. [The Hebrew University of Jerusalem, Safra Campus, Jerusalem (Israel). Dept. of Organic Chemistry; Zilm, K.W., E-mail: r.k.harris@durham.ac.uk [Yale University, New Haven, CT (United States). Dept. of Chemistry

    2008-07-01

    IUPAC has published a number of recommendations regarding the reporting of nuclear magnetic resonance (NMR) data, especially chemical shifts. The most recent publication [Pure Appl. Chem. 73, 1795 (2001)] recommended that tetramethylsilane (TMS) serve as a universal reference for reporting the shifts of all nuclides, but it deferred recommendations for several aspects of this subject. This document first examines the extent to which the {sup 1}H shielding in TMS itself is subject to change by variation in temperature, concentration, and solvent. On the basis of recently published results, it has been established that the shielding of TMS in solution [along with that of sodium-3- (trimethylsilyl)propanesulfonate, DSS, often used as a reference for aqueous solutions] varies only slightly with temperature but is subject to solvent perturbations of a few tenths of a part per million (ppm). Recommendations are given for reporting chemical shifts under most routine experimental conditions and for quantifying effects of temperature and solvent variation, including the use of magnetic susceptibility corrections and of magic-angle spinning (MAS). This document provides the first IUPAC recommendations for referencing and reporting chemical shifts in solids, based on high-resolution MAS studies. Procedures are given for relating {sup 13}C NMR chemical shifts in solids to the scales used for high resolution studies in the liquid phase. The notation and terminology used for describing chemical shift and shielding tensors in solids are reviewed in some detail, and recommendations are given for best practice. (author)

  13. Magnetic couplings in the chemical shift of paramagnetic NMR.

    Science.gov (United States)

    Vaara, Juha; Rouf, Syed Awais; Mareš, Jiří

    2015-10-13

    We apply the Kurland-McGarvey (J. Magn. Reson. 1970, 2, 286) theory for the NMR shielding of paramagnetic molecules, particularly its special case limited to the ground-state multiplet characterized by zero-field splitting (ZFS) interaction of the form S·D·S. The correct formulation for this problem was recently presented by Soncini and Van den Heuvel (J. Chem. Phys. 2013, 138, 054113). With the effective electron spin quantum number S, the theory involves 2S+1 states, of which all but one are low-lying excited states, between which magnetic couplings take place by Zeeman and hyperfine interactions. We investigate these couplings as a function of temperature, focusing on both the high- and low-temperature behaviors. As has been seen in work by others, the full treatment of magnetic couplings is crucial for a realistic description of the temperature behavior of NMR shielding up to normal measurement temperatures. At high temperatures, depending on the magnitude of ZFS, the effect of magnetic couplings diminishes, and the Zeeman and hyperfine interactions become effectively averaged in the thermally occupied states of the multiplet. At still higher temperatures, the ZFS may be omitted altogether, and the shielding properties may be evaluated using a doublet-like formula, with all the 2S+1 states becoming effectively degenerate at the limit of vanishing magnetic field. We demonstrate these features using first-principles calculations of Ni(II), Co(II), Cr(II), and Cr(III) complexes, which have ZFS of different sizes and signs. A non-monotonic inverse temperature dependence of the hyperfine shift is predicted for axially symmetric integer-spin systems with a positive D parameter of ZFS. This is due to the magnetic coupling terms that are proportional to kT at low temperatures, canceling the Curie-type 1/kT prefactor of the hyperfine shielding in this case.

  14. Effect of shifting cultivation on soil physical and chemical properties in Bandarban hill district, Bangladesh

    Institute of Scientific and Technical Information of China (English)

    Khandakar Showkat Osman; M. Jashimuddin; S. M. Sirajul Haque; Sohag Miah

    2013-01-01

    This study reports the effects of shifting cultivation at slashing stage on soil physicochemical properties at Bandarban Sadar Upazila in Chittagong Hill Tracts of Bangladesh. At this initial stage of shifting cultivation no general trend was found for moisture content, maximum water holding capacity, field capacity, dry and moist bulk density, parti-cle density for some chemical properties between shifting cultivated land and forest having similar soil texture. Organic matter was significantly (p≤0.05) lower in 1-year and 3-year shifting cultivated lands and higher in 2-year shifting cultivation than in adjacent natural forest. Significant differences were also found for total N, exchangeable Ca, Mg and K and in CEC as well as for available P. Slashed area showed higher soil pH. Deterioration in land quality starts from burning of slashing materials and continues through subsequent stages of shifting cultivation.

  15. Chemical composition of selected Saudi medicinal plants

    Directory of Open Access Journals (Sweden)

    Ihsanullah Daur

    2015-05-01

    Full Text Available Medicinal plants are important in traditional medicine and modern pharmaceutical drugs; therefore, the interest in the analysis of their chemical composition is increasing. In this study, selected medicinal plants including Achillea fragrantissima (Forssk Sch., Amaranthus viridis L., Asteriscus graveolens (Forssk. Less., Chenopodium album L., and Conyza bonariensis (L. Cronquist were collected from the rangeland of western regions (Bahra and Hada areas of Saudi Arabia to study their chemical composition. Eight minerals (Mg, Ca, Cr, Mn, Fe, Co, Cu, and Zn, total phenolic contents, antioxidant activity, and free-radical scavenging ability were examined in order to evaluate the medicinal potential of these plants. All the plants were found to be rich sources of minerals and antioxidants, although there were significant differences (p < 0.05 in their chemical composition, which may provide a rationale for generating custom extracts from specific plants depending on the application. The findings of this study will thus facilitate herbalists in their efforts to incorporate these plants into various formulations based on their chemical composition.

  16. Prediction algorithm for amino acid types with their secondary structure in proteins (PLATON) using chemical shifts.

    Science.gov (United States)

    Labudde, D; Leitner, D; Krüger, M; Oschkinat, H

    2003-01-01

    The algorithm PLATON is able to assign sets of chemical shifts derived from a single residue to amino acid types with its secondary structure (amino acid species). A subsequent ranking procedure using optionally two different penalty functions yields predictions for possible amino acid species for the given set of chemical shifts. This was demonstrated in the case of the alpha-spectrin SH3 domain and applied to 9 further protein data sets taken from the BioMagRes database. A database consisting of reference chemical shift patterns (reference CSPs) was generated from assigned chemical shifts of proteins with known 3D-structure. This reference CSP database is used in our approach for extracting distributions of amino acid types with their most likely secondary structure elements (namely alpha-helix, beta-sheet, and coil) for single amino acids by comparison with query CSPs. Results obtained for the 10 investigated proteins indicates that the percentage of correct amino acid species in the first three positions in the ranking list, ranges from 71.4% to 93.2% for the more favorable penalty function. Where only the top result of the ranking list for these 10 proteins is considered, 36.5% to 83.1% of the amino acid species are correctly predicted. The main advantage of our approach, over other methods that rely on average chemical shift values is the ability to increase database content by incorporating newly derived CSPs, and therefore to improve PLATON's performance over time.

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

    CERN Document Server

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

    2013-01-01

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

  18. A NMR experiment for simultaneous correlations of valine and leucine/isoleucine methyls with carbonyl chemical shifts in proteins.

    Science.gov (United States)

    Tugarinov, Vitali; Venditti, Vincenzo; Marius Clore, G

    2014-01-01

    A methyl-detected 'out-and-back' NMR experiment for obtaining simultaneous correlations of methyl resonances of valine and isoleucine/leucine residues with backbone carbonyl chemical shifts, SIM-HMCM(CGCBCA)CO, is described. The developed pulse-scheme serves the purpose of convenience in recording a single data set for all Ile(δ1), Leu(δ) and Val(γ) (ILV) methyl positions instead of acquiring two separate spectra selective for valine or leucine/isoleucine residues. The SIM-HMCM(CGCBCA)CO experiment can be used for ILV methyl assignments in moderately sized protein systems (up to ~100 kDa) where the backbone chemical shifts of (13)C(α), (13)Cβ and (13)CO are known from prior NMR studies and where some losses in sensitivity can be tolerated for the sake of an overall reduction in NMR acquisition time.

  19. The Effect of Molecular Conformation on the Accuracy of Theoretical (1)H and (13)C Chemical Shifts Calculated by Ab Initio Methods for Metabolic Mixture Analysis.

    Science.gov (United States)

    Chikayama, Eisuke; Shimbo, Yudai; Komatsu, Keiko; Kikuchi, Jun

    2016-04-14

    NMR spectroscopy is a powerful method for analyzing metabolic mixtures. The information obtained from an NMR spectrum is in the form of physical parameters, such as chemical shifts, and construction of databases for many metabolites will be useful for data interpretation. To increase the accuracy of theoretical chemical shifts for development of a database for a variety of metabolites, the effects of sets of conformations (structural ensembles) and the levels of theory on computations of theoretical chemical shifts were systematically investigated for a set of 29 small molecules in the present study. For each of the 29 compounds, 101 structures were generated by classical molecular dynamics at 298.15 K, and then theoretical chemical shifts for 164 (1)H and 123 (13)C atoms were calculated by ab initio quantum chemical methods. Six levels of theory were used by pairing Hartree-Fock, B3LYP (density functional theory), or second order Møller-Plesset perturbation with 6-31G or aug-cc-pVDZ basis set. The six average fluctuations in the (1)H chemical shift were ±0.63, ± 0.59, ± 0.70, ± 0.62, ± 0.75, and ±0.66 ppm for the structural ensembles, and the six average errors were ±0.34, ± 0.27, ± 0.32, ± 0.25, ± 0.32, and ±0.25 ppm. The results showed that chemical shift fluctuations with changes in the conformation because of molecular motion were larger than the differences between computed and experimental chemical shifts for all six levels of theory. In conclusion, selection of an appropriate structural ensemble should be performed before theoretical chemical shift calculations for development of an accurate database for a variety of metabolites.

  20. From NMR chemical shifts to amino acid types: Investigation of the predictive power carried by nuclei

    Energy Technology Data Exchange (ETDEWEB)

    Marin, Antoine; Malliavin, Therese E. [Institut de Biologie Physico-Chimique, Laboratoire de Biochimie Theorique, CNRS UPR 9080 (France)], E-mail: therese.malliavin@ibpc.fr; Nicolas, Pierre; Delsuc, Marc-Andre [INRA - Domaine de Vilvert, Unite Mathematique Informatique et Genome (France)

    2004-09-15

    An approach to automatic prediction of the amino acid type from NMR chemical shift values of its nuclei is presented here, in the frame of a model to calculate the probability of an amino acid type given the set of chemical shifts. The method relies on systematic use of all chemical shift values contained in the BioMagResBank (BMRB). Two programs were designed, one (BMRB stats) for extracting statistical chemical shift parameters from the BMRB and another one (RESCUE2) for computing the probabilities of each amino acid type, given a set of chemical shifts. The Bayesian prediction scheme presented here is compared to other methods already proposed: PROTYP (Grzesiek and Bax, J. Biomol. NMR, 3, 185-204, 1993) RESCUE (Pons and Delsuc, J. Biomol. NMR, 15, 15-26, 1999) and PLATON (Labudde et al., J. Biomol. NMR, 25, 41-53, 2003) and is found to be more sensitive and more specific. Using this scheme, we tested various sets of nuclei. The two nuclei carrying the most information are C{sub {beta}} and H{sub {beta}}, in agreement with observations made in Grzesiek and Bax, 1993. Based on four nuclei: H{sub {beta}}, C{sub {beta}}, C{sub {alpha}} and C', it is possible to increase correct predictions to a rate of more than 75%. Taking into account the correlations between the nuclei chemical shifts has only a slight impact on the percentage of correct predictions: indeed, the largest correlation coefficients display similar features on all amino acids.

  1. Deuterium isotope effects on 13C chemical shifts of negatively charged NH.N systems

    DEFF Research Database (Denmark)

    Hansen, Poul Erik; Pietrzak, Mariusz; Grech, Eugeniusz

    2013-01-01

    Deuterium isotope effects on 13C chemical shifts are investigated in anions of 1,8-bis(4-toluenesulphonamido)naphthalenes together with N,N-(naphthalene-1,8-diyl)bis(2,2,2-trifluoracetamide) all with bis(1,8-dimethylamino)napthaleneH+ as counter ion. These compounds represent both “static......” and equilibrium cases. NMR assignments of the former have been revised. The NH proton is deuteriated. The isotope effects on 13C chemical shifts are rather unusual in these strongly hydrogen bonded systems between a NH and a negatively charged nitrogen atom. The formal four-bond effects are found to be negative...

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

    DEFF Research Database (Denmark)

    Bratholm, Lars Andersen

    In this thesis, my work involving dierent aspects of protein structure determination by computer modeling is presented. Determination of several protein's native fold were carried out with Markov chain Monte Carlo simulations in the PHAISTOS protein structure simulation framework, utilizing...... to within 3 A. Furthermore, a fast quantum mechanics based chemical shift predictor was developed together with methodology for using chemical shifts in structure simulations. The developed predictor was used for renement of several protein structures and for reducing the computational cost of quantum...

  3. Ontogenetic shift in response to prey-derived chemical cues in prairie rattlesnakes Crotalus viridis viridis

    Institute of Scientific and Technical Information of China (English)

    Anthony J.SAVIOLA; David CHISZAR; Stephen P.MACKESSY

    2012-01-01

    Snakes often have specialized diets that undergo a shift from one prey type to another depending on the life stage of the snake.Crotalus viridis viridis (prairie rattlesnake) takes different prey at different life stages,and neonates typically prey on ectotherms,while adults feed almost entirely on small endotherms.We hypothesized that elevated rates of tongue flicking to chemical stimuli should correlate with particular prey consumed,and that this response shifts from one prey type to another as individuals age.To examine if an ontogenetic shift in response to chemical cues occurred,we recorded the rate of tongue flicking for 25 neonate,20 subadult,and 20 adult (average SVL=280.9,552,789.5 mm,respectively) wild-caught C.v.viridis to chemical stimuli presented on a cotton-tipped applicator; water-soluble cues from two ectotherms (prairie lizard,Sceloporus undulatus,and house gecko,Hemidactylusfrenatus),two endotherms (deer mouse,Peromyscus maniculatus and lab mouse,Mus musculus),and water controls were used.Neonates tongue flicked significantly more to chemical cues of their common prey,S.undulatus,than to all other chemical cues; however,the response to this lizard's chemical cues decreased in adult rattlesnakes.Subadults tongue flicked with a higher rate of tongue flicking to both S.undulatus and P.maniculatus than to all other treatments,and adults tongue flicked significantly more to P.maniculatus than to all other chemical cues.In addition,all three sub-classes demonstrated a greater response for natural prey chemical cues over chemical stimuli of prey not encountered in the wild (M.musculus and H.frenatus).This shift in chemosensory response correlated with the previously described ontogenetic shifts in C.v.viridis diet.Because many vipers show a similar ontogenetic shift in diet and venom composition,we suggest that this shift in prey cue discrimination is likely a general phenomenon among viperid snakes.

  4. Energy gap in tunneling spectroscopy: effect of the chemical potential shift

    Science.gov (United States)

    Fedotov, N. I.; Zaitsev-Zotov, S. V.

    2016-12-01

    We study the effect of a shift of the chemical potential level on the tunneling conductance spectra. In the systems with gapped energy spectra, significant chemical-potential dependent distortions of the differential tunneling conductance curves, dI/dV, arise in the gap region. An expression is derived for the correction of the dI/dV, which in a number of cases was found to be large. The sign of the correction depends on the chemical potential level position with respect to the gap. The correction of the dI/dV associated with the chemical potential shift has a nearly linear dependence on the tip-sample separation z and vanishes at z → 0.

  5. Sequence correction of random coil chemical shifts: correlation between neighbor correction factors and changes in the Ramachandran distribution

    DEFF Research Database (Denmark)

    Kjærgaard, Magnus; Poulsen, Flemming Martin

    2011-01-01

    Random coil chemical shifts are necessary for secondary chemical shift analysis, which is the main NMR method for identification of secondary structure in proteins. One of the largest challenges in the determination of random coil chemical shifts is accounting for the effect of neighboring residues....... The contributions from the neighboring residues are typically removed by using neighbor correction factors determined based on each residue's effect on glycine chemical shifts. Due to its unusual conformational freedom, glycine may be particularly unrepresentative for the remaining residue types. In this study, we...... in the conformational ensemble are an important source of neighbor effects in disordered proteins. Glutamine derived random coil chemical shifts and correction factors modestly improve our ability to predict (13)C chemical shifts of intrinsically disordered proteins compared to existing datasets, and may thus improve...

  6. Chemically modified field effect transistors with nitrite or fluoride selectivity

    NARCIS (Netherlands)

    Antonisse, Martijn M.G.; Snellink-Ruël, Bianca H.M.; Engbersen, Johan F.J.; Reinhoudt, David N.

    1998-01-01

    Polysiloxanes with different types of polar substituents are excellent membrane materials for nitrite and fluoride selective chemically modified field effect transistors (CHEMFETs). Nitrite selectivity has been introduced by incorporation of a cobalt porphyrin into the membrane; fluoride selectivity

  7. Using NMR chemical shifts to calculate the propensity for structural order and disorder in proteins

    NARCIS (Netherlands)

    Tamiola, Kamil; Mulder, Frans A. A.

    2012-01-01

    NMR spectroscopy offers the unique possibility to relate the structural propensities of disordered proteins and loop segments of folded peptides to biological function and aggregation behaviour. Backbone chemical shifts are ideally suited for this task, provided that appropriate reference data are a

  8. Isotope effects on chemical shifts in the study of intramolecular hydrogen bonds

    DEFF Research Database (Denmark)

    Hansen, Poul Erik

    2015-01-01

    The paper deals with the use of isotope effects on chemical shifts in characterizing intramolecular hydrogen bonds. Both so-called resonance-assisted (RAHB) and non-RAHB systems are treated. The importance of RAHB will be discussed. Another very important issue is the borderline between “static” ...

  9. Can the current density map topology be extracted from the nucleus independent chemical shifts?

    NARCIS (Netherlands)

    Van Damme, Sofie; Acke, Guillaume; Havenith, Remco W. A.; Bultinck, Patrick

    2016-01-01

    Aromatic compounds are characterised by the presence of a ring current when in a magnetic field. As a consequence, current density maps are used to assess (the degree of) aromaticity of a compound. However, often a more discrete set of so-called Nucleus Independent Chemical Shift (NICS) values is us

  10. Computation of Chemical Shifts for Paramagnetic Molecules: A Laboratory Experiment for the Undergraduate Curriculum

    Science.gov (United States)

    Pritchard, Benjamin P.; Simpson, Scott; Zurek, Eva; Autschbach, Jochen

    2014-01-01

    A computational experiment investigating the [superscript 1]H and [superscript 13]C nuclear magnetic resonance (NMR) chemical shifts of molecules with unpaired electrons has been developed and implemented. This experiment is appropriate for an upper-level undergraduate laboratory course in computational, physical, or inorganic chemistry. The…

  11. The statistical shift of the chemical potential causing anomalous conductivity in hydrogenated microcrystalline silicon

    NARCIS (Netherlands)

    Lof, R.W.; Schropp, R.E.I.

    2010-01-01

    The behavior of the electrical conductivity in hydrogenated microcrystalline silicon (μ c-Si:H) that is frequently observed is explained by considering the statistical shift in the chemical potential as a function of the crystalline fraction (Xc), the dangling bond density (N db), and the doping den

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

    DEFF Research Database (Denmark)

    Christensen, Anders Steen; Linnet, Troels Emtekær; Borg, Mikael;

    2013-01-01

    We present the ProCS method for the rapid and accurate prediction of protein backbone amide proton chemical shifts - sensitive probes of the geometry of key hydrogen bonds that determine protein structure. ProCS is parameterized against quantum mechanical (QM) calculations and reproduces high level...

  13. Elucidating the Link between NMR Chemical Shifts and Electronic Structure in d(0) Olefin Metathesis Catalysts.

    Science.gov (United States)

    Halbert, Stéphanie; Copéret, Christophe; Raynaud, Christophe; Eisenstein, Odile

    2016-02-24

    The nucleophilic carbon of d(0) Schrock alkylidene metathesis catalysts, [M] = CHR, display surprisingly low downfield chemical shift (δ(iso)) and large chemical shift anisotropy. State-of-the-art four-component relativistic calculations of the chemical shift tensors combined with a two-component analysis in terms of localized orbitals allow a molecular-level understanding of their orientations, the magnitude of their principal components (δ11 > δ22 > δ33) and associated δ(iso). This analysis reveals the dominating influence of the paramagnetic contribution yielding a highly deshielded alkylidene carbon. The largest paramagnetic contribution, which originates from the coupling of alkylidene σ(MC) and π*(MC) orbitals under the action of the magnetic field, is analogous to that resulting from coupling σ(CC) and π*(CC) in ethylene; thus, δ11 is in the MCH plane and is perpendicular to the MC internuclear direction. The higher value of carbon-13 δ(iso) in alkylidene complexes relative to ethylene is thus due to the smaller energy gap between σ(MC) and π*(MC) vs this between σ(CC) and π*(CC) in ethylene. This effect also explains why the highest value of δ(iso) is observed for Mo and the lowest for Ta, the values for W and Re being in between. In the presence of agostic interaction, the chemical shift tensor principal components orientation (δ22 or δ33 parallel or perpendicular to π(MX)) is influenced by the MCH angle because it determines the orientation of the alkylidene CHR fragment relative to the MC internuclear axis. The orbital analysis shows how the paramagnetic terms, understood with a localized bond model, determine the chemical shift tensor and thereby δ(iso).

  14. Early Visual Cortex Dynamics during Top-Down Modulated Shifts of Feature-Selective Attention.

    Science.gov (United States)

    Müller, Matthias M; Trautmann, Mireille; Keitel, Christian

    2016-04-01

    Shifting attention from one color to another color or from color to another feature dimension such as shape or orientation is imperative when searching for a certain object in a cluttered scene. Most attention models that emphasize feature-based selection implicitly assume that all shifts in feature-selective attention underlie identical temporal dynamics. Here, we recorded time courses of behavioral data and steady-state visual evoked potentials (SSVEPs), an objective electrophysiological measure of neural dynamics in early visual cortex to investigate temporal dynamics when participants shifted attention from color or orientation toward color or orientation, respectively. SSVEPs were elicited by four random dot kinematograms that flickered at different frequencies. Each random dot kinematogram was composed of dashes that uniquely combined two features from the dimensions color (red or blue) and orientation (slash or backslash). Participants were cued to attend to one feature (such as color or orientation) and respond to coherent motion targets of the to-be-attended feature. We found that shifts toward color occurred earlier after the shifting cue compared with shifts toward orientation, regardless of the original feature (i.e., color or orientation). This was paralleled in SSVEP amplitude modulations as well as in the time course of behavioral data. Overall, our results suggest different neural dynamics during shifts of attention from color and orientation and the respective shifting destinations, namely, either toward color or toward orientation.

  15. Magnetic Shift of the Chemical Freeze-out and Electric Charge Fluctuations

    Science.gov (United States)

    Fukushima, Kenji; Hidaka, Yoshimasa

    2016-09-01

    We discuss the effect of a strong magnetic field on the chemical freeze-out points in ultrarelativistic heavy-ion collisions. As a result of inverse magnetic catalysis or magnetic inhibition, the crossover onset to hot and dense matter out of quarks and gluons should be shifted to a lower temperature. To quantify this shift we employ the hadron resonance gas model and an empirical condition for the chemical freeze-out. We point out that the charged particle abundances are significantly affected by the magnetic field so that the electric charge fluctuation is largely enhanced, especially at high baryon density. The charge conservation partially cancels the enhancement, but our calculation shows that the electric charge fluctuation could serve as a magnetometer. We find that the fluctuation exhibits a crossover behavior rapidly increased for e B ≳(0.4 GeV )2, while the charge chemical potential has smoother behavior with an increasing magnetic field.

  16. Detecting Location Shifts during Model Selection by Step-Indicator Saturation

    Directory of Open Access Journals (Sweden)

    Jennifer L. Castle

    2015-04-01

    Full Text Available To capture location shifts in the context of model selection, we propose selecting significant step indicators from a saturating set added to the union of all of the candidate variables. The null retention frequency and approximate non-centrality of a selection test are derived using a ‘split-half’ analysis, the simplest specialization of a multiple-path block-search algorithm. Monte Carlo simulations, extended to sequential reduction, confirm the accuracy of nominal significance levels under the null and show retentions when location shifts occur, improving the non-null retention frequency compared to the corresponding impulse-indicator saturation (IIS-based method and the lasso.

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

    Science.gov (United States)

    Shen, Yang; Bax, Ad

    2015-01-01

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

  18. Stereoelectronic effects on 1H nuclear magnetic resonance chemical shifts in methoxybenzenes

    DEFF Research Database (Denmark)

    Lambert, Maja; Olsen, Lars; Jaroszewski, Jerzy W

    2006-01-01

    the Ar-OCH3 torsion out of the ring plane, resulting in large stereoelectronic effects on the chemical shift of Hpara. Conformational searches and geometry optimizations for 3-16 at the B3LYP/6-31G** level, followed by B3LYP/6-311++G(2d,2p) calculations for all low-energy conformers, gave excellent......Investigation of all O-methyl ethers of 1,2,3-benzenetriol and 4-methyl-1,2,3-benzenetriol (3-16) by 1H NMR spectroscopy and density-functional calculations disclosed practically useful conformational effects on 1H NMR chemical shifts in the aromatic ring. While the conversion of phenol (2......) to anisole (1) causes only small positive changes of 1H NMR chemical shifts (Delta delta Hmeta > Hpara, the experimental O-methylation induced shifts in ortho-disubstituted phenols are largest for Hpara, Delta delta equals; 0.19 +/- 0.02 ppm (n = 11...

  19. Guide to good practices for the selection, training, and qualification of shift technical advisors

    Energy Technology Data Exchange (ETDEWEB)

    1993-02-01

    The DOE Guide to Good Practices For The Selection, Training, and Qualification of Shift Technical Advisors can be used by any DOE nuclear facility that has implemented the shift technical advisor position. DOE Order 5480-20, ``Personnel Selection, Qualification, Training, and Staffing Requirements at DOE Reactor and Non-Reactor Nuclear Facilities,`` states that only Category A reactors must use shift technical advisor position. However, many DOE nuclear facilities have implemented the shift technical advisor position to provide independent on-shift technical advice and counsel to the shift operating personnel to help determine cause and mitigation of facility accidents. Those DOE nuclear facilities that have implemented or are going to implement the shift technical advisor position will find this guide useful. This guide addresses areas that may be covered by other training programs. In these cases, it is unnecessary (and undesirable) to duplicate these areas in the STA training program as long as the specific skills and knowledge essential for STAs are addressed. The guide is presented based on the premise that the trainee has not completed any facility-specific training other than general employee training.

  20. Guide to good practices for the selection, training, and qualification of shift technical advisors

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1993-02-01

    The DOE Guide to Good Practices For the Selection, Training, and Qualification of Shift Technical Advisors can be used by any DOE nuclear facility that has implemented the shift technical advisor (STA) position. DOE Order 5480.20A, Personnel Selection, Qualification and Training Requirements for DOE Nuclear Facilities, states that only Category A reactors must have a shift technical advisor. However, many DOE nuclear facilities have implemented the shift technical advisor position to provide independent on-shift technical advice and counsel to the shift operating personnel to help determine cause and mitigation of facility accidents. Those DOE nuclear facilities that have implemented or are going to implement the shift technical advisor position will find this guide useful. This guide addresses areas that may be covered by other training programs. In these cases, it is unnecessary (and undesirable) to duplicate these areas in the STA training program as long as the specific skills and knowledge essential for STAs are addressed. The guide is based on the premise that the trainee has not completed any facility-specific training other than general employee training.

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

    Science.gov (United States)

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

    2013-06-04

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

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

    Science.gov (United States)

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

    2012-10-01

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

  3. Identifying Stereoisomers by ab-initio Calculation of Secondary Isotope Shifts on NMR Chemical Shieldings

    Directory of Open Access Journals (Sweden)

    Karl-Heinz Böhm

    2014-04-01

    Full Text Available We present ab-initio calculations of secondary isotope effects on NMR chemical shieldings. The change of the NMR chemical shift of a certain nucleus that is observed if another nucleus is replaced by a different isotope can be calculated by computing vibrational corrections on the NMR parameters using electronic structure methods. We demonstrate that the accuracy of the computational results is sufficient to even distinguish different conformers. For this purpose, benchmark calculations for fluoro(2-2Hethane in gauche and antiperiplanar conformation are carried out at the HF, MP2 and CCSD(T level of theory using basis sets ranging from double- to quadruple-zeta quality. The methodology is applied to the secondary isotope shifts for 2-fluoronorbornane in order to resolve an ambiguity in the literature on the assignment of endo- and exo-2-fluoronorbornanes with deuterium substituents in endo-3 and exo-3 positions, also yielding insight into mechanistic details of the corresponding synthesis.

  4. Caterpillar seed predators mediate shifts in selection on flowering phenology in their host plant.

    Science.gov (United States)

    Valdés, Alicia; Ehrlén, Johan

    2017-01-01

    Variation in selection among populations and years has important implications for evolutionary trajectories of populations. Yet, the agents of selection causing this variation have rarely been identified. Selection on the time of reproduction within a season in plants might differ both among populations and among years, and selection can be mediated by both mutualists and antagonists. We investigated if differences in the direction of phenotypic selection on flowering phenology among 20 populations of Gentiana pneumonanthe during 2 yr were related to the presence of the butterfly seed predator Phengaris alcon, and if butterfly incidence was associated with the abundance of the butterfly's second host, Myrmica ants. In plant populations without the butterfly, phenotypic selection favored earlier flowering. In populations where the butterfly was present, caterpillars preferentially attacked early-flowering individuals, shifting the direction of selection to favoring later flowering. Butterfly incidence in plant populations increased with ant abundance. Our results demonstrate that antagonistic interactions can shift the direction of selection on flowering phenology, and suggest that such shifts might be associated with differences in the community context.

  5. First-principles calculation of core-level binding energy shift in surface chemical processes

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    Combined with third generation synchrotron radiation light sources, X-ray photoelectron spectroscopy (XPS) with higher energy resolution, brilliance, enhanced surface sensitivity and photoemission cross section in real time found extensive applications in solid-gas interface chemistry. This paper reports the calculation of the core-level binding energy shifts (CLS) using the first-principles density functional theory. The interplay between the CLS calculations and XPS measurements to uncover the structures, adsorption sites and chemical reactions in complex surface chemical processes are highlight. Its application on clean low index (111) and vicinal transition metal surfaces, molecular adsorption in terms of sites and configuration, and reaction kinetics are domonstrated.

  6. Relationship between electrophilicity index, Hammett constant and nucleus-independent chemical shift

    Indian Academy of Sciences (India)

    M Elango; R Parthasarathi; G Karthik Narayanan; A Md Sabeelullah; U Sarkar; N S Venkatasubramaniyan; V Subramanian; P K Chattaraj

    2005-01-01

    Inter-relationships between the electrophilicity index (), Hammett constant (ó) and nucleusindependent chemical shift (NICS (1) - NICS value one å ngstrom above the ring centre) have been investigated for a series of meta- and para-substituted benzoic acids. Good linear relationships between Hammett constant vs electrophilicity and Hammett constant vs NICS (1) values have been observed. However, the variation of NICS (1) against shows only a low correlation coefficient.

  7. Crime Scene Investigation: Clinical Application of Chemical Shift Imaging as a Problem Solving Tool

    Science.gov (United States)

    2016-02-26

    MDW/SGVU SUBJECT: Professional Presentation Approva l 26 FEB 2016 1. Your paper, entitled Crime Scene Investigation: Clinical Aoolication of...or technical information as a publication/presentation, a new 59 MDW Form 3039 must be submitted for review and approval.] Crime Scene Investiga...tion: Clinical Application of Chemical Shift Imaging as a Problem Solving Tool 1. TITLE OF MATERIAL TO BE PUBLISHED OR PRESENTED Crime Scene

  8. Effects of Protein-pheromone Complexation on Correlated Chemical Shift Modulations

    Energy Technology Data Exchange (ETDEWEB)

    Perazzolo, Chiara; Wist, Julien [Ecole Polytechnique Federale de Lausanne, Institut des Sciences et Ingenierie Chimiques (Switzerland); Loth, Karine; Poggi, Luisa [Ecole Normale Superieure, Departement de chimie, associe au CNRS (France); Homans, Steve [University of Leeds, School of Biochemistry and Microbiology (United Kingdom); Bodenhausen, Geoffrey [Ecole Polytechnique Federale de Lausanne, Institut des Sciences et Ingenierie Chimiques (Switzerland)], E-mail: Geoffrey.Bodenhausen@ens.fr

    2005-12-15

    Major urinary protein (MUP) is a pheromone-carrying protein of the lipocalin family. Previous studies by isothermal titration calorimetry (ITC) show that the affinity of MUP for the pheromone 2-methoxy-3-isobutylpyrazine (IBMP) is mainly driven by enthalpy, with a small unfavourable entropic contribution. Entropic terms can be attributed in part to changes in internal motions of the protein upon binding. Slow internal motions can lead to correlated or anti-correlated modulations of the isotropic chemical shifts of carbonyl C' and amide N nuclei. Correlated chemical shift modulations (CSM/CSM) in MUP have been determined by measuring differences of the transverse relaxation rates of zero- and double-quantum coherences ZQC{l_brace}C'N{r_brace} and DQC{l_brace}C'N{r_brace}, and by accounting for the effects of correlated fluctuations of dipole-dipole couplings (DD/DD) and chemical shift anisotropies (CSA/CSA). The latter can be predicted from tensor parameters of C' and N nuclei that have been determined in earlier work. The effects of complexation on slow time-scale protein dynamics can be determined by comparing the temperature dependence of the relaxation rates of APO-MUP (i.e., without ligand) and HOLO-MUP (i.e., with IBMP as a ligand)

  9. Substituent effects in the 13C NMR chemical shifts of alpha-mono-substituted acetonitriles.

    Science.gov (United States)

    Reis, Adriana K C A; Rittner, Roberto

    2007-03-01

    13C chemical shifts empirical calculations, through a very simple additivity relationship, for the alpha-methylene carbon of some alpha-mono-substituted acetonitriles, Y-CH(2)-CN (Y=H, F, Cl, Br, I, OMe, OEt, SMe, SEt, NMe(2), NEt(2), Me and Et), lead to similar, or even better, results in comparison to the reported values obtained through Quantum Mechanics methods. The observed deviations, for some substituents, are very similar for both approaches. This divergence between experimental and calculated, either empirically or theoretically, values are smaller than for the corresponding acetones, amides, acetic acids and methyl esters, which had been named non-additivity effects (or intramolecular interaction chemical shifts, ICS) and attributed to some orbital interactions. Here, these orbital interactions do not seem to be the main reason for the non-additivity effects in the empirical calculations, which must be due solely to the magnetic anisotropy of the heavy atom present in the substituent. These deviations, which were also observed in the theoretical calculations, were attributed in that case to the non-inclusion of relativistic effects and spin-orbit coupling in the Hamiltonian. Some divergence is also observed for the cyano carbon chemical shifts, probably due to the same reasons.

  10. DOE handbook: Guide to good practices for the selection, training, and qualification of shift supervisors

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1999-04-01

    This Department of Energy (DOE) handbook is approved for use by all DOE Components and their contractors. The Handbook incorporates editorial changes to DOE-STD-1061-93, ``Guide to Good Practices for the Selection, Training, and Qualification of shift Supervisors,`` and supersedes DOE-STD-1061-93. Technical content of this Handbook has not changed from the original technical standard. Changes are primarily editorial improvements, redesignation of the standard to a Handbook, and format changes to conform with current Technical Standards Program procedures. This guide, used in conjunction with a facility-specific job analysis, provides a framework for the selection, training, qualification, and professional development of reactor facility and non-reactor nuclear facility shift supervisors. Training and qualification programs based on this guide should provide assurance that shift supervisors perform their jobs safely and competently.

  11. Temperature dependence of contact and dipolar NMR chemical shifts in paramagnetic molecules.

    Science.gov (United States)

    Martin, Bob; Autschbach, Jochen

    2015-02-07

    Using a recently proposed equation for NMR nuclear magnetic shielding for molecules with unpaired electrons [A. Soncini and W. Van den Heuvel, J. Chem. Phys. 138, 021103 (2013)], equations for the temperature (T) dependent isotropic shielding for multiplets with an effective spin S equal to 1/2, 1, 3/2, 2, and 5/2 in terms of electron paramagnetic resonance spin Hamiltonian parameters are derived and then expanded in powers of 1/T. One simplifying assumption used is that a matrix derived from the zero-field splitting (ZFS) tensor and the Zeeman coupling matrix (g-tensor) share the same principal axis system. The influence of the rhombic ZFS parameter E is only investigated for S = 1. Expressions for paramagnetic contact shielding (from the isotropic part of the hyperfine coupling matrix) and pseudo-contact or dipolar shielding (from the anisotropic part of the hyperfine coupling matrix) are considered separately. The leading order is always 1/T. A temperature dependence of the contact shielding as 1/T and of the dipolar shielding as 1/T(2), which is sometimes assumed in the assignment of paramagnetic chemical shifts, is shown to arise only if S ≥ 1 and zero-field splitting is appreciable, and only if the Zeeman coupling matrix is nearly isotropic (Δg = 0). In such situations, an assignment of contact versus dipolar shifts may be possible based only on linear and quadratic fits of measured variable-temperature chemical shifts versus 1/T. Numerical data are provided for nickelocene (S = 1). Even under the assumption of Δg = 0, a different leading order of contact and dipolar shifts in powers of 1/T is not obtained for S = 3/2. When Δg is not very small, dipolar and contact shifts both depend in leading order in 1/T in all cases, with sizable contributions in order 1/T(n) with n = 2 and higher.

  12. Chemical tailoring of teicoplanin with site-selective reactions.

    Science.gov (United States)

    Pathak, Tejas P; Miller, Scott J

    2013-06-05

    Semisynthesis of natural product derivatives combines the power of fermentation with orthogonal chemical reactions. Yet, chemical modification of complex structures represents an unmet challenge, as poor selectivity often undermines efficiency. The complex antibiotic teicoplanin eradicates bacterial infections. However, as resistance emerges, the demand for improved analogues grows. We have discovered chemical reactions that achieve site-selective alteration of teicoplanin. Utilizing peptide-based additives that alter reaction selectivities, certain bromo-teicoplanins are accessible. These new compounds are also scaffolds for selective cross-coupling reactions, enabling further molecular diversification. These studies enable two-step access to glycopeptide analogues not available through either biosynthesis or rapid total chemical synthesis alone. The new compounds exhibit a spectrum of activities, revealing that selective chemical alteration of teicoplanin may lead to analogues with attenuated or enhanced antibacterial properties, in particular against vancomycin- and teicoplanin-resistant strains.

  13. SiC-BASED HYDROGEN SELECTIVE MEMBRANES FOR WATER-GAS-SHIFT REACTION

    Energy Technology Data Exchange (ETDEWEB)

    Paul K.T. Liu

    2001-10-16

    This technical report summarizes our activities conducted in Yr II. In Yr I we successfully demonstrated the feasibility of preparing the hydrogen selective SiC membrane with a chemical vapor deposition (CVD) technique. In addition, a SiC macroporous membrane was fabricated as a substrate candidate for the proposed SiC membrane. In Yr II we have focused on the development of a microporous SiC membrane as an intermediate layer between the substrate and the final membrane layer prepared from CVD. Powders and supported thin silicon carbide films (membranes) were prepared by a sol-gel technique using silica sol precursors as the source of silicon, and phenolic resin as the source of carbon. The powders and films were prepared by the carbothermal reduction reaction between the silica and the carbon source. The XRD analysis indicates that the powders and films consist of SiC, while the surface area measurement indicates that they contain micropores. SEM and AFM studies of the same films also validate this observation. The powders and membranes were also stable under different corrosive and harsh environments. The effects of these different treatments on the internal surface area, pore size distribution, and transport properties, were studied for both the powders and the membranes using the aforementioned techniques and XPS. Finally the SiC membrane materials are shown to have satisfactory hydrothermal stability for the proposed application. In Yr III, we will focus on the demonstration of the potential benefit using the SiC membrane developed from Yr I and II for the water-gas-shift (WGS) reaction.

  14. DFT calculations of 1H and 13C NMR chemical shifts in transition metal hydrides.

    Science.gov (United States)

    del Rosal, I; Maron, L; Poteau, R; Jolibois, F

    2008-08-14

    Transition metal hydrides are of great interest in chemistry because of their reactivity and their potential use as catalysts for hydrogenation. Among other available techniques, structural properties in transition metal (TM) complexes are often probed by NMR spectroscopy. In this paper we will show that it is possible to establish a viable methodological strategy in the context of density functional theory, that allows the determination of 1H NMR chemical shifts of hydride ligands attached to transition metal atoms in mononuclear systems and clusters with good accuracy with respect to experiment. 13C chemical shifts have also been considered in some cases. We have studied mononuclear ruthenium complexes such as Ru(L)(H)(dppm)2 with L = H or Cl, cationic complex [Ru(H)(H2O)(dppm)2]+ and Ru(H)2(dppm)(PPh3)2, in which hydride ligands are characterized by a negative 1H NMR chemical shift. For these complexes all calculations are in relatively good agreement compared to experimental data with errors not exceeding 20% except for the hydrogen atom in Ru(H)2(dppm)(PPh3)2. For this last complex, the relative error increases to 30%, probably owing to the necessity to take into account dynamical effects of phenyl groups. Carbonyl ligands are often encountered in coordination chemistry. Specific issues arise when calculating 1H or 13C NMR chemical shifts in TM carbonyl complexes. Indeed, while errors of 10 to 20% with respect to experiment are often considered good in the framework of density functional theory, this difference in the case of mononuclear carbonyl complexes culminates to 80%: results obtained with all-electron calculations are overall in very satisfactory agreement with experiment, the error in this case does not exceed 11% contrary to effective core potentials (ECPs) calculations which yield errors always larger than 20%. We conclude that for carbonyl groups the use of ECPs is not recommended, although their use could save time for very large systems, for

  15. Complete (1)H and (13)C NMR chemical shift assignments of mono-, di-, and trisaccharides as basis for NMR chemical shift predictions of polysaccharides using the computer program casper.

    Science.gov (United States)

    Roslund, Mattias U; Säwén, Elin; Landström, Jens; Rönnols, Jerk; Jonsson, K Hanna M; Lundborg, Magnus; Svensson, Mona V; Widmalm, Göran

    2011-08-16

    The computer program casper uses (1)H and (13)C NMR chemical shift data of mono- to trisaccharides for the prediction of chemical shifts of oligo- and polysaccharides. In order to improve the quality of these predictions the (1)H and (13)C, as well as (31)P when applicable, NMR chemical shifts of 30 mono-, di-, and trisaccharides were assigned. The reducing sugars gave two distinct sets of NMR resonances due to the α- and β-anomeric forms. In total 35 (1)H and (13)C NMR chemical shift data sets were obtained from the oligosaccharides. One- and two-dimensional NMR experiments were used for the chemical shift assignments and special techniques were employed in some cases such as 2D (1)H,(13)C-HSQC Hadamard Transform methodology which was acquired approximately 45 times faster than a regular t(1) incremented (1)H,(13)C-HSQC experiment and a 1D (1)H,(1)H-CSSF-TOCSY experiment which was able to distinguish spin-systems in which the target protons were only 3.3Hz apart. The (1)H NMR chemical shifts were subsequently refined using total line-shape analysis with the PERCH NMR software. The acquired NMR data were then utilized in the casper program (http://www.casper.organ.su.se/casper/) for NMR chemical shift predictions of the O-antigen polysaccharides from Klebsiella O5, Shigella flexneri serotype X, and Salmonella arizonae O62. The data were compared to experimental data of the polysaccharides from the two former strains and the lipopolysaccharide of the latter strain showing excellent agreement between predicted and experimental (1)H and (13)C NMR chemical shifts.

  16. Parameter-free calculation of K alpha chemical shifts for Al, Si, and Ge oxides

    DEFF Research Database (Denmark)

    Lægsgaard, Jesper

    2001-01-01

    The chemical shifts of the K alpha radiation line from Al, Si, and Ge ions between their elemental and oxide forms are calculated within the framework of density functional theory using ultrasoft pseudopotentials. It is demonstrated that this theoretical approach yields quantitatively accurate...... results fur the systems investigated, provided that relaxations of the valence electrons upon the core-hole transition are properly accounted for. Therefore, such calculations provide a powerful tool for identification of impurity states based on x-ray fluorescence data. Results for an Al impurity...

  17. NMR Chemical Shift Ranges of Urine Metabolites in Various Organic Solvents

    Directory of Open Access Journals (Sweden)

    Benjamin Görling

    2016-09-01

    Full Text Available Signal stability is essential for reliable multivariate data analysis. Urine samples show strong variance in signal positions due to inter patient differences. Here we study the exchange of the solvent of a defined urine matrix and how it affects signal and integral stability of the urinary metabolites by NMR spectroscopy. The exchange solvents were methanol, acetonitrile, dimethyl sulfoxide, chloroform, acetone, dichloromethane, and dimethyl formamide. Some of these solvents showed promising results with a single batch of urine. To evaluate further differences between urine samples, various acid, base, and salt solutions were added in a defined way mimicking to some extent inter human differences. Corresponding chemical shift changes were monitored.

  18. NMR Chemical Shift Ranges of Urine Metabolites in Various Organic Solvents

    Science.gov (United States)

    Görling, Benjamin; Bräse, Stefan; Luy, Burkhard

    2016-01-01

    Signal stability is essential for reliable multivariate data analysis. Urine samples show strong variance in signal positions due to inter patient differences. Here we study the exchange of the solvent of a defined urine matrix and how it affects signal and integral stability of the urinary metabolites by NMR spectroscopy. The exchange solvents were methanol, acetonitrile, dimethyl sulfoxide, chloroform, acetone, dichloromethane, and dimethyl formamide. Some of these solvents showed promising results with a single batch of urine. To evaluate further differences between urine samples, various acid, base, and salt solutions were added in a defined way mimicking to some extent inter human differences. Corresponding chemical shift changes were monitored. PMID:27598217

  19. Three model space experiments on chemical reactions. [Gibbs adsorption, equilibrium shift and electrodeposition

    Science.gov (United States)

    Grodzka, P.; Facemire, B.

    1977-01-01

    Three investigations conducted aboard Skylab IV and Apollo-Soyuz involved phenomena that are of interest to the biochemistry community. The formaldehyde clock reaction and the equilibrium shift reaction experiments conducted aboard Apollo Soyuz demonstrate the effect of low-g foams or air/liquid dispersions on reaction rate and chemical equilibrium. The electrodeposition reaction experiment conducted aboard Skylab IV demonstrate the effect of a low-g environment on an electrochemical displacement reaction. The implications of the three space experiments for various applications are considered.

  20. Prediction of spectral shifts proportional to source distances by time-varying frequency or wavelength selection

    CERN Document Server

    Guruprasad, V

    2008-01-01

    Any frequency selective device with an ongoing drift will cause observed spectra to be variously and simultaneously scaled in proportion to their source distances. The reason is that detectors after the drifting selection will integrate instantaneous electric or magnetic field values from successive sinusoids, and these sinusoids would differ in both frequency and phase. Phase differences between frequencies are ordinarily irrelevant, and recalibration procedures at most correct for frequency differences. With drifting selection, however, each integrated field value comes from *the sinusoid of the instantaneously selected frequency at its instantaneous received phase*, hence the waveform constructed by the integration will follow the drifting selection with a phase acceleration given by the drift rate times the slope of the received phase spectrum. A phase acceleration is literally a frequency shift, and the phase spectrum slope of a received waveform is an asymptotic measure of the source distance, as the pa...

  1. Optimal voxel size for measuring global gray and white matter proton metabolite concentrations using chemical shift imaging

    DEFF Research Database (Denmark)

    Hanson, Lars Peter Grüner; Adalsteinsson, E; Pfefferbaum, A;

    2000-01-01

    Quantification of gray and white matter levels of spectroscopically visible metabolites can provide important insights into brain development and pathological conditions. Chemical shift imaging offers a gain in efficiency for estimation of global gray and white matter metabolite concentrations...

  2. Predicting Pt-195 NMR chemical shift using new relativistic all-electron basis set.

    Science.gov (United States)

    Paschoal, D; Guerra, C Fonseca; de Oliveira, M A L; Ramalho, T C; Dos Santos, H F

    2016-10-01

    Predicting NMR properties is a valuable tool to assist the experimentalists in the characterization of molecular structure. For heavy metals, such as Pt-195, only a few computational protocols are available. In the present contribution, all-electron Gaussian basis sets, suitable to calculate the Pt-195 NMR chemical shift, are presented for Pt and all elements commonly found as Pt-ligands. The new basis sets identified as NMR-DKH were partially contracted as a triple-zeta doubly polarized scheme with all coefficients obtained from a Douglas-Kroll-Hess (DKH) second-order scalar relativistic calculation. The Pt-195 chemical shift was predicted through empirical models fitted to reproduce experimental data for a set of 183 Pt(II) complexes which NMR sign ranges from -1000 to -6000 ppm. Furthermore, the models were validated using a new set of 75 Pt(II) complexes, not included in the descriptive set. The models were constructed using non-relativistic Hamiltonian at density functional theory (DFT-PBEPBE) level with NMR-DKH basis set for all atoms. For the best model, the mean absolute deviation (MAD) and the mean relative deviation (MRD) were 150 ppm and 6%, respectively, for the validation set (75 Pt-complexes) and 168 ppm (MAD) and 5% (MRD) for all 258 Pt(II) complexes. These results were comparable with relativistic DFT calculation, 200 ppm (MAD) and 6% (MRD). © 2016 Wiley Periodicals, Inc.

  3. Feature Selection for Chemical Sensor Arrays Using Mutual Information

    Science.gov (United States)

    Wang, X. Rosalind; Lizier, Joseph T.; Nowotny, Thomas; Berna, Amalia Z.; Prokopenko, Mikhail; Trowell, Stephen C.

    2014-01-01

    We address the problem of feature selection for classifying a diverse set of chemicals using an array of metal oxide sensors. Our aim is to evaluate a filter approach to feature selection with reference to previous work, which used a wrapper approach on the same data set, and established best features and upper bounds on classification performance. We selected feature sets that exhibit the maximal mutual information with the identity of the chemicals. The selected features closely match those found to perform well in the previous study using a wrapper approach to conduct an exhaustive search of all permitted feature combinations. By comparing the classification performance of support vector machines (using features selected by mutual information) with the performance observed in the previous study, we found that while our approach does not always give the maximum possible classification performance, it always selects features that achieve classification performance approaching the optimum obtained by exhaustive search. We performed further classification using the selected feature set with some common classifiers and found that, for the selected features, Bayesian Networks gave the best performance. Finally, we compared the observed classification performances with the performance of classifiers using randomly selected features. We found that the selected features consistently outperformed randomly selected features for all tested classifiers. The mutual information filter approach is therefore a computationally efficient method for selecting near optimal features for chemical sensor arrays. PMID:24595058

  4. Learning from Chemical Visualizations: Comparing Generation and Selection

    Science.gov (United States)

    Zhang, Zhihui Helen; Linn, Marcia C.

    2013-01-01

    Dynamic visualizations can make unseen phenomena such as chemical reactions visible but students need guidance to benefit from them. This study explores the value of generating drawings versus selecting among alternatives to guide students to learn chemical reactions from a dynamic visualization of hydrogen combustion as part of an online inquiry…

  5. SiC-BASED HYDROGEN SELECTIVE MEMBRANES FOR WATER-GAS-SHIFT REACTION

    Energy Technology Data Exchange (ETDEWEB)

    Unknown

    2000-12-01

    A hydrogen selective membrane as a membrane reactor (MR) can significantly improve the power generation efficiency with a reduced capital and operating cost for the waster-gas-shift reaction. Existing hydrogen selective ceramic membranes are not suitable for the proposed MR due to their poor hydrothermal stability. In this project we have focused on the development of innovative silicon carbide (SiC) based hydrogen selective membranes, which can potentially overcome this technical barrier. During Year I, we have successfully fabricated SiC macro porous membranes via extrusion of commercially available SiC powder, which were then deposited with thin, micro-porous (6 to 40{angstrom} in pore size) films via sol-gel technique as intermediate layers. Finally, an SiC hydrogen selective thin film was deposited on this substrate via our CVD/I technique. The composite membrane thus prepared demonstrated excellent hydrogen selectivity at high temperature ({approx}600 C). More importantly, this membrane also exhibited a much improved hydrothermal stability at 600 C with 50% steam (atmospheric pressure) for nearly 100 hours. In parallel, we have explored an alternative approach to develop a H{sub 2} selective SiC membrane via pyrolysis of selected pre-ceramic polymers. Building upon the positive progress made in the Year I preliminary study, we will conduct an optimization study in Year II to develop an optimized H{sub 2} selective SiC membrane with sufficient hydrothermal stability suitable for the WGS environment.

  6. 125Te NMR chemical-shift trends in PbTe–GeTe and PbTe–SnTe alloys

    Energy Technology Data Exchange (ETDEWEB)

    Njegic, Bosiljka [Ames Laboratory; Levin, Evgenii M. [Ames Laboratory; Schmidt-Rohr, Klaus [Ames Laboratory

    2013-10-08

    Complex tellurides, such as doped PbTe, GeTe, and their alloys, are among the best thermoelectric materials. Knowledge of the change in 125Te NMR chemical shift due to bonding to dopant or “solute” atoms is useful for determination of phase composition, peak assignment, and analysis of local bonding. We have measured the 125Te NMR chemical shifts in PbTe-based alloys, Pb1-xGexTe and Pb1-xSnxTe, which have a rocksalt-like structure, and analyzed their trends. For low x, several peaks are resolved in the 22-kHz MAS 125Te NMR spectra. A simple linear trend in chemical shifts with the number of Pb neighbors is observed. No evidence of a proposed ferroelectric displacement of Ge atoms in a cubic PbTe matrix is detected at low Ge concentrations. The observed chemical shift trends are compared with the results of DFT calculations, which confirm the linear dependence on the composition of the first-neighbor shell. The data enable determination of the composition of various phases in multiphase telluride materials. They also provide estimates of the 125Te chemical shifts of GeTe and SnTe (+970 and +400±150 ppm, respectively, from PbTe), which are otherwise difficult to access due to Knight shifts of many hundreds of ppm in neat GeTe and SnTe.

  7. 125Te NMR chemical-shift trends in PbTe-GeTe and PbTe-SnTe alloys.

    Science.gov (United States)

    Njegic, B; Levin, E M; Schmidt-Rohr, K

    2013-01-01

    Complex tellurides, such as doped PbTe, GeTe, and their alloys, are among the best thermoelectric materials. Knowledge of the change in (125)Te NMR chemical shift due to bonding to dopant or "solute" atoms is useful for determination of phase composition, peak assignment, and analysis of local bonding. We have measured the (125)Te NMR chemical shifts in PbTe-based alloys, Pb1-xGexTe and Pb1-xSnxTe, which have a rocksalt-like structure, and analyzed their trends. For low x, several peaks are resolved in the 22-kHz MAS (125)Te NMR spectra. A simple linear trend in chemical shifts with the number of Pb neighbors is observed. No evidence of a proposed ferroelectric displacement of Ge atoms in a cubic PbTe matrix is detected at low Ge concentrations. The observed chemical shift trends are compared with the results of DFT calculations, which confirm the linear dependence on the composition of the first-neighbor shell. The data enable determination of the composition of various phases in multiphase telluride materials. They also provide estimates of the (125)Te chemical shifts of GeTe and SnTe (+970 and +400±150 ppm, respectively, from PbTe), which are otherwise difficult to access due to Knight shifts of many hundreds of ppm in neat GeTe and SnTe.

  8. Reassigning the Structures of Natural Products Using NMR Chemical Shifts Computed with Quantum Mechanics: A Laboratory Exercise

    Science.gov (United States)

    Palazzo, Teresa A.; Truong, Tiana T.; Wong, Shirley M. T.; Mack, Emma T.; Lodewyk, Michael W.; Harrison, Jason G.; Gamage, R. Alan; Siegel, Justin B.; Kurth, Mark J.; Tantillo, Dean J.

    2015-01-01

    An applied computational chemistry laboratory exercise is described in which students use modern quantum chemical calculations of chemical shifts to assign the structure of a recently isolated natural product. A pre/post assessment was used to measure student learning gains and verify that students demonstrated proficiency of key learning…

  9. Chemical genetics approaches for selective intervention in epigenetics.

    Science.gov (United States)

    Runcie, Andrew C; Chan, Kwok-Ho; Zengerle, Michael; Ciulli, Alessio

    2016-08-01

    Chemical genetics is the use of biologically active small molecules (chemical probes) to investigate the functions of gene products, through the modulation of protein activity. Recent years have seen significant progress in the application of chemical genetics to study epigenetics, following the development of new chemical probes, a growing appreciation of the role of epigenetics in disease and a recognition of the need and utility of high-quality, cell-active chemical probes. In this review, we single out the bromodomain reader domains as a prime example of both the success, and challenges facing chemical genetics. The difficulty in generating single-target selectivity has long been a thorn in the side of chemical genetics, however, recent developments in advanced forms of chemical genetics promise to bypass this, and other, limitations. The 'bump-and-hole' approach has now been used to probe - for the first time - the BET bromodomain subfamily with single-target selectivity and may be applicable to other epigenetic domains. Meanwhile, PROTAC compounds have been shown to be significantly more efficacious than standard domain inhibitors, and have the potential to enhance target selectivity.

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

    Science.gov (United States)

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

    2016-09-01

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

  11. Moving attention - Evidence for time-invariant shifts of visual selective attention

    Science.gov (United States)

    Remington, R.; Pierce, L.

    1984-01-01

    Two experiments measured the time to shift spatial selective attention across the visual field to targets 2 or 10 deg from central fixation. A central arrow cued the most likely target location. The direction of attention was inferred from reaction times to expected, unexpected, and neutral locations. The development of a spatial attentional set with time was examined by presenting target probes at varying times after the cue. There were no effects of distance on the time course of the attentional set. Reaction times for far locations were slower than for near, but the effects of attention were evident by 150 msec in both cases. Spatial attention does not shift with a characteristic, fixed velocity. Rather, velocity is proportional to distance, resulting in a movement time that is invariant over the distances tested.

  12. The interplay between transient a-helix formation and side chain rotamer distributions in disordered proteins probed by methyl chemical shifts

    DEFF Research Database (Denmark)

    Kjærgaard, Magnus; Iesmantavicius, Vytautas; Poulsen, Flemming M

    2011-01-01

    and retinoid receptors (ACTR). We find that small differences in the methyl carbon chemical shifts due to the ¿-gauche effect may provide information about the side chain rotamer distributions. However, the effects of neighboring residues on the methyl group chemical shifts obscure the direct observation...... of ¿-gauche effect. To overcome this, we reference the chemical shifts to those in a more disordered state resulting in residue specific random coil chemical shifts. The (13)C secondary chemical shifts of the methyl groups of valine, leucine, and isoleucine show sequence specific effects, which allow...

  13. Sequential acquisition of multi-dimensional heteronuclear chemical shift correlation spectra with 1H detection

    Science.gov (United States)

    Bellstedt, Peter; Ihle, Yvonne; Wiedemann, Christoph; Kirschstein, Anika; Herbst, Christian; Görlach, Matthias; Ramachandran, Ramadurai

    2014-03-01

    RF pulse schemes for the simultaneous acquisition of heteronuclear multi-dimensional chemical shift correlation spectra, such as {HA(CA)NH & HA(CACO)NH}, {HA(CA)NH & H(N)CAHA} and {H(N)CAHA & H(CC)NH}, that are commonly employed in the study of moderately-sized protein molecules, have been implemented using dual sequential 1H acquisitions in the direct dimension. Such an approach is not only beneficial in terms of the reduction of experimental time as compared to data collection via two separate experiments but also facilitates the unambiguous sequential linking of the backbone amino acid residues. The potential of sequential 1H data acquisition procedure in the study of RNA is also demonstrated here.

  14. Ab Initio Calculations of Deuterium Isotope Effects on Chemical Shifts of Salt-Bridged Lysines

    DEFF Research Database (Denmark)

    Ullah, Saif; Ishimoto, Takayoshi; Williamson, Mike P.;

    2011-01-01

    Deuterium isotope effects measure the change in chemical shift on substitution of a proton by deuterium. They have been calculated by direct treatment of the H/D nuclear quantum effect using a multicomponent ab initio molecular orbital method based on a non-Born−Oppenheimer approximation....... This method enables the determination of both the electronic and the protonic (deuteronic) wave functions simultaneously and can directly calculate the geometrical difference induced by H/D isotope effects. The calculations show that the one-bond deuterium isotope effects on 15N nuclear shielding, 1Δ15N......(D), in ammonium and amines decrease as a counterion or water molecule moves closer to the nitrogen. 1Δ15N(D) and 2Δ1H(D) of the NH3+ groups of lysine residues in the B1 domain of protein G have been calculated using truncated side chains and also determined experimentally by NMR. Comparisons show...

  15. Study of wavelength-shifting chemicals for use in large-scale water Cherenkov detectors

    CERN Document Server

    Sweany, M; Dazeley, S; Dunmore, J; Felde, J; Svoboda, R; Tripathi, M

    2011-01-01

    Cherenkov detectors employ various methods to maximize light collection at the photomultiplier tubes (PMTs). These generally involve the use of highly reflective materials lining the interior of the detector, reflective materials around the PMTs, or wavelength-shifting sheets around the PMTs. Recently, the use of water-soluble wavelength-shifters has been explored to increase the measurable light yield of Cherenkov radiation in water. These wave-shifting chemicals are capable of absorbing light in the ultravoilet and re-emitting the light in a range detectable by PMTs. Using a 250 L water Cherenkov detector, we have characterized the increase in light yield from three compounds in water: 4-Methylumbelliferone, Carbostyril-124, and Amino-G Salt. We report the gain in PMT response at a concentration of 1 ppm as: 1.88 $\\pm$ 0.02 for 4-Methylumbelliferone, stable to within 0.5% over 50 days, 1.37 $\\pm$ 0.03 for Carbostyril-124, and 1.20 $\\pm$ 0.02 for Amino-G Salt. The response of 4-Methylumbelliferone was modele...

  16. Handling the influence of chemical shift in amplitude-modulated heteronuclear dipolar recoupling solid-state NMR

    Science.gov (United States)

    Basse, Kristoffer; Shankar, Ravi; Bjerring, Morten; Vosegaard, Thomas; Nielsen, Niels Chr.; Nielsen, Anders B.

    2016-09-01

    We present a theoretical analysis of the influence of chemical shifts on amplitude-modulated heteronuclear dipolar recoupling experiments in solid-state NMR spectroscopy. The method is demonstrated using the Rotor Echo Short Pulse IRrAdiaTION mediated Cross-Polarization (RESPIRATIONCP) experiment as an example. By going into the pulse sequence rf interaction frame and employing a quintuple-mode operator-based Floquet approach, we describe how chemical shift offset and anisotropic chemical shift affect the efficiency of heteronuclear polarization transfer. In this description, it becomes transparent that the main attribute leading to non-ideal performance is a fictitious field along the rf field axis, which is generated from second-order cross terms arising mainly between chemical shift tensors and themselves. This insight is useful for the development of improved recoupling experiments. We discuss the validity of this approach and present quaternion calculations to determine the effective resonance conditions in a combined rf field and chemical shift offset interaction frame transformation. Based on this, we derive a broad-banded version of the RESPIRATIONCP experiment. The new sequence is experimentally verified using SNNFGAILSS amyloid fibrils where simultaneous 15N → 13CO and 15N → 13Cα coherence transfer is demonstrated on high-field NMR instrumentation, requiring great offset stability.

  17. 50 years anniversary of the discovery of the core level chemical shifts. The early years of photoelectron spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Mårtensson, Nils [Department of Physics and Astronomy, Uppsala University, Box 516, 751 20 Uppsala (Sweden); Sokolowski, Evelyn [Tvär-Ramsdal 1, 611 99 Tystberga (Sweden); Svensson, Svante, E-mail: Svante.Svensson@fysik.uu.se [Department of Physics and Astronomy, Uppsala University, Box 516, 751 20 Uppsala (Sweden)

    2014-03-01

    Highlights: • 50 years since the discovery of t the core level chemical shift. • The pioneering years of ESCA. • A critical review of the first core electron chemical shift results. - Abstract: The pioneering years of photoelectron spectroscopy in Uppsala are discussed, especially the work leading to the discovery of the core level chemical shifts. At a very early stage of the project, the pioneering group observed what they described as evidence for chemical shifts in the core level binding energies. However, it can now be seen that the initial observations to a large extent was due to charging of the samples. It is interesting to note that the decisive experiment was realized, not as a result of a systematic study, but was obtained with a large element of serendipity. Only when a chemical binding energy shift was observed between two S2p electron lines in the same molecule, the results were accepted internationally, and the fascinating expansion of modern core level photoelectron spectroscopy could start.

  18. Harnessing the Big Data Paradigm for ICME: Shifting from Materials Selection to Materials Enabled Design

    Science.gov (United States)

    Broderick, Scott R.; Santhanam, Ganesh Ram; Rajan, Krishna

    2016-08-01

    As the size of databases has significantly increased, whether through high throughput computation or through informatics-based modeling, the challenge of selecting the optimal material for specific design requirements has also arisen. Given the multiple, and often conflicting, design requirements, this selection process is not as trivial as sorting the database for a given property value. We suggest that the materials selection process should minimize selector bias, as well as take data uncertainty into account. For this reason, we discuss and apply decision theory for identifying chemical additions to Ni-base alloys. We demonstrate and compare results for both a computational array of chemistries and standard commercial superalloys. We demonstrate how we can use decision theory to select the best chemical additions for enhancing both property and processing, which would not otherwise be easily identifiable. This work is one of the first examples of introducing the mathematical framework of set theory and decision analysis into the domain of the materials selection process.

  19. Chemical shift tensor determination using magnetically oriented microcrystal array (MOMA): 13C solid-state CP NMR without MAS

    Science.gov (United States)

    Kusumi, R.; Kimura, F.; Song, G.; Kimura, T.

    2012-10-01

    Chemical shift tensors for the carboxyl and methyl carbons of L-alanine crystals were determined using a magnetically oriented microcrystal array (MOMA) prepared from a microcrystalline powder sample of L-alanine. A MOMA is a single-crystal-like composite in which microcrystals are aligned three-dimensionally in a matrix resin. The single-crystal rotation method was applied to the MOMA to determine the principal values and axes of the chemical shift tensors. The result showed good agreement with the literature data for the single crystal of L-alanine. This demonstrates that the present technique is a powerful tool for determining the chemical shift tensor of a crystal from a microcrystal powder sample.

  20. Chemical shift assignments of zinc finger domain of methionine aminopeptidase 1 (MetAP1) from Homo sapiens.

    Science.gov (United States)

    Rachineni, Kavitha; Arya, Tarun; Singarapu, Kiran Kumar; Addlagatta, Anthony; Bharatam, Jagadeesh

    2015-10-01

    Methionine aminopeptidase Type I (MetAP1) cleaves the initiator methionine from about 70 % of all newly synthesized proteins in almost every living cell. Human MetAP1 is a two domain protein with a zinc finger on the N-terminus and a catalytic domain on the C-terminus. Here, we report the chemical shift assignments of the amino terminal zinc binding domain (ZBD) (1-83 residues) of the human MetAP1 derived by using advanced NMR spectroscopic methods. We were able to assign the chemical shifts of ZBD of MetAP1 nearly complete, which reveal two helical fragments involving residues P44-L49 (α1) and Q59-K82 (α2). The protein structure unfolds upon complex formation with the addition of 2 M excess EDTA, indicated by the appearance of amide resonances in the random coil chemical shift region of (15)NHSQC spectrum.

  1. Additives initiate selective production of chemicals from biomass pyrolysis.

    Science.gov (United States)

    Leng, Shuai; Wang, Xinde; Wang, Lei; Qiu, Huizhe; Zhuang, Guilin; Zhong, Xing; Wang, Jianguo; Ma, Fengyun; Liu, Jingmei; Wang, Qiang

    2014-03-01

    To improve chemicals selectivity under low temperature, a new method that involves the injection of additives into biomass pyrolysis is introduced. This method allows biomass pyrolysis to achieve high selectivity to chemicals under low temperature (300°C), while nothing was obtained in typical pyrolysis under 300°C. However, by using the new method, the first liquid drop emerged at the interval between 140°C and 240°C. Adding methanol to mushroom scrap pyrolysis obtained high selectivity to acetic acid (98.33%), while adding ethyl acetate gained selectivity to methanol (65.77%) in bagasse pyrolysis and to acetone (72.51%) in corncob pyrolysis. Apart from basic chemicals, one high value-added chemical (2,3-dihydrobenzofuran) was also detected, which obtained the highest selectivity (10.33%) in corncob pyrolysis through the addition of ethyl acetate. Comparison of HZSM-5 and CaCO3 catalysis showed that benzene emerged in the liquid because of the larger degree of cracking and hydrodeoxygenation over HZSM-5.

  2. Origin of the conformational modulation of the 13C NMR chemical shift of methoxy groups in aromatic natural compounds.

    Science.gov (United States)

    Toušek, Jaromír; Straka, Michal; Sklenář, Vladimír; Marek, Radek

    2013-01-24

    The interpretation of nuclear magnetic resonance (NMR) parameters is essential to understanding experimental observations at the molecular and supramolecular levels and to designing new and more efficient molecular probes. In many aromatic natural compounds, unusual (13)C NMR chemical shifts have been reported for out-of-plane methoxy groups bonded to the aromatic ring (~62 ppm as compared to the typical value of ~56 ppm for an aromatic methoxy group). Here, we analyzed this phenomenon for a series of aromatic natural compounds using Density Functional Theory (DFT) calculations. First, we checked the methodology used to optimize the structure and calculate the NMR chemical shifts in aromatic compounds. The conformational effects of the methoxy group on the (13)C NMR chemical shift then were interpreted by the Natural Bond Orbital (NBO) and Natural Chemical Shift (NCS) approaches, and by excitation analysis of the chemical shifts, breaking down the total nuclear shielding tensor into the contributions from the different occupied orbitals and their magnetic interactions with virtual orbitals. We discovered that the atypical (13)C NMR chemical shifts observed are not directly related to a different conjugation of the lone pair of electrons of the methoxy oxygen with the aromatic ring, as has been suggested. Our analysis indicates that rotation of the methoxy group induces changes in the virtual molecular orbital space, which, in turn, correlate with the predominant part of the contribution of the paramagnetic deshielding connected with the magnetic interactions of the BD(CMet-H)→BD*(CMet-OMet) orbitals, resulting in the experimentally observed deshielding of the (13)C NMR resonance of the out-of-plane methoxy group.

  3. Quantitative and qualitative shifts in defensive metabolites define chemical defense investment during leaf development in Inga, a genus of tropical trees.

    Science.gov (United States)

    Wiggins, Natasha L; Forrister, Dale L; Endara, María-José; Coley, Phyllis D; Kursar, Thomas A

    2016-01-01

    Selective pressures imposed by herbivores are often positively correlated with investments that plants make in defense. Research based on the framework of an evolutionary arms race has improved our understanding of why the amount and types of defenses differ between plant species. However, plant species are exposed to different selective pressures during the life of a leaf, such that expanding leaves suffer more damage from herbivores and pathogens than mature leaves. We hypothesize that this differential selective pressure may result in contrasting quantitative and qualitative defense investment in plants exposed to natural selective pressures in the field. To characterize shifts in chemical defenses, we chose six species of Inga, a speciose Neotropical tree genus. Focal species represent diverse chemical, morphological, and developmental defense traits and were collected from a single site in the Amazonian rainforest. Chemical defenses were measured gravimetrically and by characterizing the metabolome of expanding and mature leaves. Quantitative investment in phenolics plus saponins, the major classes of chemical defenses identified in Inga, was greater for expanding than mature leaves (46% and 24% of dry weight, respectively). This supports the theory that, because expanding leaves are under greater selective pressure from herbivores, they rely more upon chemical defense as an antiherbivore strategy than do mature leaves. Qualitatively, mature and expanding leaves were distinct and mature leaves contained more total and unique metabolites. Intraspecific variation was greater for mature leaves than expanding leaves, suggesting that leaf development is canalized. This study provides a snapshot of chemical defense investment in a speciose genus of tropical trees during the short, few-week period of leaf development. Exploring the metabolome through quantitative and qualitative profiling enables a more comprehensive examination of foliar chemical defense investment.

  4. Regional Differences in Muscle Energy Metabolism in Human Muscle by 31P-Chemical Shift Imaging.

    Science.gov (United States)

    Kime, Ryotaro; Kaneko, Yasuhisa; Hongo, Yoshinori; Ohno, Yusuke; Sakamoto, Ayumi; Katsumura, Toshihito

    2016-01-01

    Previous studies have reported significant region-dependent differences in the fiber-type composition of human skeletal muscle. It is therefore hypothesized that there is a difference between the deep and superficial parts of muscle energy metabolism during exercise. We hypothesized that the inorganic phosphate (Pi)/phosphocreatine (PCr) ratio of the superficial parts would be higher, compared with the deep parts, as the work rate increases, because the muscle fiber-type composition of the fast-type may be greater in the superficial parts compared with the deep parts. This study used two-dimensional 31Phosphorus Chemical Shift Imaging (31P-CSI) to detect differences between the deep and superficial parts of the human leg muscles during dynamic knee extension exercise. Six healthy men participated in this study (age 27±1 year, height 169.4±4.1 cm, weight 65.9±8.4 kg). The experiments were carried out with a 1.5-T superconducting magnet with a 5-in. diameter circular surface coil. The subjects performed dynamic one-legged knee extension exercise in the prone position, with the transmit-receive coil placed under the right quadriceps muscles in the magnet. The subjects pulled down an elastic rubber band attached to the ankle at a frequency of 0.25, 0.5 and 1 Hz for 320 s each. The intracellular pH (pHi) was calculated from the median chemical shift of the Pi peak relative to PCr. No significant difference in Pi/PCr was observed between the deep and the superficial parts of the quadriceps muscles at rest. The Pi/PCr of the superficial parts was not significantly increased with increasing work rate. Compared with the superficial areas, the Pi/PCr of the deep parts was significantly higher (p<0.05) at 1 Hz. The pHi showed no significant difference between the two parts. These results suggest that muscle oxidative metabolism is different between deep and superficial parts of quadriceps muscles during dynamic exercise.

  5. Priority setting for existing chemicals : automated data selection routine

    NARCIS (Netherlands)

    Haelst, A.G. van; Hansen, B.G.

    2000-01-01

    One of the four steps within Council Regulation 793/93/EEC on the evaluation and control of existing chemicals is the priority setting step. The priority setting step is concerned with selecting high-priority substances from a large number of substances, initially starting with 2,474 high-production

  6. SIC-BASED HYDROGEN SELECTIVE MEMBRANES FOR WATER-GAS-SHIFT REACTION

    Energy Technology Data Exchange (ETDEWEB)

    Paul K.T. Liu

    2003-12-01

    A hydrogen selective membrane as a membrane reactor (MR) can significantly improve the power generation efficiency with a reduced capital and operating cost for the waster-gas-shift reaction. Existing hydrogen selective ceramic membranes are not suitable for the proposed MR due to their poor hydrothermal stability. In this project we have focused on the development of innovative silicon carbide (SiC) based hydrogen selective membranes, which can potentially overcome this technical barrier. SiC macro-porous membranes have been successfully fabricated via extrusion of commercially available SiC powder. Also, an SiC hydrogen selective thin film was prepared via our CVD/I technique. This composite membrane demonstrated excellent hydrogen selectivity at high temperature ({approx}600 C). More importantly, this membrane also exhibited a much improved hydrothermal stability at 600 C with 50% steam (atmospheric pressure) for nearly 100 hours. In parallel, we have explored an alternative approach to develop a H{sub 2} selective SiC membrane via pyrolysis of selected pre-ceramic polymers and sol-gel techniques. Building upon the positive progress made in the membrane development study, we conducted an optimization study to develop an H{sub 2} selective SiC membrane with sufficient hydrothermal stability suitable for the WGS environment. In addition, mathematical simulation has been performed to compare the performance of the membrane reactor (MR) vs conventional packed bed reactor for WGS reaction. Our result demonstrates that >99.999% conversion can be accomplished via WGS-MR using the hydrogen selective membrane developed by us. Further, water/CO ratio can be reduced, and >97% hydrogen recovery and <200 ppm CO can be accomplished according to the mathematical simulation. Thus, we believe that the operating economics of WGS can be improved significantly based upon the proposed MR concept. In parallel, gas separations and hydrothermal and long-term-storage stability of the

  7. Effects of Irritant Chemicals on Aedes aegypti Resting Behavior: Is There a Simple Shift to Untreated "Safe Sites"?

    Science.gov (United States)

    2011-07-26

    Effects of Irritant Chemicals on Aedes aegypti Resting Behavior: Is There a Simple Shift to Untreated ‘‘Safe Sites’’? Hortance Manda*, Luana M. Arce... aegypti to irritant and repellent chemicals that can be exploited to reduce man-vector contact. Maximum efficacy of interventions based on irritant...overall impact. Methods: Using a laboratory box assay, resting patterns of two population strains of female Ae. aegypti (THAI and PERU) were evaluated

  8. SUBSTITUENT CHEMICAL SHIFT (SCS) AND THE SEQUENCE STRUCTURE OF ETHYLENE-VINYL ALCOHOL COPOLYMERS

    Institute of Scientific and Technical Information of China (English)

    ZHOU Zinan; TIAN Wenjing; WU Shengrong; DAI Yingkun; FENG Zhiliu; SHEN Lianfang; YUAN Hanzhen

    1992-01-01

    Three ethylene-vinyl alcohol copolymers were studied by means of the substituent chemical shift(SCS) method. The SCS parameters of hydroxy (-OH)in two different solvents were obtained: in deuterium oxide/phenol (20/80 W/W ) the parameters are S1 = 42.77 ± 0.08ppm, S2 = 7.15 ±0.06 ppm,S3(s )=-4.08±0.02ppm, S3(t)=-3.09±0.20ppm,S4=0.48±0.03ppm, S5 =0.26±0.05ppm. In o-dichlorobenzen-d4 S1(s)=44.79±0.61ppm, S2=7.40±0.00ppm, S3 (s)=-4.51±0.17ppm, S3 (t)= -3.13± 0.00 ppm, S4 =0 . 63±0.04ppm, S5=0.36±0.00ppm. Simultaneously the 13CNMR spectra of EVA copolymers were assigned by using the SCS parameters obtained.

  9. Chemical shift imaging and localised magnetic resonance spectroscopy in full-term asphyxiated neonates

    Energy Technology Data Exchange (ETDEWEB)

    Brissaud, Olivier [Children' s Hospital, Paediatric Intensive Care Unit, Bordeaux (France); Chateil, Jean-Francois; Bordessoules, Martine; Brun, Muriel [Children' s Hospital, Radiology Unit, Bordeaux (France)

    2005-10-01

    Diagnosis of brain lesions after birth anoxia-ischemia is essential for appropriate management. Clinical evaluation is not sufficient. MRI has been proven to provide useful information. To compare abnormalities observed with MRI, including diffusion-weighted imaging (DWI), localised magnetic resonance spectroscopy (MRS) and chemical shift imaging (CSI) and correlate these findings with the clinical outcome. Fourteen full-term neonates with birth asphyxia were studied. MRI, MRS and CSI were performed within the first 4 days of life. Lesions observed with DWI were correlated with outcome, but the apparent diffusion coefficient (ADC) did improve diagnostic confidence. The mean value of Lac/Cr for the neonates with a favourable outcome was statically lower than for those who died (0.22 vs 1.04; P = 0.01). The same results were observed for the Lac/NAA ratio (0.21 vs 1.23; P = 0.01). Data obtained with localised MRS and CSI were correlated for the ratio N-acetyl-aspartate/choline, but not for the other metabolites. No correlation was found between the ADC values and the metabolite ratios. Combination of these techniques could be helpful in our understanding of the physiopathological events occurring in neonates with asphyxia. (orig.)

  10. Effects of side-chain orientation on the {sup 13}C chemical shifts of antiparallel {beta}-sheet model peptides

    Energy Technology Data Exchange (ETDEWEB)

    Villegas, Myriam E.; Vila, Jorge A. [Facultad de Ciencias Fisico Matematicas y Naturales, Instituto de Matematica Aplicada San Luis, Universidad Nacional de San Luis, CONICET (Argentina); Scheraga, Harold A. [Cornell University, Baker Laboratory of Chemistry and Chemical Biology (United States)], E-mail: has5@cornell.edu

    2007-02-15

    The dependence of the {sup 13}C chemical shift on side-chain orientation was investigated at the density functional level for a two-strand antiparallel {beta}-sheet model peptide represented by the amino acid sequence Ac-(Ala){sub 3}-X-(Ala){sub 12}-NH{sub 2} where X represents any of the 17 naturally occurring amino acids, i.e., not including alanine, glycine and proline. The dihedral angles adopted for the backbone were taken from, and fixed at, observed experimental values of an antiparallel {beta}-sheet. We carried out a cluster analysis of the ensembles of conformations generated by considering the side-chain dihedral angles for each residue X as variables, and use them to compute the {sup 13}C chemical shifts at the density functional theory level. It is shown that the adoption of the locally-dense basis set approach for the quantum chemical calculations enabled us to reduce the length of the chemical-shift calculations while maintaining good accuracy of the results. For the 17 naturally occurring amino acids in an antiparallel {beta}-sheet, there is (i) good agreement between computed and observed {sup 13}C{sup {alpha}} and {sup 13}C{sup {beta}} chemical shifts, with correlation coefficients of 0.95 and 0.99, respectively; (ii) significant variability of the computed {sup 13}C{sup {alpha}} and {sup 13}C{sup {beta}} chemical shifts as a function of {chi}{sup 1} for all amino acid residues except Ser; and (iii) a smaller, although significant, dependence of the computed {sup 13}C{sup {alpha}} chemical shifts on {chi}{sup {xi}} (with {xi} {>=} 2) compared to {chi}{sup 1} for eleven out of seventeen residues. Our results suggest that predicted {sup 13}C{sup {alpha}} and {sup 13}C{sup {beta}} chemical shifts, based only on backbone ({phi},{psi}) dihedral angles from high-resolution X-ray structure data or from NMR-derived models, may differ significantly from those observed in solution if the dihedral-angle preferences for the side chains are not taken into

  11. Motivational Shifts in Aging Monkeys and the Origins of Social Selectivity.

    Science.gov (United States)

    Almeling, Laura; Hammerschmidt, Kurt; Sennhenn-Reulen, Holger; Freund, Alexandra M; Fischer, Julia

    2016-07-11

    As humans age, they become more selective regarding their personal goals [1] and social partners [2]. Whereas the selectivity in goals has been attributed to losses in resources (e.g., physical strength) [3], the increasing focus on emotionally meaningful partners is, according to socioemotional selectivity theory, driven by the awareness of one's decreasing future lifetime [2]. Similar to humans, aging monkeys show physical losses [4] and reductions in social activity [2, 5-7]. To disentangle a general resource loss and the awareness of decreasing time, we combined field experiments with behavioral observations in a large age-heterogeneous population of Barbary macaques (Macaca sylvanus) at La Forêt des Singes. Novel object tests revealed a loss of interest in the nonsocial environment in early adulthood, which was modulated by the availability of a food reward. Experiments using vocal and visual representations of social partners indicated that monkeys maintained an interest in social stimuli and a preferential interest in friends and socially important individuals into old age. Old females engaged in fewer social interactions, although other group members continued to invest in relationships with them. Consequently, reductions in sociality were not due to a decrease in social interest. In conclusion, some of the motivational shifts observed in aging humans, particularly the increasing focus on social over nonsocial stimuli, may occur in the absence of a limited time perspective and are most likely deeply rooted in primate evolution. Our findings highlight the value of nonhuman primates as valuable models for understanding human aging [8, 9].

  12. Analysis of {sup 13}C{sup {alpha}} and {sup 13}C{sup {beta}} chemical shifts of cysteine and cystine residues in proteins: a quantum chemical approach

    Energy Technology Data Exchange (ETDEWEB)

    Martin, Osvaldo A.; Villegas, Myriam E.; Vila, Jorge A. [Universidad Nacional de San Luis, Instituto de Matematica Aplicada San Luis (Argentina); Scheraga, Harold A., E-mail: has5@cornell.ed [Cornell University, Baker Laboratory of Chemistry and Chemical Biology (United States)

    2010-03-15

    Cysteines possess a unique property among the 20 naturally occurring amino acids: it can be present in proteins in either the reduced or oxidized form, and can regulate the activity of some proteins. Consequently, to augment our previous treatment of the other types of residues, the {sup 13}C{sup {alpha}} and {sup 13}C{sup {beta}} chemical shifts of 837 cysteines in disulfide-bonded cystine from a set of seven non-redundant proteins, determined by X-ray crystallography and NMR spectroscopy, were computed at the DFT level of theory. Our results indicate that the errors between observed and computed {sup 13}C{sup {alpha}} chemical shifts of such oxidized cysteines can be attributed to several effects such as: (a) the quality of the NMR-determined models, as evaluated by the conformational-average (ca) rmsd value; (b) the existence of high B-factor or crystal-packing effects for the X-ray-determined structures; (c) the dynamics of the disulfide bonds in solution; and (d) the differences in the experimental conditions under which the observed {sup 13}C{sup {alpha}} chemical shifts and the protein models were determined by either X-ray crystallography or NMR-spectroscopy. These quantum-chemical-based calculations indicate the existence of two, almost non-overlapped, basins for the oxidized and reduced -SH {sup 13}C{sup {beta}}, but not for the {sup 13}C{sup {alpha}}, chemical shifts, in good agreement with the observation of 375 {sup 13}C{sup {alpha}} and 337 {sup 13}C{sup {beta}} resonances from 132 proteins by Sharma and Rajarathnam (2000). Overall, our results indicate that explicit consideration of the disulfide bonds is a necessary condition for an accurate prediction of {sup 13}C{sup {alpha}} and {sup 13}C{sup {beta}} chemical shifts of cysteines in cystines.

  13. Analysis of the contributions of ring current and electric field effects to the chemical shifts of RNA bases.

    Science.gov (United States)

    Sahakyan, Aleksandr B; Vendruscolo, Michele

    2013-02-21

    Ring current and electric field effects can considerably influence NMR chemical shifts in biomolecules. Understanding such effects is particularly important for the development of accurate mappings between chemical shifts and the structures of nucleic acids. In this work, we first analyzed the Pople and the Haigh-Mallion models in terms of their ability to describe nitrogen base conjugated ring effects. We then created a database (DiBaseRNA) of three-dimensional arrangements of RNA base pairs from X-ray structures, calculated the corresponding chemical shifts via a hybrid density functional theory approach and used the results to parametrize the ring current and electric field effects in RNA bases. Next, we studied the coupling of the electric field and ring current effects for different inter-ring arrangements found in RNA bases using linear model fitting, with joint electric field and ring current, as well as only electric field and only ring current approximations. Taken together, our results provide a characterization of the interdependence of ring current and electric field geometric factors, which is shown to be especially important for the chemical shifts of non-hydrogen atoms in RNA bases.

  14. Elucidation of the substitution pattern of 9,10-anthraquinones through the chemical shifts of peri-hydroxyl protons

    DEFF Research Database (Denmark)

    Schripsema, Jan; Danigno, Denise

    1996-01-01

    In 9,10-anthraquinones the chemical shift of a peri-hydroxyl proton is affected by the substituents in the other benzenoid ring. These effects are additive. They are useful for the determination of substitution patterns and have been used to revise the structures of six previously reported anthra...

  15. The local order of supercooled water in solution with LiCl studied by NMR proton chemical shift

    Science.gov (United States)

    Corsaro, C.; Mallamace, D.; Vasi, S.; Cicero, N.; Dugo, G.; Mallamace, F.

    2016-05-01

    We study by means of Nuclear Magnetic Resonance (NMR) spectroscopy the local order of water molecules in solution with lithium chloride at eutectic concentration. In particular, by measuring the proton chemical shift as a function of the temperature in the interval 203{ K}Widom line for water supporting the liquid-liquid transition hypothesis.

  16. Correlation of 1H NMR Chemical Shift for Aqueous Solutions by Statistical Associating Fluid Theory Association Model

    Institute of Scientific and Technical Information of China (English)

    许波; 李浩然; 王从敏; 许映杰; 韩世钧

    2005-01-01

    1H NMR chemical shifts of binary aqueous mixtures of acylamide, alcohol, dimethyl sulphoxide (DMSO), and acetone are correlated by statistical associating fluid theory (SAFT) association model. The comparison between SAFT association model and Wilson equation shows that the former is better for dealing with aqueous solutions. Finally, the specialties of both models are discussed.

  17. Monte Carlo optimization for site selection of new chemical plants.

    Science.gov (United States)

    Cai, Tianxing; Wang, Sujing; Xu, Qiang

    2015-11-01

    Geographic distribution of chemical manufacturing sites has significant impact on the business sustainability of industrial development and regional environmental sustainability as well. The common site selection rules have included the evaluation of the air quality impact of a newly constructed chemical manufacturing site to surrounding communities. In order to achieve this target, the simultaneous consideration should cover the regional background air-quality information, the emissions of new manufacturing site, and statistical pattern of local meteorological conditions. According to the above information, the risk assessment can be conducted for the potential air-quality impacts from candidate locations of a new chemical manufacturing site, and thus the optimization of the final site selection can be achieved by minimizing its air-quality impacts. This paper has provided a systematic methodology for the above purpose. There are total two stages of modeling and optimization work: i) Monte Carlo simulation for the purpose to identify background pollutant concentration based on currently existing emission sources and regional statistical meteorological conditions; and ii) multi-objective (simultaneous minimization of both peak pollutant concentration and standard deviation of pollutant concentration spatial distribution at air-quality concern regions) Monte Carlo optimization for optimal location selection of new chemical manufacturing sites according to their design data of potential emission. This study can be helpful to both determination of the potential air-quality impact for geographic distribution of multiple chemical plants with respect to regional statistical meteorological conditions, and the identification of an optimal site for each new chemical manufacturing site with the minimal environment impact to surrounding communities. The efficacy of the developed methodology has been demonstrated through the case studies.

  18. Intermolecular Interactions in Crystalline Theobromine as Reflected in Electron Deformation Density and (13)C NMR Chemical Shift Tensors.

    Science.gov (United States)

    Bouzková, Kateřina; Babinský, Martin; Novosadová, Lucie; Marek, Radek

    2013-06-11

    An understanding of the role of intermolecular interactions in crystal formation is essential to control the generation of diverse crystalline forms which is an important concern for pharmaceutical industry. Very recently, we reported a new approach to interpret the relationships between intermolecular hydrogen bonding, redistribution of electron density in the system, and NMR chemical shifts (Babinský et al. J. Phys. Chem. A, 2013, 117, 497). Here, we employ this approach to characterize a full set of crystal interactions in a sample of anhydrous theobromine as reflected in (13)C NMR chemical shift tensors (CSTs). The important intermolecular contacts are identified by comparing the DFT-calculated NMR CSTs for an isolated theobromine molecule and for clusters composed of several molecules as selected from the available X-ray diffraction data. Furthermore, electron deformation density (EDD) and shielding deformation density (SDD) in the proximity of the nuclei involved in the proposed interactions are calculated and visualized. In addition to the recently reported observations for hydrogen bonding, we focus here particularly on the stacking interactions. Although the principal relations between the EDD and CST for hydrogen bonding (HB) and stacking interactions are similar, the real-space consequences are rather different. Whereas the C-H···X hydrogen bonding influences predominantly and significantly the in-plane principal component of the (13)C CST perpendicular to the HB path and the C═O···H hydrogen bonding modulates both in-plane components of the carbonyl (13)C CST, the stacking modulates the out-of-plane electron density resulting in weak deshielding (2-8 ppm) of both in-plane principal components of the CST and weak shielding (∼ 5 ppm) of the out-of-plane component. The hydrogen-bonding and stacking interactions may add to or subtract from one another to produce total values observed experimentally. On the example of theobromine, we demonstrate

  19. Halogen effect on structure and 13C NMR chemical shift of 3,6-disubstituted-N-alkyl carbazoles

    DEFF Research Database (Denmark)

    Radula-Janik, Klaudia; Kupka, Teobald; Ejsmont, Krzysztof

    2013-01-01

    Structures of selected 3,6-dihalogeno-N-alkyl carbazole derivatives were calculated at the B3LYP/6-311++G(3df,2pd) level of theory and their 13C NMR isotropic nuclear shieldings were predicted using density functional theory (DFT). The model compounds contained 9H-, N-methyl and N-ethyl derivatives......). The decreasing electronegativity of the halogen substituent (F, Cl, Br and I) was reflected in both nonrelativistic and relativistic NMR results as decreased values of chemical shifts of carbon atoms attached to halogen (C3 and C6) leading to a strong sensitivity to halogen atom type at 3 and 6 positions...

  20. Female sea lamprey shift orientation toward a conspecific chemical cue to escape a sensory trap

    Science.gov (United States)

    Brant, Cory O.; Johnson, Nicholas; Li, Ke; Buchinger, Tyler J.; Li, Weiming

    2016-01-01

    The sensory trap model of signal evolution hypothesizes that signalers adapt to exploit a cue used by the receiver in another context. Although exploitation of receiver biases can result in conflict between the sexes, deceptive signaling systems that are mutually beneficial drive the evolution of stable communication systems. However, female responses in the nonsexual and sexual contexts may become uncoupled if costs are associated with exhibiting a similar response to a trait in both contexts. Male sea lamprey (Petromyzon marinus) signal with a mating pheromone, 3-keto petromyzonol sulfate (3kPZS), which may be a match to a juvenile cue used by females during migration. Upstream movement of migratory lampreys is partially guided by 3kPZS, but females only move toward 3kPZS with proximal accuracy during spawning. Here, we use in-stream behavioral assays paired with gonad histology to document the transition of female preference for juvenile- and male-released 3kPZS that coincides with the functional shift of 3kPZS as a migratory cue to a mating pheromone. Females became increasingly biased toward the source of synthesized 3kPZS as their maturation progressed into the reproductive phase, at which point, a preference for juvenile odor (also containing 3kPZS naturally) ceased to exist. Uncoupling of female responses during migration and spawning makes the 3kPZS communication system a reliable means of synchronizing mate search. The present study offers a rare example of a transition in female responses to a chemical cue between nonsexual and sexual contexts, provides insights into the origins of stable communication signaling systems.

  1. Selection of materials for pressure vessels and chemical plants

    Energy Technology Data Exchange (ETDEWEB)

    Huppertz, P.H.; Retter, A. (Linde A.G., Hoellriegelskreuth (Germany, F.R.). Werksgruppe Tieftemperatur und Verfahrenstechnik)

    1980-04-01

    The selection of materials for pressure vessels and chemical plants depends on a number of factors such as operating, operating temperature, operating medium, regulations in force in the country of the plant user concerned and manufacturing possibilities. The essay clearly explains how the above specified factors individually influence the selection of materials. The article also deals with the ranges of application of certain material groups such as unalloyed and low-alloy steels, fine-grained steels, austenitic chromium-nickel steels, unalloyed ferritic chromium steels and other materials. The article closes with remarks on the operational safety of pressure vessels.

  2. Novel selection methods for DNA-encoded chemical libraries.

    Science.gov (United States)

    Chan, Alix I; McGregor, Lynn M; Liu, David R

    2015-06-01

    Driven by the need for new compounds to serve as biological probes and leads for therapeutic development and the growing accessibility of DNA technologies including high-throughput sequencing, many academic and industrial groups have begun to use DNA-encoded chemical libraries as a source of bioactive small molecules. In this review, we describe the technologies that have enabled the selection of compounds with desired activities from these libraries. These methods exploit the sensitivity of in vitro selection coupled with DNA amplification to overcome some of the limitations and costs associated with conventional screening methods. In addition, we highlight newer techniques with the potential to be applied to the high-throughput evaluation of DNA-encoded chemical libraries.

  3. Frequency-Shift Zero-Forcing Time-Varying Equalization for Doubly Selective SIMO Channels

    Directory of Open Access Journals (Sweden)

    Verde Francesco

    2006-01-01

    Full Text Available This paper deals with the problem of designing linear time-varying (LTV finite-impulse response zero-forcing (ZF equalizers for time- and frequency-selective (so-called doubly selective single-input multiple-output (SIMO channels. Specifically, relying on a basis expansion model (BEM of the rapidly time-varying channel impulse response, we derive the canonical frequency-domain representation of the minimal norm LTV-ZF equalizer, which allows one to implement it as a parallel bank of linear time-invariant filters having, as input signals, different frequency-shift (FRESH versions of the received data. Moreover, on the basis of this FRESH representation, we propose a simple and effective low-complexity version of the minimal norm LTV-ZF equalizer and we discuss the relationships between the devised FRESH equalizers and a LTV-ZF equalizer recently proposed in the literature. The performance analysis, carried out by means of computer simulations, shows that the proposed FRESH-LTV-ZF equalizers significantly outperform their competitive alternative.

  4. Chemical recycling of mixed waste plastics by selective pyrolysis

    Energy Technology Data Exchange (ETDEWEB)

    Tatsumoto, K.; Meglen, R.; Evans, R. [National Renewable Energy Laboratory, Golden, CO (United States)

    1995-05-01

    The goal of this work is to use selective pyrolysis to produce high-value chemicals from waste plastics mixtures. Selectivity is achieved by exploiting differences in reaction rates, catalysis, and coreactants. Target wastes are molecular mixtures such as; blends or composites, or mixtures from manufactured products such as; carpets and post-consumer mixed-plastic wastes. The experimental approach has been to use small-scale experiments using molecular beam mass spectrometry (MBMS), which provides rapid analysis of reaction products and permits rapid screening of process parameters. Rapid screening experiments permit exploration of many potential waste stream applications for the selective pyrolysis process. After initial screening, small-scale, fixed-bed and fluidized-bed reactors are used to provide products for conventional chemical analysis, to determine material balances, and to test the concept under conditions that will be used at a larger scale. Computer assisted data interpretation and intelligent chemical processing are used to extract process-relevant information from these experiments. An important element of this project employs technoeconomic assessments and market analyses of durables, the availability of other wastes, and end-product uses to identify target applications that have the potential for economic success.

  5. DNA abasic site-selective enhancement of sanguinarine fluorescence with a large emission shift.

    Directory of Open Access Journals (Sweden)

    Fei Wu

    Full Text Available Small molecules that can specifically bind to a DNA abasic site (AP site have received much attention due to their importance in DNA lesion identification, drug discovery, and sensor design. Herein, the AP site binding behavior of sanguinarine (SG, a natural alkaloid, was investigated. In aqueous solution, SG has a short-wavelength alkanolamine emission band and a long-wavelength iminium emission band. At pH 8.3, SG experiences a fluorescence quenching for both bands upon binding to fully matched DNAs without the AP site, while the presence of the AP site induces a strong SG binding and the observed fluorescence enhancement for the iminium band are highly dependent on the nucleobases flanking the AP site, while the alkanolamine band is always quenched. The bases opposite the AP site also exert some modifications on the SG's emission behavior. It was found that the observed quenching for DNAs with Gs and Cs flanking the AP site is most likely caused by electron transfer between the AP site-bound excited-state SG and the nearby Gs. However, the flanking As and Ts that are not easily oxidized favor the enhanced emission. This AP site-selective enhancement of SG fluorescence accompanies a band conversion in the dominate emission from the alkanolamine to iminium band thus with a large emission shift of about 170 nm. Absorption spectra, steady-state and transient-state fluorescence, DNA melting, and electrolyte experiments confirm that the AP site binding of SG occurs and the stacking interaction with the nearby base pairs is likely to prevent the converted SG iminium form from contacting with water that is thus emissive when the AP site neighbors are bases other than guanines. We expect that this fluorophore would be developed as a promising AP site binder having a large emission shift.

  6. Nanoporous membranes with electrochemically switchable, chemically stabilized ionic selectivity.

    Science.gov (United States)

    Small, Leo J; Wheeler, David R; Spoerke, Erik D

    2015-10-28

    Nanopore size, shape, and surface charge all play important roles in regulating ionic transport through nanoporous membranes. The ability to control these parameters in situ provides a means to create ion transport systems tunable in real time. Here, we present a new strategy to address this challenge, utilizing three unique electrochemically switchable chemistries to manipulate the terminal functional group and control the resulting surface charge throughout ensembles of gold plated nanopores in ion-tracked polycarbonate membranes 3 cm(2) in area. We demonstrate the diazonium mediated surface functionalization with (1) nitrophenyl chemistry, (2) quinone chemistry, and (3) previously unreported trimethyl lock chemistry. Unlike other works, these chemistries are chemically stabilized, eliminating the need for a continuously applied gate voltage to maintain a given state and retain ionic selectivity. The effect of surface functionalization and nanopore geometry on selective ion transport through these functionalized membranes is characterized in aqueous solutions of sodium chloride at pH = 5.7. The nitrophenyl surface allows for ionic selectivity to be irreversibly switched in situ from cation-selective to anion-selective upon reduction to an aminophenyl surface. The quinone-terminated surface enables reversible changes between no ionic selectivity and a slight cationic selectivity. Alternatively, the trimethyl lock allows ionic selectivity to be reversibly switched by up to a factor of 8, approaching ideal selectivity, as a carboxylic acid group is electrochemically revealed or hidden. By varying the pore shape from cylindrical to conical, it is demonstrated that a controllable directionality can be imparted to the ionic selectivity. Combining control of nanopore geometry with stable, switchable chemistries facilitates superior control of molecular transport across the membrane, enabling tunable ion transport systems.

  7. Natural selection drives chemical resistance of Datura stramonium

    Science.gov (United States)

    Miranda-Pérez, Adán; Castillo, Guillermo; Hernández-Cumplido, Johnattan; Valverde, Pedro L.; Borbolla, María; Cruz, Laura L.; Tapia-López, Rosalinda; Fornoni, Juan; Flores-Ortiz, César M.

    2016-01-01

    Plant resistance to herbivores involves physical and chemical plant traits that prevent or diminish damage by herbivores, and hence may promote coevolutionary arm-races between interacting species. Although Datura stramonium’s concentration of tropane alkaloids is under selection by leaf beetles, it is not known whether chemical defense reduces seed predation by the specialist weevil, Trichobaris soror, and if it is evolving by natural selection. We measured infestation by T. soror as well as the concentration of the plants’ two main tropane alkaloids in 278 D. stramonium plants belonging to 31 populations in central Mexico. We assessed whether the seed predator exerted preferences on the levels of both alkaloids and whether they affect plant fitness. Results show great variation across populations in the concentration of scopolamine and atropine in both leaves and seeds of plants of D. stramonium, as well as in the intensity of infestation and the proportion of infested fruits by T. soror. The concentration of scopolamine in seeds and leaves are negatively associated across populations. We found that scopolamine concentration increases plant fitness. Our major finding was the detection of a positive relationship between the population average concentrations of scopolamine with the selection differentials of scopolamine. Such spatial variation in the direction and intensity of selection on scopolamine may represent a coevolutionary selective mosaic. Our results support the view that variation in the concentration of scopolamine among-populations of D. stramonium in central Mexico is being driven, in part, by selection exerted by T. soror, pointing an adaptive role of tropane alkaloids in this plant species. PMID:27114866

  8. Shift endpoint trace selection algorithm and wavelet analysis to detect the endpoint using optical emission spectroscopy

    Science.gov (United States)

    Ben Zakour, Sihem; Taleb, Hassen

    2016-06-01

    Endpoint detection (EPD) is very important undertaking on the side of getting a good understanding and figuring out if a plasma etching process is done on the right way. It is truly a crucial part of supplying repeatable effects in every single wafer. When the film to be etched has been completely erased, the endpoint is reached. In order to ensure the desired device performance on the produced integrated circuit, many sensors are used to detect the endpoint, such as the optical, electrical, acoustical/vibrational, thermal, and frictional. But, except the optical sensor, the other ones show their weaknesses due to the environmental conditions which affect the exactness of reaching endpoint. Unfortunately, some exposed area to the film to be etched is very low (signal and showing the incapacity of the traditional endpoint detection method to determine the wind-up of the etch process. This work has provided a means to improve the endpoint detection sensitivity by collecting a huge numbers of full spectral data containing 1201 spectra for each run, then a new unsophisticated algorithm is proposed to select the important endpoint traces named shift endpoint trace selection (SETS). Then, a sensitivity analysis of linear methods named principal component analysis (PCA) and factor analysis (FA), and the nonlinear method called wavelet analysis (WA) for both approximation and details will be studied to compare performances of the methods mentioned above. The signal to noise ratio (SNR) is not only computed based on the main etch (ME) period but also the over etch (OE) period. Moreover, a new unused statistic for EPD, coefficient of variation (CV), is proposed to reach the endpoint in plasma etches process.

  9. Hundreds of Genes Experienced Convergent Shifts in Selective Pressure in Marine Mammals.

    Science.gov (United States)

    Chikina, Maria; Robinson, Joseph D; Clark, Nathan L

    2016-09-01

    Mammal species have made the transition to the marine environment several times, and their lineages represent one of the classical examples of convergent evolution in morphological and physiological traits. Nevertheless, the genetic mechanisms of their phenotypic transition are poorly understood, and investigations into convergence at the molecular level have been inconclusive. While past studies have searched for convergent changes at specific amino acid sites, we propose an alternative strategy to identify those genes that experienced convergent changes in their selective pressures, visible as changes in evolutionary rate specifically in the marine lineages. We present evidence of widespread convergence at the gene level by identifying parallel shifts in evolutionary rate during three independent episodes of mammalian adaptation to the marine environment. Hundreds of genes accelerated their evolutionary rates in all three marine mammal lineages during their transition to aquatic life. These marine-accelerated genes are highly enriched for pathways that control recognized functional adaptations in marine mammals, including muscle physiology, lipid-metabolism, sensory systems, and skin and connective tissue. The accelerations resulted from both adaptive evolution as seen in skin and lung genes, and loss of function as in gustatory and olfactory genes. In regard to sensory systems, this finding provides further evidence that reduced senses of taste and smell are ubiquitous in marine mammals. Our analysis demonstrates the feasibility of identifying genes underlying convergent organism-level characteristics on a genome-wide scale and without prior knowledge of adaptations, and provides a powerful approach for investigating the physiological functions of mammalian genes.

  10. Seasonal variation in microhabitat of salamanders: environmental variation or shift of habitat selection?

    Directory of Open Access Journals (Sweden)

    Enrico Lunghi

    2015-08-01

    Full Text Available Relationships between species and their habitats are not always constant. Different processes may determine changes in species-habitat association: individuals may prefer different habitat typologies in different periods, or they may be forced to occupy a different habitat in order to follow the changing environment. The aim of our study was to assess whether cave salamanders change their habitat association pattern through the year, and to test whether such changes are determined by environmental changes or by changes in preferences. We monitored multiple caves in Central Italy through one year, and monthly measured biotic and abiotic features of microhabitat and recorded Italian cave salamanders distribution. We used mixed models and niche similarity tests to assess whether species-habitat relationships remain constant through the year. Microhabitat showed strong seasonal variation, with the highest variability in the superficial sectors. Salamanders were associated to relatively cold and humid sectors in summer, but not during winter. Such apparent shift in habitat preferences mostly occurred because the environmental gradient changed through the year, while individuals generally selected similar conditions. Nevertheless, juveniles were more tolerant to dry sectors during late winter, when food demand was highest. This suggests that tolerance for suboptimal abiotic conditions may change through time, depending on the required resources. Differences in habitat use are jointly determined by environmental variation through time, and by changes in the preferred habitat. The trade-offs between tolerance and resources requirement are major determinant of such variation.

  11. Cuticular hydrocarbon divergence in the jewel wasp Nasonia : evolutionary shifts in chemical communication channels?

    NARCIS (Netherlands)

    Buellesbach, J.; Gadau, J.; Beukeboom, L. W.; Echinger, F.; Raychoudhury, R.; Werren, J. H.; Schmitt, T.

    2013-01-01

    The evolution and maintenance of intraspecific communication channels constitute a key feature of chemical signalling and sexual communication. However, how divergent chemical communication channels evolve while maintaining their integrity for both sender and receiver is poorly understood. In this s

  12. Computer programming for nucleic acid studies. II. Total chemical shifts calculation of all protons of double-stranded helices.

    Science.gov (United States)

    Giessner-Prettre, C; Ribas Prado, F; Pullman, B; Kan, L; Kast, J R; Ts'o, P O

    1981-01-01

    A FORTRAN computer program called SHIFTS is described. Through SHIFTS, one can calculate the NMR chemical shifts of the proton resonances of single and double-stranded nucleic acids of known sequences and of predetermined conformations. The program can handle RNA and DNA for an arbitrary sequence of a set of 4 out of the 6 base types A,U,G,C,I and T. Data files for the geometrical parameters are available for A-, A'-, B-, D- and S-conformations. The positions of all the atoms are calculated using a modified version of the SEQ program [1]. Then, based on this defined geometry three chemical shift effects exerted by the atoms of the neighboring nucleotides on the protons of each monomeric unit are calculated separately: the ring current shielding effect: the local atomic magnetic susceptibility effect (including both diamagnetic and paramagnetic terms); and the polarization or electric field effect. Results of the program are compared with experimental results for a gamma (ApApGpCpUpU) 2 helical duplex and with calculated results on this same helix based on model building of A'-form and B-form and on graphical procedure for evaluating the ring current effects.

  13. Selective edge modification in graphene and graphite by chemical oxidation.

    Science.gov (United States)

    Yang, Min; Moriyama, Satoshi; Higuchi, Masayoshi

    2014-04-01

    The effect of edge structures in graphene sheets has been well investigated theoretically but most experimental demonstrations of the functionalization have been for the bulk structures because of only a few reports on chemical methods to modify the edges selectively. We herein report a chemical method using the Lemieux-von Rudloff reagent that selectively oxidizes only the edges of graphene sheets. The selective oxidation at the edges of the graphene sheet was confirmed by thermogravimetric analysis (TGA), Raman mapping measurements, and X-ray photoelectron spectroscopy (XPS). The TGA result of the oxidized graphite with different particle sizes showed a slight weight loss at approximately 350 degrees C (2.29% for the middle particles (35 microm)), which indicates thermal decomposition of the oxidized edge part. The Raman mapping measurement in the inner part of graphene sheets didn't detect any defects or translational symmetry breaking after the oxidation. The XPS data clearly showed that the total carbon atom content present as C--O, C==O, and O--C==C increased from 4.65 to 6.18% by the oxidation. Using the obtained edge-oxidized graphene as a starting material, various functionalizations of the edge structure are expected in the future.

  14. Towards the versatile DFT and MP2 computational schemes for 31P NMR chemical shifts taking into account relativistic corrections.

    Science.gov (United States)

    Fedorov, Sergey V; Rusakov, Yury Yu; Krivdin, Leonid B

    2014-11-01

    The main factors affecting the accuracy and computational cost of the calculation of (31)P NMR chemical shifts in the representative series of organophosphorous compounds are examined at the density functional theory (DFT) and second-order Møller-Plesset perturbation theory (MP2) levels. At the DFT level, the best functionals for the calculation of (31)P NMR chemical shifts are those of Keal and Tozer, KT2 and KT3. Both at the DFT and MP2 levels, the most reliable basis sets are those of Jensen, pcS-2 or larger, and those of Pople, 6-311G(d,p) or larger. The reliable basis sets of Dunning's family are those of at least penta-zeta quality that precludes their practical consideration. An encouraging finding is that basically, the locally dense basis set approach resulting in a dramatic decrease in computational cost is justified in the calculation of (31)P NMR chemical shifts within the 1-2-ppm error. Relativistic corrections to (31)P NMR absolute shielding constants are of major importance reaching about 20-30 ppm (ca 7%) improving (not worsening!) the agreement of calculation with experiment. Further better agreement with the experiment by 1-2 ppm can be obtained by taking into account solvent effects within the integral equation formalism polarizable continuum model solvation scheme. We recommend the GIAO-DFT-KT2/pcS-3//pcS-2 scheme with relativistic corrections and solvent effects taken into account as the most versatile computational scheme for the calculation of (31)P NMR chemical shifts characterized by a mean absolute error of ca 9 ppm in the range of 550 ppm.

  15. Chemical shift of Mn and Cr K-edges in X-ray absorption spectroscopy with synchrotron radiation

    Indian Academy of Sciences (India)

    D Joseph; A K Yadav; S N Jha; D Bhattacharyya

    2013-11-01

    Mn and Cr K X-ray absorption edges were measured in various compounds containing Mn in Mn2+, Mn3+ and Mn4+ oxidation states and Cr in Cr3+ and Cr6+ oxidation states. Few compounds possess tetrahedral coordination in the 1st shell surrounding the cation while others possess octahedral coordination. Measurements have been carried out at the energy dispersive EXAFS beamline at INDUS-2 Synchrotron Radiation Source at Raja Ramanna Centre for Advanced Technology, Indore. Energy shifts of ∼8–16 eV were observed for Mn K edge in the Mn-compounds while a shift of 13–20 eV was observed for Cr K edge in Cr-compounds compared to values in elementalMn and Cr, respectively. The different chemical shifts observed for compounds having the same oxidation state of the cation but different anions or ligands show the effect of different chemical environments surrounding the cations in determining their X-ray absorption edges in the above compounds. The above chemical effect has been quantitatively described by determining the effective charges on Mn and Cr cations in the above compounds.

  16. Differential dynamic engagement within 24 SH3 domain: peptide complexes revealed by co-linear chemical shift perturbation analysis.

    Directory of Open Access Journals (Sweden)

    Elliott J Stollar

    Full Text Available There is increasing evidence for the functional importance of multiple dynamically populated states within single proteins. However, peptide binding by protein-protein interaction domains, such as the SH3 domain, has generally been considered to involve the full engagement of peptide to the binding surface with minimal dynamics and simple methods to determine dynamics at the binding surface for multiple related complexes have not been described. We have used NMR spectroscopy combined with isothermal titration calorimetry to comprehensively examine the extent of engagement to the yeast Abp1p SH3 domain for 24 different peptides. Over one quarter of the domain residues display co-linear chemical shift perturbation (CCSP behavior, in which the position of a given chemical shift in a complex is co-linear with the same chemical shift in the other complexes, providing evidence that each complex exists as a unique dynamic rapidly inter-converting ensemble. The extent the specificity determining sub-surface of AbpSH3 is engaged as judged by CCSP analysis correlates with structural and thermodynamic measurements as well as with functional data, revealing the basis for significant structural and functional diversity amongst the related complexes. Thus, CCSP analysis can distinguish peptide complexes that may appear identical in terms of general structure and percent peptide occupancy but have significant local binding differences across the interface, affecting their ability to transmit conformational change across the domain and resulting in functional differences.

  17. Predicting Heats of Explosion of Nitroaromatic Compounds through NBO Charges and 15N NMR Chemical Shifts of Nitro Groups

    Directory of Open Access Journals (Sweden)

    Ricardo Infante-Castillo

    2012-01-01

    Full Text Available This work presents a new quantitative model to predict the heat of explosion of nitroaromatic compounds using the natural bond orbital (NBO charge and 15N NMR chemical shifts of the nitro groups (15NNitro as structural parameters. The values of the heat of explosion predicted for 21 nitroaromatic compounds using the model described here were compared with experimental data. The prediction ability of the model was assessed by the leave-one-out cross-validation method. The cross-validation results show that the model is significant and stable and that the predicted accuracy is within 0.146 MJ kg−1, with an overall root mean squared error of prediction (RMSEP below 0.183 MJ kg−1. Strong correlations were observed between the heat of explosion and the charges (R2 = 0.9533 and 15N NMR chemical shifts (R2 = 0.9531 of the studied compounds. In addition, the dependence of the heat of explosion on the presence of activating or deactivating groups of nitroaromatic explosives was analyzed. All calculations, including optimizations, NBO charges, and 15NNitro NMR chemical shifts analyses, were performed using density functional theory (DFT and a 6-311+G(2d,p basis set. Based on these results, this practical quantitative model can be used as a tool in the design and development of highly energetic materials (HEM based on nitroaromatic compounds.

  18. Etch selectivity of a wet chemical formulation for premetal cleaning

    Science.gov (United States)

    Epton, Jeremy W.; Jarrett, Deborah L.; Doohan, Ian J.

    2001-04-01

    This paper examines the relative etching rates of doped and thermal silicon dioxide when using NSSL etchant, comprising of a mixture of ammonium fluoride, water and ammonium dihydrogen phosphate [(NH4)H2PO4] and investigates their dependence on both temperature and mixture composition. The possible reaction mechanism is discussed and compared with the known mechanism for standard buffered oxide etchants (BOE). The observed etch selectivity and mechanisms of BOE and NSSL are also compared with the behavior of a third chemical formulation, referred to as mixed oxide etchant, which comprises of ammonium fluoride (NH4F) solution, diammonium hydrogen phosphate [(NH4)2HPO4] and orthophosphoric acid (H3PO4). It is concluded that no major change in oxide selectivity is observed if either BOE or NSSL etchants are used in the metal pre-clean process.

  19. Identification of zinc-ligated cysteine residues based on 13Calpha and 13Cbeta chemical shift data.

    Science.gov (United States)

    Kornhaber, Gregory J; Snyder, David; Moseley, Hunter N B; Montelione, Gaetano T

    2006-04-01

    Although a significant number of proteins include bound metals as part of their structure, the identification of amino acid residues coordinated to non-paramagnetic metals by NMR remains a challenge. Metal ligands can stabilize the native structure and/or play critical catalytic roles in the underlying biochemistry. An atom's chemical shift is exquisitely sensitive to its electronic environment. Chemical shift data can provide valuable insights into structural features, including metal ligation. In this study, we demonstrate that overlapped 13Cbeta chemical shift distributions of Zn-ligated and non-metal-ligated cysteine residues are largely resolved by the inclusion of the corresponding 13Calpha chemical shift information, together with secondary structural information. We demonstrate this with a bivariate distribution plot, and statistically with a multivariate analysis of variance (MANOVA) and hierarchical logistic regression analysis. Using 287 13Calpha/13Cbeta shift pairs from 79 proteins with known three-dimensional structures, including 86 13Calpha and 13Cbeta shifts for 43 Zn-ligated cysteine residues, along with corresponding oxidation state and secondary structure information, we have built a logistic regression model that distinguishes between oxidized cystines, reduced (non-metal ligated) cysteines, and Zn-ligated cysteines. Classifying cysteines/cystines with a statistical model incorporating all three phenomena resulted in a predictor of Zn ligation with a recall, precision and F-measure of 83.7%, and an accuracy of 95.1%. This model was applied in the analysis of Bacillus subtilis IscU, a protein involved in iron-sulfur cluster assembly. The model predicts that all three cysteines of IscU are metal ligands. We confirmed these results by (i) examining the effect of metal chelation on the NMR spectrum of IscU, and (ii) inductively coupled plasma mass spectrometry analysis. To gain further insight into the frequency of occurrence of non-cysteine Zn

  20. Structural Expression of Chemical Environment and C-13 NMR Chemical Shift for Carbons in Alcohols%脂肪醇分子碳环境结构表征与碳谱化学位移

    Institute of Scientific and Technical Information of China (English)

    刘树深; 徐红

    2000-01-01

    A novel atomic electronegative distance vector (AEDV) has been developed to express the chemical environment of various equivalent carbon in alcohols and four 4-parameter linear relationship between chemical shift and AEDV are created by using multiple linear regression.

  1. An atomic electronegative distance vector and carbon-13 nuclear magnetic resonance chemical shifts of alcohols and alkanes

    Institute of Scientific and Technical Information of China (English)

    LIU, Shu-Shea; XIA, Zhi-Ning; CAI, Shao-Xi; LIU, Yan

    2000-01-01

    A novel atomic electronegative distance vector (AEDV) has been developed to express the chemical environment of various chemically equivalent carbon atoms in alcohols and alkanes.Combining AEDV and γ parameter, four five-parameter Iinear relationship equations of chemical shift for four types of carbon atoms are created by using multiple linear regression.Correlation coefficients are R = 0.9887, 0.9972, 0.9978 and 0.9968 and roots of mean square error are RMS = 0.906, 0.821, 1.091and 1.091of four types of carbons, i.e., type1,2, 3, and 4 for primary, secondary, tertiary, and quaternary carbons, respectively. The stability and prediction capacity for external samples of four models have been tested by cross- validation.

  2. Mean shift texture surface detection based on WT and COM feature image selection

    Institute of Scientific and Technical Information of China (English)

    HAN Yan-fang; SHI Peng-fei

    2006-01-01

    Mean shift is a widely used clustering algorithm in image segmentation. However, the segmenting results are not so good as expected when dealing with the texture surface due to the influence of the textures. Therefore, an approach based on wavelet transform (WT), co-occurrence matrix (COM) and mean shift is proposed in this paper. First, WT and COM are employed to extract the optimal resolution approximation of the original image as feature image. Then, mean shift is successfully used to obtain better detection results. Finally, experiments are done to show this approach is effective.

  3. Thalassiosira spp. community composition shifts in response to chemical and physical forcing in the northeast Pacific Ocean.

    Science.gov (United States)

    Chappell, P Dreux; Whitney, Leeann P; Haddock, Traci L; Menden-Deuer, Susanne; Roy, Eric G; Wells, Mark L; Jenkins, Bethany D

    2013-01-01

    Diatoms are genetically diverse unicellular photosynthetic eukaryotes that are key primary producers in the ocean. Many of the over 100 extant diatom species in the cosmopolitan genus Thalassiosira are difficult to distinguish in mixed populations using light microscopy. Here, we examine shifts in Thalassiosira spp. composition along a coastal to open ocean transect that encountered a 3-month-old Haida eddy in the northeast Pacific Ocean. To quantify shifts in Thalassiosira species composition, we developed a targeted automated ribosomal intergenic spacer analysis (ARISA) method to identify Thalassiosira spp. in environmental samples. As many specific fragment lengths are indicative of individual Thalassiosira spp., the ARISA method is a useful screening tool to identify changes in the relative abundance and distribution of specific species. The method also enabled us to assess changes in Thalassiosira community composition in response to chemical and physical forcing. Thalassiosira spp. community composition in the core of a 3-month-old Haida eddy remained largely (>80%) similar over a 2-week period, despite moving 24 km southwestward. Shifts in Thalassiosira species correlated with changes in dissolved iron (Fe) and temperature throughout the sampling period. Simultaneously tracking community composition and relative abundance of Thalassiosira species within the physical and chemical context they occurred allowed us to identify quantitative linkages between environmental conditions and community response.

  4. Thalassiosira spp. community composition shifts in response to chemical and physical forcing in the northeast Pacific Ocean.

    Directory of Open Access Journals (Sweden)

    Phoebe Dreux Chappell

    2013-09-01

    Full Text Available Diatoms are genetically diverse unicellular photosynthetic eukaryotes that are key primary producers in the ocean. Many of the over 100 extant diatom species in the cosmopolitan genus Thalassiosira are difficult to distinguish in mixed populations using light microscopy. Here we examine shifts in Thalassiosira spp. composition along a coastal to open ocean transect that encountered a three-month-old Haida eddy in the northeast Pacific Ocean. To quantify shifts in Thalassiosira species composition, we developed a targeted automated ribosomal intergenic spacer analysis (ARISA method to identify Thalassiosira spp. in environmental samples. As many specific fragment lengths are indicative of individual Thalassiosira spp., the ARISA method is a useful screening tool to identify changes in the relative abundance and distribution of specific species. The method also enabled us to assess changes in Thalassiosira community composition in response to chemical and physical forcing. Thalassiosira spp. community composition in the core of a three-month-old Haida eddy remained largely (>80% similar over a two-week period, despite moving 24 km southwestward. Shifts in Thalassiosira species correlated with changes in dissolved iron (Fe and temperature throughout the sampling period. Simultaneously tracking community composition and relative abundance of Thalassiosira species within the physical and chemical context they occurred allowed us to identify quantitative linkages between environmental conditions and community response.

  5. Selective Electrochemical versus Chemical Oxidation of Bulky Phenol.

    Science.gov (United States)

    Zabik, Nicole L; Virca, Carolyn N; McCormick, Theresa M; Martic-Milne, Sanela

    2016-09-01

    The electrochemical oxidation of selected tert-butylated phenols 2,6-di-tert-butyl-4-methylphenol (1), 2,6-di-tert-butylphenol (2), 2,4,6-tri-tert-butylphenol (3), 2-tert-butylphenol (4), and 4-tert-butylphenol (5) was studied in an aprotic environment using cyclic voltammetry, square-wave voltammetry, and UV-vis spectroscopy. All compounds exhibited irreversible oxidation of the corresponding phenol or phenolate ion. Compound 2 was selectively electrochemically oxidized, while other phenol analogues underwent mostly chemical oxidation. The electrochemical oxidation of 2 produced a highly absorbing product, 3,5,3',5'-tetra-tert-butyl-4,4'-diphenoquinone, which was characterized by X-ray crystal diffraction. The electrochemical oxidation was monitored as a function of electrochemical parameters and concentration. Experimental and theoretical data indicated that the steric hindrance, phenoxyl radical stability, and hydrogen bonding influenced the outcome of the electrochemical oxidation. The absence of the substituent at the para position and the presence of the bulky substituents at ortho positions were structural and electrostatic requirements for the selective electrochemical oxidation.

  6. Rotating night shift work, sleep quality, selected lifestyle factors and prolactin concentration in nurses and midwives.

    Science.gov (United States)

    Bukowska, Agnieszka; Sobala, Wojciech; Peplonska, Beata

    2015-04-01

    The pattern of secretion of many hormones, including prolactin, is dependent on the circadian rhythm. Night shift work involves exposure to artificial light at night and sleep deficiency, which in turn can affect prolactin synthesis. The aim of this study was to evaluate a possible association between night shift work characteristics, sleep quality, lifestyle factors and prolactin concentration, using data from a cross-sectional study of nurses and midwives. A cross-sectional study was conducted among 327 nurses and midwives currently working on rotating night shifts, and 330 nurses and midwives working during the day (aged 40-60 years) (388 premenopausal and 269 postmenopausal). Information about night shift work characteristics, lifestyle, reproductive factors, sleep pattern and other covariates was collected through a face-to-face interview, and from a one-week work and sleep diary completed by the subjects. Weight and height were measured. Prolactin concentration was measured in the morning blood sample using the electrochemiluminesence immunoassay method. Associations were analyzed using linear regression models adjusted for important confounders. Analyses were carried out separately in pre- and postmenopausal women. None of the night shift work or sleep characteristics was significantly associated with prolactin concentration. Prolactin concentration was significantly (p prolactin among premenopausal women, but inversely among postmenopausal. Age was related to prolactin among postmenopausal women only. Our study indicates that rotating night shift work is not associated with prolactin concentration. Smoking, parity, time of blood collection and age among postmenopausal women were significant determinants of prolactin.

  7. Observed and calculated 1H and 13C chemical shifts induced by the in situ oxidation of model sulfides to sulfoxides and sulfones.

    Science.gov (United States)

    Dracínský, Martin; Pohl, Radek; Slavetínská, Lenka; Budesínský, Milos

    2010-09-01

    A series of model sulfides was oxidized in the NMR sample tube to sulfoxides and sulfones by the stepwise addition of meta-chloroperbenzoic acid in deuterochloroform. Various methods of quantum chemical calculations have been tested to reproduce the observed (1)H and (13)C chemical shifts of the starting sulfides and their oxidation products. It has been shown that the determination of the energy-minimized conformation is a very important condition for obtaining realistic data in the subsequent calculation of the NMR chemical shifts. The correlation between calculated and observed chemical shifts is very good for carbon atoms (even for the 'cheap' DFT B3LYP/6-31G* method) and somewhat less satisfactory for hydrogen atoms. The calculated chemical shifts induced by oxidation (the Delta delta values) agree even better with the experimental values and can also be used to determine the oxidation state of the sulfur atom (-S-, -SO-, -SO(2)-).

  8. Fractional enrichment of proteins using [2-{sup 13}C]-glycerol as the carbon source facilitates measurement of excited state {sup 13}Cα chemical shifts with improved sensitivity

    Energy Technology Data Exchange (ETDEWEB)

    Ahlner, Alexandra; Andresen, Cecilia; Khan, Shahid N. [Linköping University, Division of Chemistry, Department of Physics, Chemistry and Biology (Sweden); Kay, Lewis E. [The University of Toronto, Departments of Molecular Genetics, Biochemistry and Chemistry, One King’s College Circle (Canada); Lundström, Patrik, E-mail: patlu@ifm.liu.se [Linköping University, Division of Chemistry, Department of Physics, Chemistry and Biology (Sweden)

    2015-07-15

    A selective isotope labeling scheme based on the utilization of [2-{sup 13}C]-glycerol as the carbon source during protein overexpression has been evaluated for the measurement of excited state {sup 13}Cα chemical shifts using Carr–Purcell–Meiboom–Gill (CPMG) relaxation dispersion (RD) experiments. As expected, the fractional incorporation of label at the Cα positions is increased two-fold relative to labeling schemes based on [2-{sup 13}C]-glucose, effectively doubling the sensitivity of NMR experiments. Applications to a binding reaction involving an SH3 domain from the protein Abp1p and a peptide from the protein Ark1p establish that accurate excited state {sup 13}Cα chemical shifts can be obtained from RD experiments, with errors on the order of 0.06 ppm for exchange rates ranging from 100 to 1000 s{sup −1}, despite the small fraction of {sup 13}Cα–{sup 13}Cβ spin-pairs that are present for many residue types. The labeling approach described here should thus be attractive for studies of exchanging systems using {sup 13}Cα spin probes.

  9. Predicting paramagnetic 1H NMR chemical shifts and state-energy separations in spin-crossover host-guest systems.

    Science.gov (United States)

    Isley, William C; Zarra, Salvatore; Carlson, Rebecca K; Bilbeisi, Rana A; Ronson, Tanya K; Nitschke, Jonathan R; Gagliardi, Laura; Cramer, Christopher J

    2014-06-14

    The behaviour of metal-organic cages upon guest encapsulation can be difficult to elucidate in solution. Paramagnetic metal centres introduce additional dispersion of signals that is useful for characterisation of host-guest complexes in solution using nuclear magnetic resonance (NMR). However, paramagnetic centres also complicate spectral assignment due to line broadening, signal integration error, and large changes in chemical shifts, which can be difficult to assign even for known compounds. Quantum chemical predictions can provide information that greatly facilitates the assignment of NMR signals and identification of species present. Here we explore how the prediction of paramagnetic NMR spectra may be used to gain insight into the spin crossover (SCO) properties of iron(II)-based metal organic coordination cages, specifically examining how the structure of the local metal coordination environment affects SCO. To represent the tetrahedral metal-organic cage, a model system is generated by considering an isolated metal-ion vertex: fac-ML3(2+) (M = Fe(II), Co(II); L = N-phenyl-2-pyridinaldimine). The sensitivity of the (1)H paramagnetic chemical shifts to local coordination environments is assessed and utilised to shed light on spin crossover behaviour in iron complexes. Our data indicate that expansion of the metal coordination sphere must precede any thermal SCO. An attempt to correlate experimental enthalpies of SCO with static properties of bound guests shows that no simple relationship exists, and that effects are likely due to nuanced dynamic response to encapsulation.

  10. Pressure dependence of backbone chemical shifts in the model peptides Ac-Gly-Gly-Xxx-Ala-NH2.

    Science.gov (United States)

    Erlach, Markus Beck; Koehler, Joerg; Crusca, Edson; Kremer, Werner; Munte, Claudia E; Kalbitzer, Hans Robert

    2016-06-01

    For a better understanding of nuclear magnetic resonance (NMR) detected pressure responses of folded as well as unstructured proteins the availability of data from well-defined model systems are indispensable. In this work we report the pressure dependence of chemical shifts of the backbone atoms (1)H(α), (13)C(α) and (13)C' in the protected tetrapeptides Ac-Gly-Gly-Xxx-Ala-NH2 (Xxx one of the 20 canonical amino acids). Contrary to expectation the chemical shifts of these nuclei have a nonlinear dependence on pressure in the range from 0.1 to 200 MPa. The polynomial pressure coefficients B 1 and B 2 are dependent on the type of amino acid studied. The coefficients of a given nucleus show significant linear correlations suggesting that the NMR observable pressure effects in the different amino acids have at least partly the same physical cause. In line with this observation the magnitude of the second order coefficients of nuclei being direct neighbors in the chemical structure are also weakly correlated.

  11. Information-Theoretical Complexity Analysis of Selected Elementary Chemical Reactions

    Science.gov (United States)

    Molina-Espíritu, M.; Esquivel, R. O.; Dehesa, J. S.

    We investigate the complexity of selected elementary chemical reactions (namely, the hydrogenic-abstraction reaction and the identity SN2 exchange reaction) by means of the following single and composite information-theoretic measures: disequilibrium (D), exponential entropy(L), Fisher information (I), power entropy (J), I-D, D-L and I-J planes and Fisher-Shannon (FS) and Lopez-Mancini-Calbet (LMC) shape complexities. These quantities, which are functionals of the one-particle density, are computed in both position (r) and momentum (p) spaces. The analysis revealed that the chemically significant regions of these reactions can be identified through most of the single information-theoretic measures and the two-component planes, not only the ones which are commonly revealed by the energy, such as the reactant/product (R/P) and the transition state (TS), but also those that are not present in the energy profile such as the bond cleavage energy region (BCER), the bond breaking/forming regions (B-B/F) and the charge transfer process (CT). The analysis of the complexities shows that the energy profile of the abstraction reaction bears the same information-theoretical features of the LMC and FS measures, however for the identity SN2 exchange reaction does not hold a simple behavior with respect to the LMC and FS measures. Most of the chemical features of interest (BCER, B-B/F and CT) are only revealed when particular information-theoretic aspects of localizability (L or J), uniformity (D) and disorder (I) are considered.

  12. Chemical Compositions of Kinematically Selected Outer Halo Stars

    CERN Document Server

    Zhang, Lan; Aoki, Wako; Zhao, Gang; Chiba, Masashi

    2009-01-01

    Chemical abundances of 26 metal-poor dwarfs and giants are determined from high-resolution and high signal-to-noise ratio spectra obtained with Subaru/HDS. The sample is selected so that most of the objects have outer-halo kinematics. Self-consistent atmospheric parameters were determined by an iterative procedure based on spectroscopic analysis. Abundances of 13 elements, including $\\alpha$-elements (Mg, Si, Ca, Ti), odd-Z light elements (Na, Sc), iron-peak elements (Cr, Mn, Fe, Ni, Zn) and neutron-capture elements (Y, Ba), are determined by two independent data reduction and LTE analysis procedures, confirming the consistency of the stellar parameters and abundances results. We find a decreasing trend of [$\\alpha$/Fe] with increasing [Fe/H] for the range of $-3.5 <$ [Fe/H]$ < -1$, as found by Stephens and Boesgaard (2002). [Zn/Fe] values of most objects in our sample are slightly lower than the bulk of halo stars previously studied. These results are discussed as possible chemical properties of the ou...

  13. Phage Selection of Chemically Stabilized α-Helical Peptide Ligands.

    Science.gov (United States)

    Diderich, Philippe; Bertoldo, Davide; Dessen, Pierre; Khan, Maola M; Pizzitola, Irene; Held, Werner; Huelsken, Joerg; Heinis, Christian

    2016-05-20

    Short α-helical peptides stabilized by linkages between constituent amino acids offer an attractive format for ligand development. In recent years, a range of excellent ligands based on stabilized α-helices were generated by rational design using α-helical peptides of natural proteins as templates. Herein, we developed a method to engineer chemically stabilized α-helical ligands in a combinatorial fashion. In brief, peptides containing cysteines in position i and i + 4 are genetically encoded by phage display, the cysteines are modified with chemical bridges to impose α-helical conformations, and binders are isolated by affinity selection. We applied the strategy to affinity mature an α-helical peptide binding β-catenin. We succeeded in developing ligands with Kd's as low as 5.2 nM, having >200-fold improved affinity. The strategy is generally applicable for affinity maturation of any α-helical peptide. Compared to hydrocarbon stapled peptides, the herein evolved thioether-bridged peptide ligands can be synthesized more easily, as no unnatural amino acids are required and the cyclization reaction is more efficient and yields no stereoisomers. A further advantage of the thioether-bridged peptide ligands is that they can be expressed recombinantly as fusion proteins.

  14. Halodemetallation of (Z)-1-[2-(Triarylstannyl)vinyl]-cyclooctanol and Correlation of Proton Chemical Shift with Electronegativity

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    @@ Introduction Organotin compounds have attracted attention as an optimal model for antitumour agents due to the function of the interesting intramolecular O→Sn coordination[1,2]. Our recent concern has been focused on the preparation of (Z)-1-[2-(triarylstannyl)vinyl]-cyclooctanol[3]. In order to find more appropriate compounds used as anticancer agents and explore the effect of the coordinate O→Sn interaction to the antitumor activity, the new compounds were halodemetallated and characterized. During the course of the process, some linear correlations between proton chemical shifts and the sum of the electronegativities of the tin substituents of halogens were found for the first time.

  15. Predicting Heats of Explosion of Nitroaromatic Compounds through NBO Charges and 15N NMR Chemical Shifts of Nitro Groups

    OpenAIRE

    Ricardo Infante-Castillo; Samuel P. Hernández-Rivera

    2012-01-01

    This work presents a new quantitative model to predict the heat of explosion of nitroaromatic compounds using the natural bond orbital (NBO) charge and 15N NMR chemical shifts of the nitro groups (15NNitro) as structural parameters. The values of the heat of explosion predicted for 21 nitroaromatic compounds using the model described here were compared with experimental data. The prediction ability of the model was assessed by the leave-one-out cross-validation method. The cross-validation re...

  16. Effect of pH, urea, peptide length, and neighboring amino acids on alanine alpha-proton random coil chemical shifts.

    Science.gov (United States)

    Carlisle, Elizabeth A; Holder, Jessica L; Maranda, Abby M; de Alwis, Adamberage R; Selkie, Ellen L; McKay, Sonya L

    2007-01-01

    Accurate random coil alpha-proton chemical shift values are essential for precise protein structure analysis using chemical shift index (CSI) calculations. The current study determines the chemical shift effects of pH, urea, peptide length and neighboring amino acids on the alpha-proton of Ala using model peptides of the general sequence GnXaaAYaaGn, where Xaa and Yaa are Leu, Val, Phe, Tyr, His, Trp or Pro, and n = 1-3. Changes in pH (2-6), urea (0-1M), and peptide length (n = 1-3) had no effect on Ala alpha-proton chemical shifts. Denaturing concentrations of urea (8M) caused significant downfield shifts (0.10 +/- 0.01 ppm) relative to an external DSS reference. Neighboring aliphatic residues (Leu, Val) had no effect, whereas aromatic amino acids (Phe, Tyr, His and Trp) and Pro caused significant shifts in the alanine alpha-proton, with the extent of the shifts dependent on the nature and position of the amino acid. Smaller aromatic residues (Phe, Tyr, His) caused larger shift effects when present in the C-terminal position (approximately 0.10 vs. 0.05 ppm N-terminal), and the larger aromatic tryptophan caused greater effects in the N-terminal position (0.15 ppm vs. 0.10 C-terminal). Proline affected both significant upfield (0.06 ppm, N-terminal) and downfield (0.25 ppm, C-terminal) chemical shifts. These new Ala correction factors detail the magnitude and range of variation in environmental chemical shift effects, in addition to providing insight into the molecular level interactions that govern protein folding.

  17. NMR chemical shift as analytical derivative of the Helmholtz free energy.

    Science.gov (United States)

    Van den Heuvel, Willem; Soncini, Alessandro

    2013-02-07

    We present a theory for the temperature-dependent nuclear magnetic shielding tensor of molecules with arbitrary electronic structure. The theory is a generalization of Ramsey's theory for closed-shell molecules. The shielding tensor is defined as a second derivative of the Helmholtz free energy of the electron system in equilibrium with the applied magnetic field and the nuclear magnetic moments. This derivative is analytically evaluated and expressed as a sum over states formula. Special consideration is given to a system with an isolated degenerate ground state for which the size of the degeneracy and the composition of the wave functions are arbitrary. In this case, the paramagnetic part of the shielding tensor is expressed in terms of the g and A tensors of the electron paramagnetic resonance spin Hamiltonian of the degenerate state. As an illustration of the proposed theory, we provide an explicit formula for the paramagnetic shift of the central lanthanide ion in endofullerenes Ln@C(60), with Ln = Ce(3+), Nd(3+), Sm(3+), Dy(3+), Er(3+), and Yb(3+), where the ground state can be a strongly spin-orbit coupled icosahedral sextet for which the paramagnetic shift cannot be described by previous theories.

  18. Modeling the chemical shift of lanthanide 4f electron binding energies

    NARCIS (Netherlands)

    Dorenbos, P.

    2012-01-01

    Lanthanides in compounds can adopt the tetravalent [Xe]4fn−1 (like Ce4+, Pr4+, Tb4+), the trivalent [Xe]4fn (all lanthanides), or the divalent [Xe]4f n+1 configuration (like Eu2+, Yb2+, Sm2+, Tm2+). The 4f-electron binding energy depends on the charge Q of the lanthanide ion and its chemical environ

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

    Science.gov (United States)

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

    2015-11-17

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

  20. Heat Integration of the Water-Gas Shift Reaction System for Carbon Sequestration Ready IGCC Process with Chemical Looping

    Energy Technology Data Exchange (ETDEWEB)

    Juan M. Salazara; Stephen E. Zitney; Urmila M. Diwekara

    2010-01-01

    Integrated gasification combined cycle (IGCC) technology has been considered as an important alternative for efficient power systems that can reduce fuel consumption and CO2 emissions. One of the technological schemes combines water-gas shift reaction and chemical-looping combustion as post gasification techniques in order to produce sequestration-ready CO2 and potentially reduce the size of the gas turbine. However, these schemes have not been energetically integrated and process synthesis techniques can be applied to obtain an optimal flowsheet. This work studies the heat exchange network synthesis (HENS) for the water-gas shift reaction train employing a set of alternative designs provided by Aspen energy analyzer (AEA) and combined in a process superstructure that was simulated in Aspen Plus (AP). This approach allows a rigorous evaluation of the alternative designs and their combinations avoiding all the AEA simplifications (linearized models of heat exchangers). A CAPE-OPEN compliant capability which makes use of a MINLP algorithm for sequential modular simulators was employed to obtain a heat exchange network that provided a cost of energy that was 27% lower than the base case. Highly influential parameters for the pos gasification technologies (i.e. CO/steam ratio, gasifier temperature and pressure) were calculated to obtain the minimum cost of energy while chemical looping parameters (oxidation and reduction temperature) were ensured to be satisfied.

  1. Theory of NMR chemical shift in an electronic state with arbitrary degeneracy

    CERN Document Server

    Heuvel, Willem Van den

    2012-01-01

    We present a theory of nuclear magnetic resonance (NMR) shielding tensors for electronic states with arbitrary degeneracy. The shieldings are here expressed in terms of generalized Zeeman ($g^{(k)}$) and hyperfine ($A^{(k)}$) tensors, of all ranks $k$ allowed by the size of degeneracy. Contrary to recent proposals [T. O. Pennanen and J. Vaara, Phys. Rev. Lett. 100, 133002 (2008)], our theory is valid in the strong spin-orbit coupling limit. Ab initio calculations for the 4-fold degenerate $\\Gamma_8$ ground state of lanthanide-doped fluorite crystals CaF$_2$:Ln (Ln = Pr$^{2+}$, Nd$^{3+}$, Sm$^{3+}$, and Dy$^{3+}$) show that previously neglected contributions can account for more than 50% of the paramagnetic shift.

  2. Quantitative analysis of deuterium using the isotopic effect on quaternary {sup 13}C NMR chemical shifts

    Energy Technology Data Exchange (ETDEWEB)

    Darwish, Tamim A., E-mail: tamim.darwish@ansto.gov.au [National Deuteration Facility, Australian Nuclear Science and Technology Organisation, Locked Bag 21, Kirrawee DC, NSW 2232 (Australia); Yepuri, Nageshwar Rao; Holden, Peter J. [National Deuteration Facility, Australian Nuclear Science and Technology Organisation, Locked Bag 21, Kirrawee DC, NSW 2232 (Australia); James, Michael [Australian Synchrotron, 800 Blackburn Road, Clayton, Victoria 3168 (Australia)

    2016-07-13

    Quantitative analysis of specifically deuterated compounds can be achieved by a number of conventional methods, such as mass spectroscopy, or by quantifying the residual {sup 1}H NMR signals compared to signals from internal standards. However, site specific quantification using these methods becomes challenging when dealing with non-specifically or randomly deuterated compounds that are produced by metal catalyzed hydrothermal reactions in D{sub 2}O, one of the most convenient deuteration methods. In this study, deuterium-induced NMR isotope shifts of quaternary {sup 13}C resonances neighboring deuterated sites have been utilized to quantify the degree of isotope labeling of molecular sites in non-specifically deuterated molecules. By probing {sup 13}C NMR signals while decoupling both proton and deuterium nuclei, it is possible to resolve {sup 13}C resonances of the different isotopologues based on the isotopic shifts and the degree of deuteration of the carbon atoms. We demonstrate that in different isotopologues, the same quaternary carbon, neighboring partially deuterated carbon atoms, are affected to an equal extent by relaxation. Decoupling both nuclei ({sup 1}H, {sup 2}H) resolves closely separated quaternary {sup 13}C signals of the different isotopologues, and allows their accurate integration and quantification under short relaxation delays (D1 = 1 s) and hence fast accumulative spectral acquisition. We have performed a number of approaches to quantify the deuterium content at different specific sites to demonstrate a convenient and generic analysis method for use in randomly deuterated molecules, or in cases of specifically deuterated molecules where back-exchange processes may take place during work up. - Graphical abstract: The relative intensities of quaternary {sup 13}C {"1H,"2H} resonances are equal despite the different relaxation delays, allowing the relative abundance of the different deuterated isotopologues to be calculated using NMR fast

  3. Understanding Molecular Interactions within Chemically Selective Layered Polymer Assemblies

    Energy Technology Data Exchange (ETDEWEB)

    Gary J. Blanchard

    2009-06-30

    This work focuses on two broad issues. These are (1) the molecular origin of the chemical selectivity achieved with ultrathin polymer multilayers, and (2) how the viscoelastic properties of the polymer layers are affected by exposure to solvent and analytes. These issues are inter-related, and to understand them we need to design experiments that probe both the energetic and kinetic aspects of interfacial adsorption processes. This project focuses on controling the chemical structure, thickness, morphology and sequential ordering of polymer layers bound to interfaces using maleimide-vinyl ether and closely related alternating copolymerization chemistry and efficient covalent cross-linking reactions that allow for layer-by-layer polymer deposition. This chemistry has been developed during the funding cycle of this Grant. We have measure the equilibrium constants for interactions between specific layers within the polymer interfaces and size-controlled, surface-functionalized gold nanoparticles. The ability to control both size and functionality of gold nanoparticle model analytes allows us to evaluate the average “pore size” that characterizes our polymer films. We have measured the “bulk” viscosity and shear modulus of the ultrathin polymer films as a function of solvent overlayer identity using quartz crystal microbalance complex impedance measurements. We have measured microscopic viscosity at specific locations within the layered polymer interfaces with time-resolved fluorescence lifetime and depolarization techniques. We combine polymer, cross-linking and nanoparticle synthetic expertise with a host of characterization techniques, including QCM gravimetry and complex impedance analysis, steady state and time-resolved spectroscopies.

  4. Parallel shifts in ecology and natural selection in an island lizard

    Directory of Open Access Journals (Sweden)

    Smith Thomas B

    2009-01-01

    Full Text Available Abstract Background Natural selection is a potent evolutionary force that shapes phenotypic variation to match ecological conditions. However, we know little about the year-to-year consistency of selection, or how inter-annual variation in ecology shapes adaptive landscapes and ultimately adaptive radiations. Here we combine remote sensing data, field experiments, and a four-year study of natural selection to show that changes in vegetation structure associated with a severe drought altered both habitat use and natural selection in the brown anole, Anolis sagrei. Results In natural populations, lizards increased their use of vegetation in wet years and this was correlated with selection on limb length but not body size. By contrast, a die-back of vegetation caused by drought was followed by reduced arboreality, selection on body size, and relaxed selection on limb length. With the return of the rains and recovery of vegetation, selection reverted back to pre-drought pattern of selection acting on limb length but not body size. To test for the impact of vegetation loss on natural selection during the drought, we experimentally removed vegetation on a separate study island in a naturally wet year. The experiment revealed similar inter-annual changes in selection on body size but not limb length. Conclusion Our results illustrate the dynamic nature of ecology driving natural selection on Anolis morphology and emphasize the importance of inter-annual environmental variation in shaping adaptive variation. In addition, results illustrate the utility of using remote sensing data to examine ecology's role in driving natural selection.

  5. Parallel shifts in ecology and natural selection in an island lizard

    OpenAIRE

    Smith Thomas B; Buermann Wolfgang; Calsbeek Ryan

    2009-01-01

    Abstract Background Natural selection is a potent evolutionary force that shapes phenotypic variation to match ecological conditions. However, we know little about the year-to-year consistency of selection, or how inter-annual variation in ecology shapes adaptive landscapes and ultimately adaptive radiations. Here we combine remote sensing data, field experiments, and a four-year study of natural selection to show that changes in vegetation structure associated with a severe drought altered b...

  6. Chemical vapor synthesis of size-selected zinc oxide nanoparticles.

    Science.gov (United States)

    Polarz, Sebastian; Roy, Abhijit; Merz, Michael; Halm, Simon; Schröder, Detlef; Schneider, Lars; Bacher, Gerd; Kruis, Frank E; Driess, Matthias

    2005-05-01

    ZnO can be regarded as one of the most important metal oxide semiconductors for future applications. Similar to silicon in microelectronics, it is not only important to obtain nanoscale building blocks of ZnO, but also extraordinary purity has to be ensured. A new gas-phase approach to obtain size-selected, nanocrystalline ZnO particles is presented. The tetrameric alkyl-alkoxy zinc compound [CH(3)ZnOCH(CH(3))(2)](4) is chemically transformed into ZnO, and the mechanism of gas-phase transformation is studied in detail. Furthermore, the morphological genesis of particles via gas-phase sintering is investigated, and for the first time a detailed model of the gas-phase sintering processes of ZnO is presented. Various analytical techniques (powder XRD, TEM/energy-dispersive X-ray spectroscopy, magic-angle spinning NMR spectroscopy, FTIR spectroscopy, etc.) are used to investigate the structure and purity of the samples. In particular, the defect structure of the ZnO was studied by photoluminescence spectroscopy.

  7. NMR chemical shift as analytical derivative of the Helmholtz free energy

    CERN Document Server

    Heuvel, Willem Van den

    2012-01-01

    We present a theory for the temperature-dependent nuclear magnetic shielding tensor of molecules with arbitrary electronic structure. The theory is a generalization of Ramsey's theory for closed-shell molecules. The shielding tensor is defined as a second derivative of the Helmholtz free energy of the electron system in equilibrium with the applied magnetic field and the nuclear magnetic moments. This derivative is analytically evaluated and expressed as a sum over states formula. Special consideration is given to a system with an isolated degenerate ground state for which the size of the degeneracy and the composition of the wave functions are arbitrary. In this case the paramagnetic part of the shielding tensor is expressed in terms of the $g$ and $A$ tensors of the EPR spin Hamiltonian of the degenerate state. As an illustration of the proposed theory, we provide an explicit formula for the paramagnetic shift of the central lanthanide ion in endofullerenes Ln@C$_{60}$, with Ln=Ce$^{3+}$, Nd$^{3+}$, Sm$^{3+...

  8. (1) H NMR Spectra. Part 28: Proton chemical shifts and couplings in three-membered rings. A ring current model for cyclopropane and a novel dihedral angle dependence for (3) J(HH) couplings involving the epoxy proton.

    Science.gov (United States)

    Abraham, Raymond J; Leonard, Paul; Tormena, Cláudio F

    2012-04-01

    The (1) H chemical shifts of selected three-membered ring compounds in CDCl(3) solvent were obtained. This allowed the determination of the substituent chemical shifts of the substituents in the three-membered rings and the long-range effect of these rings on the distant protons. The substituent chemical shifts of common substituents in the cyclopropane ring differ considerably from the same substituents in acyclic fragments and in cyclohexane and were modelled in terms of a three-bond (γ)-effect. For long-range protons (more than three bonds removed), the substituent effects of the cyclopropane ring were analysed in terms of the cyclopropane magnetic anisotropy and steric effect. The cyclopropane magnetic anisotropy (ring current) shift was modelled by (a) a single equivalent dipole perpendicular to and at the centre of the cyclopropane ring and (b) by three identical equivalent dipoles perpendicular to the ring placed at each carbon atom. Model (b) gave a more accurate description of the (1) H chemical shifts and was the selected model. After parameterization, the overall root mean square error for the dataset of 289 entries was 0.068 ppm. The anisotropic effects are significant for the cyclopropane protons (ca 1 ppm) but decrease rapidly with distance. The heterocyclic rings of oxirane, thiirane and aziridine do not possess a ring current. (3) J(HH) couplings of the epoxy ring proton with side-chain protons were obtained and shown to be dependent on both the H-C-C-H and H-C-C-O orientations. Both density functional theory calculations and a simple Karplus-type equation gave general agreement with the observed couplings (root mean square error 0.5 Hz over a 10-Hz range).

  9. Liver fat quantification: Comparison of dual-echo and triple-echo chemical shift MRI to MR spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Satkunasingham, Janakan; Besa, Cecilia [Department of Radiology, Body MRI, Icahn School of Medicine at Mount Sinai, One Gustave Levy Place, New York, NY 10029 (United States); Translational and Molecular Imaging Institute, Icahn School of Medicine at Mount Sinai, One Gustave Levy Place, New York, NY 10029 (United States); Bane, Octavia [Translational and Molecular Imaging Institute, Icahn School of Medicine at Mount Sinai, One Gustave Levy Place, New York, NY 10029 (United States); Shah, Ami [Department of Radiology, Body MRI, Icahn School of Medicine at Mount Sinai, One Gustave Levy Place, New York, NY 10029 (United States); Oliveira, André de; Gilson, Wesley D.; Kannengiesser, Stephan [Siemens AG, Healthcare Sector, Erlangen (Germany); Taouli, Bachir, E-mail: bachir.taouli@mountsinai.org [Department of Radiology, Body MRI, Icahn School of Medicine at Mount Sinai, One Gustave Levy Place, New York, NY 10029 (United States); Translational and Molecular Imaging Institute, Icahn School of Medicine at Mount Sinai, One Gustave Levy Place, New York, NY 10029 (United States)

    2015-08-15

    Highlights: • We present a large cohort of patients who underwent dual and triple echo chemical shift imaging against multi-echo T{sub 2} corrected MR spectroscopy (MRS) for liver fat quantification. • Our data suggests that a triple-echo sequence is highly accurate for detection of liver fat, even in the presence of T{sub 2}{sup *} shortening, with minor discrepancies when compared with the advanced fat quantification method. - Abstract: Purpose: To assess the diagnostic value of MRI using dual-echo (2PD) and triple-echo (3PD) chemical shift imaging for liver fat quantification against multi-echo T{sub 2} corrected MR spectroscopy (MRS) used as the reference standard, and examine the effect of T{sub 2}{sup *} imaging on accuracy of MRI for fat quantification. Materials and methods: Patients who underwent 1.5 T liver MRI that incorporated 2PD, 3PD, multi-echo T{sub 2}{sup *} and MRS were included in this IRB approved prospective study. Regions of interest were placed in the liver to measure fat fraction (FF) with 2PD and 3PD and compared with MRS-FF. A random subset of 25 patients with a wide range of MRS-FF was analyzed with an advanced FF calculation method, to prove concordance with the 3PD. The statistical analysis included correlation stratified according to T{sub 2}{sup *}, Bland-Altman analysis, and calculation of diagnostic accuracy for detection of MRS-FF > 6.25%. Results: 220 MRI studies were identified in 217 patients (mean BMI 28.0 ± 5.6). 57/217 (26.2%) patients demonstrated liver steatosis (MRS-FF > 6.25%). Bland-Altman analysis revealed strong agreement between 3PD and MRS (mean ± 1.96 SD: −0.5% ± 4.6%) and weaker agreement between 2PD and MRS (4.7% ± 16.0%). Sensitivity of 3PD for diagnosing FF> 6.25% was higher than that of 2PD. 3PD-FF showed minor discrepancies (coefficient of variation <10%) from FF measured with the advanced method. Conclusion: Our large series study validates the use of 3PD chemical shift sequence for detection of

  10. Chemical structure elucidation from ¹³C NMR chemical shifts: efficient data processing using bipartite matching and maximal clique algorithms.

    Science.gov (United States)

    Koichi, Shungo; Arisaka, Masaki; Koshino, Hiroyuki; Aoki, Atsushi; Iwata, Satoru; Uno, Takeaki; Satoh, Hiroko

    2014-04-28

    Computer-assisted chemical structure elucidation has been intensively studied since the first use of computers in chemistry in the 1960s. Most of the existing elucidators use a structure-spectrum database to obtain clues about the correct structure. Such a structure-spectrum database is expected to grow on a daily basis. Hence, the necessity to develop an efficient structure elucidation system that can adapt to the growth of a database has been also growing. Therefore, we have developed a new elucidator using practically efficient graph algorithms, including the convex bipartite matching, weighted bipartite matching, and Bron-Kerbosch maximal clique algorithms. The utilization of the two matching algorithms especially is a novel point of our elucidator. Because of these sophisticated algorithms, the elucidator exactly produces a correct structure if all of the fragments are included in the database. Even if not all of the fragments are in the database, the elucidator proposes relevant substructures that can help chemists to identify the actual chemical structures. The elucidator, called the CAST/CNMR Structure Elucidator, plays a complementary role to the CAST/CNMR Chemical Shift Predictor, and together these two functions can be used to analyze the structures of organic compounds.

  11. Chemical composition of buckwheat plant parts and selected buckwheat products

    Directory of Open Access Journals (Sweden)

    Petra Vojtíšková

    2014-11-01

    Full Text Available Chemical composition plant parts (roots, stalks, leaves, blossoms of common buckwheat (Fagopyrum esculentum Moench and selected products made from its seeds (peels, whole seed, wholemeal flour, broken seeds, crunchy products Natural and Cocoa, flour, and pasta was determined. Samples were dried and ground to a fine powder. All analyses were performed according to the Commission Regulation no. 152/2009, while rutin concentration was determined by the modified HPLC method. The lowest content of moisture was found in roots (4.3% and in peels (almost 8% and the highest moisture (nearly 11% was discovered in seeds. The lowest amount of crude protein (3.5% was found in peels, the highest crude protein amount (>13% in both flours and leaves (23%. The starch content (>50% in dry matter differs from one sample to another. Only in peels the content of starch was about 3.5%. From all examined samples, the lowest content of fat was found in crunchy products Cocoa, 1.7%. The lowest amount of histidine was determined in all studied samples, except peels, the highest content of glutamic acid was determined in almost all samples, except peels. Whole-meal flour is very rich source of Ca and Fe. The content of these elements was 1172 mg.kg-1 and 45.9 mg.kg-1, respectively. On the other hand, the highest content of Pb (>1 mg.kg-1 was found in broken seeds. The greatest concentration of rutin was determined in blossoms and leaves (83.6 and 69.9 mg.g-1, respectively. On the other hand, the lowest concentrations of rutin were found in buckwheat products (generally less then 1 mg.g-1, i.e. in wholemeal flour, 702 μg.kg-1, the lowest almost 10 μg.kg-1 in pasta.

  12. Chemical shift powder spectra enhanced by multiple-contact cross-polarization under slow magic-angle spinning

    Science.gov (United States)

    Raya, Jésus; Perrone, Barbara; Hirschinger, Jérôme

    2013-02-01

    A simple multiple-contact cross-polarization (CP) scheme is applied to a powder sample of ferrocene and β-calcium formate under static and magic-angle spinning (MAS) conditions. The method is described analytically through the density matrix formalism. We show that multiple equilibrations-re-equilibrations with the proton spin bath improves the polarization transfer efficiency at short contact times and provides higher signal enhancements than state-of-the art techniques such as adiabatic passage through the Hartmann-Hahn condition CP (APHH-CP) when MAS is applied. The resulting chemical shift powder spectra then are identical to the ones obtained by using ROtor-Directed Exchange of Orientations CP (APHH-RODEO-CP) with intensity gains of a factor 1.1-1.3.

  13. 13C-NMR chemical shift databases as a quick tool to evaluate structural models of humic substances

    DEFF Research Database (Denmark)

    Nyrop Albers, Christian; Hansen, Poul Erik

    2010-01-01

    Models for humic and fulvic acids are discussed based on 13C liquid state NMR spectra combined with results from elemental analysis and titration studies. The analysis of NMR spectra is based on a full reconstruction of the NMR spectrum done with help of 13C-NMR data bases by adding up chemical...... side missing structural elements in the models can be suggested. A number of proposed structures for humic and fulvic acids are discussed based on the above analysis....... shifts of all substructures from the proposed models. A full reconstruction makes sure that all carbons are accounted for and enables on the negative side to discuss structural elements identified from recorded spectra of humic substances that cannot be observed in the simulated spectrum. On the positive...

  14. Chemical shift powder spectra enhanced by multiple-contact cross-polarization under slow magic-angle spinning.

    Science.gov (United States)

    Raya, Jésus; Perrone, Barbara; Hirschinger, Jérôme

    2013-02-01

    A simple multiple-contact cross-polarization (CP) scheme is applied to a powder sample of ferrocene and β-calcium formate under static and magic-angle spinning (MAS) conditions. The method is described analytically through the density matrix formalism. We show that multiple equilibrations-re-equilibrations with the proton spin bath improves the polarization transfer efficiency at short contact times and provides higher signal enhancements than state-of-the art techniques such as adiabatic passage through the Hartmann-Hahn condition CP (APHH-CP) when MAS is applied. The resulting chemical shift powder spectra then are identical to the ones obtained by using ROtor-Directed Exchange of Orientations CP (APHH-RODEO-CP) with intensity gains of a factor 1.1-1.3.

  15. Portable Sequentially Shifted Excitation Raman spectroscopy as an innovative tool for in situ chemical interrogation of painted surfaces.

    Science.gov (United States)

    Conti, Claudia; Botteon, Alessandra; Bertasa, Moira; Colombo, Chiara; Realini, Marco; Sali, Diego

    2016-08-07

    We present the first validation and application of portable Sequentially Shifted Excitation (SSE) Raman spectroscopy for the survey of painted layers in art. The method enables the acquisition of shifted Raman spectra and the recovery of the spectral data through the application of a suitable reconstruction algorithm. The technique has a great potentiality in art where commonly a strong fluorescence obscures the Raman signal of the target, especially when conventional portable Raman spectrometers are used for in situ analyses. Firstly, the analytical capability of portable SSE Raman spectroscopy is critically discussed using reference materials and laboratory specimens, comparing its results with other conventional high performance laboratory instruments (benchtop FT-Raman and dispersive Raman spectrometers with an external fiber optic probe); secondly, it is applied directly in situ to study the complex polychromy of Italian prestigious terracotta sculptures of the 16(th) century. Portable SSE Raman spectroscopy represents a new investigation modality in art, expanding the portfolio of non-invasive, chemically specific analytical tools.

  16. Microscopic structures of ionic liquids 1-ethyl-3-methylimidazolium tetrafluoroborate in water probed by the relative chemical shift

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    The relative chemical shifts (△δ) △δwere put forward to investigate the microscopic structure of 1-ethyl-3-methyl-imidazolium tetrafluoroborate (EmimBF4) during the dilution process with water.The concentration-dependent △δ(C2)H-(C4)H,△δ(C2)H-(C5)H and △δ(C4)H-(C5)H were analyzed.The results reveal that the variations of the microscopic structures of three aromatic protons are inconsistent.The strength of the H-bond between water and three aromatic protons follows the order:(C2)H···O > (C4)H···O > (C5)H···O.The concentration-dependent △δ(C6)H-(C7)H and △δ(C6)H-(C8)H indicate the formation of the H-bonds of (Calkyl)H···O is impossible,and more water is located around (C6)H than around (C7)H or (C8)H.The concentration-dependent △δ(C2)H-(C4)H and △δ(C2)H-(C5)H both increase rapidly when xwater > 0.9 or so,suggesting the ionic pairs of EmimBF4 are dissociated rapidly.The turning points of concentration-dependent △δ(C2)H-(C4)H and △δ(C2)H-(C5)H indicate that some physical properties of the EmimBF4/water mixtures also change at the corresponding concentration point.The microscopic structures of EmimBF4 in water could be clearly detected by the relative chemical shifts.

  17. Thickness-Dependent Binding Energy Shift in Few-Layer MoS2 Grown by Chemical Vapor Deposition.

    Science.gov (United States)

    Lin, Yu-Kai; Chen, Ruei-San; Chou, Tsu-Chin; Lee, Yi-Hsin; Chen, Yang-Fang; Chen, Kuei-Hsien; Chen, Li-Chyong

    2016-08-31

    The thickness-dependent surface states of MoS2 thin films grown by the chemical vapor deposition process on the SiO2-Si substrates are investigated by X-ray photoelectron spectroscopy. Raman and high-resolution transmission electron microscopy suggest the thicknesses of MoS2 films to be ranging from 3 to 10 layers. Both the core levels and valence band edges of MoS2 shift downward ∼0.2 eV as the film thickness increases, which can be ascribed to the Fermi level variations resulting from the surface states and bulk defects. Grainy features observed from the atomic force microscopy topographies, and sulfur-vacancy-induced defect states illustrated at the valence band spectra imply the generation of surface states that causes the downward band bending at the n-type MoS2 surface. Bulk defects in thick MoS2 may also influence the Fermi level oppositely compared to the surface states. When Au contacts with our MoS2 thin films, the Fermi level downshifts and the binding energy reduces due to the hole-doping characteristics of Au and easy charge transfer from the surface defect sites of MoS2. The shift of the onset potentials in hydrogen evolution reaction and the evolution of charge-transfer resistances extracted from the impedance measurement also indicate the Fermi level varies with MoS2 film thickness. The tunable Fermi level and the high chemical stability make our MoS2 a potential catalyst. The observed thickness-dependent properties can also be applied to other transition-metal dichalcogenides (TMDs), and facilitates the development in the low-dimensional electronic devices and catalysts.

  18. Zero discharge tanning: a shift from chemical to biocatalytic leather processing.

    Science.gov (United States)

    Thanikaivelan, Palanisamy; Rao, Jonnalagadda Raghava; Nair, Balachandran Unni; Ramasami, Thirumalachari

    2002-10-01

    Beam house processes (Beam house processes generally mean liming-reliming processes, which employ beam.) contribute more than 60% of the total pollution from leather processing. The use of lime and sodium sulfide is of environmental concern (1, 2). Recently, the authors have developed an enzyme-based dehairing assisted with a very low amount of sodium sulfide, which completely avoids the use of lime. However, the dehaired pelt requires opening up of fiber bundles for further processing, where lime is employed to achieve this through osmotic swelling. Huge amounts of lime sludge and total solids are the main drawbacks of lime. An alternative bioprocess, based on alpha-amylase for fiber opening, has been attempted after enzymatic unhairing. This totally eliminates the use of lime in leather processing. This method enables subsequent processes and operations in leather making feasible without a deliming process. A control experiment was run in parallel using conventional liming-reliming processes. It has been found that the extent of opening up of fiber bundles using alpha-amylase is comparable to that of the control. This has been substantiated through scanning electron microscopic, stratigraphic chrome distribution analysis, and softness measurements. Performance of the leathers is shown to be on a par with leathers produced by the conventional process through physical and hand evaluation. Importantly, softness of the leathers is numerically proven to be comparable with that of control. The process also demonstrates reduction in chemical oxygen demand load by 45% and total solids load by 20% compared to the conventional process. The total dry sludge from the beam house processes is brought down from 152 to 8 kg for processing 1 ton of raw hides.

  19. Comparison of experimental and DFT-calculated NMR chemical shifts of 2-amino and 2-hydroxyl substituted phenyl benzimidazoles, benzoxazoles and benzothiazoles in four solvents using the IEF-PCM solvation model.

    Science.gov (United States)

    Pierens, Gregory K; Venkatachalam, T K; Reutens, David C

    2016-04-01

    A comparative study of experimental and calculated NMR chemical shifts of six compounds comprising 2-amino and 2-hydroxy phenyl benzoxazoles/benzothiazoles/benzimidazoles in four solvents is reported. The benzimidazoles showed interesting spectral characteristics, which are discussed. The proton and carbon chemical shifts were similar for all solvents. The largest chemical shift deviations were observed in benzene. The chemical shifts were calculated with density functional theory using a suite of four functionals and basis set combinations. The calculated chemical shifts revealed a good match to the experimentally observed values in most of the solvents. The mean absolute error was used as the primary metric. The use of an additional metric is suggested, which is based on the order of chemical shifts. The DP4 probability measures were also used to compare the experimental and calculated chemical shifts for each compound in the four solvents. Copyright © 2015 John Wiley & Sons, Ltd.

  20. CHEMICALLY MODIFIED FIELD-EFFECT TRANSISTORS - POTENTIOMETRIC AG+ SELECTIVITY OF PVC MEMBRANES BASED ON MACROCYCLIC THIOETHERS

    NARCIS (Netherlands)

    BRZOZKA, Z; COBBEN, PLHM; REINHOUDT, DN; EDEMA, JJH; KELLOGG, RM

    1993-01-01

    A chemically modified field-effect transistor (CHEMFET) with satisfactory Ag+ selectivity is described. The potentiometric Ag+ selectivities of CHEMFETs with plasticized PVC membranes based on macrocyclic thioethers have been determined. All the macrocyclic thioethers tested showed silver response a

  1. High-Frequency (1)H NMR Chemical Shifts of Sn(II) and Pb(II) Hydrides Induced by Relativistic Effects: Quest for Pb(II) Hydrides.

    Science.gov (United States)

    Vícha, Jan; Marek, Radek; Straka, Michal

    2016-10-17

    The role of relativistic effects on (1)H NMR chemical shifts of Sn(II) and Pb(II) hydrides is investigated by using fully relativistic DFT calculations. The stability of possible Pb(II) hydride isomers is studied together with their (1)H NMR chemical shifts, which are predicted in the high-frequency region, up to 90 ppm. These (1)H signals are dictated by sizable relativistic contributions due to spin-orbit coupling at the heavy atom and can be as large as 80 ppm for a hydrogen atom bound to Pb(II). Such high-frequency (1)H NMR chemical shifts of Pb(II) hydride resonances cannot be detected in the (1)H NMR spectra with standard experimental setup. Extended (1)H NMR spectral ranges are thus suggested for studies of Pb(II) compounds. Modulation of spin-orbit relativistic contribution to (1)H NMR chemical shift is found to be important also in the experimentally known Sn(II) hydrides. Because the (1)H NMR chemical shifts were found to be rather sensitive to the changes in the coordination sphere of the central metal in both Sn(II) and Pb(II) hydrides, their application for structural investigation is suggested.

  2. Predictions of the fluorine NMR chemical shifts of perfluorinated carboxylic acids, CnF(2n+1)COOH (n = 6-8).

    Science.gov (United States)

    Liu, Zizhong; Goddard, John D

    2009-12-17

    Perfluorinated carboxylic acids (PFCAs) are a class of persistent environmental pollutants. Commercially available PFCAs are mixtures of linear and branched isomers, possibly with impurities. Different isomers have different physical and chemical properties and toxicities. However, little is known about the properties and the finer details of the structures of the individual branched isomers. Full geometry optimizations for the linear n-alkane (C(6)-C(27)) PFCAs indicated that all have helical structures. The helical angle increases slightly with increasing chain length, from 16.3 degrees in C(6)F(13)COOH to 17.0 degrees in C(27)F(55)COOH. This study predicts (19)F NMR parameters for 69 linear and branched isomers of the perfluoro carboxylic acids C(6)F(13)COOH, C(7)F(15)COOH, and C(8)F(17)COOH. B3LYP-GIAO/6-31++G(d,p)//B3LYP/6-31G(d,p) was used for the NMR calculations with analysis of the chemical shifts by the natural bond orbital method. The predictions of the (19)F chemical shifts revealed the differences among the CF(3), CF(2), and CF groups. In general, the absolute values for the chemical shifts for the CF(3) group are smaller than 90 ppm, for the CF larger than 160 ppm, and for the CF(2) between 110 and 130 ppm. The chemical shifts of the branched isomers are smaller in magnitude than the linear ones. The decrease is correlated with the steric hindrance of the CF(3) groups, the more hindered the CF(3), the greater the decrease in the (19)F chemical shifts. The predicted (19)F chemical shifts are similar to those for analogous perfluoro compounds with other terminal functional groups such as -SO(3)H or -SO(3)NH(2)CH(2)CH(3).

  3. National toxicology program chemical nomination and selection process

    Energy Technology Data Exchange (ETDEWEB)

    Selkirk, J.K. [National Institute of Environmental Health Sciences, Research Triangle Park, NC (United States)

    1990-12-31

    The National Toxicology Program (NTP) was organized to support national public health programs by initiating research designed to understand the physiological, metabolic, and genetic basis for chemical toxicity. The primary mandated responsibilities of NTP were in vivo and vitro toxicity testing of potentially hazardous chemicals; broadening the spectrum of toxicological information on known hazardous chemicals; validating current toxicological assay systems as well as developing new and innovative toxicity testing technology; and rapidly communicating test results to government agencies with regulatory responsibilities and to the medical and scientific communities. 2 figs.

  4. High accuracy NMR chemical shift corrected for bulk magnetization as a tool for structural elucidation of dilutable microemulsions. Part 1 - Proof of concept.

    Science.gov (United States)

    Hoffman, Roy E; Darmon, Eliezer; Aserin, Abraham; Garti, Nissim

    2016-02-01

    In microemulsions, changes in droplet size and shape and possible transformations occur under various conditions. They are difficult to characterize by most analytical tools because of their nano-sized structure and dynamic nature. Several methods are usually combined to obtain reliable information, guiding the scientist in understanding their physical behavior. We felt that there is a need for a technique that complements those in use today in order to provide more information on the microemulsion behavior, mainly as a function of dilution with water. The improvement of NMR chemical shift measurements independent of bulk magnetization effects makes it possible to study the very weak intermolecular chemical shift effects. In the present study, we used NMR high resolution magic angle spinning to measure the chemical shift very accurately, free of bulk magnetization effects. The chemical shift of microemulsion components is measured as a function of the water content in order to validate the method in an interesting and promising, U-type dilutable microemulsion, which had been previously studied by a variety of techniques. Phase transition points of the microemulsion (O/W, bicontinuous, W/O) and changes in droplet shape were successfully detected using high-accuracy chemical shift measurements. We analyzed the results and found them to be compatible with the previous studies, paving the way for high-accuracy chemical shifts to be used for the study of other microemulsion systems. We detected two transition points along the water dilution line of the concentrate (reverse micelles) corresponding to the transition from swollen W/O nano-droplets to bicontinuous to the O/W droplets along with the changes in the droplets' sizes and shapes. The method seems to be in excellent agreement with other previously studied techniques and shows the advantage of this easy and valid technique.

  5. Selection for adaptation to dietary shifts: towards sustainable breeding of carnivorous fish.

    Directory of Open Access Journals (Sweden)

    Richard Le Boucher

    Full Text Available Genetic adaptation to dietary environments is a key process in the evolution of natural populations and is of great interest in animal breeding. In fish farming, the use of fish meal and fish oil has been widely challenged, leading to the rapidly increasing use of plant-based products in feed. However, high substitution rates impair fish health and growth in carnivorous species. We demonstrated that survival rate, mean body weight and biomass can be improved in rainbow trout (Oncorhynchus mykiss after a single generation of selection for the ability to adapt to a totally plant-based diet (15.1%, 35.3% and 54.4%, respectively. Individual variability in the ability to adapt to major diet changes can be effectively used to promote fish welfare and a more sustainable aquaculture.

  6. Selective blockade of 5-HT7 receptors facilitates attentional set-shifting in stressed and control rats.

    Science.gov (United States)

    Nikiforuk, Agnieszka

    2012-01-01

    Preclinical data demonstrate that the selective blockade of 5-HT7 receptors produces antidepressant-like behavioural effects. Although the involvement of 5-HT7 receptors in cognitive processes has been previously suggested, little is known about their role in the prefrontal cortex (PFC)-dependent processes that may be impaired in stress-related states. According to our previous study, repeated restraint stress induces the long-lasting cognitive impairment in a rat model of PFC-dependent attentional set-shifting task (ASST). Therefore, the first aim of the present experiments was to examine the impact of the selective 5-HT7 receptor antagonist, SB-269970, on ASST performance of stressed and control rats. Since the selective blockade of 5-HT7 receptors has been previously demonstrated to enhance the behavioural effects of antidepressants, the second goal was to examine the impact of the joint administration of inactive doses of SB-269970 and escitalopram in the ASST. SB-269970 (0.3 and 1mg/kg) given to stressed rats 30min before testing reversed the restraint-induced impairment of the extra-dimensional (ED) set-shifting ability. Additionally, SB-269970 (1mg/kg) also improved ED performance of the unstressed control group. Moreover, SB-269970, given at an inactive dose, enhanced the pro-cognitive efficacy of escitalopram. In conclusion, these results highlight the possibility that 5-HT7 receptor antagonism may represent a useful pharmacological approach in the treatment of frontal-like cognitive disturbances in stress-related psychiatric disorders.

  7. A review of selected chemical additives in cosmetic products.

    Science.gov (United States)

    Juhász, Margit Lai Wun; Marmur, Ellen S

    2014-01-01

    The addition of chemical additives to consumer cosmetic products is a common practice to increase cosmetic effectiveness, maintain cosmetic efficacy, and produce a longer-lasting, more viable product. Recently, manufacturers have come under attack for the addition of chemicals including dioxane, formaldehyde, lead/lead acetate, parabens, and phthalate, as these additives may prove harmful to consumer health. Although reports show that these products may indeed adversely affect human health, these studies are conducted using levels of the aforementioned chemicals at much higher levels of exposure than those found in cosmetic products. When cosmeceuticals are used as per manufacturer's instructions, it is estimated that the levels of harmful additives found in these products are considerably lower than reported toxic concentrations.

  8. Selective observation of Goos-H\\"anchen and Imbert-Federov shifts in partial reflection via optimized weak measurements in linear and elliptical polarization basis

    CERN Document Server

    Goswami, S; Pal, M; Nandi, A; Panigrahi, P K; Ghosh, N

    2015-01-01

    The spatial and the angular variants of the Goos-H\\"anchen (GH) and the Imbert-Federov (IF) beam shifts contribute in a complex interrelated way to the resultant beam shift in partial reflection at planar dielectric interfaces. Here, we show that the angular GH and the two variants of the IF effects can be decoupled, amplified and separately observed by weak value amplification and subsequent conversion of spatial$\\leftrightarrow$angular nature of the beam shifts using appropriate pre and post selection of polarization states. We experimentally demonstrate such decoupling and illustrate various other intriguing manifestations of weak measurements by employing optimized pre and post selections (based on the eigen polarization states of the shifts) elliptical and / or linear polarization basis. The demonstrated ability to amplify, controllably decouple or combine the beam shifts via weak measurements may prove to be valuable for understanding the different physical contributions of the effects and for their app...

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

    Science.gov (United States)

    Galdeano, Carles; Ciulli, Alessio

    2016-09-01

    Targeting epigenetic proteins is a rapidly growing area for medicinal chemistry and drug discovery. Recent years have seen an explosion of interest in developing small molecules binding to bromodomains, the readers of acetyl-lysine modifications. A plethora of co-crystal structures has motivated focused fragment-based design and optimization programs within both industry and academia. These efforts have yielded several compounds entering the clinic, and many more are increasingly being used as chemical probes to interrogate bromodomain biology. High selectivity of chemical probes is necessary to ensure biological activity is due to an on-target effect. Here, we review the state-of-the-art of bromodomain-targeting compounds, focusing on the structural basis for their on-target selectivity or lack thereof. We also highlight chemical biology approaches to enhance on-target selectivity.

  10. Physico-Chemical Studies of the Pvc K+ - Selective Membrane

    Directory of Open Access Journals (Sweden)

    Ana COROIAN

    2002-12-01

    Full Text Available A plasticized ion-selective membrane based on PVC matrix which tricrezylphosphate (TCP and containing K+ - ionophores (dibenzo-18-crown-6 and decyl-18-crown-6 was used to obtain a potentiometric potassium sensor. The potassium selective membranes were characterized in terms of their electrochemical and physical properties, surface morphology and structural parameters. The a.c. impedance, UV/VIS analysis of the membranes was also studied.

  11. Selection and Evaluation of Chemical Indicators for Waste Stream Identification

    Science.gov (United States)

    DeVita, W. M.; Hall, J.

    2015-12-01

    Human and animal wastes pose a threat to the quality of groundwater, surface water and drinking water. This is especially of concern for private and public water supplies in agricultural areas of Wisconsin where land spreading of livestock waste occurs on thin soils overlaying fractured bedrock. Current microbial source tracking (MST) methods for source identification requires the use of polymerase chain reaction (PCR) techniques. Due to cost, these tests are often not an option for homeowners, municipalities or state agencies with limited resources. The Water and Environmental Analysis Laboratory sought to develop chemical methods to provide lower cost processes to determine sources of fecal waste using fecal sterols, pharmaceuticals (human and veterinary) and human care/use products in ground and surface waters using solid phase extraction combined with triple quadrupole mass spectrometry. The two separate techniques allow for the detection of fecal sterol and other chemical markers in the sub part per billion-range. Fecal sterol ratios from published sources were used to evaluate drinking water samples and wastewater from onsite waste treatment systems and municipal wastewater treatment plants. Pharmaceuticals and personal care products indicative of human waste included: acetaminophen, caffeine, carbamazepine, cotinine, paraxanthine, sulfamethoxazole, and the artificial sweeteners; acesulfame, saccharin, and sucralose. The bovine antibiotic sulfamethazine was also targeted. Well water samples with suspected fecal contamination were analyzed for fecal sterols and PPCPs. Results were compared to traditional MST results from the Wisconsin State Laboratory of Hygiene. Chemical indicators were found in 6 of 11 drinking water samples, and 5 of 11 were in support of MST results. Lack of detection of chemical indicators in samples contaminated with fecal waste supports the need for confirmatory methods and advancement of chemical indicator detection technologies.

  12. Shifting Phases for Patchy Particles - Effect of mutagenesis and chemical modification on the phase diagram of human gamma D crystallin

    Science.gov (United States)

    McManus, Jennifer J.; James, Susan; McNamara, Ruth; Quinn, Michelle

    2014-03-01

    Single mutations in human gamma D crystallin (HGD), a protein found in the eye lens are associated with several childhood cataracts. Phase diagrams for several of these protein mutants have been measured and reveal that phase boundaries are shifted compared with the native protein, leading to condensation of protein in a physiologically relevant regime. Using HGD as a model protein, we have constructed phase diagrams for double mutants of the protein, incorporating two single amino acid substitutions for which phase diagrams are already known. In doing so, the characteristics of each of the single mutations are maintained but both are now present in the same protein particle. While these proteins are not of interest physiologically, this strategy allows the controlled synthesis of nano-scale patchy particles in which features associated with a known phase behavior can be included. It can also provide a strategy for the controlled crystallisation of proteins. Phase boundaries also change after the chemical modification of the protein, through the covalent attachment of fluorescent labels, for example, and this will also be discussed. The authors acknowledge Science Foundation Ireland Stokes Lectureship and Grant 11/RFP.1/PHY/3165. The authors also acknowledge the Irish Research Council and the John and Pat Hume Scholarship.

  13. Molecular structure and vibrational and chemical shift assignments of 3'-chloro-4-dimethylamino azobenzene by DFT calculations.

    Science.gov (United States)

    Toy, Mehmet; Tanak, Hasan

    2016-01-05

    In the present work, a combined experimental and theoretical study on ground state molecular structure, spectroscopic and nonlinear optical properties of azo compound 3'-chloro-4-dimethlamino azobenzene are reported. The molecular geometry, vibrational wavenumbers and the first order hyperpolarizability of the title compound were calculated with the help of density functional theory computations. The optimized geometric parameters obtained by using DFT (B3LYP/6-311++G(d,p)) show good agreement with the experimental data. The vibrational transitions were identified based on the recorded FT-IR spectra in the range of 4000-400cm(-1) for solid state. The (1)H isotropic chemical shifts with respect to TMS were also calculated using the gauge independent atomic orbital (GIAO) method and compared with the experimental data. Using the TD-DFT method, electronic absorption spectra of the title compound have been predicted, and good agreement is determined with the experimental ones. To investigate the NLO properties of the title compound, the polarizability and the first hyperpolarizability were calculated using the density functional B3LYP method with the 6-311++G(d,p) basis set. According to results, the title compound exhibits non-zero first hyperpolarizability value revealing second order NLO behavior. In addition, DFT calculations of the title compound, molecular electrostatic potential and frontier molecular orbitals were also performed at 6-311++G(d,p) level of theory.

  14. 13C-detected NMR experiments for measuring chemical shifts and coupling constants in nucleic acid bases.

    Science.gov (United States)

    Fiala, Radovan; Sklenár, Vladimír

    2007-10-01

    The paper presents a set of two-dimensional experiments that utilize direct (13)C detection to provide proton-carbon, carbon-carbon and carbon-nitrogen correlations in the bases of nucleic acids. The set includes a (13)C-detected proton-carbon correlation experiment for the measurement of (13)C-(13)C couplings, the CaCb experiment for correlating two quaternary carbons, the HCaCb experiment for the (13)C-(13)C correlations in cases where one of the carbons has a proton attached, the HCC-TOCSY experiment for correlating a proton with a network of coupled carbons, and a (13)C-detected (13)C-(15)N correlation experiment for detecting the nitrogen nuclei that cannot be detected via protons. The IPAP procedure is used for extracting the carbon-carbon couplings and/or carbon decoupling in the direct dimension, while the S(3)E procedure is preferred in the indirect dimension of the carbon-nitrogen experiment to obtain the value of the coupling constant. The experiments supply accurate values of (13)C and (15)N chemical shifts and carbon-carbon and carbon-nitrogen coupling constants. These values can help to reveal structural features of nucleic acids either directly or via induced changes when the sample is dissolved in oriented media.

  15. Chemical shifts assignments of the archaeal MC1 protein and a strongly bent 15 base pairs DNA duplex in complex.

    Science.gov (United States)

    Loth, Karine; Landon, Céline; Paquet, Françoise

    2015-04-01

    MC1 is the most abundant architectural protein present in Methanosarcina thermophila CHTI55 in laboratory growth conditions and is structurally unrelated to other DNA-binding proteins. MC1 functions are to shape and to protect DNA against thermal denaturation by binding to it. Therefore, MC1 has a strong affinity for any double-stranded DNA. However, it recognizes and preferentially binds to bent DNA, such as four-way junctions and negatively supercoiled DNA minicircles. Combining NMR data, electron microscopy data, biochemistry, molecular modelisation and docking approaches, we proposed recently a new type of DNA/protein complex, in which the monomeric protein MC1 binds on the concave side of a strongly bent 15 base pairs DNA. We present here the NMR chemical shifts assignments of each partner in the complex, (1)H (15)N MC1 protein and (1)H (13)C (15)N bent duplex DNA, as first step towards the first experimental 3D structure of this new type of DNA/protein complex.

  16. Fragment-Based Approach for the Evaluation of NMR Chemical Shifts for Large Biomolecules Incorporating the Effects of the Solvent Environment.

    Science.gov (United States)

    Jose, K V Jovan; Raghavachari, Krishnan

    2017-03-14

    We present an efficient implementation of the molecules-in-molecules (MIM) fragment-based quantum chemical method for the evaluation of NMR chemical shifts of large biomolecules. Density functional techniques have been employed in conjunction with large basis sets and including the effects of the solvent environment in these calculations. The MIM-NMR method is initially benchmarked on a set of (alanine)10 conformers containing strong intramolecular interactions. The incorporation of a second low level of theory to recover the missing long-range interactions in the primary fragmentation scheme is critical to yield reliable chemical shifts, with a mean absolute deviation (MAD) from direct unfragmented calculations of 0.01 ppm for (1)H chemical shifts and 0.07 ppm for (13)C chemical shifts. In addition, the performance of MIM-NMR has been assessed on two large peptides: the helical portion of ubiquitin ( 1UBQ ) containing 12 residues where the X-ray structure is known, and E6-binding protein of papilloma virus ( 1RIJ ) containing 23 residues where the structure has been derived from solution-phase NMR analysis. The solvation environment is incorporated in these MIM-NMR calculations, either through an explicit, implicit, or a combination of both solvation models. Using an explicit treatment of the solvent molecules within the first solvation sphere (3 Å) and an implicit solvation model for the rest of the interactions, the (1)H and (13)C chemical shifts of ubiquitin show excellent agreement with experiment (mean absolute deviation of 0.31 ppm for (1)H and 1.72 ppm for (13)C), while the larger E6-binding protein yields a mean absolute deviation of 0.34 ppm for (1)H chemical shifts. The proposed MIM-NMR method is computationally cost-effective and provides a substantial speedup relative to conventional full calculations, the largest density functional NMR calculation included in this work involving more than 600 atoms and over 10,000 basis functions. The MIM

  17. Highly Selective Hg (II Ion Detection Based on Linear Blue-Shift of the Maximum Absorption Wavelength of Silver Nanoparticles

    Directory of Open Access Journals (Sweden)

    Li Ping Wu

    2012-01-01

    Full Text Available A new method of detecting Hg (II ion with silver nanoparticles (AgNPs is developed in this contribution. When Hg (II ions were added into AgNPs solution, the solution displayed rapid color change and blue shift of the maximum absorption wavelength (Δλ, which was in proportion to the Hg (II ion concentration over the range of 2.0 × 10−7–6.0 × 10−6 mol/L, with detection limit (3σ of 6.6 × 10−9 mol/L. Under the same experimental conditions, other metal ions did not interfere. Thus, we propose a rapid, simple and highly selective method for detecting Hg (II ion.

  18. Selection of material for building pressure vessels and chemical plants

    Energy Technology Data Exchange (ETDEWEB)

    Huppertz, P.H.; Retter, A.

    1979-06-01

    The authors give on extensive survey on the materials used in building pressure vessels and chemical plants for a temperature region of -200 to +1000/sup 0/C. The effect of various influences on the material behaviour is critically examined on the existing control plant, where the differences to foreign control are indicated. NE metals also come into consideration apart from steels, especially with low-temperature application.

  19. Chemical shift as a probe of molecular interfaces: NMR studies of DNA binding by the three amino-terminal zinc finger domains from transcription factor IIIA

    Energy Technology Data Exchange (ETDEWEB)

    Foster, Mark P.; Wuttke, Deborah S.; Clemens, Karen R.; Jahnke, Wolfgang; Radhakrishnan, Ishwar; Tennant, Linda; Reymond, Martine; Chung, John; Wright, Peter E. [Scripps Research Institute, Department of Molecular Biology and Skaggs Institute for Chemical Biology (United States)

    1998-07-15

    We report the NMR resonance assignments for a macromolecular protein/DNA complex containing the three amino-terminal zinc fingers (92 amino acid residues) of Xenopus laevis TFIIIA (termed zf1-3) bound to the physiological DNA target (15 base pairs), and for the free DNA. Comparisons are made of the chemical shifts of protein backbone{sup 1} H{sup N}, {sup 15}N,{sup 13} C{sup {alpha}} and{sup 13} C{sup {beta}} and DNA base and sugar protons of the free and bound species. Chemical shift changes are analyzed in the context of the structures of the zf1-3/DNA complex to assess the utility of chemical shift change as a probe of molecular interfaces. Chemical shift perturbations that occur upon binding in the zf1-3/DNA complex do not correspond directly to the structural interface, but rather arise from a number of direct and indirect structural and dynamic effects.

  20. Multilinear relations between {sup 13} C NMR chemical shifts of aliphatic halides; Relacoes lineares multiplas entre deslocamentos quimicos em RMN {sup 13} C de haletos alifaticos

    Energy Technology Data Exchange (ETDEWEB)

    Doyama, Julio Toshimi [UNESP, Botucatu, SP (Brazil). Inst. de Biociencias. Dept. de Quimica e Bioquimica; Tornero, Maria Teresinha Trovarelli [UNESP, Botucatu, SP (Brazil). Inst. de Biociencias. Dept. de Bioestatistica; Yoshida, Massayoshi [UNESP, Araraquara, SP (Brazil). Inst. de Quimica. Dept. de Quimica Organica

    1999-07-01

    The {sup 13} C NMR chemical shifts of the {alpha}, {beta}, {gamma} and {delta} carbons of 17 sets of aliphatic halides (F, Cl, Br and I), including mono, bi and tricyclic compounds, can be reproduced by a linear equation composed with two constants and two variables: {delta}{sub RX} = A{sup *} {delta}{sub R-X2}, where A and B are constants derived from multilinear regression of {sup 13} C chemical shifts observed; {delta}{sub R-X}, the chemical shifts of aliphatic halide (R-X); and {delta}{sub R-X1}, {delta}{sub R-X2} the chemical shifts of other halides. It was observed a better correlation for aliphatic bromides (R-X) by using data of aliphatic fluorides (R-X 1) and aliphatic iodides (R-X 2), resulting R{sup 2} of 0.9989 and average absolute deviation (AVG) of 0.39 ppm. For the chlorides (R-X), the better correlation was observed by using data of bromides (R-X 1) was observed better correlation with data of bromides (R-X 1) and iodides (R-X 2), R{sup 2} of 0.997 and AVG of 1.10 ppm. For the iodides (R-X) was observed better correlation with data of fluorides (R-X 1) and bromides (R-X 2), R{sup 2} of 0.9972 and AVG of 0.60 ppm. (author)

  1. Chemically Patterned Inverse Opal Created by a Selective Photolysis Modification Process.

    Science.gov (United States)

    Tian, Tian; Gao, Ning; Gu, Chen; Li, Jian; Wang, Hui; Lan, Yue; Yin, Xianpeng; Li, Guangtao

    2015-09-01

    Anisotropic photonic crystal materials have long been pursued for their broad applications. A novel method for creating chemically patterned inverse opals is proposed here. The patterning technique is based on selective photolysis of a photolabile polymer together with postmodification on released amine groups. The patterning method allows regioselective modification within an inverse opal structure, taking advantage of selective chemical reaction. Moreover, combined with the unique signal self-reporting feature of the photonic crystal, the fabricated structure is capable of various applications, including gradient photonic bandgap and dynamic chemical patterns. The proposed method provides the ability to extend the structural and chemical complexity of the photonic crystal, as well as its potential applications.

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

    Energy Technology Data Exchange (ETDEWEB)

    Brothers, Michael C [University of Illinois, Urbana-Champaign; Nesbitt, Anna E [University of Illinois, Urbana-Champaign; Hallock, Michael J [University of Illinois, Urbana-Champaign; Rupasinghe, Sanjeewa [University of Illinois, Urbana-Champaign; Tang, Ming [University of Illinois, Urbana-Champaign; Harris, Jason B [ORNL; Baudry, Jerome Y [ORNL; Schuler, Mary A [University of Illinois, Urbana-Champaign; Rienstra, Chad M [University of Illinois, Urbana-Champaign

    2011-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

    Brothers, Michael C.; Nesbitt, Anna E.; Hallock, Michael J. [University of Illinois at Urbana-Champaign, Department of Chemistry (United States); Rupasinghe, Sanjeewa G. [University of Illinois at Urbana-Champaign, Department of Cell and Developmental Biology (United States); Tang Ming [University of Illinois at Urbana-Champaign, Department of Chemistry (United States); Harris, Jason; Baudry, Jerome [University of Tennessee, Department of Biochemistry, Cellular and Molecular Biology (United States); Schuler, Mary A. [University of Illinois at Urbana-Champaign, Department of Cell and Developmental Biology (United States); Rienstra, Chad M., E-mail: rienstra@illinois.edu [University of Illinois at Urbana-Champaign, Department of Chemistry (United States)

    2012-01-15

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

  4. From prebiotic chemistry to cellular metabolism--the chemical evolution of metabolism before Darwinian natural selection.

    Science.gov (United States)

    Meléndez-Hevia, Enrique; Montero-Gómez, Nancy; Montero, Francisco

    2008-06-07

    It is generally assumed that the complex map of metabolism is a result of natural selection working at the molecular level. However, natural selection can only work on entities that have three basic features: information, metabolism and membrane. Metabolism must include the capability of producing all cellular structures, as well as energy (ATP), from external sources; information must be established on a material that allows its perpetuity, in order to safeguard the goals achieved; and membranes must be able to preserve the internal material, determining a selective exchange with external material in order to ensure that both metabolism and information can be individualized. It is not difficult to understand that protocellular entities that boast these three qualities can evolve through natural selection. The problem is rather to explain the origin of such features under conditions where natural selection could not work. In the present work we propose that these protocells could be built by chemical evolution, starting from the prebiotic primordial soup, by means of chemical selection. This consists of selective increases of the rates of certain specific reactions because of the kinetic or thermodynamic features of the process, such as stoichiometric catalysis or autocatalysis, cooperativity and others, thereby promoting their prevalence among the whole set of chemical possibilities. Our results show that all chemical processes necessary for yielding the basic materials that natural selection needs to work may be achieved through chemical selection, thus suggesting a way for life to begin.

  5. Morphological and chemical characteristics of fruits of selected Rosa sp.

    Directory of Open Access Journals (Sweden)

    Agnieszka Najda

    2013-04-01

    Full Text Available The aim of this study was to evaluate the morphological and chemical parameters, antioxidant activity (DPPH of five rose species (Rosa rugosa, R. villosa, R. californica, R. spinosissima, and R. × damascene and grouping them according to the harvest date. On the basis of the study, rose species grown in eastern Poland were grouped according to their harvest time, and three dates of cumulative ripeness of pseudofruits were distinguished. Rosehips of studied species varied referring to their harvest date and morphological properties and were characterized by diverse contents of primary metabolites analyzed. In addition, obtained extracts showed high antioxidant activity, which has a significant impact on their value for processing.

  6. CO2 SELECTIVE CERAMIC MEMBRANE FOR WATER-GAS-SHIFT REACTION WITH CONCOMITANT RECOVERY OF CO2

    Energy Technology Data Exchange (ETDEWEB)

    Paul K.T. Liu

    2005-07-15

    A high temperature membrane reactor (MR) has been developed to enhance the water-gas-shift (WGS) reaction efficiency with concomitant CO{sub 2} removal for sequestration. This improved WGS-MR with CO{sub 2} recovery capability is ideally suitable for integration into the Integrated Gasification Combined-Cycle (IGCC) power generation system. Two different CO{sub 2}-affinity materials were selected in this study. The Mg-Al-CO{sub 3}-layered double hydroxide (LDH) was investigated as an adsorbent or a membrane for CO{sub 2} separation. The adsorption isotherm and intraparticle diffusivity for the LDH-based adsorbent were experimentally determined, and suitable for low temperature shift (LTS) of WGS. The LDH-based membranes were synthesized using our commercial ceramic membranes as substrate. These experimental membranes were characterized comprehensively in terms of their morphology, and CO{sub 2} permeance and selectivity to demonstrate the technical feasibility. In parallel, an alternative material-base membrane, carbonaceous membrane developed by us, was characterized, which also demonstrated enhanced CO{sub 2} selectivity at the LTS-WGS condition. With optimization on membrane defect reduction, these two types of membrane could be used commercially as CO{sub 2}-affinity membranes for the proposed application. Based upon the unique CO{sub 2} affinity of the LDHs at the LTS/WGS environment, we developed an innovative membrane reactor, Hybrid Adsorption and Membrane Reactor (HAMR), to achieve {approx}100% CO conversion, produce a high purity hydrogen product and deliver a concentrated CO{sub 2} stream for disposal. A mathematical model was developed to simulate this unique one -step process. Finally a benchtop reactor was employed to generate experimental data, which were consistent with the prediction from the HAMR mathematical model. In summary, the project objective, enhancing WGS efficiency for hydrogen production with concomitant CO{sub 2} removal for

  7. Chemical shift of U L3 edges in different uranium compounds obtained by X-ray absorption spectroscopy with synchrotron radiation

    Indian Academy of Sciences (India)

    D Joseph; C Nayak; P Venu Babu; S N Jha; D Bhattacharyya

    2014-05-01

    Uranium L3 X-ray absorption edge was measured in various compounds containing uranium in U4+, U5+ and U6+ oxidation states. The measurements have been carried out at the Energy Dispersive EXAFS beamline (BL-08) at INDUS-2 synchrotron radiation source at RRCAT, Indore. Energy shifts of ∼ 2–3 eV were observed for U L3 edge in the U-compounds compared to their value in elemental U. The different chemical shifts observed for the compounds having the same oxidation state of the cation but different anions or ligands show the effect of different chemical environments surrounding the cations in determining their X-ray absorption edges in the above compounds. The above chemical effect has been quantitatively described by determining the effective charges on U cation in the above compounds.

  8. Combining ambiguous chemical shift mapping with structure-based backbone and NOE assignment from 15N-NOESY

    KAUST Repository

    Jang, Richard

    2011-01-01

    Chemical shift mapping is an important technique in NMRbased drug screening for identifying the atoms of a target protein that potentially bind to a drug molecule upon the molecule\\'s introduction in increasing concentrations. The goal is to obtain a mapping of peaks with known residue assignment from the reference spectrum of the unbound protein to peaks with unknown assignment in the target spectrum of the bound protein. Although a series of perturbed spectra help to trace a path from reference peaks to target peaks, a one-to-one mapping generally is not possible, especially for large proteins, due to errors, such as noise peaks, missing peaks, missing but then reappearing, overlapped, and new peaks not associated with any peaks in the reference. Due to these difficulties, the mapping is typically done manually or semi-automatically. However, automated methods are necessary for high-throughput drug screening. We present PeakWalker, a novel peak walking algorithm for fast-exchange systems that models the errors explicitly and performs many-to-one mapping. On the proteins: hBclXL, UbcH5B, and histone H1, it achieves an average accuracy of over 95% with less than 1.5 residues predicted per target peak. Given these mappings as input, we present PeakAssigner, a novel combined structure-based backbone resonance and NOE assignment algorithm that uses just 15N-NOESY, while avoiding TOCSY experiments and 13C- labeling, to resolve the ambiguities for a one-toone mapping. On the three proteins, it achieves an average accuracy of 94% or better. Copyright © 2011 ACM.

  9. Chemical tools selectively target components of the PKA system

    Directory of Open Access Journals (Sweden)

    Drewianka Stephan

    2009-02-01

    Full Text Available Abstract Background In the eukaryotic cell the cAMP-dependent protein kinase (PKA is a key enzyme in signal transduction and represents the main target of the second messenger cAMP. Here we describe the design, synthesis and characterisation of specifically tailored cAMP analogs which can be utilised as a tool for affinity enrichment and purification as well as for proteomics based analyses of cAMP binding proteins. Results Two sets of chemical binders were developed based on the phosphorothioate derivatives of cAMP, Sp-cAMPS and Rp-cAMPS acting as cAMP-agonists and -antagonists, respectively. These compounds were tested via direct surface plasmon resonance (SPR analyses for their binding properties to PKA R-subunits and holoenzyme. Furthermore, these analogs were used in an affinity purification approach to analyse their binding and elution properties for the enrichment and improvement of cAMP binding proteins exemplified by the PKA R-subunits. As determined by SPR, all tested Sp-analogs provide valuable tools for affinity chromatography. However, Sp-8-AEA-cAMPS displayed (i superior enrichment properties while maintaining low unspecific binding to other proteins in crude cell lysates, (ii allowing mild elution conditions and (iii providing the capability to efficiently purify all four isoforms of active PKA R-subunit in milligram quantities within 8 h. In a chemical proteomics approach both sets of binders, Rp- and Sp-cAMPS derivatives, can be employed. Whereas Sp-8-AEA-cAMPS preferentially binds free R-subunit, Rp-AHDAA-cAMPS, displaying antagonist properties, not only binds to the free PKA R-subunits but also to the intact PKA holoenzyme both from recombinant and endogenous sources. Conclusion In summary, all tested cAMP analogs were useful for their respective application as an affinity reagent which can enhance purification of cAMP binding proteins. Sp-8-AEA-cAMPS was considered the most efficient analog since Sp-8-AHA-cAMPS and Sp-2-AHA

  10. Chemical and biological insecticides select distinct gene expression patterns in Aedes aegypti mosquito.

    Science.gov (United States)

    Després, Laurence; Stalinski, Renaud; Faucon, Frédéric; Navratil, Vincent; Viari, Alain; Paris, Margot; Tetreau, Guillaume; Poupardin, Rodolphe; Riaz, Muhammad Asam; Bonin, Aurélie; Reynaud, Stéphane; David, Jean-Philippe

    2014-12-01

    Worldwide evolution of mosquito resistance to chemical insecticides represents a major challenge for public health, and the future of vector control largely relies on the development of biological insecticides that can be used in combination with chemicals (integrated management), with the expectation that populations already resistant to chemicals will not become readily resistant to biological insecticides. However, little is known about the metabolic pathways affected by selection with chemical or biological insecticides. Here we show that Aedes aegypti, a laboratory mosquito strain selected with a biological insecticide (Bacillus thuringiensis israelensis, Bti) evolved increased transcription of many genes coding for endopeptidases while most genes coding for detoxification enzymes were under-expressed. By contrast, in strains selected with chemicals, genes encoding detoxification enzymes were mostly over-expressed. In all the resistant strains, genes involved in immune response were under-transcribed, suggesting that basal immunity might be a general adjustment variable to compensate metabolic costs caused by insecticide selection. Bioassays generally showed no evidence for an increased susceptibility of selected strains towards the other insecticide type, and all chemical-resistant strains were as susceptible to Bti as the unselected parent strain, which is a good premise for sustainable integrated management of mosquito populations resistant to chemicals.

  11. Surface etching, chemical modification and characterization of silicon nitride and silicon oxide - Selective functionalization of Si

    NARCIS (Netherlands)

    Liu, Li Hong; Michalak, David J.; Chopra, Tatiana P.; Pujari, Sidharam P.; Zuilhof, Han

    2016-01-01

    The ability to selectively chemically functionalize silicon nitride (Si3N4) or silicon dioxide (SiO2) surfaces after cleaning would open interesting technological applications. In order to achieve this goal, the chemical composition of surfaces needs to be careful

  12. Relativistic four-component DFT calculations of 1H NMR chemical shifts in transition-metal hydride complexes: unusual high-field shifts beyond the Buckingham-Stephens model.

    Science.gov (United States)

    Hrobárik, Peter; Hrobáriková, Veronika; Meier, Florian; Repiský, Michal; Komorovský, Stanislav; Kaupp, Martin

    2011-06-09

    State-of-the-art relativistic four-component DFT-GIAO-based calculations of (1)H NMR chemical shifts of a series of 3d, 4d, and 5d transition-metal hydrides have revealed significant spin-orbit-induced heavy atom effects on the hydride shifts, in particular for several 4d and 5d complexes. The spin-orbit (SO) effects provide substantial, in some cases even the dominant, contributions to the well-known characteristic high-field hydride shifts of complexes with a partially filled d-shell, and thereby augment the Buckingham-Stephens model of off-center paramagnetic ring currents. In contrast, complexes with a 4d(10) and 5d(10) configuration exhibit large deshielding SO effects on their hydride (1)H NMR shifts. The differences between the two classes of complexes are attributed to the dominance of π-type d-orbitals for the true transition-metal systems compared to σ-type orbitals for the d(10) systems.

  13. MORPHOLOGICAL AND CHEMICAL PROPERTIES OF SELECTED SWEET VIOLET POPULATIONS

    Directory of Open Access Journals (Sweden)

    Renata ERHATIĆ

    2010-10-01

    Full Text Available Sweet violet (Viola odorata L. blooms in continental climate conditions in early spring (March-April with delicate flowers of attractive scent because of which it is frequently gathered from its natural habitats. Differences among the populations were established according to their morphological properties of twelve populations from Križevci area. Stated information indicates that the populations gathered from meadow – habitat are shorter and have a smaller diameter than the populations gathered from the habitat in forest, whereas the population from the orchards has the highest number of leaves and flowers. Correlation analysis shows strong (P<0.01 positive connection of the root mass, leaves mass, number of leaves with the total mass of the plants, as well as connection of the plant mass with the number of flowers. Chemical analysis established agrochemical soil properties and nutrient concentrations in plants. Correlations between the examined properties of violets and soil properties indicate that the potassium concentration in the roots is in strong (P <0.01 correlation with potassium in the soil, whereas phosphorus concentration in flower is in a considerably strong (P<0.05 positive correlation with the phosphorus in the soil.

  14. Effect of prolonged chemical challenges on selected properties of silorane

    DEFF Research Database (Denmark)

    de Jesus, Vivian CBR; Martinelli, Natan Luiz; Pascotto, Renata Corrêa;

    Objectives: The purpose of this study was to investigate the effect of prolonged chemical challenges on water sorption, solubility, and roughness of a silorane-based material when compared to methacrylate-based composites. Methods: Initial roughness and mass were registered for specimens (n=24......) fabricated from methacrylate (Filtek Z250, 3M ESPE; Filtek Z350XT, 3M ESPE; Master Fill, Biodinâmica) or silorane-based (Filtek P90, 3M ESPE) composites. The volume of all specimens was also calculated. Specimens were divided in four groups (n=6) and individually stored at 37°C in 0.02N citric acid, 0.02N...... submitted to two-way analysis of variance or analysis of variance for repeated measures, and Tukey’s multiple comparison test (a=0.05). Results: The silorane-based composite was the roughest (pcomposite (Ra=0.06±0.01) when compared to the other investigated materials (Ra=0.05±0.01). Significant...

  15. Antimicrobial, antioxidant activities and chemical composition of selected Thai spices

    Directory of Open Access Journals (Sweden)

    Juraithip Wungsintaweekul

    2010-12-01

    Full Text Available Nine volatile oils and six methanol extracts from Ocimum americanum, O. basilicum, O. sanctum, Citrus hystrix,Alpinia galanga, Curcuma zedoaria, Kaempferia parviflora and Zingiber cassumunar were assessed for antimicrobial andantioxidant activities. The volatile oils and extracts were investigated against eight bacteria and three fungi. The resultsillustrated that O. americanum volatile oil exhibited broad spectrum activity against tested bacteria with the MICs ranging1.4-3.6 mg/ml and Candida spp. with the MICs ranging from 0.5-0.6 mg/ml. The O. sanctum volatile oil showed a considerableactivity against only Candida spp. with the MICs ranging from 0.8-1.4 mg/ml. Interestingly, growth of Mycobacteriumphlei was inhibited by the volatiles of O. americanum, C. hystrix peel, and C. zedoaria with MIC of 1.7, 3.5 and 1.2 mg/ml,respectively. For antioxidant activity evaluation, the methanol extracts of C. hystrix (leaf and peel and K. parviflora hadpotent antioxidant activity by the radical-scavenging DPPH method with IC50 of 24.6, 66.3 and 61.5 mg/ml, respectively.GC-MS analysis revealed the typical chemical profiles of the volatile oils. The major component showed the characteristicsof the volatile oils and was probably responsible for the antimicrobial effect.

  16. A Multiphilic Descriptor for Chemical Reactivity and Selectivity

    CERN Document Server

    Padmanabhan, J; Elango, M; Subramanian, V; Krishnamoorthy, B S; Gutierrez-Oliva, S; Toro-Labbe, A; Roy, D R; Chattaraj, P K

    2007-01-01

    In line with the local philicity concept proposed by Chattaraj et al. (Chattaraj, P. K.; Maiti, B.; Sarkar, U. J. Phys. Chem. A. 2003, 107, 4973) and a dual descriptor derived by Toro-Labbe and coworkers (Morell, C.; Grand, A.; Toro-Labbe, A. J. Phys. Chem. A. 2005, 109, 205), we propose a multiphilic descriptor. It is defined as the difference between nucleophilic (Wk+) and electrophilic (Wk-) condensed philicity functions. This descriptor is capable of simultaneously explaining the nucleophilicity and electrophilicity of the given atomic sites in the molecule. Variation of these quantities along the path of a soft reaction is also analyzed. Predictive ability of this descriptor has been successfully tested on the selected systems and reactions. Corresponding force profiles are also analyzed in some representative cases. Also, to study the intra- and intermolecular reactivities another related descriptor namely, the nucleophilicity excess (DelW-+) for a nucleophile, over the electrophilicity in it has been d...

  17. SELECTING SAGITTARIUS: IDENTIFICATION AND CHEMICAL CHARACTERIZATION OF THE SAGITTARIUS STREAM

    Energy Technology Data Exchange (ETDEWEB)

    Hyde, E. A. [University of Western Sydney, Locked Bag 1797, Penrith South DC, NSW 1797 (Australia); Keller, S. [Research School of Astronomy and Astrophysics, Australian National University, Canberra, ACT 2601 (Australia); Zucker, D. B. [Macquarie University, Physics and Astronomy, NSW 2109 (Australia); Ibata, R.; Siebert, A. [Observatoire astronomique de Strasbourg, Université de Strasbourg, CNRS, UMR 7550, 11 rue de l’Université, F-67000 Strasbourg (France); Lewis, G. F.; Conn, A. R. [Sydney Institute for Astronomy, School of Physics, The University of Sydney, NSW 2006 (Australia); Penarrubia, J. [ROE, The University of Edinburgh, Institute for Astronomy, Edinburgh EH9 3HJ (United Kingdom); Irwin, M.; Gilmore, G. [Institute of Astronomy, University of Cambridge, Madingley Road, Cambridge CB3 0HA (United Kingdom); Lane, R. R. [Departamento de Astronomía Universidad de Concepción, Casilla 160 C, Concepción (Chile); Koch, A. [Landessternwarte, Zentrum für Astronomie der Universität Heidelberg, Königstuhl 12, D-69117 Heidelberg (Germany); Diakogiannis, F. I. [International Center for Radio Astronomy Research, University of Western Australia, 35 Stirling Highway, Crawley, WA 6009 (Australia); Martell, S., E-mail: E.Hyde@uws.edu.au [Department of Astrophysics, School of Physics, University of New South Wales, Sydney, NSW 2052 (Australia)

    2015-06-01

    Wrapping around the Milky Way, the Sagittarius stream is the dominant substructure in the halo. Our statistical selection method has allowed us to identify 106 highly likely members of the Sagittarius stream. Spectroscopic analysis of metallicity and kinematics of all members provides us with a new mapping of the Sagittarius stream. We find correspondence between the velocity distribution of stream stars and those computed for a triaxial model of the Milky Way dark matter halo. The Sagittarius trailing arm exhibits a metallicity gradient, ranging from −0.59 to −0.97 dex over 142°. This is consistent with the scenario of tidal disruption from a progenitor dwarf galaxy that possessed an internal metallicity gradient. We note high metallicity dispersion in the leading arm, causing a lack of detectable gradient and possibly indicating orbital phase mixing. We additionally report on a potential detection of the Sextans dwarf spheroidal in our data.

  18. Proton-detected 3D (15)N/(1)H/(1)H isotropic/anisotropic/isotropic chemical shift correlation solid-state NMR at 70kHz MAS.

    Science.gov (United States)

    Pandey, Manoj Kumar; Yarava, Jayasubba Reddy; Zhang, Rongchun; Ramamoorthy, Ayyalusamy; Nishiyama, Yusuke

    2016-01-01

    Chemical shift anisotropy (CSA) tensors offer a wealth of information for structural and dynamics studies of a variety of chemical and biological systems. In particular, CSA of amide protons can provide piercing insights into hydrogen-bonding interactions that vary with the backbone conformation of a protein and dynamics. However, the narrow span of amide proton resonances makes it very difficult to measure (1)H CSAs of proteins even by using the recently proposed 2D (1)H/(1)H anisotropic/isotropic chemical shift (CSA/CS) correlation technique. Such difficulties due to overlapping proton resonances can in general be overcome by utilizing the broad span of isotropic chemical shifts of low-gamma nuclei like (15)N. In this context, we demonstrate a proton-detected 3D (15)N/(1)H/(1)H CS/CSA/CS correlation experiment at fast MAS frequency (70kHz) to measure (1)H CSA values of unresolved amide protons of N-acetyl-(15)N-l-valyl-(15)N-l-leucine (NAVL).

  19. A Chemically Synthesized Capture Agent Enables the Selective, Sensitive, and Robust Electrochemical Detection of Anthrax Protective Antigen

    Science.gov (United States)

    2014-08-01

    A Chemically Synthesized Capture Agent Enables the Selective, Sensitive, and Robust Electrochemical Detection of Anthrax Protective Antigen...A Chemically Synthesized Capture Agent Enables the Selective, Sensitive, and Robust Electrochemical Detection of Anthrax Protective Antigen...AND SUBTITLE A Chemically Synthesized Capture Agent Enables the Selective, Sensitive, and Robust Electrochemical Detection of Anthrax Protective

  20. Non-Precious Bimetallic Catalysts for Selective Dehydrogenation of an Organic Chemical Hydride System

    KAUST Repository

    Shaikh Ali, Anaam

    2015-07-06

    Methylcyclohexane (MCH)-Toluene (TOL) chemical hydride cycles as a hydrogen carrier system is successful with the selective dehydrogenation reaction of MCH to TOL, which has been achieved only using precious Pt-based catalysts. Herein, we report improved selectivity using non-precious metal nickel-based bimetallic catalysts, where the second metal occupies the unselective step sites.

  1. Solvent-induced chemical shifts of methoxyl nuclear resonance signals in chalcones by benzene and trifluoroacetic acid

    Science.gov (United States)

    Khurana, Shashi K.; Krishnamoorthy, V.; Parmar, Virinder S.

    The 1H NMR spectra of eight different methoxylated chalcones have separately been recorded, (1) in deuterated chloroform; (2) in a mixture (1:1) of deuterated chloroform and benzene; and (3) in a mixture of deuterated chloroform, benzene and trifluoroacetic acid (2:2:1) and the benzene induced and TFA induced shift values have been assigned to different methoxyl groups. These shift values can serve as a guide in determining the structures of natural or new chalcones. The steric, electronic and conformational factors are discussed to explain the shift values.

  2. A highly selective ratiometric fluorescent pH probe based on a PAMAM wavelength-shifting bichromophoric system

    Science.gov (United States)

    Alamry, Khalid A.; Georgiev, Nikolai I.; El-Daly, Samy Abdullah; Taib, Layla A.; Bojinov, Vladimir B.

    2015-01-01

    A novel PAMAM wavelength-shifting bichromophoric system has been successfully developed. Novel compound was configured as a light harvesting antenna where the system surface is labeled with yellow-green emitting 4-(N,N-dimethylamino)ethylamino-1,8-naphthalimide "donor" units capable of absorbing light and efficiently transferring the energy to a focal Rhodamine 6G "acceptor". The periphery of the system was designed on the "fluorophore-spacer-receptor" format, capable of acting as a molecular fluorescence photoinduced electron transfer based probe. Due to the both effects, photoinduced electron transfer in the periphery of the system and pH dependent rhodamine core absorption, novel antenna is able to act as a selective ratiometric pH fluorescence probe in aqueous medium. Thus, the distinguishing features of the fluorescence resonance energy transfer systems were successfully combined with the properties of classical ring-opening charge transfer systems, which may be beneficially for monitoring pH variations in complex samples.

  3. Precision Measurement of the Quadrupole Coupling and Chemical Shift Tensors of the Deuterons in α-Calcium Formate

    Science.gov (United States)

    Schmitt, Heike; Zimmermann, H.; Körner, O.; Stumber, M.; Meinel, C.; Haeberlen, U.

    2001-07-01

    Using calcium formate, α-Ca(DCOO)2, as a test sample, we explore how precisely deuteron quadrupole coupling (QC) and chemical shift (CS) tensors Q and σ can currently be measured. The error limits, ±0.09 kHz for the components of Q and ±0.06 ppm for those of σ, are at least three times lower than in any comparable previous experiment. The concept of a new receiver is described. A signal/noise ratio of 100 is realized in single-shot FT spectra. The measurement strategies and a detailed error analysis are presented. The precision of the measurement of Q is limited by the uncertainty of the rotation angles of the sample and that of σ by the uncertainty of the phase correction parameters needed in FT spectroscopy. With a 4-sigma confidence, it is demonstrated for the first time that the unique QC tensor direction of a deuteron attached to a carbon deviates from the bond direction; the deviation found is (1.2±0.3°). Evidence is provided for intermolecular QC contributions. In terms of Q, their size is roughly 4 kHz. The deuteron QC tensors in α-Ca(DCOO)2 (two independent deuteron sites) are remarkable in three respects. For deuterons attached to sp2 carbons, first, the asymmetry factors η and, second, the quadrupole coupling constants CQ, are unusually small, η1=0.018, η2=0.011, and CQ1=(151.27±0.06) kHz, CQ2=(154.09±0.06) kHz. Third, the principal direction associated with the largest negative QC tensor component lies in and not, as usual, perpendicular to the molecular plane. A rationalization is provided for these observations. The CS tensors obtained are in quantitative agreement with the results of an earlier, less precise, line-narrowing multiple-pulse study of α-Ca(HCOO)2. The assignment proposed in that work is confirmed. Finally we argue that a further 10-fold increase of the measurement precision of deuteron QC tensors, and a 2-fold increase of that of CS tensors, should be possible. We indicate the measures that need to be taken.

  4. 化工设备材料的选择%Chemical Equipment Material Selection

    Institute of Scientific and Technical Information of China (English)

    邓建国

    2012-01-01

    化工生产过程复杂,大多数都具有有毒、有害、腐蚀性,化工设备材料的选择至关重要,其决定了化工设备在化工生产使用的安全性和经济性。%Chemical production is a complex process,most are harmful,toxic,corrosive,chemical equipment and materials selection is very important,it determines the chemical equipment in the chemical used in the production of safety and economy

  5. Detection of chemical vapor with high sensitivity by using the symmetrical metal-cladding waveguide-enhanced Goos-Hänchen shift.

    Science.gov (United States)

    Nie, Yiyou; Li, Yuanhua; Wu, Zhijing; Wang, Xianping; Yuan, Wen; Sang, Minghuang

    2014-04-21

    We present a novel and simple optical structure, i.e., the symmetrical metal-cladding waveguide, in which a polymer layer is added into the guiding layer, for sensitive detection of chemical vapor by using the enhanced Goos-Hänchen (GH) shift (nearly a millimeter scale). Owing to the high sensitivity of the excited ultrahigh-order modes, the vapor-induced effect (swelling effect and refractive index change) in the polymer layer will lead to a dramatic variation of the GH shift. The detected GH shift signal is irrelevant to the power fluctuation of the incident light. The detection limit of 9.5 ppm for toluene and 28.5 ppm for benzene has been achieved.

  6. Chemically selective coated quartz-crystal-microbalance (QCM) array for detection of volatile organic chemicals

    Science.gov (United States)

    Schneider, Thomas W.; Frye-Mason, Gregory C.; Martin, Stephen J.; Spates, James J.; Bohuszewicz, Teresa V.; Osbourn, Gordon C.; Bartholomew, John W.

    1998-12-01

    Liquid flow cells have been fabricated to prepare an array of QCMs operating simultaneously for detection and identification of VOCs in water. Two signals, a frequency response and a damping voltage response, were obtained per resonator. A blank QCM was used as a reference to account for changes in liquid density and viscosity. Nine different polymer coatings applied using a spin coat technique have been examined for VOC response under liquid flow conditions. A matrix of three classes of VOCs were examined for each coating with four chemicals in each class. The three classes of VOCs are polar, nonpolar and chlorinated. A pattern recognition technique, called visually empirical region of influence, was used to cluster the responses in n- dimensional space. Chemicals within a class varying by only one methyl group (e.g., toluene and xylene) are easily discriminated using only two different coatings with three different QCM responses. All chemicals were easily separated and detected with a total of 5 films and 6 responses with >99% accuracy.

  7. Chemical shifts of K-X-ray absorption edges on copper in different compounds by X-ray absorption spectroscopy (XAS) with Synchrotron radiation

    Energy Technology Data Exchange (ETDEWEB)

    Joseph, D., E-mail: djoseph@barc.gov.in [Nuclear Physics Division, Bhabha Atomic Research Centre, Mumbai 400085 (India); Basu, S.; Jha, S.N.; Bhattacharyya, D. [Applied Spectroscopy Division, Bhabha Atomic Research Centre, Mumbai 400085 (India)

    2012-03-01

    Cu K X-ray absorption edges were measured in compounds such as CuO, Cu(CH{sub 3}CO{sub 2}){sub 2}, Cu(CO{sub 3}){sub 2}, and CuSO{sub 4} where Cu is present in oxidation state of 2+, using the energy dispersive EXAFS beamline at INDUS-2 Synchrotron radiation source at RRCAT, Indore. Energy shifts of {approx}4-7 eV were observed for Cu K X-ray absorption edge in the above compounds compared to its value in elemental copper. The difference in the Cu K edge energy shifts in the different compounds having same oxidation state of Cu shows the effect of different chemical environments surrounding the cation in the above compounds. The above chemical effect has been quantitatively described by determining the effective charges on Cu cations in the above compounds.

  8. Chemical shifts of K-X-ray absorption edges on copper in different compounds by X-ray absorption spectroscopy (XAS) with Synchrotron radiation

    Science.gov (United States)

    Joseph, D.; Basu, S.; Jha, S. N.; Bhattacharyya, D.

    2012-03-01

    Cu K X-ray absorption edges were measured in compounds such as CuO, Cu(CH3CO2)2, Cu(CO3)2, and CuSO4 where Cu is present in oxidation state of 2+, using the energy dispersive EXAFS beamline at INDUS-2 Synchrotron radiation source at RRCAT, Indore. Energy shifts of ˜4-7 eV were observed for Cu K X-ray absorption edge in the above compounds compared to its value in elemental copper. The difference in the Cu K edge energy shifts in the different compounds having same oxidation state of Cu shows the effect of different chemical environments surrounding the cation in the above compounds. The above chemical effect has been quantitatively described by determining the effective charges on Cu cations in the above compounds.

  9. Solid state NMR of proteins at high MAS frequencies: symmetry-based mixing and simultaneous acquisition of chemical shift correlation spectra

    Energy Technology Data Exchange (ETDEWEB)

    Bellstedt, Peter [Fritz Lipmann Institute, Biomolecular NMR spectroscopy, Leibniz Institute for Age Research (Germany); Herbst, Christian [Ubon Ratchathani University, Department of Physics, Faculty of Science (Thailand); Haefner, Sabine; Leppert, Joerg; Goerlach, Matthias; Ramachandran, Ramadurai, E-mail: raman@fli-leibniz.de [Fritz Lipmann Institute, Biomolecular NMR spectroscopy, Leibniz Institute for Age Research (Germany)

    2012-12-15

    We have carried out chemical shift correlation experiments with symmetry-based mixing sequences at high MAS frequencies and examined different strategies to simultaneously acquire 3D correlation spectra that are commonly required in the structural studies of proteins. The potential of numerically optimised symmetry-based mixing sequences and the simultaneous recording of chemical shift correlation spectra such as: 3D NCAC and 3D NHH with dual receivers, 3D NC Prime C and 3D C Prime NCA with sequential {sup 13}C acquisitions, 3D NHH and 3D NC Prime H with sequential {sup 1}H acquisitions and 3D CANH and 3D C'NH with broadband {sup 13}C-{sup 15}N mixing are demonstrated using microcrystalline samples of the {beta}1 immunoglobulin binding domain of protein G (GB1) and the chicken {alpha}-spectrin SH3 domain.

  10. Free magnesium levels in normal human brain and brain tumors: sup 31 P chemical-shift imaging measurements at 1. 5 T

    Energy Technology Data Exchange (ETDEWEB)

    Taylor, J.S.; Vigneron, D.B.; Murphy-Boesch, J.; Nelson, S.J.; Kessler, H.B.; Coia, L.; Curran, W.; Brown, T.R. (Fox Chase Cancer Center, Philadelphia, PA (United States))

    1991-08-01

    The authors have studied a series of normal subjects and patients with brain tumors, by using {sup 31}P three-dimensional chemical shift imaging to obtain localized {sup 31}P spectra of the brain. A significant proportion of brain cytosolic ATP in normal brain is not complexed to Mg{sup 2+}, as indicated by the chemical shift {delta} of the {beta}-P resonance of ATP. The ATP {beta}P resonance position in brain thus is sensitive to changes in intracellular free Mg{sup 2+} concentration and in the proportion of ATP complexed with Mg because this shift lies on the rising portion of the {delta} vs. Mg{sup 2+} titration curve for ATP. They have measured the ATP {beta}-P shift and compared intracellular free Mg{sup 2+} concentration and fractions of free ATP for normal individuals and a limited series of patients with brain tumors. In four of the five spectra obtained from brain tissue containing a substantial proportion of tumor, intracellular free Mg{sup 2+} was increased, and the fraction of free ATP was decreased, compared with normal brain.

  11. Evidence of chemical-potential shift with hole doping in Bi sub 2 Sr sub 2 CaCu sub 2 O sub 8+. delta

    Energy Technology Data Exchange (ETDEWEB)

    Shen, Z.; Dessau, D.S.; Wells, B.O. (Stanford Electronics Laboratory, Stanford University, Stanford, California 94305 (United States)); Olson, C.G. (Ames Laboratory, Iowa State University, Ames, Iowa 50011 (United States)); Mitzi, D.B.; Lombado, L. (Department of Applied Physics, Stanford University, Stanford, California 94305 (United States)); List, R.S.; Arko, A.J. (Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States))

    1991-12-01

    We have performed photoemission studies on high-quality Bi{sub 2}Sr{sub 2}CaCu{sub 2}O{sub 8+{delta}} samples with various {delta}. Our results show a clear chemical-potential shift (0.15--0.2 eV) as a function of doping. This result and the existing angle-resolved-photoemission data give a rather standard doping behavior of this compound in its highly doped regime.

  12. Progress in spin dynamics solid-state nuclear magnetic resonance with the application of Floquet-Magnus expansion to chemical shift anisotropy.

    Science.gov (United States)

    Mananga, Eugene Stephane

    2013-01-01

    The purpose of this article is to present an historical overview of theoretical approaches used for describing spin dynamics under static or rotating experiments in solid state nuclear magnetic resonance. The article gives a brief historical overview for major theories in nuclear magnetic resonance and the promising theories. We present the first application of Floquet-Magnus expansion to chemical shift anisotropy when irradiated by BABA pulse sequence.

  13. All-atom Molecular Dynamic Simulations Combined with the Chemical Shifts Study on the Weak Interactions of Ethanol-water System

    Institute of Scientific and Technical Information of China (English)

    ZHANG Rong; LUO San-Lai; WU Wen-Juan

    2008-01-01

    All-atom molecular dynamics(MD)simulation combined with chemical shifts was performed to investigate the interactions over the entire concentration range of the ethanol(EtOH)-water system.The results of the simulation were adopted to explain the NMR experiments by hydrogen bonding analysis.The strong hydrogen bonds and weak C-H…O contacts coexist in the mixtures through the analysis of the radial distribution functions.And the liquid structures in the whole concentration of EtOH-water mixtures can be classified into three regions by the statistic analysis of the hydrogen-bonding network in the MD simulations.Moreover,the chemical shifts of the hydrogen atom are in agreement witb the statistical results of the average number hydrogen bonds in the MD simulations.Interestingly,the excess relative extent Eηrel calculated by the MD simulations and chemical shifts in the EtOH aqueous solutions shows the largest deviation at XEtOH≈0.18.The excess properties present good agreement with the excess enthalpy in the concentration dependence.

  14. Homonuclear chemical shift correlation in rotating solids via RN{sup {nu}}{sub n} symmetry-based adiabatic RF pulse schemes

    Energy Technology Data Exchange (ETDEWEB)

    Riedel, Kerstin; Leppert, Joerg; Haefner, Sabine; Ohlenschlaeger, Oliver; Goerlach, Matthias; Ramachandran, Ramadurai [Institut fuer Molekulare Biotechnologie, Abteilung Molekulare Biophysik/NMR-Spektroskopie (Germany)], E-mail: raman@imb-jena.de

    2004-12-15

    The efficacy of RN{sup {nu}}{sub n} symmetry-based adiabatic Zero-Quantum (ZQ) dipolar recoupling schemes for obtaining chemical shift correlation data at moderate magic angle spinning frequencies has been evaluated. RN{sub n}{sup {nu}} sequences generally employ basic inversion elements that correspond to a net 180 deg. rotation about the rotating frame x-axis. It is shown here via numerical simulations and experimental measurements that it is also possible to achieve efficient ZQ dipolar recoupling via RN{sub n}{sup {nu}} schemes employing adiabatic pulses. Such an approach was successfully used for obtaining {sup 1}3C chemical shift correlation spectra of a uniformly labelled sample of (CUG){sub 9}7- a triplet repeat expansion RNA that has been implicated in the neuromuscular disease myotonic dystrophy. An analysis of the {sup 1}3C sugar carbon chemical shifts suggests, in agreement with our recent {sup 1}5N MAS-NMR studies, that this RNA adopts an A-helical conformation.

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

    Science.gov (United States)

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

    2015-07-01

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

  16. Chemically Selective Coated Quartz Crystal Microbalance (QCM) Array for Detection of Volatile Organic Chemicals

    Energy Technology Data Exchange (ETDEWEB)

    Bohuszewicz, T.V.; Frye-Mason, G.C.; Martin, S.J.; Osbourn, G.C. Bartholomew, J.W.; Schneider, T.W.; Spates, J.J.

    1998-11-04

    Liquid flow cells have been fabricated to prepare an array of QCMS operating simultaneously for detection and identification of VOCS in water. TWO signals, a tlequency response and a damping voltage response, were obtained per resonator. A blank QCM was used as a reference to account for changes in liquid density and viscosity. Nine different polymer coatings applied using a spin coat technique have been examined for VOC response under liquid flow conditions. A matrix of three classes of VOCS were examined for each coating with four chemicals in each class. The three classes of VOCS are polar, nonpolar and chlorinated. A pattern recognition technique, called visually empirical region of influence (VERI), was used to cluster the responses in n-dimensional space. Chemicals within a class varying by only one methyl group (e.g., toluene and xylene) are easily discriminated using only two different coatings with three different QCM responses. All chemicak were easily separated and detected with a total of 5 films and 6 responses with >99% accuracy.

  17. Identification of Zinc-ligated Cysteine Residues Based on {sup 13}C{alpha} and {sup 13}C{beta} Chemical Shift Data

    Energy Technology Data Exchange (ETDEWEB)

    Kornhaber, Gregory J.; Snyder, David; Moseley, Hunter N. B.; Montelione, Gaetano T. [Rutgers University, Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry (United States)], E-mail: guy@cabm.rutgers.edu

    2006-04-15

    Although a significant number of proteins include bound metals as part of their structure, the identification of amino acid residues coordinated to non-paramagnetic metals by NMR remains a challenge. Metal ligands can stabilize the native structure and/or play critical catalytic roles in the underlying biochemistry. An atom's chemical shift is exquisitely sensitive to its electronic environment. Chemical shift data can provide valuable insights into structural features, including metal ligation. In this study, we demonstrate that overlapped {sup 13}C{beta} chemical shift distributions of Zn-ligated and non-metal-ligated cysteine residues are largely resolved by the inclusion of the corresponding {sup 13}C{alpha} chemical shift information, together with secondary structural information. We demonstrate this with a bivariate distribution plot, and statistically with a multivariate analysis of variance (MANOVA) and hierarchical logistic regression analysis. Using 287 {sup 13}C{alpha}/{sup 13}C{beta} shift pairs from 79 proteins with known three-dimensional structures, including 86 {sup 13}C{alpha} and{sup 13}C{beta} shifts for 43 Zn-ligated cysteine residues, along with corresponding oxidation state and secondary structure information, we have built a logistic regression model that distinguishes between oxidized cystines, reduced (non-metal ligated) cysteines, and Zn-ligated cysteines. Classifying cysteines/cystines with a statisical model incorporating all three phenomena resulted in a predictor of Zn ligation with a recall, precision and F-measure of 83.7%, and an accuracy of 95.1%. This model was applied in the analysis of Bacillus subtilis IscU, a protein involved in iron-sulfur cluster assembly. The model predicts that all three cysteines of IscU are metal ligands. We confirmed these results by (i) examining the effect of metal chelation on the NMR spectrum of IscU, and (ii) inductively coupled plasma mass spectrometry analysis. To gain further insight into

  18. Uncovering symmetry-breaking vector and reliability order for assigning secondary structures of proteins from atomic NMR chemical shifts in amino acids

    Energy Technology Data Exchange (ETDEWEB)

    Yu, Wookyung [Pusan National University, Department of Physics, Center for Proteome Biophysics (Korea, Republic of); Lee, Woonghee; Lee, Weontae [Yonsei University, Department of Biochemistry, Structural Biochemistry and Molecular Biophysics Laboratory (Korea, Republic of); Kim, Suhkmann [Pusan National University, Department of Chemistry, Biochemistry and Bio-NMR Laboratory (Korea, Republic of); Chang, Iksoo, E-mail: iksoochang@pusan.ac.kr [Pusan National University, Department of Physics, Center for Proteome Biophysics (Korea, Republic of)

    2011-12-15

    Unravelling the complex correlation between chemical shifts of {sup 13}C{sup {alpha}}, {sup 13}C{sup {beta}}, {sup 13}C Prime , {sup 1}H{sup {alpha}}, {sup 15}N, {sup 1}H{sup N} atoms in amino acids of proteins from NMR experiment and local structural environments of amino acids facilitates the assignment of secondary structures of proteins. This is an important impetus for both determining the three-dimensional structure and understanding the biological function of proteins. The previous empirical correlation scores which relate chemical shifts of {sup 13}C{sup {alpha}}, {sup 13}C{sup {beta}}, {sup 13}C Prime , {sup 1}H{sup {alpha}}, {sup 15}N, {sup 1}H{sup N} atoms to secondary structures resulted in progresses toward assigning secondary structures of proteins. However, the physical-mathematical framework for these was elusive partly due to both the limited and orthogonal exploration of higher-dimensional chemical shifts of hetero-nucleus and the lack of physical-mathematical understanding underlying those correlation scores. Here we present a simple multi-dimensional hetero-nuclear chemical shift score function (MDHN-CSSF) which captures systematically the salient feature of such complex correlations without any references to a random coil state of proteins. We uncover the symmetry-breaking vector and its reliability order not only for distinguishing different secondary structures of proteins but also for capturing the delicate sensitivity interplayed among chemical shifts of {sup 13}C{sup {alpha}}, {sup 13}C{sup {beta}}, {sup 13}C Prime , {sup 1}H{sup {alpha}}, {sup 15}N, {sup 1}H{sup N} atoms simultaneously, which then provides a straightforward framework toward assigning secondary structures of proteins. MDHN-CSSF could correctly assign secondary structures of training (validating) proteins with the favourable (comparable) Q3 scores in comparison with those from the previous correlation scores. MDHN-CSSF provides a simple and robust strategy for the

  19. Chemical interaction of Ce-Fe mixed oxides for methane selective oxidation

    Institute of Scientific and Technical Information of China (English)

    祝星; 杜云鹏; 王华; 魏永刚; 李孔斋; 孙令玥

    2014-01-01

    Chemical interaction of Ce-Fe mixed oxides was investigated in methane selective oxidation via methane temperature pro-grammed reduction and methane isothermal reaction tests over Ce-Fe oxygen carriers. In methane temperature programmed reduction test, Ce-Fe oxide behaved complete oxidation at the lower temperature and selective oxidation at higher temperatures. Ce-Fe mixed oxides with the Fe content in the range of 0.1-0.5 was able to produce syngas with high selectivity in high-temperature range (800-900 °C), and a higher Fe amount over 0.5 seemed to depress the CO formation. In isothermal reaction, complete oxidation oc-curred at beginning following with selective oxidation later. Ce1-xFexO2-δ oxygen carriers (x≤0.5) were proved to be suitable for the selective oxidation of methane. Ce-Fe mixed oxides had the well-pleasing reducibility with high oxygen releasing rate and CO selec-tivity due to the interaction between Ce and Fe species. Strong chemical interaction of Ce-Fe mixed oxides originated from both Fe* activated CeO2 and Ce3+ activated iron oxides (FeOm), and those chemical interaction greatly enhanced the oxygen mobility and se-lectivity.

  20. Selected bibliography for the extraction of uranium from seawater: chemical process and plant design feasibility study

    Energy Technology Data Exchange (ETDEWEB)

    Binney, S.E.; Polkinghorne, S.T.; Jante, R.R.; Rodman, M.R.; Chen, A.C.T.; Gordon, L.I.

    1979-02-01

    A selected annotated bibliography of 521 references was prepared as a part of a feasibility study of the extraction of uranium from seawater. For the most part, these references are related to the chemical processes whereby the uranium is removed from the seawater. A companion docment contains a similar bibliography of 471 references related to oceanographic and uranium extraction plant siting considerations, although some of the references are in common. The bibliography was prepared by computer retrieval from Chemical Abstracts, Nuclear Science Abstracts, Energy Data Base, NTIS, and Oceanic Abstracts. References are listed by author, country of author, and selected keywords.

  1. In Situ Solid-State Reactions Monitored by X-ray Absorption Spectroscopy: Temperature-Induced Proton Transfer Leads to Chemical Shifts.

    Science.gov (United States)

    Stevens, Joanna S; Walczak, Monika; Jaye, Cherno; Fischer, Daniel A

    2016-10-24

    The dramatic colour and phase alteration with the solid-state, temperature-dependent reaction between squaric acid and 4,4'-bipyridine has been probed in situ with X-ray absorption spectroscopy. The electronic and chemical sensitivity to the local atomic environment through chemical shifts in the near-edge X-ray absorption fine structure (NEXAFS) revealed proton transfer from the acid to the bipyridine base through the change in nitrogen protonation state in the high-temperature form. Direct detection of proton transfer coupled with structural analysis elucidates the nature of the solid-state process, with intermolecular proton transfer occurring along an acid-base chain followed by a domino effect to the subsequent acid-base chains, leading to the rapid migration along the length of the crystal. NEXAFS thereby conveys the ability to monitor the nature of solid-state chemical reactions in situ, without the need for a priori information or long-range order.

  2. Induction of a heat shock response (HSP 72) in rat embryos exposed to selected chemical teratogens.

    Science.gov (United States)

    Mirkes, P E; Doggett, B; Cornel, L

    1994-02-01

    A monoclonal antibody to the 72 kD heat shock protein (HSP 72), Western blot analysis and 2-D gel electrophoresis/autoradiography were used to determine whether selected chemical teratogens induced the synthesis and accumulation of HSP 72 in postimplantation rat embryos exposed in vitro. The chemical teratogens studied include N-Acetoxy-2-acetylaminofluorene (N-Ac-AAF), cadmium chloride (CAD), cyclophosphamide (CP), sodium arsenite (AS), and sodium salicylate (SAL). Exposures to test chemicals were selected that produced obvious embryotoxicity characterized by abnormal development and growth retardation. Of the five chemical teratogens studied, AS and SAL induced the synthesis and accumulation of HSP 72 in day 10 rat embryos. The kinetics of HSP 72 accumulation, however, differed between AS- and SAL-treated embryos. Maximal levels of HSP 72 were observed 24 hours after AS exposure and 10 hours after SAL exposure. N-Ac-AAF, CD, and CP induced obvious embryotoxicity; however, none of these chemical teratogens induced HSP 72 at any of the timepoints assayed. Although only a small sample of chemical teratogens was studied, our results suggest that the heat shock response, characterized by the synthesis and accumulation of HSP 72, is not a general biomarker for chemical teratogens.

  3. Mass spectrometry analysis of polychlorinated biphenyls: chemical ionization and selected ion chemical ionization using methane as a reagent gas

    Directory of Open Access Journals (Sweden)

    RAYMOND E. MARCH

    2000-06-01

    Full Text Available In the present paper a quadrupole ion trap mass spectrometer, coupled with a gas chromatograph, was used to compare the electron impact ionization (EI and chemical ionization (Cl technique, in terms of their selectivity in polychlorinated biphenyls (PCBs quantitative analysis. The experiments were carried out with a modified Varian SATURN III quadrupole ion-storage mass spectrometer equipped with Varian waveform generator, coupled with a gas chromatograph with DB-5 capillary column. The disadvantage of using EI in the analysis of PCBs congeners is the extensive fragmentation of the molecular ion. The main fragmentation pattern recorded in the EI mass spectra of PCBs was the loss of a chlorine atom from the molecular ion. Therefore the fragment-ion signal overlapped with the molecular-ion cluster of lower mass congener. The fragmentation reactions of PCBs are suppressed if methane is used as a reagent gas for chemical ionization, but fragment ions are also present in the spectrum as an obstruction for quantitative analysis. The most selective method for PCBs quantitative analysis appears to be Cl with mass-selected C2H5+ ions from methane, which results in a mass spectrum with a negligible amount of fragment ions.

  4. Target-based drug discovery for human African trypanosomiasis: selection of molecular target and chemical matter.

    Science.gov (United States)

    Gilbert, Ian H

    2014-01-01

    Target-based approaches for human African trypanosomiasis (HAT) and related parasites can be a valuable route for drug discovery for these diseases. However, care needs to be taken in selection of both the actual drug target and the chemical matter that is developed. In this article, potential criteria to aid target selection are described. Then the physiochemical properties of typical oral drugs are discussed and compared to those of known anti-parasitics.

  5. Using Fisher Information Criteria for Chemical Sensor Selection via Convex Optimization Methods

    Science.gov (United States)

    2016-11-16

    best sensors after an optimization procedure. Due to the positive definite nature of the Fisher information matrix, convex optimization may be used to...parametrized to select the best sensors after an optimization procedure. Due to the positive definite nature of the Fisher information matrix, convex op...Naval Research Laboratory Washington, DC 20375-5320 NRL/MR/6180--16-9711 Using Fisher Information Criteria for Chemical Sensor Selection via Convex

  6. Effects of irritant chemicals on Aedes aegypti resting behavior: is there a simple shift to untreated "safe sites"?

    Directory of Open Access Journals (Sweden)

    Hortance Manda

    2011-07-01

    Full Text Available BACKGROUND: Previous studies have identified the behavioral responses of Aedes aegypti to irritant and repellent chemicals that can be exploited to reduce man-vector contact. Maximum efficacy of interventions based on irritant chemical actions will, however, require full knowledge of variables that influence vector resting behavior and how untreated "safe sites" contribute to overall impact. METHODS: Using a laboratory box assay, resting patterns of two population strains of female Ae. aegypti (THAI and PERU were evaluated against two material types (cotton and polyester at various dark:light surface area coverage (SAC ratio and contrast configuration (horizontal and vertical under chemical-free and treated conditions. Chemicals evaluated were alphacypermethrin and DDT at varying concentrations. RESULTS: Under chemical-free conditions, dark material had significantly higher resting counts compared to light material at all SAC, and significantly increased when material was in horizontal configuration. Cotton elicited stronger response than polyester. Within the treatment assays, significantly higher resting counts were observed on chemical-treated dark material compared to untreated light fabric. However, compared to matched controls, significantly less resting observations were made on chemical-treated dark material overall. Most importantly, resting observations on untreated light material (or "safe sites" in the treatment assay did not significantly increase for many of the tests, even at 25% SAC. Knockdown rates were ≤5% for all assays. Significantly more observations of flying mosquitoes were made in test assays under chemical-treatment conditions as compared to controls. CONCLUSIONS/SIGNIFICANCE: When preferred Ae. aegypti resting sites are treated with chemicals, even at reduced treatment coverage area, mosquitoes do not simply move to safe sites (untreated areas following contact with the treated material. Instead, they become agitated

  7. Transport-induced shifts in condensate dew-point and composition in multicomponent systems with chemical reaction

    Science.gov (United States)

    Rosner, D. E.; Nagarajan, R.

    1985-01-01

    Partial heterogeneous condensation phenomena in multicomponent reacting systems are analyzed taking into consideration the chemical element transport phenomena. It is demonstrated that the dew-point surface temperature in chemically reactive systems is not a purely thermodynamic quantity, but is influenced by the multicomponent diffusion and Soret-mass diffusion phenomena. Several distinct dew-points are shown to exist in such systems and, as a result of transport constraints, the 'sharp' locus between two chemically distinct condensates is systematically moved to a difference mainstream composition.

  8. Chemical deactivation of Cu-SSZ-13 ammonia selective catalytic reduction (NH3-SCR) systems

    NARCIS (Netherlands)

    Lezcano-Gonzalez, I.; Deka, U.; van der Bij, H. E.; Paalanen, P.; Arstad, B.; Weckhuysen, B. M.; Beale, A. M.

    2014-01-01

    The chemical deactivation of Cu-SSZ-13 Ammonia Selective Catalytic Reduction (NH3-SCR) catalysts by Pt, Zn, Ca and P has been systematically investigated using a range of analytical techniques in order to study the influence on both the zeolitic framework and the active Cu2+ ions. The results obtain

  9. Physical, chemical, and biological data for selected streams in Chester County, Pennsylvania, 1981-94

    Science.gov (United States)

    Reif, Andrew G.

    1999-01-01

    Physical, chemical, and biological data were collected at 51 sampling sites in Chester County, Pa., from 1970 through 1994 as part of the Stream Conditions of Chester County Program. This report presents data collected from 1981 through 1994. Physical data include water temperature, instantaneous stream discharge, pH, alkalinity, specific conductance, and dissolved oxygen. Chemical data include laboratory determinations of nutrients, major ions, and selected metals in whole water samples and selected metals, pesticides, gross polychlorinated biphenyls (PCB?s), gross polychlorinated napthalenes (PCN?s), and total carbon in stream-bottom sediment samples. The biological data consists of benthic macroinvertebrate population analyses and diversity indices. Chester County is undergoing rapid urbanization as agricultural lands are converted to residential, commercial, and industrial areas. The purpose of the Stream Conditions of Chester County Program is to further the understanding of stream habitat and chemical changes in response to this urbanization.

  10. 平衡电负性与烷烃核磁共振碳谱位移%EQUILIBRIUM ELECTRONEGATIVITY AND 13C NMR CHEMICAL SHIFTS OF ALKANES

    Institute of Scientific and Technical Information of China (English)

    聂长明; 文松年

    2001-01-01

    In this paper, the atomic equilibrium electronegativity in a molecule has been defined and the model of 13C NMR chemical shifts of alkanes has been studied with the atomic equilibrium electronegativity and the structural information parameters NiH(i=0,α,β,γ) and NjC(j=α,β,γ). The results indicate that the 13C NMR chemical shifts of alkanes can be described as follows: CS=-1736.776+755.118AEE+5.2539N0H+1.8837NβH-0.2066NγH By the use of the formula the chemical shifts of 99 carbon atoms are predicated, and the standard error is only 0.9861ppm. The average absolute error is 0.78ppm, The calculated values conform very much to the observed values.%定义了烷烃分子中碳原子的平衡电负性(AEE),用平衡电负性和NiH(i=0,α,β,γ)和NjC(j=α,β,γ)结构信息参数研究了烷烃的13C NMR化学位移模型.结果表明,烷烃13C NMR化学位移(CS)可用下式来定量描述: CS=-1736.776+755.118AEE+5.2539N0H+1.8837NβH-0.2066NγH   用上式估算了99个碳原子的化学位移,标准差为0.9861ppm,平均绝对误差0.78ppm,预测值与实验值十分吻合.

  11. Prediction of microvascular invasion of hepatocellular carcinomas with gadoxetic acid-enhanced MR imaging: Impact of intra-tumoral fat detected on chemical-shift images

    Energy Technology Data Exchange (ETDEWEB)

    Min, Ji Hye [Department of Radiology and Center for Imaging Science, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul (Korea, Republic of); Kim, Young Kon, E-mail: jmyr@dreamwiz.com [Department of Radiology and Center for Imaging Science, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul (Korea, Republic of); Lim, Sanghyeok [Department of Radiology, Guri Hospital, Hanyang University College of Medicine, Guri (Korea, Republic of); Jeong, Woo Kyoung; Choi, Dongil; Lee, Won Jae [Department of Radiology and Center for Imaging Science, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul (Korea, Republic of)

    2015-06-15

    Highlights: • Intra-tumoral fat detected with MR imaging may suggest lower risk for MVI of HCC. • Alfa-fetoprotein, tumor size, and fat component were associated with MVI of HCC. • Chemical shift MRI should be considered for the evaluation of HCC. - Abstract: Purpose: To investigate the impact of intra-tumoral fat detected by chemical-shift MR imaging in predicting the MVI of HCC. Materials and methods: Gadoxetic acid-enhanced MR imaging of 365 surgically proven HCCs from 365 patients (306 men, 59 women; mean age, 55.6 years) were evaluated. HCCs were classified into two groups, fat-containing and non-fat-containing, based on the presence of fat on chemical-shift images. Fat-containing HCCs were subdivided into diffuse or focal fatty change groups. Logistic regression analyses were used to identify clinical and MR findings associated with MVI. Results: Based on MR imaging, 66 tumors were classified as fat-containing HCCs and 299 as non-fat-containing HCCs. Among the 66 fat-containing HCCs, 38 (57.6%) showed diffuse fatty changes and 28 (42.4%) showed focal fatty changes. MVI was present in 18 (27.3%) fat-containing HCCs and in 117 (39.1%) non-fat-containing HCCs (P = 0.07). Univariate analysis revealed that serum alpha-fetoprotein (AFP) and tumor size were significantly associated with MVI (P < 0.001). A multiple logistic regression analysis showed that log AFP (odds ratio 1.178, P = 0.0016), tumor size (odds ratio 1.809, P < 0.001), and intra-tumoral fat (odds ratio 0.515, P = 0.0387) were independent variables associated with MVI. Conclusion: Intra-tumoral fat detected with MR imaging may suggest lower risk for MVI of HCC and, therefore, a possibly more favorable prognosis, but the clinical value of this finding is uncertain.

  12. Chemical shift magnetic resonance imaging in differentiation of benign from malignant vertebral collapse in a rural tertiary care hospital in North India

    Science.gov (United States)

    Mittal, Puneet; Gupta, Ranjana; Mittal, Amit; Joshi, Sandeep

    2016-01-01

    Introduction: Magnetic resonance imaging (MRI) is the modality of the first choice for evaluation of vertebral compression/collapse. Many MRI qualitative features help to differentiate benign from malignant collapse. We conducted this study to look for a quantitative difference in chemical shift values in benign and malignant collapse using dual-echo gradient echo in-phase/out-phase imaging. Materials and Methods: MRI examinations of a total of 38 patients were retrospectively included in the study who had vertebral compression/collapse with marrow edema in which final diagnosis was available at the time of imaging/follow-up. Signal intensity value in the region of abnormal marrow signal and adjacent normal vertebra was measured on in phase/out phase images. Signal intensity ratio (SIR) was measured by dividing signal intensity value on opposite phase images to that on in phase images. SIR was compared in normal vertebrae and benign and malignant vertebral collapse. Results: There were 21 males and 17 females with mean age of 52.4 years (range 28–76 years). Out of total 38 patients, 18 were of benign vertebral collapse and 20 of malignant vertebral collapse. SIR in normal vertebrae was 0.30 ± 0.14, 0.67 ± 0.18 in benign vertebral collapse, and 1.20 ± 0.27 in malignant vertebral collapse with significant difference in SIR of normal vertebrae versus benign collapse (P < 0.01) and in benign collapse versus malignant collapse (P < 0.01). Assuming a cutoff of <0.95 for benign collapse and ≥0.95 for malignant collapse, chemical shift imaging had a sensitivity of 90% and specificity of 94.4%. Conclusion: Chemical shift imaging is a rapid and useful sequence in differentiating benign from malignant vertebral collapse with good specificity and sensitivity.

  13. 1H NMR spectra. Part 30(+): 1H chemical shifts in amides and the magnetic anisotropy, electric field and steric effects of the amide group.

    Science.gov (United States)

    Abraham, Raymond J; Griffiths, Lee; Perez, Manuel

    2013-03-01

    The (1)H spectra of 37 amides in CDCl(3) solvent were analysed and the chemical shifts obtained. The molecular geometries and conformational analysis of these amides were considered in detail. The NMR spectral assignments are of interest, e.g. the assignments of the formamide NH(2) protons reverse in going from CDCl(3) to more polar solvents. The substituent chemical shifts of the amide group in both aliphatic and aromatic amides were analysed using an approach based on neural network data for near (≤3 bonds removed) protons and the electric field, magnetic anisotropy, steric and for aromatic systems π effects of the amide group for more distant protons. The electric field is calculated from the partial atomic charges on the N.C═O atoms of the amide group. The magnetic anisotropy of the carbonyl group was reproduced with the asymmetric magnetic anisotropy acting at the midpoint of the carbonyl bond. The values of the anisotropies Δχ(parl) and Δχ(perp) were for the aliphatic amides 10.53 and -23.67 (×10(-6) Å(3)/molecule) and for the aromatic amides 2.12 and -10.43 (×10(-6) Å(3)/molecule). The nitrogen anisotropy was 7.62 (×10(-6) Å(3)/molecule). These values are compared with previous literature values. The (1)H chemical shifts were calculated from the semi-empirical approach and also by gauge-independent atomic orbital calculations with the density functional theory method and B3LYP/6-31G(++) (d,p) basis set. The semi-empirical approach gave good agreement with root mean square error of 0.081 ppm for the data set of 280 entries. The gauge-independent atomic orbital approach was generally acceptable, but significant errors (ca. 1 ppm) were found for the NH and CHO protons and also for some other protons.

  14. Magnetic moments in chemically ordered mass-selected CoPt and FePt clusters

    Energy Technology Data Exchange (ETDEWEB)

    Dupuis, V., E-mail: Veronique.Dupuis@univ-lyon1.fr [Institut Lumière Matière, UMR5306 Université Lyon 1-CNRS, Université de Lyon, 69622 Villeurbanne cedex (France); Khadra, G.; Linas, S.; Hillion, A. [Institut Lumière Matière, UMR5306 Université Lyon 1-CNRS, Université de Lyon, 69622 Villeurbanne cedex (France); Gragnaniello, L. [Institute of Condensed Matter Physics, EPFL, CH-1015 Lausanne (Switzerland); Tamion, A.; Tuaillon-Combes, J.; Bardotti, L.; Tournus, F. [Institut Lumière Matière, UMR5306 Université Lyon 1-CNRS, Université de Lyon, 69622 Villeurbanne cedex (France); Otero, E.; Ohresser, P. [Synchrotron SOLEIL, L’Orme des Merisiers, Saint-Aubin BP 48, F-91192 Gif-sur-Yvette Cedex (France); Rogalev, A.; Wilhelm, F. [European Synchrotron Radiation Facility, BP 220, F-38043 Grenoble Cedex (France)

    2015-06-01

    By combining high photon flux and chemical selectivity, X-ray absorption spectroscopy and X-ray magnetic circular dichroism (XMCD) have been used to study the magnetism of CoPt and FePt clusters before and after their transition to the chemically ordered L1{sub 0}-like phase. Compared to the bulk, we find larger magnetic spin and orbital moments of Fe, Co and Pt atoms in nanoalloys. - Highlights: • Study of magnetism on well-defined CoPt and FePt clusters embedded in carbon matrix • X-ray magnetic circular dichroism (XMCD) at each specific Fe, Co and Pt edges, before and after annealing to induce transition to the chemically L1{sub 0}-like phase. • Quantitative values of the spin and orbital magnetic moments of Co (resp. Fe) and Pt after the chemical ordering transition. • Specific nanoalloy effects.

  15. Energy and chemicals from the selective electrooxidation of renewable diols by organometallic fuel cells.

    Science.gov (United States)

    Bellini, Marco; Bevilacqua, Manuela; Filippi, Jonathan; Lavacchi, Alessandro; Marchionni, Andrea; Miller, Hamish A; Oberhauser, Werner; Vizza, Francesco; Annen, Samuel P; Grützmacher, H

    2014-09-01

    Organometallic fuel cells catalyze the selective electrooxidation of renewable diols, simultaneously providing high power densities and chemicals of industrial importance. It is shown that the unique organometallic complex [Rh(OTf)(trop2NH)(PPh3)] employed as molecular active site in an anode of an OMFC selectively oxidizes a number of renewable diols, such as ethylene glycol , 1,2-propanediol (1,2-P), 1,3-propanediol (1,3-P), and 1,4-butanediol (1,4-B) to their corresponding mono-carboxylates. The electrochemical performance of this molecular catalyst is discussed, with the aim to achieve cogeneration of electricity and valuable chemicals in a highly selective electrooxidation from diol precursors.

  16. How to distinguish conformational selection and induced fit based on chemical relaxation rates

    CERN Document Server

    Paul, Fabian

    2016-01-01

    Protein binding often involves conformational changes. Important questions are whether a conformational change occurs prior to a binding event ('conformational selection') or after a binding event ('induced fit'), and how conformational transition rates can be obtained from experiments. In this article, we present general results for the chemical relaxation rates of conformational-selection and induced-fit binding processes that hold for all concentrations of proteins and ligands and, thus, go beyond the standard pseudo-first-order approximation of large ligand concentration. These results allow to distinguish conformational-selection from induced-fit processes - also in cases in which such a distinction is not possible under pseudo-first-order conditions - and to extract conformational transition rates of proteins from chemical relaxation data.

  17. Other compounds isolated from Simira glaziovii and the {sup 1}H and {sup 13}C NMR chemical shift assignments of new 1-epi-castanopsol

    Energy Technology Data Exchange (ETDEWEB)

    Araujo, Marcelo F. de; Vieira, Ivo J. Curcino [Universidade Federal Rural do Rio de Janeiro, Seropedica, RJ (Brazil). Dept. de Quimica; Braz-Filho, Raimundo [Universidade Estadual do Norte Fluminense (UENF), Campos dos Goytacases, RJ (Brazil). Centro de Ciencias Tecnologicas. Lab. de Ciencias Quimicas; Carvalho, Mario G. de, E-mail: mgeraldo@ufrrj.br [Universidade Federal do Rio de Janeiro (NPPN/UFRJ), RJ (Brazil). Centro de Ciencias da Saude. Nucleo de Pesquisa em Produtos Naturais

    2012-07-01

    A new triterpene, 1-epi-castanopsol, besides eleven known compounds: sitosterol, stigmasterol, campesterol, lupeol, lupenone, simirane B, syringaresinol, scopoletin, isofraxidin, 6,7,8-trimethoxycoumarin and harman, were isolated from the wood of Simira glaziovii. The structures of the known compounds were defined by 1D, 2D {sup 1}H, {sup 13}C NMR spectra data analyses and comparison with literature data. The detailed spectral data analyses allowed the definition of the structure of the new 1-epi isomer of castanopsol and performance of {sup 1}H and {sup 13}C NMR chemical shift assignments. (author)

  18. Accurate calculation of chemical shifts in highly dynamic H2@C60 through an integrated quantum mechanics/molecular dynamics scheme.

    Science.gov (United States)

    Jiménez-Osés, Gonzalo; García, José I; Corzana, Francisco; Elguero, José

    2011-05-20

    A new protocol combining classical MD simulations and DFT calculations is presented to accurately estimate the (1)H NMR chemical shifts of highly mobile guest-host systems and their thermal dependence. This strategy has been successfully applied for the hydrogen molecule trapped into C(60) fullerene, an unresolved and challenging prototypical case for which experimental values have never been reproduced. The dependence of the final values on the theoretical method and their implications to avoid over interpretation of the obtained results are carefully described.

  19. 1H, 13C and 15N backbone and side-chain chemical shift assignment of the Fyn SH2 domain and its complex with a phosphotyrosine peptide.

    Science.gov (United States)

    Huculeci, Radu; Buts, Lieven; Lenaerts, Tom; van Nuland, Nico A J

    2011-10-01

    SH2 domains are interaction modules uniquely dedicated to recognize phosphotyrosine sites, playing a central role in for instance the activation of tyrosine kinases or phosphatases. Here we report the (1)H, (15)N and (13)C backbone and side-chain chemical shift assignments of the SH2 domain of the human protein tyrosine kinase Fyn, both in its free state and bound to a high-affinity phosphotyrosine peptide corresponding to a specific sequence in the hamster middle-T antigen. The BMRB accession numbers are 17,368 and 17,369, respectively.

  20. Liver steatosis (LS) evaluated through chemical-shift magnetic resonance imaging liver enzymes in morbid obesity; effect of weight loss obtained with intragastric balloon gastric banding.

    Science.gov (United States)

    Folini, Laura; Veronelli, Annamaria; Benetti, Alberto; Pozzato, Carlo; Cappelletti, Marco; Masci, Enzo; Micheletto, Giancarlo; Pontiroli, Antonio E

    2014-01-01

    The aim of this study was to evaluate in morbid obesity clinical and metabolic effects related to weight loss on liver steatosis (LS), measured through chemical-shift magnetic resonance imaging (MRI) and liver enzymes. Forty obese subjects (8 M/32 W; BMI 42.8 ± 7.12 kg/m(2), mean ± SD) were evaluated for LS through ultrasound (US-LS), chemical-shift MRI (MRI-LS), liver enzymes [aspartate aminotransferase (AST), alanine aminotransferase (ALT), γ-glutamyltransferase (GGT), alkaline phosphatase (ALP)], anthropometric parameters [weight, BMI, waist circumference (WC)], lipids, insulin, insulin resistance (HOMA-IR), glycated hemoglobin (HbA1c), oral glucose tolerance test, and body composition [fat mass (FM) and fat-free mass (FFM) at bio-impedance analysis (BIA)]. Anthropometric measures, MRI-LS, BIA, and biochemical parameters were reevaluated 6 months later in 18 subjects undergoing restrictive bariatric approach, i.e., intragastric balloon (BIB, n = 13) or gastric banding (LAGB, n = 5), and in 13 subjects receiving hypocaloric diet. At baseline, US-LS correlates only with MRI-LS, and the latter correlates with ALT, AST, and GGT. After 6 months, subjects undergoing BIB or LAGB had significant changes of BMI, weight, WC, ALT, AST, GGT, ALP, HbA1c, insulin, HOMA-IR, FM, FFM, and MRI-LS. Diet-treated obese subjects had no significant change of any parameter under study; change of BMI, fat mass, and fat-free mass was significantly greater in LAGB/BIB subjects than in diet-treated subjects. Change of MRI-LS showed a significant correlation with changes in weight, BMI, WC, GGT, ALP, and basal MRI-LS. Significant weight loss after BIB or LAGB is associated with decrease in chemical-shift MRI-LS and with reduction in liver enzymes; chemical-shift MRI and liver enzymes allow monitoring of LS in follow-up studies.

  1. Double-echo gradient chemical shift MR imaging fails to differentiate minimal fat renal angiomyolipomas from other homogeneous solid renal tumors

    Energy Technology Data Exchange (ETDEWEB)

    Ferré, R., E-mail: kn638@yahoo.fr [Department of Radiology, Necker Hospital, 149 rue de Sèvres, 75730 Paris (France); Cornelis, F. [Department of Radiology, Pellegrin Hospital, Place Amélie Raba Léon, 33076 Bordeaux (France); Verkarre, V. [Department of Pathology, Necker Hospital, 149 rue de Sèvres, 75730 Paris (France); Eiss, D.; Correas, J.M. [Department of Radiology, Necker Hospital, 149 rue de Sèvres, 75730 Paris (France); Grenier, N. [Department of Radiology, Pellegrin Hospital, Place Amélie Raba Léon, 33076 Bordeaux (France); Hélénon, O. [Department of Radiology, Necker Hospital, 149 rue de Sèvres, 75730 Paris (France)

    2015-03-15

    Highlights: •Diagnosis of AMLs with minimal fat (mfAMLs) is still challenging with MRI. •Drop of signal on opposed-phase MR imaging is not specific of mfAMLs. •Double-echo gradient-echo sequences cannot accurately differentiate renal mfAMLs from other renal tumors. -- Abstract: Objectives: The purpose of this retrospective study was to evaluate the diagnostic performance of double-echo gradient chemical shift (GRE) magnetic resonance (MR) imaging for the differentiation of angiomyolipomas with minimal fat (mfAML) from other homogeneous solid renal tumors. Methods: Between 2005 and 2010 in two institutions, all histologically proven homogenous solid renal tumors imaged with computed tomography and MR imaging, including GRE sequences, have been retrospectively selected. A total of 118 patients (mean age: 61 years; range: 20–87) with 119 tumors were included. Two readers measured independently the signal intensity (SI) on GRE images and calculated SI index (SII) and tumor-to-spleen ratio (TSR) on in-phase and opposed-phase images. Intra- and interreader agreement was obtained. Cut-off values were derived from the receiver operating characteristic (ROC) curve analysis. Results: Twelve mfAMLs in 11 patients were identified (mean size: 2.8 cm; range: 1.2–3.5), and 107 non-AML tumors (3.2 cm; 1–7.8) in 107 patients. The intraobserver reproducibility of SII and TSR was excellent with an intraclass correlation coefficient equal to 0.99 [0.98–0.99]. The coefficient of correlation between the readers was 0.99. The mean values of TSR for mfAMLs and non-mfAMLs were −7.0 ± 22.8 versus −8.2 ± 21.2 for reader 1 and −6.7 ± 22.8 versus −8.4 ± 20.9 for reader 2 respectively. No significant difference was noticed between the two groups for SII (p = 0.98) and TSR (p = 0.86). Only 1 out of 12 mfAMLs and 11 of 107 non-AML tumors presented with a TSR inferior to −30% (p = 0.83). Conclusion: In a routine practice, GRE sequences cannot be a confident tool to

  2. Altering the interfacial activation mechanism of a lipase by solid-phase selective chemical modification.

    Science.gov (United States)

    López-Gallego, Fernando; Abian, Olga; Guisán, Jose Manuel

    2012-09-04

    This study presents a combined protein immobilization, directed mutagenesis, and site-selective chemical modification approach, which was used to create a hyperactivated semisynthetic variant of BTL2. Various alkane chains were tethered at three different positions in order to mimic the lipase interfacial activation exogenously triggered by detergents. Optimum results were obtained when a dodecane chain was introduced at position 320 by solid-phase site-selective chemical modification. The resulting semisynthetic variant showed a 2.5-fold higher activity than the wild-type nonmodified variant in aqueous conditions. Remarkably, this is the maximum hyperactivation ever observed for BTL2 in the presence of detergents such as Triton X-100. We present evidence to suggest that the endogenous dodecane chain hyperactivates the enzyme in a similar fashion as an exogenous detergent molecule. In this way, we also observe a faster irreversible enzyme inhibition and an altered detergent sensitivity profile promoted by the site-selective chemical modification. These findings are also supported by fluorescence studies, which reveal that the structural conformation changes of the semisynthetic variant are different to those of the wild type, an effect that is more pronounced in the presence of detergent. Finally, the optimal immobilized semisynthetic variant was successfully applied to the selective synthesis of oxiran-2-yl butyrate. Significantly, this biocatalyst is 12-fold more efficient than the immobilized wild-type enzyme, producing the S-enantiomer with higher enantiospecificity (ee = 92%).

  3. Toward structural dynamics: protein motions viewed by chemical shift modulations and direct detection of C'N multiple-quantum relaxation.

    Science.gov (United States)

    Mori, Mirko; Kateb, Fatiha; Bodenhausen, Geoffrey; Piccioli, Mario; Abergel, Daniel

    2010-03-17

    Multiple quantum relaxation in proteins reveals unexpected relationships between correlated or anti-correlated conformational backbone dynamics in alpha-helices or beta-sheets. The contributions of conformational exchange to the relaxation rates of C'N coherences (i.e., double- and zero-quantum coherences involving backbone carbonyl (13)C' and neighboring amide (15)N nuclei) depend on the kinetics of slow exchange processes, as well as on the populations of the conformations and chemical shift differences of (13)C' and (15)N nuclei. The relaxation rates of C'N coherences, which reflect concerted fluctuations due to slow chemical shift modulations (CSMs), were determined by direct (13)C detection in diamagnetic and paramagnetic proteins. In well-folded proteins such as lanthanide-substituted calbindin (CaLnCb), copper,zinc superoxide dismutase (Cu,Zn SOD), and matrix metalloproteinase (MMP12), slow conformational exchange occurs along the entire backbone. Our observations demonstrate that relaxation rates of C'N coherences arising from slow backbone dynamics have positive signs (characteristic of correlated fluctuations) in beta-sheets and negative signs (characteristic of anti-correlated fluctuations) in alpha-helices. This extends the prospects of structure-dynamics relationships to slow time scales that are relevant for protein function and enzymatic activity.

  4. Optical Red shift in ZnO Nanoflowers Fabricated on Non-Seeded Substrates by Soft Wet Chemical Route

    Science.gov (United States)

    Murali, K. V.; Preetha, K. C.; Ragina, A. J.; Deepa, K.; Remadevi, T. L.

    2011-10-01

    Zinc oxide (ZnO) nanoflowers were fabricated on non-seeded glass substrates by successive ionic layer adsorption and reaction (SILAR) method using different complex agents. Influence of complex agents ammonia, lithium hydroxide and hexamine on the optical properties of the as-synthesized and the samples annealed at 400 °C was studied. Optical red shift was observed in ZnO samples and was analyzed with respect to the complex agents. All samples possessed a steep absorption edge in the wavelength range 375-425 nm. ZnO nanostructures except that synthesized using hexamine have low and steady absorbance and show higher transmittance (70-85%) in the entire visible region. SEM, XRD and EDAX studies confirmed the high surface-to-volume ratio, good optical quality, excellent crystalline nature and purity of the formed and annealed ZnO nanostructures.

  5. Final Technical Report: A Paradigm Shift in Chemical Processing: New Sustainable Chemistries for Low-VOC Coatings

    Energy Technology Data Exchange (ETDEWEB)

    Smith, Kenneth F.

    2006-07-26

    The project employed new processes to make emulsion polymers from reduced levels of petroleum-derived chemical feedstocks. Most waterborne paints contain spherical, emulsion polymer particles that serve as the film-forming binder phase. Our goal was to make emulsion polymer particles containing 30 percent feedstock that would function as effectively as commercial emulsions made from higher level feedstock. The processes developed yielded particles maintained their film formation capability and binding capacity while preserving the structural integrity of the particles after film formation. Rohm and Haas Company (ROH) and Archer Daniels Midland Company (ADM) worked together to employ novel polymer binders (ROH) and new, non-volatile, biomass-derived coalescing agents (ADM). The University of Minnesota Department of Chemical Engineering and Material Science utilized its unique microscopy capabilities to characterize films made from the New Emulsion Polymers (NEP).

  6. Diversity selection of compounds based on 'protein affinity fingerprints' improves sampling of bioactive chemical space.

    Science.gov (United States)

    Nguyen, Ha P; Koutsoukas, Alexios; Mohd Fauzi, Fazlin; Drakakis, Georgios; Maciejewski, Mateusz; Glen, Robert C; Bender, Andreas

    2013-09-01

    Diversity selection is a frequently applied strategy for assembling high-throughput screening libraries, making the assumption that a diverse compound set increases chances of finding bioactive molecules. Based on previous work on experimental 'affinity fingerprints', in this study, a novel diversity selection method is benchmarked that utilizes predicted bioactivity profiles as descriptors. Compounds were selected based on their predicted activity against half of the targets (training set), and diversity was assessed based on coverage of the remaining (test set) targets. Simultaneously, fingerprint-based diversity selection was performed. An original version of the method exhibited on average 5% and an improved version on average 10% increase in target space coverage compared with the fingerprint-based methods. As a typical case, bioactivity-based selection of 231 compounds (2%) from a particular data set ('Cutoff-40') resulted in 47.0% and 50.1% coverage, while fingerprint-based selection only achieved 38.4% target coverage for the same subset size. In conclusion, the novel bioactivity-based selection method outperformed the fingerprint-based method in sampling bioactive chemical space on the data sets considered. The structures retrieved were structurally more acceptable to medicinal chemists while at the same time being more lipophilic, hence bioactivity-based diversity selection of compounds would best be combined with physicochemical property filters in practice.

  7. Structure-based predictions of 13C-NMR chemical shifts for a series of 2-functionalized 5-(methylsulfonyl)-1-phenyl-1H-indoles derivatives using GA-based MLR method

    Science.gov (United States)

    Ghavami, Raouf; Sadeghi, Faridoon; Rasouli, Zolikha; Djannati, Farhad

    2012-12-01

    Experimental values for the 13C NMR chemical shifts (ppm, TMS = 0) at 300 K ranging from 96.28 ppm (C4' of indole derivative 17) to 159.93 ppm (C4' of indole derivative 23) relative to deuteride chloroform (CDCl3, 77.0 ppm) or dimethylsulfoxide (DMSO, 39.50 ppm) as internal reference in CDCl3 or DMSO-d6 solutions have been collected from literature for thirty 2-functionalized 5-(methylsulfonyl)-1-phenyl-1H-indole derivatives containing different substituted groups. An effective quantitative structure-property relationship (QSPR) models were built using hybrid method combining genetic algorithm (GA) based on stepwise selection multiple linear regression (SWS-MLR) as feature-selection tools and correlation models between each carbon atom of indole derivative and calculated descriptors. Each compound was depicted by molecular structural descriptors that encode constitutional, topological, geometrical, electrostatic, and quantum chemical features. The accuracy of all developed models were confirmed using different types of internal and external procedures and various statistical tests. Furthermore, the domain of applicability for each model which indicates the area of reliable predictions was defined.

  8. Nanoscale arrays of antimony telluride single crystals by selective chemical vapor deposition

    Science.gov (United States)

    Huang, Ruomeng; Benjamin, Sophie L.; Gurnani, Chitra; Wang, Yudong; Hector, Andrew L.; Levason, William; Reid, Gillian; De Groot, C. H. (Kees)

    2016-01-01

    Arrays of individual single nanocrystals of Sb2Te3 have been formed using selective chemical vapor deposition (CVD) from a single source precursor. Crystals are self-assembled reproducibly in confined spaces of 100 nm diameter with pitch down to 500 nm. The distribution of crystallite sizes across the arrays is very narrow (standard deviation of 15%) and is affected by both the hole diameter and the array pitch. The preferred growth of the crystals in the orientation along the diagonal of the square holes strongly indicates that the diffusion of adatoms results in a near thermodynamic equilibrium growth mechanism of the nuclei. A clear relationship between electrical resistivity and selectivity is established across a range of metal selenides and tellurides, showing that conductive materials result in more selective growth and suggesting that electron donation is of critical importance for selective deposition. PMID:27283116

  9. On the sensitivity, selectivity, sensory information and optimal size of resistive chemical sensors

    CERN Document Server

    Kish, L B; Heszler, P; Smulko, J; Granqvist, Claes-Goran; Heszler, Peter; Kish, Laszlo B.; Smulko, Janusz

    2007-01-01

    Information theoretical tools are applied for the study of the sensitivity and selectivity enhancements of resistive fluctuation-enhanced sensors. General considerations are given for the upper limit of selectivity enhancement. The signal-to-noise ratio and information channel capacity of fluctuation-enhanced chemical sensors is compared to that of classical sensors providing a single output. The considerations are done at the generic level with a few concrete examples and include the estimation of scaling relations between the sensor size, the signal power, the noise power and the speed of measurements versus the size, sampling rate and measurement time.

  10. Selective olfactory attention of a specialised predator to intraspecific chemical signals of its prey

    Science.gov (United States)

    Cárdenas, Manuel; Jiroš, Pavel; Pekár, Stano

    2012-08-01

    Prey-specialised predators have evolved specific cognitive adaptations that increase their prey searching efficiency. In particular, when the prey is social, selection probably favours the use of prey intraspecific chemical signals by predatory arthropods. Using a specialised ant-eating zodariid spider, Zodarion rubidum, which is known to prey on several ant species and possesses capture and venom adaptations more effective on Formicinae ants, we tested its ability to recognise chemical cues produced by several ant species. Using an olfactometer, we tested the response of Z. rubidum towards air with chemical cues from six different ant species: Camponotus ligniperda, Lasius platythorax and Formica rufibarbis (all Formicinae); and Messor structor, Myrmica scabrinodis and Tetramorium caespitum (all Myrmicinae). Z. rubidum was attracted to air carrying chemical cues only from F. rufibarbis and L. platythorax. Then, we identified that the spiders were attracted to airborne cues coming from the F. rufibarbis gaster and Dufour's gland, in particular. Finally, we found that among several synthetic blends, the decyl acetate and undecane mixture produced significant attraction of spiders. These chemicals are produced only by three Formicine genera. Furthermore, we investigated the role of these chemical cues in the communication of F. rufibarbis and found that this blend reduces their movement. This study demonstrates the chemical cognitive capacity of Z. rubidum to locate its ant prey using chemical signals produced by the ants. The innate capacity of Z. rubidum to olfactory detect different ant species is narrow, as it includes only two ant genera, confirming trophic specialisation at lower than subfamily level. The olfactory cue detected by Zodarion spiders is probably a component of the recruitment or trail pheromone.

  11. Correlations of the chemical shift on fasly rotating biological solids by means of NMR spectroscopy; Korrelationen der chemischen Verschiebung an schnell rotierenden biologischen Festkoerpern mittels NMR-Spektroskopie

    Energy Technology Data Exchange (ETDEWEB)

    Herbst, Christian

    2010-04-27

    The basic aim of the thesis was the development and improvement of homo- and heteronuclear feedback sequences for the generation of correlation spectra of the chemical shift. In a first step the possibility of the acquisition of {sup 13}C-{sup 13} correlation spectra of the chemical shift by means of inversion pulses with low RF power factor was studied. Furthermore it was shown that broad-band phase-modulated inversion and universal rotational pulses can be constructed by means of global optimization procedures like the genetic algorithms under regardment of the available RF field strength. By inversion, universal rotational, and 360 pulses as starting values of the optimization efficient homonuclear CN{sub n}{sup {nu}} and RN{sub n}{sup {nu}} mixing sequences as well as heteronuclear RN{sub n}{sup {nu}{sub s},{nu}{sub k}} feedback sequences were generated. The satisfactory power of the numerically optimized sequences was shown by means of the simulation as well by means of correlation experiments of the chemical shift of L-histidine, L-arginine, and the (CUG){sub 97}-RNA. This thesis deals furthermore with the possibility to acquire simultaneously different signals with several receivers. By means of numerically optimized RN{sub n}{sup {nu}{sub s},{nu}{sub k}} pulse sequences both {sup 15}N-{sup 13}C and {sup 13}C-{sup 15}N correlation spectra were simultaneously generated. Furthermore it could be shown that the simultaneous acquisition of 3D-{sup 15}N-{sup 13}C-{sup 13}C and {sup 13}C-{sup 15}N-({sup 1}H)-{sup 1}H correlation spectra is possible. By this in only one measurement process resonance assignments can be met and studies of the global folding performed. A further application of several receivers is the simultaneous acquisition of CHHC, NHHN, NHHC, as well as CHHN spectra. By such experiments it is possible to characterize the hydrogen-bonding pattern and the glycosidic torsion angle {sup {chi}} in RNA. This was demonstrated by means of the (CUG){sub 97

  12. Selective pharmacological blockade of the 5-HT7 receptor attenuates light and 8-OH-DPAT induced phase shifts of mouse circadian wheel running activity.

    Science.gov (United States)

    Shelton, Jonathan; Yun, Sujin; Losee Olson, Susan; Turek, Fred; Bonaventure, Pascal; Dvorak, Curt; Lovenberg, Timothy; Dugovic, Christine

    2014-01-01

    Recent reports have illustrated a reciprocal relationship between circadian rhythm disruption and mood disorders. The 5-HT7 receptor may provide a crucial link between the two sides of this equation since the receptor plays a critical role in sleep, depression, and circadian rhythm regulation. To further define the role of the 5-HT7 receptor as a potential pharmacotherapy to correct circadian rhythm disruptions, the current study utilized the selective 5-HT7 antagonist JNJ-18038683 (10 mg/kg) in three different circadian paradigms. While JNJ-18038683 was ineffective at phase shifting the onset of wheel running activity in mice when administered at different circadian time (CT) points across the circadian cycle, pretreatment with JNJ-18038683 blocked non-photic phase advance (CT6) induced by the 5-HT1A/7 receptor agonist 8-OH-DPAT (3 mg/kg). Since light induced phase shifts in mammals are partially mediated via the modulation of the serotonergic system, we determined if JNJ-18038683 altered phase shifts induced by a light pulse at times known to phase delay (CT15) or advance (CT22) wheel running activity in free running mice. Light exposure resulted in a robust shift in the onset of activity in vehicle treated animals at both times tested. Administration of JNJ-18038683 significantly attenuated the light induced phase delay and completely blocked the phase advance. The current study demonstrates that pharmacological blockade of the 5-HT7 receptor by JNJ-18038683 blunts both non-photic and photic phase shifts of circadian wheel running activity in mice. These findings highlight the importance of the 5-HT7 receptor in modulating circadian rhythms. Due to the opposite modulating effects of light resetting between diurnal and nocturnal species, pharmacotherapy targeting the 5-HT7 receptor in conjunction with bright light therapy may prove therapeutically beneficial by correcting the desynchronization of internal rhythms observed in depressed individuals.

  13. Selective pharmacological blockade of the 5-HT7 receptor attenuates light and 8-OH-DPAT induced phase shifts of mouse circadian wheel running activity

    Directory of Open Access Journals (Sweden)

    Jonathan eShelton

    2015-01-01

    Full Text Available Recent reports have illustrated a reciprocal relationship between circadian rhythm disruption and mood disorders. The 5-HT7 receptor may provide a crucial link between the two sides of this equation since the receptor plays a critical role in sleep, depression, and circadian rhythm regulation. To further define the role of the 5-HT7 receptor as a potential pharmacotherapy to correct circadian rhythm disruptions, the current study utilized the selective 5-HT7 antagonist JNJ-18038683 (10 mg/kg in three different circadian paradigms. While JNJ-18038683 was ineffective at phase shifting the onset of wheel running activity in mice when administered at different circadian time (CT points across the circadian cycle, pretreatment with JNJ-18038683 blocked non-photic phase advance (CT6 induced by the 5-HT1A/7 receptor agonist 8-OH-DPAT (3 mg/kg. Since light induced phase shifts in mammals are partially mediated via the modulation of the serotonergic system, we determined if JNJ-18038683 altered phase shifts induced by a light pulse at times known to phase delay (CT15 or advance (CT22 wheel running activity in free running mice. Light exposure resulted in a robust shift in the onset of activity in vehicle treated animals at both times tested. Administration of JNJ-18038683 significantly attenuated the light-induced phase delay and completely blocked the phase advance. The current study demonstrates that pharmacological blockade of the 5-HT7 receptor by JNJ-18038683 blunts both non-photic and photic phase shifts of circadian wheel running activity in mice. These findings highlight the importance of the 5-HT7 receptor in modulating circadian rhythms. Due to the opposite modulating effects of light resetting between diurnal and nocturnal species, pharmacotherapy targeting the 5-HT7 receptor in conjunction with bright light therapy may prove therapeutically beneficial by correcting the desynchronization of internal rhythms observed in depressed individuals.

  14. Review of selective accumudation of photosensitizers with different chemical structure in tumor tissue

    Directory of Open Access Journals (Sweden)

    E. A. Machinskaya

    2013-01-01

    Full Text Available The review of available theories explaining mechanisms of photosensitizer selective accumulation in tumor tissue is represented in the article. Variants associated with both targeted delivery of compounds with different chemical structure to tumor and low elimination rate of photosensitizers in the tumor are described. Details of tumor cell up-take of photosensitizer bounded with lipoproteins due to increased expression of low solidity lipoproteins receptors comparing with normal cells; mechanisms of photosensitizer accumulation in tumor tissue due to phagocytosis by macrophages localized in this area; mechanisms of binding of porphyrin-based photosensitizer by collagen fibers, production of which is increased in tumor cells, and other mechanisms are reviewed. Perspectives of practical application of knowledge about mechanisms of selective accumulation for induced increase in selectiveness of photosensitizer accumulation in tumor through targeted delivery of agent to pathological tissues are shown. Analysis of world trends in the search of transport systems for photosensitizers is performed. 

  15. Characterization of mu s-ms dynamics of proteins using a combined analysis of N-15 NMR relaxation and chemical shift: Conformational exchange in plastocyanin induced by histidine protonations

    DEFF Research Database (Denmark)

    Hass, M. A. S.; Thuesen, Marianne Hallberg; Christensen, Hans Erik Mølager

    2004-01-01

    An approach is presented that allows a detailed, quantitative characterization of conformational exchange processes in proteins on the mus-ms time scale. The approach relies on a combined analysis of NMR relaxation rates and chemical shift changes and requires that the chemical shift...... variabilis (A.v. PCu) (Ma, L.; Hass, M. A. S.; Vierick, N.; Kristensen, S. M.; Ulstrup, J.; Led, J. J. Biochemistry 2003, 42, 320-330). The R-1 and R-2 relaxation rates of the backbone N-15 nuclei were measured at a series of pH and temperatures on an 15N labeled sample of A.v. PCu, and the 15 N chemical...... quantitatively by the correlation between the R-ex terms and the corresponding chemical shift differences of the exchanging species. By this approach, the R-ex terms of N-15 nuclei belonging to contiguous regions in the protein could be assigned to the same exchange process. Furthermore, the analysis...

  16. Stereochemistry of Complex Marine Natural Products by Quantum Mechanical Calculations of NMR Chemical Shifts: Solvent and Conformational Effects on Okadaic Acid

    Directory of Open Access Journals (Sweden)

    Humberto J. Domínguez

    2014-01-01

    Full Text Available Marine organisms are an increasingly important source of novel metabolites, some of which have already inspired or become new drugs. In addition, many of these molecules show a high degree of novelty from a structural and/or pharmacological point of view. Structure determination is generally achieved by the use of a variety of spectroscopic methods, among which NMR (nuclear magnetic resonance plays a major role and determination of the stereochemical relationships within every new molecule is generally the most challenging part in structural determination. In this communication, we have chosen okadaic acid as a model compound to perform a computational chemistry study to predict 1H and 13C NMR chemical shifts. The effect of two different solvents and conformation on the ability of DFT (density functional theory calculations to predict the correct stereoisomer has been studied.

  17. Species Selection Favors Dispersive Life Histories in Sea Slugs, but Higher Per-Offspring Investment Drives Shifts to Short-Lived Larvae.

    Science.gov (United States)

    Krug, Patrick J; Vendetti, Jann E; Ellingson, Ryan A; Trowbridge, Cynthia D; Hirano, Yayoi M; Trathen, Danielle Y; Rodriguez, Albert K; Swennen, Cornelis; Wilson, Nerida G; Valdés, Ángel A

    2015-11-01

    For 40 years, paleontological studies of marine gastropods have suggested that species selection favors lineages with short-lived (lecithotrophic) larvae, which are less dispersive than long-lived (planktotrophic) larvae. Although lecithotrophs appeared to speciate more often and accumulate over time in some groups, lecithotrophy also increased extinction rates, and tests for state-dependent diversification were never performed. Molecular phylogenies of diverse groups instead suggested lecithotrophs accumulate without diversifying due to frequent, unidirectional character change. Although lecithotrophy has repeatedly originated in most phyla, no adult trait has been correlated with shifts in larval type. Thus, both the evolutionary origins of lecithotrophy and its consequences for patterns of species richness remain poorly understood. Here, we test hypothesized links between development mode and evolutionary rates using likelihood-based methods and a phylogeny of 202 species of gastropod molluscs in Sacoglossa, a clade of herbivorous sea slugs. Evolutionary quantitative genetics modeling and stochastic character mapping supported 27 origins of lecithotrophy. Tests for correlated evolution revealed lecithotrophy evolved more often in lineages investing in extra-embryonic yolk, the first adult trait associated with shifts in development mode across a group. However, contrary to predictions from paleontological studies, species selection actually favored planktotrophy; most extant lecithotrophs originated through recent character change, and did not subsequently diversify. Increased offspring provisioning in planktotrophs thus favored shifts to short-lived larvae, which led to short-lived lineages over macroevolutionary time scales. These findings challenge long-standing assumptions about the effects of alternative life histories in the sea. Species selection can explain the long-term persistence of planktotrophy, the ancestral state in most clades, despite frequent

  18. Examination of anticipated chemical shift and shape distortion effect on materials commonly used in prosthetic socket fabrication when measured using MRI: a validation study.

    Science.gov (United States)

    Safari, Mohammad Reza; Rowe, Philip; Buis, Arjan

    2013-01-01

    The quality of lower-limb prosthetic socket fit is influenced by shape and volume consistency during the residual limb shape-capturing process (i.e., casting). Casting can be quantified with magnetic resonance imaging (MRI) technology. However, chemical shift artifact and image distortion may influence the accuracy of MRI when common socket/casting materials are used. We used a purpose-designed rig to examine seven different materials commonly used in socket fabrication during exposure to MRI. The rig incorporated glass marker tubes filled with water doped with 1 g/L copper sulfate (CS) and 9 plastic sample vials (film containers) to hold the specific material specimens. The specimens were scanned 9 times in different configurations. The absolute mean difference of the glass marker tube length was 1.39 mm (2.98%) (minimum = 0.13 mm [0.30%], maximum = 5.47 mm [14.03%], standard deviation = 0.89 mm). The absolute shift for all materials was <1.7 mm. This was less than the measurement tolerance of +/-2.18 mm based on voxel (three-dimensional pixel) dimensions. The results show that MRI is an accurate and repeatable method for dimensional measurement when using matter containing water. Additionally, silicone and plaster of paris plus 1 g/L CS do not show a significant shape distortion nor do they interfere with the MRI image of the residual limb.

  19. Examination of anticipated chemical shift and shape distortion effect on materials commonly used in prosthetic socket fabrication when measured using MRI: A validation study

    Directory of Open Access Journals (Sweden)

    Mohammad Reza Safari, PhD

    2013-02-01

    Full Text Available The quality of lower-limb prosthetic socket fit is influenced by shape and volume consistency during the residual limb shape-capturing process (i.e., casting. Casting can be quantified with magnetic resonance imaging (MRI technology. However, chemical shift artifact and image distortion may influence the accuracy of MRI when common socket/casting materials are used. We used a purpose-designed rig to examine seven different materials commonly used in socket fabrication during exposure to MRI. The rig incorporated glass marker tubes filled with water doped with 1 g/L copper sulfate (CS and 9 plastic sample vials (film containers to hold the specific material specimens. The specimens were scanned 9 times in different configurations. The absolute mean difference of the glass marker tube length was 1.39 mm (2.98% (minimum = 0.13 mm [0.30%], maximum = 5.47 mm [14.03%], standard deviation = 0.89 mm. The absolute shift for all materials was <1.7 mm. This was less than the measurement tolerance of +/–2.18 mm based on voxel (three-dimensional pixel dimensions. The results show that MRI is an accurate and repeatable method for dimensional measurement when using matter containing water. Additionally, silicone and plaster of paris plus 1 g/L CS do not show a significant shape distortion nor do they interfere with the MRI image of the residual limb.

  20. Study of the Chemical Space of Selected Bacteriostatic Sulfonamides from an Information Theory Point of View.

    Science.gov (United States)

    López-Rosa, Sheila; Molina-Espíritu, Moyocoyani; Esquivel, Rodolfo O; Soriano-Correa, Catalina; Dehesa, Jésus S

    2016-12-05

    The relative structural location of a selected group of 27 sulfonamide-like molecules in a chemical space defined by three information theory quantities (Shannon entropy, Fisher information, and disequilibrium) is discussed. This group is composed of 15 active bacteriostatic molecules, 11 theoretically designed ones, and para-aminobenzoic acid. This endeavor allows molecules that share common chemical properties through the molecular backbone, but with significant differences in the identity of the chemical substituents, which might result in bacteriostatic activity, to be structurally classified and characterized. This is performed by quantifying the structural changes on the electron density distribution due to different functional groups and number of electrons. The macroscopic molecular features are described by means of the entropy-like notions of spatial electronic delocalization, order, and uniformity. Hence, an information theory three-dimensional space (IT-3D) emerges that allows molecules with common properties to be gathered. This space witnesses the biological activity of the sulfonamides. Some structural aspects and information theory properties can be associated, as a result of the IT-3D chemical space, with the bacteriostatic activity of these molecules. Most interesting is that the active bacteriostatic molecules are more similar to para-aminobenzoic acid than to the theoretically designed analogues.

  1. Efficient and selective chemical transformations under flow conditions: The combination of supported catalysts and supercritical fluids

    Directory of Open Access Journals (Sweden)

    M. Isabel Burguete

    2011-09-01

    Full Text Available This paper reviews the current trends in the combined use of supported catalytic systems, either on solid supports or in liquid phases and supercritical fluids (scFs, to develop selective and enantioselective chemical transformations under continuous and semi-continuous flow conditions. The results presented have been selected to highlight how the combined use of those two elements can contribute to: (i Significant improvements in productivity as a result of the enhanced diffusion of substrates and reagents through the interfaces favored by the scF phase; (ii the long term stability of the catalytic systems, which also contributes to the improvement of the final productivity, as the use of an appropriate immobilization strategy facilitates catalyst isolation and reuse; (iii the development of highly efficient selective or, when applicable, enantioselective chemical transformations. Although the examples reported in the literature and considered in this review are currently confined to a limited number of fields, a significant development in this area can be envisaged for the near future due to the clear advantages of these systems over the conventional ones.

  2. Size-selective predation and predator-induced life-history shifts alter the outcome of competition between planktonic grazers

    NARCIS (Netherlands)

    Hülsmann, S.; Rinke, K.; Mooij, W.M.

    2011-01-01

    1.We studied the effect of size-selective predation on the outcome of competition between two differently sized prey species in a homogenous environment. 2. Using a physiologically structured population model, we calculated equilibrium food concentrations for a range of predation scenarios defined b

  3. Physical, chemical, and biological data for selected streams in Chester County, Pennsylvania, 1995-97

    Science.gov (United States)

    Reif, Andrew G.

    2000-01-01

    Physical, chemical, and biological data were collected at 51 sampling sites in Chester County, Pa., from 1970 through 1997 as part of the Stream Conditions of Chester County Program. This report presents data collected from 43 sites from 1995 through 1997 that constitute a continuation of the program. Physical data include water temperature, instantaneous stream discharge, pH, alkalinity, specific conductance, and dissolved oxygen. Chemical data collected include laboratory determinations of nutrients and major ions in whole water samples and selected metals, pesticides, gross polychlorinated biphenyls (PCB's), gross polychlorinated napthalenes (PCN's), and total carbon in stream-sediment samples. The biological data include benthic-macroinvertebrate populations. The data are presented without interpretation. Chester County is undergoing urbanization as agricultural land is converted to residential developments, commercial areas, and industrial and corporate parks. The major goal of the Stream Conditions of Chester County Program is to further the understanding of stream changes in response to urbanization.

  4. Diffusion, Thermal Properties and Chemical Compatibilities of Select MAX Phases with Materials For Advanced Nuclear Systems

    Energy Technology Data Exchange (ETDEWEB)

    Barsoum, Michel [Drexel Univ., Philadelphia, PA (United States); Bentzel, Grady [Drexel Univ., Philadelphia, PA (United States); Tallman, Darin J. [Drexel Univ., Philadelphia, PA (United States); Sindelar, Robert [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL); Garcia-Diaz, Brenda [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL); Hoffman, Elizabeth [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL)

    2016-04-04

    The demands of Gen IV nuclear power plants for long service life under neutron irradiation at high temperature are severe. Advanced materials that would withstand high temperatures (up to 1000+ ºC) to high doses in a neutron field would be ideal for reactor internal structures and would add to the long service life and reliability of the reactors. The objective of this work is to investigate the chemical compatibility of select MAX with potential materials that are important for nuclear energy, as well as to measure the thermal transport properties as a function of neutron irradiation. The chemical counterparts chosen for this work are: pyrolytic carbon, SiC, U, Pd, FLiBe, Pb-Bi and Na, the latter 3 in the molten state. The thermal conductivities and heat capacities of non-irradiated MAX phases will be measured.

  5. Chemical proteomics with sulfonyl fluoride probes reveals selective labeling of functional tyrosines in glutathione transferases.

    Science.gov (United States)

    Gu, Christian; Shannon, D Alexander; Colby, Tom; Wang, Zheming; Shabab, Mohammed; Kumari, Selva; Villamor, Joji Grace; McLaughlin, Christopher J; Weerapana, Eranthie; Kaiser, Markus; Cravatt, Benjamin F; van der Hoorn, Renier A L

    2013-04-18

    Chemical probes have great potential for identifying functional residues in proteins in crude proteomes. Here we studied labeling sites of chemical probes based on sulfonyl fluorides (SFs) on plant and animal proteomes. Besides serine proteases and many other proteins, SF-based probes label Tyr residues in glutathione transferases (GSTs). The labeled GSTs represent four different GST classes that share less than 30% sequence identity. The targeted Tyr residues are located at similar positions in the promiscuous substrate binding site and are essential for GST function. The high selectivity of SF-based probes for functional Tyr residues in GSTs illustrates how these probes can be used for functional studies of GSTs and other proteins in crude proteomes.

  6. Highly Chemical and Regio-selective Catalytic Oxidation with a Novel Manganese Catalyst

    Institute of Scientific and Technical Information of China (English)

    刘斌; 陈怡; 余成志; 沈征武

    2003-01-01

    The chemical selectivity of a novel active manganese compound [Mn2IVμ-O)3(TMTACN)2] (PF6)2 (1) in catalytic oxidation reactions depended on the structure of substrates and 1 was able to catalyze the oxidation of toluene into benzaldehyde and/or benzoic acid under very mild conditions. The following results were obtained: (1) The selectivity of the oxidation depended on the electronic density of double bonds. Reactivity was absent when strong electron-witherawing groups were conjugated with double bonds. (2) Allylic oxidation reactions mostly take place when double bond is present inside a ring system, whilst epoxiclarion reactions occur when the alkene moiety is part of linear chain. (3) In ring systems, the methylene group was more likely to be oxidized than the methyl group on ailylic position. As expected, the C--H bonds at the bridgeheads were unreactive.The secondary hydroxyl groups are more easily to be oxidized than the primary hydroxyl groups.

  7. Selecting the right bird model in experimental studies on endocrine disrupting chemicals

    Directory of Open Access Journals (Sweden)

    Veerle L.B. Jaspers

    2015-05-01

    Full Text Available Birds have been used as model species in ecotoxicological research for decades but have only recently been included in toxicity testing schemes. However, the avian fauna is very diverse. Given this diversity the ecology, behavior and reproduction should be considered when selecting the appropriate bird model in ecotoxicological studies. This article focusses on choosing the right bird model species for experimental studies with endocrine disrupting chemicals (EDCs. EDCs have been associated with adverse effects on the reproduction and development in birds and other wildlife. In addition, new EDCs continue to emerge and the concern for potential effects in humans and wildlife is calling for increased toxicity testing and hence appropriate model species. Common bird model species used in ecotoxicological studies investigating EDCs will be reviewed. In addition, considerations for selecting the right bird model, along with potential drawbacks and restrictions on the use of certain species will be discussed.

  8. Measurement of the principal values of the chemical-shift tensors of overlapping protonated and unprotonated carbons with the 2D-SUPER technique and dipolar dephasing (DD-SUPER)

    Science.gov (United States)

    Liu, Wei; Wang, Wei D.; Wang, Wei; Bai, Shi; Dybowski, Cecil

    2010-09-01

    A modified 2D-SUPER technique is demonstrated to allow independent measurement of the principal values of the chemical-shift tensors of overlapping protonated and unprotonated carbons. The insertion of a dipolar-dephasing period into the sequence causes loss of signal from protonated carbons. The spectrum obtained with this modification allows one to determine the principal values of the unprotonated carbons with high precision. Subsequent fitting of the usual 2D-SUPER spectrum, with the chemical-shift parameters of the unprotonated carbons fixed, gives the parameters of the overlapped resonances of the protonated carbons. As an example, we report the determination of the 13C chemical-shift parameters of the carbons of form II of piroxicam. The experimental results are compared with those obtained from calculations using the DFT/GIAO method. Potential applications of this method are discussed.

  9. Antioxidant and chemical properties of essential oil extracted from blend of selected spices

    Institute of Scientific and Technical Information of China (English)

    Ochuko Lucky Erukainure; Funmi Olabisi Kayode; Olubanke Adetutu Adeyoju; Sunday Oluwaseun Adenekan; Godfrey Asieba; Atinuke Ajayi; Mosebolatan Victoria Adegbola; Bolanle Basirat Sarumi

    2015-01-01

    Objective:To investigate the chemical properties of essential oil extracted from blends of selected Nigerian spices as well as its antioxidant protective potentials against free radicalin vitro. Methods: Essential oil was extracted from selected spices blend consisting ofMonodora myristica, Myristica fragrans, Tetrapleura tetraptera, andAframomum sceptrum using a Clevenger type apparatus. Oil obtained was subjected to phytochemical and gas chromatography-mass spectrometer analysis as well as analyzed for antioxidant activity which covers for 1,1-diphenyl-2 picrylhydrazyl, nitric oxide scavenging activities and reducing property. Results: Gas chromatography-mass spectrometer analysis revealed over 50 compoundfs withα-phellandrene being the most predominant compound (27.32%), which was followed by (-)-β-bourbonene (15.78%) and 5-(1-methylethyl)-α-phellandrene (11.80%). Phytochemical analysis showed high flavonoid content and a lower phenolic content. The oil showed a dose like dependent effect on the1-diphenyl-2 picrylhydrazyl and nitric oxide scavenging activities, these activities increased with increasing concentration. The same was also observed for the reducing power properties of the oil. Conclusions: The antioxidant activities exhibited by the essential oilin vitro signify its protective potential against free radicals. The chemical constituents,α-phellandrene in particular and the studied phytochemicals may be responsible for these effects. However,in vivo study is needed to further authenticate this potency.

  10. Exact probability distributions of selected species in stochastic chemical reaction networks.

    Science.gov (United States)

    López-Caamal, Fernando; Marquez-Lago, Tatiana T

    2014-09-01

    Chemical reactions are discrete, stochastic events. As such, the species' molecular numbers can be described by an associated master equation. However, handling such an equation may become difficult due to the large size of reaction networks. A commonly used approach to forecast the behaviour of reaction networks is to perform computational simulations of such systems and analyse their outcome statistically. This approach, however, might require high computational costs to provide accurate results. In this paper we opt for an analytical approach to obtain the time-dependent solution of the Chemical Master Equation for selected species in a general reaction network. When the reaction networks are composed exclusively of zeroth and first-order reactions, this analytical approach significantly alleviates the computational burden required by simulation-based methods. By building upon these analytical solutions, we analyse a general monomolecular reaction network with an arbitrary number of species to obtain the exact marginal probability distribution for selected species. Additionally, we study two particular topologies of monomolecular reaction networks, namely (i) an unbranched chain of monomolecular reactions with and without synthesis and degradation reactions and (ii) a circular chain of monomolecular reactions. We illustrate our methodology and alternative ways to use it for non-linear systems by analysing a protein autoactivation mechanism. Later, we compare the computational load required for the implementation of our results and a pure computational approach to analyse an unbranched chain of monomolecular reactions. Finally, we study calcium ions gates in the sarco/endoplasmic reticulum mediated by ryanodine receptors.

  11. Antioxidant and chemical properties of essential oil extracted from blend of selected spices

    Directory of Open Access Journals (Sweden)

    Ochuko Lucky Erukainure

    2015-07-01

    Full Text Available Objective: To investigate the chemical properties of essential oil extracted from blends of selected Nigerian spices as well as its antioxidant protective potentials against free radical in vitro. Methods: Essential oil was extracted from selected spices blend consisting of Monodora myristica, Myristica fragrans, Tetrapleura tetraptera, and Aframomum sceptrum using a Clevenger type apparatus. Oil obtained was subjected to phytochemical and gas chromatography-mass spectrometer analysis as well as analyzed for antioxidant activity which covers for 1,1-diphenyl-2 picrylhydrazyl, nitric oxide scavenging activities and reducing property. Results: Gas chromatography-mass spectrometer analysis revealed over 50 compoundfs with α-phellandrene being the most predominant compound (27.32%, which was followed by (--β-bourbonene (15.78% and 5-(1-methylethyl-α-phellandrene (11.80%. Phytochemical analysis showed high flavonoid content and a lower phenolic content. The oil showed a dose like dependent effect on the1-diphenyl-2 picrylhydrazyl and nitric oxide scavenging activities, these activities increased with increasing concentration. The same was also observed for the reducing power properties of the oil. Conclusions: The antioxidant activities exhibited by the essential oil in vitro signify its protective potential against free radicals. The chemical constituents, α-phellandrene in particular and the studied phytochemicals may be responsible for these effects. However, in vivo study is needed to further authenticate this potency.

  12. Speciation of heavy metals in garden soils. Evidences from selective and sequential chemical leaching

    Energy Technology Data Exchange (ETDEWEB)

    Cheng, Zhongqi; Lee, Leda; Dayan, Sara; Grinshtein, Michael [Brooklyn College of The City Univ. of New York, Brooklyn, NY (United States). Environmental Sciences Analytical Cnter; Shaw, Richard [USDA-NRCS NYC Soil Survey, Staten Island, NY (United States)

    2011-06-15

    Purpose: Gardening (especially food growing) in urban areas is becoming popular, but urban soils are often very contaminated for historical reasons. There is lack of sufficient information as to the bioavailability of soil heavy metals to plants and human in urban environments. This study examines the relative leachability of Cr, Ni, As, Cd, Zn, and Pb for soils with varying characteristics. The speciation and mobility of these metals can be qualitatively inferred from the leaching experiments. The goal is to use the data to shed some light on their bioavailability to plant and human, as well as the basis for soil remediation. Materials and methods: Selective and sequential chemical leaching methods were both used to evaluate the speciation of Cr, Ni, As, Cd, Zn, and Pb in soil samples collected from New York City residential and community gardens. The sequential leaching experiment followed a standard BCR four-step procedure, while selective leaching involved seven different chemical extractants. Results and discussion: The results from selective and sequential leaching methods are consistent. In general, very little of the heavy metals were found in the easily soluble or exchangeable fractions. Larger fractions of Cd and Zn can be leached out than other metals. Lead appears predominantly in the organic or carbonate fractions, of which {proportional_to} 30-60% is in the easily soluble organic fraction. Most As cannot be leached out by any of the extractants used, but it could have been complicated by the ineffective dissolution of oxides by ammonium hydroxylamine. Ni and Cr were mostly in the residual fractions but some released in the oxidizable fractions. Therefore, the leachability of metals follow the order Cd/Zn > Pb > Ni/Cr. Conclusions: Despite of the controversy and inaccuracy surrounding chemical leaching methods for the speciation of metals, chemical leaching data provide important, general, and easy-to-access information on the mobility of heavy metals

  13. Advancing alternatives analysis: The role of predictive toxicology in selecting safer chemical products and processes.

    Science.gov (United States)

    Malloy, Timothy; Zaunbrecher, Virginia; Beryt, Elizabeth; Judson, Richard; Tice, Raymond; Allard, Patrick; Blake, Ann; Cote, Ila; Godwin, Hilary; Heine, Lauren; Kerzic, Patrick; Kostal, Jakub; Marchant, Gary; McPartland, Jennifer; Moran, Kelly; Nel, Andre; Oguseitan, Oladele; Rossi, Mark; Thayer, Kristina; Tickner, Joel; Whittaker, Margaret; Zarker, Ken

    2017-03-01

    Alternatives analysis (AA) is a method used in regulation and product design to identify, assess, and evaluate the safety and viability of potential substitutes for hazardous chemicals. It requires toxicological data for the existing chemical and potential alternatives. Predictive toxicology uses in silico and in vitro approaches, computational models, and other tools to expedite toxicological data generation in more cost-effective manner than traditional approaches. This article briefly reviews the challenges associated with using predictive toxicology in regulatory AA, then presents four recommendations for its advancement. It recommends using case studies to advance the integration of predictive toxicology into AA; adopting a stepwise process to employing predicative toxicology in AA beginning with prioritization of chemicals of concern; leveraging existing resources to advance the integration of predictive toxicology into the practice of AA, and supporting trans-disciplinary efforts. The further incorporation of predictive toxicology into AA would advance the ability of companies and regulators to select alternatives to harmful ingredients, and potentially increase the use of predictive toxicology in regulation more broadly. This article is protected by copyright. All rights reserved.

  14. Ecotoxicological and chemical characterization of selected treatment process effluents of municipal sewage treatment plant.

    Science.gov (United States)

    Wang, Chunxia; Wang, Yi; Kiefer, F; Yediler, A; Wang, Zijian; Kettrup, A

    2003-10-01

    The triolein-containing semipermeable membrane devices (SPMDs) were deployed for 4 weeks in a sewage treatment plant in Beijing, China, to sample and concentrate priority hydrophobic organic pollutants in a sewage treatment process. The chemical analyses and ecotoxicities of the residuals of SPMDs dialysate were examined. The data from the chemical analyses by gas chromatography-mass spectrometry selected ion monitoring mode indicated the lower removal for polychlorinated biphenyls (PCB) congeners and polycyclic aromatic hydrocarbons (PAHs) coincided with the persistence of them in the environment. The acute toxicity examined by bioluminescence test with Vibrio fischeri revealed approximately only 20% decrease in the overall toxicity of the influent after the activate sludge treatment process. The ethoxy resorufin-O-deethylase (EROD) induction with a micro-EROD assay in vitro using H4-IIE rat hepatoma cell cultures demonstrated the presence of persistent organics in influent and sequency effluents. Results obtained suggested that integration of the SPMD technique and chemical analyses and bioassay might be a valuable approach for the risk assessment of hydrophobic organic pollutants in water ecosystem. It revealed the necessity for organic pollutants monitoring and ecotoxicities examining of sewage treatment plants.

  15. Selection of the best chemical pretreatment for lignocellulosic substrate Prosopis juliflora.

    Science.gov (United States)

    Naseeruddin, Shaik; Srilekha Yadav, K; Sateesh, L; Manikyam, Ananth; Desai, Suseelendra; Venkateswar Rao, L

    2013-05-01

    Pretreatment is a pre-requisite step in bioethanol production from lignocellulosic biomass required to remove lignin and increase the porosity of the substrate for saccharification. In the present study, chemical pretreatment of Prosopis juliflora was performed using alkali (NaOH, KOH, and NH3), reducing agents (Na2S2O4, Na2SO3) and NaClO2 in different concentration ranges at room temperature (30±2 °C) to remove maximum lignin with minimum sugar loss. Further, biphasic acid hydrolysis of the various pretreated substrates was performed at mild temperatures. Considering the amount of holocellulose hydrolyzed and inhibitors released during hydrolysis, best chemical pretreatment was selected. Among all the chemicals investigated, pretreatment with sodium dithionite at concentration of 2% (w/v) removed maximum lignin (80.46±1.35%) with a minimum sugar loss (2.56±0.021%). Subsequent biphasic acid hydrolysis of the sodium dithionite pretreated substrate hydrolyzed 40.09±1.22% of holocellulose and released minimum amount of phenolics (1.04±0.022 g/L) and furans (0.41±0.012 g/L) in the hydrolysate.

  16. Chemical tagging of the Ursa Major moving group. A northern selection of FGK stars

    Science.gov (United States)

    Tabernero, H. M.; Montes, D.; González Hernández, J. I.; Ammler-von Eiff, M.

    2017-01-01

    Context. Stellar kinematic groups are kinematically coherent groups of stars that might have a common origin. These groups spread through the Galaxy over time owing to tidal effects caused by Galactic rotation and disk heating. However, the chemical information survives these processes. Aims: The information provided by analysis of chemical elements can reveal the origin of these kinematic groups. Here we investigate the origin of the stars that belong to the Ursa Major (UMa) moving group (MG). Methods: We present high-resolution spectroscopic observations obtained from three different spectrographs of kinematically selected FGK stars of the Ursa Major moving group. Stellar atmospheric parameters (Teff, log g, ξ, and [Fe/H]) were determined using our own automatic code (StePar), which makes use of the sensitivity of iron equivalent widths (EWs) measured in the spectra. We critically compared the StePar results with other methods (Teff values derived using the infrared flux method (IRFM) and log g values based on Hipparcos parallaxes). We derived the chemical abundances of 20 elements and their [X/Fe] ratios for all stars in the sample. We performed a differential abundance analysis with respect to a reference star of the UMa MG (HD 115043). We also carried out a systematic comparison of the abundance pattern of the Ursa Major MG and the Hyades SC with the thin disk stellar abundances. Results: Our chemical tagging analysis indicates that the Ursa Major MG is less affected by field star contamination than other moving groups (such as the Hyades SC). We find a roughly solar iron composition [Fe/H] = 0.03 ± 0.07 dex for the finally selected stars, whereas the [X/Fe] ratios are roughly subsolar except for super-solar Barium abundance. Conclusions: We conclude that 29 out of 44 (i.e., 66%) candidate stars have similar chemical compositions. In addition, we find that the abundance pattern of the Ursa Major MG might be marginally different from that of the Hyades SC

  17. Chemically Functionalized Arrays Comprising Micro and Nano-Electro-Mechanizal Systems for Reliable and Selective Characterization of Tank Waste

    Energy Technology Data Exchange (ETDEWEB)

    Michael J. Sepaniak

    2008-10-08

    Innovative technology of sensory and selective chemical monitoring of hazardous wastes present in storage tanks are of continued importance to the environment. This multifaceted research program exploits the unique characteristics of micro and nano-fabricated cantilever-based, micro-electro-mechanical systems (MEMES) and nano-electro-mechanical systems (NEMS) in chemical sensing.

  18. Acute pharmacologically induced shifts in serotonin availability abolish emotion-selective responses to negative face emotions in distinct brain networks

    DEFF Research Database (Denmark)

    Grady, Cheryl Lynn; Siebner, Hartwig R; Hornboll, Bettina

    2013-01-01

    enhanced the neural response of this set of regions to angry faces, relative to Control, and CIT also enhanced activity for neutral faces. The net effect of these changes in both networks was to abolish the selective response to fearful expressions. These results suggest that a normal level of serotonin...... distributed brain responses identified two brain networks with modulations of activity related to face emotion and serotonin level. The first network included the left amygdala, bilateral striatum, and fusiform gyri. During the Control session this network responded only to fearful faces; increasing serotonin...... decreased this response to fear, whereas reducing serotonin enhanced the response of this network to angry faces. The second network involved bilateral amygdala and ventrolateral prefrontal cortex, and these regions also showed increased activity to fear during the Control session. Both drug challenges...

  19. The effects of librations on the 13C chemical shift and 2H electric field gradient tensors in β-calcium formate

    Science.gov (United States)

    Hallock, Kevin J.; Lee, Dong Kuk; Ramamoorthy, A.

    2000-12-01

    The magnitudes and orientations of the principal elements of the 13C chemical shift anisotropy (CSA) tensor in the molecular frame of the formate ion in β-calcium formate is determined using one-dimensional dipolar-shift spectroscopy. The magnitudes of the principal elements of the 13C CSA tensor are σ11C=104 ppm, σ22C=179 ppm, and σ33C=233 ppm. The least shielding element of the 13C CSA tensor, σ33C, is found to be collinear with the C-H bond. The temperature dependence of the 13C CSA and the 2H quadrupole coupling tensors in β-calcium formate are analyzed for a wide range of temperature (173-373 K). It was found that the span of the 13C CSA and the magnitude of the 2H quadrupole coupling interactions are averaged with the increasing temperature. The experimental results also show that the 2H quadrupole coupling tensor becomes more asymmetric with increasing temperature. A librational motion about the σ22C axis of the 13C CSA tensor is used to model the temperature dependence of the 13C CSA tensor. The temperature dependence of the mean-square amplitude of the librational motion is found to be =2.6×10-4(T) rad2 K-1. The same librational motion also accounts for the temperature-dependence of the 2H quadrupole coupling tensor after the relative orientation of the 13C CSA and 2H electric field gradient tensors are taken into account. Reconsideration of the results of a previous study found that the librational motion, not the vibrational motion, accounts for an asymmetry in the 1H-13C dipolar coupling tensor of α-calcium formate at room temperature.

  20. A lanthanide complex with dual biosensing properties: CEST (chemical exchange saturation transfer) and BIRDS (biosensor imaging of redundant deviation in shifts) with europium DOTA-tetraglycinate.

    Science.gov (United States)

    Coman, Daniel; Kiefer, Garry E; Rothman, Douglas L; Sherry, A Dean; Hyder, Fahmeed

    2011-12-01

    Responsive contrast agents (RCAs) composed of lanthanide(III) ion (Ln3R) complexes with a variety of1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetate (DOTA4S) derivatives have shown great potential as molecular imaging agents for MR. A variety of LnDOTA–tetraamide complexes have been demonstrated as RCAs for molecular imaging using chemical exchange saturation transfer (CEST). The CEST method detects proton exchange between bulk water and any exchangeable sites on the ligand itself or an inner sphere of bound water that is shifted by a paramagnetic Ln3R ion bound in the core of the macrocycle. It has also been shown that molecular imaging is possible when the RCA itself is observed (i.e. not its effect on bulk water) using a method called biosensor imaging of redundant deviation in shifts (BIRDS). The BIRDS method utilizes redundant information stored in the nonexchangeable proton resonances emanating from the paramagnetic RCA for ambient factors such as temperature and/or pH.Thus, CEST and BIRDS rely on exchangeable and nonexchangeable protons, respectively, for biosensing. We posited that it would be feasible to combine these two biosensing features into the same RCA (i.e. dual CEST and BIRDS properties). A complex between europium(III) ion (Eu3R) and DOTA–tetraglycinate [DOTA–(gly)S4] was used to demonstrate that its CEST characteristics are preserved, while its BIRDS properties are also detectable. The in vitro temperature sensitivity of EuDOTA–(gly)S4 was used to show that qualitative MR contrast with CEST can be calibrated using quantitative MR mapping with BIRDS, thereby enabling quantitative molecular imaging at high spatial resolution.

  1. Concurrent Increases and Decreases in Local Stability and Conformational Heterogeneity in Cu, Zn Superoxide Dismutase Variants Revealed by Temperature-Dependence of Amide Chemical Shifts.

    Science.gov (United States)

    Doyle, Colleen M; Rumfeldt, Jessica A; Broom, Helen R; Sekhar, Ashok; Kay, Lewis E; Meiering, Elizabeth M

    2016-03-08

    The chemical shifts of backbone amide protons in proteins are sensitive reporters of local structural stability and conformational heterogeneity, which can be determined from their readily measured linear and nonlinear temperature-dependences, respectively. Here we report analyses of amide proton temperature-dependences for native dimeric Cu, Zn superoxide dismutase (holo pWT SOD1) and structurally diverse mutant SOD1s associated with amyotrophic lateral sclerosis (ALS). Holo pWT SOD1 loses structure with temperature first at its periphery and, while having extremely high global stability, nevertheless exhibits extensive conformational heterogeneity, with ∼1 in 5 residues showing evidence for population of low energy alternative states. The holo G93A and E100G ALS mutants have moderately decreased global stability, whereas V148I is slightly stabilized. Comparison of the holo mutants as well as the marginally stable immature monomeric unmetalated and disulfide-reduced (apo(2SH)) pWT with holo pWT shows that changes in the local structural stability of individual amides vary greatly, with average changes corresponding to differences in global protein stability measured by differential scanning calorimetry. Mutants also exhibit altered conformational heterogeneity compared to pWT. Strikingly, substantial increases as well as decreases in local stability and conformational heterogeneity occur, in particular upon maturation and for G93A. Thus, the temperature-dependence of amide shifts for SOD1 variants is a rich source of information on the location and extent of perturbation of structure upon covalent changes and ligand binding. The implications for potential mechanisms of toxic misfolding of SOD1 in disease and for general aspects of protein energetics, including entropy-enthalpy compensation, are discussed.

  2. Investigation into the Effect of Concentration of Benzotriazole on the Selective Layer Surface in the Chemical Mechanical Planarization Process

    Science.gov (United States)

    Ilie, Filip; Laurian, Tiberiu

    2015-12-01

    During selective layer chemical mechanical planarization (CMP), the surface layer is selectively oxidized and removed. Material removal rate in selective layer CMP depends on the depth of removal, pH of the solution, slurry chemistry, potential, percentage of oxidizer, and the applied load. Benzotriazole (BTA) has been used as a corrosion inhibitor in the CMP process. The role of BTA is to prevent corrosion of a pattern via a chemical reaction that forms a Cu-BTA passive film on the selective-layer surface. This paper focuses on the concentration effect of BTA in the slurry of a selective layer CMP process by measuring the friction force during CMP and the modification of the selective layer films immersed in slurries containing various concentrations of BTA. Additionally; the friction characteristics with the concentration of BTA in the selective layer CMP slurry. The effect of BTA concentration was verified using an empirical model based on the friction energy ( E f).

  3. Chemical variation in a dominant tree species: population divergence, selection and genetic stability across environments.

    Directory of Open Access Journals (Sweden)

    Julianne M O'Reilly-Wapstra

    Full Text Available Understanding among and within population genetic variation of ecologically important plant traits provides insight into the potential evolutionary processes affecting those traits. The strength and consistency of selection driving variability in traits would be affected by plasticity in differences among genotypes across environments (G×E. We investigated population divergence, selection and environmental plasticity of foliar plant secondary metabolites (PSMs in a dominant tree species, Eucalyptus globulus. Using two common garden trials we examined variation in PSMs at multiple genetic scales; among 12 populations covering the full geographic range of the species and among up to 60 families within populations. Significant genetic variation in the expression of many PSMs resides both among and within populations of E. globulus with moderate (e.g., sideroxylonal A h(2op = 0.24 to high (e.g., macrocarpal G h(2op = 0.48 narrow sense heritabilities and high coefficients of additive genetic variation estimated for some compounds. A comparison of Qst and Fst estimates suggest that variability in some of these traits may be due to selection. Importantly, there was no genetic by environment interaction in the expression of any of the quantitative chemical traits despite often significant site effects. These results provide evidence that natural selection has contributed to population divergence in PSMs in E. globulus, and identifies the formylated phloroglucinol compounds (particularly sideroxylonal and a dominant oil, 1,8-cineole, as candidates for traits whose genetic architecture has been shaped by divergent selection. Additionally, as the genetic differences in these PSMs that influence community phenotypes is stable across environments, the role of plant genotype in structuring communities is strengthened and these genotypic differences may be relatively stable under global environmental changes.

  4. Chemical Reaction Route Selection Based on Green Chemical Engineering%基于绿色化工的化学反应路径选择

    Institute of Scientific and Technical Information of China (English)

    何潮洪; 葛挺峰; S.H.Yang; D.W.Edwards

    2004-01-01

    In the preliminary stage of chemical process design, the choice of chemical reaction route is the key design decision, and the concepts of atom utilization and environmental quotient have become extremely useful tools. However, the waste quality such as chemical toxicity and other engineering factors have not been taken into account. Therefore, a synthetic route selection index, Iroute, is proposed to determine the suitability of a chemical route in this paper. Iroute considers the effects of "extended atom economy", material renewability, chemical characteristics and some engineering factors. The extended atom economy concept regards not only the value of the desired product but also the value of byproducts. The methodology by using Iroute to compare different routes is illustrated in case study of cyclohexanone oxime and acrylonitrile manufacture.

  5. Chemical constituents of Ottonia corcovadensis Miq. from Amazon forest: {sup 1}H and {sup 13}C chemical shift assignments; Constituintes quimicos de Ottonia corcovadensis Miq. da floresta Amazonica - atribuicao dos deslocamentos quimicos dos atomos de hidrogenio e carbono

    Energy Technology Data Exchange (ETDEWEB)

    Facundo, Valdir A. [Rondonia Univ., Porto Velho, RO (Brazil). Dept. de Quimica; Morais, Selene M. [Ceara Univ., Fortaleza, CE (Brazil). Dept. de Quimica e Fisica; Braz Filho, Raimundo [Universidade Estadual do Norte Fluminense (UENF), Campos dos Goytacases, RJ (Brazil). Setor de Quimica de Produtos Naturais. Lab. de Ciencias Quimicas. Setor de Quimica de Produtos Naturais]. E-mail: braz@uenf.br

    2004-02-01

    In an ethanolic extract of leaves of Ottonia corcovadensis (Piperaceae) were identified sixteen terpenoids of essential oil and the three flavonoids 3',4',5,5',7-penta methoxyflavone (1), 3',4',5,7-tetra methoxyflavone (2) and 5-hydroxy-3',4',5',7-tetra methoxyflavone (3) and cafeic acid (4). Two amides (5 and 6) were isolated from an ethanolic extract of the roots. The structures were established by spectral analysis, meanly NMR (1D and 2D) and mass spectra. Extensive NMR analysis was also used to complete {sup 1}H and {sup 13}C chemical shift assignments of the flavonoids and amides. The components of the essential oil were identified by computer library search, retention indices and visual interpretation of mass spectra. (author)

  6. Chemical library subset selection algorithms: a unified derivation using spatial statistics.

    Science.gov (United States)

    Hamprecht, Fred A; Thiel, Walter; van Gunsteren, Wilfred F

    2002-01-01

    If similar compounds have similar activity, rational subset selection becomes superior to random selection in screening for pharmacological lead discovery programs. Traditional approaches to this experimental design problem fall into two classes: (i) a linear or quadratic response function is assumed (ii) some space filling criterion is optimized. The assumptions underlying the first approach are clear but not always defendable; the second approach yields more intuitive designs but lacks a clear theoretical foundation. We model activity in a bioassay as realization of a stochastic process and use the best linear unbiased estimator to construct spatial sampling designs that optimize the integrated mean square prediction error, the maximum mean square prediction error, or the entropy. We argue that our approach constitutes a unifying framework encompassing most proposed techniques as limiting cases and sheds light on their underlying assumptions. In particular, vector quantization is obtained, in dimensions up to eight, in the limiting case of very smooth response surfaces for the integrated mean square error criterion. Closest packing is obtained for very rough surfaces under the integrated mean square error and entropy criteria. We suggest to use either the integrated mean square prediction error or the entropy as optimization criteria rather than approximations thereof and propose a scheme for direct iterative minimization of the integrated mean square prediction error. Finally, we discuss how the quality of chemical descriptors manifests itself and clarify the assumptions underlying the selection of diverse or representative subsets.

  7. The ECVAM international validation study on in vitro tests for acute skin irritation: selection of test chemicals.

    Science.gov (United States)

    Eskes, Chantra; Cole, Thomas; Hoffmann, Sebastian; Worth, Andrew; Cockshott, Amanda; Gerner, Ingrid; Zuang, Valérie

    2007-12-01

    The ECVAM-funded skin irritation validation study (SIVS) was initiated in 2003, with the aim to evaluate whether the EpiDerm, EPISKIN and the SIFT alternative methods were able to reliably identify skin irritant and non-irritant chemicals, and could therefore be candidates for replacing the rabbit Draize test for skin irritation. The primary goal of the study was to evaluate the predictive capacity of the assays with regard to the EU classification system, which employs the risk phrases, "R38", for skin irritants, and "no label" for non-irritants. A secondary objective was the retrospective analysis of the data, to assess whether the in vitro tests would be able to discriminate between strong irritants (category 2), mild irritants (category 3) and non-irritants (no category), as defined by the OECD and United Nations proposal for a Globally Harmonised System (GHS) for the classification and labelling of dermal irritancy. A Chemicals Selection Sub-Committee (CSSC) was appointed to identify test chemicals to be used in the SIVS, for which existing, high quality in vivo data were available, with which to correlate the in vitro measurements. Since chemicals from the European Centre for the Ecotoxicology and Toxicology of Chemicals (ECETOC) database of reference chemicals for skin irritation/skin corrosion had been extensively used in preceding studies, the CSSC made use of novel sources for potential test chemicals. The first source of chemicals screened was the New Chemicals Database (NCD), which is the central archive within the EU notification scheme for 'new' commercial chemicals. Data registered in the NCD originate from standard assays, submitted in compliance with the legislation which regulates the marketing of industrial chemicals, and are subject to quality assurance by the competent authorities of the EU Member States. In addition, to obtain 'existing' chemicals which were readily available from major manufacturing and/or distribution sources, additional

  8. Selective growth of graphene in layer-by-layer via chemical vapor deposition

    Science.gov (United States)

    Park, Jaehyun; An, Hyosub; Choi, Dong-Chul; Hussain, Sajjad; Song, Wooseok; An, Ki-Seok; Lee, Won-Jun; Lee, Naesung; Lee, Wan-Gyu; Jung, Jongwan

    2016-07-01

    Selective and precise control of the layer number of graphene remains a critical issue for the practical applications of graphene. First, it is highly challenging to grow a continuous and uniform few-layer graphene since once the monolayer graphene fully covers a copper (Cu) surface, the growth of the second layer stops, resulting in mostly nonhomogeneous films. Second, from the selective adlayer growth point of view, there is no clear pathway for achieving this. We have developed the selective growth of a graphene adlayer in layer-by-layer via chemical vapor deposition (CVD) which makes it possible to stack graphene on a specific position. The key idea is to deposit a thin Cu layer (~40 nm thick) on pre-grown monolayer graphene and to apply additional growth. The thin Cu atop the graphene/Cu substrate acts as a catalyst to decompose methane (CH4) gas during the additional growth. The adlayer is grown selectively on the pre-grown graphene, and the thin Cu is removed through evaporation during CVD, eventually forming large-area and uniform double layer graphene. With this technology, highly uniform graphene films with precise thicknesses of 1 to 5 layers and graphene check patterns with 1 to 3 layers were successfully demonstrated. This method provides precise LBL growth for a uniform graphene film and a technique for the design of new graphene devices.Selective and precise control of the layer number of graphene remains a critical issue for the practical applications of graphene. First, it is highly challenging to grow a continuous and uniform few-layer graphene since once the monolayer graphene fully covers a copper (Cu) surface, the growth of the second layer stops, resulting in mostly nonhomogeneous films. Second, from the selective adlayer growth point of view, there is no clear pathway for achieving this. We have developed the selective growth of a graphene adlayer in layer-by-layer via chemical vapor deposition (CVD) which makes it possible to stack graphene

  9. Noise tolerance in wavelength-selective switching of optical differential quadrature-phase-shift-keying pulse train by collinear acousto-optic devices.

    Science.gov (United States)

    Goto, Nobuo; Miyazaki, Yasumitsu

    2014-06-01

    Optical switching of high-bit-rate quadrature-phase-shift-keying (QPSK) pulse trains using collinear acousto-optic (AO) devices is theoretically discussed. Since the collinear AO devices have wavelength selectivity, the switched optical pulse trains suffer from distortion when the bandwidth of the pulse train is comparable to the pass bandwidth of the AO device. As the AO device, a sidelobe-suppressed device with a tapered surface-acoustic-wave (SAW) waveguide and a Butterworth-type filter device with a lossy SAW directional coupler are considered. Phase distortion of optical pulse trains at 40 to 100  Gsymbols/s in QPSK format is numerically analyzed. Bit-error-rate performance with additive Gaussian noise is also evaluated by the Monte Carlo method.

  10. Long-term effects of soil management practices on selected indicators of chemical soil quality

    Directory of Open Access Journals (Sweden)

    Alicja Pecio

    2016-06-01

    Full Text Available The study was conducted in scope of Catch-C project “Compatibility of agricultural management practices and types of farming in the EU to enhance climate change mitigation and soil health” (7FP, realized in 2012–2014 by the consortium of partners from 10 European countries (http://www.catch-c.eu. This work reports the effects of soil management practices – under different soil and climatic conditions – on the selected soil chemical quality indicators, based on the analysis of data extracted from literature on long term experiments (LTEs in Europe, as well as from LTEs held by the Catch-C consortium partners. The dataset related to soil chemical quality indicators consisted of 1044 records and referred to 59 long-term trials. The following indicators of chemical soil quality were analyzed: pH, N total content, N total stock, C:N ratio, N mineral content, P and K availability. They are the most frequently used indicators in the European literature on long-term experiments collected in the Catch-C project database. Soil organic carbon, however, the most important indicator was not presented here, due to it was covered by a separate study on indicators for climate change mitigation. The indicators were analyzed using their response ratio (RR to a management practice. For a given treatment (management practice, this ratio was calculated as the quotient between the indicator value obtained in the treatment, and the indicator value in the reference treatment. The examples were: rotation (with cereals, with legume crops, with tuber or root crops, with grassland vs. adequate monoculture, catch/cover crops vs. no catch/cover crops, no-tillage and no-inversion tillage vs. conventional tillage, mineral fertilization vs. no fertilization, organic fertilization (compost, farmyard manure, slurry vs. mineral fertilization at the same available nitrogen input, crop residue incorporation vs. removal. All tested practices influenced soil chemical quality

  11. Determination of the Orientation and Dynamics of Ergosterol in Model Membranes Using Uniform 13C Labeling and Dynamically Averaged 13C Chemical Shift Anisotropies as Experimental Restraints

    Science.gov (United States)

    Soubias, O.; Jolibois, F.; Massou, S.; Milon, A.; Réat, V.

    2005-01-01

    A new strategy was established to determine the average orientation and dynamics of ergosterol in dimyristoylphosphatidylcholine model membranes. It is based on the analysis of chemical shift anisotropies (CSAs) averaged by the molecular dynamics. Static 13C CSA tensors were computed by quantum chemistry, using the gauge-including atomic-orbital approach within Hartree-Fock theory. Uniformly 13C-labeled ergosterol was purified from Pichia pastoris cells grown on labeled methanol. After reconstitution into dimyristoylphosphatidylcholine lipids, the complete 1H and 13C assignment of ergosterol's resonances was performed using a combination of magic-angle spinning two-dimensional experiments. Dynamically averaged CSAs were determined by standard side-band intensity analysis for isolated 13C resonances (C3 and ethylenic carbons) and by off-magic-angle spinning experiments for other carbons. A set of 18 constraints was thus obtained, from which the sterol's molecular order parameter and average orientation could be precisely defined. The validity of using computed CSAs in this strategy was verified on cholesterol model systems. This new method allowed us to quantify ergosterol's dynamics at three molar ratios: 16 mol % (Ld phase), 30 mol % (Lo phase), and 23 mol % (mixed phases). Contrary to cholesterol, ergosterol's molecular diffusion axis makes an important angle (14°) with the inertial axis of the rigid four-ring system. PMID:15923221

  12. ¹³C solid-state NMR analysis of the most common pharmaceutical excipients used in solid drug formulations, Part I: Chemical shifts assignment.

    Science.gov (United States)

    Pisklak, Dariusz Maciej; Zielińska-Pisklak, Monika Agnieszka; Szeleszczuk, Łukasz; Wawer, Iwona

    2016-04-15

    Solid-state NMR is an excellent and useful method for analyzing solid-state forms of drugs. In the (13)C CP/MAS NMR spectra of the solid dosage forms many of the signals originate from the excipients and should be distinguished from those of active pharmaceutical ingredient (API). In this work the most common pharmaceutical excipients used in the solid drug formulations: anhydrous α-lactose, α-lactose monohydrate, mannitol, sucrose, sorbitol, sodium starch glycolate type A and B, starch of different origin, microcrystalline cellulose, hypromellose, ethylcellulose, methylcellulose, hydroxyethylcellulose, sodium alginate, magnesium stearate, sodium laurilsulfate and Kollidon(®) were analyzed. Their (13)C CP/MAS NMR spectra were recorded and the signals were assigned, employing the results (R(2): 0.948-0.998) of GIPAW calculations and theoretical chemical shifts. The (13)C ssNMR spectra for some of the studied excipients have not been published before while for the other signals in the spectra they were not properly assigned or the assignments were not correct. The results summarize and complement the data on the (13)C ssNMR analysis of the most common pharmaceutical excipients and are essential for further NMR studies of API-excipient interactions in the pharmaceutical formulations.

  13. Reproducibility of Intra- and Inter-scanner Measurements of Liver Fat Using Complex Confounder-corrected Chemical Shift Encoded MRI at 3.0 Tesla

    Science.gov (United States)

    Wu, Bing; Han, Wei; Li, Zhenhong; Zhao, Yonghua; Ge, Mingmei; Guo, Xueqing; Wu, Xinhuai

    2016-01-01

    The purpose of this study was to prospectively evaluate the reproducibility of the proton density fat-fraction (PDFF) of the liver using the IDEAL algorithm, a quantitative confounder-corrected chemical-shift-encoded MRI method. Data were obtained from 15 volunteers on four different days. The first and the third examinations were conducted on scanner one with one-week intervals, while the second and the fourth tests were performed on scanner two with same time interval. For each test, two MR scans were performed, one before and one after a meal. Regions-of-interest measurements were manually calculated to estimate the PDFF in the right and left lobes on the PDFF images. Reproducibility was measured using the intra-class correlation coefficient (ICC). The ICCs of the PDFF in the right and left lobes were 0.935 and 0.878, respectively. The intra-scanner ICCs of the right lobe before and after a meal or at a one-week interval were 0.924 and 0.953, respectively. The inter-scanner ICCs of PDFF the next day and at a one-week interval were 0.920 and 0.864, respectively. The PDFF of liver derived from IDEAL demonstrated high intra- and inter-scanner measurement reproducibility. The PDFF of the right lobe before a meal was more reproducible than after-meal measurements. PMID:26763303

  14. Scan time reduction in {sup 23}Na-Magnetic Resonance Imaging using the chemical shift imaging sequence. Evaluation of an iterative reconstruction method

    Energy Technology Data Exchange (ETDEWEB)

    Weingaertner, Sebastian; Konstandin, Simon; Schad, Lothar R. [Heidelberg Univ., Mannheim (Germany). Computer Assisted Clinical Medicine; Wetterling, Friedrich [Heidelberg Univ., Mannheim (Germany). Computer Assisted Clinical Medicine; Dublin Univ. (Ireland) Trinity Inst. of Neuroscience; Fatar, Marc [Heidelberg Univ., Mannheim (Germany). Dept. of Neurology; Neumaier-Probst, Eva [Heidelberg Univ., Mannheim (Germany). Dept. of Neuroradiology

    2015-07-01

    To evaluate potential scan time reduction in {sup 23}Na-Magnetic Resonance Imaging with the chemical shift imaging sequence (CSI) using undersampled data of high-quality datasets, reconstructed with an iterative constrained reconstruction, compared to reduced resolution or reduced signal-to-noise ratio. CSI {sup 23}Na-images were retrospectively undersampled and reconstructed with a constrained reconstruction scheme. The results were compared to conventional methods of scan time reduction. The constrained reconstruction scheme used a phase constraint and a finite object support, which was extracted from a spatially registered {sup 1}H-image acquired with a double-tuned coil. The methods were evaluated using numerical simulations, phantom images and in-vivo images of a healthy volunteer and a patient who suffered from cerebral ischemic stroke. The constrained reconstruction scheme showed improved image quality compared to a decreased number of averages, images with decreased resolution or circular undersampling with weighted averaging for any undersampling factor. Brain images of a stroke patient, which were reconstructed from three-fold undersampled k-space data, resulted in only minor differences from the original image (normalized root means square error < 12%) and an almost identical delineation of the stroke region (mismatch < 6%). The acquisition of undersampled {sup 23}Na-CSI images enables up to three-fold scan time reduction with improved image quality compared to conventional methods of scan time saving.

  15. Tribochemical interaction between nanoparticles and surfaces of selective layer during chemical mechanical polishing

    Energy Technology Data Exchange (ETDEWEB)

    Ilie, Filip, E-mail: filip@meca.omtr.pub.ro [Polytechnic University of Bucharest, Department of Machine Elements and Tribology (Romania)

    2013-11-15

    Nanoparticles have been widely used in polish slurries such as those in the chemical mechanical polishing (CMP) process. For understanding the mechanisms of CMP, an atomic force microscope (AFM) is used to characterize polished surfaces of selective layers, after a set of polishing experiments. To optimize the CMP polishing process, one needs to get information on the interaction between the nano-abrasive slurry nanoparticles and the surface of selective layer being polished. The slurry used in CMP process of the solid surfaces is slurry with large nanoparticle size colloidal silica sol nano-abrasives. Silica sol nano-abrasives with large nanoparticle are prepared and characterized by transmission electron microscopy, particles colloidal size, and Zeta potential in this paper. The movement of nanoparticles in liquid and the interaction between nanoparticles and solid surfaces coating with selective layer are very important to obtain an atomic alloy smooth surface in the CMP process. We investigate the nanoparticle adhesion and removal processes during CMP and post-CMP cleaning. The mechanical interaction between nanoparticles and the wafer surface was studied using a microcontact wear model. This model considers the nanoparticle effects between the polishing interfaces during load balancing. Experimental results on polishing and cleaning are compared with numerical analysis. This paper suggests that during post-CMP cleaning, a combined effort in chemical and mechanical interaction (tribochemical interactions) would be effective in removal of small nanoparticles during cleaning. For large nanoparticles, more mechanical forces would be more effective. CMP results show that the removal rate has been improved to 367 nm/min and root mean square (RMS) of roughness has been reduced from 4.4 to 0.80 nm. Also, the results show that the silica sol nano-abrasives about 100 nm are of higher stability (Zeta potential is −65 mV) and narrow distribution of nanoparticle

  16. Carbon dots (C-dots) from cow manure with impressive subcellular selectivity tuned by simple chemical modification.

    Science.gov (United States)

    D'Angelis do E S Barbosa, Cintya; Corrêa, José R; Medeiros, Gisele A; Barreto, Gabrielle; Magalhães, Kelly G; de Oliveira, Aline L; Spencer, John; Rodrigues, Marcelo O; Neto, Brenno A D

    2015-03-23

    Improved cellular selectivity for nucleoli staining was achieved by simple chemical modification of carbon dots (C-dots) synthesized from waste carbon sources such as cow manure (or from glucose). The C-dots were characterized and functionalized (amine-passivated) with ethylenediamine, affording amide bonds that resulted in bright green fluorescence. The new modified C-dots were successfully applied as selective live-cell fluorescence imaging probes with impressive subcellular selectivity and the ability to selectively stain nucleoli in breast cancer cell lineages (MCF-7). The C-dots were also tested in four other cellular models and showed the same cellular selection in live-cell imaging experiments.

  17. Chemical analysis of succinylacetone and 4-hydroxyphenyllactate in amniotic fluid using selective ion monitoring.

    Science.gov (United States)

    Jakobs, C; Sweetman, L; Nyhan, W L

    1984-01-01

    A method for the measurement of the concentration of succinylacetone and 4-hydroxyphenyllactic acid in amniotic fluid was developed for the prenatal diagnosis of hereditary tyrosinemia. Succinylacetone was converted to 5-methyl-3-isoxazolepropionic acid and isolated with 4-hydroxyphenyllactic acid by liquid partition chromatography and the trimethylsilyl derivatives quantified by ammonia chemical ionization selected ion monitoring gas chromatography-mass spectrometry with 2-hydroxy-n-caproic acid as the internal standard. The concentration of 4-hydroxyphenyllactic acid in normal amniotic fluid was 1.97 +/- 0.75 (S.D.) mumol/l while succinylacetone was undetectable. A pregnancy at risk for tyrosinemia type II was monitored. The concentration of 4-hydroxyphenyllactic acid was within the normal range and a healthy child was born.

  18. Comparative performances of selected chiral HPLC, SFC, and CE systems with a chemically diverse sample set.

    Science.gov (United States)

    Borman, Phil; Boughtflower, Bob; Cattanach, Kaye; Crane, Kathy; Freebairn, Keith; Jonas, Greg; Mutton, Ian; Patel, Asha; Sanders, Matt; Thompson, Duncan

    2003-01-01

    Pharmaceutical companies have a continuous need to resolve new racemates. Analysis may be required in aqueous and nonaqueous media, or in the presence of several different sets of potentially interfering compounds. There is often a preparative requirement. For these reasons analysts may require a number of different separation systems capable of resolving a given pair of enantiomers. We wished to improve upon existing approaches that address this situation and undertook a program of work to screen over 100 racemates, selected for their chemical diversity, on over 100 different chiral HPLC, SFC, and CE systems. Here we report results of this comparison and illustrate the use of rapid gradient screening as a valuable tool for chiral method development.

  19. Effect of selected spices on chemical and sensory markers in fortified rye-buckwheat cakes.

    Science.gov (United States)

    Przygodzka, Małgorzata; Zieliński, Henryk; Ciesarová, Zuzana; Kukurová, Kristina; Lamparski, Grzegorz

    2016-07-01

    The aim of this study was to find out the effect of selected spices on chemical and sensorial markers in cakes formulated on rye and light buckwheat flour fortified with spices. Among collection of spices, rye-buckwheat cakes fortified individually with cloves, nutmeg, allspice, cinnamon, vanilla, and spice mix revealed the highest sensory characteristics and overall quality. Cakes fortified with cloves, allspice, and spice mix showed the highest antioxidant capacity, total phenolics, rutin, and almost threefold higher available lysine contents. The reduced furosine content as well as free and total fluorescent intermediatory compounds were observed as compared to nonfortified cakes. The FAST index was significantly lowered in all cakes enriched with spices, especially with cloves, allspice, and mix. In contrast, browning index increased in compare to cakes without spices. It can be suggested that clove, allspice, vanilla, and spice mix should be used for production of safety and good quality cakes.

  20. Stirring competes with chemical induction in chiral selection of Langmuir monolayer domains

    Directory of Open Access Journals (Sweden)

    Petit-Garrido Nuria

    2013-08-01

    Full Text Available Chirality, the absence of mirror symmetry, can be equally invoked in relation to physical forces and chemical induction processes, yet a competition between these two types of influences is rarely reported. Here, we employ Langmuir monolayers of azobenzene surfactants as a prototypical self-assembled two-dimensional system in which chiral selection is controlled by the combined independent action of a chiral dopant and vortical stirring. The two effects can be arbitrarily coupled, either constructively or destructively, leading to a situation of perfect compensation. The induced enantiomorphic excess is measured in terms of the statistical imbalance of an ensemble of sub-millimeter monolayer domains, where achiral molecules self-assemble with a well-defined orientational chirality, which is unambiguously resolved using Brewster angle microscopy.

  1. Improving N(6)-methyladenosine site prediction with heuristic selection of nucleotide physical-chemical properties.

    Science.gov (United States)

    Zhang, Ming; Sun, Jia-Wei; Liu, Zi; Ren, Ming-Wu; Shen, Hong-Bin; Yu, Dong-Jun

    2016-09-01

    N(6)-methyladenosine (m(6)A) is one of the most common and abundant post-transcriptional RNA modifications found in viruses and most eukaryotes. m(6)A plays an essential role in many vital biological processes to regulate gene expression. Because of its widespread distribution across the genomes, the identification of m(6)A sites from RNA sequences is of significant importance for better understanding the regulatory mechanism of m(6)A. Although progress has been achieved in m(6)A site prediction, challenges remain. This article aims to further improve the performance of m(6)A site prediction by introducing a new heuristic nucleotide physical-chemical property selection (HPCS) algorithm. The proposed HPCS algorithm can effectively extract an optimized subset of nucleotide physical-chemical properties under the prescribed feature representation for encoding an RNA sequence into a feature vector. We demonstrate the efficacy of the proposed HPCS algorithm under different feature representations, including pseudo dinucleotide composition (PseDNC), auto-covariance (AC), and cross-covariance (CC). Based on the proposed HPCS algorithm, we implemented an m(6)A site predictor, called M6A-HPCS, which is freely available at http://csbio.njust.edu.cn/bioinf/M6A-HPCS. Experimental results over rigorous jackknife tests on benchmark datasets demonstrated that the proposed M6A-HPCS achieves higher success rates and outperforms existing state-of-the-art sequence-based m(6)A site predictors.

  2. Optimization of chemical structure of Schottky-type selection diode for crossbar resistive memory.

    Science.gov (United States)

    Kim, Gun Hwan; Lee, Jong Ho; Jeon, Woojin; Song, Seul Ji; Seok, Jun Yeong; Yoon, Jung Ho; Yoon, Kyung Jean; Park, Tae Joo; Hwang, Cheol Seong

    2012-10-24

    The electrical performances of Pt/TiO(2)/Ti/Pt stacked Schottky-type diode (SD) was systematically examined, and this performance is dependent on the chemical structures of the each layer and their interfaces. The Ti layers containing a tolerable amount of oxygen showed metallic electrical conduction characteristics, which was confirmed by sheet resistance measurement with elevating the temperature, transmission line measurement (TLM), and Auger electron spectroscopy (AES) analysis. However, the chemical structure of SD stack and resulting electrical properties were crucially affected by the dissolved oxygen concentration in the Ti layers. The lower oxidation potential of the Ti layer with initially higher oxygen concentration suppressed the oxygen deficiency of the overlying TiO(2) layer induced by consumption of the oxygen from TiO(2) layer. This structure results in the lower reverse current of SDs without significant degradation of forward-state current. Conductive atomic force microscopy (CAFM) analysis showed the current conduction through the local conduction paths in the presented SDs, which guarantees a sufficient forward-current density as a selection device for highly integrated crossbar array resistive memory.

  3. Selective production of chemicals from biomass pyrolysis over metal chlorides supported on zeolite.

    Science.gov (United States)

    Leng, Shuai; Wang, Xinde; Cai, Qiuxia; Ma, Fengyun; Liu, Yue'e; Wang, Jianguo

    2013-12-01

    Direct biomass conversion into chemicals remains a great challenge because of the complexity of the compounds; hence, this process has attracted less attention than conversion into fuel. In this study, we propose a simple one-step method for converting bagasse into furfural (FF) and acetic acid (AC). In this method, bagasse pyrolysis over ZnCl2/HZSM-5 achieved a high FF and AC yield (58.10%) and a 1.01 FF/AC ratio, but a very low yield of medium-boiling point components. However, bagasse pyrolysis using HZSM-5 alone or ZnCl2 alone still remained large amounts of medium-boiling point components or high-boiling point components. The synergistic effect of HZSM-5 and ZnCl2, which combines pyrolysis, zeolite cracking, and Lewis acid-selective catalysis results in highly efficient bagasse conversion into FF and AC. Therefore, our study provides a novel, simple method for directly converting biomass into high-yield useful chemical.

  4. A Comprehensive Framework for Surfactant Selection and Design for Emulsion Based Chemical Product Design

    DEFF Research Database (Denmark)

    Mattei, Michele; Kontogeorgis, Georgios; Gani, Rafiqul

    2014-01-01

    The manufacture of emulsified products is of increasing interest in the consumer oriented chemical indus-try. Several cosmetic, house-hold and pharmaceutical products are in the emulsified form when soldand/or they are expected to form an emulsion when used. Therefore, there is a need for the dev......The manufacture of emulsified products is of increasing interest in the consumer oriented chemical indus-try. Several cosmetic, house-hold and pharmaceutical products are in the emulsified form when soldand/or they are expected to form an emulsion when used. Therefore, there is a need...... ingredientsis consequently necessary to tackle this problem with computer-aided methods and tools. A compre-hensive framework for the selection and design of surfactants, the main responsible for the formationand the stability of emulsions, is presented here together with the modeling of the cloud point, a key......-property of nonionic surfactants, with a group-contribution model. The mathematical formulation of astandard product design problem is presented, together with the list of both the pure component prop-erties (related to nonionic surfactants) and the mixture properties (relevant to the overall products asan emulsion...

  5. The JaCVAM international validation study on the in vivo comet assay: Selection of test chemicals.

    Science.gov (United States)

    Morita, Takeshi; Uno, Yoshifumi; Honma, Masamitsu; Kojima, Hajime; Hayashi, Makoto; Tice, Raymond R; Corvi, Raffaella; Schechtman, Leonard

    2015-07-01

    The Japanese Center for the Validation of Alternative Methods (JaCVAM) sponsored an international prevalidation and validation study of the in vivo rat alkaline pH comet assay. The main objective of the study was to assess the sensitivity and specificity of the assay for correctly identifying genotoxic carcinogens, as compared with the traditional rat liver unscheduled DNA synthesis assay. Based on existing carcinogenicity and genotoxicity data and chemical class information, 90 chemicals were identified as primary candidates for use in the validation study. From these 90 chemicals, 46 secondary candidates and then 40 final chemicals were selected based on a sufficiency of carcinogenic and genotoxic data, differences in chemical class or genotoxic or carcinogenic mode of action (MOA), availability, price, and ease of handling. These 40 chemicals included 19 genotoxic carcinogens, 6 genotoxic non-carcinogens, 7 non-genotoxic carcinogens and 8 non-genotoxic non-carcinogens. "Genotoxicity" was defined as positive in the Ames mutagenicity test or in one of the standard in vivo genotoxicity tests (primarily the erythrocyte micronucleus assay). These chemicals covered various chemicals classes, MOAs, and genotoxicity profiles and were considered to be suitable for the purpose of the validation study. General principles of chemical selection for validation studies are discussed.

  6. Determination of the Tautomeric Equilibria of Pyridoyl Benzoyl -Diketones in the Liquid and Solid State through the use of Deuterium Isotope Effects on 1H and 13C NMR Chemical Shifts and Spin Coupling Constants

    DEFF Research Database (Denmark)

    Hansen, Poul Erik; Borisov, Eugeny V.; Lindon, John C.

    2015-01-01

    The tautomeric equilibria for 2-pyridoyl-, 3-pyridoyl-, and 4-pyridoyl-benzoyl methane have been investigated using deuterium isotope effects on 1H and 13C chemical shifts both in the liquid and the solid state. Equilibria are established both in the liquid and the solid state. In addition, in th...

  7. Chemically selective polymer substrate based direct isotope dilution alpha spectrometry of Pu.

    Science.gov (United States)

    Paul, Sumana; Pandey, Ashok K; Shah, R V; Aggarwal, S K

    2015-06-01

    Quantification of actinides in the complex environmental, biological, process and waste streams samples requires multiple steps like selective preconcentration and matrix elimination, solid source preparations generally by evaporation or electrodeposition, and finally alpha spectrometry. To minimize the sample manipulation steps, a membrane based isotope dilution alpha spectrometry method was developed for the determination of plutonium concentrations in the complex aqueous solutions. The advantages of this method are that it is Pu(IV) selective at 3M HNO3, high preconcentration factor can be achieved, and obviates the need of solid source preparation. For this, a thin phosphate-sulfate bifunctional polymer layer was anchored on the surface of microporous poly(ethersulfone) membrane by UV induced surface grafting. The thickness of the bifunctional layer on one surface of the poly(ethersulfone) membrane was optimized. The thickness, physical and chemical structures of the bifunctional layer were studied by secondary ionization mass spectrometry (SIMS), scanning electron microscopy (SEM) and SEM-EDS (energy-dispersive spectroscopy). The optimized membrane was used for preconcentration of Pu(IV) from aqueous solutions having 3-4M HNO3, followed by direct quantification of the preconcentrated Pu(IV) by isotope dilution alpha spectrometry using (238)Pu spike. The chemical recovery efficiency of Pu(IV) was found to be 86±3% below Pu(IV) loading capacity (1.08 μg in 2×1 cm(2)) of the membrane sample. The experiments with single representative actinides indicated that Am(III) did not sorb to significant extent (7%) but U(VI) sorbed with 78±3% efficiency from the solutions having 3M HNO3 concentration. However, Pu(IV) chemical recovery in the membrane remained unaffected from the solution containing 1:1000 wt. proportion of Pu(IV) to U(VI). Pu concentrations in the (U, Pu)C samples and in the irradiated fuel dissolver solutions were determined. The results thus obtained

  8. Feasibility study of the microforming combined with selective chemical vapor deposition

    Directory of Open Access Journals (Sweden)

    Koshimizu Kazushi

    2015-01-01

    Full Text Available Microforming has been received much attention in the recent decades due to the wide use of microparts in electronics and medical applications. For the further functionalization of these micro devices, high functional surfaces with noble metals and nanomaterials are strongly required in bio- and medical fields, such as bio-sensors. To realize an efficient manufacturing process, which can deform the submillimeter scale bulk structure and can construct the micro to nanometer scale structures in one process, the present study proposes a combined process of microforming for metal foils with a selective chemical vapor deposition (SCVD on the active surfaces of the working material. To demonstrate feasibility of this proposed process, feasibility of SCVD of functional materials onto active surfaces of titanium (Ti was investigated. CVD of iron (Fe and carbon nanotubes (CNTs which construct CNTs on the patterned surfaces of the active Ti and non-active Ti oxidation layers were conducted. Ti thin films on silicon substrate and Fe were used as working materials and functional materials respectively. CNTs were grown only on the Ti surface. Consequently, selectivity of the active surface of Ti to the synthesis of Fe particles in CVD was confirmed.

  9. Influence of temperature and chemical composition on phase transformations of selected oxide melts

    Directory of Open Access Journals (Sweden)

    J. Dobrovská

    2013-07-01

    Full Text Available The paper deals with structural changes of solid phase of selected oxide systems during their transition into liquid state. Analyses concerned poly-component systems forming basis of casting powders for CCM mould. Industrially used oxide system with prevailing contents of CaO–Al2O3–SiO2 components and with numerous accompanying admixtures was tested. Investigation was focused on temperatures, during which individual phases disappear and precipitate, as well as on influence of CaO content on phase composition at selected temperatures. The experiments were realised with use of original methodology consisting of shock cooling of the tested melt in liquid nitrogen. Thus obtained samples were further investigated by X-ray diffraction phase analyses at ambient temperatures. The obtained results provide additional data on physical-chemical properties of oxide systems, such as surface tension, viscosity, sintering intervals, etc., which can be used in technological practice for appropriate lubrication effect of casting powders in the mould.

  10. CHEMICALLY FABRICATED SILVER NANOPARTICLES ENHANCES THE ACTIVITY OF ANTIBIOTICS AGAINST SELECTED HUMAN BACTERIAL PATHOGENS

    Directory of Open Access Journals (Sweden)

    S. Thangapandiyan and P. Prema*

    2012-05-01

    Full Text Available Due to the outbreak of infectious diseases caused by different pathogenic bacteria and the development of antibiotic resistance, the pharmaceutical companies and the researchers are now searching for new unconventional antibacterial agents. Nanotechnology represents a modern and innovative approach to develop new formulations based on metallic nanoparticles with antimicrobial properties. The potential bioactivity of chemically fabricated silver nanoparticles has been extensively studied. However, the antibacterial activity of silver nanoparticles individually or in combination with different antibiotics has not been demonstrated. In the present investigations, the effect of silver nanoparticles on the antibacterial activity of different antibiotics was evaluated against selected human bacterial pathogens such as Staphylococcus aureus, Streptococcus epidermis, Escherichia coli, Pseudomonas aeruginosa, and Bacillus cereus by disc diffusion method. In the presence of sub - inhibitory concentration of silver nanoparticles (100µL/disc, the antibacterial activities of all antibiotics are increased from 1 mm to 10 mm. The maximum fold increase was noticed for vancomycin against Pseudomonas aeruginosa (66.67%, Escherichia coli (62.50%, and Staphylococcus aureus (46% followed by rifampicin against Bacillus cereus (66.67% and kanamycin against Streptococcus epidermis (25%. These results signify that the silver nanoparticles showed potential antibacterial action of ß-lactams, glycopeptides, aminoglycosides, sulphonamides suggesting a possible utilization of silver nanocompounds in combination therapy against selected pathogens used in the experiment.

  11. Structural Plasticity of Malaria Dihydroorotate Dehydrogenase Allows Selective Binding of Diverse Chemical Scaffolds

    Energy Technology Data Exchange (ETDEWEB)

    Deng, Xiaoyi; Gujjar, Ramesh; El Mazouni, Farah; Kaminsky, Werner; Malmquist, Nicholas A.; Goldsmith, Elizabeth J.; Rathod, Pradipsinh K.; Phillips, Margaret A.; (UWASH); (UTSMC)

    2010-01-20

    Malaria remains a major global health burden and current drug therapies are compromised by resistance. Plasmodium falciparum dihydroorotate dehydrogenase (PfDHODH) was validated as a new drug target through the identification of potent and selective triazolopyrimidine-based DHODH inhibitors with anti-malarial activity in vivo. Here we report x-ray structure determination of PfDHODH bound to three inhibitors from this series, representing the first of the enzyme bound to malaria specific inhibitors. We demonstrate that conformational flexibility results in an unexpected binding mode identifying a new hydrophobic pocket on the enzyme. Importantly this plasticity allows PfDHODH to bind inhibitors from different chemical classes and to accommodate inhibitor modifications during lead optimization, increasing the value of PfDHODH as a drug target. A second discovery, based on small molecule crystallography, is that the triazolopyrimidines populate a resonance form that promotes charge separation. These intrinsic dipoles allow formation of energetically favorable H-bond interactions with the enzyme. The importance of delocalization to binding affinity was supported by site-directed mutagenesis and the demonstration that triazolopyrimidine analogs that lack this intrinsic dipole are inactive. Finally, the PfDHODH-triazolopyrimidine bound structures provide considerable new insight into species-selective inhibitor binding in this enzyme family. Together, these studies will directly impact efforts to exploit PfDHODH for the development of anti-malarial chemotherapy.

  12. REMOVAL OF SELECTED CONGENERS OF POLYCYCLIC AROMATIC HYDROCARBONS FROM THE BOTTOM SEDIMENTS USING CHEMICAL OXIDATION

    Directory of Open Access Journals (Sweden)

    Sabina Książek

    2016-06-01

    Full Text Available Bottom sediments are the part of the aquatic ecosystem, which accumulates most of pollution emitted into environment and flowing into surface waters. This concerns of nutrients, heavy metals and Persistent Organic Pollutants, which include, among others, polycyclic aromatic hydrocarbons (PAHs. PAHs are toxic, carcinogenic mutagenic and teratogenic compounds. The aim of this study was to evaluate the usefulness of chemical oxidation to remove selected PAH contained in bottom sediments. Oxidation of the impurities were carried out using 30% solution of hydrogen peroxide and with the addition of H2O2 with the catalyst FeSO4x7H2O (the Fenton’s method. The efficiency of oxidation was evaluated on the basis of changes in the content of tested impurities, which was determined by gas chromatography coupled with the mass spectrometer (GC-MS after extraction of analytes from bottom sediments. Preliminary studies have shown the efficacy of the use of H2O2 and the Fenton’s method to remove of selected PAHs.

  13. Shifting Attention

    Science.gov (United States)

    Ingram, Jenni

    2014-01-01

    This article examines the shifts in attention and focus as one teacher introduces and explains an image that represents the processes involved in a numeric problem that his students have been working on. This paper takes a micro-analytic approach to examine how the focus of attention shifts through what the teacher and students do and say in the…

  14. Tough Shift

    DEFF Research Database (Denmark)

    Brewer, Robert S.; Verdezoto, Nervo; Holst, Thomas;

    2015-01-01

    in a student dormitory and found that players did not shift their electricity use, because they were unwilling to change their schedules and found it easier to focus on reducing electricity use. Based on our findings, we discuss the implications for encouraging shifting, and also the challenges of integrating...

  15. Chemical composition and enzymatic digestibility of sugarcane clones selected for varied lignin content

    Directory of Open Access Journals (Sweden)

    Masarin Fernando

    2011-12-01

    Full Text Available Abstract Background The recalcitrance of lignocellulosic materials is a major limitation for their conversion into fermentable sugars. Lignin depletion in new cultivars or transgenic plants has been identified as a way to diminish this recalcitrance. In this study, we assessed the success of a sugarcane breeding program in selecting sugarcane plants with low lignin content, and report the chemical composition and agronomic characteristics of eleven experimental hybrids and two reference samples. The enzymatic digestion of untreated and chemically delignified samples was evaluated to advance the performance of the sugarcane residue (bagasse in cellulosic-ethanol production processes. Results The ranges for the percentages of glucan, hemicellulose, lignin, and extractive (based on oven-dry biomass of the experimental hybrids and reference samples were 38% to 43%, 25% to 32%, 17% to 24%, and 1.6% to 7.5%, respectively. The samples with the smallest amounts of lignin did not produce the largest amounts of total polysaccharides. Instead, a variable increase in the mass of a number of components, including extractives, seemed to compensate for the reduction in lignin content. Hydroxycinnamic acids accounted for a significant part of the aromatic compounds in the samples, with p-coumaric acid predominating, whereas ferulic acid was present only in low amounts. Hydroxycinnamic acids with ester linkage to the hemicelluloses varied from 2.3% to 3.6%. The percentage of total hydroxycinnamic acids (including the fraction linked to lignin through ether linkages varied from 5.0% to 9.2%, and correlated to some extent with the lignin content. These clones released up to 31% of glucose after 72 hours of digestion with commercial cellulases, whereas chemically delignified samples led to cellulose conversion values of more than 80%. However, plants with lower lignin content required less delignification to reach higher efficiencies of cellulose conversion during

  16. Elucidation of Mechanisms and Selectivities of Metal-Catalyzed Reactions using Quantum Chemical Methodology.

    Science.gov (United States)

    Santoro, Stefano; Kalek, Marcin; Huang, Genping; Himo, Fahmi

    2016-05-17

    Quantum chemical techniques today are indispensable for the detailed mechanistic understanding of catalytic reactions. The development of modern density functional theory approaches combined with the enormous growth in computer power have made it possible to treat quite large systems at a reasonable level of accuracy. Accordingly, quantum chemistry has been applied extensively to a wide variety of catalytic systems. A huge number of problems have been solved successfully, and vast amounts of chemical insights have been gained. In this Account, we summarize some of our recent work in this field. A number of examples concerned with transition metal-catalyzed reactions are selected, with emphasis on reactions with various kinds of selectivities. The discussed cases are (1) copper-catalyzed C-H bond amidation of indoles, (2) iridium-catalyzed C(sp(3))-H borylation of chlorosilanes, (3) vanadium-catalyzed Meyer-Schuster rearrangement and its combination with aldol- and Mannich-type additions, (4) palladium-catalyzed propargylic substitution with phosphorus nucleophiles, (5) rhodium-catalyzed 1:2 coupling of aldehydes and allenes, and finally (6) copper-catalyzed coupling of nitrones and alkynes to produce β-lactams (Kinugasa reaction). First, the methodology adopted in these studies is presented briefly. The electronic structure method in the great majority of these kinds of mechanistic investigations has for the last two decades been based on density functional theory. In the cases discussed here, mainly the B3LYP functional has been employed in conjunction with Grimme's empirical dispersion correction, which has been shown to improve the calculated energies significantly. The effect of the surrounding solvent is described by implicit solvation techniques, and the thermochemical corrections are included using the rigid-rotor harmonic oscillator approximation. The reviewed examples are chosen to illustrate the usefulness and versatility of the adopted methodology in

  17. The use of chemical shift temperature gradients to establish the paramagnetic susceptibility tensor orientation: Implication for structure determination/refinement in paramagnetic metalloproteins

    Energy Technology Data Exchange (ETDEWEB)

    Xia Zhicheng; Nguyen, Bao D.; La Mar, Gerd N. [University of California, Department of Chemistry (United States)

    2000-06-15

    The use of dipolar shifts as important constraints in refining molecular structure of paramagnetic metalloproteins by solution NMR is now well established. A crucial initial step in this procedure is the determination of the orientation of the anisotropic paramagnetic susceptibility tensor in the molecular frame which is generated interactively with the structure refinement. The use of dipolar shifts as constraints demands knowledge of the diamagnetic shift, which, however, is very often not directly and easily accessible. We demonstrate that temperature gradients of dipolar shifts can serve as alternative constraints for determining the orientation of the magnetic axes, thereby eliminating the need to estimate the diamagnetic shifts. This approach is tested on low-spin, ferric sperm whale cyanometmyoglobin by determining the orientation, anisotropies and anisotropy temperature gradients by the alternate routes of using dipolar shifts and dipolar shift gradients as constraints. The alternate routes ultimately lead to very similar orientation of the magnetic axes, magnetic anisotropies and magnetic anisotropy temperature gradients which, by inference, would lead to an equally valid description of the molecular structure. It is expected that the use of the dipolar shift temperature gradients, rather than the dipolar shifts directly, as constraints will provide an accurate shortcut in a solution structure determination of a paramagnetic metalloprotein.

  18. Selective desulfurization of cysteine in the presence of Cys(Acm) in polypeptides obtained by native chemical ligation.

    Science.gov (United States)

    Pentelute, Brad L; Kent, Stephen B H

    2007-02-15

    Increased versatility for the synthesis of proteins and peptides by native chemical ligation requires the ability to ligate at positions other than Cys. Here, we report that Raney nickel can be used under standard conditions for the selective desulfurization of Cys in the presence of Cys(Acm). This simple and practical tactic enables the more common Xaa-Ala junctions to be used as ligation sites for the chemical synthesis of Cys-containing peptides and proteins. [reaction: see text].

  19. Chemical Constituents and Combined Larvicidal Effects of Selected Essential Oils against Anopheles cracens (Diptera: Culicidae

    Directory of Open Access Journals (Sweden)

    Jitrawadee Intirach

    2012-01-01

    Full Text Available A preliminary study on larvicidal activity against laboratory-colonized Anopheles cracens mosquitos revealed that five of ten plant oils at concentration of 100 ppm showed 95–100% larval mortality. The essential oils of five plants, including Piper sarmentosum, Foeniculum vulgare, Curcuma longa, Myristica fragrans, and Zanthoxylum piperitum, were then selected for chemical analysis, dose-response larvicidal experiments, and combination-based bioassays. Chemical compositions analyzed by gas chromatography coupled to mass spectrometry demonstrated that the main component in the oil derived from P. sarmentosum, F. vulgare, C. longa, M. fragrans, and Z. piperitum was croweacin (71.01%, anethole (63.00%, ar-turmerone (30.19%, safrole (46.60%, and 1,8-cineole (21.27%, respectively. For larvicidal bioassay, all five essential oils exerted promising efficacy in a dose-dependent manner and different performances on A. cracens after 24 hours of exposure. The strongest larvicidal potential was established from P. sarmentosum, followed by F. vulgare, C. longa, M. fragrans, and Z. piperitum, with LC50 values of 16.03, 32.77, 33.61, 40.00, and 63.17 ppm, respectively. Binary mixtures between P. sarmentosum, the most effective oil, and the others at the highest ratio were proved to be highly efficacious with a cotoxicity coefficient value greater than 100, indicating synergistic activity. Results of mixed formulations of different essential oils generating synergistic effects may prove helpful in developing effective, economical, and ecofriendly larvicides, as favorable alternatives for mosquito management.

  20. Effect of Grain Size on Selected Physico-Chemical Properties of Clay

    Directory of Open Access Journals (Sweden)

    Osumanu H. Ahmed

    2009-01-01

    Full Text Available Problem statement: Mixture of the right proportion of expanding and non-expanding clays to improve plasticity (moldability of clays used in the pot industry of Malaysia is yet to be well investigated. In addition, little is known about the choice of the right clay size to eliminate or reduce the content of undesirable compounds such as Fe2O3, Al2O3 to improve the strength of pots and roofing tiles in the country. The objective of this study was to investigate how selected physico-chemical properties of pottery clay relate to grain size of Nyalau series ((Typic Paleudults. Approach: Soil samples were refined into 25, 20 and 63 µm using size grading method. The mineralogical composition of the samples was determined using X-Ray Diffraction (XRD. The chemical composition of the samples was also determined using standard procedures. Firing was done at 800°C in a muffle furnace and the cracks of the samples recorded. Results: The clay particles with sizes 20 and 25 µm were higher in LOI and total C than that those of 63 µm regardless of grain size, the clay investigated had quartz (SiO2, illite-montmorillonite, Anatase ((TiO2 and kaolinite. Grading affected the concentrations of Fe, Al and Si as clays with particle sizes 20 and 25 µm had higher contents of the aforementioned elements compared with those of 63 µm. The clay with particles 63 µm had the best strength and this was so because the clay particles had the lowest amount of Fe, Al and Si. Conclusion: The strength of Malaysian pots could be improved upon proper grading of the clay particles.

  1. Chemically engineering ligand selectivity at the free fatty acid receptor 2 based on pharmacological variation between species orthologs

    DEFF Research Database (Denmark)

    Hudson, Brian D; Christiansen, Elisabeth; Tikhonova, Irina G

    2012-01-01

    When it is difficult to develop selective ligands within a family of related G-protein-coupled receptors (GPCRs), chemically engineered receptors activated solely by synthetic ligands (RASSLs) are useful alternatives for probing receptor function. In the present work, we explored whether a RASSL...... on this receptor and demonstrates that exploitation of pharmacological variation between species orthologs is a powerful method to generate novel chemically engineered GPCRs.-Hudson, B. D., Christiansen, E., Tikhonova, I. G., Grundmann, M., Kostenis, E., Adams, D. R., Ulven, T., Milligan, G. Chemically engineering...

  2. A Molecular and Chemical Perspective in Defining Melatonin Receptor Subtype Selectivity

    Directory of Open Access Journals (Sweden)

    Yung Hou Wong

    2013-09-01

    Full Text Available Melatonin is primarily synthesized and secreted by the pineal gland during darkness in a normal diurnal cycle. In addition to its intrinsic antioxidant property, the neurohormone has renowned regulatory roles in the control of circadian rhythm and exerts its physiological actions primarily by interacting with the G protein-coupled MT1 and MT2 transmembrane receptors. The two melatonin receptor subtypes display identical ligand binding characteristics and mediate a myriad of signaling pathways, including adenylyl cyclase inhibition, phospholipase C stimulation and the regulation of other effector molecules. Both MT1 and MT2 receptors are widely expressed in the central nervous system as well as many peripheral tissues, but each receptor subtype can be linked to specific functional responses at the target tissue. Given the broad therapeutic implications of melatonin receptors in chronobiology, immunomodulation, endocrine regulation, reproductive functions and cancer development, drug discovery and development programs have been directed at identifying chemical molecules that bind to the two melatonin receptor subtypes. However, all of the melatoninergics in the market act on both subtypes of melatonin receptors without significant selectivity. To facilitate the design and development of novel therapeutic agents, it is necessary to understand the intrinsic differences between MT1 and MT2 that determine ligand binding, functional efficacy, and signaling specificity. This review summarizes our current knowledge in differentiating MT1 and MT2 receptors and their signaling capacities. The use of homology modeling in the mapping of the ligand-binding pocket will be described. Identification of conserved and distinct residues will be tremendously useful in the design of highly selective ligands.

  3. Origin of the chemical shift in X-ray absorption near-edge spectroscopy at the Mn K-Edge in manganese oxide compounds

    NARCIS (Netherlands)

    de Vries, AH; Hozoi, L; Broer, R; Broer-Braam, H.B.

    2003-01-01

    The absorption edge in Mn K-edge X-ray absorption spectra of manganese oxide compounds shows a shift of several electronvolts in going from MnO through LaMnO3 to CaMnO3. On the other hand, in X-ray photoelectron spectra much smaller shifts are observed. To identify the mechanisms that cause the obse

  4. Chemical characterization of selected high copper dental amalgams using XPS and XRD techniques

    Energy Technology Data Exchange (ETDEWEB)

    Talik, E. [A. Chelkowski Institute of Physics, University of Silesia, Uniwersytecka 4, 40-007 Katowice (Poland)]. E-mail: talik@us.edu.pl; Babiarz-Zdyb, R. [A. Chelkowski Institute of Physics, University of Silesia, Uniwersytecka 4, 40-007 Katowice (Poland); Dziedzic, A. [Medical University of Silesia, Department of Conservative Dentistry and Periodontology, Akademicki 17 Sqr., 41-209 Bytom (Poland)

    2005-08-02

    The study was carried out to analyze some dependencies between the composition of seven high copper dental amalgams and mercury release behavior, as well as oxygen reactivity of metallic elements. Chemical comparative analysis of selected dental amalgams was carried out using X-ray photoelectron spectroscopy (XPS) technique and X-ray diffraction (XRD) method. The X-ray powder diffraction measurements revealed two main phases for measured amalgams: {gamma}{sub 1}-(Ag{sub 2}Hg{sub 3}) and {eta}'-(Cu{sub 6}Sn{sub 5}). The amount of mercury obtained by the XPS method was lower than the value quoted in the manufacturer's literature, which suggested evaporation of mercury under the UHV conditions. A linear decrease of oxygen and carbon contamination with the growing amount of Cu and Ag was observed. The XPS analysis showed that a high Sn concentration caused less resistance to oxidation. Some of the amalgams contained some extra elements, such as Bi, In, and Zn. All samples contained lead in metallic state and oxides. The amount of Ag, Cu, Sn ingredients determines the main properties of high copper amalgams and plays an important role in mercury evaporation. High tin concentration combined with the presence of smaller amounts of silver and copper (high Sn/Ag ratio) may influence the increase of mercury vaporization.

  5. Acoustic Aposematism and Evasive Action in Select Chemically Defended Arctiine (Lepidoptera: Erebidae) Species: Nonchalant or Not?

    Science.gov (United States)

    Dowdy, Nicolas J; Conner, William E

    2016-01-01

    Tiger moths (Erebidae: Arctiinae) have experienced intense selective pressure from echolocating, insectivorous bats for over 65 million years. One outcome has been the evolution of acoustic signals that advertise the presence of toxins sequestered from the moths' larval host plants, i.e. acoustic aposematism. Little is known about the effectiveness of tiger moth anti-bat sounds in their natural environments. We used multiple infrared cameras to reconstruct bat-moth interactions in three-dimensional (3-D) space to examine how functional sound-producing organs called tymbals affect predation of two chemically defended tiger moth species: Pygarctia roseicapitis (Arctiini) and Cisthene martini (Lithosiini). P. roseicapitis and C. martini with intact tymbals were 1.8 and 1.6 times less likely to be captured by bats relative to those rendered silent. 3-D flight path and acoustic analyses indicated that bats actively avoided capturing sound-producing moths. Clicking behavior differed between the two tiger moth species, with P. roseicapitis responding in an earlier phase of bat attack. Evasive flight behavior in response to bat attacks was markedly different between the two tiger moth species. P. roseicapitis frequently paired evasive dives with aposematic sound production. C. martini were considerably more nonchalant and employed evasion in fewer interactions. Our results show that acoustic aposematism is effective at deterring bat predation in a natural context and that this strategy is likely to be the ancestral function of tymbal organs within the Arctiinae.

  6. DNA aptamers for selective identification and separation of flame retardant chemicals.

    Science.gov (United States)

    Kim, Un-Jung; Kim, Byoung Chan

    2016-09-14

    Polybrominated diphenyl ethers (PBDEs) are group of chemicals which are representative persistent organic pollutants (POPs) and used as brominated flame retardants for many consumer products. PBDEs were phased out since 2009 but are still frequently observed in various environmental matrices and human body. Here, we report ssDNA aptamers which bind to BDE47, one of the PBDE congeners commonly found in various environmental matrices, and show affinity to other major tri-to hepta- BDE congeners. The PBDE specific aptamers were isolated from random library of ssDNA using Mag-SELEX. Two out of 15 sequences, based on their alignment and hairpin loop structures, were chosen to determine dissociation constant with BDE47 and showed from picomolar to nanomolar affinities (200 pM and 1.53 nM). The aptamers displayed high selectivity to the original target, BDE47, and implying general specificity to PBDE backbone with varying affinities to other congeners. Further, we showed that the use of two aptamers together could enhance the separation efficiency of BDE47 and other BDE congeners when dissolved in a solvent compared to use of single aptamer. These aptamers are expected to provide a tool for preliminary screening or quick separation of PBDEs in environmental samples prior to trace quantitative analysis.

  7. Physical and chemical conditions in methanol maser selected hot-cores and UCHII regions

    CERN Document Server

    Purcell, C R; Burton, M G; Walsh, A J; Minier, V; Cunningham, M R; Balasubramanyam, R

    2008-01-01

    We present the results of a targeted 3-mm spectral line survey towards the eighty-three 6.67 GHz methanol maser selected star forming clumps observed by Purcell et al. 2006. In addition to the previously reported measurements of HCO+ (1 - 0), H13CO+ (1 - 0), and CH3CN (5 - 4) & (6 -5), we used the Mopra antenna to detect emission lines of N2H+ (1 - 0), HCN (1 - 0) and HNC (1 - 0) towards 82/83 clumps (99 per cent), and CH3OH (2 - 1) towards 78/83 clumps (94 per cent). The molecular line data have been used to derive virial and LTE masses, rotational temperatures and chemical abundances in the clumps, and these properties have been compared between sub-samples associated with different indicators of evolution. The greatest differences are found between clumps associated with 8.6 GHz radio emission, indicating the presence of an Ultra-Compact HII region, and `isolated' masers (without associated radio emission), and between clumps exhibiting CH3CN emission and those without. In particular, thermal CH3OH is ...

  8. Utility of chemical-shift MR imaging in detecting small amounts of fat in extrahepatic abdominal tumors; Utilidad de la tecnica de desplazamiento quimico den RM para la deteccion de pequenas cantidades de grasa en tumores abdominales extrahepaticos

    Energy Technology Data Exchange (ETDEWEB)

    Martin, J.; Falco, J.; Puig, J.; Donoso, L. [Unidad de Diagnostico por Imagen de Alta Tecnologia (UDIAT). Sabadell (Spain)

    1999-07-01

    To determine the utility of the chemical shift technique in magnetic resonance imaging (MRI) to confirm small amounts of fat in extrahepatic intraabdominal tumours. 7 extrahepatic abdominal tumours that are suspected to have fat as seen in the axial computed tomography (TC) are analysed retrospectively. In order to confirm the fat content, the chemical displacement technique with gradient echo sequences (GE) in phase (P) and in opposite phase (OP) was used with MRI 1 T equipment. The tumours corresponded to renal angiomyolipoma (AML) (n=4), intraperitoneal liposarcoma (n=1), retroperitoneal liposarcoma (n=1) and intraabdominal extramedular hematopoiesis (n=1). To confirm the existence of fat in the tumours, we used a quantitative percentage variation parameter of the intensity of the signals (VIS) between the images in P and OP, according to the formula: IS{sub (}p)-IS({sub o}p)x100/IS{sub (}op), where IS is the intensity of the signal. The chemical shift technique showed fat in the seven tumours. Upon visual inspection, all the tumoral areas that were suspected to have fat showed a notable difference in the signal intensity, being hypointense in OP and hyperintense in P. In these areas the average VIS percentage was 170% while in the rest of the tumour the average VIS percentage was 3%. The chemical shift technique with RG sequences can be easily used in MRI equipment and allows us to confirm if a specific abdominal tumour has fat, even if there is only a small quantity. (Author) 13 refs.

  9. Mental rotation impairs attention shifting and short-term memory encoding: neurophysiological evidence against the response-selection bottleneck model of dual-task performance.

    Science.gov (United States)

    Pannebakker, Merel M; Jolicœur, Pierre; van Dam, Wessel O; Band, Guido P H; Ridderinkhof, K Richard; Hommel, Bernhard

    2011-09-01

    Dual tasks and their associated delays have often been used to examine the boundaries of processing in the brain. We used the dual-task procedure and recorded event-related potentials (ERPs) to investigate how mental rotation of a first stimulus (S1) influences the shifting of visual-spatial attention to a second stimulus (S2). Visual-spatial attention was monitored by using the N2pc component of the ERP. In addition, we examined the sustained posterior contralateral negativity (SPCN) believed to index the retention of information in visual short-term memory. We found modulations of both the N2pc and the SPCN, suggesting that engaging mechanisms of mental rotation impairs the deployment of visual-spatial attention and delays the passage of a representation of S2 into visual short-term memory. Both results suggest interactions between mental rotation and visual-spatial attention in capacity-limited processing mechanisms indicating that response selection is not pivotal in dual-task delays and all three processes are likely to share a common resource like executive control.

  10. CHEMICALS

    CERN Multimedia

    Medical Service

    2002-01-01

    It is reminded that all persons who use chemicals must inform CERN's Chemistry Service (TIS-GS-GC) and the CERN Medical Service (TIS-ME). Information concerning their toxicity or other hazards as well as the necessary individual and collective protection measures will be provided by these two services. Users must be in possession of a material safety data sheet (MSDS) for each chemical used. These can be obtained by one of several means : the manufacturer of the chemical (legally obliged to supply an MSDS for each chemical delivered) ; CERN's Chemistry Service of the General Safety Group of TIS ; for chemicals and gases available in the CERN Stores the MSDS has been made available via EDH either in pdf format or else via a link to the supplier's web site. Training courses in chemical safety are available for registration via HR-TD. CERN Medical Service : TIS-ME :73186 or service.medical@cern.ch Chemistry Service : TIS-GS-GC : 78546

  11. Transfer Rate Edited experiment for the selective detection of Chemical Exchange via Saturation Transfer (TRE-CEST).

    Science.gov (United States)

    Friedman, Joshua I; Xia, Ding; Regatte, Ravinder R; Jerschow, Alexej

    2015-07-01

    Chemical Exchange Saturation Transfer (CEST) magnetic resonance experiments have become valuable tools in magnetic resonance for the detection of low concentration solutes with far greater sensitivity than direct detection methods. Accurate measures of rates of chemical exchange provided by CEST are of particular interest to biomedical imaging communities where variations in chemical exchange can be related to subtle variations in biomarker concentration, temperature and pH within tissues using MRI. Despite their name, however, traditional CEST methods are not truly selective for chemical exchange and instead detect all forms of magnetization transfer including through-space NOE. This ambiguity crowds CEST spectra and greatly complicates subsequent data analysis. We have developed a Transfer Rate Edited CEST experiment (TRE-CEST) that uses two different types of solute labeling in order to selectively amplify signals of rapidly exchanging proton species while simultaneously suppressing 'slower' NOE-dominated magnetization transfer processes. This approach is demonstrated in the context of both NMR and MRI, where it is used to detect the labile amide protons of proteins undergoing chemical exchange (at rates⩾30s(-1)) while simultaneously eliminating signals originating from slower (∼5s(-1)) NOE-mediated magnetization transfer processes. TRE-CEST greatly expands the utility of CEST experiments in complex systems, and in-vivo, in particular, where it is expected to improve the quantification of chemical exchange and magnetization transfer rates while enabling new forms of imaging contrast.

  12. In vitro evolution of chemically-modified nucleic acid aptamers: Pros and cons, and comprehensive selection strategies.

    Science.gov (United States)

    Lipi, Farhana; Chen, Suxiang; Chakravarthy, Madhuri; Rakesh, Shilpa; Veedu, Rakesh N

    2016-12-01

    Nucleic acid aptamers are single-stranded DNA or RNA oligonucleotide sequences that bind to a specific target molecule with high affinity and specificity through their ability to adopt 3-dimensional structure in solution. Aptamers have huge potential as targeted therapeutics, diagnostics, delivery agents and as biosensors. However, aptamers composed of natural nucleotide monomers are quickly degraded in vivo and show poor pharmacodynamic properties. To overcome this, chemically-modified nucleic acid aptamers are developed by incorporating modified nucleotides after or during the selection process by Systematic Evolution of Ligands by EXponential enrichment (SELEX). This review will discuss the development of chemically-modified aptamers and provide the pros and cons, and new insights on in vitro aptamer selection strategies by using chemically-modified nucleic acid libraries.

  13. Synthesis, NMR spectroscopic characterization and structure of a divinyldisilazane-(triphenylphosphine)platinum(0) complex: observation of isotope-induced chemical shifts (1)Δ(12/13)C((195)Pt).

    Science.gov (United States)

    Wrackmeyer, Bernd; Klimkina, Elena V; Schmalz, Thomas; Milius, Wolfgang

    2013-05-01

    Tetramethyldivinyldisilazane-(triphenylphosphine)platinum(0) was prepared, characterized in solid state by X-ray crystallography and in solution by multinuclear magnetic resonance spectroscopy ((1)H, (13)C, (15)N, (29)Si, (31)P and (195)Pt NMR). Numerous signs of spin-spin coupling constants were determined by two-dimensional heteronuclear shift correlations (HETCOR) and two-dimensional (1)H/(1)H COSY experiments. Isotope-induced chemical shifts (1)Δ(12/13)C((195)Pt) were measured from (195)Pt NMR spectra of the title compound as well as of other Pt(0), Pt(II) and Pt(IV) compounds for comparison. In contrast to other heavy nuclei such as (199)Hg or (207)Pb, the "normal" shifts of the heavy isotopomers to low frequencies are found, covering a range of >500 ppb.

  14. Estimation of sediment sources using selected chemical tracers in the Perry lake basin,Kansas,USA

    Institute of Scientific and Technical Information of China (English)

    K.E.JURACEK; A.C.ZIEGLER

    2009-01-01

    The ability to achieve meaningful decreases in sediment loads to reservoirs requires a determination of the relative importance of sediment sources within the contributing basins.In an investigation of sources of fine-grained sediment (clay and silt) within the Perry Lake Basin in northeast Kansas,representative samples of channel-bank sources,surface-soil sources (cropland and grassland),and reservoir bottom sediment were collected,chemically analyzed,and compared.The samples were sieved to isolate the <63μ m fraction and analyzed for selected nutrients (total nitrogen and total phosphorus),organic and total carbon,25 trace elements,and the radionuclide cesium-137 (137Cs).On the basis of substantial and consistent compositional differences among the source types,total nitrogen (TN),total phosphorus (TP),total organic carbon (TOC),and 137Cs were selected for use in the estimation of sediment sources.To further account for differences in particle-size composition between the sources and the reservoir bottom sediment,constituent ratio and clay-normalization techniques were used.Computed ratios included TOC to TN,TOC to TP,and TN to TP.Constituent concentrations (TN,TP,TOC) and activities (137Cs) were normalized by dividing by the percentage of clay.Thus,the sediment-source estimations involved the use of seven sediment-source indicators.Within the Perry Lake Basin,the consensus of the seven indicators was that both channel-bank and surface-soil sources were important in the Atchison County Lake and Banner Creek Reservoir subbasins,whereas channel-bank sources were dominant in the Mission Lake subbasin.On the sole basis of 137Cs activity,surface-soil sources contributed the most fine-grained sediment to Atchison County Lake,and channel-bank sources contributed the most fine-grained sediment to Banner Creek Reservoir and Mission Lake.Both the seven-indicator consensus and 137Cs indicated that channelbank sources were dominant for Perry Lake and that channel

  15. Determination of pKa values of tenoxicam from 1H NMR chemical shifts and of oxicams from electrophoretic mobilities (CZE) with the aid of programs SQUAD and HYPNMR.

    Science.gov (United States)

    Rodríguez-Barrientos, Damaris; Rojas-Hernández, Alberto; Gutiérrez, Atilano; Moya-Hernández, Rosario; Gómez-Balderas, Rodolfo; Ramírez-Silva, María Teresa

    2009-12-15

    In this work it is explained, by the first time, the application of programs SQUAD and HYPNMR to refine equilibrium constant values through the fit of electrophoretic mobilities determined by capillary zone electrophoresis experiments, due to the mathematical isomorphism of UV-vis absorptivity coefficients, NMR chemical shifts and electrophoretic mobilities as a function of pH. Then, the pK(a) values of tenoxicam in H(2)O/DMSO 1:4 (v/v) have been obtained from (1)H NMR chemical shifts, as well as of oxicams in aqueous solution from electrophoretic mobilities determined by CZE, at 25 degrees C. These values are in very good agreement with those reported by spectrophotometric and potentiometric measurements.

  16. Selection of appropriate training and validation set chemicals for modelling dermal permeability by U-optimal design.

    Science.gov (United States)

    Xu, G; Hughes-Oliver, J M; Brooks, J D; Yeatts, J L; Baynes, R E

    2013-01-01

    Quantitative structure-activity relationship (QSAR) models are being used increasingly in skin permeation studies. The main idea of QSAR modelling is to quantify the relationship between biological activities and chemical properties, and thus to predict the activity of chemical solutes. As a key step, the selection of a representative and structurally diverse training set is critical to the prediction power of a QSAR model. Early QSAR models selected training sets in a subjective way and solutes in the training set were relatively homogenous. More recently, statistical methods such as D-optimal design or space-filling design have been applied but such methods are not always ideal. This paper describes a comprehensive procedure to select training sets from a large candidate set of 4534 solutes. A newly proposed 'Baynes' rule', which is a modification of Lipinski's 'rule of five', was used to screen out solutes that were not qualified for the study. U-optimality was used as the selection criterion. A principal component analysis showed that the selected training set was representative of the chemical space. Gas chromatograph amenability was verified. A model built using the training set was shown to have greater predictive power than a model built using a previous dataset [1].

  17. E-2-Benzylidenebenzocycloalkanones. IV. Studies on transmission of substituent effects on 13C NMR chemical shifts of E-2-(X-benzylidene)-1-tetralones, and -benzosuberones. Comparison with the 13C NMR data of chalcones and E-2-(X-benzylidene)-1-indanones

    Science.gov (United States)

    Perjési, Pál; Linnanto, Juha; Kolehmainen, Erkki; Ősz, Erzsébet; Virtanen, Elina

    2005-04-01

    Single substituent parameter (SSP) and dual substituent parameter (DSP) analyses were applied to study the transmission of substituent effects on selected 13C NMR chemical shifts of the cyclic chalcone analogues, E-2-(4'-X-benzylidene)-1-tetralones ( 2) and E-2-(4'-X-benzylidene)-1-benzosuberones ( 3). In order to study how the geometry of the cyclic chalcone analogues affects the transmission of substituent effects similar investigations with the respective chalcones ( 4) were also performed. The results obtained earlier with the five-membered analogue E-2-(4'-X-benzylidene)-1-indanones ( 1) were also involved in the comparisons. Geometry optimization of the unsubstituted 1a, 2a, 3a and 4a as well as the substituted 2 and 3 was performed by ab initio quantum chemical calculations. Both SSP and DSP analyses reflected that resonance effects contribute more to the chemical shift of C-α (C2), while inductive effects primarily affect that of C-β (C10) of the enone moiety of all the four series. This latter effect, however, is far not as pronounced as that of the former one. It was found that DSP analysis data ( ρF and ρR values) of transmission of substituent effects on the δC2 data can serve as a measure of choice to study the conformation (planarity) of the investigated enones in the four series.

  18. Bioactive Ti metal analogous to human cancellous bone: Fabrication by selective laser melting and chemical treatments.

    Science.gov (United States)

    Pattanayak, Deepak K; Fukuda, A; Matsushita, T; Takemoto, M; Fujibayashi, S; Sasaki, K; Nishida, N; Nakamura, T; Kokubo, T

    2011-03-01

    Selective laser melting (SLM) is a useful technique for preparing three-dimensional porous bodies with complicated internal structures directly from titanium (Ti) powders without any intermediate processing steps, with the products being expected to be useful as a bone substitute. In this study the necessary SLM processing conditions to obtain a dense product, such as the laser power, scanning speed, and hatching pattern, were investigated using a Ti powder of less than 45 μm particle size. The results show that a fully dense plate thinner than 1.8 mm was obtained when the laser power to scanning speed ratio was greater than 0.5 and the hatch spacing was less than the laser diameter, with a 30 μm thick powder layer. Porous Ti metals with structures analogous to human cancellous bone were fabricated and the compressive strength measured. The compressive strength was in the range 35-120 MPa when the porosity was in the range 75-55%. Porous Ti metals fabricated by SLM were heat-treated at 1300 °C for 1h in an argon gas atmosphere to smooth the surface. Such prepared specimens were subjected to NaOH, HCl, and heat treatment to provide bioactivity. Field emission scanning electron micrographs showed that fine networks of titanium oxide were formed over the whole surface of the porous body. These treated porous bodies formed bone-like apatite on their surfaces in a simulated body fluid within 3 days. In vivo studies showed that new bone penetrated into the pores and directly bonded to the walls within 12 weeks after implantation into the femur of Japanese white rabbits. The percentage bone affinity indices of the chemical- and heat-treated porous bodies were significantly higher than that of untreated implants.

  19. Lanthanide ion (III) complexes of 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraaminophosphonate for dual biosensing of pH with chemical exchange saturation transfer (CEST) and biosensor imaging of redundant deviation in shifts (BIRDS).

    Science.gov (United States)

    Huang, Yuegao; Coman, Daniel; Ali, Meser M; Hyder, Fahmeed

    2015-01-01

    Relaxivity-based magnetic resonance of phosphonated ligands chelated with gadolinium (Gd(3+)) shows promise for pH imaging. However instead of monitoring the paramagnetic effect of lanthanide complexes on the relaxivity of water protons, biosensor (or molecular) imaging with magnetic resonance is also possible by detecting either the nonexchangeable or the exchangeable protons on the lanthanide complexes themselves. The nonexchangeable protons (e.g. -CHx, where 3 ≥ x ≥ 1) are detected using a three-dimensional chemical shift imaging method called biosensor imaging of redundant deviation in shifts (BIRDS), whereas the exchangeable protons (e.g. -OH or -NHy , where 2 ≥ y ≥ 1) are measured with chemical exchange saturation transfer (CEST) contrast. Here we tested the feasibility of BIRDS and CEST for pH imaging of 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraaminophosphonate (DOTA-4AmP(8-)) chelated with thulium (Tm(3+) ) and ytterbium (Yb(3+)). BIRDS and CEST experiments show that both complexes are responsive to pH and temperature changes. Higher pH and temperature sensitivities are obtained with BIRDS for either complex when using the chemical shift difference between two proton resonances vs using the chemical shift of a single proton resonance, thereby eliminating the need to use water resonance as reference. While CEST contrast for both agents is linearly dependent on pH within a relatively large range (i.e. 6.3-7.9), much stronger CEST contrast is obtained with YbDOTA-4AmP(5-) than with TmDOTA-4AmP(5-). In addition, we demonstrate the prospect of using BIRDS to calibrate CEST as new platform for quantitative pH imaging.

  20. Power Shift

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    @@ "We are entering a new era of world history: the end of Western domination and the arrival of the Asian century. The question is: will Washington wake up to this reality?" This is the central premise of Kishore Mahbubani's provocative new book The New Asian Hemisphere: The Irresistible Shift of Global Power to the East.

  1. Combination of TRAIL with bortezomib shifted apoptotic signaling from DR4 to DR5 death receptor by selective internalization and degradation of DR4.

    Directory of Open Access Journals (Sweden)

    Maxim L Bychkov

    Full Text Available TRAIL (tumor necrosis factor-related apoptosis-inducing ligand mediates apoptosis in cancer cells through death receptors DR4 and DR5 preferring often one receptor over another in the cells expressing both receptors. Receptor selective mutant variants of TRAIL and agonistic antibodies against DR4 and DR5 are highly promising anticancer agents. Here using DR5 specific mutant variant of TRAIL--DR5-B we have demonstrated for the first time that the sensitivity of cancer cells can be shifted from one TRAIL death receptor to another during co-treatment with anticancer drugs. First we have studied the contribution of DR4 and DR5 in HCT116 p53+/+ and HCT116 p53-/- cells and demonstrated that in HCT116 p53+/+ cells the both death receptors are involved in TRAIL-induced cell death while in HCT116 p53-/- cells prevailed DR4 signaling. The expression of death (DR4 and DR5 as well as decoy (DcR1 and DcR2 receptors was upregulated in the both cell lines either by TRAIL or by bortezomib. However, combined treatment of cells with two drugs induced strong time-dependent and p53-independent internalization and further lysosomal degradation of DR4 receptor. Interestingly DR5-B variant of TRAIL which do not bind with DR4 receptor also induced elimination of DR4 from cell surface in combination with bortezomib indicating the ligand-independent mechanism of the receptor internalization. Eliminatory internalization of DR4 resulted in activation of DR5 receptor thus DR4-dependent HCT116 p53-/- cells became highly sensitive to DR5-B in time-dependent manner. Internalization and degradation of DR4 receptor depended on activation of caspases as well as of lysosomal activity as it was completely inhibited by Z-VAD-FMK, E-64 and Baf-A1. In light of our findings, it is important to explore carefully which of the death receptors is active, when sensitizing drugs are combined with agonistic antibodies to the death receptors or receptor selective variants of TRAIL to enhance

  2. Combination of TRAIL with bortezomib shifted apoptotic signaling from DR4 to DR5 death receptor by selective internalization and degradation of DR4.

    Science.gov (United States)

    Bychkov, Maxim L; Gasparian, Marine E; Dolgikh, Dmitry A; Kirpichnikov, Mikhail P

    2014-01-01

    TRAIL (tumor necrosis factor-related apoptosis-inducing ligand) mediates apoptosis in cancer cells through death receptors DR4 and DR5 preferring often one receptor over another in the cells expressing both receptors. Receptor selective mutant variants of TRAIL and agonistic antibodies against DR4 and DR5 are highly promising anticancer agents. Here using DR5 specific mutant variant of TRAIL--DR5-B we have demonstrated for the first time that the sensitivity of cancer cells can be shifted from one TRAIL death receptor to another during co-treatment with anticancer drugs. First we have studied the contribution of DR4 and DR5 in HCT116 p53+/+ and HCT116 p53-/- cells and demonstrated that in HCT116 p53+/+ cells the both death receptors are involved in TRAIL-induced cell death while in HCT116 p53-/- cells prevailed DR4 signaling. The expression of death (DR4 and DR5) as well as decoy (DcR1 and DcR2) receptors was upregulated in the both cell lines either by TRAIL or by bortezomib. However, combined treatment of cells with two drugs induced strong time-dependent and p53-independent internalization and further lysosomal degradation of DR4 receptor. Interestingly DR5-B variant of TRAIL which do not bind with DR4 receptor also induced elimination of DR4 from cell surface in combination with bortezomib indicating the ligand-independent mechanism of the receptor internalization. Eliminatory internalization of DR4 resulted in activation of DR5 receptor thus DR4-dependent HCT116 p53-/- cells became highly sensitive to DR5-B in time-dependent manner. Internalization and degradation of DR4 receptor depended on activation of caspases as well as of lysosomal activity as it was completely inhibited by Z-VAD-FMK, E-64 and Baf-A1. In light of our findings, it is important to explore carefully which of the death receptors is active, when sensitizing drugs are combined with agonistic antibodies to the death receptors or receptor selective variants of TRAIL to enhance cancer treatment

  3. Phenomenological description of selected elementary chemical reaction mechanisms: An information-theoretic study

    Energy Technology Data Exchange (ETDEWEB)

    Esquivel, R.O., E-mail: esquivel@xanum.uam.m [Departamento de Quimica, Universidad Autonoma Metropolitana, 09340 Mexico D.F. (Mexico); Departamento de Fisica Atomica, Molecular y Nuclear, Universidad de Granada, 18071-Granada (Spain); Instituto Carlos I de Fisica Teorica y Computacional, Universidad de Granada, 18071-Granada (Spain); Flores-Gallegos, N.; Iuga, C.; Carrera, E.M. [Departamento de Quimica, Universidad Autonoma Metropolitana, 09340 Mexico D.F. (Mexico); Angulo, J.C. [Departamento de Fisica Atomica, Molecular y Nuclear, Universidad de Granada, 18071-Granada (Spain); Instituto Carlos I de Fisica Teorica y Computacional, Universidad de Granada, 18071-Granada (Spain); Antolin, J. [Departamento de Fisica Aplicada, EUITIZ, Universidad de Zaragoza, 50018-Zaragoza (Spain); Instituto Carlos I de Fisica Teorica y Computacional, Universidad de Granada, 18071-Granada (Spain)

    2010-02-01

    The information-theoretic description of the course of two elementary chemical reactions allows a phenomenological description of the chemical course of the hydrogenic abstraction and the S{sub N}2 identity reactions by use of Shannon entropic measures in position and momentum spaces. The analyses reveal their synchronous/asynchronous mechanistic behavior.

  4. Selective-Area Growth of Thick Diamond Films Using Chemically Stable Masks of Ru/Au and Mo/Au

    Science.gov (United States)

    Nagase, Masanori; Watanabe, Katsumi; Umezawa, Hitoshi; Shikata, Shinichi

    2012-07-01

    Selective-area growth of diamond films in microwave-plasma chemical vapor deposition was performed using newly developed masks. By forming chemically stable masks made of Ru/Au or Mo/Au, which have high melting points, good adhesion to diamond, and difficulty in forming carbide compounds, patterned diamond films with a large thickness of 50 µm, a large area of 5 mm2, and a high orientation in the [001] direction were successfully grown on (001) diamond substrates without degradation of the crystal quality of masked areas.

  5. Chemical biology based on target-selective degradation of proteins and carbohydrates using light-activatable organic molecules.

    Science.gov (United States)

    Toshima, Kazunobu

    2013-05-01

    Proteins and carbohydrates play crucial roles in a wide range of biological processes, including serious diseases. The development of novel and innovative methods for selective control of specific proteins and carbohydrates functions has attracted much attention in the field of chemical biology. In this account article, the development of novel chemical tools, which can degrade target proteins and carbohydrates by irradiation with a specific wavelength of light under mild conditions without any additives, is introduced. This novel class of photochemical agents promise bright prospects for finding not only molecular-targeted bioprobes for understanding of the structure-activity relationships of proteins and carbohydrates but also novel therapeutic drugs targeting proteins and carbohydrates.

  6. Understanding boron through size-selected clusters: structure, chemical bonding, and fluxionality.

    Science.gov (United States)

    Sergeeva, Alina P; Popov, Ivan A; Piazza, Zachary A; Li, Wei-Li; Romanescu, Constantin; Wang, Lai-Sheng; Boldyrev, Alexander I

    2014-04-15

    believed that the electronic transmutation concept will be effective and valuable in aiding the design of new boride materials with predictable properties. The study of boron clusters with intermediate properties between those of individual atoms and bulk solids has given rise to a unique opportunity to broaden the frontier of boron chemistry. Understanding boron clusters has spurred experimentalists and theoreticians to find new boron-based nanomaterials, such as boron fullerenes, nanotubes, two-dimensional boron, and new compounds containing boron clusters as building blocks. Here, a brief and timely overview is presented addressing the recent progress made on boron clusters and the approaches used in the authors' laboratories to determine the structure, stability, and chemical bonding of size-selected boron clusters by joint photoelectron spectroscopy and theoretical studies. Specifically, key findings on all-boron hydrocarbon analogues, metal-centered boron wheels, and electronic transmutation in boron clusters are summarized.

  7. Understanding Boron through Size-Selected Clusters: Structure, Chemical Bonding, and Fluxionality

    Energy Technology Data Exchange (ETDEWEB)

    Sergeeva, Alina P.; Popov, Ivan A.; Piazza, Zachary A.; Li, Wei-Li; Romanescu, Constantin; Wang, Lai S.; Boldyrev, Alexander I.

    2014-04-15

    /C analogy. It is believed that the electronic transmutation concept will be effective and valuable in aiding the design of new boride materials with predictable properties. The study of boron clusters with intermediate properties between those of individual atoms and bulk solids has given rise to a unique opportunity to broaden the frontier of boron chemistry. Understanding boron clusters has spurred experimentalists and theoreticians to find new boron-based nanomaterials, such as boron fullerenes, nanotubes, two-dimensional boron, and new compounds containing boron clusters as building blocks. Here, a brief and timely overview is presented addressing the recent progress made on boron clusters and the approaches used in the authors’ laboratories to determine the structure, stability, and chemical bonding of size-selected boron clusters by joint photoelectron spectroscopy and theoretical studies. Specifically, key findings on all-boron hydrocarbon analogues, metal-centered boron wheels, and electronic transmutation in boron clusters are summarized.

  8. Prediction of (195) Pt NMR chemical shifts of dissolution products of H2 [Pt(OH)6 ] in nitric acid solutions by DFT methods: how important are the counter-ion effects?

    Science.gov (United States)

    Tsipis, Athanassios C; Karapetsas, Ioannis N

    2016-08-01

    (195) Pt NMR chemical shifts of octahedral Pt(IV) complexes with general formula [Pt(NO3 )n (OH)6 - n ](2-) , [Pt(NO3 )n (OH2 )6 - n ](4 - n) (n = 1-6), and [Pt(NO3 )6 - n  - m (OH)m (OH2 )n ](-2 + n - m) formed by dissolution of platinic acid, H2 [Pt(OH)6 ], in aqueous nitric acid solutions are calculated employing density functional theory methods. Particularly, the gauge-including atomic orbitals (GIAO)-PBE0/segmented all-electron relativistically contracted-zeroth-order regular approximation (SARC-ZORA)(Pt) ∪ 6-31G(d,p)(E)/Polarizable Continuum Model computational protocol performs the best. Excellent second-order polynomial plots of δcalcd ((195) Pt) versus δexptl ((195) Pt) chemical shifts and δcalcd ((195) Pt) versus the natural atomic charge QPt are obtained. Despite of neglecting relativistic and spin orbit effects the good agreement of the calculated δ (195) Pt chemical shifts with experimental values is probably because of the fact that the contribution of relativistic and spin orbit effects to computed σ(iso) (195) Pt magnetic shielding of Pt(IV) coordination compounds is effectively cancelled in the computed δ (195) Pt chemical shifts, because the relativistic corrections are expected to be similar in the complexes and the proper reference standard used. To probe the counter-ion effects on the (195) Pt NMR chemical shifts of the anionic [Pt(NO3 )n (OH)6 - n ](2-) and cationic [Pt(NO3 )n (OH2 )6 - n ](4 - n) (n = 0-3) complexes we calculated the (195) Pt NMR chemical shifts of the neutral (PyH)2 [Pt(NO3 )n (OH)6 - n ] (n = 1-6; PyH = pyridinium cation, C5 H5 NH(+) ) and [Pt(NO3 )n (H2 O)6 - n ](NO3 )4 - n (n = 0-3) complexes. Counter-anion effects are very important for the accurate prediction of the (195) Pt NMR chemical shifts of the cationic [Pt(NO3 )n (OH2 )6 - n ](4 - n) complexes, while counter-cation effects are less important for the anionic [Pt(NO3 )n (OH)6

  9. Electrochemical evaluation of chemical selectivity of glutamate receptor ion channel proteins with a multi-channel sensor.

    Science.gov (United States)

    Sugawara, M; Hirano, A; Rehák, M; Nakanishi, J; Kawai, K; Sato, H; Umezawa, Y

    1997-01-01

    A new method for evaluating chemical selectivity of agonists towards receptor ion channel proteins is proposed by using glutamate receptor (GluR) ion channel proteins and their agonists N-methyl-D-aspartic acid (NMDA), L-glutamate, and (2S, 3R, 4S) isomer of 2-(carboxycyclopropyl)glycine (L-CCG-IV). Integrated multi-channel currents, corresponding to the sum of total amount of ions passed through the multiple open channels, were used as a measure of agonists' selectivity to recognize ion channel proteins and induce channel currents. GluRs isolated from rat synaptic plasma membranes were incorporated into planar bilayer lipid membranes (BLMs) formed by the folding method. The empirical factors that affect the selectivity were demonstrated: (i) the number of GluRs incorporated into BLMs varied from one membrane to another; (ii) each BLM contained different subtypes of GluRs (NMDA and/or non-NMDA subtypes); and (iii) the magnitude of multi-channel responses induced by L-glutamate at negative applied potentials was larger than at positive potentials, while those by NMDA and L-CCG-IV were linearly related to applied potentials. The chemical selectivity among NMDA, L-glutamate and L-CCG-IV for NMDA subtype of GluRs was determined with each single BLM in which only NMDA subtype of GluRs was designed to be active by inhibiting the non-NMDA subtypes using a specific antagonist DNQX. The order of selectivity among the relevant agonists for the NMDA receptor subtype was found to be L-CCG-IV > L-glutamate > NMDA, which is consistent with the order of binding affinity of these agonists towards the same NMDA subtypes. The potential use of this approach for evaluating chemical selectivity towards non-NMDA receptor subtypes of GluRs and other receptor ion channel proteins is discussed.

  10. Down Select Report of Chemical Hydrogen Storage Materials, Catalysts, and Spent Fuel Regeneration Processes

    Energy Technology Data Exchange (ETDEWEB)

    Ott, Kevin; Linehan, Sue; Lipiecki, Frank; Aardahl, Christopher L.

    2008-08-24

    The DOE Hydrogen Storage Program is focused on identifying and developing viable hydrogen storage systems for onboard vehicular applications. The program funds exploratory research directed at identifying new materials and concepts for storage of hydrogen having high gravimetric and volumetric capacities that have the potential to meet long term technical targets for onboard storage. Approaches currently being examined are reversible metal hydride storage materials, reversible hydrogen sorption systems, and chemical hydrogen storage systems. The latter approach concerns materials that release hydrogen in endothermic or exothermic chemical bond-breaking processes. To regenerate the spent fuels arising from hydrogen release from such materials, chemical processes must be employed. These chemical regeneration processes are envisioned to occur offboard the vehicle.

  11. Importance of asparagine on the conformational stability and chemical reactivity of selected anti-inflammatory peptides

    Energy Technology Data Exchange (ETDEWEB)

    Soriano-Correa, Catalina, E-mail: csorico@comunidad.unam.mx [Química Computacional, Facultad de Estudios Superiores (FES)-Zaragoza, Universidad Nacional Autónoma de México (UNAM), Iztapalapa, C.P. 09230 México, D.F. (Mexico); Barrientos-Salcedo, Carolina [Laboratorio de Química Médica y Quimiogenómica, Facultad de Bioanálisis Campus Veracruz-Boca del Río, Universidad Veracruzana, C.P. 91700 Veracruz (Mexico); Campos-Fernández, Linda; Alvarado-Salazar, Andres [Química Computacional, Facultad de Estudios Superiores (FES)-Zaragoza, Universidad Nacional Autónoma de México (UNAM), Iztapalapa, C.P. 09230 México, D.F. (Mexico); Esquivel, Rodolfo O. [Departamento de Química, Universidad Autónoma Metropolitana-Iztapalapa (UAM-Iztapalapa), C.P. 09340 México, D.F. (Mexico)

    2015-08-18

    Highlights: • Asparagine plays an important role to anti-inflammatory effect of peptides. • The electron-donor substituent groups favor the formation of the hydrogen bonds, which contribute in the structural stability of peptides. • Chemical reactivity and the physicochemical features are crucial in the biological functions of peptides. - Abstract: Inflammatory response events are initiated by a complex series of molecular reactions that generate chemical intermediaries. The structure and properties of peptides and proteins are determined by the charge distribution of their side chains, which play an essential role in its electronic structure and physicochemical properties, hence on its biological functionality. The aim of this study was to analyze the effect of changing one central amino acid, such as substituting asparagine for aspartic acid, from Cys–Asn–Ser in aqueous solution, by assessing the conformational stability, physicochemical properties, chemical reactivity and their relationship with anti-inflammatory activity; employing quantum-chemical descriptors at the M06-2X/6-311+G(d,p) level. Our results suggest that asparagine plays a more critical role than aspartic acid in the structural stability, physicochemical features, and chemical reactivity of these tripeptides. Substituent groups in the side chain cause significant changes on the conformational stability and chemical reactivity, and consequently on their anti-inflammatory activity.

  12. Fluid Shifts

    Science.gov (United States)

    Stenger, M. B.; Hargens, A. R.; Dulchavsky, S. A.; Arbeille, P.; Danielson, R. W.; Ebert, D. J.; Garcia, K. M.; Johnston, S. L.; Laurie, S. S.; Lee, S. M. C.; Liu, J.; Macias, B.; Martin, D. S.; Minkoff, L.; Ploutz-Snyder, R.; Ribeiro, L. C.; Sargsyan, A.; Smith, S. M.

    2017-01-01

    Introduction. NASA's Human Research Program is focused on addressing health risks associated with long-duration missions on the International Space Station (ISS) and future exploration-class missions beyond low Earth orbit. Visual acuity changes observed after short-duration missions were largely transient, but now more than 50 percent of ISS astronauts have experienced more profound, chronic changes with objective structural findings such as optic disc edema, globe flattening and choroidal folds. These structural and functional changes are referred to as the visual impairment and intracranial pressure (VIIP) syndrome. Development of VIIP symptoms may be related to elevated intracranial pressure (ICP) secondary to spaceflight-induced cephalad fluid shifts, but this hypothesis has not been tested. The purpose of this study is to characterize fluid distribution and compartmentalization associated with long-duration spaceflight and to determine if a relation exists with vision changes and other elements of the VIIP syndrome. We also seek to determine whether the magnitude of fluid shifts during spaceflight, as well as any VIIP-related effects of those shifts, are predicted by the crewmember's pre-flight status and responses to acute hemodynamic manipulations, specifically posture changes and lower body negative pressure. Methods. We will examine a variety of physiologic variables in 10 long-duration ISS crewmembers using the test conditions and timeline presented in the figure below. Measures include: (1) fluid compartmentalization (total body water by D2O, extracellular fluid by NaBr, intracellular fluid by calculation, plasma volume by CO rebreathe, interstitial fluid by calculation); (2) forehead/eyelids, tibia, and calcaneus tissue thickness (by ultrasound); (3) vascular dimensions by ultrasound (jugular veins, cerebral and carotid arteries, vertebral arteries and veins, portal vein); (4) vascular dynamics by MRI (head/neck blood flow, cerebrospinal fluid

  13. Tree resin composition, collection behavior and selective filters shape chemical profiles of tropical bees (Apidae: Meliponini).

    Science.gov (United States)

    Leonhardt, Sara D; Schmitt, Thomas; Blüthgen, Nico

    2011-01-01

    The diversity of species is striking, but can be far exceeded by the chemical diversity of compounds collected, produced or used by them. Here, we relate the specificity of plant-consumer interactions to chemical diversity applying a comparative network analysis to both levels. Chemical diversity was explored for interactions between tropical stingless bees and plant resins, which bees collect for nest construction and to deter predators and microbes. Resins also function as an environmental source for terpenes that serve as appeasement allomones and protection against predators when accumulated on the bees' body surfaces. To unravel the origin of the bees' complex chemical profiles, we investigated resin collection and the processing of resin-derived terpenes. We therefore analyzed chemical networks of tree resins, foraging networks of resin collecting bees, and their acquired chemical networks. We revealed that 113 terpenes in nests of six bee species and 83 on their body surfaces comprised a subset of the 1,117 compounds found in resins from seven tree species. Sesquiterpenes were the most variable class of terpenes. Albeit widely present in tree resins, they were only found on the body surface of some species, but entirely lacking in others. Moreover, whereas the nest profile of Tetragonula melanocephala contained sesquiterpenes, its surface profile did not. Stingless bees showed a generalized collecting behavior among resin sources, and only a hitherto undescribed species-specific "filtering" of resin-derived terpenes can explain the variation in chemical profiles of nests and body surfaces from different species. The tight relationship between bees and tree resins of a large variety of species elucidates why the bees' surfaces contain a much higher chemodiversity than other hymenopterans.

  14. Improved transgene expression in doxycycline-inducible embryonic stem cells by repeated chemical selection or cell sorting

    Directory of Open Access Journals (Sweden)

    Renáta Bencsik

    2016-09-01

    Full Text Available Transgene-mediated programming is a preeminent strategy to direct cellular identity. To facilitate cell fate switching, lineage regulating genes must be efficiently and uniformly induced. However, gene expression is often heterogeneous in transgenic systems. Consistent with this notion, a non-uniform reporter gene expression was detected in our doxycycline (DOX-regulated, murine embryonic stem (ES cell clones. Interestingly, a significant fraction of cells within each clone failed to produce any reporter signals upon DOX treatment. We found that the majority of these non-responsive cells neither carry reporter transgene nor geneticin/G418 resistance. This observation suggested that our ES cell clones contained non-recombined cells that survived the G418 selection which was carried out during the establishment of these clones. We successfully eliminated most of these corrupted cells with repeated chemical (G418 selection, however, even after prolonged G418 treatments, a few cells remained non-responsive due to epigenetic silencing. We found that cell sorting has been the most efficient approach to select those cells which can uniformly and stably induce the integrated transgene in this ES cell based platform. Together, our data revealed that post-cloning chemical re-selection or cell sorting strongly facilitate the production of ES cell lines with a uniform transgene induction capacity.

  15. Site-specific protein backbone and side-chain NMR chemical shift and relaxation analysis of human vinexin SH3 domain using a genetically encoded {sup 15}N/{sup 19}F-labeled unnatural amino acid

    Energy Technology Data Exchange (ETDEWEB)

    Shi, Pan [National Laboratory for Physical Science at Microscale, University of Science and Technology of China, Hefei, Anhui 230026 (China); School of Life Science, University of Science and Technology of China, Hefei, Anhui 230026 (China); Xi, Zhaoyong; Wang, Hu [School of Chemistry, University of Science and Technology of China, Hefei, Anhui 230026 (China); Shi, Chaowei [National Laboratory for Physical Science at Microscale, University of Science and Technology of China, Hefei, Anhui 230026 (China); School of Life Science, University of Science and Technology of China, Hefei, Anhui 230026 (China); Xiong, Ying, E-mail: yxiong73@ustc.edu.cn [School of Life Science, University of Science and Technology of China, Hefei, Anhui 230026 (China); Tian, Changlin, E-mail: cltian@ustc.edu.cn [National Laboratory for Physical Science at Microscale, University of Science and Technology of China, Hefei, Anhui 230026 (China)

    2010-11-19

    Research highlights: {yields} Chemical synthesis of {sup 15}N/{sup 19}F-trifluomethyl phenylalanine. {yields} Site-specific incorporation of {sup 15}N/{sup 19}F-trifluomethyl phenylalanine to SH3. {yields} Site-specific backbone and side chain chemical shift and relaxation analysis. {yields} Different internal motions at different sites of SH3 domain upon ligand binding. -- Abstract: SH3 is a ubiquitous domain mediating protein-protein interactions. Recent solution NMR structural studies have shown that a proline-rich peptide is capable of binding to the human vinexin SH3 domain. Here, an orthogonal amber tRNA/tRNA synthetase pair for {sup 15}N/{sup 19}F-trifluoromethyl-phenylalanine ({sup 15}N/{sup 19}F-tfmF) has been applied to achieve site-specific labeling of SH3 at three different sites. One-dimensional solution NMR spectra of backbone amide ({sup 15}N){sup 1}H and side-chain {sup 19}F were obtained for SH3 with three different site-specific labels. Site-specific backbone amide ({sup 15}N){sup 1}H and side-chain {sup 19}F chemical shift and relaxation analysis of SH3 in the absence or presence of a peptide ligand demonstrated different internal motions upon ligand binding at the three different sites. This site-specific NMR analysis might be very useful for studying large-sized proteins or protein complexes.

  16. High-value chemicals obtained from selective photo-oxidation of glucose in the presence of nanostructured titanium photocatalysts.

    Science.gov (United States)

    Colmenares, Juan C; Magdziarz, Agnieszka; Bielejewska, Anna

    2011-12-01

    Glucose was oxidized in the presence of powdered TiO(2) photocatalysts synthesized by an ultrasound-promoted sol-gel method. The catalysts were more selective towards glucaric acid, gluconic acid and arabitol (total selectivity approx. 70%) than the most popular photocatalyst, Degussa P-25. The photocatalytic systems worked at mild reaction conditions: 30°C, atmospheric pressure and very short reaction time (e.g. 5 min). Such relatively good selectivity towards high-valued molecules are attributed to the physico-chemical properties (e.g. high specific surface area, nanostructured anatase phase, and visible light absorption) of novel TiO(2) materials and the reaction conditions. The TiO(2) photocatalysts have potential for water purification and energy production and for use in the pharmaceutical, food, perfume and fuel industries.

  17. Fiber array based hyperspectral Raman imaging for chemical selective analysis of malaria-infected red blood cells

    Energy Technology Data Exchange (ETDEWEB)

    Brückner, Michael [Leibniz Institute of Photonic Technology, 07745 Jena (Germany); Becker, Katja [Justus Liebig University Giessen, Biochemistry and Molecular Biology, 35392 Giessen (Germany); Popp, Jürgen [Leibniz Institute of Photonic Technology, 07745 Jena (Germany); Friedrich Schiller University Jena, Institute for Physical Chemistry, 07745 Jena (Germany); Friedrich Schiller University Jena, Abbe Centre of Photonics, 07745 Jena (Germany); Frosch, Torsten, E-mail: torsten.frosch@uni-jena.de [Leibniz Institute of Photonic Technology, 07745 Jena (Germany); Friedrich Schiller University Jena, Institute for Physical Chemistry, 07745 Jena (Germany); Friedrich Schiller University Jena, Abbe Centre of Photonics, 07745 Jena (Germany)

    2015-09-24

    A new setup for Raman spectroscopic wide-field imaging is presented. It combines the advantages of a fiber array based spectral translator with a tailor-made laser illumination system for high-quality Raman chemical imaging of sensitive biological samples. The Gaussian-like intensity distribution of the illuminating laser beam is shaped by a square-core optical multimode fiber to a top-hat profile with very homogeneous intensity distribution to fulfill the conditions of Koehler. The 30 m long optical fiber and an additional vibrator efficiently destroy the polarization and coherence of the illuminating light. This homogeneous, incoherent illumination is an essential prerequisite for stable quantitative imaging of complex biological samples. The fiber array translates the two-dimensional lateral information of the Raman stray light into separated spectral channels with very high contrast. The Raman image can be correlated with a corresponding white light microscopic image of the sample. The new setup enables simultaneous quantification of all Raman spectra across the whole spatial area with very good spectral resolution and thus outperforms other Raman imaging approaches based on scanning and tunable filters. The unique capabilities of the setup for fast, gentle, sensitive, and selective chemical imaging of biological samples were applied for automated hemozoin analysis. A special algorithm was developed to generate Raman images based on the hemozoin distribution in red blood cells without any influence from other Raman scattering. The new imaging setup in combination with the robust algorithm provides a novel, elegant way for chemical selective analysis of the malaria pigment hemozoin in early ring stages of Plasmodium falciparum infected erythrocytes. - Highlights: • Raman hyperspectral imaging allows for chemical selective analysis of biological samples with spatial heterogeneity. • A homogeneous, incoherent illumination is essential for reliable

  18. Chemical conditions in present and future ecosystems in Forsmark - implications for selected radionuclides in the safety assessment SR-Site

    Energy Technology Data Exchange (ETDEWEB)

    Troejbom, Mats (Mats Troejbom Konsult AB (Sweden)); Grolander, Sara (Facilia AB (Sweden))

    2010-12-15

    This report is a background report for the biosphere analysis of the SR-Site Safety Assessment. This work aims to describe the future development of the chemical conditions at Forsmark, based on the present chemical conditions at landscape level taking landscape development and climate cases into consideration. The results presented contribute to the overall understanding of the present and future chemistry in the Forsmark area, and specifically, to the understanding of the behaviour of some selected radionuclides in the surface system. The future development of the chemistry at the site is qualitatively discussed with focus on the interglacial within the next 10,000 years. The effects on the chemical environment of future climate cases as Global Warming and cold permafrost climates are also briefly discussed. The work is presented in two independent parts describing background radionuclide activities in the Forsmark area and the distribution and behaviour of a large number of stable elements in the landscape. In a concluding section, implications of the future chemical environment of a selection of radionuclides important in the Safety Assessment are discussed based on the knowledge of stable elements. The broad range of elements studied show that there are general and expected patterns for the distribution and behaviour in the landscape of different groups of elements. Mass balances reveal major sources and sinks, pool estimations show where elements are accumulated in the landscape and estimations of time-scales give indications of the potential future development. This general knowledge is transferred to radionuclides not measured in order to estimate their behaviour and distribution in the landscape. It could be concluded that the future development of the chemical environment in the Forsmark area might affect element specific parameters used in de radionuclide model in different directions depending on element. The alternative climate cases, Global Warming

  19. Efficient and Selective Chemical Labeling of Electrochemically Generated Peptides Based on Spirolactone Chemistry

    NARCIS (Netherlands)

    Zhang, Tao; Niu, Xiaoyu; Yuan, Tao; Tessari, Marco; de Vries, Marcel P.; Permentier, Hjalmar P.; Bischoff, Rainer

    2016-01-01

    Specific digestion of proteins is an essential step for mass spectrometry-based proteomics, and the chemical labeling of the resulting peptides is often used for peptide enrichment or the introduction of desirable tags. Cleavage of the peptide bond following electrochemical oxidation of Tyr or Trp r

  20. Selective chemical binding enhances cesium tolerance in plants through inhibition of cesium uptake

    DEFF Research Database (Denmark)

    Adams, Eri; Chaban, Vitaly; Khandelia, Himanshu;

    2015-01-01

    High concentrations of cesium (Cs(+)) inhibit plant growth but the detailed mechanisms of Cs(+) uptake, transport and response in plants are not well known. In order to identify small molecules with a capacity to enhance plant tolerance to Cs(+), chemical library screening was performed using Ara...

  1. The Reduction of Microbial and Chemical Contaminants with Selected POU/POE Systems

    Science.gov (United States)

    Centralized drinking water treatment and distribution alone may not always be the most practical or cost-effective option. Also, some consumers seeking a proactive measure to reduce exposure to pathogens and chemicals not currently monitored or regulated might consider employing...

  2. Linear solvation energy relationships for toxicity of selected organic chemicals to Daphnia pulex and Daphnia magna

    Science.gov (United States)

    Passino, Dora R.M.; Hickey, James P.; Frank, Anthony M.

    1988-01-01

    In the Laurentian Great Lakes, more than 300 contaminants have been identified in fish, other biota, water, and sediment. Current hazard assessment of these chemicals by the National Fisheries Research Center-Great Lakes is based on their toxicity, occurrence in the environment, and source. Although scientists at the Center have tested over 70 chemicals with the crustacean Daphnia pulex, the number of experimental data needed to screen the huge array of chemicals in the Great Lakes exceeds the practical capabilities of conducting bioassays. This limitation can be partly circumvented, however, by using mathematical models based on quantitative structure-activity relationships (QSAR) to provide rapid, inexpensive estimates of toxicity. Many properties of chemicals, including toxicity, bioaccumulation and water solubility are well correlated and can be predicted by equations of the generalized linear solvation energy relationships (LSER). The equation we used to model solute toxicity is Toxicity = constant + mVI/100 + s (π* + dδ) + bβm + aαm where VI = intrinsic (Van der Waals) molar volume; π* = molecular dipolarity/polarizability; δ = polarizability 'correction term'; βm = solute hydrogen bond acceptor basicity; and αm = solute hydrogen bond donor acidity. The subscript m designates solute monomer values for α and β. We applied the LSER model to 48-h acute toxicity data (measured as immobilization) for six classes of chemicals detected in Great Lakes fish. The following regression was obtained for Daphnia pulex (concentration = μM): log EC50 = 4.86 - 4.35 VI/100; N = 38, r2 = 0.867, sd = 0.403 We also used the LSER modeling approach to analyze to a large published data set of 24-h acute toxicity for Daphnia magna; the following regression resulted, for eight classes of compounds (concentration = mM): log EC50 = 3.88 - 4.52 VI/100 - 1.62 π* + 1.66 βm - 0.916 αm; N = 62, r2 = 0.859, sd = 0.375 In addition we developed computer software that identifies

  3. Tuning the chemical selectivity of SWNT-FETs for detection of heavy-metal ions.

    Science.gov (United States)

    Forzani, Erica S; Li, Xiulan; Zhang, Peiming; Tao, Nongjian; Zhang, Ruth; Amlani, Islamshah; Tsui, Raymond; Nagahara, Larry A

    2006-11-01

    A method to functionalize single-walled carbon nanotubes (SWNTs) in a field-effect transistor (FET) device for the selective detection of heavy-metal ions is presented. In this method, peptide-modified polymers were electrochemically deposited onto SWNTs and the selective detection of metal ions was demonstrated by choosing appropriate peptide sequences. The signal transduction mechanism of the peptide-modified SWNT-FETs has also been studied.

  4. Chemically engineering ligand selectivity at the free fatty acid receptor 2 based on pharmacological variation between species orthologs

    Science.gov (United States)

    Hudson, Brian D.; Christiansen, Elisabeth; Tikhonova, Irina G.; Grundmann, Manuel; Kostenis, Evi; Adams, David R.; Ulven, Trond; Milligan, Graeme

    2012-01-01

    When it is difficult to develop selective ligands within a family of related G-protein-coupled receptors (GPCRs), chemically engineered receptors activated solely by synthetic ligands (RASSLs) are useful alternatives for probing receptor function. In the present work, we explored whether a RASSL of the free fatty acid receptor 2 (FFA2) could be developed on the basis of pharmacological variation between species orthologs. For this, bovine FFA2 was characterized, revealing distinct ligand selectivity compared with human FFA2. Homology modeling and mutational analysis demonstrated a single mutation in human FFA2 of C4.57G resulted in a human FFA2 receptor with ligand selectivity similar to the bovine receptor. This was exploited to generate human FFA2-RASSL by the addition of a second mutation at a known orthosteric ligand interaction site, H6.55Q. The resulting FFA2-RASSL displayed a >100-fold loss of activity to endogenous ligands, while responding to the distinct ligand sorbic acid with pEC50 values for inhibition of cAMP, 5.83 ± 0.11; Ca2+ mobilization, 4.63 ± 0.05; ERK phosphorylation, 5.61 ± 0.06; and dynamic mass redistribution, 5.35 ± 0.06. This FFA2-RASSL will be useful in future studies on this receptor and demonstrates that exploitation of pharmacological variation between species orthologs is a powerful method to generate novel chemically engineered GPCRs.—Hudson, B. D., Christiansen, E., Tikhonova, I. G., Grundmann, M., Kostenis, E., Adams, D. R., Ulven, T., Milligan, G. Chemically engineering ligand selectivity at the free fatty acid receptor 2 based on pharmacological variation between species orthologs. PMID:22919070

  5. Mental rotation impairs attention shifting and short-term memory encoding: neurophysiological evidence against the response-selection bottleneck model of dual-task performance

    NARCIS (Netherlands)

    M.M. Pannebakker; W.O. van Dam; G.P.H. Band; K.R. Ridderinkhof; B. Hommel

    2011-01-01

    Dual tasks and their associated delays have often been used to examine the boundaries of processing in the brain. We used the dual-task procedure and recorded event-related potentials (ERPs) to investigate how mental rotation of a first stimulus (S1) influences the shifting of visual-spatial attenti

  6. Antibacterial activity of coffee extracts and selected coffee chemical compounds against enterobacteria.

    Science.gov (United States)

    Almeida, Ana Amélia P; Farah, Adriana; Silva, Daniela A M; Nunan, Elzíria A; Glória, M Beatriz A

    2006-11-15

    The in vitro antimicrobial activity of commercial coffee extracts and chemical compounds was investigated on nine strains of enterobacteria. The antimicrobial activity investigated by the disc diffusion method was observed in both the extracts and tested chemical compounds. Even though pH, color, and the contents of trigonelline, caffeine, and chlorogenic acids differed significantly among the coffee extracts, no significant differences were observed in their antimicrobial activity. Caffeic acid and trigonelline showed similar inhibitory effect against the growth of the microorganisms. Caffeine, chlorogenic acid, and protocatechuic acid showed particularly strong effect against Serratia marcescens and Enterobacter cloacae. The IC(50) and IC(90) for the compounds determined by the microtiter plate method indicated that trigonelline, caffeine, and protocatechuic acids are potential natural antimicrobial agents against Salmonella enterica. The concentrations of caffeine found in coffee extracts are enough to warrant 50% of the antimicrobial effect against S. enterica, which is relevant to human safety.

  7. Selective chemical binding enhances cesium tolerance in plants through inhibition of cesium uptake

    Science.gov (United States)

    Adams, Eri; Chaban, Vitaly; Khandelia, Himanshu; Shin, Ryoung

    2015-03-01

    High concentrations of cesium (Cs+) inhibit plant growth but the detailed mechanisms of Cs+ uptake, transport and response in plants are not well known. In order to identify small molecules with a capacity to enhance plant tolerance to Cs+, chemical library screening was performed using Arabidopsis. Of 10,000 chemicals tested, five compounds were confirmed as Cs+ tolerance enhancers. Further investigation and quantum mechanical modelling revealed that one of these compounds reduced Cs+ concentrations in plants and that the imidazole moiety of this compound bound specifically to Cs+. Analysis of the analogous compounds indicated that the structure of the identified compound is important for the effect to be conferred. Taken together, Cs+ tolerance enhancer isolated here renders plants tolerant to Cs+ by inhibiting Cs+ entry into roots via specific binding to the ion thus, for instance, providing a basis for phytostabilisation of radiocesium-contaminated farmland.

  8. Physico-Chemical Analysis of Selected Groundwater Samples of Inkollu Mandal, Prakasam District, Andhra Pradesh, India

    Directory of Open Access Journals (Sweden)

    G. Arun Kumar

    2015-04-01

    Full Text Available Physico-chemical parameters of groundwater quality based on Physic-chemical parameters at Inkollu mandal, Prakasam district, Andhra Pradesh, India have been taken up to evaluate its suitability for Drinking purpose. Nine ground water samples were collected from different places of Inkollu mandal of Prakasam district. The quality analysis has been made through the pH, EC, TDS, Total Hardness, Sodium, Potassium, Calcium, Magnesium, Chloride, Sulphate, Nitrate, Fluoride and Iron. By observing the results, it was shown that the parameters from the water samples were compared with WHO (World Health Organization and BIS (Bureau of Indian Standards, USPH (United state Public health for ground water .The results revealed that some parameters were in high concentration and quality of the potable water has deteriorated to a large extent at some sampling locations.

  9. Chemical analysis of selected pothole water sources in Southwestern National Parks, Monuments, and Recreation Areas

    Energy Technology Data Exchange (ETDEWEB)

    Gladney, E.S.; Ferenbaugh, R.W.; Bell, M.G.; Burns, C.; Morgan, J.D.; Nickell, E.J. [Los Alamos National Lab., NM (United States); Graham, T. [US Department of the Interior, National Park Service (United States)

    1993-10-01

    Environmental data related to the evaluation of inorganic air pollution input to pothole ecosystems in the desert Southwest have been collected over the past several years. Chemical composition of pothole waters and associated sediments are reported. The enrichment factor approach has been applied to the sediments in an effort to identify elemental levels that diverge from mean crustal abundances. These data provide a baseline for determining changes in elemental concentration and enrichment status in the future.

  10. Application of Photocured Polymer Ion Selective Membranes for Solid-State Chemical Sensors

    Directory of Open Access Journals (Sweden)

    Natalia Abramova

    2015-06-01

    Full Text Available Application of conducting polymers with additional functional groups for a solid contact formation and photocurable membranes as sensitive elements of solid-state chemical sensors is discussed. Problems associated with application of UV-curable polymers for sensors are analyzed. A method of sensor fabrication using copolymerized conductive layer and sensitive membrane is presented and the proof of concept is confirmed by two examples of solid-contact electrodes for Ca ions and pH.

  11. A corona discharge atmospheric pressure chemical ionization source with selective NO(+) formation and its application for monoaromatic VOC detection.

    Science.gov (United States)

    Sabo, Martin; Matejčík, Štefan

    2013-11-21

    We have developed a new type of corona discharge (CD) for atmospheric pressure chemical ionization (APCI) for application in ion mobility spectrometry (IMS) as well as in mass spectrometry (MS). While the other CD-APCI sources are able to generate H3O(+)·(H2O)n as the major reactant ions in N2 or in zero air, the present CD-APCI source has the ability to generate up to 84% NO(+)·(H2O)n reactant ions in zero air. The change of the working gas from zero air to N2 allows us to change the major reactant ions from NO(+)·(H2O)n to H3O(+)·(H2O)n. In this paper we present the description of the new CD-APCI and discuss the processes associated with the NO(+) formation. The selective formation of NO(+)·(H2O)n reactant ions offers chemical ionization based on these ions which can be of great advantage for some classes of chemicals. We demonstrate here a significant increase in the sensitivity of the IMS-MS instrument for monoaromatic volatile organic compound (VOC) detection upon NO(+)·(H2O)n chemical ionization.

  12. Chemical contaminants on DOE lands and selection of contaminant mixtures for subsurface science research

    Energy Technology Data Exchange (ETDEWEB)

    Riley, R.G.; Zachara, J.M. [Pacific Northwest Lab., Richland, WA (United States)

    1992-04-01

    This report identifies individual contaminants and contaminant mixtures that have been measured in the ground at 91 waste sites at 18 US Department of Energy (DOE) facilities within the weapons complex. The inventory of chemicals and mixtures was used to identify generic chemical mixtures to be used by DOE`s Subsurface Science Program in basic research on the subsurface geochemical and microbiological behavior of mixed contaminants (DOE 1990a and b). The generic mixtures contain specific radionuclides, metals, organic ligands, organic solvents, fuel hydrocarbons, and polychlorinated biphenyls (PCBs) in various binary and ternary combinations. The mixtures are representative of in-ground contaminant associations at DOE facilities that are likely to exhibit complex geochemical behavior as a result of intercontaminant reactions and/or microbiologic activity stimulated by organic substances. Use of the generic mixtures will focus research on important mixed contaminants that are likely to be long-term problems at DOE sites and that will require cleanup or remediation. The report provides information on the frequency of associations among different chemicals and compound classes at DOE waste sites that require remediation.

  13. Chemical contaminants on DOE lands and selection of contaminant mixtures for subsurface science research

    Energy Technology Data Exchange (ETDEWEB)

    Riley, R.G.; Zachara, J.M. (Pacific Northwest Lab., Richland, WA (United States))

    1992-04-01

    This report identifies individual contaminants and contaminant mixtures that have been measured in the ground at 91 waste sites at 18 US Department of Energy (DOE) facilities within the weapons complex. The inventory of chemicals and mixtures was used to identify generic chemical mixtures to be used by DOE's Subsurface Science Program in basic research on the subsurface geochemical and microbiological behavior of mixed contaminants (DOE 1990a and b). The generic mixtures contain specific radionuclides, metals, organic ligands, organic solvents, fuel hydrocarbons, and polychlorinated biphenyls (PCBs) in various binary and ternary combinations. The mixtures are representative of in-ground contaminant associations at DOE facilities that are likely to exhibit complex geochemical behavior as a result of intercontaminant reactions and/or microbiologic activity stimulated by organic substances. Use of the generic mixtures will focus research on important mixed contaminants that are likely to be long-term problems at DOE sites and that will require cleanup or remediation. The report provides information on the frequency of associations among different chemicals and compound classes at DOE waste sites that require remediation.

  14. Chemical effect on the K shell absorption parameters of some selected cerium compounds

    Science.gov (United States)

    Akman, F.; Kaçal, M. R.; Durak, R.

    2016-08-01

    In this study, the photoelectric cross section values of Ce, CeCl3.7H2O, Ce2(SO4)3, Ce(OH)4 and Ce2O3 samples were measured in the energy range from 31.82 keV up to 51.70 keV by adopting in narrow beam geometry. Using these photoelectric cross sections, the K shell photoelectric cross sections at the K-edge, the K shell absorption jump ratios and jump factors, the Davisson-Kirchner ratios and K shell oscillator strength values were estimated experimentally. The measured parameters were compared with the theoretical calculated values. It is observed that the K shell photoelectric cross section at the K-edge and K shell oscillator strength values of an element are affected by the chemical environment of material while the K shell absorption jump ratio, K shell absorption jump factor and Davisson-Kirchner ratio are not affected by the chemical environment of material for the present samples. To the best of our knowledge, the chemical effects on the Davisson-Kirchner ratio and K shell oscillator strength have not been discussed for any element by now.

  15. Plakilactones G and H from a marine sponge. Stereochemical determination of highly flexible systems by quantitative NMR-derived interproton distances combined with quantum mechanical calculations of 13C chemical shifts

    Directory of Open Access Journals (Sweden)

    Simone Di Micco

    2013-12-01

    Full Text Available In this paper the stereostructural investigation of two new oxygenated polyketides, plakilactones G and H, isolated from the marine sponge Plakinastrella mamillaris collected at Fiji Islands, is reported. The stereostructural studies began on plakilactone H by applying an integrated approach of the NOE-based protocol and quantum mechanical calculations of 13C chemical shifts. In particular, plakilactone H was used as a template to extend the application of NMR-derived interproton distances to a highly flexible molecular system with simultaneous assignment of four non-contiguous stereocenters. Chemical derivatization and quantum mechanical calculations of 13C on plakilactone G along with a plausible biogenetic interconversion between plakilactone G and plakilactone H allowed us to determine the absolute configuration in this two new oxygenated polyketides.

  16. Design and Use of Nanostructured Single-Site Heterogeneous Catalysts for the Selective Transformation of Fine Chemicals

    Directory of Open Access Journals (Sweden)

    Vladimiro Dal Santo

    2010-05-01

    Full Text Available Nanostructured single-site heterogeneous catalysts possess the advantages of classical solid catalysts, in terms of easy recovery and recycling, together with a defined tailored chemical and steric environment around the catalytically active metal site. The use of inorganic oxide supports with selected shape and porosity at a nanometric level may have a relevant impact on the regio- and stereochemistry of the catalytic reaction. Analogously, by choosing the optimal preparation techniques to obtain spatially isolated and well-characterised active sites, it is possible to achieve performances that are comparable to (or, in the most favourable cases, better than those obtained with homogeneous systems. Such catalysts are therefore particularly suitable for the transformation of highly-functionalised fine chemicals and some relevant examples where high chemo-, regio- and stereoselectivity are crucial will be described.

  17. Protective clothing for pesticide operators: part I--selection of a reference test chemical for penetration testing.

    Science.gov (United States)

    Shaw, Anugrah; Schiffelbein, Paul

    2016-01-01

    A systematic approach was taken to develop a database for protective clothing for pesticide operators; results are reported as a two-part series. Part I describes the research studies that led to identification of a pesticide formulation that could serve as a reference test chemical for further testing. Measurement of pesticide penetration was conducted using different types of pesticide formulations. Six fabrics were tested using 10 formulations at different concentrations. Three formulations were subsequently selected for further testing. Analysis of the data indicated that, when compared with other formulations, mean percent penetration of 5% Prowl 3.3 EC [emulsifiable concentrate diluted to 5% active ingredient (pendimethalin)] is either similar to or higher than most test chemicals. Those results led to choosing 5% Prowl 3.3 EC as a reference test liquid. Part II of the study, published as a separate paper, includes data on a wide range of textile materials.

  18. Selected Physical, Chemical, and Biological Data for 30 Urbanizing Streams in the North Carolina Piedmont Ecoregion, 2002-2003

    Science.gov (United States)

    Giddings, E.M.; Moorman, Michelle; Cuffney, Thomas F.; McMahon, Gerard; Harned, Douglas A.

    2007-01-01

    This report provides summarized physical, chemical, and biological data collected during a study of the effects of urbanization on stream ecosystems as part of the U.S. Geological Survey's National Water-Quality Assessment study. The purpose of this study was to examine differences in biological, chemical, and physical characteristics of streams across a gradient of urban intensity. Thirty sites were selected along an urbanization gradient that represents conditions in the North Carolina Piedmont ecoregion, including the cities of Raleigh, Durham, Cary, Greensboro, Winston-Salem, High Point, Asheboro, and Oxford. Data collected included streamflow variability, stream temperature, instream chemistry, instream aquatic habitat, and collections of the algal, macroinvertebrate, and fish communities. In addition, ancillary data describing land use, socioeconomic conditions, and urban infrastructure were compiled for each basin using a geographic information system analysis. All data were processed and summarized for analytical use and are presented in downloadable data tables, along with the methods of data collection and processing.

  19. Polynuclear Nickel Hexacyanoferrate/Graphitized Mesoporous Carbon Hybrid Chemically Modified Electrode for Selective Hydrazine Detection

    OpenAIRE

    Palani Barathi; Annamalai Senthil Kumar; Minnal Ranjan Babu Karthick

    2011-01-01

    A hybrid polynuclear nickel hexacyanoferrate (NiHCFe)/graphitized mesoporous carbon- (GMC-) modified glassy carbon electrode (GCE/NiHCFe@GMC) has been prepared by a sequential method using electrodeposited Ni on a GMC-modified glassy carbon electrode (GCE/Ni@GMC) as a template and [Fe(CN)6]3− as an in-situ chemical precipitant, without any additional interlinking agent. Physicochemical and electrochemical characterizations reveal the presence of NiHCFe units within the porous sites of the GM...

  20. Evidence for porphyrins bound, via ester bonds, to the Messel oil shale kerogen by selective chemical degradation experiments

    Science.gov (United States)

    Huseby, B.; Ocampo, R.

    1997-09-01

    High amounts of nickel mono- and di-acid porphyrins were released from Messel oil shale kerogen (Eocene, Germany) by selective chemical degradation (acid and base hydrolysis). The released porphyrin fractions were quantified (UV-vis) and their constituents isolated and characterized at the molecular level (UV-vis, MS, NMR). The mono-acid porphyrin fraction released contained four compounds of similar abundance which arise from an obvious chlorophyll or bacteriochlorophyll precursor. The di-acid porphyrin fraction was, however, dominated by far by one compound, mesoporphyrin IX, which must have originated from heme-like precursors (heme, cytochromes, etc.). These results show unambigously that the released mono- and di-acid porphyrins were linked to the macromolecular kerogen network via ester bonds and suggest that precursor heme-like pigments could be selectively and/or more readily incorporated into the macromolecular kerogen network than precursor chlorophylls and bacteriochlorophylls.

  1. Application of high-throughput affinity-selection mass spectrometry for screening of chemical compound libraries in lead discovery.

    Science.gov (United States)

    Zehender, Hartmut; Mayr, Lorenz M

    2007-02-01

    High-throughput screening of chemical libraries for compounds that interfere with a particular molecular target is among the most powerful methodologies applied in lead discovery at present. In this review, the authors describe a label-free, homogeneous, affinity-selection-based technology developed at Novartis, termed SpeedScreen, which is compared with similar technologies used for high-throughput screening in the pharmaceutical and biotechnology industries. The focus at present of SpeedScreen is twofold: first, this technology is applied to orphan genomic targets and to those targets that are non-tractable by a functional assay; second, this technology is applied complementary to the well-established traditional methodologies for the screening of molecular targets. In summary, the authors discuss the value of affinity-selection-based high-throughput screening as a complementary technology to the common functional screening platforms and the benefits as well as the limitations of this new technology are outlined.

  2. Influence of Chemical Effect on the Kβ/Kα Intensity Ratios and Kβ Energy Shift of Co, Ni, Cu, and Zn Complexes

    Institute of Scientific and Technical Information of China (English)

    G. Apaydma, V. Ayhkg; Z. Biyiklioglu; E. Tirasoglu; H. Kantekin

    2008-01-01

    Chemical effects on the Kβ/Kα intensity ratios and ΔE energy differences for Co, Ni, Cu, and Zn complexes were investigated. The samples were excited by 59.5 keV γ-rays from a 241 Am annular radioactive source. K X-rays emitted by samples were counted by an Ultra-LEGe detector with a resolution of 150 eV at 5.9 keV. We observed the effects of different ligands on the Kβ/Kα intensity ratios and ΔE energy differences for Co, Ni, Cu, and Zn complexes. We tried to investigate chemical effects on central atoms using the behaviors of different ligands in these complexes. The experimental values of Kβ/Kα were compared with the theoretical and other experimental values of pure Co, Ni, Cu, and Zn.

  3. Physical and chemical effects of acoustic cavitation in selected ultrasonic cleaning applications.

    Science.gov (United States)

    Yusof, Nor Saadah Mohd; Babgi, Bandar; Alghamdi, Yousef; Aksu, Mecit; Madhavan, Jagannathan; Ashokkumar, Muthupandian

    2016-03-01

    Acoustic cavitation in a liquid medium generates several physical and chemical effects. The oscillation and collapse of cavitation bubbles, driven at low ultrasonic frequencies (e.g., 20 kHz), can generate strong shear forces, microjets, microstreaming and shockwaves. Such strong physical forces have been used in cleaning and flux improvement of ultrafiltration processes. These physical effects have also been shown to deactivate pathogens. The efficiency of deactivation of pathogens is not only dependent on ultrasonic experimental parameters, but also on the properties of the pathogens themselves. Bacteria with thick shell wall are found to be resistant to ultrasonic deactivation process. Some evidence does suggest that the chemical effects (radicals) of acoustic cavitation are also effective in deactivating pathogens. Another aspect of cleaning, namely, purification of water contaminated with organic and inorganic pollutants, has also been discussed in detail. Strong oxidising agents produced within acoustic cavitation bubbles could be used to degrade organic pollutants and convert toxic inorganic pollutants to less harmful substances. The effect of ultrasonic frequency and surface activity of solutes on the sonochemical degradation efficiency has also been discussed in this overview.

  4. Density functional theory molecular modeling, chemical synthesis, and antimicrobial behaviour of selected benzimidazole derivatives

    Science.gov (United States)

    Marinescu, Maria; Tudorache, Diana Gabriela; Marton, George Iuliu; Zalaru, Christina-Marie; Popa, Marcela; Chifiriuc, Mariana-Carmen; Stavarache, Cristina-Elena; Constantinescu, Catalin

    2017-02-01

    Eco-friendly, one-pot, solvent-free synthesis of biologically active 2-substituted benzimidazoles is presented and discussed herein. Novel N-Mannich bases are synthesized from benzimidazoles, secondary amines and formaldehyde, and their structures are confirmed by 1H nuclear magnetic resonance (NMR), Fourier transform infrared (FTIR), and elemental analysis. All benzimidazole derivatives are evaluated by qualitative and quantitative methods against 9 bacterial strains. The largest microbicide and anti-biofilm effect is observed for the 2-(1-hydroxyethyl)-compounds. Density functional theory (DFT) modeling of the molecular structure and frontier molecular orbitals, i.e. highest occupied molecular orbital and lowest unoccupied molecular orbital (HOMO/LUMO), is accomplished by using the GAMESS 2012 software. Antimicrobial activity is correlated with the electronic parameters (chemical hardness, electronic chemical potential, global electrophilicity index), Mullikan atomic charges and geometric parameters of the benzimidazole compounds. The planarity of the compound, symmetry of the molecule, and the presence of a nucleophilic group, are advantages for a high antimicrobial activity. Finally, we briefly show that further accurate processing of such compounds into thin films and hybrid structures, e.g. by laser ablation matrix-assisted pulsed laser evaporation and/or laser-induced forward transfer, may indeed provide simple and environmental friendly, state-of-the-art solutions for antimicrobial coatings.

  5. Influence of clinoptilolite rock on chemical speciation of selected heavy metals in sewage sludge

    Energy Technology Data Exchange (ETDEWEB)

    Sprynskyy, M.; Kosobucki, P.; Kowalkowski, T. [Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, 7 Gagarina Str., 87-100 Torun (Poland); Buszewski, B. [Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, 7 Gagarina Str., 87-100 Torun (Poland)], E-mail: bbusz@chem.uni.torun.pl

    2007-10-22

    The chemical speciation of Cd, Cu, Pb, Cr and Ni in Torun municipal sewage sludge is investigated with addition of a natural sorbent (clinoptilolite rock). The total contents of the heavy metals in the sludge are substantially lower than the corresponding limits established by European or Polish legislation excepting nickel only. But the metals concentrations excepting lead exceed significantly the natural background (average contents in soils and in the Earth's crust) in dozens. Application of the sequential chemical extraction indicated that the metals in the sewage sludge are bound mainly (over 50%) in the residual fraction. The metals form the following order by parts of the mobile form: Ni > Cd >> Cr > Cu >> Pb. Addition of the clinoptilolite to the sludge leads to the metals contents fall in all four fractions of the sequential procedure. Concentrations of mobile forms of cadmium, chromium, copper and nickel decrease by 87, 64, 35 and 24%, respectively, as a result of addition of 9.09% of the clinoptilolite. The total decreases of the metals amount after 9.09% clinoptilolite addition to the sludge are around 11, 15, 25, 41 and 51% for copper, nickel, chromium, cadmium and lead, respectively.

  6. Selection of potential cold water marine species for testing of oil dispersants, and chemically dispersed oil

    Energy Technology Data Exchange (ETDEWEB)

    Perkins, R.A. [Alaska Univ., Fairbanks, AK (United States). Dept. of Civil and Environmental Engineering

    2000-07-01

    A study regarding marine species for toxicity testing for Alaska conditions was presented and the potential adverse impacts of a large marine oil spill in cold water were discussed with the objective to determine if the spill should be treated by the use of oil dispersants. Without dispersion, the oil can pollute marine epifauna and can deposit on beaches. The decision to apply dispersants to a marine oil spill requires knowledge of the toxicity of the undispersed oil to pelagic marine life occurring via natural dispersion as opposed to the toxicity of the oil-dispersant mixture. Most standard toxicity tests apply to warm water species. This paper discussed the need to have a standard test species relevant to Alaska waters for toxicity testing. In this study, toxicity testing was done according to the methods of the Chemical Response to Oil Spills : Ecological Effects Research Forum (CROSERF). The testing included capturing adult species in the winter and holding them until larval hatching. Toxicity testing was completed in a narrow time frame before hatching ceased. Many chemical samples were tested. Topsmelt, urchins, shellfish, mysids, copepods, pink salmon fry, and tidepool sculpin were considered by the author to be the most useful for certain types of toxicity testing. 29 refs.

  7. PHYSICO-CHEMICAL ANALYSIS OF SELECTED GROUND WATER SAMPLES OF RURAL AREAS OF JAIPUR, RAJASTHAN

    Directory of Open Access Journals (Sweden)

    Priyanka Dhingra

    2014-12-01

    Full Text Available The aim of present study was to assess the status of the groundwater in rural areas of Jaipur city. People on globe are under tremendous threat due to undesired changes in the physical, chemical and biological characteristics of air, water and soil. Due to increased population, urbanization, industrialization, use of fertilizers water is highly polluted with different harmful contaminants Natural water resources are being contaminated due to weathering of rocks and leaching of soil, mining processing etc. It is necessary that quality of drinking water should be checked at regular time interval to prevent various water born diseases. In present analysis physico-chemical parameter of drinking water viz. pH, hardness, TDS, residual chlorine, dissolved oxygen, electrical conductivity, Free CO2 have been analyzed. Drinking water quality of 8 villages of Amber District Jaipur, Rajasthan was analyzed to identify the nature and quality of water. The drinking water samples were collected in clean polythene one liter cans and subjected for analysis in laboratory. The main objective of the present paper is to aware people of concerned area about the water quality and concerned health hazards.

  8. Chemical-technological approach to the selection of ceramic materials with predetermined thermistor properties

    Energy Technology Data Exchange (ETDEWEB)

    Plewa, J.; Altenburg, H. [Fachhochschule Muenster, Steinfurt (Germany). SIMa and Supraleiter-Keramik-Kristalle; Brunner, M. [Fachhochschule Koeln (Germany). Elektronische Bauelemente; Shpotyuk, O.; Vakiv, M. [Scientific Research Co. ' ' Carat' ' , Lviv Scientific Research Inst. of Materials, Lviv (Ukraine)

    2002-07-01

    The selection possibilities of quaternary Cu-Ni-Co-Mn oxide system restricted by cubic spinels (CuMn{sub 2}O{sub 4}, MnCo{sub 2}O{sub 4} and NiMn{sub 2}O{sub 4}) for NTC thermistors application were discussed. Phase compositions, microstructural features and electrical properties of the investigated spinel-structured ceramics were studied in tight connection with technological regimes of their sintering. (orig.)

  9. Selective Laser Sintering And Melting Of Pristine Titanium And Titanium Ti6Al4V Alloy Powders And Selection Of Chemical Environment For Etching Of Such Materials

    Directory of Open Access Journals (Sweden)

    Dobrzański L.A.

    2015-09-01

    Full Text Available The aim of the investigations described in this article is to present a selective laser sintering and melting technology to fabricate metallic scaffolds made of pristine titanium and titanium Ti6Al4V alloy powders. Titanium scaffolds with different properties and structure were manufactured with this technique using appropriate conditions, notably laser power and laser beam size. The purpose of such elements is to replace the missing pieces of bones, mainly cranial and facial bones in the implantation treatment process. All the samples for the investigations were designed in CAD/CAM (3D MARCARM ENGINEERING AutoFab (Software for Manufacturing Applications software suitably integrated with an SLS/SLM system. Cube-shaped test samples dimensioned 10×10×10 mm were designed for the investigations using a hexagon-shaped base cell. The so designed 3D models were transferred to the machine software and the actual rapid manufacturing process was commenced. The samples produced according to the laser sintering technology were subjected to chemical processing consisting of etching the scaffolds’ surface in different chemical mediums. Etching was carried out to remove the loosely bound powder from the surface of scaffolds, which might detach from their surface during implantation treatment and travel elsewhere in an organism. The scaffolds created were subjected to micro- and spectroscopic examinations

  10. Effective, Facile, and Selective Hydrolysis of the Chemical Warfare Agent VX Using Zr6-Based Metal-Organic Frameworks.

    Science.gov (United States)

    Moon, Su-Young; Wagner, George W; Mondloch, Joseph E; Peterson, Gregory W; DeCoste, Jared B; Hupp, Joseph T; Farha, Omar K

    2015-11-16

    The nerve agent VX is among the most toxic chemicals known to mankind, and robust solutions are needed to rapidly and selectively deactivate it. Herein, we demonstrate that three Zr6-based metal-organic frameworks (MOFs), namely, UiO-67, UiO-67-NH2, and UiO-67-N(Me)2, are selective and highly active catalysts for the hydrolysis of VX. Utilizing UiO-67, UiO-67-NH2, and UiO-67-N(Me)2 in a pH 10 buffered solution of N-ethylmorpholine, selective hydrolysis of the P-S bond in VX was observed. In addition, UiO-67-N(Me)2 was found to catalyze VX hydrolysis with an initial half-life of 1.8 min. This half-life is nearly 3 orders of magnitude shorter than that of the only other MOF tested to date for hydrolysis of VX and rivals the activity of the best nonenzymatic materials. Hydrolysis utilizing Zr-based MOFs is also selective and facile in the absence of pH 10 buffer (just water) and for the destruction of the toxic byproduct EA-2192.

  11. Separation of selected stable isotopes by liquid-phase thermal diffusion and by chemical exchange

    Science.gov (United States)

    Rutherford, W. M.; Jepson, B. E.; Michaels, E. D.

    Useful applications of enriched stable nuclides are unduly restricted by high cost and limited availability. Recent research on liquid phase thermal diffusion (LTD) has resulted in practical processes for separating S34, CL35, and CL37 in significant quantities (100 to 500 g/yr) at costs much lower than those associated with the electromagnetic (Calutron) process. The separation of the isotopes of bromine by LTD is now in progress and BR79 is being produced in relatively simple equivalent at a rate on the order of 0.5 g/day. The results of recent measurements show that the isotopes of Zn can be separated by LTD of zinc alkyls. The isotopes of calcium can be separated by LTD and by chemical exchange. The LTD process is based on the use of aqueous Ca(NO3)2 as a working fluid.

  12. SELECTED CHEMICAL ANALYSES AND GEOTHERMOMETRY OF HOT SPRING WATERS FROM THE CALABOZOS CALDERA, CENTRAL CHILE.

    Science.gov (United States)

    Thompson, J.M.; Grunder, A.L.; Hildreth, Wes

    1983-01-01

    Hot springs discharging from the active hydrothermal system associated with the Calabozos caldera, Chile, have measured orifice temperatures as high as 98. 5 degree C and calculated geothermometer temperatures as high as 250 degree C. Three types of spring waters can be identified from the chemical analyses: a Na-Cl type, a Na-HCO//3 type and a Na-mixed anion type. Chloride-enthalpy relations indicate that the hydrothermal reservoir water may attain temperatures near 342 degree C and that most spring waters are mixed with cold meteoric water. Despite the proximity of Mesozoic marine gypsum deposits, the Cl/Br weight ratio of the Calabozos spring waters does not appear to indicate that these waters have a significant 'marine' signature. Refs.

  13. Physical and chemical properties of selected agricultural byproduct-based activated carbons and their ability to adsorb geosmin.

    Science.gov (United States)

    Ng, Chilton; Losso, Jack N; Marshall, Wayne E; Rao, Ramu M

    2002-09-01

    The objectives of this study were to evaluate selected physical and chemical properties of agricultural byproduct-based activated carbons made from pecan shells and sugarcane bagasse, and compare those properties to a commercial coal-based activated carbon as well as to compare the adsorption efficiency of these carbons for geosmin. Comparison of the physical and chemical properties of pecan shell- and bagasse-based carbons to the commercial carbon, Calgon Filtrasorb 400, showed that pecan shell carbon, but not the bagasse carbon, compared favorably to Filtrasorb 400, especially in terms of surface area, bulk density, ash and attrition. A carbon dosage study done in a model system showed the amount of geosmin adsorbed to be greater for Filtrasorb 400 and the bagasse-based carbon at low carbon concentrations than for the pecan shell carbons, but geosmin adsorption was similar in all carbons at higher carbon dosages. Application of the Freundlich isotherm model to the adsorption data showed that carbons made by steam activation of pecan shells or sugarcane bagasse had geosmin adsorption characteristics most like those of the commercial carbon. In terms of physical, chemical and adsorptive properties, steam-activated pecan shell carbon most resembled the commercial carbon and has the potential to replace Filtrasorb 400 in applications involving removal of geosmin from aqueous environments.

  14. Chemical Dynamics of State-Selected Atomic and Diatomic Ions of Aerospace Relevance

    Science.gov (United States)

    2008-11-01

    modified the triple - quadrupole -double-octopole y<t&te Cy» LJMW • • Figure 1. Schematic diagram of the comprehensive VUV laser system, which...H. Xu, and C. Y. Ng, "The Study of State-Selected Ion-Molecule Reactions using the Pulsed-Field Ionization- Photoion Technique ", J. Chem. Phys...8217==0-4) + He collisions in the ET range of 0-3 eV have also been measured using the VUV-photoionization-guided-ion beam mass spectrometric technique

  15. Selectivity of Chemoresistive Sensors Made of Chemically Functionalized Carbon Nanotube Random Networks for Volatile Organic Compounds (VOC

    Directory of Open Access Journals (Sweden)

    Jean-François Feller

    2014-01-01

    Full Text Available Different grades of chemically functionalized carbon nanotubes (CNT have been processed by spraying layer-by-layer (sLbL to obtain an array of chemoresistive transducers for volatile organic compound (VOC detection. The sLbL process led to random networks of CNT less conductive, but more sensitive to vapors than filtration under vacuum (bucky papers. Shorter CNT were also found to be more sensitive due to the less entangled and more easily disconnectable conducting networks they are making. Chemical functionalization of the CNT’ surface is changing their selectivity towards VOC, which makes it possible to easily discriminate methanol, chloroform and tetrahydrofuran (THF from toluene vapors after the assembly of CNT transducers into an array to make an e-nose. Interestingly, the amplitude of the CNT transducers’ responses can be enhanced by a factor of five (methanol to 100 (chloroform by dispersing them into a polymer matrix, such as poly(styrene (PS, poly(carbonate (PC or poly(methyl methacrylate (PMMA. COOH functionalization of CNT was found to penalize their dispersion in polymers and to decrease the sensors’ sensitivity. The resulting conductive polymer nanocomposites (CPCs not only allow for a more easy tuning of the sensors’ selectivity by changing the chemical nature of the matrix, but they also allow them to adjust their sensitivity by changing the average gap between CNT (acting on quantum tunneling in the CNT network. Quantum resistive sensors (QRSs appear promising for environmental monitoring and anticipated disease diagnostics that are both based on VOC analysis.

  16. Fiber array based hyperspectral Raman imaging for chemical selective analysis of malaria-infected red blood cells.

    Science.gov (United States)

    Brückner, Michael; Becker, Katja; Popp, Jürgen; Frosch, Torsten

    2015-09-24

    A new setup for Raman spectroscopic wide-field imaging is presented. It combines the advantages of a fiber array based spectral translator with a tailor-made laser illumination system for high-quality Raman chemical imaging of sensitive biological samples. The Gaussian-like intensity distribution of the illuminating laser beam is shaped by a square-core optical multimode fiber to a top-hat profile with very homogeneous intensity distribution to fulfill the conditions of Koehler. The 30 m long optical fiber and an additional vibrator efficiently destroy the polarization and coherence of the illuminating light. This homogeneous, incoherent illumination is an essential prerequisite for stable quantitative imaging of complex biological samples. The fiber array translates the two-dimensional lateral information of the Raman stray light into separated spectral channels with very high contrast. The Raman image can be correlated with a corresponding white light microscopic image of the sample. The new setup enables simultaneous quantification of all Raman spectra across the whole spatial area with very good spectral resolution and thus outperforms other Raman imaging approaches based on scanning and tunable filters. The unique capabilities of the setup for fast, gentle, sensitive, and selective chemical imaging of biological samples were applied for automated hemozoin analysis. A special algorithm was developed to generate Raman images based on the hemozoin distribution in red blood cells without any influence from other Raman scattering. The new imaging setup in combination with the robust algorithm provides a novel, elegant way for chemical selective analysis of the malaria pigment hemozoin in early ring stages of Plasmodium falciparum infected erythrocytes.

  17. Combined chemical oxidation and membrane filtration techniques applied to the removal of some selected pharmaceuticals from water systems.

    Science.gov (United States)

    Real, Francisco J; Benitez, F Javier; Acero, Juan L; Roldan, Gloria

    2012-01-01

    The elimination of five selected pharmaceuticals (amoxicillin, hydrochlorothiazide, metoprolol, naproxen and phenacetin) dissolved in different water systems (two natural water matrices and a secondary effluent) was carried out by sequential processes constituted by membrane filtration and chemical oxidation stages. Different configurations of those two stages were applied. In a first group, a pretreatment consisting in a membrane filtration (ultrafiltration or nanofiltration) was conducted; and the permeate and retentate effluents produced were afterwards treated by chemical oxidation, using ozone or chlorine. In a second group, the pretreatment consisted in a chemical oxidation stage (by using ozone, chlorine, O(3)/H(2)O(2), UV or UV/H(2)O(2)) followed by a nanofiltration process. The main objective of this set of experiments was the comparison of the efficiencies reached by using different systems and configurations in order to optimize the elimination of those pollutants from the selected water matrices. Results of removals and rejection coefficients for the five pharmaceuticals showed that the combined treatments involving UV radiation (254 nm monochromatic radiation during 30 min) followed by nanofiltration were very effective, with global removals over 80 % in most of the experiments. Ozonation (initial dose of 2.25 mg L(-1)) followed by nanofiltration also showed high levels of efficiency, with removals over 70 % in the permeate stream generated in experiments carried out with natural waters. The opposite sequence, nanofiltration followed by ozonation, reached removals over 97 % in the natural waters by using an ozone dose of 2.25 mg L(-1); and over 90 % in the secondary effluent with an initial ozone dose of 3.75 mg L(-1).

  18. How Do I Know? A Guide to the Selection of Personal Protective Equipment for Use in Responding to A Release of Chemical Warfare Agents

    Energy Technology Data Exchange (ETDEWEB)

    Foust, C.B.

    1999-05-01

    An incident involving chemical warfare agents requires a unique hazardous materials (HAZMAT) response. As with an HAZMAT event, federal regulations prescribe that responders must be protected from exposure to the chemical agents. But unlike other HAZMAT events, special considerations govern selection of personal protective equipment (PPE). PPE includes all clothing, respirators and monitoring devices used to respond to a chemical release. PPE can differ depending on whether responders are military or civilian personnel.

  19. Interfacial structure of tungsten layers formed by selective low pressure chemical vapor deposition

    Energy Technology Data Exchange (ETDEWEB)

    Stacy, W.T.; Broadbent, E.K.; Norcott, M.H.

    1985-02-01

    We have analyzed the interfacial structure of selectively deposited LPCVD tungsten on monocrystalline silicon, polycrystalline silicon, and polycrystalline aluminum substrates. Cross-sectional specimens were examined by transmission electron microscopy to determine the amount of substrate consumed by the selective deposition process and to assess the degree of lateral encroachment under masking SiO/sub 2/ layers for different conditions of deposition and surface preparation. The tungsten-silicon interfacial structure was found to depend strongly on the initia surface preparation. Immersion in a dilute HF solution resulted in a smooth interface, while a glow-discharge treatment (CF/sub 4/ + O/sub 2/) led to highly irregular interfaces, which, in extreme cases, contained tunnels extending 1 ..mu..m or more into the silicon substrate. Layers formed in WF/sub 6/ plus H/sub 2/ were found to consist of two layers, of which the lower layer i formed by the substrate reduction of WF/sub 6/.

  20. Selected bibliography of the physical, chemical, and biological oceanographic literature for the waters surrounding Guam

    Energy Technology Data Exchange (ETDEWEB)

    Eldredge, L.G.; Kropp, R.K.

    1981-09-01

    An ocean thermal energy conversion (OTEC) plant has been proposed to be built at Guam. A study of the impact of such a plant would be needed, since the movement of deep, cold water into shallow, warm water may have significant effects on the biota and the surrounding physical environment. No comprehensive overview of the ocean at Guam exists. The Lawrence Berkeley Laboratory at the University of California, Berkeley, contracted the Guam Natural Energy Institute at the University of Guam Marine Laboratory to carry out a review of the existing oceanoraphic data and scientific literature about the ocean water surrounding the island of Guam. This selected bibliography of 262 titles is the initial product of the contract. This bibliography includes the major literature pertaining to the ocean at Guam. It is selected for numerous reasons. Many titles appear in at least two forms - thesis or technical report and journal article. The published article is preferentially cited. A great deal of information is in manuscript or unpublished form which will be printed at a later date.

  1. Synthesis, antimicrobial evaluation and theoretical prediction of NMR chemical shifts of thiazole and selenazole derivatives with high antifungal activity against Candida spp.

    Science.gov (United States)

    Łączkowski, Krzysztof Z.; Motylewska, Katarzyna; Baranowska-Łączkowska, Angelika; Biernasiuk, Anna; Misiura, Konrad; Malm, Anna; Fernández, Berta

    2016-03-01

    Synthesis and investigation of antimicrobial activities of novel thiazoles and selenazoles is presented. Their structures were determined using NMR, FAB(+)-MS, HRMS and elemental analyses. To support the experiment, theoretical calculations of the 1H NMR shifts were carried out for representative systems within the DFT B3LYP/6-311++G** approximation which additionally confirmed the structure of investigated compounds. Among the derivatives, compounds 4b, 4h, 4j and 4l had very strong activity against reference strains of Candida albicans ATCC and Candida parapsilosis ATCC 22019 with MIC = 0.49-7.81 μg/ml. In the case of compounds 4b, 4c, 4h - 4j and 4l, the activity was very strong against of Candida spp. isolated from clinical materials, i.e. C. albicans, Candida krusei, Candida inconspicua, Candida famata, Candida lusitaniae, Candida sake, C. parapsilosis and Candida dubliniensis with MIC = 0.24-15.62 μg/ml. The activity of several of these was similar to the activity of commonly used antifungal agent fluconazole. Additionally, compounds 4m - 4s were found to be active against Gram-positive bacteria, both pathogenic staphylococci Staphylococcus aureus ATCC with MIC = 31.25-125 μg/ml and opportunistic bacteria, such as Staphylococcus epidermidis ATCC 12228 and Micrococcus luteus ATCC 10240 with MIC = 7.81-31.25 μg/ml.

  2. Characteristics and chemical compositions of particulate matter collected at the selected metro stations of Shanghai, China

    Energy Technology Data Exchange (ETDEWEB)

    Guo, Li; Hu, Yunjie; Hu, Qingqing [Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention, Department of Environmental Science and Engineering, Fudan University, Shanghai 200433 (China); Lin, Jun [Key Laboratory of Nuclear Analysis Techniques, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800 (China); Li, Chunlin; Chen, Jianmin [Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention, Department of Environmental Science and Engineering, Fudan University, Shanghai 200433 (China); Li, Lina [Key Laboratory of Nuclear Analysis Techniques, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800 (China); Fu, Hongbo [Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention, Department of Environmental Science and Engineering, Fudan University, Shanghai 200433 (China)

    2014-10-15

    A campaign was conducted to assess and compare the air quality at the different metro platforms at Shanghai City, focusing on particulate matter (PM) levels, chemical compositions, morphology and mineralogy, as well as species of iron. Our results indicated that the average PM{sub 2.5} concentrations for the three metro lines were 177.7 μg/m{sup 3}, 105.7 μg/m{sup 3} and 82.5 μg/m{sup 3}, respectively, and the average PM{sub 1} concentrations for the three lines were 122.3 μg/m{sup 3}, 84.1 μg/m{sup 3} and 59.6 μg/m{sup 3}, respectively. Fe, Mn, Cr, Cu, Sr, Ba and Pb concentrations in all of the sampling sites were significantly higher than that in the urban ambient air, implicating that these trace metals may be associated with the metro systems working. Individual airborne dusts were studied for morphology and mineralogy characteristics. The results revealed that the presence of most individual particles were with no definite shape and most of them were with a large metal content. Furthermore, Fe-rich particles had significantly higher abundance in the metro systems, which were more frequently encountered in the underground lines than the aboveground line. The 2D distribution map of an interested Fe-rich particle showed an uneven Fe distribution, implying that a hollow or core of other substance exists in the particle center during the formation process. Cluster analysis revealed that Fe-rich particles were possibly a mixture of Fe species. Fitting of X-ray absorption near-edge fine structure spectra (XANES) showed the main iron species within the particles collected from the three contrasting metro lines of Shanghai to be hematite, magnetite, iron-metal and mineral Fe. Hematite and mineral Fe were all found in three lines, while magnetite only existed in aboveground metro line. Iron-metal was determined in both the older and younger underground lines, based on the X-ray diffraction (XRD) analysis. As diverse Fe species have different physical–chemical

  3. Liquidus temperature and chemical durability of selected glasses to immobilize rare earth oxides waste

    Energy Technology Data Exchange (ETDEWEB)

    Mohd Fadzil, Syazwani Binti; Hrma, Pavel R.; Schweiger, Michael J.; Riley, Brian J.

    2015-06-30

    Pyroprocessing is a reprocessing method for managing and reusing used nuclear fuel (UNF) by dissolving it in an electrorefiner with a molten alkali or alkaline earth chloride salt mixture while avoiding wet reprocessing. Pyroprocessing UNF with a LiCl-KCl eutectic salt releases the fission products from the fuel and generates a variety of metallic and salt-based species, including rare earth (RE) chlorides. If the RE-chlorides are converted to oxides, borosilicate glass is a prime candidate for their immobilization because of its durability and ability to dissolve almost any RE waste component into the matrix at high loadings. Crystallization that occurs in waste glasses as the waste loading increases may complicate glass processing and affect the product quality. This work compares three types of borosilicate glasses in terms of liquidus temperature (TL): the International Simple Glass designed by the International Working Group, sodium borosilicate glass developed by Korea Hydro and Nuclear Power, and the lanthanide aluminoborosilicate (LABS) glass established in the United States. The LABS glass allows the highest waste loadings (over 50 mass% RE2O3) while possessing an acceptable chemical durability.

  4. Statistical Significance of the Maximum Hardness Principle Applied to Some Selected Chemical Reactions

    Directory of Open Access Journals (Sweden)

    Ranajit Saha

    2016-11-01

    Full Text Available The validity of the maximum hardness principle (MHP is tested in the cases of 50 chemical reactions, most of which are organic in nature and exhibit anomeric effect. To explore the effect of the level of theory on the validity of MHP in an exothermic reaction, B3LYP/6-311++G(2df,3pd and LC-BLYP/6-311++G(2df,3pd (def2-QZVP for iodine and mercury levels are employed. Different approximations like the geometric mean of hardness and combined hardness are considered in case there are multiple reactants and/or products. It is observed that, based on the geometric mean of hardness, while 82% of the studied reactions obey the MHP at the B3LYP level, 84% of the reactions follow this rule at the LC-BLYP level. Most of the reactions possess the hardest species on the product side. A 50% null hypothesis is rejected at a 1% level of significance.

  5. Statistical Significance of the Maximum Hardness Principle Applied to Some Selected Chemical Reactions.

    Science.gov (United States)

    Saha, Ranajit; Pan, Sudip; Chattaraj, Pratim K

    2016-11-05

    The validity of the maximum hardness principle (MHP) is tested in the cases of 50 chemical reactions, most of which are organic in nature and exhibit anomeric effect. To explore the effect of the level of theory on the validity of MHP in an exothermic reaction, B3LYP/6-311++G(2df,3pd) and LC-BLYP/6-311++G(2df,3pd) (def2-QZVP for iodine and mercury) levels are employed. Different approximations like the geometric mean of hardness and combined hardness are considered in case there are multiple reactants and/or products. It is observed that, based on the geometric mean of hardness, while 82% of the studied reactions obey the MHP at the B3LYP level, 84% of the reactions follow this rule at the LC-BLYP level. Most of the reactions possess the hardest species on the product side. A 50% null hypothesis is rejected at a 1% level of significance.

  6. Emissions of Selected Semivolatile Organic Chemicals from Forest and Savannah Fires.

    Science.gov (United States)

    Wang, Xianyu; Thai, Phong K; Mallet, Marc; Desservettaz, Maximilien; Hawker, Darryl W; Keywood, Melita; Miljevic, Branka; Paton-Walsh, Clare; Gallen, Michael; Mueller, Jochen F

    2017-02-07

    The emission factors (EFs) for a broad range of semivolatile organic chemicals (SVOCs) from subtropical eucalypt forest and tropical savannah fires were determined for the first time from in situ investigations. Significantly higher (t test, P < 0.01) EFs (μg kg(-1) dry fuel, gas + particle-associated) for polycyclic aromatic hydrocarbons (∑13 PAHs) were determined from the subtropical forest fire (7,000 ± 170) compared to the tropical savannah fires (1,600 ± 110), due to the approximately 60-fold higher EFs for 3-ring PAHs from the former. EF data for many PAHs from the eucalypt forest fire were comparable with those previously reported from pine and fir forest combustion events. EFs for other SVOCs including polychlorinated biphenyl (PCB), polychlorinated naphthalene (PCN), and polybrominated diphenyl ether (PBDE) congeners as well as some pesticides (e.g., permethrin) were determined from the subtropical eucalypt forest fire. The highest concentrations of total suspended particles, PAHs, PCBs, PCNs, and PBDEs, were typically observed in the flaming phase of combustion. However, concentrations of levoglucosan and some pesticides such as permethrin peaked during the smoldering phase. Along a transect (10-150-350 m) from the forest fire, concentration decrease for PCBs during flaming was faster compared to PAHs, while levoglucosan concentrations increased.

  7. Evaluation, Selection and Assessment of Guidelines for Chemical Stabilization of Tropical Residual Soils

    Directory of Open Access Journals (Sweden)

    Bujang B.K. Huat

    2008-01-01

    Full Text Available Soil stabilization has been widely used as an alternative to substitute the lacking of suitable materials on site. Guidelines and standards have been developed to assist practitioners in designing structures such as road by mean of stabilization. This paper presents the results of an investigation aimed at evaluating and assessing the suitable guidelines for the stabilization of tropical residual soils. Two types of tropical residual soils namely granite residual and sedimentary residual soil were tested by using conventional methods practiced in Malaysiaand two guidelines, namely the TRL and PWD were evaluated. From the results of this study, it appeared that the TRL gave a simplified and satisfactory route in selection of suitable binder for the stabilization processes of tropical residual soils.

  8. Evaluation of chemical data from selected sites in the Surface-Water Ambient Monitoring Program (SWAMP) in Florida

    Science.gov (United States)

    Katz, B.G.; Collins, J.J.

    1998-01-01

    A cooperative study between the Florida Department of Environmental Protection (FDEP) and the U.S. Geological Survey was conducted to assess the integrity of selected water-quality data collected at 150 sites in the FDEP Surface-Water Ambient Monitoring Program (SWAMP) in Florida. The assessment included determining the consistency of the water-quality data collected statewide, including commonality of monitoring procedures and analytes, screening of the gross validity of a chemical analysis, and quality assurance and quality control (QA/QC) procedures. Four tests were used to screen data at selected SWAMP sites to estimate the gross validity of selected chemical data: (1) the ratio of dissolved solids (in milligrams per liter) to specific conductance (in microsiemens per centimeter); (2) the ratio of total cations (in milliequivalents per liter) multiplied by 100 to specific conductance (in microsiemens per centimeter); (3) the ratio of total anions (in milliequivalents per liter) multiplied by 100 to specific conductance (in microsiemens per centimeter); and (4) the ionic charge-balance error. Although the results of the four screening tests indicate that the chemical data generally are quite reliable, the extremely small number of samples (less than 5 percent of the total number of samples) with sufficient chemical information to run the tests may not provide a representative indication of the analytical accuracy of all laboratories in the program. In addition to the four screening tests, unusually low or high values were flagged for field and laboratory pH (less than 4.0 and greater than 9.0) and specific conductance (less than 10 and greater than 10,000 microsiemens per centimeter). The numbers of flagged data were less than 1 percent of the 19,937 water samples with pH values and less than 0.6 percent of the 16,553 water samples with specific conductance values. Thirty-four agencies responded to a detailed questionnaire that was sent to more than 60 agencies

  9. Unusual Physical and Chemical Properties of Ni in Ce1-xNixO2-y Oxides: Structural Characterization and Catalytic Activity for the Water Gas Shift Reaction

    Energy Technology Data Exchange (ETDEWEB)

    Barrio, L.; Kubacka, A; Zhou, G; Estrella, M; Martinez-Arias, A; Hanson, J; Fernandez-Garcia, M; Rodriguez, J

    2010-01-01

    The structural and electronic properties of Ce{sub 1-x}Ni{sub x}O{sub 2-y} nanosystems prepared by a reverse microemulsion method were characterized with synchrotron-based X-ray diffraction, X-ray absorption spectroscopy, Raman spectroscopy, and density functional calculations. The Ce{sub 1-x}Ni{sub x}O{sub 2-y} systems adopt a lattice with a fluorite-type structure with an acute local order where Ni displays a strongly distorted (oxygen) nearest-neighbor coordination and the presence of Ni atoms as first cation distances, pointing to the existence of Ni-O-Ni entities embedded into the ceria lattice. A Ni {leftrightarrow} Ce exchange within the CeO{sub 2} leads to a charge redistribution and the appearance of O vacancies. The Ni-O bonds in Ce{sub 1-x}Ni{sub x}O{sub 2-y} are more difficult to reduce than the bonds in pure NiO. The specific structural configuration of Ni inside the mixed-metal oxide leads to a unique catalyst with a high activity for the water gas shift (CO + H{sub 2}O {yields} H{sub 2} + CO{sub 2}) reaction and a simultaneous reduction of the methanation activity of nickel. Characterization results indicate that small particles of metallic Ni at the interface position of a ceria network may be the key for high WGS activity and that the formate-carbonate route is operative for the production of hydrogen.

  10. Unusual Physical and Chemical Properties of Ni in Ce1-xNixO2-y Oxides: Structural Characterization and Catalytic Activity for the Water Gas Shift Reaction

    Energy Technology Data Exchange (ETDEWEB)

    Rodriguez, J.A.; Barrio, L.; Kubacka, A.; Zhou, G.; Estrella, M.; Mart& #305; nez-Arias, A.; Hanson, J.C.; Fernandez-Garc& #305; a, M.

    2010-07-29

    The structural and electronic properties of Ce{sub 1-x}Ni{sub x}O{sub 2-y} nanosystems prepared by a reverse microemulsion method were characterized with synchrotron-based X-ray diffraction, X-ray absorption spectroscopy, Raman spectroscopy, and density functional calculations. The Ce{sub 1-x}Ni{sub x}O{sub 2-y} systems adopt a lattice with a fluorite-type structure with an acute local order where Ni displays a strongly distorted (oxygen) nearest-neighbor coordination and the presence of Ni atoms as first cation distances, pointing to the existence of Ni-O-Ni entities embedded into the ceria lattice. A Ni {leftrightarrow} Ce exchange within the CeO{sub 2} leads to a charge redistribution and the appearance of O vacancies. The Ni?O bonds in Ce{sub 1-x}Ni{sub x}O{sub 2-y} are more difficult to reduce than the bonds in pure NiO. The specific structural configuration of Ni inside the mixed-metal oxide leads to a unique catalyst with a high activity for the water gas shift (CO + H{sub 2}O {yields} H{sub 2} + CO{sub 2}) reaction and a simultaneous reduction of the methanation activity of nickel. Characterization results indicate that small particles of metallic Ni at the interface position of a ceria network may be the key for high WGS activity and that the formate?carbonate route is operative for the production of hydrogen.

  11. Selective and Efficient Elimination of Vibrio cholerae with a Chemical Modulator that Targets Glucose Metabolism

    Science.gov (United States)

    Oh, Young Taek; Kim, Hwa Young; Kim, Eun Jin; Go, Junhyeok; Hwang, Wontae; Kim, Hyoung Rae; Kim, Dong Wook; Yoon, Sang Sun

    2016-01-01

    Vibrio cholerae, a Gram-negative bacterium, is the causative agent of pandemic cholera. Previous studies have shown that the survival of the seventh pandemic El Tor biotype V. cholerae strain N16961 requires production of acetoin in a glucose-rich environment. The production of acetoin, a neutral fermentation end-product, allows V. cholerae to metabolize glucose without a pH drop, which is mediated by the production of organic acid. This finding suggests that inhibition of acetoin fermentation can result in V. cholerae elimination by causing a pH imbalance under glucose-rich conditions. Here, we developed a simple high-throughput screening method and identified an inducer of medium acidification (iMAC). Of 8364 compounds screened, we identified one chemical, 5-(4-chloro-2-nitrobenzoyl)-6-hydroxy-1,3-dimethylpyrimidine-2,4(1H,3H)-dione, that successfully killed glucose-metabolizing N16961 by inducing acidic stress. When N16961 was grown with abundant glucose in the presence of iMAC, acetoin production was completely suppressed and concomitant accumulation of lactate and acetate was observed. Using a beta-galactosidase activity assay with a single-copy palsD::lacZ reporter fusion, we show that that iMAC likely inhibits acetoin production at the transcriptional level. Thin-layer chromatography revealed that iMAC causes a significantly reduced accumulation of intracellular (p)ppGpp, a bacterial stringent response alarmone known to positively regulate acetoin production. In vivo bacterial colonization and fluid accumulation were also markedly decreased after iMAC treatment. Finally, we demonstrate iMAC-induced bacterial killing for 22 different V. cholerae strains belonging to diverse serotypes. Together, our results suggest that iMAC, acting as a metabolic modulator, has strong potential as a novel antibacterial agent for treatment against cholera. PMID:27900286

  12. Chemical composition and efficacy of some selected plant oils against Pediculus humanus capitis in vitro.

    Science.gov (United States)

    Yones, Doaa A; Bakir, Hanaa Y; Bayoumi, Soad A L

    2016-08-01

    Natural compounds have been suggested as alternative sources for pediculosis capitis control. We aimed to investigate the chemical composition and evaluate the pediculicidal activity of spearmint, clove, cassia, thyme, eucalyptus, and anise essential oils in addition to sesame oil against human head lice in vitro. A filter paper contact bioassay method was used by applying 0.25 and 0.5 mg/cm(2) of each tested oil to filter paper in Petri dishes with 15 females head lice and another with ten nits. The lice mortalities were reported every 5 min for 180 min. The percentage of inhibition of hatch (PIH) was used to calculate ovicidal activity by daily microscopic inspections 5 days after the hatching of controls. Comparison with the widely used pediculicide (malathion) was performed. The most effective essential oil was spearmint followed by cassia and clove with KT50 values of 4.06, 7.62, and 12.12 at 0.5 mg/cm(2) and 8.84, 11.38, and 19.73 at 0.25 mg/cm(2), respectively. Thyme, eucalyptus, and anise were also effective adulticides with KT50 values of 18.61, 32.65, and 37.34 at 0.5 mg/cm(2) and 29.92, 43.16, and 45.37 at 0.25 mg/cm(2), respectively. Essential oils were also successful in inhibiting nymph emergence. Spearmint oil was the most effective, with a complete inhibition of emergence at 0.5 mg/cm(2). Sesame fixed oil did not show any adulticidal or ovicidal activity against head lice in vitro. The observed insecticidal activity was comparable to malathion. The results herein described the effectiveness of these essential oils as potential pediculicides for head lice control. Incorporation of essential oils in pediculicide formulations needs proper formulation and clinical trials.

  13. Linking selective chemical extraction of iron oxyhydroxides to arsenic bioaccessibility in soil.

    Science.gov (United States)

    Palumbo-Roe, Barbara; Wragg, Joanna; Cave, Mark

    2015-12-01

    The relationship between As bioaccessibility using the physiologically based extraction test (PBET) and As extracted by hydroxylamine hydrochloride (HH), targeting the dissolution of amorphous Fe oxyhydroxides, is established in soils from the British Geological Survey Geochemical Baseline Survey of SW England, UK, to represent low As background and high As mineralised/mined soils. The HH-extracted As was of the same order of magnitude as the As extracted in the bioaccessibility test and proved to be a better estimate of bioaccessible As than total As (bioaccessible As - total As: r = 0.955; bioaccessible As - HH-extracted As: r = 0.974; p-values = 0.000). These results provide a means of estimating soil As bioaccessibility on the basis of the HH extraction. Further selective extraction data, using hydrochloride acid that seeks to dissolve both amorphous and crystalline Fe oxyhydroxides, indicates a decrease in the As bioaccessible fraction with the increase of the soil Fe oxyhydroxide crystallinity.

  14. Chemical Composition of Selected Beetroot Juices in Relation to Beetroot Production System and Processing Technology

    Directory of Open Access Journals (Sweden)

    Renata KAZIMIERCZAK

    2016-12-01

    Full Text Available Market offer of vegetable juices in Europe is growing, and the vegetable species and processing technologies used become more diversified resulting in a large range of juice types. At the same time consumers look for natural and safe products with pro-health properties. The aim of this study was to evaluate the nutritional composition of selected juices based on beetroots coming from different agricultural systems and processed according to different technologies. Research material consisted of conventional and organic juices marketed in Poland, in that pure pressed juices, fermented juice and juices from concentrate, pure and combined with apple or lemon juice. The concentration of vitamin C, organic acids, total and reducing sugars, phenolic acids, flavonoids and betalains has been determined in the juices. All beetroot juices were abundant in betalains, with higher concentrations of these compounds found in pure beetroot juices when compared to juices combined with apple or lemon. Highest concentration of betanin-3-O-glucoside was found in pure conventional juice from concentrate, while highest betanidin content was found in pure organic fermented juice. Highest vitamin C contents were found in pressed organic juices combined with apple and lemon. All juices were abundant in polyphenols, mainly phenolic acids, with highest concentrations of these antioxidants found in conventional pure pressed juice. The study shows that beetroot juices, independently on the beetroot processing technology and agricultural production system, are very valuable products due to the presence of numerous bioactive compounds, especially betalains, in their composition. Therefore beetroot juice consumption should be promoted among consumers.

  15. Iboga alkaloids from Peschiera affinis (Apocynaceae) - unequivocal {sup 1}H and {sup 13}C chemical shift assignments: antioxidant activity; Alcaloides iboga de Peschiera affinis (Apocynaceae) - atribuicao inequivoca dos deslocamentos quimicos dos atomos de hidrogenio e carbono: atividade antioxidante

    Energy Technology Data Exchange (ETDEWEB)

    Santos, Allana Kellen L.; Magalhaes, Ticiane S.; Monte, Francisco Jose Q.; Mattos, Marcos Carlos de; Oliveira, Maria Conceicao F. de; Almeida, Maria Mozarina B.; Lemos, Telma L.G.; Braz-Filho, Raimundo [Universidade Federal do Ceara (UFC), Fortaleza, CE (Brazil). Dept. de Quimica Organica e Inorganica], e-mail: tlemos@dqoi.ufc.br

    2009-07-01

    Six known alkaloids iboga type and the triterpene {alpha}- and {beta}-amyrin acetate were isolated from the roots and stems of Peschiera affinis. Their structures were characterized on the basis of spectral data mainly NMR and mass spectra. 1D and 2D NMR spectra were also used to unequivocal {sup 1}H and {sup 13}C chemical shift assignments of alkaloids. The ethanolic extract of roots, alkaloidic and no-alkaloidic fractions and iso-voacristine hydroxyindolenine and voacangine were evaluated for their antioxidative properties using an autographic assay based on {beta}-carotene bleaching on TLC plates, and also spectrophotometric detection by reduction of the stable DPPH (2,2-diphenyl-1-picrylhydrazyl) free radical. (author)

  16. Growth of selective tungsten films on self-aligned CoSi/sub 2/ by low pressure chemical vapor deposition

    Energy Technology Data Exchange (ETDEWEB)

    van der Putte, P.; Sadana, D.K.; Broadbent, E.K.; Morgan, A.E.

    1986-12-22

    The selective deposition of tungsten films onto CoSi/sub 2/ and onto Co by low pressure chemical vapor deposition and their material properties have been investigated with Auger electron spectroscopy, transmission electron microscopy, and Rutherford backscattering. When using WF/sub 6/ and H/sub 2/, uniformly thick tungsten films can be deposited onto CoSi/sub 2/ without substrate alteration. In patterned structures, however, void formation was found at the perimeters of CoSi/sub 2/ contacts to silicon, indicating encroachment of WF/sub 6/ down the edge of the silicide-Si interface. In WF/sub 6/ and Ar, the film thickness was limited to 10 nm and some Si was locally consumed from the upper part of the CoSi/sub 2/ film. Transmission electron diffraction showed evidence of Co/sub 2/Si formation in these areas.

  17. Effect of Different Ages of a Rehabilitated Forest on Selected Physico-chemical Properties

    Directory of Open Access Journals (Sweden)

    Rajeswari A.P. Murugayah

    2009-01-01

    Full Text Available Problem statement: This research was important because of still lack of information about rehabilitated tropical forest age effect on infiltration rate. The objectives of this study were to determine the influence of age of forest on soil water infiltration rate and to evaluate the influence of forest age on the relationship between water infiltration rate, soil organic matter and soil texture. Approach: This study was conducted under a rehabilitated forest at Bukit Nyabau (University Putra Malaysia Bintulu Campus, UPMKB Forest. Soil organic matter, soil texture and infiltration rate were investigated in randomly selected blocks representing different age classes, namely two, four, six, eight and ten years. Results: The results indicated that 2, 4, 6 and 8 year old forest were not significantly different in organic matter content with the mean of 8.10+2.75, 9.32+3.50, 9.55+1.71 and 8.10+2.75% respectively. Besides, 10 year forest showed no significant differences compared with two and eight year forests. Soil texture for all the forests was sandy loam, except for the 4 year old forest which was a sandy clay loam. The lowest value of sand content was observed in four year forest. However, the clay content in this forest was statistically the highest compared with 2, 4, 8 and 10 year old forest. The infiltration rate of 6 years old forest was significantly greater in soil water infiltration rate with the mean of 5.0±0.02 mm m-1, compared with 2, 4, 8 and 10 years old forest with the means of 2.6±0.02, 4.2±0.03, 3.6±0.03 and 3.5±0.03 mm m-1 respectively. Eight and 10 year old forests showed no significant differences in terms of soil water infiltration rate and the lowest value of water infiltration rate was observed in the two year old forest. Conclusion: From the results, it can be concluded that the soil water infiltration rate in the forest is mainly influenced by soil texture and organic matter content, but not by forest age. However, the

  18. Development of a risk management tool for prioritizing chemical hazard-food pairs and demonstration for selected mycotoxins.

    Science.gov (United States)

    Stornetta, Alessia; Engeli, Barbara E; Zarn, Jürg A; Gremaud, Gérard; Sturla, Shana J

    2015-07-01

    We developed a simple tool for ranking chemical hazard-food pairs to assist policy makers and risk managers selecting the hazard-food pairs that deserve more attention and need to be monitored during food safety inspections. The tool is based on the derivation of a "Priority Index" (PI) that results from the ratio of the potency of the hazard and the consumer exposure. The potency corresponds to a toxicity reference value of the hazard, whereas the exposure results from the combination of the concentration of the hazard in the food, and the food consumption. Tool's assumptions and limitations are demonstrated and discussed by ranking a dataset of 13 mycotoxins in 26 food items routinely analyzed in Switzerland. The presented ranking of mycotoxin-food pairs has to be considered as relative due to scarce exposure data availability, and uncertainties in toxicity reference values. However, this representative example allows demonstrating the simplicity and the ability of the PI tool to prioritize chemical hazard-food pairs.

  19. Combining Non Selective Gas Sensors on a Mobile Robot for Identification and Mapping of Multiple Chemical Compounds

    Directory of Open Access Journals (Sweden)

    Victor Hernandez Bennetts

    2014-09-01

    Full Text Available In this paper, we address the task of gas distribution modeling in scenarios where multiple heterogeneous compounds are present. Gas distribution modeling is particularly useful in emission monitoring applications where spatial representations of the gaseous patches can be used to identify emission hot spots. In realistic environments, the presence of multiple chemicals is expected and therefore, gas discrimination has to be incorporated in the modeling process. The approach presented in this work addresses the task of gas distribution modeling by combining different non selective gas sensors. Gas discrimination is addressed with an open sampling system, composed by an array of metal oxide sensors and a probabilistic algorithm tailored to uncontrolled environments. For each of the identified compounds, the mapping algorithm generates a calibrated gas distribution model using the classification uncertainty and the concentration readings acquired with a photo ionization detector. The meta parameters of the proposed modeling algorithm are automatically learned from the data. The approach was validated with a gas sensitive robot patrolling outdoor and indoor scenarios, where two different chemicals were released simultaneously. The experimental results show that the generated multi compound maps can be used to accurately predict the location of emitting gas sources.

  20. Combining non selective gas sensors on a mobile robot for identification and mapping of multiple chemical compounds.

    Science.gov (United States)

    Bennetts, Victor Hernandez; Schaffernicht, Erik; Pomareda, Victor; Lilienthal, Achim J; Marco, Santiago; Trincavelli, Marco

    2014-09-17

    In this paper, we address the task of gas distribution modeling in scenarios where multiple heterogeneous compounds are present. Gas distribution modeling is particularly useful in emission monitoring applications where spatial representations of the gaseous patches can be used to identify emission hot spots. In realistic environments, the presence of multiple chemicals is expected and therefore, gas discrimination has to be incorporated in the modeling process. The approach presented in this work addresses the task of gas distribution modeling by combining different non selective gas sensors. Gas discrimination is addressed with an open sampling system, composed by an array of metal oxide sensors and a probabilistic algorithm tailored to uncontrolled environments. For each of the identified compounds, the mapping algorithm generates a calibrated gas distribution model using the classification uncertainty and the concentration readings acquired with a photo ionization detector. The meta parameters of the proposed modeling algorithm are automatically learned from the data. The approach was validated with a gas sensitive robot patrolling outdoor and indoor scenarios, where two different chemicals were released simultaneously. The experimental results show that the generated multi compound maps can be used to accurately predict the location of emitting gas sources.

  1. Hard X-ray photoelectron spectra (HXPES) of bulk non-conductor vitreous SiO{sub 2}: Minimum linewidths and surface chemical shifts

    Energy Technology Data Exchange (ETDEWEB)

    Hu, Y.F., E-mail: Yongfeng.hu@lightsource.ca [Canadian Light Source, Saskatoon, SK (Canada); Xiao, Q.; Wang, D.; Cui, X. [Canadian Light Source, Saskatoon, SK (Canada); Nesbitt, H.W. [Department of Earth Sciences, University of Western Ontario, London, ONT (Canada); Bancroft, G.M. [Department of Chemistry, University of Western Ontario, London, ONT (Canada)

    2015-07-15

    Highlights: • Electronic structure of non-conducting glass studied by hard X-ray photoelectron spectroscopy. • A thin film of Cr was deposited on the vitreous SiO{sub 2} glass to overcome the sample charging. • Excellent O 1s and Si 1s linewidths were obtained, matching those reported using the laboratory based Kratos Axis Ultra spectrometer equipped with a magnetic compensation system. • The bulk and interface states of non-conducting samples are studied as a function of photon energy. - Abstract: Hard X-ray photoelectron spectra (2200 eV to 5000 eV photon energies) have been obtained for the first time on a bulk non-conductor, vitreous SiO{sub 2}, on a high resolution (E/ΔE of 10,000) synchrotron beamline at the Canadian Light Source (CLS). To minimize charging and differential charging, the SiO{sub 2} was coated with very thin layers (0.5 to 1.5 nm) of Cr metal. The O 1s linewidth obtained at 2500 eV photon energy was 1.26 eV—the minimum linewidth for SiO{sub 2}—and in good agreement with that obtained at 1486 eV on a Kratos Axis Ultra spectrometer equipped with a magnetic charge compensation system. The Si 1s linewidth of 1.5 eV, somewhat broader than that previously obtained at 1486 eV on the Si 2p{sub 3/2} line of 1.16 eV, is mainly due to the much larger inherent Si 1s linewidth (0.5 eV) compared to the inherent Si 2p linewidth (<0.1 eV). Both linewidths are dominated by the large final state vibrational broadening previously described. The Cr coating produces surface monolayers of interfacial Cr “suboxide” (Cr-subox), Cr metal, and a surface Cr oxide (Cr-surfox). Cr-subox (Si−O−Cr) gives rise to the weak near-surface Si 1s peak, while both oxides give rise to both the weak surface O 1s peak and the Cr 2p oxide peak. Both the O 1s and Si 1s surface peaks are shifted by ∼2 eV relative to the large bulk Si 1s and O 1s peaks. The weak Si 1s and O 1s surface peaks along with the Cr 2p oxide peak decrease in intensity greatly as the photon

  2. 英语名词动用中选择性制约的认知解释%A Cognitive Study of Selective Restriction in N-V Shift

    Institute of Scientific and Technical Information of China (English)

    周小文

    2014-01-01

    在认知语法框架下,以英语处所类动词与移位类动词为例,解释名词动用中产生选择性制约的原因,并从类型学的角度对研究结论加以佐证。文章认为,在名词动用时,被凸显的名词继续保留其名词性质,具有担当宾语的典型价值,它转化为动词的可能性因此受到限制。而不那么被凸显的名词更可能转化为动词。在致使-移动类事件中,受事的凸显度高于地点,因此表示地点的名词类转为动词,即处所类动词;在致使-领有类事件中,领有者的凸显度高于受事,因此指示受事的名词类转为动词,即移位类动词。名词动用的制约性最终是由主体对事件的认知模式与概念结构决定的。%Within the framework of cognitive grammar theories, this paper proposes an account of the selective restriction in N-V shift illustrated by denominal locatum and location verbs. The paper proposes that in the N-V shift, the noun with greater prominence will have the prototypical value as an object, so its possibility of being transformed into a verb is greatly restricted, hence the noun with less prominence will be used as a verb. In the cause-move event, the prominence of the patient is greater than the location, so the noun with the location role is shifted to verb, i.e., a location verb. In the cause-possess event, the prominence of a recipient is greater than a patient, so the noun with the patient role is shifted to verb, i.e., a locatum verb. The selective restriction in N-V shift is ultimately determined by one’s cognitive mode and conceptual structure.

  3. PREFACE: Selected papers from the Fourth Topical Conference on Nanoscale Science and Engineering of the American Institute of Chemical Engineers

    Science.gov (United States)

    Wong, Michael S.; Lee, Gil U.

    2005-07-01

    systems and tissue engineering; nanotechnology for drug delivery and imaging; bionanotechnology in cancer and cardiovascular disease; nanostructured biomaterials; nanotechnology in bioengineering; nanofabrication of biosensing devices. We are pleased to present a selection of research papers in this special issue of Nanotechnology on behalf of the Nanoscale Science and Engineering Forum (NSEF). NSEF was established in 2001 as a new division of AIChE to promote nanotechnology efforts in chemical engineering. The chemical engineering discipline deals with the production and processing of chemicals and materials, and does so through a fundamental understanding of the core issues of transport, thermodynamics, and kinetics that exist at multiple length scales. Thus, it should come as no surprise that chemical engineers have been pursuing nanotechnology research for the last fifty years. For example, fuel production has benefited immensely from improved catalysts in which their pore structure is controlled with nanoscale precision, and polymer properties have been improved by controlling the polymer supramolecular structure at the nanometre scale. Chemical engineering will continue to make important contributions to nanotechnology, and will play a critical role in the transition from basic science and engineering research to commercial applications. We would like to thank all of the authors who contributed to this special issue; the three NSEF poster presentation award winners for their papers (Sureshkumar, Sunkara, and Rinaldi groups); Dr Nina Couzin, Publisher of Nanotechnology, for her support and enthusiasm for this project; Drs Sharon Glotzer and Dan Coy who chaired the topical conference; and Drs Meyya Meyyappan and Brett Cruden (NASA Ames Research Center) for their assistance in the initial planning stages. We also take this opportunity to thank the many people and organizations who have supported the 2004 topical conference along the way, which include all the session

  4. CO{sub 2} SELECTIVE CERAMIC MEMBRANE FOR WATER-GAS-SHIFT REACTION WITH CONCOMITANT RECOVERY OF CO{sub 2}

    Energy Technology Data Exchange (ETDEWEB)

    Paul K. T. Liu

    2005-01-31

    Our CO{sub 2}-affinity material synthesis activities thus far have offered two base materials suitable for hydrogen production via low temperature water gas shift reaction (LTS-WGS) with concomitant removal of CO{sub 2} for sequestration. They include (i) a nanoporous CO{sub 2}-affinity membrane and (ii) a hydrotalcite based CO-affinity adsorbent. These two materials offer a commercially viable opportunity for implementing an innovative process concept termed the hybrid adsorbent-membrane reactor (HAMR) for LTS-WGS, proposed by us in a previous quarterly report. A complete mathematical model has been developed in this quarter to describe the HAMR system, which offers process flexibility to incorporate both catalysts and adsorbents in the reactor as well as permeate sides. In comparison with the preliminary mathematical model we reported previously, this improved model incorporates ''time'' as an independent variable to realistically simulate the unsteady state nature of the adsorptive portion of the process. In the next quarterly report, we will complete the simulation to demonstrate the potential benefit of the proposed process based upon the performance parameters experimentally obtained from the CO{sub 2}-affinity adsorbent and membrane developed from this project.

  5. Using Selected Chemical and Physical Factors to Cross-link a BioCo Polymer Binder - Mineral Matrix System

    Directory of Open Access Journals (Sweden)

    B. Grabowska

    2013-04-01

    Full Text Available This publication describes research on the course of the process of cross-linking new BioCo polymer binders - in the form of water-based polymer compositions of poly(acrylic acid or poly(sodium acrylate/modified polysaccharide - using selected physical and chemical factors. It has been shown that the type of cross-linking factor used influences the strength parameters of the moulding sand. The crosslinking factors selected during basic research make it possible to obtain sand strengths similar to those of samples of sands bonded with commercial binders. Microwave radiation turned out to be the most effective cross-linking factor in a binder-matrix system. It was proven that adsorption in the microwave radiation field leads to the formation of polymer lattices with hydrogen bonds which play a major role in maintaining the formed cross-linked structures in the binder-matrix system. As a result, the process improves the strength parameters of the sand, whereas the hardening process in a microwave field significantly shortens the setting time.

  6. Effects of Gene Duplication, Positive Selection, and Shifts in Gene Expression on the Evolution of the Venom Gland Transcriptome in Widow Spiders.

    Science.gov (United States)

    Haney, Robert A; Clarke, Thomas H; Gadgil, Rujuta; Fitzpatrick, Ryan; Hayashi, Cheryl Y; Ayoub, Nadia A; Garb, Jessica E

    2016-01-05

    Gene duplication and positive selection can be important determinants of the evolution of venom, a protein-rich secretion used in prey capture and defense. In a typical model of venom evolution, gene duplicates switch to venom gland expression and change function under the action of positive selection, which together with further duplication produces large gene families encoding diverse toxins. Although these processes have been demonstrated for individual toxin families, high-throughput multitissue sequencing of closely related venomous species can provide insights into evolutionary dynamics at the scale of the entire venom gland transcriptome. By assembling and analyzing multitissue transcriptomes from the Western black widow spider and two closely related species with distinct venom toxicity phenotypes, we do not find that gene duplication and duplicate retention is greater in gene families with venom gland biased expression in comparison with broadly expressed families. Positive selection has acted on some venom toxin families, but does not appear to be in excess for families with venom gland biased expression. Moreover, we find 309 distinct gene families that have single transcripts with venom gland biased expression, suggesting that the switching of genes to venom gland expression in numerous unrelated gene families has been a dominant mode of evolution. We also find ample variation in protein sequences of venom gland-specific transcripts, lineage-specific family sizes, and ortholog expression among species. This variation might contribute to the variable venom toxicity of these species.

  7. Dempster-Shafer theory applied to regulatory decision process for selecting safer alternatives to toxic chemicals in consumer products.

    Science.gov (United States)

    Park, Sung Jin; Ogunseitan, Oladele A; Lejano, Raul P

    2014-01-01

    Regulatory agencies often face a dilemma when regulating chemicals in consumer products-namely, that of making decisions in the face of multiple, and sometimes conflicting, lines of evidence. We present an integrative approach for dealing with uncertainty and multiple pieces of evidence in toxics regulation. The integrative risk analytic framework is grounded in the Dempster-Shafer (D-S) theory that allows the analyst to combine multiple pieces of evidence and judgments from independent sources of information. We apply the integrative approach to the comparative risk assessment of bisphenol-A (BPA)-based polycarbonate and the functionally equivalent alternative, Eastman Tritan copolyester (ETC). Our results show that according to cumulative empirical evidence, the estimated probability of toxicity of BPA is 0.034, whereas the toxicity probability for ETC is 0.097. However, when we combine extant evidence with strength of confidence in the source (or expert judgment), we are guided by a richer interval measure, (Bel(t), Pl(t)). With the D-S derived measure, we arrive at various intervals for BPA, with the low-range estimate at (0.034, 0.250), and (0.097,0.688) for ETC. These new measures allow a reasonable basis for comparison and a justifiable procedure for decision making that takes advantage of multiple sources of evidence. Through the application of D-S theory to toxicity risk assessment, we show how a multiplicity of scientific evidence can be converted into a unified risk estimate, and how this information can be effectively used for comparative assessments to select potentially less toxic alternative chemicals.

  8. VP Anaphors and Object Shift

    DEFF Research Database (Denmark)

    Ørsnes, Bjarne

    2013-01-01

    The article discusses the placement of the VP anaphor det ‘it’ as a complement of verbs selecting VP complements in Danish. With verbs that only allow a VP complement, the VP anaphor must be in SpecCP regardless of its information structure properties. If SpecCP is occupied by an operator, the an...... be in situ. The article argues that a shifted pronominal in Danish must be categorially licensed by the verb and extends this analysis to shifting locatives. An Optimality Theory analysis is proposed that accounts for the observed facts......., the anaphor can be in situ, but it cannot shift. With verbs that allow its VP complement to alternate with an NP complement, the VP anaphor can be in SpecCP, shifted or in situ according to the information structural properties of the anaphor. Only if SpecCP is occupied by an operator, must a topical anaphor...

  9. On the calculation of Mossbauer isomer shift

    NARCIS (Netherlands)

    Filatov, Michael

    2007-01-01

    A quantum chemical computational scheme for the calculation of isomer shift in Mossbauer spectroscopy is suggested. Within the described scheme, the isomer shift is treated as a derivative of the total electronic energy with respect to the radius of a finite nucleus. The explicit use of a finite nuc

  10. Study of multi-site chemical exchange in solution state by NMR: 1D experiments with multiply selective excitation

    Indian Academy of Sciences (India)

    Samanwita Pal

    2010-07-01

    Chemical exchange in solution state has been investigated traditionally by both 1D and 2D NMR, permitting the extraction of kinetic parameters (e.g. the spin-lattice relaxation time 1, the exchange rate constant and the activation parameters). This work demonstrates a simple 1D NMR approach employing multiply selective excitation to study multi-site exchange processes in solution, applying it to systems that exhibit three-site exchange. This approach involves simultaneous excitation of all - or a chosen subset of - the exchanging sites by using an appropriately modulated shaped radiofrequency pulse. The pulse sequence, as well as analysis is summarized. Significant features of the experiment, which relies on sign labelling of the exchanging sites, include considerably shorter experiment time compared to standard 2D exchange work, clear definition of the exchange time window and uniform pulse non-ideality effects for all the exchanging sites. Complete kinetic information is reported in the study of dynamic processes in superacid solutions of two weak bases, studied by 1H NMR. An analytical solution, leading to the determination of four rate parameters, is presented for proton exchange studies on these systems, which involve a mixture of two weak bases in arbitrary concentration ratio, and stoichiometric excess of the superacid.

  11. Sulfur and ash reduction potential and selected chemical and physical properties of United States coals. [Contains glossary

    Energy Technology Data Exchange (ETDEWEB)

    Cavallaro, J.A.; Deurbrouck, A.W.; Killmeyer, R.P.; Fuchs, W. (USDOE Pittsburgh Energy Technology Center, PA (USA). Coal Preparation Div.); Jacobsen, P.S. (Burns and Roe Services Corp., Pittsburgh, PA (USA))

    1991-02-01

    This report presents the washability and comprehensive characterization results of 184 raw coal channel samples, including anthracite, bituminous and lignite coals, collected from the Central Region of the United States. This is the second of a three volume report on the coals of the United States. All the data are presented in six appendices. Statistical techniques and definitions are presented in Appendix A, and a glossary of terms is presented in Appendix B. The complete washability data and an in-depth characterization of each sample are presented alphabetically by state in Appendix C. In Appendix D, a statistical evaluation is given for the composited washability data, selected chemical and physical properties and washability data interpolated at various levels of Btu recovery. This presentation is shown by state, section, and region where four or more samples were collected. Appendix E presents coalbed codes and names for the Central Region coals. Graphical summations are presented by state, section and region showing the effects of crushing on impurity reductions, and the distribution of raw and clean coal samples meeting various levels of SO{sub 2} emissions. 35 figs., 5 tabs.

  12. Selective catalytic reduction of NO by NH3 on Cu-faujasite catalysts: an experimental and quantum chemical approach.

    Science.gov (United States)

    Delahay, Gérard; Villagomez, Enrique Ayala; Ducere, Jean-Marie; Berthomieu, Dorothée; Goursot, Annick; Coq, Bernard

    2002-08-16

    The selective catalytic reduction (SCR) of NO by NH3 in the presence of O2 on Cu-faujasite (Cu-FAU) has been studied. Substitution of some Cu2+ with H+ and Na+ cations, compensating for the negative charge of the zeolite framework, forms the various CuHNa-FAU studied. The amount of Cu was held constant and the proportion of H+ and Na+ varied in the sample. The substitution of Na+ for H+ increases sharply the SCR rate by lowering the temperature of reaction by about 150 K. It is proposed that the rate increase mainly comes from an unhindered migration of Cu from hidden to active sites and a modification of the redox properties of Cu species. The former was demonstrated by diffuse reflectance IR spectroscopy of adsorbed CO. The change in redox properties was demonstrated by a faster oxidation of Cu+ to Cu2+ (rate-determining step). Quantum chemical calculations on model clusters of CuHNa-FAU indicate that the faster rate of oxidation can be explained by a higher lability of protons in the absence of Na, which can be then removed from the catalyst more easily to yield H2O during the oxidation process.

  13. Determining soil redistribution in Dian Lake catchment by combined use of caesium-137 and selected chemical properties

    Institute of Scientific and Technical Information of China (English)

    Zhang Mingli; Yang Hao; Xu Congan; Wang Yihong

    2009-01-01

    Recent development in the use of the environmental radionuclide caesium-137 for documenting rates and patterns of soil redistribution on the cultivated or uncultivated land and estimating rates of sediment deposition on floodplains represents an important advance that overcomes many of the limitations' of the conventional techniques commonly applied in such investigations.A study on soil redistribution (including soil erosion and deposition) was carried out in the Dian Lake catchment,Yunnan Province,using 137Cs and selected chemical properties.The average soil erosion rate was 1,280.2 t km-2yr-1.Soil erosion rate occurring on different parts of the slope was significantly different on different parts of the slope,increasing from the top,the bottom to the middle slope.The average soil erosion rate is also different with the land use type and that of the cultivated land (1,672.8 t km-2 yr-1) is higher than of the uncultivated land (1,161.2 t km-2yr-1).The result shows that landform,slope gradient and land use type are key factors that influence the size of soil erosion.In addition,we also find the SOC and TN contents and amount of the soil erosion to be correlated in the soil.With the soil erosion occurring,there are land degradation and the local eco-environmental problems,such as water eutrophication in Dian Lake

  14. Chemical composition and antibacterial activity of the essential oil from green huajiao (Zanthoxylum schinifolium) against selected foodborne pathogens.

    Science.gov (United States)

    Diao, Wen-Rui; Hu, Qing-Ping; Feng, Sai-Sai; Li, Wei-Qin; Xu, Jian-Guo

    2013-06-26

    Green huajiao, which is the ripe pericarp of the fruit of Zanthoxylum schinifolium Sieb. et Zucc, is widely consumed in Asia as a spice. In this work, the chemical composition of the essential oil from green huajiao was analyzed by gas chromatography (GC) and GC/mass spectrometry (MS), and the majority of components were identified. Linalool (28.2%), limonene (13.2%), and sabinene (12.1%) were found to be the major components. The antibacterial activity, minimum inhibitory concentration (MIC), and minimum bactericidal concentration (MBC) of the essential oil were evaluated against selected bacteria, including food-borne pathogens. The results showed that the sensitivities to the essential oil were different for different bacteria tested, and the susceptibility of Gram-positive bacteria tested was observed to be greater than that of Gram-negative bacteria. The antibacterial activity of the essential oil was particularly strong against Staphylococcus epidermidis , with MIC and MBC values of 2.5 and 5.0 mg/mL, respectively. A postcontact effect assay also confirmed the essential oil had a significant effect on the growth rate of surviving S. epidermidis . The antibacterial activity of the essential oil from green huajiao may be due to the increase in permeability of cell membranes, and the leakage of intracellular constituents, on the basis of the cell constituents' release assay and electron microscopy observations.

  15. Selective adhesion of intestinal epithelial cells on patterned films with amine functionalities formed by plasma enhanced chemical vapor deposition

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Kyung Seop; Choi, Changrok; Kim, Soo Heon; Choi, Kun oh [Department of Physics, Brain Korea 21 Physics Research Division and Institute of Basic Science, Sungkyunkwan University, Suwon 440-746 (Korea, Republic of); Kim, Jeong Min [Department of Molecular Biology and Institute of Nanosensor and Biotechnology, BK21 Graduate Program for RNA Biology, Dankook University, Yongin 448-701 (Korea, Republic of); Kim, Hong Ja [Department of Internal Medicine, Dankook University College of Medicine, Cheonan 330-715 (Korea, Republic of); Yeo, Sanghak [R and D Center, ELBIO Incorporation, 426-5 Gasan-dong Geumchun-gu, Seoul (Korea, Republic of); Park, Heonyong [Department of Molecular Biology and Institute of Nanosensor and Biotechnology, BK21 Graduate Program for RNA Biology, Dankook University, Yongin 448-701 (Korea, Republic of); Jung, Donggeun, E-mail: djung@skku.ac.kr [Department of Physics, Brain Korea 21 Physics Research Division and Institute of Basic Science, Sungkyunkwan University, Suwon 440-746 (Korea, Republic of)

    2010-11-01

    Control of cell adhesion to surfaces is important to develop analytical tools in the areas of biomedical engineering. To control cell adhesiveness of the surface, we constructed a variety of plasma polymerized hexamethyldisiloxane (PPHMDSO) thin films deposited at the plasma power range of 10-100 W by plasma enhanced chemical vapor deposition (PECVD). The PPHMDSO film that was formed at 10 W was revealed to be resistant to cell adhesion. The resistance to cell adhesion is closely related to physicochemical properties of the film. Atomic force microscopic data show an increase in surface roughness from 0.52 nm to 0.74 nm with increasing plasma power. From Fourier transform infrared (FT-IR) absorption spectroscopy data, it was also determined that the methyl (-CH{sub 3}) peak intensity increases with increasing plasma power, whereas the hydroxyl (-OH) peak decreases. X-ray photoelectron spectroscopy data reveal an increase in C-O bonding with increasing plasma power. These results suggest that C-O bonding and hydroxyl (-OH) and methyl (-CH{sub 3}) functional groups play a critical part in cell adhesion. Furthermore, to enhance a diversity of film surface, we accumulated the patterned plasma polymerized ethylenediamine (PPEDA) thin film on the top of the PPHMDSO thin film. The PPEDA film is established to be strongly cell-adherent. This patterned two-layer film stacking method can be used to form the selectively limited cell-adhesive PPEDA spots over the adhesion-resistant surface.

  16. Selective adsorption of molybdenum(VI) from Mo-Re bearing effluent by chemically modified astringent persimmon.

    Science.gov (United States)

    Xiong, Ying; Wang, Haitao; Lou, Zhenning; Shan, Weijun; Xing, Zhiqiang; Deng, Guichun; Wu, Dongbei; Fang, Dawei; Biswas, Biplob Kumar

    2011-02-28

    Astringent persimmon was chemically cross-linked by formaldehyde to obtain a novel kind of adsorption gel, which was named as APF gel. The adsorption behaviors of Mo(VI) and Re(VII) along with other coexisting metals onto the APF gel were studied in the present paper. The APF gel was found to be effective for the adsorption of Mo(VI) while the gel is almost completely inert toward rhenium and calcium over the whole hydrochloric acid concentration region. The APF gel has a low affinity for iron, copper, lead, nickel, manganese and zinc ions when the concentration of HCl is higher than 1 mol/L. The gel exhibited selectivity only for Mo(VI) with a remarkably high adsorption capacity 1.05 mol/kg, and the adsorption behavior obeys the Langmuir model. According to the thermodynamic and kinetic studies, the endothermic adsorption process followed pseudo-second order kinetics. Also, its excellent adsorption characteristics for Mo(VI) were confirmed by the adsorption and elution tests using a column packed with the APF gel. The result provides a new approach for the recovery of Mo(VI) from a industrial waste effluent.

  17. Sulfur and ash reduction potential and selected chemical and physical properties of United States coals. [Contains glossary

    Energy Technology Data Exchange (ETDEWEB)

    Cavallaro, J.A.; Deurbrouck, A.W.; Killmeyer, R.P.; Fuchs, W. (USDOE Pittsburgh Energy Technology Center, PA (USA)); Jacobsen, P.S. (Burns and Roe Services Corp., Pittsburgh, PA (USA))

    1990-01-01

    This report presents the washability and comprehensive characterization results of 543 raw coal samples collected from the Eastern Region of the United States. This is the first volume of a three-volume report on the coals of the United States. All the data are presented in six appendices. Statistical techniques and definitions are presented in Appendix A, and a glossary of terms is presented in Appendix B. The complete washability data and an in- depth characterization of each sample are presented alphbetically by state in Appendix C. In Appendix D, a statistical evaluation is given for the composited washability data, selected chemical and physical properties, and washability data interpolated at various levels of Btu recovery. This presentation is shown by state, section, and region where four or more samples were collected. Appendix E presents coalbed codes and names for the Eastern Region coals. Graphical summations are presented by state, section, and region showing the effects of crushing on impurity reductions, and the distribution of raw and clean coal samples meeting various levels of SO{sub 2} emissions. 14 refs., 27 figs., 3 tabs.

  18. Surface etching, chemical modification and characterization of silicon nitride and silicon oxide—selective functionalization of Si3N4 and SiO2

    Science.gov (United States)

    Liu, Li-Hong; Michalak, David J.; Chopra, Tatiana P.; Pujari, Sidharam P.; Cabrera, Wilfredo; Dick, Don; Veyan, Jean-François; Hourani, Rami; Halls, Mathew D.; Zuilhof, Han; Chabal, Yves J.

    2016-03-01

    The ability to selectively chemically functionalize silicon nitride (Si3N4) or silicon dioxide (SiO2) surfaces after cleaning would open interesting technological applications. In order to achieve this goal, the chemical composition of surfaces needs to be carefully characterized so that target chemical reactions can proceed on only one surface at a time. While wet-chemically cleaned silicon dioxide surfaces have been shown to be terminated with surficial Si-OH sites, chemical composition of the HF-etched silicon nitride surfaces is more controversial. In this work, we removed the native oxide under various aqueous HF-etching conditions and studied the chemical nature of the resulting Si3N4 surfaces using infrared absorption spectroscopy (IRAS), x-ray photoelectron spectroscopy (XPS), low energy ion scattering (LEIS), and contact angle measurements. We find that HF-etched silicon nitride surfaces are terminated by surficial Si-F and Si-OH bonds, with slightly subsurface Si-OH, Si-O-Si, and Si-NH2 groups. The concentration of surficial Si-F sites is not dependent on HF concentration, but the distribution of oxygen and Si-NH2 displays a weak dependence. The Si-OH groups of the etched nitride surface are shown to react in a similar manner to the Si-OH sites on SiO2, and therefore no selectivity was found. Chemical selectivity was, however, demonstrated by first reacting the -NH2 groups on the etched nitride surface with aldehyde molecules, which do not react with the Si-OH sites on a SiO2 surface, and then using trichloro-organosilanes for selective reaction only on the SiO2 surface (no reactivity on the aldehyde-terminated Si3N4 surface).

  19. Surface etching, chemical modification and characterization of silicon nitride and silicon oxide--selective functionalization of Si3N4 and SiO2.

    Science.gov (United States)

    Liu, Li-Hong; Michalak, David J; Chopra, Tatiana P; Pujari, Sidharam P; Cabrera, Wilfredo; Dick, Don; Veyan, Jean-François; Hourani, Rami; Halls, Mathew D; Zuilhof, Han; Chabal, Yves J

    2016-03-09

    The ability to selectively chemically functionalize silicon nitride (Si3N4) or silicon dioxide (SiO2) surfaces after cleaning would open interesting technological applications. In order to achieve this goal, the chemical composition of surfaces needs to be carefully characterized so that target chemical reactions can proceed on only one surface at a time. While wet-chemically cleaned silicon dioxide surfaces have been shown to be terminated with surficial Si-OH sites, chemical composition of the HF-etched silicon nitride surfaces is more controversial. In this work, we removed the native oxide under various aqueous HF-etching conditions and studied the chemical nature of the resulting Si3N4 surfaces using infrared absorption spectroscopy (IRAS), x-ray photoelectron spectroscopy (XPS), low energy ion scattering (LEIS), and contact angle measurements. We find that HF-etched silicon nitride surfaces are terminated by surficial Si-F and Si-OH bonds, with slightly subsurface Si-OH, Si-O-Si, and Si-NH2 groups. The concentration of surficial Si-F sites is not dependent on HF concentration, but the distribution of oxygen and Si-NH2 displays a weak dependence. The Si-OH groups of the etched nitride surface are shown to react in a similar manner to the Si-OH sites on SiO2, and therefore no selectivity was found. Chemical selectivity was, however, demonstrated by first reacting the -NH2 groups on the etched nitride surface with aldehyde molecules, which do not react with the Si-OH sites on a SiO2 surface, and then using trichloro-organosilanes for selective reaction only on the SiO2 surface (no reactivity on the aldehyde-terminated Si3N4 surface).

  20. Presence of selected chemicals of emerging concern in water and bottom sediment from the St. Louis River, St. Louis Bay, and Superior Bay, Minnesota and Wisconsin, 2010

    Science.gov (United States)

    Christensen, Victoria G.; Lee, Kathy E.; Kieta, Kristen A.; Elliott, Sarah M.

    2012-01-01

    The St. Louis Bay of Lake Superior receives substantial urban runoff, wastewater treatment plant effluent, and industrial effluent. In 1987, the International Joint Commission designated the St. Louis Bay portion of the lower St. Louis River as one of the Great Lakes Areas of Concern. Concerns exist about the potential effects of chemicals of emerging concern on aquatic biota because many of these chemicals, including endocrine active chemicals, have been shown to affect the endocrine systems of fish. To determine the occurrence of chemicals of emerging concern in the St. Louis River, the St. Louis Bay, and Superior Bay, the U.S. Geological Survey in cooperation with the Minnesota Pollution Control Agency and the Wisconsin Department of Natural Resources collected water and bottom-sediment samples from 40 sites from August through October 2010. The objectives of this study were to (1) identify the extent to which chemicals of emerging concern, including pharmaceuticals, hormones, and other organic chemicals, occur in the St. Louis River, St. Louis Bay, and Superior Bay, and (2) identify the extent to which the chemicals may have accumulated in bottom sediment of the study area. Samples were analyzed for selected wastewater indicators, hormones, sterols, bisphenol A, and human-health pharmaceuticals. During this study, 33 of 89 chemicals of emerging concern were detected among all water samples collected and 56 of 104 chemicals of emerging concern were detected in bottom-sediment samples. The chemical N,N-diethyl-meta-toluamide (DEET) was the most commonly detected chemical in water samples and 2,6-dimethylnaphthalene was the most commonly detected chemical in bottom-sediment samples. In general, chemicals of emerging concern were detected at a higher frequency in bottom-sediment samples than in water samples. Estrone (a steroid hormone) and hexahydrohexamethyl cyclopentabensopyran (a synthetic fragrance) were the most commonly detected endocrine active chemicals in

  1. Xinjiang Guanghui Shifts to Coal Chemical Business

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    @@ Xinjiang Guanghui Industry Co., Ltd.(Xinjiang Guanghui, SH: 600256) was established on April 10th, 1999. It is located in Urumqi Economic and Technological Development Zone,Xinjiang of western China. The company got listed in Shanghai Stock Exchange on May 26th, 2000.

  2. The test chemical selection procedure of the European Centre for the Validation of Alternative Methods for the EU Project ReProTect.

    Science.gov (United States)

    Pazos, Patricia; Pellizzer, Cristian; Stummann, Tina C; Hareng, Lars; Bremer, Susanne

    2010-08-01

    The selection of reference compounds is crucial for a successful in vitro test development in order to proof the relevance of the test system. This publication describes the criteria and the selection strategy leading to a list of more than 130 chemicals suitable for test development within the ReProTect project. The presented chemical inventory aimed to support the development and optimization of in vitro tests that seek to fulfill ECVAM's criteria for entering into the prevalidation. In order to select appropriate substances, a primary database was established compiling information from existing databases. In a second step, predefined selection criteria have been applied to obtain a comprehensive list ready to undergo a peer review process from independent experts with industrial, academic and regulatory background. Finally, a peer reviewed chemical list containing 13 substances challenging endocrine disrupter tests, additional 50 substances serving as reference chemicals for various tests evaluating effects on male and female fertility, and finally 61 substances were identified as known to provoke effects on the early development of mammalian offspring. The final list aims to cover relevant and specific mode/site of actions as they are known to be relevant for various substance classes. However, the recommended list should not be interpreted as a list of reproductive toxicants, because such a description requires proven associations with adverse effects of mammalian reproduction, which are subject of regulatory decisions done by involved competent authorities.

  3. Comparison of clinical semi-quantitative assessment of muscle fat infiltration with quantitative assessment using chemical shift-based water/fat separation in MR studies of the calf of post-menopausal women

    Energy Technology Data Exchange (ETDEWEB)

    Alizai, Hamza; Nardo, Lorenzo; Karampinos, Dimitrios C.; Joseph, Gabby B.; Yap, Samuel P.; Baum, Thomas; Krug, Roland; Majumdar, Sharmila; Link, Thomas M. [University of California, San Francisco, Musculoskeletal and Quantitati