WorldWideScience

Sample records for state chemical shift

  1. An extrapolation scheme for solid-state NMR chemical shift calculations

    Science.gov (United States)

    Nakajima, Takahito

    2017-06-01

    Conventional quantum chemical and solid-state physical approaches include several problems to accurately calculate solid-state nuclear magnetic resonance (NMR) properties. We propose a reliable computational scheme for solid-state NMR chemical shifts using an extrapolation scheme that retains the advantages of these approaches but reduces their disadvantages. Our scheme can satisfactorily yield solid-state NMR magnetic shielding constants. The estimated values have only a small dependence on the low-level density functional theory calculation with the extrapolation scheme. Thus, our approach is efficient because the rough calculation can be performed in the extrapolation scheme.

  2. Measuring 13Cβ chemical shifts of invisible excited states in proteins by relaxation dispersion NMR spectroscopy

    International Nuclear Information System (INIS)

    Lundstroem, Patrik; Lin Hong; Kay, Lewis E.

    2009-01-01

    A labeling scheme is introduced that facilitates the measurement of accurate 13 C β chemical shifts of invisible, excited states of proteins by relaxation dispersion NMR spectroscopy. The approach makes use of protein over-expression in a strain of E. coli in which the TCA cycle enzyme succinate dehydrogenase is knocked out, leading to the production of samples with high levels of 13 C enrichment (30-40%) at C β side-chain carbon positions for 15 of the amino acids with little 13 C label at positions one bond removed (∼5%). A pair of samples are produced using [1- 13 C]-glucose/NaH 12 CO 3 or [2- 13 C]-glucose as carbon sources with isolated and enriched (>30%) 13 C β positions for 11 and 4 residues, respectively. The efficacy of the labeling procedure is established by NMR spectroscopy. The utility of such samples for measurement of 13 C β chemical shifts of invisible, excited states in exchange with visible, ground conformations is confirmed by relaxation dispersion studies of a protein-ligand binding exchange reaction in which the extracted chemical shift differences from dispersion profiles compare favorably with those obtained directly from measurements on ligand free and fully bound protein samples

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

    International Nuclear Information System (INIS)

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

    2013-01-01

    We introduce a Python-based program that utilizes the large database of 13 C and 15 N chemical shifts in the Biological Magnetic Resonance Bank to rapidly predict the amino acid type and secondary structure from correlated chemical shifts. The program, called PACSYlite Unified Query (PLUQ), is designed to help assign peaks obtained from 2D 13 C– 13 C, 15 N– 13 C, or 3D 15 N– 13 C– 13 C magic-angle-spinning correlation spectra. We show secondary-structure specific 2D 13 C– 13 C correlation maps of all twenty amino acids, constructed from a chemical shift database of 262,209 residues. The maps reveal interesting conformation-dependent chemical shift distributions and facilitate searching of correlation peaks during amino-acid type assignment. Based on these correlations, PLUQ outputs the most likely amino acid types and the associated secondary structures from inputs of experimental chemical shifts. We test the assignment accuracy using four high-quality protein structures. Based on only the Cα and Cβ chemical shifts, the highest-ranked PLUQ assignments were 40–60 % correct in both the amino-acid type and the secondary structure. For three input chemical shifts (CO–Cα–Cβ or N–Cα–Cβ), the first-ranked assignments were correct for 60 % of the residues, while within the top three predictions, the correct assignments were found for 80 % of the residues. PLUQ and the chemical shift maps are expected to be useful at the first stage of sequential assignment, for combination with automated sequential assignment programs, and for highly disordered proteins for which secondary structure analysis is the main goal of structure determination.

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

    Energy Technology Data Exchange (ETDEWEB)

    Fritzsching, K. J.; Yang, Y.; Schmidt-Rohr, K.; Hong Mei, E-mail: mhong@iastate.edu [Iowa State University, Department of Chemistry (United States)

    2013-06-15

    We introduce a Python-based program that utilizes the large database of {sup 13}C and {sup 15}N chemical shifts in the Biological Magnetic Resonance Bank to rapidly predict the amino acid type and secondary structure from correlated chemical shifts. The program, called PACSYlite Unified Query (PLUQ), is designed to help assign peaks obtained from 2D {sup 13}C-{sup 13}C, {sup 15}N-{sup 13}C, or 3D {sup 15}N-{sup 13}C-{sup 13}C magic-angle-spinning correlation spectra. We show secondary-structure specific 2D {sup 13}C-{sup 13}C correlation maps of all twenty amino acids, constructed from a chemical shift database of 262,209 residues. The maps reveal interesting conformation-dependent chemical shift distributions and facilitate searching of correlation peaks during amino-acid type assignment. Based on these correlations, PLUQ outputs the most likely amino acid types and the associated secondary structures from inputs of experimental chemical shifts. We test the assignment accuracy using four high-quality protein structures. Based on only the C{alpha} and C{beta} chemical shifts, the highest-ranked PLUQ assignments were 40-60 % correct in both the amino-acid type and the secondary structure. For three input chemical shifts (CO-C{alpha}-C{beta} or N-C{alpha}-C{beta}), the first-ranked assignments were correct for 60 % of the residues, while within the top three predictions, the correct assignments were found for 80 % of the residues. PLUQ and the chemical shift maps are expected to be useful at the first stage of sequential assignment, for combination with automated sequential assignment programs, and for highly disordered proteins for which secondary structure analysis is the main goal of structure determination.

  5. Criteria to average out the chemical shift anisotropy in solid-state NMR when irradiated with BABA I, BABA II, and C7 radiofrequency pulse sequences.

    Science.gov (United States)

    Stephane Mananga, Eugene

    2013-01-01

    Floquet-Magnus expansion is used to study the effect of chemical shift anisotropy in solid-state NMR of rotating solids. The chemical shift interaction is irradiated with two types of radiofrequency pulse sequences: BABA and C7. The criteria for the chemical shift anisotropy to be averaged out in each rotor period are obtained. Copyright © 2013 Elsevier Inc. All rights reserved.

  6. Spin-echo based diagonal peak suppression in solid-state MAS NMR homonuclear chemical shift correlation spectra

    Science.gov (United States)

    Wang, Kaiyu; Zhang, Zhiyong; Ding, Xiaoyan; Tian, Fang; Huang, Yuqing; Chen, Zhong; Fu, Riqiang

    2018-02-01

    The feasibility of using the spin-echo based diagonal peak suppression method in solid-state MAS NMR homonuclear chemical shift correlation experiments is demonstrated. A complete phase cycling is designed in such a way that in the indirect dimension only the spin diffused signals are evolved, while all signals not involved in polarization transfer are refocused for cancellation. A data processing procedure is further introduced to reconstruct this acquired spectrum into a conventional two-dimensional homonuclear chemical shift correlation spectrum. A uniformly 13C, 15N labeled Fmoc-valine sample and the transmembrane domain of a human protein, LR11 (sorLA), in native Escherichia coli membranes have been used to illustrate the capability of the proposed method in comparison with standard 13C-13C chemical shift correlation experiments.

  7. Chemical shift imaging: a review

    International Nuclear Information System (INIS)

    Brateman, L.

    1986-01-01

    Chemical shift is the phenomenon that is seen when an isotope possessing a nuclear magnetic dipole moment resonates at a spectrum of resonance frequencies in a given magnetic field. These resonance frequencies, or chemical shifts, depend on the chemical environments of particular nuclei. Mapping the spatial distribution of nuclei associated with a particular chemical shift (e.g., hydrogen nuclei associated with water molecules or with lipid groups) is called chemical shift imaging. Several techniques of proton chemical shift imaging that have been applied in vivo are presented, and their clinical findings are reported and summarized. Acquiring high-resolution spectra for large numbers of volume elements in two or three dimensions may be prohibitive because of time constraints, but other methods of imaging lipid of water distributions (i.e., selective excitation, selective saturation, or variations in conventional magnetic resonance imaging pulse sequences) can provide chemical shift information. These techniques require less time, but they lack spectral information. Since fat deposition seen by chemical shift imaging may not be demonstrated by conventional magnetic resonance imaging, certain applications of chemical shift imaging, such as in the determination of fatty liver disease, have greater diagnostic utility than conventional magnetic resonance imaging. Furthermore, edge artifacts caused by chemical shift effects can be eliminated by certain selective methods of data acquisition employed in chemical shift imaging

  8. Chemical shift homology in proteins

    International Nuclear Information System (INIS)

    Potts, Barbara C.M.; Chazin, Walter J.

    1998-01-01

    The degree of chemical shift similarity for homologous proteins has been determined from a chemical shift database of over 50 proteins representing a variety of families and folds, and spanning a wide range of sequence homologies. After sequence alignment, the similarity of the secondary chemical shifts of C α protons was examined as a function of amino acid sequence identity for 37 pairs of structurally homologous proteins. A correlation between sequence identity and secondary chemical shift rmsd was observed. Important insights are provided by examining the sequence identity of homologous proteins versus percentage of secondary chemical shifts that fall within 0.1 and 0.3 ppm thresholds. These results begin to establish practical guidelines for the extent of chemical shift similarity to expect among structurally homologous proteins

  9. pH-Dependent spin state population and 19F NMR chemical shift via remote ligand protonation in an iron(ii) complex.

    Science.gov (United States)

    Gaudette, Alexandra I; Thorarinsdottir, Agnes E; Harris, T David

    2017-11-30

    An Fe II complex that features a pH-dependent spin state population, by virtue of a variable ligand protonation state, is described. This behavior leads to a highly pH-dependent 19 F NMR chemical shift with a sensitivity of 13.9(5) ppm per pH unit at 37 °C, thereby demonstrating the potential utility of the complex as a 19 F chemical shift-based pH sensor.

  10. Measurements of relative chemical shift tensor orientations in solid-state NMR: new slow magic angle spinning dipolar recoupling experiments.

    Science.gov (United States)

    Jurd, Andrew P S; Titman, Jeremy J

    2009-08-28

    Solid-state NMR experiments can be used to determine conformational parameters, such as interatomic distances and torsion angles. The latter can be obtained from measurements of the relative orientation of two chemical shift tensors, if the orientation of these with respect to the surrounding bonds is known. In this paper, a new rotor-synchronized magic angle spinning (MAS) dipolar correlation experiment is described which can be used in this way. Because the experiment requires slow MAS rates, a novel recoupling sequence, designed using symmetry principles, is incorporated into the mixing period. This recoupling sequence is based in turn on a new composite cyclic pulse referred to as COAST (for combined offset and anisotropy stabilization). The new COAST-C7(2)(1) sequence is shown to give good theoretical and experimental recoupling efficiency, even when the CSA far exceeds the MAS rate. In this regime, previous recoupling sequences, such as POST-C7(2)(1), exhibit poor recoupling performance. The effectiveness of the new method has been explored by a study of the dipeptide L-phenylalanyl-L-phenylalanine.

  11. chemical shift tensors in helical peptides by dipolar-modulated chemical shift recoupling NMR

    International Nuclear Information System (INIS)

    Yao Xiaolan; Yamaguchi, Satoru; Hong Mei

    2002-01-01

    The Cα chemical shift tensors of proteins contain information on the backbone conformation. We have determined the magnitude and orientation of the Cα chemical shift tensors of two peptides with α-helical torsion angles: the Ala residue in G*AL (φ=-65.7 deg., ψ=-40 deg.), and the Val residue in GG*V (φ=-81.5 deg., ψ=-50.7 deg.). The magnitude of the tensors was determined from quasi-static powder patterns recoupled under magic-angle spinning, while the orientation of the tensors was extracted from Cα-Hα and Cα-N dipolar modulated powder patterns. The helical Ala Cα chemical shift tensor has a span of 36 ppm and an asymmetry parameter of 0.89. Its σ 11 axis is 116 deg. ± 5 deg. from the Cα-Hα bond while the σ 22 axis is 40 deg. ± 5 deg. from the Cα-N bond. The Val tensor has an anisotropic span of 25 ppm and an asymmetry parameter of 0.33, both much smaller than the values for β-sheet Val found recently (Yao and Hong, 2002). The Val σ 33 axis is tilted by 115 deg. ± 5 deg. from the Cα-Hα bond and 98 deg. ± 5 deg. from the Cα-N bond. These represent the first completely experimentally determined Cα chemical shift tensors of helical peptides. Using an icosahedral representation, we compared the experimental chemical shift tensors with quantum chemical calculations and found overall good agreement. These solid-state chemical shift tensors confirm the observation from cross-correlated relaxation experiments that the projection of the Cα chemical shift tensor onto the Cα-Hα bond is much smaller in α-helices than in β-sheets

  12. Empirical isotropic chemical shift surfaces

    International Nuclear Information System (INIS)

    Czinki, Eszter; Csaszar, Attila G.

    2007-01-01

    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 φ and ψ 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(φ,ψ) surfaces obtained for the model peptides For-(l-Ala) n -NH 2 , with n = 1, 3, and 5, resulted in so-called empirical ICS(φ,ψ) surfaces for all major nuclei of the 20 naturally occurring α-amino acids. Out of the many empirical surfaces determined, it is the 13C α ICS(φ,ψ) surface which seems to be most promising for identifying major secondary structure types, α-helix, β-strand, left-handed helix (α D ), and polyproline-II. Detailed tests suggest that Ala is a good model for many naturally occurring α-amino acids. Two-dimensional empirical 13C α - 1 H α ICS(φ,ψ) 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

  13. NMR spectroscopic studies of a TAT-derived model peptide in imidazolium-based ILs: influence on chemical shifts and the cis/trans equilibrium state.

    Science.gov (United States)

    Wiedemann, Christoph; Ohlenschläger, Oliver; Mrestani-Klaus, Carmen; Bordusa, Frank

    2017-09-13

    NMR spectroscopy was used to study systematically the impact of imidazolium-based ionic liquid (IL) solutions on a TAT-derived model peptide containing Xaa-Pro peptide bonds. The selected IL anions cover a wide range of the Hofmeister series of ions. Based on highly resolved one- and two-dimensional NMR spectra individual 1 H and 13 C peptide chemical shift differences were analysed and a classification of IL anions according to the Hofmeister series was derived. The observed chemical shift changes indicate significant interactions between the peptide and the ILs. In addition, we examined the impact of different ILs towards the cis/trans equilibrium state of the Xaa-Pro peptide bonds. In this context, the IL cations appear to be of exceptional importance for inducing an alteration of the native cis/trans equilibrium state of Xaa-Pro bonds in favour of the trans-isomers.

  14. De novo protein structure generation from incomplete chemical shift assignments

    Energy Technology Data Exchange (ETDEWEB)

    Shen Yang [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States); Vernon, Robert; Baker, David [University of Washington, Department of Biochemistry and Howard Hughes Medical Institute (United States); Bax, Ad [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States)], E-mail: bax@nih.gov

    2009-02-15

    NMR chemical shifts provide important local structural information for proteins. Consistent structure generation from NMR chemical shift data has recently become feasible for proteins with sizes of up to 130 residues, and such structures are of a quality comparable to those obtained with the standard NMR protocol. This study investigates the influence of the completeness of chemical shift assignments on structures generated from chemical shifts. The Chemical-Shift-Rosetta (CS-Rosetta) protocol was used for de novo protein structure generation with various degrees of completeness of the chemical shift assignment, simulated by omission of entries in the experimental chemical shift data previously used for the initial demonstration of the CS-Rosetta approach. In addition, a new CS-Rosetta protocol is described that improves robustness of the method for proteins with missing or erroneous NMR chemical shift input data. This strategy, which uses traditional Rosetta for pre-filtering of the fragment selection process, is demonstrated for two paramagnetic proteins and also for two proteins with solid-state NMR chemical shift assignments.

  15. MR chemical shift imaging of human atheroma

    International Nuclear Information System (INIS)

    Mohiaddin, R.H.; Underwood, R.; Firmin, D.; Abdulla, A.K.; Rees, S.; Longmore, D.

    1988-01-01

    The lipid content of atheromatous plaques has been measured with chemical shift MR imaging by taking advantage of the different resonance frequencies of protons in lipid and water. Fifteen postmortem aortic specimens of the human descending aorta and the aortae of seven patients with documented peripheral vascular disease were studied at 0.5 T. Spin-echo images were used to localize the lesions before acquisition of the chemical shift images. The specimens were examined histologically, and the lipid distribution in the plaque showed good correlation with the chemical shift data. Validation in vivo and clinical applications remain to be established

  16. Molecular and Silica-Supported Molybdenum Alkyne Metathesis Catalysts: Influence of Electronics and Dynamics on Activity Revealed by Kinetics, Solid-State NMR, and Chemical Shift Analysis.

    Science.gov (United States)

    Estes, Deven P; Gordon, Christopher P; Fedorov, Alexey; Liao, Wei-Chih; Ehrhorn, Henrike; Bittner, Celine; Zier, Manuel Luca; Bockfeld, Dirk; Chan, Ka Wing; Eisenstein, Odile; Raynaud, Christophe; Tamm, Matthias; Copéret, Christophe

    2017-12-06

    Molybdenum-based molecular alkylidyne complexes of the type [MesC≡Mo{OC(CH 3 ) 3-x (CF 3 ) x } 3 ] (MoF 0 , x = 0; MoF 3 , x = 1; MoF 6 , x = 2; MoF 9 , x = 3; Mes = 2,4,6-trimethylphenyl) and their silica-supported analogues are prepared and characterized at the molecular level, in particular by solid-state NMR, and their alkyne metathesis catalytic activity is evaluated. The 13 C NMR chemical shift of the alkylidyne carbon increases with increasing number of fluorine atoms on the alkoxide ligands for both molecular and supported catalysts but with more shielded values for the supported complexes. The activity of these catalysts increases in the order MoF 0 molecular and supported species. Detailed solid-state NMR analysis of molecular and silica-supported metal alkylidyne catalysts coupled with DFT/ZORA calculations rationalize the NMR spectroscopic signatures and discernible activity trends at the frontier orbital level: (1) increasing the number of fluorine atoms lowers the energy of the π*(M≡C) orbital, explaining the more deshielded chemical shift values; it also leads to an increased electrophilicity and higher reactivity for catalysts up to MoF 6 , prior to a sharp decrease in reactivity for MoF 9 due to the formation of stable metallacyclobutadiene intermediates; (2) the silica-supported catalysts are less active than their molecular analogues because they are less electrophilic and dynamic, as revealed by their 13 C NMR chemical shift tensors.

  17. 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. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  18. 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.

  19. Combined chemical shift changes and amino acid specific chemical shift mapping of protein-protein interactions

    Energy Technology Data Exchange (ETDEWEB)

    Schumann, Frank H.; Riepl, Hubert [University of Regensburg, Institute of Biophysics and Physical Biochemistry (Germany); Maurer, Till [Boehringer Ingelheim Pharma GmbH and Co. KG, Analytical Sciences Department (Germany); Gronwald, Wolfram [University of Regensburg, Institute of Biophysics and Physical Biochemistry (Germany); Neidig, Klaus-Peter [Bruker BioSpin GmbH, Software Department (Germany); Kalbitzer, Hans Robert [University of Regensburg, Institute of Biophysics and Physical Biochemistry (Germany)], E-mail: hans-robert.kalbitzer@biologie.uni-regensburg.de

    2007-12-15

    Protein-protein interactions are often studied by chemical shift mapping using solution NMR spectroscopy. When heteronuclear data are available the interaction interface is usually predicted by combining the chemical shift changes of different nuclei to a single quantity, the combined chemical shift perturbation {delta}{delta}{sub comb}. In this paper different procedures (published and non-published) to calculate {delta}{delta}{sub comb} are examined that include a variety of different functional forms and weighting factors for each nucleus. The predictive power of all shift mapping methods depends on the magnitude of the overlap of the chemical shift distributions of interacting and non-interacting residues and the cut-off criterion used. In general, the quality of the prediction on the basis of chemical shift changes alone is rather unsatisfactory but the combination of chemical shift changes on the basis of the Hamming or the Euclidian distance can improve the result. The corrected standard deviation to zero of the combined chemical shift changes can provide a reasonable cut-off criterion. As we show combined chemical shifts can also be applied for a more reliable quantitative evaluation of titration data.

  20. Solid-state NMR chemical-shift perturbations indicate domain reorientation of the DnaG primase in the primosome of Helicobacter pylori

    Energy Technology Data Exchange (ETDEWEB)

    Gardiennet, Carole [Université de Lorraine, CNRS, CRM2, UMR 7036 (France); Wiegand, Thomas [ETH Zurich, Physical Chemistry (Switzerland); Bazin, Alexandre [Université de Lyon 1, Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS (France); Cadalbert, Riccardo [ETH Zurich, Physical Chemistry (Switzerland); Kunert, Britta; Lacabanne, Denis [Université de Lyon 1, Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS (France); Gutsche, Irina [Université Grenoble Alpes, Institut de Biologie Structurale (IBS), CNRS, IBS, CEA, IBS (France); Terradot, Laurent, E-mail: l.terradot@ibcp.fr [Université de Lyon 1, Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS (France); Meier, Beat H., E-mail: beme@ethz.ch [ETH Zurich, Physical Chemistry (Switzerland); Böckmann, Anja, E-mail: a.bockmann@ibcp.fr [Université de Lyon 1, Molecular Microbiology and Structural Biochemistry, Labex Ecofect, UMR 5086 CNRS (France)

    2016-03-15

    We here investigate the interactions between the DnaB helicase and the C-terminal domain of the corresponding DnaG primase of Helicobacter pylori using solid-state NMR. The difficult crystallization of this 387 kDa complex, where the two proteins interact in a six to three ratio, is circumvented by simple co-sedimentation of the two proteins directly into the MAS-NMR rotor. While the amount of information that can be extracted from such a large protein is still limited, we can assign a number of amino-acid residues experiencing significant chemical-shift perturbations upon helicase-primase complex formation. The location of these residues is used as a guide to model the interaction interface between the two proteins in the complex. Chemical-shift perturbations also reveal changes at the interaction interfaces of the hexameric HpDnaB assembly on HpDnaG binding. A structural model of the complex that explains the experimental findings is obtained.

  1. A simple method for measuring signs of {sup 1}H{sup N} chemical shift differences between ground and excited protein states

    Energy Technology Data Exchange (ETDEWEB)

    Bouvignies, Guillaume; Korzhnev, Dmitry M.; Neudecker, Philipp; Hansen, D. Flemming [University of Toronto, Departments of Molecular Genetics, Biochemistry and Chemistry (Canada); Cordes, Matthew H. J. [University of Arizona, Department of Chemistry and Biochemistry (United States); Kay, Lewis E., E-mail: kay@pound.med.utoronto.c [University of Toronto, Departments of Molecular Genetics, Biochemistry and Chemistry (Canada)

    2010-06-15

    NMR relaxation dispersion spectroscopy is a powerful method for studying protein conformational dynamics whereby visible, ground and invisible, excited conformers interconvert on the millisecond time-scale. In addition to providing kinetics and thermodynamics parameters of the exchange process, the CPMG dispersion experiment also allows extraction of the absolute values of the chemical shift differences between interconverting states, |{Delta}{omega}-tilde|, opening the way for structure determination of excited state conformers. Central to the goal of structural analysis is the availability of the chemical shifts of the excited state that can only be obtained once the signs of {Delta}{omega}-tilde are known. Herein we describe a very simple method for determining the signs of {sup 1}H{sup N} {Delta}{omega}-tilde values based on a comparison of peak positions in the directly detected dimensions of a pair of {sup 1}H{sup N}-{sup 15}N correlation maps recorded at different static magnetic fields. The utility of the approach is demonstrated for three proteins that undergo millisecond time-scale conformational rearrangements. Although the method provides fewer signs than previously published techniques it does have a number of strengths: (1) Data sets needed for analysis are typically available from other experiments, such as those required for measuring signs of {sup 15}N {Delta}{omega}-tilde values, thus requiring no additional experimental time, (2) acquisition times in the critical detection dimension can be as long as necessary and (3) the signs obtained can be used to cross-validate those from other approaches.

  2. 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 the solution state the 2-bond and 3-bond J(1H–13C) coupling constants have been used to confirm the equilibrium positions. The isotope effects due to deuteriation at the OH position are shown to be superior to chemical shift in determination of equilibrium positions of these almost symmetrical -pyridoyl......-benzoyl methanes. The assignments of the NMR spectra are supported by calculations of the chemical shifts at the DFT level. The equilibrium positions are shown to be different in the liquid and the solid state. In the liquid state the 4-pyridoyl derivative is at the B-form (C-1 is OH), whereas the 2-and 3-pyridoyl...

  3. Protein Structure Determination Using Chemical Shifts

    DEFF Research Database (Denmark)

    Christensen, Anders Steen

    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...

  4. Steady State Shift Damage Localization

    DEFF Research Database (Denmark)

    Sekjær, Claus; Bull, Thomas; Markvart, Morten Kusk

    2017-01-01

    The steady state shift damage localization (S3DL) method localizes structural deterioration, manifested as either a mass or stiffness perturbation, by interrogating the damage-induced change in the steady state vibration response with damage patterns cast from a theoretical model. Damage is, thus...... the required accuracy when examining complex structures, an extensive amount of degrees of freedom (DOF) must often be utilized. Since the interrogation matrix for each damage pattern depends on the size of the system matrices constituting the FE-model, the computational time quickly becomes of first......-order importance. The present paper investigates two sub-structuring approaches, in which the idea is to employ Craig-Bampton super-elements to reduce the amount of interrogation distributions while still providing an acceptable localization resolution. The first approach operates on a strict super-element level...

  5. 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.

  6. 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...

  7. Proton chemical shift imaging after myocardial infarction

    International Nuclear Information System (INIS)

    Bouchard, A.; Doyle, M.; Pohost, G.M.

    1989-01-01

    The present study was undertaken to test whether chemical shift imaging could detect spatially the lipids known to accumulate in myocardium after an ischemic insult. Seven dogs underwent a 24-hour coronary artery occlusion. Hearts were removed and imaged ex vivo by the Dixon method (1.5 T), and myocardial samples were obtained for high-resolution H-1 spectroscopy. Lipid images revealed regions of increased signal intensity in the periphery f the myocardial infarction. The zones of high lipid signal corresponded to zones with elevated mobile lipids as detected by H-1 spectroscopy

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

    International Nuclear Information System (INIS)

    Bellstedt, Peter; Herbst, Christian; Häfner, Sabine; Leppert, Jörg; Görlach, Matthias; Ramachandran, Ramadurai

    2012-01-01

    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′C and 3D C′NCA with sequential 13 C acquisitions, 3D NHH and 3D NC′H with sequential 1 H acquisitions and 3D CANH and 3D C’NH with broadband 13 C– 15 N mixing are demonstrated using microcrystalline samples of the β1 immunoglobulin binding domain of protein G (GB1) and the chicken α-spectrin SH3 domain.

  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. Determination of accurate 1H positions of an alanine tripeptide with anti-parallel and parallel β-sheet structures by high resolution 1H solid state NMR and GIPAW chemical shift calculation.

    Science.gov (United States)

    Yazawa, Koji; Suzuki, Furitsu; Nishiyama, Yusuke; Ohata, Takuya; Aoki, Akihiro; Nishimura, Katsuyuki; Kaji, Hironori; Shimizu, Tadashi; Asakura, Tetsuo

    2012-11-25

    The accurate (1)H positions of alanine tripeptide, A(3), with anti-parallel and parallel β-sheet structures could be determined by highly resolved (1)H DQMAS solid-state NMR spectra and (1)H chemical shift calculation with gauge-including projector augmented wave calculations.

  11. The PROSECCO server for chemical shift predictions in ordered and disordered proteins.

    Science.gov (United States)

    Sanz-Hernández, Máximo; De Simone, Alfonso

    2017-11-01

    The chemical shifts measured in solution-state and solid-state nuclear magnetic resonance (NMR) are powerful probes of the structure and dynamics of protein molecules. The exploitation of chemical shifts requires methods to correlate these data with the protein structures and sequences. We present here an approach to calculate accurate chemical shifts in both ordered and disordered proteins using exclusively the information contained in their sequences. Our sequence-based approach, protein sequences and chemical shift correlations (PROSECCO), achieves the accuracy of the most advanced structure-based methods in the characterization of chemical shifts of folded proteins and improves the state of the art in the study of disordered proteins. Our analyses revealed fundamental insights on the structural information carried by NMR chemical shifts of structured and unstructured protein states.

  12. The calculation of proton chemical shifts in hydrocarbons

    Energy Technology Data Exchange (ETDEWEB)

    Abraham, Raymond J [Liverpool Univ. (United Kingdom). Dept. of Chemistry

    1994-12-31

    Novel extension of the CHARGE3 semi-empirical calculation of the partial atomic charges in molecules are described which allow the accurate calculation of the proton chemical shifts of a variety of acyclic alkanes. This simple scheme predicts the proton chemical shifts of all the simple alkanes, cyclohexane and methyl cyclohexanes, norbornane, trans-decalin and trans perhydrophenanthrene, comprising a range of chemical shifts from 0.3 to 2.2 {delta} with the known substituent chemical shifts of other functional groups this could allow the general prediction of proton chemical shifts in a simple and useful format. (author) 13 refs., 2 figs.

  13. Measurement of the signs of methyl {sup 13}C chemical shift differences between interconverting ground and excited protein states by R{sub 1{rho}}: an application to {alpha}B-crystallin

    Energy Technology Data Exchange (ETDEWEB)

    Baldwin, Andrew J.; Kay, Lewis E., E-mail: kay@pound.med.utoronto.ca [University of Toronto, Departments of Molecular Genetics, Biochemistry and Chemistry (Canada)

    2012-05-15

    Carr-Purcell-Meiboom-Gill relaxation dispersion (CPMG RD) NMR spectroscopy has emerged as a powerful tool for quantifying the kinetics and thermodynamics of millisecond time-scale exchange processes involving the interconversion between a visible ground state and one or more minor, sparsely populated invisible 'excited' conformational states. Recently it has also become possible to determine atomic resolution structural models of excited states using a wide array of CPMG RD approaches. Analysis of CPMG RD datasets provides the magnitudes of the chemical shift differences between the ground and excited states, {Delta}{omega}, but not the sign. In order to obtain detailed structural insights from, for example, excited state chemical shifts and residual dipolar coupling measurements, these signs are required. Here we present an NMR experiment for obtaining signs of {sup 13}C chemical shift differences of {sup 13}CH{sub 3} methyl groups using weak field off-resonance R{sub 1{rho}} relaxation measurements. The accuracy of the method is established by using an exchanging system where the invisible, excited state can be converted to the visible, ground state by altering sample conditions so that the signs of {Delta}{omega} values obtained from the spin-lock approach can be validated against those measured directly. Further, the spin-lock experiments are compared with the established H(S/M)QC approach for measuring signs of chemical shift differences and the relative strengths of each method are discussed. In the case of the 650 kDa human {alpha}B-crystallin complex where there are large transverse relaxation differences between ground and excited state spins the R{sub 1{rho}} method is shown to be superior to more 'traditional' experiments for sign determination.

  14. Anisotropy of the fluorine chemical shift tensor in UF6

    International Nuclear Information System (INIS)

    Rigny, P.

    1965-04-01

    An 19 F magnetic resonance study of polycrystalline UF 6 is presented. The low temperature complex line can be analyzed as the superposition of two distinct lines, which is attributed to a distortion of the UF 6 octahedron in the solid. The shape of the two components is studied. Their width is much larger than the theoretical dipolar width, and must be explained by large anisotropies of the fluorine chemical shift tensors. The resulting shape functions of the powder spectra are determined. The values of the parameters of the chemical shift tensors yield estimates of the characters of the U-F bonds, and this gives some information on the ground state electronic wave function of the UF 6 molecule in the solid. (author) [fr

  15. Design of high-power, broadband 180o pulses and mixing sequences for fast MAS solid state chemical shift correlation NMR spectroscopy

    International Nuclear Information System (INIS)

    Herbst, Christian; Herbst, Jirada; Kirschstein, Anika; Leppert, Joerg; Ohlenschlaeger, Oliver; Goerlach, Matthias; Ramachandran, Ramadurai

    2009-01-01

    An approach for the design of high-power, broadband 180 o pulses and mixing sequences for generating dipolar and scalar coupling mediated 13 C- 13 C chemical shift correlation spectra of isotopically labelled biological systems at fast magic-angle spinning frequencies without 1 H decoupling during mixing is presented. Considering RF field strengths in the range of 100-120 kHz, as typically available in MAS probes employed at high spinning speeds, and limited B 1 field inhomogeneities, the Fourier coefficients defining the phase modulation profile of the RF pulses were optimised numerically to obtain broadband inversion and refocussing pulses and mixing sequences. Experimental measurements were carried out to assess the performance characteristics of the mixing sequences reported here

  16. Stopping powers from the inverted doppler shift attenuation method: Z-oscillations; Bragg's rule or chemical effects; solid and liquid state effects

    International Nuclear Information System (INIS)

    Pietsch, W.; Hauser, U.; Neuwirth, W.

    1976-01-01

    With the 'Inverted Doppler Shift Attenuation (IDSA)' method stopping cross sections for swift ions can be measured with an accuracy of about 1%. Here results are reported with lithium and carbon projectiles in very different stopping materials. It turns out that the stopping cross section around Bohr's velocity is linearly dependent on the velocity. Stopping cross sections of elements show the expected Z 2 -oscillations. With compound targets strong deviations from Bragg's rule were found which means that the stopping cross section is influenced by the chemical bonding. In electrolytic solutions effects due to ion-dipole interactions can be observed. These phenomena demonstrate the strong sensitivity of electronic stopping cross sections on the specific distribution of the outer electrons of the target atoms. Further Lindhard's formula has been modified which gives a good description of this influence. (Auth.)

  17. Chemical shift-dependent apparent scalar couplings: An alternative concept of chemical shift monitoring in multi-dimensional NMR experiments

    International Nuclear Information System (INIS)

    Kwiatkowski, Witek; Riek, Roland

    2003-01-01

    The paper presents an alternative technique for chemical shift monitoring in a multi-dimensional NMR experiment. The monitored chemical shift is coded in the line-shape of a cross-peak through an apparent residual scalar coupling active during an established evolution period or acquisition. The size of the apparent scalar coupling is manipulated with an off-resonance radio-frequency pulse in order to correlate the size of the coupling with the position of the additional chemical shift. The strength of this concept is that chemical shift information is added without an additional evolution period and accompanying polarization transfer periods. This concept was incorporated into the three-dimensional triple-resonance experiment HNCA, adding the information of 1 H α chemical shifts. The experiment is called HNCA coded HA, since the chemical shift of 1 H α is coded in the line-shape of the cross-peak along the 13 C α dimension

  18. Using chemical shift perturbation to characterise ligand binding.

    Science.gov (United States)

    Williamson, Mike P

    2013-08-01

    Chemical shift perturbation (CSP, chemical shift mapping or complexation-induced changes in chemical shift, CIS) follows changes in the chemical shifts of a protein when a ligand is added, and uses these to determine the location of the binding site, the affinity of the ligand, and/or possibly the structure of the complex. A key factor in determining the appearance of spectra during a titration is the exchange rate between free and bound, or more specifically the off-rate koff. When koff is greater than the chemical shift difference between free and bound, which typically equates to an affinity Kd weaker than about 3μM, then exchange is fast on the chemical shift timescale. Under these circumstances, the observed shift is the population-weighted average of free and bound, which allows Kd to be determined from measurement of peak positions, provided the measurements are made appropriately. (1)H shifts are influenced to a large extent by through-space interactions, whereas (13)Cα and (13)Cβ shifts are influenced more by through-bond effects. (15)N and (13)C' shifts are influenced both by through-bond and by through-space (hydrogen bonding) interactions. For determining the location of a bound ligand on the basis of shift change, the most appropriate method is therefore usually to measure (15)N HSQC spectra, calculate the geometrical distance moved by the peak, weighting (15)N shifts by a factor of about 0.14 compared to (1)H shifts, and select those residues for which the weighted shift change is larger than the standard deviation of the shift for all residues. Other methods are discussed, in particular the measurement of (13)CH3 signals. Slow to intermediate exchange rates lead to line broadening, and make Kd values very difficult to obtain. There is no good way to distinguish changes in chemical shift due to direct binding of the ligand from changes in chemical shift due to allosteric change. Ligand binding at multiple sites can often be characterised, by

  19. Rapid and reliable protein structure determination via chemical shift threading.

    Science.gov (United States)

    Hafsa, Noor E; Berjanskii, Mark V; Arndt, David; Wishart, David S

    2018-01-01

    Protein structure determination using nuclear magnetic resonance (NMR) spectroscopy can be both time-consuming and labor intensive. Here we demonstrate how chemical shift threading can permit rapid, robust, and accurate protein structure determination using only chemical shift data. Threading is a relatively old bioinformatics technique that uses a combination of sequence information and predicted (or experimentally acquired) low-resolution structural data to generate high-resolution 3D protein structures. The key motivations behind using NMR chemical shifts for protein threading lie in the fact that they are easy to measure, they are available prior to 3D structure determination, and they contain vital structural information. The method we have developed uses not only sequence and chemical shift similarity but also chemical shift-derived secondary structure, shift-derived super-secondary structure, and shift-derived accessible surface area to generate a high quality protein structure regardless of the sequence similarity (or lack thereof) to a known structure already in the PDB. The method (called E-Thrifty) was found to be very fast (often chemical shift refinement, these results suggest that protein structure determination, using only NMR chemical shifts, is becoming increasingly practical and reliable. E-Thrifty is available as a web server at http://ethrifty.ca .

  20. Relative Configuration of Natural Products Using NMR Chemical Shifts

    Science.gov (United States)

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

  1. A probabilistic approach for validating protein NMR chemical shift assignments

    International Nuclear Information System (INIS)

    Wang Bowei; Wang, Yunjun; Wishart, David S.

    2010-01-01

    It has been estimated that more than 20% of the proteins in the BMRB are improperly referenced and that about 1% of all chemical shift assignments are mis-assigned. These statistics also reflect the likelihood that any newly assigned protein will have shift assignment or shift referencing errors. The relatively high frequency of these errors continues to be a concern for the biomolecular NMR community. While several programs do exist to detect and/or correct chemical shift mis-referencing or chemical shift mis-assignments, most can only do one, or the other. The one program (SHIFTCOR) that is capable of handling both chemical shift mis-referencing and mis-assignments, requires the 3D structure coordinates of the target protein. Given that chemical shift mis-assignments and chemical shift re-referencing issues should ideally be addressed prior to 3D structure determination, there is a clear need to develop a structure-independent approach. Here, we present a new structure-independent protocol, which is based on using residue-specific and secondary structure-specific chemical shift distributions calculated over small (3-6 residue) fragments to identify mis-assigned resonances. The method is also able to identify and re-reference mis-referenced chemical shift assignments. Comparisons against existing re-referencing or mis-assignment detection programs show that the method is as good or superior to existing approaches. The protocol described here has been implemented into a freely available Java program called 'Probabilistic Approach for protein Nmr Assignment Validation (PANAV)' and as a web server (http://redpoll.pharmacy.ualberta.ca/PANAVhttp://redpoll.pharmacy.ualberta.ca/PANAV) which can be used to validate and/or correct as well as re-reference assigned protein chemical shifts.

  2. Random coil chemical shifts in acidic 8 M urea: Implementation of random coil shift data in NMRView

    International Nuclear Information System (INIS)

    Schwarzinger, Stephan; Kroon, Gerard J.A.; Foss, Ted R.; Wright, Peter E.; Dyson, H. Jane

    2000-01-01

    Studies of proteins unfolded in acid or chemical denaturant can help in unraveling events during the earliest phases of protein folding. In order for meaningful comparisons to be made of residual structure in unfolded states, it is necessary to use random coil chemical shifts that are valid for the experimental system under study. We present a set of random coil chemical shifts obtained for model peptides under experimental conditions used in studies of denatured proteins. This new set, together with previously published data sets, has been incorporated into a software interface for NMRView, allowing selection of the random coil data set that fits the experimental conditions best

  3. Validation of archived chemical shifts through atomic coordinates

    Science.gov (United States)

    Rieping, Wolfgang; Vranken, Wim F

    2010-01-01

    The public archives containing protein information in the form of NMR chemical shift data at the BioMagResBank (BMRB) and of 3D structure coordinates at the Protein Data Bank are continuously expanding. The quality of the data contained in these archives, however, varies. The main issue for chemical shift values is that they are determined relative to a reference frequency. When this reference frequency is set incorrectly, all related chemical shift values are systematically offset. Such wrongly referenced chemical shift values, as well as other problems such as chemical shift values that are assigned to the wrong atom, are not easily distinguished from correct values and effectively reduce the usefulness of the archive. We describe a new method to correct and validate protein chemical shift values in relation to their 3D structure coordinates. This method classifies atoms using two parameters: the per-atom solvent accessible surface area (as calculated from the coordinates) and the secondary structure of the parent amino acid. Through the use of Gaussian statistics based on a large database of 3220 BMRB entries, we obtain per-entry chemical shift corrections as well as Z scores for the individual chemical shift values. In addition, information on the error of the correction value itself is available, and the method can retain only dependable correction values. We provide an online resource with chemical shift, atom exposure, and secondary structure information for all relevant BMRB entries (http://www.ebi.ac.uk/pdbe/nmr/vasco) and hope this data will aid the development of new chemical shift-based methods in NMR. Proteins 2010. © 2010 Wiley-Liss, Inc. PMID:20602353

  4. Probabilistic validation of protein NMR chemical shift assignments

    International Nuclear Information System (INIS)

    Dashti, Hesam; Tonelli, Marco; Lee, Woonghee; Westler, William M.; Cornilescu, Gabriel; Ulrich, Eldon L.; Markley, John L.

    2016-01-01

    Data validation plays an important role in ensuring the reliability and reproducibility of studies. NMR investigations of the functional properties, dynamics, chemical kinetics, and structures of proteins depend critically on the correctness of chemical shift assignments. We present a novel probabilistic method named ARECA for validating chemical shift assignments that relies on the nuclear Overhauser effect data. ARECA has been evaluated through its application to 26 case studies and has been shown to be complementary to, and usually more reliable than, approaches based on chemical shift databases. ARECA is available online at http://areca.nmrfam.wisc.edu/ http://areca.nmrfam.wisc.edu/

  5. Probabilistic validation of protein NMR chemical shift assignments

    Energy Technology Data Exchange (ETDEWEB)

    Dashti, Hesam [University of Wisconsin-Madison, Graduate Program in Biophysics, Biochemistry Department (United States); Tonelli, Marco; Lee, Woonghee; Westler, William M.; Cornilescu, Gabriel [University of Wisconsin-Madison, Biochemistry Department, National Magnetic Resonance Facility at Madison (United States); Ulrich, Eldon L. [University of Wisconsin-Madison, BioMagResBank, Biochemistry Department (United States); Markley, John L., E-mail: markley@nmrfam.wisc.edu, E-mail: jmarkley@wisc.edu [University of Wisconsin-Madison, Biochemistry Department, National Magnetic Resonance Facility at Madison (United States)

    2016-01-15

    Data validation plays an important role in ensuring the reliability and reproducibility of studies. NMR investigations of the functional properties, dynamics, chemical kinetics, and structures of proteins depend critically on the correctness of chemical shift assignments. We present a novel probabilistic method named ARECA for validating chemical shift assignments that relies on the nuclear Overhauser effect data. ARECA has been evaluated through its application to 26 case studies and has been shown to be complementary to, and usually more reliable than, approaches based on chemical shift databases. ARECA is available online at http://areca.nmrfam.wisc.edu/ http://areca.nmrfam.wisc.edu/.

  6. SimShiftDB; local conformational restraints derived from chemical shift similarity searches on a large synthetic database

    International Nuclear Information System (INIS)

    Ginzinger, Simon W.; Coles, Murray

    2009-01-01

    We present SimShiftDB, a new program to extract conformational data from protein chemical shifts using structural alignments. The alignments are obtained in searches of a large database containing 13,000 structures and corresponding back-calculated chemical shifts. SimShiftDB makes use of chemical shift data to provide accurate results even in the case of low sequence similarity, and with even coverage of the conformational search space. We compare SimShiftDB to HHSearch, a state-of-the-art sequence-based search tool, and to TALOS, the current standard tool for the task. We show that for a significant fraction of the predicted similarities, SimShiftDB outperforms the other two methods. Particularly, the high coverage afforded by the larger database often allows predictions to be made for residues not involved in canonical secondary structure, where TALOS predictions are both less frequent and more error prone. Thus SimShiftDB can be seen as a complement to currently available methods

  7. SimShiftDB; local conformational restraints derived from chemical shift similarity searches on a large synthetic database

    Energy Technology Data Exchange (ETDEWEB)

    Ginzinger, Simon W. [Center of Applied Molecular Engineering, University of Salzburg, Department of Molecular Biology, Division of Bioinformatics (Austria)], E-mail: simon@came.sbg.ac.at; Coles, Murray [Max-Planck-Institute for Developmental Biology, Department of Protein Evolution (Germany)], E-mail: Murray.Coles@tuebingen.mpg.de

    2009-03-15

    We present SimShiftDB, a new program to extract conformational data from protein chemical shifts using structural alignments. The alignments are obtained in searches of a large database containing 13,000 structures and corresponding back-calculated chemical shifts. SimShiftDB makes use of chemical shift data to provide accurate results even in the case of low sequence similarity, and with even coverage of the conformational search space. We compare SimShiftDB to HHSearch, a state-of-the-art sequence-based search tool, and to TALOS, the current standard tool for the task. We show that for a significant fraction of the predicted similarities, SimShiftDB outperforms the other two methods. Particularly, the high coverage afforded by the larger database often allows predictions to be made for residues not involved in canonical secondary structure, where TALOS predictions are both less frequent and more error prone. Thus SimShiftDB can be seen as a complement to currently available methods.

  8. 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.

  9. Chemical shifts of oxygen-17 NMR in polyoxotungstates

    International Nuclear Information System (INIS)

    Kazanskij, L.P.; Fedotov, M.A.; Spitsyn, V.I.

    1977-01-01

    17 O NMR spectra of aqueous solutions containing paratungstate BH 2 W 12 O 42 10- and metatungstate H 2 W 12 O 40 6- anions have been measured. On the basis of the obtained data a scale of chemical shifts for oxygen atoms connected by various bonds with tungsten atoms is suggested. The obtained data are compared with the Raman spectra of crystalline salts and their aqueous solutions. Chemical shifts of 17 O NMR spectra have been also measured in other heteropolyanions

  10. Chemical Shift Imaging (CSI) by precise object displacement

    OpenAIRE

    Leclerc, Sebastien; Trausch, Gregory; Cordier, Benoit; Grandclaude, Denis; Retournard, Alain; Fraissard, Jacques; Canet, Daniel

    2006-01-01

    International audience; A mechanical device (NMR lift) has been built for displacing vertically an object (typically a NMR sample tube) inside the NMR probe with an accuracy of 1 Μm. A series of single pulse experiments are performed for incremented vertical positions of the sample. With a sufficiently spatially selective rf field, one obtains chemical shift information along the displacement direction (one dimensional Chemical Shift Imaging – CSI). Knowing the vertical radio-frequency (rf) f...

  11. Unraveling the meaning of chemical shifts in protein NMR.

    Science.gov (United States)

    Berjanskii, Mark V; Wishart, David S

    2017-11-01

    Chemical shifts are among the most informative parameters in protein NMR. They provide wealth of information about protein secondary and tertiary structure, protein flexibility, and protein-ligand binding. In this report, we review the progress in interpreting and utilizing protein chemical shifts that has occurred over the past 25years, with a particular focus on the large body of work arising from our group and other Canadian NMR laboratories. More specifically, this review focuses on describing, assessing, and providing some historical context for various chemical shift-based methods to: (1) determine protein secondary and super-secondary structure; (2) derive protein torsion angles; (3) assess protein flexibility; (4) predict residue accessible surface area; (5) refine 3D protein structures; (6) determine 3D protein structures and (7) characterize intrinsically disordered proteins. This review also briefly covers some of the methods that we previously developed to predict chemical shifts from 3D protein structures and/or protein sequence data. It is hoped that this review will help to increase awareness of the considerable utility of NMR chemical shifts in structural biology and facilitate more widespread adoption of chemical-shift based methods by the NMR spectroscopists, structural biologists, protein biophysicists, and biochemists worldwide. This article is part of a Special Issue entitled: Biophysics in Canada, edited by Lewis Kay, John Baenziger, Albert Berghuis and Peter Tieleman. Copyright © 2017 Elsevier B.V. All rights reserved.

  12. 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.

  13. ¹H, ¹³C, and ¹⁵N backbone and side-chain chemical shift assignment of the toxin Doc in the unbound state.

    Science.gov (United States)

    De Gieter, Steven; Loris, Remy; van Nuland, Nico A J; Garcia-Pino, Abel

    2014-04-01

    Toxin-antitoxin (TA) modules in bacteria are involved in pathogenesis, antibiotic stress response, persister formation and programmed cell death. The toxin Doc, from the phd/doc module, blocks protein synthesis by targeting the translation machinery. Despite a large wealth of biophysical and biochemical data on the regulatory aspects of the operon transcription and role of Doc co-activator and co-repressor, little is still know on the molecular basis of Doc toxicity. Structural information about this toxin is only available for its inhibited state bound to the antitoxin Phd. Here we report the (1)H, (15)N and (13)C backbone and side chain chemical shift assignments of the toxin Doc from of bacteriophage P1 (the model protein from this family of TA modules) in its free state. The BMRB accession number is 18899.

  14. Evaluating amber force fields using computed NMR chemical shifts.

    Science.gov (United States)

    Koes, David R; Vries, John K

    2017-10-01

    NMR chemical shifts can be computed from molecular dynamics (MD) simulations using a template matching approach and a library of conformers containing chemical shifts generated from ab initio quantum calculations. This approach has potential utility for evaluating the force fields that underlie these simulations. Imperfections in force fields generate flawed atomic coordinates. Chemical shifts obtained from flawed coordinates have errors that can be traced back to these imperfections. We use this approach to evaluate a series of AMBER force fields that have been refined over the course of two decades (ff94, ff96, ff99SB, ff14SB, ff14ipq, and ff15ipq). For each force field a series of MD simulations are carried out for eight model proteins. The calculated chemical shifts for the 1 H, 15 N, and 13 C a atoms are compared with experimental values. Initial evaluations are based on root mean squared (RMS) errors at the protein level. These results are further refined based on secondary structure and the types of atoms involved in nonbonded interactions. The best chemical shift for identifying force field differences is the shift associated with peptide protons. Examination of the model proteins on a residue by residue basis reveals that force field performance is highly dependent on residue position. Examination of the time course of nonbonded interactions at these sites provides explanations for chemical shift differences at the atomic coordinate level. Results show that the newer ff14ipq and ff15ipq force fields developed with the implicitly polarized charge method perform better than the older force fields. © 2017 Wiley Periodicals, Inc.

  15. Nucleic acid helix structure determination from NMR proton chemical shifts

    Energy Technology Data Exchange (ETDEWEB)

    Werf, Ramon M. van der; Tessari, Marco; Wijmenga, Sybren S., E-mail: S.Wijmenga@science.ru.nl [Radboud University Nijmegen, Department of Biophysical Chemistry, Institute of Molecules and Materials (Netherlands)

    2013-06-15

    We present a method for de novo derivation of the three-dimensional helix structure of nucleic acids using non-exchangeable proton chemical shifts as sole source of experimental restraints. The method is called chemical shift de novo structure derivation protocol employing singular value decomposition (CHEOPS) and uses iterative singular value decomposition to optimize the structure in helix parameter space. The correct performance of CHEOPS and its range of application are established via an extensive set of structure derivations using either simulated or experimental chemical shifts as input. The simulated input data are used to assess in a defined manner the effect of errors or limitations in the input data on the derived structures. We find that the RNA helix parameters can be determined with high accuracy. We finally demonstrate via three deposited RNA structures that experimental proton chemical shifts suffice to derive RNA helix structures with high precision and accuracy. CHEOPS provides, subject to further development, new directions for high-resolution NMR structure determination of nucleic acids.

  16. Islamic State and Chemical Weapons

    Directory of Open Access Journals (Sweden)

    Lukáš Rafay

    2016-09-01

    Full Text Available The article deals with topic of Islamic State and chemical weapons. The issue is analysed in three dimensions: origin of used chemical weapons and possibility of independent production; known chemical attacks and tactical regularities in their execution; and traits of future chemical terrorist attacks. By providing a thorough examination of the problem, the article aims at predicting the future development of the group’s chemical program as well as describing any prospective chemical terrorist attacks in Europe

  17. Difference in the structures of alanine tri- and tetra-peptides with antiparallel β-sheet assessed by X-ray diffraction, solid-state NMR and chemical shift calculations by GIPAW.

    Science.gov (United States)

    Asakura, Tetsuo; Yazawa, Koji; Horiguchi, Kumiko; Suzuki, Furitsu; Nishiyama, Yusuke; Nishimura, Katsuyuki; Kaji, Hironori

    2014-01-01

    Alanine oligomers provide a key structure for silk fibers from spider and wild silkworms.We report on structural analysis of L-alanyl-L-alanyl-L-alanyl-L-alanine (Ala)4 with anti-parallel (AP) β-structures using X-ray and solid-state NMR. All of the Ala residues in the (Ala)4 are in equivalent positions, whereas for alanine trimer (Ala)3 there are two alternative locations in a unit cell as reported previously (Fawcett and Camerman, Acta Cryst., 1975, 31, 658-665). (Ala)4 with AP β-structure is more stable than AP-(Ala)3 due to formation of the stronger hydrogen bonds. The intermolecular structure of (Ala)4 is also different from polyalanine fiber structure, indicating that the interchain arrangement of AP β-structure changes with increasing alanine sequencelength. Furthermore the precise (1)H positions, which are usually inaccesible by X-ray diffraction method, are determined by high resolution (1)H solid state NMR combined with the chemical shift calculations by the gauge-including projector augmented wave method. Copyright © 2013 Wiley Periodicals, Inc.

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

    International Nuclear Information System (INIS)

    Zhang, Rongchun; Mroue, Kamal H.; Ramamoorthy, Ayyalusamy

    2015-01-01

    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), 1 H MAS NMR spectra of rigid solids still suffer from poor resolution and severe peak overlap caused by the strong 1 H– 1 H homonuclear dipolar couplings and narrow 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) 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 1 H– 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-level structural and dynamical

  19. 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)

  20. Equilibrium simulations of proteins using molecular fragment replacement and NMR chemical shifts.

    Science.gov (United States)

    Boomsma, Wouter; Tian, Pengfei; Frellsen, Jes; Ferkinghoff-Borg, Jesper; Hamelryck, Thomas; Lindorff-Larsen, Kresten; Vendruscolo, Michele

    2014-09-23

    Methods of protein structure determination based on NMR chemical shifts are becoming increasingly common. The most widely used approaches adopt the molecular fragment replacement strategy, in which structural fragments are repeatedly reassembled into different complete conformations in molecular simulations. Although these approaches are effective in generating individual structures consistent with the chemical shift data, they do not enable the sampling of the conformational space of proteins with correct statistical weights. Here, we present a method of molecular fragment replacement that makes it possible to perform equilibrium simulations of proteins, and hence to determine their free energy landscapes. This strategy is based on the encoding of the chemical shift information in a probabilistic model in Markov chain Monte Carlo simulations. First, we demonstrate that with this approach it is possible to fold proteins to their native states starting from extended structures. Second, we show that the method satisfies the detailed balance condition and hence it can be used to carry out an equilibrium sampling from the Boltzmann distribution corresponding to the force field used in the simulations. Third, by comparing the results of simulations carried out with and without chemical shift restraints we describe quantitatively the effects that these restraints have on the free energy landscapes of proteins. Taken together, these results demonstrate that the molecular fragment replacement strategy can be used in combination with chemical shift information to characterize not only the native structures of proteins but also their conformational fluctuations.

  1. Identifying inter-residue resonances in crowded 2D {sup 13}C-{sup 13}C chemical shift correlation spectra of membrane proteins by solid-state MAS NMR difference spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Miao Yimin; Cross, Timothy A. [Florida State University, Department of Chemistry and Biochemistry (United States); Fu Riqiang, E-mail: rfu@magnet.fsu.edu [National High Magnet Field Lab (United States)

    2013-07-15

    The feasibility of using difference spectroscopy, i.e. subtraction of two correlation spectra at different mixing times, for substantially enhanced resolution in crowded two-dimensional {sup 13}C-{sup 13}C chemical shift correlation spectra is presented. With the analyses of {sup 13}C-{sup 13}C spin diffusion in simple spin systems, difference spectroscopy is proposed to partially separate the spin diffusion resonances of relatively short intra-residue distances from the longer inter-residue distances, leading to a better identification of the inter-residue resonances. Here solid-state magic-angle-spinning NMR spectra of the full length M2 protein embedded in synthetic lipid bilayers have been used to illustrate the resolution enhancement in the difference spectra. The integral membrane M2 protein of Influenza A virus assembles as a tetrameric bundle to form a proton-conducting channel that is activated by low pH and is essential for the viral lifecycle. Based on known amino acid resonance assignments from amino acid specific labeled samples of truncated M2 sequences or from time-consuming 3D experiments of uniformly labeled samples, some inter-residue resonances of the full length M2 protein can be identified in the difference spectra of uniformly {sup 13}C labeled protein that are consistent with the high resolution structure of the M2 (22-62) protein (Sharma et al., Science 330(6003):509-512, 2010)

  2. Solvent Effects on Oxygen-17 Chemical Shifts in Amides. Quantitative Linear Solvation Shift Relationships

    Science.gov (United States)

    Díez, Ernesto; Fabián, Jesús San; Gerothanassis, Ioannis P.; Esteban, Angel L.; Abboud, José-Luis M.; Contreras, Ruben H.; de Kowalewski, Dora G.

    1997-01-01

    A multiple-linear-regression analysis (MLRA) has been carried out using the Kamlet-Abboud-Taft (KAT) solvatochromic parameters in order to elucidate and quantify the solvent effects on the17O chemical shifts ofN-methylformamide (NMF),N,N-dimethylformamide (DMF),N-methylacetamide (NMA), andN,N-dimethylacetamide (DMA). The chemical shifts of the four molecules show the same dependence (in ppm) on the solvent polarity-polarizability, i.e., -22π*. The influence of the solvent hydrogen-bond-donor (HBD) acidities is slightly larger for the acetamides NMA and DMA, i.e., -48α, than for the formamides NMF and DMF, i.e., -42α. The influence of the solvent hydrogen-bond-acceptor (HBA) basicities is negligible for the nonprotic molecules DMF and DMA but significant for the protic molecules NMF and NMA, i.e., -9β. The effect of substituting the N-H hydrogen by a methyl group amounts to -5.9 ppm in NMF and 5.4 ppm in NMA. The effect of substituting the O=C-H hydrogen amounts to 5.5 ppm in NMF and 16.8 ppm in DMF. The model of specific hydration sites of amides by I. P. Gerothanassis and C. Vakka [J. Org. Chem.59,2341 (1994)] is settled in a more quantitative basis and the model by M. I. Burgar, T. E. St. Amour, and D. Fiat [J. Phys. Chem.85,502 (1981)] is critically evaluated.17O hydration shifts have been calculated for formamide (FOR) by the ab initio LORG method at the 6-31G* level. For a formamide surrounded by the four in-plane molecules of water in the first hydration shell, the calculated17O shift change due to the four hydrogen bonds, -83.2 ppm, is smaller than the empirical hydration shift, -100 ppm. The17O shift change from each out-of-plane water molecule hydrogen-bonded to the amide oxygen is -18.0 ppm. These LORG results support the conclusion that no more than four water molecules are hydrogen-bonded to the amide oxygen in formamide.

  3. 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...

  4. NMR chemical shifts in amino acids: Effects of environments, electric field, and amine group rotation

    International Nuclear Information System (INIS)

    Yoon, Young-Gui; Pfrommer, Bernd G.; Louie, Steven G.; Canning, Andrew

    2002-01-01

    The authors present calculations of NMR chemical shifts in crystalline phases of some representative amino acids such as glycine, alanine, and alanyl-alanine. To get an insight on how different environments affect the chemical shifts, they study the transition from the crystalline phase to completely isolated molecules of glycine. In the crystalline limit, the shifts are dominated by intermolecular hydrogen-bonds. In the molecular limit, however, dipole electric field effects dominate the behavior of the chemical shifts. They show that it is necessary to average the chemical shifts in glycine over geometries. Tensor components are analyzed to get the angle dependent proton chemical shifts, which is a more refined characterization method

  5. Characterization of the conformational equilibrium between the two major substates of RNase A using NMR chemical shifts.

    Science.gov (United States)

    Camilloni, Carlo; Robustelli, Paul; De Simone, Alfonso; Cavalli, Andrea; Vendruscolo, Michele

    2012-03-07

    Following the recognition that NMR chemical shifts can be used for protein structure determination, rapid advances have recently been made in methods for extending this strategy for proteins and protein complexes of increasing size and complexity. A remaining major challenge is to develop approaches to exploit the information contained in the chemical shifts about conformational fluctuations in native states of proteins. In this work we show that it is possible to determine an ensemble of conformations representing the free energy surface of RNase A using chemical shifts as replica-averaged restraints in molecular dynamics simulations. Analysis of this surface indicates that chemical shifts can be used to characterize the conformational equilibrium between the two major substates of this protein. © 2012 American Chemical Society

  6. Role of quantitative chemical shift magnetic resonance imaging and chemical shift subtraction technique in discriminating adenomatous from non adenomatous adrenal solid lesions

    Directory of Open Access Journals (Sweden)

    Ahmed H. Afifi

    2017-03-01

    Conclusion: The signal intensity index and adrenal to spleen ratio are the most reliable quantitative chemical shift MRI methods in differentiation of adrenal adenomas from other non-adenomatous adrenal solid lesions. Chemical shift subtraction MRI is a recent technique that gives highly confident discrimination between two categories of pathology without using of any reference organ.

  7. Accuracy and precision of protein-ligand interaction kinetics determined from chemical shift titrations

    Energy Technology Data Exchange (ETDEWEB)

    Markin, Craig J.; Spyracopoulos, Leo, E-mail: leo.spyracopoulos@ualberta.ca [University of Alberta, Department of Biochemistry (Canada)

    2012-12-15

    NMR-monitored chemical shift titrations for the study of weak protein-ligand interactions represent a rich source of information regarding thermodynamic parameters such as dissociation constants (K{sub D}) in the micro- to millimolar range, populations for the free and ligand-bound states, and the kinetics of interconversion between states, which are typically within the fast exchange regime on the NMR timescale. We recently developed two chemical shift titration methods wherein co-variation of the total protein and ligand concentrations gives increased precision for the K{sub D} value of a 1:1 protein-ligand interaction (Markin and Spyracopoulos in J Biomol NMR 53: 125-138, 2012). In this study, we demonstrate that classical line shape analysis applied to a single set of {sup 1}H-{sup 15}N 2D HSQC NMR spectra acquired using precise protein-ligand chemical shift titration methods we developed, produces accurate and precise kinetic parameters such as the off-rate (k{sub off}). For experimentally determined kinetics in the fast exchange regime on the NMR timescale, k{sub off} {approx} 3,000 s{sup -1} in this work, the accuracy of classical line shape analysis was determined to be better than 5 % by conducting quantum mechanical NMR simulations of the chemical shift titration methods with the magnetic resonance toolkit GAMMA. Using Monte Carlo simulations, the experimental precision for k{sub off} from line shape analysis of NMR spectra was determined to be 13 %, in agreement with the theoretical precision of 12 % from line shape analysis of the GAMMA simulations in the presence of noise and protein concentration errors. In addition, GAMMA simulations were employed to demonstrate that line shape analysis has the potential to provide reasonably accurate and precise k{sub off} values over a wide range, from 100 to 15,000 s{sup -1}. The validity of line shape analysis for k{sub off} values approaching intermediate exchange ({approx}100 s{sup -1}), may be facilitated by

  8. Accuracy and precision of protein–ligand interaction kinetics determined from chemical shift titrations

    International Nuclear Information System (INIS)

    Markin, Craig J.; Spyracopoulos, Leo

    2012-01-01

    NMR-monitored chemical shift titrations for the study of weak protein–ligand interactions represent a rich source of information regarding thermodynamic parameters such as dissociation constants (K D ) in the micro- to millimolar range, populations for the free and ligand-bound states, and the kinetics of interconversion between states, which are typically within the fast exchange regime on the NMR timescale. We recently developed two chemical shift titration methods wherein co-variation of the total protein and ligand concentrations gives increased precision for the K D value of a 1:1 protein–ligand interaction (Markin and Spyracopoulos in J Biomol NMR 53: 125–138, 2012). In this study, we demonstrate that classical line shape analysis applied to a single set of 1 H– 15 N 2D HSQC NMR spectra acquired using precise protein–ligand chemical shift titration methods we developed, produces accurate and precise kinetic parameters such as the off-rate (k off ). For experimentally determined kinetics in the fast exchange regime on the NMR timescale, k off ∼ 3,000 s −1 in this work, the accuracy of classical line shape analysis was determined to be better than 5 % by conducting quantum mechanical NMR simulations of the chemical shift titration methods with the magnetic resonance toolkit GAMMA. Using Monte Carlo simulations, the experimental precision for k off from line shape analysis of NMR spectra was determined to be 13 %, in agreement with the theoretical precision of 12 % from line shape analysis of the GAMMA simulations in the presence of noise and protein concentration errors. In addition, GAMMA simulations were employed to demonstrate that line shape analysis has the potential to provide reasonably accurate and precise k off values over a wide range, from 100 to 15,000 s −1 . The validity of line shape analysis for k off values approaching intermediate exchange (∼100 s −1 ), may be facilitated by more accurate K D measurements from NMR

  9. Accuracy and precision of protein-ligand interaction kinetics determined from chemical shift titrations.

    Science.gov (United States)

    Markin, Craig J; Spyracopoulos, Leo

    2012-12-01

    NMR-monitored chemical shift titrations for the study of weak protein-ligand interactions represent a rich source of information regarding thermodynamic parameters such as dissociation constants (K ( D )) in the micro- to millimolar range, populations for the free and ligand-bound states, and the kinetics of interconversion between states, which are typically within the fast exchange regime on the NMR timescale. We recently developed two chemical shift titration methods wherein co-variation of the total protein and ligand concentrations gives increased precision for the K ( D ) value of a 1:1 protein-ligand interaction (Markin and Spyracopoulos in J Biomol NMR 53: 125-138, 2012). In this study, we demonstrate that classical line shape analysis applied to a single set of (1)H-(15)N 2D HSQC NMR spectra acquired using precise protein-ligand chemical shift titration methods we developed, produces accurate and precise kinetic parameters such as the off-rate (k ( off )). For experimentally determined kinetics in the fast exchange regime on the NMR timescale, k ( off ) ~ 3,000 s(-1) in this work, the accuracy of classical line shape analysis was determined to be better than 5 % by conducting quantum mechanical NMR simulations of the chemical shift titration methods with the magnetic resonance toolkit GAMMA. Using Monte Carlo simulations, the experimental precision for k ( off ) from line shape analysis of NMR spectra was determined to be 13 %, in agreement with the theoretical precision of 12 % from line shape analysis of the GAMMA simulations in the presence of noise and protein concentration errors. In addition, GAMMA simulations were employed to demonstrate that line shape analysis has the potential to provide reasonably accurate and precise k ( off ) values over a wide range, from 100 to 15,000 s(-1). The validity of line shape analysis for k ( off ) values approaching intermediate exchange (~100 s(-1)), may be facilitated by more accurate K ( D ) measurements

  10. Phase-shift calculation using continuum-discretized states

    International Nuclear Information System (INIS)

    Suzuki, Y.; Horiuchi, W.; Arai, K.

    2009-01-01

    We present a method for calculating scattering phase shifts which utilizes continuum-discretized states obtained in a bound-state type calculation. The wrong asymptotic behavior of the discretized state is remedied by means of the Green's function formalism. Test examples confirm the accuracy of the method. The α+n scattering is described using realistic nucleon-nucleon potentials. The 3/2 - and 1/2 - phase shifts obtained in a single-channel calculation are too small in comparison with experiment. The 1/2 + phase shifts are in reasonable agreement with experiment, and gain contributions both from the tensor and central components of the nucleon-nucleon potential.

  11. 13C NMR Chemical Shifts of the Triclinic and Monoclinic Crystal forms of Valinomycin

    International Nuclear Information System (INIS)

    Kameda, Tsunenori; McGeorge, Gary; Orendt, Anita M.; Grant, David M.

    2004-01-01

    Two different crystalline polymorphs of valinomycin, the triclinic and monoclinic forms, have been studied by high resolution, solid state 13 C CP-MAS NMR spectroscopy. Although the two polymorphs of the crystal are remarkably similar, there are distinct differences in the isotropic chemical shifts between the two spectra. For the triclinic form, the carbon chemical shift tensor components for the alpha carbons adjacent to oxygen in the lactic acid and hydroxyisovaleric acid residues and the ester carbonyls of the valine residue were obtained using the FIREMAT experiment. From the measured components, it was found that the behavior of the isotropic chemical shift, δ iso , for valine residue ester carbonyl carbons is predominately influenced by the intermediate component, δ 22 . Additionally it was found that the smallest shift component, δ 33 , for the L-lactic acid (L-Lac) and D-α-hydroxyisovaleric acid (D-Hyi) C α -O carbon was significantly displaced depending upon the nature of individual amino acid residues, and it is the δ 33 component that governs the behavior of δ iso in these alpha carbons

  12. Spectral stability of shifted states on star graphs

    Science.gov (United States)

    Kairzhan, Adilbek; Pelinovsky, Dmitry E.

    2018-03-01

    We consider the nonlinear Schrödinger (NLS) equation with the subcritical power nonlinearity on a star graph consisting of N edges and a single vertex under generalized Kirchhoff boundary conditions. The stationary NLS equation may admit a family of solitary waves parameterized by a translational parameter, which we call the shifted states. The two main examples include (i) the star graph with even N under the classical Kirchhoff boundary conditions and (ii) the star graph with one incoming edge and N  -  1 outgoing edges under a single constraint on coefficients of the generalized Kirchhoff boundary conditions. We obtain the general counting results on the Morse index of the shifted states and apply them to the two examples. In the case of (i), we prove that the shifted states with even N ≥slant 4 are saddle points of the action functional which are spectrally unstable under the NLS flow. In the case of (ii), we prove that the shifted states with the monotone profiles in the N  -  1 edges are spectrally stable, whereas the shifted states with non-monotone profiles in the N  -  1 edges are spectrally unstable, the two families intersect at the half-soliton states which are spectrally stable but nonlinearly unstable under the NLS flow. Since the NLS equation on a star graph with shifted states can be reduced to the homogeneous NLS equation on an infinite line, the spectral instability of shifted states is due to the perturbations breaking this reduction. We give a simple argument suggesting that the spectrally stable shifted states in the case of (ii) are nonlinearly unstable under the NLS flow due to the perturbations breaking the reduction to the homogeneous NLS equation.

  13. TALOS+: a hybrid method for predicting protein backbone torsion angles from NMR chemical shifts

    Energy Technology Data Exchange (ETDEWEB)

    Shen Yang; Delaglio, Frank [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States); Cornilescu, Gabriel [National Magnetic Resonance Facility (United States); Bax, Ad [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States)], E-mail: bax@nih.gov

    2009-08-15

    NMR chemical shifts in proteins depend strongly on local structure. The program TALOS establishes an empirical relation between {sup 13}C, {sup 15}N and {sup 1}H chemical shifts and backbone torsion angles {phi} and {psi} (Cornilescu et al. J Biomol NMR 13 289-302, 1999). Extension of the original 20-protein database to 200 proteins increased the fraction of residues for which backbone angles could be predicted from 65 to 74%, while reducing the error rate from 3 to 2.5%. Addition of a two-layer neural network filter to the database fragment selection process forms the basis for a new program, TALOS+, which further enhances the prediction rate to 88.5%, without increasing the error rate. Excluding the 2.5% of residues for which TALOS+ makes predictions that strongly differ from those observed in the crystalline state, the accuracy of predicted {phi} and {psi} angles, equals {+-}13{sup o}. Large discrepancies between predictions and crystal structures are primarily limited to loop regions, and for the few cases where multiple X-ray structures are available such residues are often found in different states in the different structures. The TALOS+ output includes predictions for individual residues with missing chemical shifts, and the neural network component of the program also predicts secondary structure with good accuracy.

  14. Protein backbone and sidechain torsion angles predicted from NMR chemical shifts using artificial neural networks

    Energy Technology Data Exchange (ETDEWEB)

    Shen Yang; Bax, Ad, E-mail: bax@nih.gov [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States)

    2013-07-15

    A new program, TALOS-N, is introduced for predicting protein backbone torsion angles from NMR chemical shifts. The program relies far more extensively on the use of trained artificial neural networks than its predecessor, TALOS+. Validation on an independent set of proteins indicates that backbone torsion angles can be predicted for a larger, {>=}90 % fraction of the residues, with an error rate smaller than ca 3.5 %, using an acceptance criterion that is nearly two-fold tighter than that used previously, and a root mean square difference between predicted and crystallographically observed ({phi}, {psi}) torsion angles of ca 12 Masculine-Ordinal-Indicator . TALOS-N also reports sidechain {chi}{sup 1} rotameric states for about 50 % of the residues, and a consistency with reference structures of 89 %. The program includes a neural network trained to identify secondary structure from residue sequence and chemical shifts.

  15. Implementation of the NMR CHEmical Shift Covariance Analysis (CHESCA): A Chemical Biologist's Approach to Allostery.

    Science.gov (United States)

    Boulton, Stephen; Selvaratnam, Rajeevan; Ahmed, Rashik; Melacini, Giuseppe

    2018-01-01

    Mapping allosteric sites is emerging as one of the central challenges in physiology, pathology, and pharmacology. Nuclear Magnetic Resonance (NMR) spectroscopy is ideally suited to map allosteric sites, given its ability to sense at atomic resolution the dynamics underlying allostery. Here, we focus specifically on the NMR CHEmical Shift Covariance Analysis (CHESCA), in which allosteric systems are interrogated through a targeted library of perturbations (e.g., mutations and/or analogs of the allosteric effector ligand). The atomic resolution readout for the response to such perturbation library is provided by NMR chemical shifts. These are then subject to statistical correlation and covariance analyses resulting in clusters of allosterically coupled residues that exhibit concerted responses to the common set of perturbations. This chapter provides a description of how each step in the CHESCA is implemented, starting from the selection of the perturbation library and ending with an overview of different clustering options.

  16. 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.

  17. MR chemical shift imaging and spectroscopy of atherosclerotic plaque

    International Nuclear Information System (INIS)

    Vinitski, S.; Consigny, P.M.; Shapiro, M.J.; Janes, N.; Smullens, S.N.; Rifkin, M.D.

    1989-01-01

    The purpose of this study was to develop a technique for in vivo imaging and characterization of atherosclerotic plaque. The authors used a spin-echo technique with a short echo time (TE) of 11 msec. Lipid/water suppression was achieved by means of hybrid chemical shift imaging. Lesions were induced in three rabbits by a combination of balloon denudation of the abdominal aorta and a high-cholesterol diet. Following in vivo imaging of these rabbit aortas and human carotid arteries (1.5 T), the animals were killed or carotid endarterectomy was performed so that the plaques could be excised. The plaques were then analyzed in vitro both histologically and with high-resolution spectroscopy (8.5 T). Use of the short TE improved lesion visualization. The fat/water suppression showed only a small amount of mobile lipids in plaque. Both MR spectroscopic and histologic analysis corroborated these images. The composition of atherosclerotic plaques in both humans and rabbits was demonstrated to be heterogeneous, with predominantly nonmobile lipids. These results suggest that the combination of short TE MR imaging and fat/water suppression can identify plaque and delineate areas containing mobile lipids

  18. Diagnostic value of chemical shift artifact in distinguishing benign lymphadenopathy

    Energy Technology Data Exchange (ETDEWEB)

    Farshchian, Nazanin, E-mail: farshchian.n@gmail.com [Department of Radiology, Kermanshah University of Medical Sciences, Kermanshah (Iran, Islamic Republic of); Tamari, Saghar; Farshchian, Negin [Department of Radiology, Kermanshah University of Medical Sciences, Kermanshah (Iran, Islamic Republic of); Madani, Hamid [Department of Pathology, Imam-Reza Hospital, Kermanshah University of Medical Sciences, Kermanshah (Iran, Islamic Republic of); Rezaie, Mansour [Department of Biostatistics, Kermanshah University of Medical Sciences, Kermanshah (Iran, Islamic Republic of); Mohammadi-Motlagh, Hamid-Reza, E-mail: mohammadimotlagh@gmail.com [Medical Biology Research Center, Kermanshah University of Medical Sciences, Kermanshah (Iran, Islamic Republic of)

    2011-11-15

    Purpose: Today, distinguishing metastatic lymph nodes from secondary benign inflammatory ones via using non-invasive methods is increasingly favorable. In this study, the diagnostic value of chemical shift artifact (CSA) in magnetic resonance imaging (MRI) was evaluated to distinguish benign lymphadenopathy. Subjects and methods: A prospective intraindividual internal review board-approved study was carried out on 15 men and 15 women having lymphadenopathic lesions in different locations of the body who underwent contrast-enhanced dynamic MR imaging at 1.5 T. Then, the imaging findings were compared with pathology reports, using the statistics analyses. Results: Due to the findings of the CSA existence in MRI, a total of 56.7% of the studied lesions (17 of 30) were identified as benign lesions and the rest were malignant, whereas the pathology reports distinguished twelve malignant and eighteen benign cases. Furthermore, the CSA findings comparing the pathology reports indicated that CSA, with confidence of 79.5%, has a significant diagnostic value to differentiate benign lesions from malignant ones. Conclusion: Our study demonstrated that CSA in MR imaging has a suitable diagnostic potential nearing readiness for clinical trials. Furthermore, CSA seems to be a feasible tool to differentiate benign lymph nodes from malignant ones; however, further studies including larger numbers of patients are required to confirm our results.

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

    Science.gov (United States)

    Kumari, Amrita; Dorai, Kavita

    2013-06-01

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

  20. Effect of shift work on mental state of factory workers.

    Science.gov (United States)

    Kaneko, Shin-Ya; Maeda, Takafumi; Sasaki, Akihiko; Sato, Akihiko; Tanaka, Kazuko; Kobayashi, Toshio; Tanaka, Masatoshi; Fukushima, Tetsuhito

    2004-06-01

    This paper examines the effects of shift work on the mental state of factory workers. As an indicator of the workers' mental condition, the authors used a scoring system (referred to below as the 'depression tendency score') based on the SRQ-D investigative report. The depression tendency score of the men was higher among the shift worker group than among the regular day worker group (p workers was higher than that of the male regular day workers among skilled workers (p worker group and the shift worker group. However, the depression tendency score of the female two-shift workers was higher than that of the female regular day workers among skilled workers (p work and that of women is affected by two-shift work because of the difference in modern societal/home role between man and woman.

  1. Temperature dependence of 1H NMR chemical shifts and its influence on estimated metabolite concentrations.

    Science.gov (United States)

    Wermter, Felizitas C; Mitschke, Nico; Bock, Christian; Dreher, Wolfgang

    2017-12-01

    Temperature dependent chemical shifts of important brain metabolites measured by localised 1 H MRS were investigated to test how the use of incorrect prior knowledge on chemical shifts impairs the quantification of metabolite concentrations. Phantom measurements on solutions containing 11 metabolites were performed on a 7 T scanner between 1 and 43 °C. The temperature dependence of the chemical shift differences was fitted by a linear model. Spectra were simulated for different temperatures and analysed by the AQSES program (jMRUI 5.2) using model functions with chemical shift values for 37 °C. Large differences in the temperature dependence of the chemical shift differences were determined with a maximum slope of about ±7.5 × 10 -4  ppm/K. For 32-40 °C, only minor quantification errors resulted from using incorrect chemical shifts, with the exception of Cr and PCr. For 1-10 °C considerable quantification errors occurred if the temperature dependence of the chemical shifts was neglected. If 1 H MRS measurements are not performed at 37 °C, for which the published chemical shift values have been determined, the temperature dependence of chemical shifts should be considered to avoid systematic quantification errors, particularly for measurements on animal models at lower temperatures.

  2. Empirical correlation between protein backbone {sup 15}N and {sup 13}C secondary chemical shifts and its application to nitrogen chemical shift re-referencing

    Energy Technology Data Exchange (ETDEWEB)

    Wang Liya [Cold Spring Harbor Laboratory (United States); Markley, John L. [University of Wisconsin, Biochemistry Department (United States)], E-mail: markley@nmrfam.wisc.edu

    2009-06-15

    The linear analysis of chemical shifts (LACS) has provided a robust method for identifying and correcting {sup 13}C chemical shift referencing problems in data from protein NMR spectroscopy. Unlike other approaches, LACS does not require prior knowledge of the three-dimensional structure or inference of the secondary structure of the protein. It also does not require extensive assignment of the NMR data. We report here a way of extending the LACS approach to {sup 15}N NMR data from proteins, so as to enable the detection and correction of inconsistencies in chemical shift referencing for this nucleus. The approach is based on our finding that the secondary {sup 15}N chemical shift of the backbone nitrogen atom of residue i is strongly correlated with the secondary chemical shift difference (experimental minus random coil) between the alpha and beta carbons of residue i - 1. Thus once alpha and beta {sup 13}C chemical shifts are available (their difference is referencing error-free), the {sup 15}N referencing can be validated, and an appropriate offset correction can be derived. This approach can be implemented prior to a structure determination and can be used to analyze potential referencing problems in database data not associated with three-dimensional structure. Application of the LACS algorithm to the current BMRB protein chemical shift database, revealed that nearly 35% of the BMRB entries have {delta}{sup 15}N values mis-referenced by over 0.7 ppm and over 25% of them have {delta}{sup 1}H{sup N} values mis-referenced by over 0.12 ppm. One implication of the findings reported here is that a backbone {sup 15}N chemical shift provides a better indicator of the conformation of the preceding residue than of the residue itself.

  3. A procedure to validate and correct the {sup 13}C chemical shift calibration of RNA datasets

    Energy Technology Data Exchange (ETDEWEB)

    Aeschbacher, Thomas; Schubert, Mario, E-mail: schubert@mol.biol.ethz.ch; Allain, Frederic H.-T., E-mail: allain@mol.biol.ethz.ch [ETH Zuerich, Institute for Molecular Biology and Biophysics (Switzerland)

    2012-02-15

    Chemical shifts reflect the structural environment of a certain nucleus and can be used to extract structural and dynamic information. Proper calibration is indispensable to extract such information from chemical shifts. Whereas a variety of procedures exist to verify the chemical shift calibration for proteins, no such procedure is available for RNAs to date. We present here a procedure to analyze and correct the calibration of {sup 13}C NMR data of RNAs. Our procedure uses five {sup 13}C chemical shifts as a reference, each of them found in a narrow shift range in most datasets deposited in the Biological Magnetic Resonance Bank. In 49 datasets we could evaluate the {sup 13}C calibration and detect errors or inconsistencies in RNA {sup 13}C chemical shifts based on these chemical shift reference values. More than half of the datasets (27 out of those 49) were found to be improperly referenced or contained inconsistencies. This large inconsistency rate possibly explains that no clear structure-{sup 13}C chemical shift relationship has emerged for RNA so far. We were able to recalibrate or correct 17 datasets resulting in 39 usable {sup 13}C datasets. 6 new datasets from our lab were used to verify our method increasing the database to 45 usable datasets. We can now search for structure-chemical shift relationships with this improved list of {sup 13}C chemical shift data. This is demonstrated by a clear relationship between ribose {sup 13}C shifts and the sugar pucker, which can be used to predict a C2 Prime - or C3 Prime -endo conformation of the ribose with high accuracy. The improved quality of the chemical shift data allows statistical analysis with the potential to facilitate assignment procedures, and the extraction of restraints for structure calculations of RNA.

  4. 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...

  5. 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...

  6. Binding energies and chemical shifts of least bound core electron excitations in cubic Asub(N)Bsub(8-N) semiconductors

    International Nuclear Information System (INIS)

    Bechstedt, F.; Enderlein, R.; Wischnewski, R.

    1981-01-01

    Core electron binding energies Esup(B) with respect to the vacuum level and their chemical shifts are calculated for the least bound core levels of cations and anions of cubic Asub(N)Bsub(8-N) semiconductors. Starting from the HF-binding energy of the free atom absolute values of Esup(B) are obtained by adding core level shifts and relaxation energies. Core level shifts are calculated by means of an electrostatic model with ionic and bond charges according to Phillips' bond charge model. For the calculation of relaxation energies the linear dielectric theory of electronic polarization is applied. Valence and core electrons, and diagonal and non-diagonal screening are taken into account. The theoretical results for chemical shifts of binding energies are compared with experimental values from XPS-measurements corrected by work function data. Good agreement is obtained in all cases within the error limit of about one eV. Chemical and atomic trends of core level shifts, relaxation energies, and binding energies are discussed in terms of changes of atomic and solid state parameters. Chemical shifts and relaxation energies are predicted for various ternary Asub(N)Bsub(8-N) compounds. (author)

  7. Hydrodynamic fluctuations, nonequilibrium equations of state, and the shift of the spinodal line in polymer solutions under flow

    International Nuclear Information System (INIS)

    Criado-Sancho, M.; Casas-Vazquez, J.; Jou, D.

    1997-01-01

    In the literature, the shift of the spinodal line of polymer solutions under flow is attributed either to an actual shift of the spinodal due to a nonequilibrium modification of the equation of state for the chemical potential, or to an apparent shift due to an increase of hydrodynamic fluctuations owing to the flow. Here we see that both approaches are compatible and that both effects add up. copyright 1997 The American Physical Society

  8. Mass shift of charmonium states in p bar A collision

    Science.gov (United States)

    Wolf, György; Balassa, Gábor; Kovács, Péter; Zétényi, Miklós; Lee, Su Houng

    2018-05-01

    The masses of the low lying charmonium states, namely, the J / Ψ, Ψ (3686), and Ψ (3770) are shifted downwards due to the second order Stark effect. In p bar +Au collisions at 6-10 GeV we study their in-medium propagation. The time evolution of the spectral functions of these charmonium states is studied with a Boltzmann-Uehling-Uhlenbeck (BUU) type transport model. We show that their in-medium mass shift can be observed in the dilepton spectrum. Therefore, by observing the dileptonic decay channel of these low lying charmonium states, especially for Ψ (3686), we can gain information about the magnitude of the gluon condensate in nuclear matter. This measurement could be performed at the upcoming PANDA experiment at FAIR.

  9. Protein backbone angle restraints from searching a database for chemical shift and sequence homology

    Energy Technology Data Exchange (ETDEWEB)

    Cornilescu, Gabriel; Delaglio, Frank; Bax, Ad [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States)

    1999-03-15

    Chemical shifts of backbone atoms in proteins are exquisitely sensitive to local conformation, and homologous proteins show quite similar patterns of secondary chemical shifts. The inverse of this relation is used to search a database for triplets of adjacent residues with secondary chemical shifts and sequence similarity which provide the best match to the query triplet of interest. The database contains 13C{alpha}, 13C{beta}, 13C', 1H{alpha} and 15N chemical shifts for 20 proteins for which a high resolution X-ray structure is available. The computer program TALOS was developed to search this database for strings of residues with chemical shift and residue type homology. The relative importance of the weighting factors attached to the secondary chemical shifts of the five types of resonances relative to that of sequence similarity was optimized empirically. TALOS yields the 10 triplets which have the closest similarity in secondary chemical shift and amino acid sequence to those of the query sequence. If the central residues in these 10 triplets exhibit similar {phi} and {psi} backbone angles, their averages can reliably be used as angular restraints for the protein whose structure is being studied. Tests carried out for proteins of known structure indicate that the root-mean-square difference (rmsd) between the output of TALOS and the X-ray derived backbone angles is about 15 deg. Approximately 3% of the predictions made by TALOS are found to be in error.

  10. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-11-15

    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 http://www.gamdy.ca.

  12. Stereospecific assignment of the asparagine and glutamine sidechain amide protons in proteins from chemical shift analysis

    Energy Technology Data Exchange (ETDEWEB)

    Harsch, Tobias; Schneider, Philipp; Kieninger, Bärbel; Donaubauer, Harald; Kalbitzer, Hans Robert, E-mail: hans-robert.kalbitzer@biologie.uni-regensburg.de [University of Regensburg, Institute of Biophysics and Physical Biochemistry and Centre of Magnetic Resonance in Chemistry and Biomedicine (Germany)

    2017-02-15

    Side chain amide protons of asparagine and glutamine residues in random-coil peptides are characterized by large chemical shift differences and can be stereospecifically assigned on the basis of their chemical shift values only. The bimodal chemical shift distributions stored in the biological magnetic resonance data bank (BMRB) do not allow such an assignment. However, an analysis of the BMRB shows, that a substantial part of all stored stereospecific assignments is not correct. We show here that in most cases stereospecific assignment can also be done for folded proteins using an unbiased artificial chemical shift data base (UACSB). For a separation of the chemical shifts of the two amide resonance lines with differences ≥0.40 ppm for asparagine and differences ≥0.42 ppm for glutamine, the downfield shifted resonance lines can be assigned to H{sup δ21} and H{sup ε21}, respectively, at a confidence level >95%. A classifier derived from UASCB can also be used to correct the BMRB data. The program tool AssignmentChecker implemented in AUREMOL calculates the Bayesian probability for a given stereospecific assignment and automatically corrects the assignments for a given list of chemical shifts.

  13. Prediction of proton chemical shifts in RNA - Their use in structure refinement and validation

    International Nuclear Information System (INIS)

    Cromsigt, Jenny A.M.T.C.; Hilbers, Cees W.; Wijmenga, Sybren S.

    2001-01-01

    An analysis is presented of experimental versus calculated chemical shifts of the non-exchangeable protons for 28 RNA structures deposited in the Protein Data Bank, covering a wide range of structural building blocks. We have used existing models for ring-current and magnetic-anisotropy contributions to calculate the proton chemical shifts from the structures. Two different parameter sets were tried: (i) parameters derived by Ribas-Prado and Giessner-Prettre (GP set) [(1981) J. Mol. Struct.,76, 81-92.]; (ii) parameters derived by Case [(1995) J. Biomol. NMR, 6, 341-346]. Both sets lead to similar results. The detailed analysis was carried using the GP set. The root-mean-square-deviation between the predicted and observed chemical shifts of the complete database is 0.16 ppm with a Pearson correlation coefficient of 0.79. For protons in the usually well-defined A-helix environment these numbers are, 0.08 ppm and 0.96, respectively. As a result of this good correspondence, a reliable analysis could be made of the structural dependencies of the 1 H chemical shifts revealing their physical origin. For example, a down-field shift of either H2' or H3' or both indicates a high-syn/syn χ-angle. In an A-helix it is essentially the 5'-neighbor that affects the chemical shifts of H5, H6 and H8 protons. The H5, H6 and H8 resonances can therefore be assigned in an A-helix on the basis of their observed chemical shifts. In general, the chemical shifts were found to be quite sensitive to structural changes. We therefore propose that a comparison between calculated and observed 1 H chemical shifts is a good tool for validation and refinement of structures derived from NOEs and J-couplings

  14. Relation between chemical shift artifact and infiltration on MR imaging of renal cell carcinoma

    International Nuclear Information System (INIS)

    Yoshigoe, Fukuo; Makino, Hideki; Yanada, Syuichi; Ohishi, Yukihiko; Mashima, Yasuoki; Yamada, Hideo.

    1994-01-01

    Retrospective study on the relation between existence of the interruption and disturbance of chemical shift artifact and tumor infiltration at the periphery of the kidney on MR imaging was evaluated in 28 cases with renal cell carcinoma. Judgement was possible in 9 out of the 11 cases with pathological stage below pT2 and 14 cases out of 17 pT3 cases. Judgement was impracticable in 5 cases because the peripheral fat tissue of the kidney was too less to observe chemical shift artifact and the tumor was spreading at the side opposite to the chemical shift artifact. Chemical shift artifact on MRI in this study correlated well with renal tumor infiltration. (author)

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

    International Nuclear Information System (INIS)

    Li, Dawei; Brüschweiler, Rafael

    2015-01-01

    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

  16. Theoretical Study of the NMR Chemical Shift of Xe in Supercritical Condition

    DEFF Research Database (Denmark)

    Lacerda Junior, Evanildo Gomes; Sauer, Stephan P. A.; Mikkelsen, Kurt Valentin

    2018-01-01

    In this work we investigate the level of theory necessary for reproducing the non-linear variation of the 129Xe nuclear magnetic resonance (NMR) chemical shift with the density of Xe in supercritical conditions. In detail we study how the 129Xe chemical shift depends under these conditions...... on electron correlation, relativistic and many-body effects. The latter are included using a sequential-QM/MM methodology, in which a classical MD simulation is performed first and the chemical shift is then obtained as an average of quantum calculations of 250 MD snapshots conformations carried out for Xen...... this approach we obtain very good agreement with the experimental data, showing that the chemical shift of 129Xe in supercritical conditions is very well described by cluster calculations at the HF level, with small contributions from relativistic and electron correlation effects....

  17. The direct measurement of the heteronuclear chemical shifts relative to tetramethylsilane

    International Nuclear Information System (INIS)

    Moritz, A.G.

    1988-12-01

    The measurement of heteronuclear chemical shifts using absolute frequencies of the heteronucleus and the 1 H resonance of tetramethylsilane has been examined. This method avoids the problems associated with external standards and gives results which can be obtained quickly and with high precision. The method has a number of advantages in the accurate measurement of chemical shifts, as for example 31 P in chemical warfare agents and related chemicals and allows multinuclear data to be obtained without dynamic range or potential interference problems. 15 refs., 4 tabs

  18. 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.

  19. 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.)

  20. Cyclohexanecarbonitriles: Assigning Configurations at Quaternary Centers From 13C NMR CN Chemical Shifts.1

    Science.gov (United States)

    Wei, Guoqing

    2009-01-01

    13C NMR chemical shifts of the nitrile carbon in cyclohexanecarbonitriles directly correlate with the configuration of the quaternary, nitrile-bearing stereocenter. Comparing 13C NMR chemical shifts for over 200 cyclohexanecarbonitriles reveals that equatorially oriented nitriles resonate 3.3 ppm downfield, on average, from their axial counterparts. Pairs of axial/equatorial diastereomers varying only at the nitrile-bearing carbon consistently exhibit downfield shifts of δ 0.4–7.2 for the equatorial nitrile carbon, even in angularly substituted decalins and hydrindanes. PMID:19348434

  1. Chemical shift assignments of the partially deuterated Fyn SH2-SH3 domain.

    Science.gov (United States)

    Kieken, Fabien; Loth, Karine; van Nuland, Nico; Tompa, Peter; Lenaerts, Tom

    2018-04-01

    Src Homology 2 and 3 (SH2 and SH3) are two key protein interaction modules involved in regulating the activity of many proteins such as tyrosine kinases and phosphatases by respective recognition of phosphotyrosine and proline-rich regions. In the Src family kinases, the inactive state of the protein is the direct result of the interaction of the SH2 and the SH3 domain with intra-molecular regions, leading to a closed structure incompetent with substrate modification. Here, we report the 1 H, 15 N and 13 C backbone- and side-chain chemical shift assignments of the partially deuterated Fyn SH3-SH2 domain and structural differences between tandem and single domains. The BMRB accession number is 27165.

  2. 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)

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

    International Nuclear Information System (INIS)

    Harris, R.K.; Menezes, S.M. Cabral de; Granger, P.; Hoffman, R.E.; Zilm, K.W.

    2008-01-01

    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 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 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)

  4. 29Si NMR Chemical Shift Calculation for Silicate Species by Gaussian Software

    Science.gov (United States)

    Azizi, S. N.; Rostami, A. A.; Godarzian, A.

    2005-05-01

    Hartree-Fock self-consistent-field (HF-SCF) theory and the Gauge-including atomic orbital (GIAO) methods are used in the calculation of 29Si NMR chemical shifts for ABOUT 90 units of 19 compounds of various silicate species of precursors for zeolites. Calculations have been performed at geometries optimized at the AM1 semi-empirical method. The GIAO-HF-SCF calculations were carried out with using three different basis sets: 6-31G*, 6-31+G** and 6-311+G(2d,p). To demonstrate the quality of the calculations the calculated chemical shifts, δ, were compared with the corresponding experimental values for the compounds in study. The results, especially with 6-31+g** are in excellent agreement with experimental values. The calculated chemical shifts, in practical point of view, appear to be accurate enough to aid in experimental peak assignments. The difference between the experimental and calculated 29Si chemical shift values not only depends on the Qn units but also it seems that basis set effects and the level of theory is more important. For the series of molecules studied here, the standard deviations and mean absolute errors for 29Si chemical shifts relative to TMS determined using Hartree--Fock 6-31+G** basis is nearly in all cases smaller than the errors for shifts determined using HF/6-311+G(2d,p).

  5. 1H NMR spectra part 31: 1H chemical shifts of amides in DMSO solvent.

    Science.gov (United States)

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

    2014-07-01

    The (1)H chemical shifts of 48 amides in DMSO solvent are assigned and presented. The solvent shifts Δδ (DMSO-CDCl3 ) are large (1-2 ppm) for the NH protons but smaller and negative (-0.1 to -0.2 ppm) for close range protons. A selection of the observed solvent shifts is compared with calculated shifts from the present model and from GIAO calculations. Those for the NH protons agree with both calculations, but other solvent shifts such as Δδ(CHO) are not well reproduced by the GIAO calculations. The (1)H chemical shifts of the amides in DMSO were analysed using a functional approach for near ( ≤ 3 bonds removed) protons and the electric field, magnetic anisotropy and steric effect of the amide group for more distant protons. The chemical shifts of the NH protons of acetanilide and benzamide vary linearly with the π density on the αN and βC atoms, respectively. The C=O anisotropy and steric effect are in general little changed from the values in CDCl3. The effects of substituents F, Cl, Me on the NH proton shifts are reproduced. The electric field coefficient for the protons in DMSO is 90% of that in CDCl3. There is no steric effect of the C=O oxygen on the NH proton in an NH…O=C hydrogen bond. The observed deshielding is due to the electric field effect. The calculated chemical shifts agree well with the observed shifts (RMS error of 0.106 ppm for the data set of 257 entries). Copyright © 2014 John Wiley & Sons, Ltd.

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

    DEFF Research Database (Denmark)

    Bratholm, Lars Andersen

    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...... mechanics / molecular mechanics (QM/MM) computations of chemical shieldings. Several improvements to the predictor is ongoing, where among other things, kernel based machine learning techniques have successfully been used to improve the quantum mechanical level of theory used in the predictions....

  7. Chemical shift imprint of intersubunit communication in a symmetric homodimer

    Science.gov (United States)

    Falk, Bradley T.; Sapienza, Paul J.; Lee, Andrew L.

    2016-01-01

    Allosteric communication is critical for protein function and cellular homeostasis, and it can be exploited as a strategy for drug design. However, unlike many protein–ligand interactions, the structural basis for the long-range communication that underlies allostery is not well understood. This lack of understanding is most evident in the case of classical allostery, in which a binding event in one protomer is sensed by a second symmetric protomer. A primary reason why study of interdomain signaling is challenging in oligomeric proteins is the difficulty in characterizing intermediate, singly bound species. Here, we use an NMR approach to isolate and characterize a singly ligated state (“lig1”) of a homodimeric enzyme that is otherwise obscured by rapid exchange with apo and saturated forms. Mixed labeled dimers were prepared that simultaneously permit full population of the lig1 state and isotopic labeling of either protomer. Direct visualization of peaks from lig1 yielded site-specific ligand-state multiplets that provide a convenient format for assessing mechanisms of intersubunit communication from a variety of NMR measurements. We demonstrate this approach on thymidylate synthase from Escherichia coli, a homodimeric enzyme known to be half-the-sites reactive. Resolving the dUMP1 state shows that active site communication occurs not upon the first dUMP binding, but upon the second. Surprisingly, for many sites, dUMP1 peaks are found beyond the limits set by apo and dUMP2 peaks, indicating that binding the first dUMP pushes the enzyme ensemble to further conformational extremes than the apo or saturated forms. The approach used here should be generally applicable to homodimers. PMID:27466406

  8. Protein backbone chemical shifts predicted from searching a database for torsion angle and sequence homology

    International Nuclear Information System (INIS)

    Shen Yang; Bax, Ad

    2007-01-01

    Chemical shifts of nuclei in or attached to a protein backbone are exquisitely sensitive to their local environment. A computer program, SPARTA, is described that uses this correlation with local structure to predict protein backbone chemical shifts, given an input three-dimensional structure, by searching a newly generated database for triplets of adjacent residues that provide the best match in φ/ψ/χ 1 torsion angles and sequence similarity to the query triplet of interest. The database contains 15 N, 1 H N , 1 H α , 13 C α , 13 C β and 13 C' chemical shifts for 200 proteins for which a high resolution X-ray (≤2.4 A) structure is available. The relative importance of the weighting factors for the φ/ψ/χ 1 angles and sequence similarity was optimized empirically. The weighted, average secondary shifts of the central residues in the 20 best-matching triplets, after inclusion of nearest neighbor, ring current, and hydrogen bonding effects, are used to predict chemical shifts for the protein of known structure. Validation shows good agreement between the SPARTA-predicted and experimental shifts, with standard deviations of 2.52, 0.51, 0.27, 0.98, 1.07 and 1.08 ppm for 15 N, 1 H N , 1 H α , 13 C α , 13 C β and 13 C', respectively, including outliers

  9. A comparison of chemical shift sensitivity of trifluoromethyl tags: optimizing resolution in {sup 19}F NMR studies of proteins

    Energy Technology Data Exchange (ETDEWEB)

    Ye, Libin; Larda, Sacha Thierry; Frank Li, Yi Feng [University of Toronto, UTM, Department of Chemistry (Canada); Manglik, Aashish [Stanford University School of Medicine, Department of Molecular and Cellular Physiology (United States); Prosser, R. Scott, E-mail: scott.prosser@utoronto.ca [University of Toronto, UTM, Department of Chemistry (Canada)

    2015-05-15

    The elucidation of distinct protein conformers or states by fluorine ({sup 19}F) NMR requires fluorinated moieties whose chemical shifts are most sensitive to subtle changes in the local dielectric and magnetic shielding environment. In this study we evaluate the effective chemical shift dispersion of a number of thiol-reactive trifluoromethyl probes [i.e. 2-bromo-N-(4-(trifluoromethyl)phenyl)acetamide (BTFMA), N-(4-bromo-3-(trifluoromethyl)phenyl)acetamide (3-BTFMA), 3-bromo-1,1,1-trifluoropropan-2-ol (BTFP), 1-bromo-3,3,4,4,4-pentafluorobutan-2-one (BPFB), 3-bromo-1,1,1-trifluoropropan-2-one (BTFA), and 2,2,2-trifluoroethyl-1-thiol (TFET)] under conditions of varying polarity. In considering the sensitivity of the {sup 19}F NMR chemical shift to the local environment, a series of methanol/water mixtures were prepared, ranging from relatively non-polar (MeOH:H{sub 2}O = 4) to polar (MeOH:H{sub 2}O = 0.25). {sup 19}F NMR spectra of the tripeptide, glutathione ((2S)-2-amino-4-{[(1R)-1-[(carboxymethyl)carbamoyl] -2-sulfanylethyl]carbamoyl}butanoic acid), conjugated to each of the above trifluoromethyl probes, revealed that the BTFMA tag exhibited a significantly greater range of chemical shift as a function of solvent polarity than did either BTFA or TFET. DFT calculations using the B3LYP hybrid functional and the 6-31G(d,p) basis set, confirmed the observed trend in chemical shift dispersion with solvent polarity.

  10. Prediction of Xaa-Pro peptide bond conformation from sequence and chemical shifts

    Energy Technology Data Exchange (ETDEWEB)

    Shen Yang; Bax, Ad, E-mail: bax@nih.go [National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Laboratory of Chemical Physics (United States)

    2010-03-15

    We present a program, named Promega, to predict the Xaa-Pro peptide bond conformation on the basis of backbone chemical shifts and the amino acid sequence. Using a chemical shift database of proteins of known structure together with the PDB-extracted amino acid preference of cis Xaa-Pro peptide bonds, a cis/trans probability score is calculated from the backbone and {sup 13}C{sup {beta}} chemical shifts of the proline and its neighboring residues. For an arbitrary number of input chemical shifts, which may include Pro-{sup 13}C{sup {gamma}}, Promega calculates the statistical probability that a Xaa-Pro peptide bond is cis. Besides its potential as a validation tool, Promega is particularly useful for studies of larger proteins where Pro-{sup 13}C{sup {gamma}} assignments can be challenging, and for on-going efforts to determine protein structures exclusively on the basis of backbone and {sup 13}C{sup {beta}} chemical shifts.

  11. Benchmarking quantum mechanical calculations with experimental NMR chemical shifts of 2-HADNT

    Science.gov (United States)

    Liu, Yuemin; Junk, Thomas; Liu, Yucheng; Tzeng, Nianfeng; Perkins, Richard

    2015-04-01

    In this study, both GIAO-DFT and GIAO-MP2 calculations of nuclear magnetic resonance (NMR) spectra were benchmarked with experimental chemical shifts. The experimental chemical shifts were determined experimentally for carbon-13 (C-13) of seven carbon atoms for the TNT degradation product 2-hydroxylamino-4,6-dinitrotoluene (2-HADNT). Quantum mechanics GIAO calculations were implemented using Becke-3-Lee-Yang-Parr (B3LYP) and other six hybrid DFT methods (Becke-1-Lee-Yang-Parr (B1LYP), Becke-half-and-half-Lee-Yang-Parr (BH and HLYP), Cohen-Handy-3-Lee-Yang-Parr (O3LYP), Coulomb-attenuating-B3LYP (CAM-B3LYP), modified-Perdew-Wang-91-Lee-Yang-Parr (mPW1LYP), and Xu-3-Lee-Yang-Parr (X3LYP)) which use the same correlation functional LYP. Calculation results showed that the GIAO-MP2 method gives the most accurate chemical shift values, and O3LYP method provides the best prediction of chemical shifts among the B3LYP and other five DFT methods. Three types of atomic partial charges, Mulliken (MK), electrostatic potential (ESP), and natural bond orbital (NBO), were also calculated using MP2/aug-cc-pVDZ method. A reasonable correlation was discovered between NBO partial charges and experimental chemical shifts of carbon-13 (C-13).

  12. DFT/GIAO calculations of the relative contributions of hyperconjugation to the chemical shifts of ethanol

    International Nuclear Information System (INIS)

    Carneiro, J. Walkimar de M.; Dias, Jacques F.; Seidl, Peter R.; Tostes, J. Glauco R.

    2002-01-01

    Our previous DFT/GIAO calculations on different types of alcohols reveal that the rotation of the hydroxyl group can affect the chemical shift of carbons and hydrogens close to the substituent in different ways. Besides the steric and electrostatic effects that have been widely studied, hyperconjugation with the lone pairs on oxygen of the hydroxyl group leads to changes in bond lengths and angles as well as to different charge distributions. As all three of these factors also affect chemical shifts, we undertook a systematic investigation of their relative contributions to the chemical shifts of ethanol, a molecule in which there is minimum interference among these factors. Calculations by the B3LYP method at the 6-31G(d) level for ethanol conformers corresponding to a rotation around the carbon-oxygen bond at 30 dec increments are used to show how relative contributions vary with the dihedral angle formed between the carbon-carbon and oxygen-hydrogen bonds (C-C-O-H). Largest contributions to carbon chemical shifts can be attributed to changes in bond lengths while for hydrogen chemical shifts also contribute significantly differences in charge distribution. (author)

  13. [Changes in functional state during occupational activities in workers at objects for chemical weapons destruction].

    Science.gov (United States)

    2010-01-01

    The authors studied functional state before and after the working shift in workers at objects for chemical weapons destruction, analyzed changes in central and peripheral hemodynamics parameters, vegetative regulation of heart rhythm, stabilographic and psychophysiologic values.

  14. Resolution of NMR chemical shift images into real and imaginary components

    International Nuclear Information System (INIS)

    Yamamoto, E.; Kohno, H.

    1986-01-01

    Fast chemical shift imaging of two-line materials is described using a modified spin-echo sequence. The method resolves the two chemical shift images into real and imaginary components representing the reconstructed image. The measuring time is reduced to half of that for the conventional method proposed by Dixon et al, and quantitative evaluation of the images becomes possible. Reference material with a single resonant line is used to eliminate the phase error caused by static field inhomogeneity and the inherent apparatus offset phase. Experiments are conducted using acetone and benzene with a medium-bore superconductive magnet operating at 0.5T. From these experiments, two chemical shift images are obtained. These images are then superimposed to produce a conventional density image. (author)

  15. /sup 1/H-NMR chemical shift imaging suitable for low field systems

    Energy Technology Data Exchange (ETDEWEB)

    Yamamoto, Etsuji; Onodera, Takashi; Shiono, Hidemi; Kohno, Hideki

    1986-12-01

    An echo-time encoding proton NMR chemical shift imaging proposed by Dixon is extended to be applicable to low filed systems. The method utilizes the small phase angle between magnetic vectors of water and lipid protons to decrease the signal decays with spin-spin relaxation. The inevitable phase error caused by the static field inhomogeneity is corrected by using phase images of phantom measured under the same conditions as the actual measurements. The experiments were carried out using CuSO/sub 4/ doped water and vegetable oil at 0.5 T. Two chemical shift images could be clearly resolved with only one scan when the field inhomogeneity was larger than the chemical shift difference.

  16. What can we learn by computing 13Cα chemical shifts for X-ray protein models?

    International Nuclear Information System (INIS)

    Arnautova, Yelena A.; Vila, Jorge A.; Martin, Osvaldo A.; Scheraga, Harold A.

    2009-01-01

    The room-temperature X-ray structures of two proteins, solved at 1.8 and 1.9 Å resolution, are used to investigate whether a set of conformations, rather than a single X-ray structure, provides better agreement with both the X-ray data and the observed 13 C α chemical shifts in solution. The room-temperature X-ray structures of ubiquitin and of the RNA-binding domain of nonstructural protein 1 of influenza A virus solved at 1.8 and 1.9 Å resolution, respectively, were used to investigate whether a set of conformations rather than a single X-ray structure provides better agreement with both the X-ray data and the observed 13 C α chemical shifts in solution. For this purpose, a set of new conformations for each of these proteins was generated by fitting them to the experimental X-ray data deposited in the PDB. For each of the generated structures, which show R and R free factors similar to those of the deposited X-ray structure, the 13 C α chemical shifts of all residues in the sequence were computed at the DFT level of theory. The sets of conformations were then evaluated by their ability to reproduce the observed 13 C α chemical shifts by using the conformational average root-mean-square-deviation (ca-r.m.s.d.). For ubiquitin, the computed set of conformations is a better representation of the observed 13 C α chemical shifts in terms of the ca-r.m.s.d. than a single X-ray-derived structure. However, for the RNA-binding domain of nonstructural protein 1 of influenza A virus, consideration of an ensemble of conformations does not improve the agreement with the observed 13 C α chemical shifts. Whether an ensemble of conformations rather than any single structure is a more accurate representation of a protein structure in the crystal as well as of the observed 13 C α chemical shifts is determined by the dispersion of coordinates, in terms of the all-atom r.m.s.d. among the generated models; these generated models satisfy the experimental X-ray data with

  17. Casimir-Polder shifts on quantum levitation states

    Science.gov (United States)

    Crépin, P.-P.; Dufour, G.; Guérout, R.; Lambrecht, A.; Reynaud, S.

    2017-03-01

    An ultracold atom above a horizontal mirror experiences quantum reflection from the attractive Casimir-Polder interaction, which holds it against gravity and leads to quantum levitation states. We analyze this system by using a Liouville transformation of the Schrödinger equation and a Langer coordinate adapted to problems with a classical turning point. Reflection on the Casimir-Polder attractive well is replaced by reflection on a repulsive wall, and the problem is then viewed as an ultracold atom trapped inside a cavity with gravity and Casimir-Polder potentials acting, respectively, as top and bottom mirrors. We calculate numerically Casimir-Polder shifts of the energies of the cavity resonances and propose an approximate treatment which is precise enough to discuss spectroscopy experiments aimed at tests of the weak-equivalence principle on antihydrogen. We also discuss the lifetimes by calculating complex energies associated with cavity resonances.

  18. Sequential nearest-neighbor effects on computed {sup 13}C{sup {alpha}} chemical shifts

    Energy Technology Data Exchange (ETDEWEB)

    Vila, Jorge A. [Cornell University, Baker Laboratory of Chemistry and Chemical Biology (United States); Serrano, Pedro; Wuethrich, Kurt [The Scripps Research Institute, Department of Molecular Biology (United States); Scheraga, Harold A., E-mail: has5@cornell.ed [Cornell University, Baker Laboratory of Chemistry and Chemical Biology (United States)

    2010-09-15

    To evaluate sequential nearest-neighbor effects on quantum-chemical calculations of {sup 13}C{sup {alpha}} chemical shifts, we selected the structure of the nucleic acid binding (NAB) protein from the SARS coronavirus determined by NMR in solution (PDB id 2K87). NAB is a 116-residue {alpha}/{beta} protein, which contains 9 prolines and has 50% of its residues located in loops and turns. Overall, the results presented here show that sizeable nearest-neighbor effects are seen only for residues preceding proline, where Pro introduces an overestimation, on average, of 1.73 ppm in the computed {sup 13}C{sup {alpha}} chemical shifts. A new ensemble of 20 conformers representing the NMR structure of the NAB, which was calculated with an input containing backbone torsion angle constraints derived from the theoretical {sup 13}C{sup {alpha}} chemical shifts as supplementary data to the NOE distance constraints, exhibits very similar topology and comparable agreement with the NOE constraints as the published NMR structure. However, the two structures differ in the patterns of differences between observed and computed {sup 13}C{sup {alpha}} chemical shifts, {Delta}{sub ca,i}, for the individual residues along the sequence. This indicates that the {Delta}{sub ca,i} -values for the NAB protein are primarily a consequence of the limited sampling by the bundles of 20 conformers used, as in common practice, to represent the two NMR structures, rather than of local flaws in the structures.

  19. Chemical equilibration due to heavy Hagedorn states

    International Nuclear Information System (INIS)

    Greiner, C; Koch-Steinheimer, P; Liu, F M; Shovkovy, I A; Stoecker, H

    2005-01-01

    A scenario of heavy resonances, called massive Hagedorn states, is proposed which exhibits a fast (t ∼ 1 fm/c) chemical equilibration of (strange) baryons and anti-baryons at the QCD critical temperature T c . For relativistic heavy ion collisions this scenario predicts that hadronization is followed by a brief expansion phase during which the equilibration rate is higher than the expansion rate, so that baryons and antibaryons reach chemical equilibrium before chemical freeze-out occurs

  20. 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...

  1. Investigation of DOTA-Metal Chelation Effects on the Chemical Shift of 129 Xe

    Energy Technology Data Exchange (ETDEWEB)

    Jeong, K; Slack, CC; Vassiliou, CC; Dao, P; Gomes, MD; Kennedy, DJ; Truxal, AE; Sperling, LJ; Francis, MB; Wemmer, DE; Pines, A

    2015-09-17

    Recent work has shown that xenon chemical shifts in cryptophane-cage sensors are affected when tethered chelators bind to metals. Here in this paper, we explore the xenon shifts in response to a wide range of metal ions binding to diastereomeric forms of 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid (DOTA) linked to cryptophane-A. The shifts induced by the binding of Ca2+, Cu2+, Ce3+, Zn2+, Cd2+, Ni2+, Co2+, Cr2+, Fe3+, and Hg2+ are distinct. In addition, the different responses of the diastereomers for the same metal ion indicate that shifts are affected by partial folding with a correlation between the expected coordination number of the metal in the DOTA complex and the chemical shift of 129Xe. Lastly, these sensors may be used to detect and quantify many important metal ions, and a better understanding of the basis for the induced shifts could enhance future designs.

  2. 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...

  3. Identification of helix capping and {beta}-turn motifs from NMR chemical shifts

    Energy Technology Data Exchange (ETDEWEB)

    Shen Yang; Bax, Ad, E-mail: bax@nih.gov [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States)

    2012-03-15

    We present an empirical method for identification of distinct structural motifs in proteins on the basis of experimentally determined backbone and {sup 13}C{sup {beta}} chemical shifts. Elements identified include the N-terminal and C-terminal helix capping motifs and five types of {beta}-turns: I, II, I Prime , II Prime and VIII. Using a database of proteins of known structure, the NMR chemical shifts, together with the PDB-extracted amino acid preference of the helix capping and {beta}-turn motifs are used as input data for training an artificial neural network algorithm, which outputs the statistical probability of finding each motif at any given position in the protein. The trained neural networks, contained in the MICS (motif identification from chemical shifts) program, also provide a confidence level for each of their predictions, and values ranging from ca 0.7-0.9 for the Matthews correlation coefficient of its predictions far exceed those attainable by sequence analysis. MICS is anticipated to be useful both in the conventional NMR structure determination process and for enhancing on-going efforts to determine protein structures solely on the basis of chemical shift information, where it can aid in identifying protein database fragments suitable for use in building such structures.

  4. Identify Beta-Hairpin Motifs with Quadratic Discriminant Algorithm Based on the Chemical Shifts.

    Directory of Open Access Journals (Sweden)

    Feng YongE

    Full Text Available Successful prediction of the beta-hairpin motif will be helpful for understanding the of the fold recognition. Some algorithms have been proposed for the prediction of beta-hairpin motifs. However, the parameters used by these methods were primarily based on the amino acid sequences. Here, we proposed a novel model for predicting beta-hairpin structure based on the chemical shift. Firstly, we analyzed the statistical distribution of chemical shifts of six nuclei in not beta-hairpin and beta-hairpin motifs. Secondly, we used these chemical shifts as features combined with three algorithms to predict beta-hairpin structure. Finally, we achieved the best prediction, namely sensitivity of 92%, the specificity of 94% with 0.85 of Mathew's correlation coefficient using quadratic discriminant analysis algorithm, which is clearly superior to the same method for the prediction of beta-hairpin structure from 20 amino acid compositions in the three-fold cross-validation. Our finding showed that the chemical shift is an effective parameter for beta-hairpin prediction, suggesting the quadratic discriminant analysis is a powerful algorithm for the prediction of beta-hairpin.

  5. Chemical shift of Mn and Cr K-edges in X-ray absorption

    Indian Academy of Sciences (India)

    ... Lecture Workshops · Refresher Courses · Symposia · Live Streaming. Home; Journals; Bulletin of Materials Science; Volume 36; Issue 6. Chemical shift of Mn and Cr K-edges in X-ray absorption spectroscopy with synchrotron radiation. D Joseph A K Yadav S N Jha D Bhattacharyya. Volume 36 Issue 6 November 2013 pp ...

  6. 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...

  7. Database proton NMR chemical shifts for RNA signal assignment and validation

    Energy Technology Data Exchange (ETDEWEB)

    Barton, Shawn; Heng Xiao [University of Maryland, Baltimore County, Howard Hughes Medical Institute (United States); Johnson, Bruce A., E-mail: bruce@onemoonscientific.com [University of Maryland, Baltimore County, Department of Chemistry and Biochemistry (United States); Summers, Michael F., E-mail: summers@hhmi.umbc.edu [University of Maryland, Baltimore County, Howard Hughes Medical Institute (United States)

    2013-01-15

    The Biological Magnetic Resonance Data Bank contains NMR chemical shift depositions for 132 RNAs and RNA-containing complexes. We have analyzed the {sup 1}H NMR chemical shifts reported for non-exchangeable protons of residues that reside within A-form helical regions of these RNAs. The analysis focused on the central base pair within a stretch of three adjacent base pairs (BP triplets), and included both Watson-Crick (WC; G:C, A:U) and G:U wobble pairs. Chemical shift values were included for all 4{sup 3} possible WC-BP triplets, as well as 137 additional triplets that contain one or more G:U wobbles. Sequence-dependent chemical shift correlations were identified, including correlations involving terminating base pairs within the triplets and canonical and non-canonical structures adjacent to the BP triplets (i.e. bulges, loops, WC and non-WC BPs), despite the fact that the NMR data were obtained under different conditions of pH, buffer, ionic strength, and temperature. A computer program (RNAShifts) was developed that enables convenient comparison of RNA {sup 1}H NMR assignments with database predictions, which should facilitate future signal assignment/validation efforts and enable rapid identification of non-canonical RNA structures and RNA-ligand/protein interaction sites.

  8. Skeletal and chlorine effects on 13C-NMR chemical shifts of chlorinated polycyclic systems

    Directory of Open Access Journals (Sweden)

    Costa V.E.U.

    1999-01-01

    Full Text Available In order to establish a comparative analysis of chemical shifts caused by ring compression effects or by the presence of a chlorine atom on strained chlorinated carbons, a series of the chlorinated and dechlorinated polycyclic structures derived from "aldrin" (5 and "isodrin" (14 was studied. Compounds were classified in four different groups, according to their conformation and number of ring such as: endo-exo and endo-endo tetracyclics, pentacyclics and hexacyclics. The 13C chemical shift comparison between the chlorinated and dechlorinated compounds showed that when C-9 and C-10 are olefinic carbons, it occurs a shielding of 0.5-2.4 ppm for endo-endo tetracyclics and of 4.7-7.6 ppm for endo-exo tetracyclic. The chemical shift variation for C-11 reaches 49-53 ppm for endo-exo and endo-endo tetracyclics, 54 ppm for pentacyclic and 56-59 ppm for hexacyclic compounds. From these data, it was possible to observe the influence of ring compression on the chemical shifts.

  9. Identification of helix capping and β-turn motifs from NMR chemical shifts

    International Nuclear Information System (INIS)

    Shen Yang; Bax, Ad

    2012-01-01

    We present an empirical method for identification of distinct structural motifs in proteins on the basis of experimentally determined backbone and 13 C β chemical shifts. Elements identified include the N-terminal and C-terminal helix capping motifs and five types of β-turns: I, II, I′, II′ and VIII. Using a database of proteins of known structure, the NMR chemical shifts, together with the PDB-extracted amino acid preference of the helix capping and β-turn motifs are used as input data for training an artificial neural network algorithm, which outputs the statistical probability of finding each motif at any given position in the protein. The trained neural networks, contained in the MICS (motif identification from chemical shifts) program, also provide a confidence level for each of their predictions, and values ranging from ca 0.7–0.9 for the Matthews correlation coefficient of its predictions far exceed those attainable by sequence analysis. MICS is anticipated to be useful both in the conventional NMR structure determination process and for enhancing on-going efforts to determine protein structures solely on the basis of chemical shift information, where it can aid in identifying protein database fragments suitable for use in building such structures.

  10. H-1 chemical shift imaging characterization of human brain tumor and edema

    NARCIS (Netherlands)

    Sijens, PE; Oudkerk, M

    Longitudinal (T1) and transverse (T2) relaxation times of metabolites in human brain tumor, peritumoral edema, and unaffected brain tissue were assessed from point resolved spectroscopy (PRESS) H-1 chemical shift imaging results at different repetition times (TR = 1500 and 5000 ms; T1: n = 19) and

  11. Chemical Mass Shifts in a Digital Linear Ion Trap as Analytical Identity of o-, m-, and p-Xylene.

    Science.gov (United States)

    Sun, Lulu; Xue, Bing; Huang, Zhengxu; Cheng, Ping; Ma, Li; Ding, Li; Zhou, Zhen

    2018-07-01

    Chemical mass shifts between isomeric ions of o-, m-, and p-xylene were measured using a digital linear ion trap, and the directions and values of the shifts were found to be correlated to the collision cross sections of the isomers. Both forward and reverse scans were used and the chemical shifts for each pair of isomers in scans of opposite directions were in opposite signs. Using different voltage settings (namely the voltage dividing ratio-VDR) of the ion trap allows adding high order field components in the quadrupole field and results in larger chemical mass shifts. The differential chemical mass shift which combined the shifts from forward and reverse scans doubled the amount of chemical shift, e.g., 0.077 Th between o- and p-xylene, enough for identification of the type of isomer without using an additional ion mobility spectrometer. The feature of equal and opposite chemical mass shifts also allowed to null out the chemical mass shift by calculating the mean m/z value between the two opposite scans and remove or reduce the mass error caused by chemical mass shift. Graphical Abstract ᅟ.

  12. Chemical Mass Shifts in a Digital Linear Ion Trap as Analytical Identity of o-, m-, and p-Xylene

    Science.gov (United States)

    Sun, Lulu; Xue, Bing; Huang, Zhengxu; Cheng, Ping; Ma, Li; Ding, Li; Zhou, Zhen

    2018-04-01

    Chemical mass shifts between isomeric ions of o-, m-, and p-xylene were measured using a digital linear ion trap, and the directions and values of the shifts were found to be correlated to the collision cross sections of the isomers. Both forward and reverse scans were used and the chemical shifts for each pair of isomers in scans of opposite directions were in opposite signs. Using different voltage settings (namely the voltage dividing ratio-VDR) of the ion trap allows adding high order field components in the quadrupole field and results in larger chemical mass shifts. The differential chemical mass shift which combined the shifts from forward and reverse scans doubled the amount of chemical shift, e.g., 0.077 Th between o- and p-xylene, enough for identification of the type of isomer without using an additional ion mobility spectrometer. The feature of equal and opposite chemical mass shifts also allowed to null out the chemical mass shift by calculating the mean m/z value between the two opposite scans and remove or reduce the mass error caused by chemical mass shift. [Figure not available: see fulltext.

  13. Application of the Fenske-Hall molecular orbital method to the calculation of 11B NMR chemical shifts. Antipodal substituent effects in deltahedral clusters

    International Nuclear Information System (INIS)

    Fehlner, T.P.; Czech, P.T.; Fenske, R.F.

    1990-01-01

    Utilizing Fenske-Hall wave functions and eigenvalues combined with the Ramsey sum over states (SOS) approximation, it is demonstrated that the sign and magnitude of the paramagnetic contribution to the shielding correlates well with the observed 11 B chemical shifts of a substantial variety of boron- and metal-containing compounds. Analysis of the molecular orbital (MO) contributions in the SOS approximation leads to an explanation of the large downfield shifts associated with metal-rich metallaboranes. A similar analysis demonstrates the importance of selected cluster occupied and unoccupied MO's in explaining both exo-cage substituent effects in which the antipodal boron resonance is shifted upfield and endo-cage substituent effects (interchange of isolobal fragments within the cage framework) in which the antipodal boron resonance is shifted downfield. Exo- and endo-cage substitution perturbs these MO's in an understandable fashion, leading to an internally consistent explanation of the observed chemical shift changes. 36 refs., 8 figs., 4 tabs

  14. Pressure-dependent {sup 13}C chemical shifts in proteins: origins and applications

    Energy Technology Data Exchange (ETDEWEB)

    Wilton, David J. [University of Sheffield, Department of Molecular Biology and Biotechnology (United Kingdom); Kitahara, Ryo [Ritsumeikan University, College of Pharmaceutical Sciences (Japan); Akasaka, Kazuyuki [Kinki University, Department of Biotechnological Science, School of Biology-Oriented Science and Technology (Japan); Williamson, Mike P. [University of Sheffield, Department of Molecular Biology and Biotechnology (United Kingdom)], E-mail: m.williamson@sheffield.ac.uk

    2009-05-15

    Pressure-dependent {sup 13}C chemical shifts have been measured for aliphatic carbons in barnase and Protein G. Up to 200 MPa (2 kbar), most shift changes are linear, demonstrating pressure-independent compressibilities. CH{sub 3}, CH{sub 2} and CH carbon shifts change on average by +0.23, -0.09 and -0.18 ppm, respectively, due to a combination of bond shortening and changes in bond angles, the latter matching one explanation for the {gamma}-gauche effect. In addition, there is a residue-specific component, arising from both local compression and conformational change. To assess the relative magnitudes of these effects, residue-specific shift changes for protein G were converted into structural restraints and used to calculate the change in structure with pressure, using a genetic algorithm to convert shift changes into dihedral angle restraints. The results demonstrate that residual {sup 13}C{alpha} shifts are dominated by dihedral angle changes and can be used to calculate structural change, whereas {sup 13}C{beta} shifts retain significant dependence on local compression, making them less useful as structural restraints.

  15. Evaluation of the application of chemical shift for the detection of lipid in brain lesion

    Energy Technology Data Exchange (ETDEWEB)

    Lim, C.J. [Department of Biomedical Imaging, Faculty of Medicine, University of Malaya Medical Centre, Kuala Lumpur (Malaysia); Ng, K.H., E-mail: ngkh@um.edu.m [Department of Biomedical Imaging, Faculty of Medicine, University of Malaya Medical Centre, Kuala Lumpur (Malaysia); Ramli, N.; Azman, R.R. [Department of Biomedical Imaging, Faculty of Medicine, University of Malaya Medical Centre, Kuala Lumpur (Malaysia)

    2011-02-15

    Non-invasive detection of the presence of lipids is particularly important in staging of intracranial tumours. Presence of lipid peak in aggressive intracranial tumours has been reported widely using MR spectroscopy. However this method has limitation due to long imaging time and artefacts formed by adjacent bones. Chemical shift MR imaging (with has shorter imaging time) is an alternative method that had been used to detect presence of lipid in vivo by means of signal intensity loss. The purpose of this study was to evaluate gradient echo in- and opposed-phase chemical shift pulse sequences for detection of lipid elements in brain lesion. Ten cylindered phantoms measuring 3 x 3 cm were filled with various mixtures of lipid and water: 0-90% lipid, in 10% step by weight. The gradient echo in- and opposed-phase chemical shift sequences were performed using a 1.5 T MRI (Magnetom Vision, Siemens) with a head coil. In addition, we performed MRI and chemical shift studies on 32 patients with brain lesion. We then analysed the association between out of phase intensity value and classification of the lesions. For phantom containing 50% lipid, maximum signal loss on opposed-phase images was observed. There were significant differences between in- and opposed-phase lipid-water phantom images (P = 0.0054). Most of the benign lesions fall into the positive out of phase intensity value, and malignant lesions fall into negative out of phase intensity value. We conclude that chemical shift artefact can be applied in detecting and characterising lipid elements in brain lesion.

  16. Evaluation of the application of chemical shift for the detection of lipid in brain lesion

    International Nuclear Information System (INIS)

    Lim, C.J.; Ng, K.H.; Ramli, N.; Azman, R.R.

    2011-01-01

    Non-invasive detection of the presence of lipids is particularly important in staging of intracranial tumours. Presence of lipid peak in aggressive intracranial tumours has been reported widely using MR spectroscopy. However this method has limitation due to long imaging time and artefacts formed by adjacent bones. Chemical shift MR imaging (with has shorter imaging time) is an alternative method that had been used to detect presence of lipid in vivo by means of signal intensity loss. The purpose of this study was to evaluate gradient echo in- and opposed-phase chemical shift pulse sequences for detection of lipid elements in brain lesion. Ten cylindered phantoms measuring 3 x 3 cm were filled with various mixtures of lipid and water: 0-90% lipid, in 10% step by weight. The gradient echo in- and opposed-phase chemical shift sequences were performed using a 1.5 T MRI (Magnetom Vision, Siemens) with a head coil. In addition, we performed MRI and chemical shift studies on 32 patients with brain lesion. We then analysed the association between out of phase intensity value and classification of the lesions. For phantom containing 50% lipid, maximum signal loss on opposed-phase images was observed. There were significant differences between in- and opposed-phase lipid-water phantom images (P = 0.0054). Most of the benign lesions fall into the positive out of phase intensity value, and malignant lesions fall into negative out of phase intensity value. We conclude that chemical shift artefact can be applied in detecting and characterising lipid elements in brain lesion.

  17. Protein energetic conformational analysis from NMR chemical shifts (PECAN) and its use in determining secondary structural elements

    Energy Technology Data Exchange (ETDEWEB)

    Eghbalnia, Hamid R.; Wang Liya; Bahrami, Arash [National Magnetic Resonance Facility at Madison, Biochemistry Department (United States); Assadi, Amir [University of Wisconsin-Madison, Mathematics Department (United States); Markley, John L. [National Magnetic Resonance Facility at Madison, Biochemistry Department (United States)], E-mail: eghbalni@nmrfam.wisc.edu

    2005-05-15

    We present an energy model that combines information from the amino acid sequence of a protein and available NMR chemical shifts for the purposes of identifying low energy conformations and determining elements of secondary structure. The model ('PECAN', Protein Energetic Conformational Analysis from NMR chemical shifts) optimizes a combination of sequence information and residue-specific statistical energy function to yield energetic descriptions most favorable to predicting secondary structure. Compared to prior methods for secondary structure determination, PECAN provides increased accuracy and range, particularly in regions of extended structure. Moreover, PECAN uses the energetics to identify residues located at the boundaries between regions of predicted secondary structure that may not fit the stringent secondary structure class definitions. The energy model offers insights into the local energetic patterns that underlie conformational preferences. For example, it shows that the information content for defining secondary structure is localized about a residue and reaches a maximum when two residues on either side are considered. The current release of the PECAN software determines the well-defined regions of secondary structure in novel proteins with assigned chemical shifts with an overall accuracy of 90%, which is close to the practical limit of achievable accuracy in classifying the states.

  18. Protein energetic conformational analysis from NMR chemical shifts (PECAN) and its use in determining secondary structural elements

    International Nuclear Information System (INIS)

    Eghbalnia, Hamid R.; Wang Liya; Bahrami, Arash; Assadi, Amir; Markley, John L.

    2005-01-01

    We present an energy model that combines information from the amino acid sequence of a protein and available NMR chemical shifts for the purposes of identifying low energy conformations and determining elements of secondary structure. The model ('PECAN', Protein Energetic Conformational Analysis from NMR chemical shifts) optimizes a combination of sequence information and residue-specific statistical energy function to yield energetic descriptions most favorable to predicting secondary structure. Compared to prior methods for secondary structure determination, PECAN provides increased accuracy and range, particularly in regions of extended structure. Moreover, PECAN uses the energetics to identify residues located at the boundaries between regions of predicted secondary structure that may not fit the stringent secondary structure class definitions. The energy model offers insights into the local energetic patterns that underlie conformational preferences. For example, it shows that the information content for defining secondary structure is localized about a residue and reaches a maximum when two residues on either side are considered. The current release of the PECAN software determines the well-defined regions of secondary structure in novel proteins with assigned chemical shifts with an overall accuracy of 90%, which is close to the practical limit of achievable accuracy in classifying the states

  19. Coronary artery atherosclerosis associated with shift work in chemical plant workers by using coronary CT angiography.

    Science.gov (United States)

    Kang, WonYang; Park, Won-Ju; Jang, Keun-Ho; Kim, Soo-Hyeon; Gwon, Do-Hyeong; Lim, Hyeong-Min; Ahn, Ji-Sung; Moon, Jai-Dong

    2016-08-01

    The aim of this study was to investigate whether shift work is related to elevated risk of coronary artery disease (CAD) by determining the coronary artery calcium (CAC) score and the presence of coronary artery stenosis by using coronary artery CT angiography (CCTA). In this study, 110 male workers participated and underwent a CCTA examination for CAC scoring, which represents coronary artery plaque, and were evaluated for luminal stenosis. All of the participants were working in the same chemical plant, of whom 70 worked day shifts and 40 worked rotating shifts. In a multivariate logistic regression analysis, including age, smoking status, alcohol consumption, regular exercise and waist circumference, shift work was associated with a 2.89-fold increase in the odds of developing coronary plaque compared with day work (OR, 2.89; 95% CI 1.07 to 7.82). The association between shift work and coronary plaque was strong after adjustment for age, low-density lipoprotein cholesterol, hypertension and diabetes mellitus (OR, 2.92; 95% CI 1.02 to 8.33). In addition, the number of years of shift work employment was associated with coronary plaque. However, no association was found between shift work and coronary artery stenosis. Shift work could induce CAD onset via the atherosclerotic process, and shift work employment duration was associated with an increased risk of atherosclerosis in male workers. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

  20. Isotope effects on chemical shifts in tautomeric systems with double proton transfer. Citronin

    International Nuclear Information System (INIS)

    Hansen, P.E.; Langgard, M.; Bolvig, S.

    1998-01-01

    Primary and secondary deuterium isotope effects on 1 H and 13 C chemical shifts are measured in citrinin, a tautomeric compound with an unusual doubly intramolecularly hydrogen bonded structure. The isotope effects are to a large extent dominated by equilibrium contributions and deuteration leads to more of the deuterated enol forms rather than the deuterated acid form. 1 H 13 C and 17 O nuclear shieldings are calculated using density functional ab initio methods. A very good correlation between calculated nuclear shieldings and experimental 1 H and 13 C chemical shifts is obtained. The tautomeric equilibrium can be analyzed based on the isotope effects on B-6 and C-8 carbons and shows an increase in the o-quinone form on lowering the temperature. Furthermore, upon deuteration the largest equilibrium shift is found for deuteration at OH-8 and the shift in the tautomeric equilibrium upon deuteration at OH-8 and the shift in the tautomeric equilibrium upon deuteration is increasing at lower temperature. (author)

  1. Dynamic shifting in thalamocortical processing during different behavioural states.

    OpenAIRE

    Nicolelis, Miguel A L; Fanselow, Erika E

    2002-01-01

    Recent experiments in our laboratory have indicated that as rats shift the behavioural strategy employed to explore their surrounding environment, there is a parallel change in the physiological properties of the neuronal ensembles that define the main thalamocortical loop of the trigeminal somatosensory system. Based on experimental evidence from several laboratories, we propose that this concurrent shift in behavioural strategy and thalamocortical physiological properties provides rats with...

  2. Modelling the acid/base 1H NMR chemical shift limits of metabolites in human urine.

    Science.gov (United States)

    Tredwell, Gregory D; Bundy, Jacob G; De Iorio, Maria; Ebbels, Timothy M D

    2016-01-01

    Despite the use of buffering agents the 1 H NMR spectra of biofluid samples in metabolic profiling investigations typically suffer from extensive peak frequency shifting between spectra. These chemical shift changes are mainly due to differences in pH and divalent metal ion concentrations between the samples. This frequency shifting results in a correspondence problem: it can be hard to register the same peak as belonging to the same molecule across multiple samples. The problem is especially acute for urine, which can have a wide range of ionic concentrations between different samples. To investigate the acid, base and metal ion dependent 1 H NMR chemical shift variations and limits of the main metabolites in a complex biological mixture. Urine samples from five different individuals were collected and pooled, and pre-treated with Chelex-100 ion exchange resin. Urine samples were either treated with either HCl or NaOH, or were supplemented with various concentrations of CaCl 2 , MgCl 2 , NaCl or KCl, and their 1 H NMR spectra were acquired. Nonlinear fitting was used to derive acid dissociation constants and acid and base chemical shift limits for peaks from 33 identified metabolites. Peak pH titration curves for a further 65 unidentified peaks were also obtained for future reference. Furthermore, the peak variations induced by the main metal ions present in urine, Na + , K + , Ca 2+ and Mg 2+ , were also measured. These data will be a valuable resource for 1 H NMR metabolite profiling experiments and for the development of automated metabolite alignment and identification algorithms for 1 H NMR spectra.

  3. 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.

  4. Assignment of protein backbone resonances using connectivity, torsion angles and 13Cα chemical shifts

    International Nuclear Information System (INIS)

    Morris, Laura C.; Valafar, Homayoun; Prestegard, James H.

    2004-01-01

    A program is presented which will return the most probable sequence location for a short connected set of residues in a protein given just 13 C α chemical shifts (δ( 13 C α )) and data restricting the φ and ψ backbone angles. Data taken from both the BioMagResBank and the Protein Data Bank were used to create a probability density function (PDF) using a multivariate normal distribution in δ( 13 C α ), φ, and ψ space for each amino acid residue. Extracting and combining probabilities for particular amino acid residues in a short proposed sequence yields a score indicative of the correctness of the proposed assignment. The program is illustrated using several proteins for which structure and 13 C α chemical shift data are available

  5. Identifying stereoisomers by ab-initio calculation of secondary isotope shifts on NMR chemical shieldings.

    Science.gov (United States)

    Böhm, Karl-Heinz; Banert, Klaus; Auer, Alexander A

    2014-04-23

    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(2-2H)ethane 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.

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

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Woonghee, E-mail: whlee@nmrfam.wisc.edu [University of Wisconsin-Madison, National Magnetic Resonance Facility at Madison, and Biochemistry Department (United States); Yu, Wookyung [Center for Proteome Biophysics, Pusan National University, Department of Physics (Korea, Republic of); Kim, Suhkmann [Pusan National University, Department of Chemistry and Chemistry Institute for Functional Materials (Korea, Republic of); Chang, Iksoo [Center for Proteome Biophysics, Pusan National University, Department of Physics (Korea, Republic of); Lee, Weontae, E-mail: wlee@spin.yonsei.ac.kr [Yonsei University, Structural Biochemistry and Molecular Biophysics Laboratory, Department of Biochemistry (Korea, Republic of); Markley, John L., E-mail: markley@nmrfam.wisc.edu [University of Wisconsin-Madison, National Magnetic Resonance Facility at Madison, and Biochemistry Department (United States)

    2012-10-15

    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.eduhttp://pacsy.nmrfam.wisc.edu.

  7. 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.

  8. 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

    2012-01-01

    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. PMID:22903636

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

    International Nuclear Information System (INIS)

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

    2012-01-01

    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.eduhttp://pacsy.nmrfam.wisc.edu.

  10. Cα and Cβ Carbon-13 Chemical Shifts in Proteins From an Empirical Database

    International Nuclear Information System (INIS)

    Iwadate, Mitsuo; Asakura, Tetsuo; Williamson, Michael P.

    1999-01-01

    We have constructed an extensive database of 13C Cα and Cβ chemical shifts in proteins of solution, for proteins of which a high-resolution crystal structure exists, and for which the crystal structure has been shown to be essentially identical to the solution structure. There is no systematic effect of temperature, reference compound, or pH on reported shifts, but there appear to be differences in reported shifts arising from referencing differences of up to 4.2 ppm. The major factor affecting chemical shifts is the backbone geometry, which causes differences of ca. 4 ppm between typical α- helix and β-sheet geometries for Cα, and of ca. 2 ppm for Cβ. The side-chain dihedral angle χ1 has an effect of up to 0.5 ppm on the Cα shift, particularly for amino acids with branched side-chains at Cβ. Hydrogen bonding to main-chain atoms has an effect of up to 0.9 ppm, which depends on the main- chain conformation. The sequence of the protein and ring-current shifts from aromatic rings have an insignificant effect (except for residues following proline). There are significant differences between different amino acid types in the backbone geometry dependence; the amino acids can be grouped together into five different groups with different φ,ψ shielding surfaces. The overall fit of individual residues to a single non-residue-specific surface, incorporating the effects of hydrogen bonding and χ1 angle, is 0.96 ppm for both Cα and Cβ. The results from this study are broadly similar to those from ab initio studies, but there are some differences which could merit further attention

  11. Conformational analysis of the chemical shifts for molecules containing diastereotopic methylene protons

    Science.gov (United States)

    Borowski, Piotr

    2012-01-01

    Quantum chemistry SCF/GIAO calculations were carried out on a set of compounds containing diastereotopic protons. Five molecules, including recently synthesized 1,3-di(2,3-epoxypropoxy)benzene, containing the chiral or pro-chiral center and the neighboring methylene group, were chosen. The rotational averages (i.e. normalized averages with respect to the rotation about the torsional angle τ with the exponential energy weight at temperature T) calculated individually for each of the methylene protons in 1,3-di(2,3-epoxypropoxy)benzene differ by ca. 0.6 ppm, which is significantly less than the value calculated for the lowest energy conformer. This value turned out to be low enough to guarantee the proper ordering of theoretical chemical shifts, supporting the interpretation of the 1H NMR spectrum of this important compound. The rotational averages of chemical shifts for methylene protons for a given type of conformer are shown to be essentially equal to the Boltzmann averages (here, the population-weighted averages for the individual conformers representing minima on the E( τ) cross-section). The calculated Boltzmann averages in the representative conformational space may exhibit completely different ordering as compared to the chemical shifts calculated for the lowest-energy conformer. This is especially true in the case of molecules, for which no significant steric effects are present. In this case, only Boltzmann averages account for the experimental pattern of proton signals. In addition, better overall agreement with experiment (lower value of the root-mean-square deviation between calculated and measured chemical shifts) is typically obtained when Boltzmann averages are used.

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

    International Nuclear Information System (INIS)

    Perazzolo, Chiara; Wist, Julien; Loth, Karine; Poggi, Luisa; Homans, Steve; Bodenhausen, Geoffrey

    2005-01-01

    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{C'N} and DQC{C'N}, 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)

  13. 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)

  14. Unusually large chemical potential shift in a degenerate semiconductor: Angle-resolved photoemission study of SnSe and Na-doped SnSe

    Science.gov (United States)

    Maeda, M.; Yamamoto, K.; Mizokawa, T.; Saini, N. L.; Arita, M.; Namatame, H.; Taniguchi, M.; Tan, G.; Zhao, L. D.; Kanatzidis, M. G.

    2018-03-01

    We have studied the electronic structure of SnSe and Na-doped SnSe by means of angle-resolved photoemission spectroscopy. The valence-band top reaches the Fermi level by the Na doping, indicating that Na-doped SnSe can be viewed as a degenerate semiconductor. However, in the Na-doped system, the chemical potential shift with temperature is unexpectedly large and is apparently inconsistent with the degenerate semiconductor picture. The large chemical potential shift and anomalous spectral shape are key ingredients for an understanding of the novel metallic state with the large thermoelectric performance in Na-doped SnSe.

  15. Dynamic two state stochastic models for ecological regime shifts

    DEFF Research Database (Denmark)

    Møller, Jan Kloppenborg; Carstensen, Niels Jacob; Madsen, Henrik

    2009-01-01

    of the model illustrates that hysteresis effect and regime shifts can be obtained for a limited range of parameter values only. The effect of multiplicative noise components entering at different levels of the model is presented and discussed. Including noise leads to very different results on the stability...

  16. Cortico-pontine theta carrier frequency phase shift across sleep/wake states following monoaminergic lesion in rat.

    Science.gov (United States)

    Kalauzi, Aleksandar; Spasic, Sladjana; Petrovic, Jelena; Ciric, Jelena; Saponjic, Jelena

    2012-06-01

    This study was aimed to explore the sleep/wake states related cortico-pontine theta carrier frequency phase shift following a systemically induced chemical axotomy of the monoaminergic afferents within a brain of the freely moving rats. Our experiments were performed in 14 adult, male Sprague Dawley rats, chronically implanted for sleep recording. We recorded sleep during baseline condition, following sham injection (saline i.p. 1 ml/kg), and every week for 5 weeks following injection of the systemic neurotoxins (DSP-4 or PCA; 1 ml/kg, i.p.) for chemical axotomy of the locus coeruleus (LC) and dorsal raphe (DR) axon terminals. After sleep/wake states identification, FFT analysis was performed on 5 s epochs. Theta carrier frequency phase shift (∆Φ) was calculated for each epoch by averaging theta Fourier component phase shifts, and the ∆Φ values were plotted for each rat in control condition and 28 days following the monoaminergic lesions, as a time for permanently established DR or LC chemical axotomy. Calculated group averages have shown that ∆Φ increased between pons and cortex significantly in all sleep/wake states (Wake, NREM and REM) following the monoaminergic lesions, with respect to controls. Monoaminergic lesions established the pontine leading role in the brain theta oscillations during all sleep/wake states.

  17. Benchmarking Hydrogen and Carbon NMR Chemical Shifts at HF, DFT, and MP2 Levels.

    Science.gov (United States)

    Flaig, Denis; Maurer, Marina; Hanni, Matti; Braunger, Katharina; Kick, Leonhard; Thubauville, Matthias; Ochsenfeld, Christian

    2014-02-11

    An extensive study of error distributions for calculating hydrogen and carbon NMR chemical shifts at Hartree-Fock (HF), density functional theory (DFT), and Møller-Plesset second-order perturbation theory (MP2) levels is presented. Our investigation employs accurate CCSD(T)/cc-pVQZ calculations for providing reference data for 48 hydrogen and 40 carbon nuclei within an extended set of chemical compounds covering a broad range of the NMR scale with high relevance to chemical applications, especially in organic chemistry. Besides the approximations of HF, a variety of DFT functionals, and conventional MP2, we also present results with respect to a spin component-scaled MP2 (GIAO-SCS-MP2) approach. For each method, the accuracy is analyzed in detail for various basis sets, allowing identification of efficient combinations of method and basis set approximations.

  18. Effect of Phase Shift in Dual-Rail Perfect State Transfer

    International Nuclear Information System (INIS)

    Wang Zhao-Ming; Zhang Zhong-Jun; Gu Yong-Jian

    2014-01-01

    We investigate the effect of phase shift on the perfect state transfer through two parallel one-dimensional ring-shaped spin chains. We find that the total success probability can be significantly enhanced by phase shift control when the communication channel consists of two odd chains. The average time to gain unit success probability is discussed, showing that a proper phase shift can be used to enhance the efficiency of state transmission. (general)

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

    International Nuclear Information System (INIS)

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

    2016-01-01

    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

  20. Carbon 13 nuclear magnetic resonance chemical shifts empiric calculations of polymers by multi linear regression and molecular modeling

    International Nuclear Information System (INIS)

    Da Silva Pinto, P.S.; Eustache, R.P.; Audenaert, M.; Bernassau, J.M.

    1996-01-01

    This work deals with carbon 13 nuclear magnetic resonance chemical shifts empiric calculations by multi linear regression and molecular modeling. The multi linear regression is indeed one way to obtain an equation able to describe the behaviour of the chemical shift for some molecules which are in the data base (rigid molecules with carbons). The methodology consists of structures describer parameters definition which can be bound to carbon 13 chemical shift known for these molecules. Then, the linear regression is used to determine the equation significant parameters. This one can be extrapolated to molecules which presents some resemblances with those of the data base. (O.L.). 20 refs., 4 figs., 1 tab

  1. 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...... anthraquinones containing methoxyl, hydroxyl, methylenedioxy and beta-methyl substituents. Because the chemical shifts of the other protons are hardly affected by substitutions in the other ring, the characteristic chemical shifts for a wide variety of substitution patterns could be derived....

  2. 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

  3. SPARTA+: a modest improvement in empirical NMR chemical shift prediction by means of an artificial neural network

    Energy Technology Data Exchange (ETDEWEB)

    Shen Yang; Bax, Ad, E-mail: bax@nih.go [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States)

    2010-09-15

    NMR chemical shifts provide important local structural information for proteins and are key in recently described protein structure generation protocols. We describe a new chemical shift prediction program, SPARTA+, which is based on artificial neural networking. The neural network is trained on a large carefully pruned database, containing 580 proteins for which high-resolution X-ray structures and nearly complete backbone and {sup 13}C{sup {beta}} chemical shifts are available. The neural network is trained to establish quantitative relations between chemical shifts and protein structures, including backbone and side-chain conformation, H-bonding, electric fields and ring-current effects. The trained neural network yields rapid chemical shift prediction for backbone and {sup 13}C{sup {beta}} atoms, with standard deviations of 2.45, 1.09, 0.94, 1.14, 0.25 and 0.49 ppm for {delta}{sup 15}N, {delta}{sup 13}C', {delta}{sup 13}C{sup {alpha}}, {delta}{sup 13}C{sup {beta}}, {delta}{sup 1}H{sup {alpha}} and {delta}{sup 1}H{sup N}, respectively, between the SPARTA+ predicted and experimental shifts for a set of eleven validation proteins. These results represent a modest but consistent improvement (2-10%) over the best programs available to date, and appear to be approaching the limit at which empirical approaches can predict chemical shifts.

  4. SPARTA+: a modest improvement in empirical NMR chemical shift prediction by means of an artificial neural network

    International Nuclear Information System (INIS)

    Shen Yang; Bax, Ad

    2010-01-01

    NMR chemical shifts provide important local structural information for proteins and are key in recently described protein structure generation protocols. We describe a new chemical shift prediction program, SPARTA+, which is based on artificial neural networking. The neural network is trained on a large carefully pruned database, containing 580 proteins for which high-resolution X-ray structures and nearly complete backbone and 13 C β chemical shifts are available. The neural network is trained to establish quantitative relations between chemical shifts and protein structures, including backbone and side-chain conformation, H-bonding, electric fields and ring-current effects. The trained neural network yields rapid chemical shift prediction for backbone and 13 C β atoms, with standard deviations of 2.45, 1.09, 0.94, 1.14, 0.25 and 0.49 ppm for δ 15 N, δ 13 C', δ 13 C α , δ 13 C β , δ 1 H α and δ 1 H N , respectively, between the SPARTA+ predicted and experimental shifts for a set of eleven validation proteins. These results represent a modest but consistent improvement (2-10%) over the best programs available to date, and appear to be approaching the limit at which empirical approaches can predict chemical shifts.

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

    International Nuclear Information System (INIS)

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

    2014-01-01

    Uranium L 3 X-ray absorption edge was measured in various compounds containing uranium in U 4+ , U 5+ and U 5+ 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 L 3 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. (author)

  6. Quantitative chemical shift-encoded MRI is an accurate method to quantify hepatic steatosis.

    Science.gov (United States)

    Kühn, Jens-Peter; Hernando, Diego; Mensel, Birger; Krüger, Paul C; Ittermann, Till; Mayerle, Julia; Hosten, Norbert; Reeder, Scott B

    2014-06-01

    To compare the accuracy of liver fat quantification using a three-echo chemical shift-encoded magnetic resonance imaging (MRI) technique without and with correction for confounders with spectroscopy (MRS) as the reference standard. Fifty patients (23 women, mean age 56.6 ± 13.2 years) with fatty liver disease were enrolled. Patients underwent T2-corrected single-voxel MRS and a three-echo chemical shift-encoded gradient echo (GRE) sequence at 3.0T. MRI fat fraction (FF) was calculated without and with T2* and T1 correction and multispectral modeling of fat and compared with MRS-FF using linear regression. The spectroscopic range of liver fat was 0.11%-38.7%. Excellent correlation between MRS-FF and MRI-FF was observed when using T2* correction (R(2)  = 0.96). With use of T2* correction alone, the slope was significantly different from 1 (1.16 ± 0.03, P fat were addressed, the results showed equivalence between fat quantification using MRI and MRS (slope: 1.02 ± 0.03, P = 0.528; intercept: 0.26% ± 0.46%, P = 0.572). Complex three-echo chemical shift-encoded MRI is equivalent to MRS for quantifying liver fat, but only with correction for T2* decay and T1 recovery and use of spectral modeling of fat. This is necessary because T2* decay, T1 recovery, and multispectral complexity of fat are processes which may otherwise bias the measurements. Copyright © 2013 Wiley Periodicals, Inc.

  7. Study of chemical shifts of the chloroform complexes with cyclic donors of electrons

    International Nuclear Information System (INIS)

    Blaszkiewicz, B.; Pajak, Z.

    1973-01-01

    Chemical shifts of chloroform complexes with the heterocyclic electron donors: pyridine, piperidine, alpha-picoline and gamma-picoline have been studied using the high resolution (5.10 -9 ) spectrometer operating at 80 MHz. An attempt has also been made to study the three - component solutions of : chloroform, a heterocyclic donor of electrons and carbon tetrachloride. The results, which have been obtained, indicate that the complex-forming power of pyridine and other electron donors is greater in carbon tetrachloride than in other solvents. (S.B.)

  8. Isomer shifts and chemical bonding in crystalline Sn(II) and Sn(IV) compounds

    International Nuclear Information System (INIS)

    Terra, J.; Guenzburger, D.

    1991-01-01

    First-principles self-consistent Local Density calculations of the electronic structure of clusters representing Sn(II) (SnO, SnF 2 , SnS, SnSe) and Sn(IV) (SnO 2 , SnF 4 ) crystalline compounds were performed. Values of the electron density at the Sn nucleus were obtained and related to measured values of the Moessbauer Isomer Shifts reported in the literature. The nuclear parameter of 119 Sn derived was ΔR/R=(1.58±0.14)x10 -4 . The chemical bonding in the solids was analysed and related to the electron densities obtained. (author)

  9. Performance test of multicomponent quantum mechanical calculation with polarizable continuum model for proton chemical shift.

    Science.gov (United States)

    Kanematsu, Yusuke; Tachikawa, Masanori

    2015-05-21

    Multicomponent quantum mechanical (MC_QM) calculations with polarizable continuum model (PCM) have been tested against liquid (1)H NMR chemical shifts for a test set of 80 molecules. Improvement from conventional quantum mechanical calculations was achieved for MC_QM calculations. The advantage of the multicomponent scheme could be attributed to the geometrical change from the equilibrium geometry by the incorporation of the hydrogen nuclear quantum effect, while that of PCM can be attributed to the change of the electronic structure according to the polarization by solvent effects.

  10. Combined echo offset (Dixon) and line volume chemical shift imaging as a clinical imaging protocol

    International Nuclear Information System (INIS)

    Listerud, J.; Chan, T.; Lenkinski, R.E.; Kressel, H.Y.; Chao, P.W.

    1989-01-01

    The authors have studied the sensitivity and specificity of the line-volume chemical-shift imaging (CSI) method as compared with the Dixon method they have recently implemented on a Signa, which supports a variety of options. Potential sources or error for the Dixon method include line broadening due to susceptibility, field inhomogeneity, and errors form olefinic resonances associated with fat, which behave like water in the Dixon regime. The authors investigate whether a combined Dixon/line-volume CSI method could be used to improve the placement of the line volume and to provide higher sensitivity and specificity than does the Dixon method alone

  11. Calculation of NMR chemical shifts. 7. Gauge-invariant INDO method

    Science.gov (United States)

    Fukui, H.; Miura, K.; Hirai, A.

    A gauge-invariant INDO method based on the coupled Hartree-Fuck perturbation theory is presented and applied to the calculation of 1H and 13C chemical shifts of hydrocarbons including ring compounds. Invariance of the diamagnetic and paramagnetic shieldings with respect to displacement of the coordinate origin is discussed. Comparison between calculated and experimental results exhibits fairly good agreement, provided that the INDO parameters of Ellis et al. (J. Am. Chem. Soc.94, 4069 (1972)) are used with the inclusion of all multicenter one-electron integrals.

  12. Determination of hydration numbers of electrolytes from temperature dependence of PMR chemical shifts

    International Nuclear Information System (INIS)

    Subramanian, N.

    1979-01-01

    The method proposed by Malinowski et al. for the determination of effective hydration numbers (h) of electrolytes leads to a consistent incrrease in the observed values of 'h' with increase in solution concentration. An attempt is made to rationalize the experimental results by cosidering the simultaneous effects of temperature and concentration on the proton chemical shift. It is suggested that Malinowski's technique might yeld 'h' values very close to the true value for those ions for which there is a fortuitous cancellation of structure-making and structure-breaking properties. (Author) [pt

  13. 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 co...

  14. Physical basis of the effect of hemoglobin on the 31P NMR chemical shifts of various phosphoryl compounds

    International Nuclear Information System (INIS)

    Kirk, K.; Kuchel, P.W.

    1988-01-01

    The marked difference between the intra- and extracellular 31 P NMR chemical shifts of various phosphoryl compounds when added to a red cell suspension may be largely understood in terms of the effects of hemoglobin on the 31 P NMR chemical shifts. The presence of [oxy- or (carbonmonoxy)-] hemoglobin inside the red cell causes the bulk magnetic susceptibility of the cell cytoplasm to be significantly less than that of the external solution. This difference is sufficient to account for the difference in the intra- and extracellular chemical shifts of the two phosphate esters trimethyl phosphate and triethyl phosphate. However, in the case of the compounds dimethyl methylphosphonate, diethyl methylphosphonate, and trimethylphosphine oxide as well as the hypophosphite, phenylphosphinate, and diphenylphosphinate ions, hemoglobin exerts an additional, much larger, effect, causing the 31 P NMR resonances to shift to lower frequency in a manner that cannot be accounted for in terms of magnetic susceptibility. Lysozyme is a protein structurally unrelated to hemoglobin and was shown to cause similar shifts to lower frequency of the resonances of these six compounds; this suggests that the mechanism may involve a property of proteins in general and not a specific property of hemoglobin. The effect of different solvents on the chemical shifts of the eight phosphoryl compounds provided an insight into the possible physical basis of the effect. It is proposed that, in addition to magnetic susceptibility effects, hemoglobin exerts its influence on phosphoryl chemical shifts by disrupting the hydrogen bonding of the phosphoryl group to solvent water

  15. Urbanization causes shifts in species' trait state frequencies

    NARCIS (Netherlands)

    Knapp, S.; Kühn, I.; Wittig, R.; Ozinga, W.A.; Poschlod, P.; Klotz, S.

    2008-01-01

    Urbanization is one of the most extreme forms of land transformation. It is supposed to change the frequencies of species trait states in species assemblages.We hypothesize that the flora of urban and rural areas differs in the frequency of trait states and ask which traits enable a plant to cope

  16. Solvation effects on chemical shifts by embedded cluster integral equation theory.

    Science.gov (United States)

    Frach, Roland; Kast, Stefan M

    2014-12-11

    The accurate computational prediction of nuclear magnetic resonance (NMR) parameters like chemical shifts represents a challenge if the species studied is immersed in strongly polarizing environments such as water. Common approaches to treating a solvent in the form of, e.g., the polarizable continuum model (PCM) ignore strong directional interactions such as H-bonds to the solvent which can have substantial impact on magnetic shieldings. We here present a computational methodology that accounts for atomic-level solvent effects on NMR parameters by extending the embedded cluster reference interaction site model (EC-RISM) integral equation theory to the prediction of chemical shifts of N-methylacetamide (NMA) in aqueous solution. We examine the influence of various so-called closure approximations of the underlying three-dimensional RISM theory as well as the impact of basis set size and different treatment of electrostatic solute-solvent interactions. We find considerable and systematic improvement over reference PCM and gas phase calculations. A smaller basis set in combination with a simple point charge model already yields good performance which can be further improved by employing exact electrostatic quantum-mechanical solute-solvent interaction energies. A larger basis set benefits more significantly from exact over point charge electrostatics, which can be related to differences of the solvent's charge distribution.

  17. Chemical constituents of Ottonia corcovadensis Miq. from Amazon forest: 1H and 13C chemical shift assignments

    International Nuclear Information System (INIS)

    Facundo, Valdir A.; Morais, Selene M.; Braz Filho, Raimundo

    2004-01-01

    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 1 H and 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)

  18. Structural analysis of flavonoids in solution through DFT 1H NMR chemical shift calculations: Epigallocatechin, Kaempferol and Quercetin

    Science.gov (United States)

    De Souza, Leonardo A.; Tavares, Wagner M. G.; Lopes, Ana Paula M.; Soeiro, Malucia M.; De Almeida, Wagner B.

    2017-05-01

    In this work, we showed that comparison between experimental and theoretical 1H NMR chemical shift patterns, calculated using Density Functional Theory (DFT), can be used for the prediction of molecular structure of flavonoids in solution, what is experimentally accessible for gas phase (electron diffraction methods) and solid samples (X-ray diffraction). The best match between B3LYP/6-31G(d,p)-PCM 1H NMR calculations for B ring rotated structures and experimental spectra can provide information on the conformation adopted by polyphenols in solution (usually DMSO-d6, acetone-d6 as solvents), which may differ from solid state and gas phase observed structures, and also DFT optimized geometry in the vacuum.

  19. Just a minute meditation: Rapid voluntary conscious state shifts in long term meditators.

    Science.gov (United States)

    Nair, Ajay Kumar; Sasidharan, Arun; John, John P; Mehrotra, Seema; Kutty, Bindu M

    2017-08-01

    Meditation induces a modified state of consciousness that remains under voluntary control. Can meditators rapidly and reversibly bring about mental state changes on demand? To check, we carried out 128 channel EEG recordings on Brahma Kumaris Rajayoga meditators (36 long term: median 14240h meditation; 25 short term: 1095h) and controls (25) while they tried to switch every minute between rest and meditation states in different conditions (eyes open and closed; before and after an engaging task). Long term meditators robustly shifted states with enhanced theta power (4-8Hz) during meditation. Short term meditators had limited ability to shift between states and showed increased lower alpha power (8-10Hz) during eyes closed meditation only when pre and post task data were combined. Controls could not shift states. Thus trained beginners can reliably meditate but it takes long term practice to exercise more refined control over meditative states. Copyright © 2017 Elsevier Inc. All rights reserved.

  20. 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…

  1. Accommodating state shifts within the conceptual framework of the wetland continuum

    Science.gov (United States)

    Mushet, David M.; McKenna, Owen; LaBaugh, James W.; Euliss, Ned H.; Rosenberry, Donald O.

    2018-01-01

    The Wetland Continuum is a conceptual framework that facilitates the interpretation of biological studies of wetland ecosystems. Recently summarized evidence documenting how a multi-decadal wet period has influenced aspects of wetland, lake and stream systems in the southern prairie-pothole region of North America has revealed the potential for wetlands to shift among alternate states. We propose that incorporation of state shifts into the Wetland Continuum, as originally proposed or as modified by Hayashi et al., is a relatively simple matter if one allows for shifts of wetlands along the horizontal, groundwater axis of the framework under conditions of extreme and sustained wet or dry conditions. We suggest that the ease by which state shifts can be accommodated within both the original and modified frameworks of the Wetland Continuum is a testament to the robustness of the concept when it is related to the alternative-stable-state concept.

  2. Correlations of the chemical shift on fasly rotating biological solids by means of NMR spectroscopy

    International Nuclear Information System (INIS)

    Herbst, Christian

    2010-01-01

    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 13 C- 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 n ν and RN n ν mixing sequences as well as heteronuclear RN n ν s ,ν 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) 97 -RNA. This thesis deals furthermore with the possibility to acquire simultaneously different signals with several receivers. By means of numerically optimized RN n ν s ,ν k pulse sequences both 15 N- 13 C and 13 C- 15 N correlation spectra were simultaneously generated. Furthermore it could be shown that the simultaneous acquisition of 3D- 15 N- 13 C- 13 C and 13 C- 15 N-( 1 H)- 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 χ in RNA. This was demonstrated by means of the (CUG) 97 -RNA. The simultaneous acquisition of all relevant crossing signals of the correlation spectra leads not only to an essential time saving, but

  3. Improvement of chemical shift selective saturation (CHESS) pulse for MR angiography

    International Nuclear Information System (INIS)

    Ishimori, Yoshiyuki; Sashie, Hiroyuki; Hiraga, Akira; Matsuda, Tsuyoshi

    2000-01-01

    We improved the fat suppression technique based on chemical shift selective saturation (CHESS). To do this, we shortened the duration of the CHESS pulse to achieve a short repetition time (TR) for MR angiography (MRA). A short-duration CHESS pulse causes broad frequency band saturation, creating extensive offset from the resonance frequency of water. In our phantom experiment, the best parameters of the short-duration CHESS pulse were 3.84 ms in duration, -650 Hz in offset frequency from water resonance, and had a 130-degree flip angle. With this technique, MRA will be able to be carried out without a significant increase in TR. Thus, better vessel contrast will be maintained in time-of-flight (TOF) MRA or contrast-enhanced MRA when using the maximum intensity projection (MIP) method. (author)

  4. Nuclear spin relaxation due to chemical shift anisotropy of gas-phase 129Xe.

    Science.gov (United States)

    Hanni, Matti; Lantto, Perttu; Vaara, Juha

    2011-08-14

    Nuclear spin relaxation provides detailed dynamical information on molecular systems and materials. Here, first-principles modeling of the chemical shift anisotropy (CSA) relaxation time for the prototypic monoatomic (129)Xe gas is carried out, both complementing and predicting the results of NMR measurements. Our approach is based on molecular dynamics simulations combined with pre-parametrized ab initio binary nuclear shielding tensors, an "NMR force field". By using the Redfield relaxation formalism, the simulated CSA time correlation functions lead to spectral density functions that, for the first time, quantitatively determine the experimental spin-lattice relaxation times T(1). The quality requirements on both the Xe-Xe interaction potential and binary shielding tensor are investigated in the context of CSA T(1). Persistent dimers Xe(2) are found to be responsible for the CSA relaxation mechanism in the low-density limit of the gas, completely in line with the earlier experimental findings.

  5. On the Confounding Effect of Temperature on Chemical Shift-Encoded Fat Quantification

    Science.gov (United States)

    Hernando, Diego; Sharma, Samir D.; Kramer, Harald; Reeder, Scott B.

    2014-01-01

    Purpose To characterize the confounding effect of temperature on chemical shift-encoded (CSE) fat quantification. Methods The proton resonance frequency of water, unlike triglycerides, depends on temperature. This leads to a temperature dependence of the spectral models of fat (relative to water) that are commonly used by CSE-MRI methods. Simulation analysis was performed for 1.5 Tesla CSE fat–water signals at various temperatures and echo time combinations. Oil–water phantoms were constructed and scanned at temperatures between 0 and 40°C using spectroscopy and CSE imaging at three echo time combinations. An explanted human liver, rejected for transplantation due to steatosis, was scanned using spectroscopy and CSE imaging. Fat–water reconstructions were performed using four different techniques: magnitude and complex fitting, with standard or temperature-corrected signal modeling. Results In all experiments, magnitude fitting with standard signal modeling resulted in large fat quantification errors. Errors were largest for echo time combinations near TEinit ≈ 1.3 ms, ΔTE ≈ 2.2 ms. Errors in fat quantification caused by temperature-related frequency shifts were smaller with complex fitting, and were avoided using a temperature-corrected signal model. Conclusion Temperature is a confounding factor for fat quantification. If not accounted for, it can result in large errors in fat quantifications in phantom and ex vivo acquisitions. PMID:24123362

  6. Increased precision for analysis of protein-ligand dissociation constants determined from chemical shift titrations

    Energy Technology Data Exchange (ETDEWEB)

    Markin, Craig J.; Spyracopoulos, Leo, E-mail: leo.spyracopoulos@ualberta.ca [University of Alberta, Department of Biochemistry (Canada)

    2012-06-15

    NMR is ideally suited for the analysis of protein-protein and protein ligand interactions with dissociation constants ranging from {approx}2 {mu}M to {approx}1 mM, and with kinetics in the fast exchange regime on the NMR timescale. For the determination of dissociation constants (K{sub D}) of 1:1 protein-protein or protein-ligand interactions using NMR, the protein and ligand concentrations must necessarily be similar in magnitude to the K{sub D}, and nonlinear least squares analysis of chemical shift changes as a function of ligand concentration is employed to determine estimates for the parameters K{sub D} and the maximum chemical shift change ({Delta}{delta}{sub max}). During a typical NMR titration, the initial protein concentration, [P{sub 0}], is held nearly constant. For this condition, to determine the most accurate parameters for K{sub D} and {Delta}{delta}{sub max} from nonlinear least squares analyses requires initial protein concentrations that are {approx}0.5 Multiplication-Sign K{sub D}, and a maximum concentration for the ligand, or titrant, of {approx}10 Multiplication-Sign [P{sub 0}]. From a practical standpoint, these requirements are often difficult to achieve. Using Monte Carlo simulations, we demonstrate that co-variation of the ligand and protein concentrations during a titration leads to an increase in the precision of the fitted K{sub D} and {Delta}{delta}{sub max} values when [P{sub 0}] > K{sub D}. Importantly, judicious choice of protein and ligand concentrations for a given NMR titration, combined with nonlinear least squares analyses using two independent variables (ligand and protein concentrations) and two parameters (K{sub D} and {Delta}{delta}{sub max}) is a straightforward approach to increasing the accuracy of measured dissociation constants for 1:1 protein-ligand interactions.

  7. The contribution of chemical shift imaging with digital subtracting images to the diagnosis of steatohepatitis

    International Nuclear Information System (INIS)

    Guo Xinghua; Wang Juanping; Zhang Chongjie; Zheng Guofang; Fan Ruiqiang; Zhu Sumei; Liu Qiwang

    2006-01-01

    Objective: To investigate the diagnosis value of chemical shift imaging with digital subtracting in steatohepatitis. Methods: The in-phase images were subtracted by the out-phase ones in 34 cases of steatohepatitis, and the CNR were measured on these subtracted images to estimate the steatosis of the liver. The relationship of CT grade of steatohepatitis and CNR from the subtracted images was analyzed to evaluate the relationship between CNR and the degree of hepatic steatosis. The sensitivity and specificity of the subtracting and eyeballing methods were compared with chi-square test. Results: On the subtracted images, the liver and spleen were seen nearly the same aspects as low signals, CNR=0.98±0.06, meanwhile the spongy vertebra and the subcutaneous or abdominal lipid were seen as obvious higher signals in 52 normal cases. On the 34 steatohepatitis, scattered high signals were seen in the liver, which made the signal of liver higher than that of spleen, CNR=3.25±0.91--14.35±6.10. There was positive correlation between CNR and CT grade in the 34 cases of steatohepatitis, r=0.893, P<0.01. The sensitivity and specificity of the subtracting method were 88.24% and 94. 23%, significantly higher than that of the eyeballing results, 32.35% and 80.77%, P<0.01 and P<0.05. Conclusion: Chemical shift imaging with digital subtracting is a sensitive, specific, objective method to diagnose steatohepatitis and it is of potential ability for quantitative diagnosis. (authors)

  8. Clinical application of 1H-chemical-shift imaging (CSI) to brain diseases

    International Nuclear Information System (INIS)

    Naruse, Shoji; Furuya, Seiichi; Ide, Mariko

    1992-01-01

    An H-1 chemical shift imaging (CSI) was developed as part of the clinical MRI system, by which magnetic resonance spectra (MRS) can be obtained from multiple small voxels and metabolite distribution in the brain can be visualized. The present study was to determine the feasibility and clinical potential of using an H-1 CSI. The device used was a Magnetom H 15 apparatus. The study population was comprised of 25 healthy subjects, 20 patients with brain tumor, 4 with ischemic disease, and 6 with miscellaneous degenerative disease. The H-1 CSI was obtained by the 3-dimensional Fourier transformation. After suppressing the lipid signal by the inversion-recovery method and the water signal by the chemical-shift selective pulse with a following dephasing gradient, 2-directional 16 x 16 phase encodings were applied to the 16 x 16∼18 x 18 cm field of view, in which a 8 x 8 x 2∼10 x 10 x 2 cm area was selected by the stimulated echo or spin-echo method. The metabolite mapping and its contour mapping were created by using the curve-fitted area, with interpolation to the 256 x 256 matrix. In the healthy group, high resolution spectra for N-acetyl aspartate (NAA), creatine, choline (Cho), and glutamine/glutamate were obtained from each voxel; and metabolite mapping and contour mapping also clearly showed metabolite distribution in the brain. In the group of brain tumor, an increased Cho and lactate and loss of NAA were observed, along with heterogeneity within the tumor and changes in the surrounding tissue; and there was a good correlation between lactate peak and tumor malignancy. The group of ischemic and degenerative disease had a decreased NAA and increased lactate on both spectra and metabolite mapping, depending on disease stage. These findings indicated that H-1 CSI is helpful for detecting spectra over the whole brain, as well as for determining metabolite distribution. (N.K.)

  9. Sensitivity of ab Initio vs Empirical Methods in Computing Structural Effects on NMR Chemical Shifts for the Example of Peptides.

    Science.gov (United States)

    Sumowski, Chris Vanessa; Hanni, Matti; Schweizer, Sabine; Ochsenfeld, Christian

    2014-01-14

    The structural sensitivity of NMR chemical shifts as computed by quantum chemical methods is compared to a variety of empirical approaches for the example of a prototypical peptide, the 38-residue kaliotoxin KTX comprising 573 atoms. Despite the simplicity of empirical chemical shift prediction programs, the agreement with experimental results is rather good, underlining their usefulness. However, we show in our present work that they are highly insensitive to structural changes, which renders their use for validating predicted structures questionable. In contrast, quantum chemical methods show the expected high sensitivity to structural and electronic changes. This appears to be independent of the quantum chemical approach or the inclusion of solvent effects. For the latter, explicit solvent simulations with increasing number of snapshots were performed for two conformers of an eight amino acid sequence. In conclusion, the empirical approaches neither provide the expected magnitude nor the patterns of NMR chemical shifts determined by the clearly more costly ab initio methods upon structural changes. This restricts the use of empirical prediction programs in studies where peptide and protein structures are utilized for the NMR chemical shift evaluation such as in NMR refinement processes, structural model verifications, or calculations of NMR nuclear spin relaxation rates.

  10. Fragment-based {sup 13}C nuclear magnetic resonance chemical shift predictions in molecular crystals: An alternative to planewave methods

    Energy Technology Data Exchange (ETDEWEB)

    Hartman, Joshua D.; Beran, Gregory J. O., E-mail: gregory.beran@ucr.edu [Department of Chemistry, University of California, Riverside, California 92521 (United States); Monaco, Stephen; Schatschneider, Bohdan [The Pennsylvania State University, The Eberly Campus, 2201 University Dr, Lemont Furnace, Pennsylvania 15456 (United States)

    2015-09-14

    We assess the quality of fragment-based ab initio isotropic {sup 13}C chemical shift predictions for a collection of 25 molecular crystals with eight different density functionals. We explore the relative performance of cluster, two-body fragment, combined cluster/fragment, and the planewave gauge-including projector augmented wave (GIPAW) models relative to experiment. When electrostatic embedding is employed to capture many-body polarization effects, the simple and computationally inexpensive two-body fragment model predicts both isotropic {sup 13}C chemical shifts and the chemical shielding tensors as well as both cluster models and the GIPAW approach. Unlike the GIPAW approach, hybrid density functionals can be used readily in a fragment model, and all four hybrid functionals tested here (PBE0, B3LYP, B3PW91, and B97-2) predict chemical shifts in noticeably better agreement with experiment than the four generalized gradient approximation (GGA) functionals considered (PBE, OPBE, BLYP, and BP86). A set of recommended linear regression parameters for mapping between calculated chemical shieldings and observed chemical shifts are provided based on these benchmark calculations. Statistical cross-validation procedures are used to demonstrate the robustness of these fits.

  11. Quantum-Chemical Approach to NMR Chemical Shifts in Paramagnetic Solids Applied to LiFePO4 and LiCoPO4.

    Science.gov (United States)

    Mondal, Arobendo; Kaupp, Martin

    2018-04-05

    A novel protocol to compute and analyze NMR chemical shifts for extended paramagnetic solids, accounting comprehensively for Fermi-contact (FC), pseudocontact (PC), and orbital shifts, is reported and applied to the important lithium ion battery cathode materials LiFePO 4 and LiCoPO 4 . Using an EPR-parameter-based ansatz, the approach combines periodic (hybrid) DFT computation of hyperfine and orbital-shielding tensors with an incremental cluster model for g- and zero-field-splitting (ZFS) D-tensors. The cluster model allows the use of advanced multireference wave function methods (such as CASSCF or NEVPT2). Application of this protocol shows that the 7 Li shifts in the high-voltage cathode material LiCoPO 4 are dominated by spin-orbit-induced PC contributions, in contrast with previous assumptions, fundamentally changing interpretations of the shifts in terms of covalency. PC contributions are smaller for the 7 Li shifts of the related LiFePO 4 , where FC and orbital shifts dominate. The 31 P shifts of both materials finally are almost pure FC shifts. Nevertheless, large ZFS contributions can give rise to non-Curie temperature dependences for both 7 Li and 31 P shifts.

  12. Experimental and DFT evaluation of the 1H and 13C NMR chemical shifts for calix[4]arenes

    Science.gov (United States)

    Guzzo, Rodrigo N.; Rezende, Michelle Jakeline Cunha; Kartnaller, Vinicius; Carneiro, José Walkimar de M.; Stoyanov, Stanislav R.; Costa, Leonardo Moreira da

    2018-04-01

    The density functional theory is employed to determine the efficiency of 11 exchange-correlation (XC) functionals to compute the 1H and 13C NMR chemical shifts of p-tert-butylcalix[4]arene (ptcx4, R1 = C(CH3)3) and congeners using the 6-31G(d,p) basis set. The statistical analysis shows that B3LYP, B3PW91 and PBE1PBE are the best XC functionals for the calculation of 1H chemical shifts. Moreover, the best results for the 13C chemical shifts are obtained using the LC-WPBE, M06-2X and wB97X-D functionals. The performance of these XC functionals is tested for three other calix[4]arenes: p-sulfonic acid calix[4]arene (sfxcx4 - R1 = SO3H), p-nitro-calix[4]arene (ncx4, R1 = NO2) and calix[4]arene (cx4 - R1 = H). For 1H chemical shifts B3LYP, B3PW91 and PBE1PBE yield similar results, although B3PW91 shows more consistency in the calculated error for the different structures. For 13C NMR chemical shifts, the XC functional that stood out as best is LC-WPBE. Indeed, the three functionals selected for each of 1H and 13C show good accuracy and can be used in future studies involving the prediction of 1H and 13C chemical shifts for this type of compounds.

  13. Shifts in Plant Chemical Defenses of Chile Pepper (Capsicum annuum L. Due to Domestication in Mesoamerica

    Directory of Open Access Journals (Sweden)

    Jose de Jesus Luna-Ruiz

    2018-04-01

    Full Text Available We propose that comparisons of wild and domesticated Capsicum species can serve as a model system for elucidating how crop domestication influences biotic and abiotic interactions mediated by plant chemical defenses. Perhaps no set of secondary metabolites (SMs used for plant defenses and human health have been better studied in the wild and in milpa agro-habitats than those found in Capsicum species. However, very few scientific studies on SM variation have been conducted in both the domesticated landraces of chile peppers and in their wild relatives in the Neotropics. In particular, capsaicinoids in Capsicum fruits and on their seeds differ in the specificity of their ecological effects from broad-spectrum toxins in other members of the Solanaceae. They do so in a manner that mediates specific ecological interactions with a variety of sympatric Neotropical vertebrates, invertebrates, nurse plants and microbes. Specifically, capsaicin is a secondary metabolite (SM in the placental tissues of the chile fruit that mediates interactions with seed dispersers such as birds, and with seed predators, ranging from fungi to insects and rodents. As with other Solanaceae, a wide range of SMs in Capsicum spp. function to ecologically mediate the effects of a variety of biotic and abiotic stresses on wild chile peppers in certain tropical and subtropical habitats. However, species in the genus Capsicum are the only ones found within any solanaceous genus that utilize capsaicinoids as their primary means of chemical defense. We demonstrate how exploring in tandem the evolutionary ecology and the ethnobotany of human-chile interactions can generate and test novel hypotheses with regard to how the domestication process shifts plant chemical defense strategies in a variety of tropical crops. To do so, we draw upon recent advances regarding the chemical ecology of a number of wild Capsicum species found in the Neotropics. We articulate three hypotheses regarding

  14. Multiparametric fat-water separation method for fast chemical-shift imaging guidance of thermal therapies.

    Science.gov (United States)

    Lin, Jonathan S; Hwang, Ken-Pin; Jackson, Edward F; Hazle, John D; Stafford, R Jason; Taylor, Brian A

    2013-10-01

    A k-means-based classification algorithm is investigated to assess suitability for rapidly separating and classifying fat/water spectral peaks from a fast chemical shift imaging technique for magnetic resonance temperature imaging. Algorithm testing is performed in simulated mathematical phantoms and agar gel phantoms containing mixed fat/water regions. Proton resonance frequencies (PRFs), apparent spin-spin relaxation (T2*) times, and T1-weighted (T1-W) amplitude values were calculated for each voxel using a single-peak autoregressive moving average (ARMA) signal model. These parameters were then used as criteria for k-means sorting, with the results used to determine PRF ranges of each chemical species cluster for further classification. To detect the presence of secondary chemical species, spectral parameters were recalculated when needed using a two-peak ARMA signal model during the subsequent classification steps. Mathematical phantom simulations involved the modulation of signal-to-noise ratios (SNR), maximum PRF shift (MPS) values, analysis window sizes, and frequency expansion factor sizes in order to characterize the algorithm performance across a variety of conditions. In agar, images were collected on a 1.5T clinical MR scanner using acquisition parameters close to simulation, and algorithm performance was assessed by comparing classification results to manually segmented maps of the fat/water regions. Performance was characterized quantitatively using the Dice Similarity Coefficient (DSC), sensitivity, and specificity. The simulated mathematical phantom experiments demonstrated good fat/water separation depending on conditions, specifically high SNR, moderate MPS value, small analysis window size, and low but nonzero frequency expansion factor size. Physical phantom results demonstrated good identification for both water (0.997 ± 0.001, 0.999 ± 0.001, and 0.986 ± 0.001 for DSC, sensitivity, and specificity, respectively) and fat (0.763 ± 0.006, 0

  15. The 40th anniversary of the discovery of NMR-chemical shift and nuclear spin-spin coupling

    International Nuclear Information System (INIS)

    Zhu Zhenghe; Gou Qingquan

    1989-01-01

    After the discovery of NMR Phenomenon in the physics laboratories of E.M.Purcell at Harvard and F.Bloch at Stanford in 1946, W.G.Proctor and F.C.Yu made the successful discovery of NMR-chemical shift and nuclear spin-spin coupling at Stanford in 1950, Which brought NMR spectroscopy from the physics laboratory to the laboratories of many different fields. This is worth memorizing. Retrospecting the past 40 years, it is sure that chemical shift theory will be much more prosperous prospects

  16. Chemical shift-based identification of monosaccharide spin-systems with NMR spectroscopy to complement untargeted glycomics.

    Science.gov (United States)

    Klukowski, Piotr; Schubert, Mario

    2018-06-15

    A better understanding of oligosaccharides and their wide-ranging functions in almost every aspect of biology and medicine promises to uncover hidden layers of biology and will support the development of better therapies. Elucidating the chemical structure of an unknown oligosaccharide is still a challenge. Efficient tools are required for non-targeted glycomics. Chemical shifts are a rich source of information about the topology and configuration of biomolecules, whose potential is however not fully explored for oligosaccharides. We hypothesize that the chemical shifts of each monosaccharide are unique for each saccharide type with a certain linkage pattern, so that correlated data measured by NMR spectroscopy can be used to identify the chemical nature of a carbohydrate. We present here an efficient search algorithm, GlycoNMRSearch, that matches either a subset or the entire set of chemical shifts of an unidentified monosaccharide spin system to all spin systems in an NMR database. The search output is much more precise than earlier search functions and highly similar matches suggest the chemical structure of the spin system within the oligosaccharide. Thus searching for connected chemical shift correlations within all electronically available NMR data of oligosaccharides is a very efficient way of identifying the chemical structure of unknown oligosaccharides. With an improved database in the future, GlycoNMRSearch will be even more efficient deducing chemical structures of oligosaccharides and there is a high chance that it becomes an indispensable technique for glycomics. The search algorithm presented here, together with a graphical user interface, is available at http://glyconmrsearch.santos.pwr.edu.pl. Supplementary data are available at Bioinformatics online.

  17. Orientation-dependent surface core-level shifts and chemical shifts on clean and H 2S-covered GaAs

    Science.gov (United States)

    Ranke, W.; Finster, J.; Kuhr, H. J.

    1987-08-01

    Photoelectron spectra of the As 3d and Ga 3d core levels were studied in situ on a cylindrically shaped GaAs single crystal for the six inequivalent orientations (001), (113), (111), (110), (11¯1) and (11¯3). On the clean surface, prepared by molecular beam epitaxy (MBE), surface core levels are shifted by 0.25 to 0.55 eV towards smaller binding energy (BE) for As 3d and -0.25 to -0.35 eV towards higher BE for Ga, depending on orientation. Additional As causes As 3d contributions shifted between -0.45 and -0.7 eV towards higher BE. The position and intensity of them is influenced by H 2S adsorption. At 150 K, H 2S adsorbs preferentially on As sites. As chemical shifts appear at -0.6 to -0.9 eV towards higher BE. Simultaneously, As accumulation occurs on all orientations with the exception of (110). High temperature adsorption (550 K, 720 K) influences mainly the Ga 3d peaks. Two peaks shifted by about -0.45 and -0.8 eV towards higher Be were found which are attributed to Ga atoms with one or two sulfur ligands, respectively. At 720 K, also As depletion is observed. The compatibility of surface core-level positions and intensities with recent structural models for the (111) and (11¯1) surfaces is discussed.

  18. Finite nuclear size and Lamb shift of p-wave atomic states

    International Nuclear Information System (INIS)

    Milstein, A.I.; Sushkov, O.P.; Terekhov, I.S.

    2003-01-01

    We consider corrections to the Lamb shift of the p-wave atomic states due to the finite nuclear size (FNS). In other words, these are radiative corrections to the atomic isotope shift related to the FNS. It is shown that the structure of the corrections is qualitatively different to that for the s-wave states. The perturbation theory expansion for the relative correction for a p 1/2 state starts with a α ln(1/Zα) term, while for the s 1/2 states it starts with a Zα 2 term. Here, α is the fine-structure constant and Z is the nuclear charge. In the present work, we calculate the α terms for that 2p states, the result for the 2p 1/2 state reads (8α/9π){ln[1/(Zα) 2 ]+0.710}. Even more interesting are the p 3/2 states. In this case the 'correction' is several orders of magnitude larger than the 'leading' FNS shift. However, absolute values of energy shifts related to these corrections are very small

  19. Atmospheric Peroxy Radical Measurements by Chemical Amplification - Cavity Attenuated Phase Shift Spectroscopy

    Science.gov (United States)

    Wood, E. C.; Charest, J. R.

    2013-12-01

    We present a new chemical amplifier for the detection of peroxy radicals using Cavity Attenuated Phase Shift spectroscopy (CAPS) detection of NO2. The amplification scheme is similar to other chemical amplifiers and involves addition of CO (8%) and NO (3 ppm) to air sampled in a PFA tube. The chain length is quantified by amplification of a known concentration of methyl peroxy radicals (CH3O2) and peroxyacetyl radicals (CH3COO2) sampled by the instrument's reactor. The CH3O2 and CH3COO2 radicals are produced by photolysis of acetone at 254 nm and quantified by conversion to NO2 by reaction with excess NO. The chain length (CL) in dry air is over 200 and constant at RO2 concentrations under 500 ppt. The CL decreases by 55% at a relative humidity of 50%. A 0.95 cm (3/8') ID PFA tube, a 0.32 cm (1/8' ID) PFA tube, and a 0.48 cm ID quartz reactor give near-identical chain lengths and RH dependence, demonstrating the small importance of wall reactions (for clean tubing) as radical termination steps. The instrument comprises two independent inlets and CAPS detectors, allowing for simultaneous measurements in ROx mode (= NO2 + O3 + RO2 + HO2) and Ox mode (= NO2 + O3) thereby greatly reducing the effect of variations in background [Ox]. The 1σ precision of the instrument at constant background [Ox] and 0% relative humidity is 0.2 ppt ROx with 100 second averaging and increases to 0.3 ppt at an RH of 50%. The absolute uncertainty of the measurements is estimated as 20% and is affected by the accuracy of the NO2 calibration, the precision of the CAPS when calibrating at low RO2 concentrations, and the uncertainty in the photolysis quantum yield for the CH3CO + CH3 channel of acetone photolysis.

  20. Dynamics-based selective 2D 1H/1H chemical shift correlation spectroscopy under ultrafast MAS conditions

    Science.gov (United States)

    Zhang, Rongchun; Ramamoorthy, Ayyalusamy

    2015-05-01

    Dynamics plays important roles in determining the physical, chemical, and functional properties of a variety of chemical and biological materials. However, a material (such as a polymer) generally has mobile and rigid regions in order to have high strength and toughness at the same time. Therefore, it is difficult to measure the role of mobile phase without being affected by the rigid components. Herein, we propose a highly sensitive solid-state NMR approach that utilizes a dipolar-coupling based filter (composed of 12 equally spaced 90° RF pulses) to selectively measure the correlation of 1H chemical shifts from the mobile regions of a material. It is interesting to find that the rotor-synchronized dipolar filter strength decreases with increasing inter-pulse delay between the 90° pulses, whereas the dipolar filter strength increases with increasing inter-pulse delay under static conditions. In this study, we also demonstrate the unique advantages of proton-detection under ultrafast magic-angle-spinning conditions to enhance the spectral resolution and sensitivity for studies on small molecules as well as multi-phase polymers. Our results further demonstrate the use of finite-pulse radio-frequency driven recoupling pulse sequence to efficiently recouple weak proton-proton dipolar couplings in the dynamic regions of a molecule and to facilitate the fast acquisition of 1H/1H correlation spectrum compared to the traditional 2D NOESY (Nuclear Overhauser effect spectroscopy) experiment. We believe that the proposed approach is beneficial to study mobile components in multi-phase systems, such as block copolymers, polymer blends, nanocomposites, heterogeneous amyloid mixture of oligomers and fibers, and other materials.

  1. Dynamics-based selective 2D 1H/1H chemical shift correlation spectroscopy under ultrafast MAS conditions

    International Nuclear Information System (INIS)

    Zhang, Rongchun; Ramamoorthy, Ayyalusamy

    2015-01-01

    Dynamics plays important roles in determining the physical, chemical, and functional properties of a variety of chemical and biological materials. However, a material (such as a polymer) generally has mobile and rigid regions in order to have high strength and toughness at the same time. Therefore, it is difficult to measure the role of mobile phase without being affected by the rigid components. Herein, we propose a highly sensitive solid-state NMR approach that utilizes a dipolar-coupling based filter (composed of 12 equally spaced 90° RF pulses) to selectively measure the correlation of 1 H chemical shifts from the mobile regions of a material. It is interesting to find that the rotor-synchronized dipolar filter strength decreases with increasing inter-pulse delay between the 90° pulses, whereas the dipolar filter strength increases with increasing inter-pulse delay under static conditions. In this study, we also demonstrate the unique advantages of proton-detection under ultrafast magic-angle-spinning conditions to enhance the spectral resolution and sensitivity for studies on small molecules as well as multi-phase polymers. Our results further demonstrate the use of finite-pulse radio-frequency driven recoupling pulse sequence to efficiently recouple weak proton-proton dipolar couplings in the dynamic regions of a molecule and to facilitate the fast acquisition of 1 H/ 1 H correlation spectrum compared to the traditional 2D NOESY (Nuclear Overhauser effect spectroscopy) experiment. We believe that the proposed approach is beneficial to study mobile components in multi-phase systems, such as block copolymers, polymer blends, nanocomposites, heterogeneous amyloid mixture of oligomers and fibers, and other materials

  2. Differentiation of osteoporotic and neoplastic vertebral fractures by chemical shift {in-phase and out-of phase} MR imaging

    International Nuclear Information System (INIS)

    Ragab, Yasser; Emad, Yasser; Gheita, Tamer; Mansour, Maged; Abou-Zeid, A.; Ferrari, Serge; Rasker, Johannes J.

    2009-01-01

    Objective: The objective of this study was to establish the cut-off value of the signal intensity drop on chemical shift magnetic resonance imaging (MRI) with appropriate sensitivity and specificity to differentiate osteoporotic from neoplastic wedging of the spine. Patients and methods: All patients with wedging of vertebral bodies were included consecutively between February 2006 and January 2007. A chemical shift MRI was performed and signal intensity after (in-phase and out-phase) images were obtained. A DXA was performed in all. Results: A total of 40 patients were included, 20 with osteoporotic wedging (group 1) and 20 neoplastic (group 2). They were 21 males and 19 females. Acute vertebral collapse was observed in 15 patients in group 1 and subacute collapse in another 5 patients, while in group 2, 11 patients showed acute collapse and 9 patients (45%) showed subacute vertebral collapse. On the chemical shift MRI a substantial reduction in signal intensity was found in all lesions in both groups. The proportional changes observed in signal intensity of bone marrow lesions on in-phase compared with out-of-phase images showed significant differences in both groups (P < 0.05). At a cut-off value of 35%, the observed sensitivity of out-of-phase images was 95%, specificity was 100%, positive predictive value was 100% and negative predictive value was 95.2%. Conclusion: A chemical shift MRI is useful in order to differentiate patients with vertebral collapse due to underlying osteoporosis or neoplastic process.

  3. Positive XPS binding energy shift of supported Cu{sub N}-clusters governed by initial state effects

    Energy Technology Data Exchange (ETDEWEB)

    Peters, S.; Peredkov, S. [Technische Universität Berlin, IOAP, Strasse des 17. Juni 135, 10623 Berlin (Germany); Al-Hada, M. [Department of Physics, College of Education and Linguistics, University of Amran (Yemen); Neeb, M., E-mail: matthias.neeb@helmholtz-berlin.de [Helmholtz-Zentrum Berlin, Wilhelm-Conrad-Röntgen-Campus Adlershof, Elektronenspeicherring BESSY II, Albert-Einstein-Straße 15, 12489 Berlin (Germany); Eberhardt, W. [Technische Universität Berlin, IOAP, Strasse des 17. Juni 135, 10623 Berlin (Germany); DESY, Center for Free Electron Laser Science (CFEL), Notkestr. 85, 22607 Hamburg (Germany)

    2014-01-01

    Highlights: • Size dependent initial and final state effects of mass-selected deposited clusters. • Initial state effect dominates positive XPS shift in supported Cu-clusters. • Size dependent Coulomb correlation shift in the Auger final state of Cu cluster. • Size-dependent Auger parameter analysis. • Positive XPS shift differs from negative surface core level shift in crystalline copper. - Abstract: An initial state effect is established as origin for the positive 2p core electron binding energy shift found for Cu{sub N}-clusters supported by a thin silica layer of a p-doped Si(1 0 0) wafer. Using the concept of the Auger parameter and taking into account the usually neglected Coulomb correlation shift in the Auger final state (M{sub 4,5}M{sub 4,5}) it is shown that the initial state shift is comparable to the measured XPS shift while the final state relaxation shift contributes only marginally to the binding energy shift. The cluster results differ from the negative surface core-level shift of crystalline copper which has been explained in terms of a final state relaxation effect.

  4. Spectral fitting for signal assignment and structural analysis of uniformly {sup 13}C-labeled solid proteins by simulated annealing based on chemical shifts and spin dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Matsuki, Yoh; Akutsu, Hideo; Fujiwara, Toshimichi [Osaka University, Institute for Protein Research (Japan)], E-mail: tfjwr@protein.osaka-u.ac.jp

    2007-08-15

    We describe an approach for the signal assignment and structural analysis with a suite of two-dimensional {sup 13}C-{sup 13}C magic-angle-spinning solid-state NMR spectra of uniformly {sup 13}C-labeled peptides and proteins. We directly fit the calculated spectra to experimental ones by simulated annealing in restrained molecular dynamics program CNS as a function of atomic coordinates. The spectra are calculated from the conformation dependent chemical shift obtained with SHIFTX and the cross-peak intensities computed for recoupled dipolar interactions. This method was applied to a membrane-bound 14-residue peptide, mastoparan-X. The obtained C', C{sup {alpha}} and C{sup {beta}} chemical shifts agreed with those reported previously at the precisions of 0.2, 0.7 and 0.4 ppm, respectively. This spectral fitting program also provides backbone dihedral angles with a precision of about 50 deg. from the spectra even with resonance overlaps. The restraints on the angles were improved by applying protein database program TALOS to the obtained chemical shifts. The peptide structure provided by these restraints was consistent with the reported structure at the backbone RMSD of about 1 A.

  5. How to distinguish elastically scattered light from Stokes shifted light for solid-state lighting?

    NARCIS (Netherlands)

    Meretska, Maryna; Lagendijk, Aart; Thyrrestrup Nielsen, Henri; Mosk, Allard; IJzerman, W.L.; Vos, Willem L.

    2016-01-01

    We have studied the transport of light through phosphor diffuser plates that are used in commercial solid-state lighting modules (Fortimo). These polymer plates contain YAG:Ce+3phosphor particles that both elastically scatter and Stokes shift light in the visible wavelength range (400–700 nm). We

  6. 1H MR chemical shift imaging detection of phenylalanine in patients suffering from phenylketonuria (PKU)

    International Nuclear Information System (INIS)

    Sijens, Paul E.; Oudkerk, Matthijs; Reijngoud, Dirk-Jan; Spronsen, Francjan J. van; Leenders, Klaas L.; Valk, Harold W. de

    2004-01-01

    Short echo time single voxel methods were used in previous MR spectroscopy studies of phenylalanine (Phe) levels in phenylketonuria (PKU) patients. In this study, apparent T 2 relaxation time of the 7.3-ppm Phe multiplet signal in the brain of PKU patients was assessed in order to establish which echo time would be optimal. 1 H chemical shift imaging (CSI) examinations of a transverse plain above the ventricles of the brain were performed in 10 PKU patients and 11 persons not suffering from PKU at 1.5 T, using four echo times (TE 20, 40, 135 and 270 ms). Phe was detectable only when the signals from all CSI voxels were summarized. In patients suffering from PKU the T 2 relaxation times of choline, creatine and N-acetyl aspartate (NAA) were similar to those previously reported for healthy volunteers (between 200 and 325 ms). The T 2 of Phe in brain tissue was 215±120 ms (standard deviation). In the PKU patients the brain tissue Phe concentrations were 141±69 μM as opposed to 58±23 μM in the persons not suffering from PKU. In the detection of Phe, MR spectroscopy performed at TE 135 or 270 ms is not inferior to that performed at TE 20 or 40 ms (all previous studies). Best results were obtained at TE=135 ms, relating to the fact that at that particular TE, the visibility of a compound with a T 2 of 215 ms still is good, while interfering signals from short-TE compounds are negligible. (orig.)

  7. {sup 1}H MR chemical shift imaging detection of phenylalanine in patients suffering from phenylketonuria (PKU)

    Energy Technology Data Exchange (ETDEWEB)

    Sijens, Paul E.; Oudkerk, Matthijs [University Hospital Groningen, Department of Radiology, Hanzeplein 1, P.O. Box 30001, Groningen (Netherlands); Reijngoud, Dirk-Jan; Spronsen, Francjan J. van [University Hospital Groningen, Department of Pediatrics, Groningen (Netherlands); Leenders, Klaas L. [University Hospital Groningen, Department of Neurology, Groningen (Netherlands); Valk, Harold W. de [University Medical Centre of Utrecht, Department of Internal Medicine, Utrecht (Netherlands)

    2004-10-01

    Short echo time single voxel methods were used in previous MR spectroscopy studies of phenylalanine (Phe) levels in phenylketonuria (PKU) patients. In this study, apparent T{sub 2} relaxation time of the 7.3-ppm Phe multiplet signal in the brain of PKU patients was assessed in order to establish which echo time would be optimal. {sup 1}H chemical shift imaging (CSI) examinations of a transverse plain above the ventricles of the brain were performed in 10 PKU patients and 11 persons not suffering from PKU at 1.5 T, using four echo times (TE 20, 40, 135 and 270 ms). Phe was detectable only when the signals from all CSI voxels were summarized. In patients suffering from PKU the T{sub 2} relaxation times of choline, creatine and N-acetyl aspartate (NAA) were similar to those previously reported for healthy volunteers (between 200 and 325 ms). The T{sub 2} of Phe in brain tissue was 215{+-}120 ms (standard deviation). In the PKU patients the brain tissue Phe concentrations were 141{+-}69 {mu}M as opposed to 58{+-}23 {mu}M in the persons not suffering from PKU. In the detection of Phe, MR spectroscopy performed at TE 135 or 270 ms is not inferior to that performed at TE 20 or 40 ms (all previous studies). Best results were obtained at TE=135 ms, relating to the fact that at that particular TE, the visibility of a compound with a T{sub 2} of 215 ms still is good, while interfering signals from short-TE compounds are negligible. (orig.)

  8. Quantification of fat using chemical shift imaging and 1H-MR spectroscopy in phantom model

    International Nuclear Information System (INIS)

    Peng Xingui; Ju Shenghong; Fang Fang; Teng Gaojun

    2010-01-01

    Objective: To evaluate the accuracy of chemical shift imaging (CSI) and MR spectroscopy (MRS) for fat quantification in phantom model. Methods: Eleven phantoms were made according to the volume percentage of fat ranging from 0 to 100% with an interval of 10%. The fat concentration in the phantoms were measured respectively by CSI and MRS and compared using one-sample t test. The correlation between the two methods was also analyzed. The concentration of saturated fatty acids (FS), unsaturated fatty acids (FU) and the poly, unsaturation degree (PUD) were calculated by using MRS. Results: The fat concentration was (48.0±1.0)%, (57.0±0.5)%, (67.3±0.6)%, (77.3± 0.6)%, (83.3±0.6)% and (91.0±1.0)% respectively with fat volume of 50% to 100% by CSI. The fat concentration was (8.3±0.6)%, (16.3±0.7)%, (27.7±0.6)%, (36.0±1.0)%, (43.5± 0.6)% and (56.5±1.0)% respectively with fat volume of 10% to 60% by MRS, the fat concentration were underestimated by CSI and MRS (P<0.05), and had high linear correlation with the real concentration in phantoms (CSI: r=0.998, MRS: r=0.996, P<0.01). There was also a linear correlation between two methods (r=0.992, P<0.01) but no statistically significant difference (paired- samples t test, t=-0.125, P=0.903). By using MRS, the relative ratio of FS and FU in fat were 0. 15 and 0.85, the PUD was 0.0325, respectively, and highly consistent with these in phantoms. Conclusion: Both CSI and MRS are efficient and accurate methods in fat quantification at 7.0 T MR. (authors)

  9. Changes of brain metabolite concentrations during maturation in different brain regions measured by chemical shift imaging.

    Science.gov (United States)

    Bültmann, Eva; Nägele, Thomas; Lanfermann, Heinrich; Klose, Uwe

    2017-01-01

    We examined the effect of maturation on the regional distribution of brain metabolite concentrations using multivoxel chemical shift imaging. From our pool of pediatric MRI examinations, we retrospectively selected patients showing a normal cerebral MRI scan or no pathologic signal abnormalities at the level of the two-dimensional 1H MRS-CSI sequence and an age-appropriate global neurological development, except for focal neurological deficits. Seventy-one patients (4.5 months-20 years) were identified. Using LC Model, spectra were evaluated from voxels in the white matter, caudate head, and corpus callosum. The concentration of total N-acetylaspartate increased in all regions during infancy and childhood except in the right caudate head where it remained constant. The concentration of total creatine decreased in the caudate nucleus and splenium and minimally in the frontal white matter and genu. It remained largely constant in the parietal white matter. The concentration of choline-containing compounds had the tendency to decrease in all regions except in the parietal white matter where it remained constant. The concentration of myoinositol decreased slightly in the splenium and right frontal white matter, remained constant on the left side and in the caudate nucleus, and rose slightly in the parietal white matter and genu. CSI determined metabolite concentrations in multiple cerebral regions during routine MRI. The obtained data will be helpful in future pediatric CSI measurements deciding whether the ratios of the main metabolites are within the range of normal values or have to be considered as probably pathologic.

  10. Changes of brain metabolite concentrations during maturation in different brain regions measured by chemical shift imaging

    International Nuclear Information System (INIS)

    Bueltmann, Eva; Lanfermann, Heinrich; Naegele, Thomas; Klose, Uwe

    2017-01-01

    We examined the effect of maturation on the regional distribution of brain metabolite concentrations using multivoxel chemical shift imaging. From our pool of pediatric MRI examinations, we retrospectively selected patients showing a normal cerebral MRI scan or no pathologic signal abnormalities at the level of the two-dimensional 1H MRS-CSI sequence and an age-appropriate global neurological development, except for focal neurological deficits. Seventy-one patients (4.5 months-20 years) were identified. Using LC Model, spectra were evaluated from voxels in the white matter, caudate head, and corpus callosum. The concentration of total N-acetylaspartate increased in all regions during infancy and childhood except in the right caudate head where it remained constant. The concentration of total creatine decreased in the caudate nucleus and splenium and minimally in the frontal white matter and genu. It remained largely constant in the parietal white matter. The concentration of choline-containing compounds had the tendency to decrease in all regions except in the parietal white matter where it remained constant. The concentration of myoinositol decreased slightly in the splenium and right frontal white matter, remained constant on the left side and in the caudate nucleus, and rose slightly in the parietal white matter and genu. CSI determined metabolite concentrations in multiple cerebral regions during routine MRI. The obtained data will be helpful in future pediatric CSI measurements deciding whether the ratios of the main metabolites are within the range of normal values or have to be considered as probably pathologic. (orig.)

  11. Quantification of liver fat with respiratory-gated quantitative chemical shift encoded MRI.

    Science.gov (United States)

    Motosugi, Utaroh; Hernando, Diego; Bannas, Peter; Holmes, James H; Wang, Kang; Shimakawa, Ann; Iwadate, Yuji; Taviani, Valentina; Rehm, Jennifer L; Reeder, Scott B

    2015-11-01

    To evaluate free-breathing chemical shift-encoded (CSE) magnetic resonance imaging (MRI) for quantification of hepatic proton density fat-fraction (PDFF). A secondary purpose was to evaluate hepatic R2* values measured using free-breathing quantitative CSE-MRI. Fifty patients (mean age, 56 years) were prospectively recruited and underwent the following four acquisitions to measure PDFF and R2*; 1) conventional breath-hold CSE-MRI (BH-CSE); 2) respiratory-gated CSE-MRI using respiratory bellows (BL-CSE); 3) respiratory-gated CSE-MRI using navigator echoes (NV-CSE); and 4) single voxel MR spectroscopy (MRS) as the reference standard for PDFF. Image quality was evaluated by two radiologists. MRI-PDFF measured from the three CSE-MRI methods were compared with MRS-PDFF using linear regression. The PDFF and R2* values were compared using two one-sided t-test to evaluate statistical equivalence. There was no significant difference in the image quality scores among the three CSE-MRI methods for either PDFF (P = 1.000) or R2* maps (P = 0.359-1.000). Correlation coefficients (95% confidence interval [CI]) for the PDFF comparisons were 0.98 (0.96-0.99) for BH-, 0.99 (0.97-0.99) for BL-, and 0.99 (0.98-0.99) for NV-CSE. The statistical equivalence test revealed that the mean difference in PDFF and R2* between any two of the three CSE-MRI methods was less than ±1 percentage point (pp) and ±5 s(-1) , respectively (P liver PDFF and R2* and are as valid as the standard breath-hold technique. © 2015 Wiley Periodicals, Inc.

  12. Changes of brain metabolite concentrations during maturation in different brain regions measured by chemical shift imaging

    Energy Technology Data Exchange (ETDEWEB)

    Bueltmann, Eva; Lanfermann, Heinrich [Hannover Medical School, Institute of Diagnostic and Interventional Neuroradiology, Hannover (Germany); Naegele, Thomas [University of Tuebingen, Department of Diagnostic and Interventional Neuroradiology, Radiological University Hospital, Tuebingen (Germany); Klose, Uwe [University of Tuebingen, Section of Experimental MR of the CNS, Department of Neuroradiology, Radiological University Hospital, Tuebingen (Germany)

    2017-01-15

    We examined the effect of maturation on the regional distribution of brain metabolite concentrations using multivoxel chemical shift imaging. From our pool of pediatric MRI examinations, we retrospectively selected patients showing a normal cerebral MRI scan or no pathologic signal abnormalities at the level of the two-dimensional 1H MRS-CSI sequence and an age-appropriate global neurological development, except for focal neurological deficits. Seventy-one patients (4.5 months-20 years) were identified. Using LC Model, spectra were evaluated from voxels in the white matter, caudate head, and corpus callosum. The concentration of total N-acetylaspartate increased in all regions during infancy and childhood except in the right caudate head where it remained constant. The concentration of total creatine decreased in the caudate nucleus and splenium and minimally in the frontal white matter and genu. It remained largely constant in the parietal white matter. The concentration of choline-containing compounds had the tendency to decrease in all regions except in the parietal white matter where it remained constant. The concentration of myoinositol decreased slightly in the splenium and right frontal white matter, remained constant on the left side and in the caudate nucleus, and rose slightly in the parietal white matter and genu. CSI determined metabolite concentrations in multiple cerebral regions during routine MRI. The obtained data will be helpful in future pediatric CSI measurements deciding whether the ratios of the main metabolites are within the range of normal values or have to be considered as probably pathologic. (orig.)

  13. Proton magnetic resonance chemical shift imaging (1H CSI)-directed stereotactic biopsy

    International Nuclear Information System (INIS)

    Son, B.-C.; Kim, B.-C.; Kang, J.-K.; Choi, B.-G.; Kim, E.-N.; Baik, H.-M.; Choe, B.-Y.; Naruse, S.

    2001-01-01

    Introduction. To add metabolic information during stereotactic biopsy target selection, the authors adopted proton chemical shift imaging ( 1 H CSI)-directed stereotactic biopsy. Currently, proton single voxel spectroscopy (SVS) technique has been reported in stereotactic biopsy. We performed 1 H CSI in combination with a stereotactic headframe and selected targets according to local metabolic information, and evaluated the pathological results. Patients and Method. The 1 H CSI-directed stereotactic biopsy was performed in four patients. 1 H CSI and conventional Gd-enhancement stereotactic MRI were performed simultaneously after the fitting of a stereotactic frame. After reconstructing the metabolic maps of N-acetylaspartate (NAA)/phosphocreatine (Cr), phosphocholine (Cho)/Cr, and Lactate/Cr ratios, focal areas of increased Cho/Cr ratio and Lac/Cr ratios were selected as target sites in the stereotactic MR images. Result. 1 H CSI is possible with the stereotactic headframe in place. No difficulty was experienced performing 1 H CSI or making a diagnosis. Pathological samples taken from areas of increased Cho/Cr ratios and decreased NAA/Cr ratios provided information upon increased cellularity, mitoses and cellular atypism, and facilitated diagnosis. Pathological samples taken from areas of increased Lac/ Cr ratio snowed predominant feature of necrosis. Conclusion. 1 H CSI was feasible with the stereotactic headframe in place. The final pathological results obtained were concordant with the local metabolic information from 1 H CSI. We believe that 1 H CSI-directed stereotactic biopsy has the potential to significantly improve the accuracy of stereotactic biopsy targeting. (author)

  14. 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.

  15. Benchmark fragment-based 1H, 13C, 15N and 17O chemical shift predictions in molecular crystals†

    Science.gov (United States)

    Hartman, Joshua D.; Kudla, Ryan A.; Day, Graeme M.; Mueller, Leonard J.; Beran, Gregory J. O.

    2016-01-01

    The performance of fragment-based ab initio 1H, 13C, 15N and 17O chemical shift predictions is assessed against experimental NMR chemical shift data in four benchmark sets of molecular crystals. Employing a variety of commonly used density functionals (PBE0, B3LYP, TPSSh, OPBE, PBE, TPSS), we explore the relative performance of cluster, two-body fragment, and combined cluster/fragment models. The hybrid density functionals (PBE0, B3LYP and TPSSh) generally out-perform their generalized gradient approximation (GGA)-based counterparts. 1H, 13C, 15N, and 17O isotropic chemical shifts can be predicted with root-mean-square errors of 0.3, 1.5, 4.2, and 9.8 ppm, respectively, using a computationally inexpensive electrostatically embedded two-body PBE0 fragment model. Oxygen chemical shieldings prove particularly sensitive to local many-body effects, and using a combined cluster/fragment model instead of the simple two-body fragment model decreases the root-mean-square errors to 7.6 ppm. These fragment-based model errors compare favorably with GIPAW PBE ones of 0.4, 2.2, 5.4, and 7.2 ppm for the same 1H, 13C, 15N, and 17O test sets. Using these benchmark calculations, a set of recommended linear regression parameters for mapping between calculated chemical shieldings and observed chemical shifts are provided and their robustness assessed using statistical cross-validation. We demonstrate the utility of these approaches and the reported scaling parameters on applications to 9-tertbutyl anthracene, several histidine co-crystals, benzoic acid and the C-nitrosoarene SnCl2(CH3)2(NODMA)2. PMID:27431490

  16. Benchmark fragment-based (1)H, (13)C, (15)N and (17)O chemical shift predictions in molecular crystals.

    Science.gov (United States)

    Hartman, Joshua D; Kudla, Ryan A; Day, Graeme M; Mueller, Leonard J; Beran, Gregory J O

    2016-08-21

    The performance of fragment-based ab initio(1)H, (13)C, (15)N and (17)O chemical shift predictions is assessed against experimental NMR chemical shift data in four benchmark sets of molecular crystals. Employing a variety of commonly used density functionals (PBE0, B3LYP, TPSSh, OPBE, PBE, TPSS), we explore the relative performance of cluster, two-body fragment, and combined cluster/fragment models. The hybrid density functionals (PBE0, B3LYP and TPSSh) generally out-perform their generalized gradient approximation (GGA)-based counterparts. (1)H, (13)C, (15)N, and (17)O isotropic chemical shifts can be predicted with root-mean-square errors of 0.3, 1.5, 4.2, and 9.8 ppm, respectively, using a computationally inexpensive electrostatically embedded two-body PBE0 fragment model. Oxygen chemical shieldings prove particularly sensitive to local many-body effects, and using a combined cluster/fragment model instead of the simple two-body fragment model decreases the root-mean-square errors to 7.6 ppm. These fragment-based model errors compare favorably with GIPAW PBE ones of 0.4, 2.2, 5.4, and 7.2 ppm for the same (1)H, (13)C, (15)N, and (17)O test sets. Using these benchmark calculations, a set of recommended linear regression parameters for mapping between calculated chemical shieldings and observed chemical shifts are provided and their robustness assessed using statistical cross-validation. We demonstrate the utility of these approaches and the reported scaling parameters on applications to 9-tert-butyl anthracene, several histidine co-crystals, benzoic acid and the C-nitrosoarene SnCl2(CH3)2(NODMA)2.

  17. Relativistic Spin-Orbit Heavy Atom on the Light Atom NMR Chemical Shifts: General Trends Across the Periodic Table Explained.

    Science.gov (United States)

    Vícha, Jan; Komorovsky, Stanislav; Repisky, Michal; Marek, Radek; Straka, Michal

    2018-05-10

    The importance of relativistic effects on the NMR parameters in heavy-atom (HA) compounds, particularly the SO-HALA (Spin-Orbit Heavy Atom on the Light Atom) effect on NMR chemical shifts, has been known for about 40 years. Yet, a general correlation between the electronic structure and SO-HALA effect has been missing. By analyzing 1 H NMR chemical shifts of the sixth-period hydrides (Cs-At), we discovered general electronic-structure principles and mechanisms that dictate the size and sign of the SO-HALA NMR chemical shifts. In brief, partially occupied HA valence shells induce relativistic shielding at the light atom (LA) nuclei, while empty HA valence shells induce relativistic deshielding. In particular, the LA nucleus is relativistically shielded in 5d 2 -5d 8 and 6p 4 HA hydrides and deshielded in 4f 0 , 5d 0 , 6s 0 , and 6p 0 HA hydrides. This general and intuitive concept explains periodic trends in the 1 H NMR chemical shifts along the sixth-period hydrides (Cs-At) studied in this work. We present substantial evidence that the introduced principles have a general validity across the periodic table and can be extended to nonhydride LAs. The decades-old question of why compounds with occupied frontier π molecular orbitals (MOs) cause SO-HALA shielding at the LA nuclei, while the frontier σ MOs cause deshielding is answered. We further derive connection between the SO-HALA NMR chemical shifts and Spin-Orbit-induced Electron Deformation Density (SO-EDD), a property that can be obtained easily from differential electron densities and can be represented graphically. SO-EDD provides an intuitive understanding of the SO-HALA effect in terms of the depletion/concentration of the electron density at LA nuclei caused by spin-orbit coupling due to HA in the presence of a magnetic field. Using an analogy between the SO-EDD concept and arguments from classic NMR theory, the complex question of the SO-HALA NMR chemical shifts becomes easily understandable for a wide

  18. Pressure dependence of side chain 13C chemical shifts in model peptides Ac-Gly-Gly-Xxx-Ala-NH2.

    Science.gov (United States)

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

    2017-10-01

    For evaluating the pressure responses of folded as well as intrinsically unfolded proteins detectable by NMR spectroscopy the availability of data from well-defined model systems is indispensable. In this work we report the pressure dependence of 13 C chemical shifts of the side chain atoms in the protected tetrapeptides Ac-Gly-Gly-Xxx-Ala-NH 2 (Xxx, one of the 20 canonical amino acids). Contrary to expectation the chemical shifts of a number of nuclei have a nonlinear dependence on pressure in the range from 0.1 to 200 MPa. The size of the polynomial pressure coefficients B 1 and B 2 is dependent on the type of atom and amino acid studied. For H N , N and C α the first order pressure coefficient B 1 is also correlated to the chemical shift at atmospheric pressure. The first and second order pressure coefficients of a given type of carbon atom 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 also are weakly correlated. The downfield shifts of the methyl resonances suggest that gauche conformers of the side chains are not preferred with pressure. The valine and leucine methyl groups in the model peptides were assigned using stereospecifically 13 C enriched amino acids with the pro-R carbons downfield shifted relative to the pro-S carbons.

  19. United States Chemical Policy: Response Considerations

    Science.gov (United States)

    1991-06-07

    nTcn aapplicable. entew induiy r~ epr dates (g.10~Saeet o ehia Jun 87.- 30 Jun 88). rot gDocuments. DOE See authorities Block 4. Title and $ubtitle...introduction of mustard gas and gas shells to the battlefield. Between World War I and the 1980’s, infrequent use of chemical warfare occurred. In 1935 and...The period just prior to World War II included at least two known cases of chemical warfare use. In 1935 -36, Italy used mustard gas against Abyssinia

  20. Vanadium NMR Chemical Shifts of (Imido)vanadium(V) Dichloride Complexes with Imidazolin-2-iminato and Imidazolidin-2-iminato Ligands: Cooperation with Quantum-Chemical Calculations and Multiple Linear Regression Analyses.

    Science.gov (United States)

    Yi, Jun; Yang, Wenhong; Sun, Wen-Hua; Nomura, Kotohiro; Hada, Masahiko

    2017-11-30

    The NMR chemical shifts of vanadium ( 51 V) in (imido)vanadium(V) dichloride complexes with imidazolin-2-iminato and imidazolidin-2-iminato ligands were calculated by the density functional theory (DFT) method with GIAO. The calculated 51 V NMR chemical shifts were analyzed by the multiple linear regression (MLR) analysis (MLRA) method with a series of calculated molecular properties. Some of calculated NMR chemical shifts were incorrect using the optimized molecular geometries of the X-ray structures. After the global minimum geometries of all of the molecules were determined, the trend of the observed chemical shifts was well reproduced by the present DFT method. The MLRA method was performed to investigate the correlation between the 51 V NMR chemical shift and the natural charge, band energy gap, and Wiberg bond index of the V═N bond. The 51 V NMR chemical shifts obtained with the present MLR model were well reproduced with a correlation coefficient of 0.97.

  1. Chemical composition and trophic state of shallow saline steppe lakes in central Asia (North Kazakhstan).

    Science.gov (United States)

    Boros, Emil; Jurecska, Laura; Tatár, Enikő; Vörös, Lajos; Kolpakova, Marina

    2017-10-09

    The purpose of this study was to identify the prevailing chemical composition and trophic state of the shallow saline steppe lakes of North Kazakhstan along a wide size range (SO 4 and Na-Cl (n = 16; 64%); the Ca, Mg, HCO 3 , and SO 4 ions precipitate with increasing salinity (2-322 g L -1 ); and ion composition shifts from Na>Mg-Cl>SO 4 to Na-Cl. The most of the chemical variables positively, but chlorophyll a negatively, correlated with total dissolved solids, and the total phosphorus had no significant correlation with any variables. The trophic state of these lakes in most cases exceeded the hypertrophic level. The increase in salinity causes change in chemical composition and effects on the phytoplankton development independently from the size of water surface, and the human disturbances had negligible effect on the trophic state of shallow saline lakes in this region of Kazakhstan.

  2. Testing for Level Shifts in Fractionally Integrated Processes: a State Space Approach

    DEFF Research Database (Denmark)

    Monache, Davide Delle; Grassi, Stefano; Santucci de Magistris, Paolo

    Short memory models contaminated by level shifts have similar long-memory features as fractionally integrated processes. This makes hard to verify whether the true data generating process is a pure fractionally integrated process when employing standard estimation methods based on the autocorrela......Short memory models contaminated by level shifts have similar long-memory features as fractionally integrated processes. This makes hard to verify whether the true data generating process is a pure fractionally integrated process when employing standard estimation methods based...... on the autocorrelation function or the periodogram. In this paper, we propose a robust testing procedure, based on an encompassing parametric specification that allows to disentangle the level shifts from the fractionally integrated component. The estimation is carried out on the basis of a state-space methodology...... and it leads to a robust estimate of the fractional integration parameter also in presence of level shifts. Once the memory parameter is correctly estimated, we use the KPSS test for presence of level shift. The Monte Carlo simulations show how this approach produces unbiased estimates of the memory parameter...

  3. Calculation of the NMR chemical shift for a 4d1 system in a strong crystal field environment of trigonal symmetry with a threefold axis of quantization

    International Nuclear Information System (INIS)

    Ahn, Sang Woon; Oh, Se Woung; Ro, Seung Woo

    1986-01-01

    The NMR chemical shift arising from 4d electron angular momentum and 4d electron angular momentum and 4d electron spin dipolar-nuclear spin angular momentum interactions for a 4d 1 system in a strong crystal field environment of trigonal symmetry, where the threefold axis is chosen to be the axis of quantization axis, has been examined. A general expression using the nonmultipole expansion method (exact method) is derived for the NMR chemical shift. From this expression all the multipolar terms are determined. we observe that along the (100), (010), (110), and (111) axes the NMR chemical shifts are positive while along the (001) axis, it is negative. We observe that the dipolar term (1/R 3 ) is the dominant contribution to the NMR chemical shift except for along the (111) axis. A comparison of the multipolar terms with the exact values shows also that the multipolar results are exactly in agreement with the exact values around R≥0.2 nm. The temperature dependence analysis on the NMR chemical shifts may imply that along the (111) axis the contribution to the NMR chemical shift is dominantly pseudo contact interaction. Separation of the contributions of the Fermi and the pseudo contact interactions would correctly imply that the dipolar interaction is the dominant contribution to the NMR chemical shifts along the (100), (010), (001), and (110) axes, but along the (111) axis the Fermi contact interaction is incorrectly the dominant contribution to the NMR chemical shift. (Author)

  4. Chemical shift of U L3 edges in different uranium compounds ...

    Indian Academy of Sciences (India)

    Administrator

    by X-ray absorption spectroscopy with synchrotron radiation. D JOSEPH†, C NAYAK††, ... Bhabha Atomic Research Centre, Mumbai 400 085, India. MS received 28 .... As has been discussed in the 'Introduction' section, the above edge shift ...

  5. Comparison of the solution and crystal structures of staphylococcal nuclease with 13C and 15N chemical shifts used as structural fingerprints

    International Nuclear Information System (INIS)

    Cole, H.B.R.; Sparks, S.W.; Torchia, D.A.

    1988-01-01

    The authors report high-resolution 13 C and 15 N NMR spectra of crystalline staphylococcal nuclease (Nase) complexed to thymidine 3',5'-diphosphate and Ca 2+ . High sensitivity and resolution are obtained by applying solid-state NMR techniques-high power proton decoupling and cross-polarization magic angle sample spinning (CPMASS)-to protein samples that have been efficiently synthesized and labeled by an overproducing strain of Escherichia coli. A comparison of CPMASS and solution spectra of Nase labeled with either [methyl- 13 C]methionine or [ 15 ]valine shows that the chemical shifts in the crystalline and solution states are virtually identical. This result is strong evidence that the protein conformations in the solution and crystalline states are nearly the same. Because of the close correspondence of the crystal and solution chemical shifts, sequential assignments obtained in solution apply to the crystal spectra. It should therefore be possible to study the molecular structure and dynamics of many sequentially assigned atomic sites in Nase crystals. Similar experiments are applicable to the growing number of proteins that can be obtained from efficient expression systems

  6. Correlates to sleepiness on night shift among male workers engaged in three-shift work in a chemical plant: its association with sleep practice and job stress.

    Science.gov (United States)

    Kageyama, Takayuki; Kobayashi, Toshio; Abe-Gotoh, Ayano

    2011-01-01

    The purpose of this study was to examine the correlation of sleepiness during night shift (SNS) in male shiftworkers with nonpharmacological self-management (nPSM) practices to facilitate good day sleep, and also with job stress. Sleepiness on the job and possible correlates to SNS among 157 male shiftworkers in a rotating three-shift schedule at a chemical plant were cross-sectionally investigated using a self-administered questionnaire. Multivariate analyses revealed that SNS was positively associated with drinking alcoholic beverages before day sleep, but inversely associated with subjective health status, being of the evening type, abstaining from caffeine before day sleep, having a bath before day sleep, job control, reward from work, feeling suited to the job, and support from colleagues. SNS correlated with certain nPSM practices and also with possible modifiers of job stress. These findings provide clues to developing countermeasures against SNS among shiftworkers. The effects of nPSM practices and job stress management on their day sleep and SNS should be examined in detail.

  7. Development of 19F-NMR chemical shift detection of DNA B-Z equilibrium using 19F-NMR.

    Science.gov (United States)

    Nakamura, S; Yang, H; Hirata, C; Kersaudy, F; Fujimoto, K

    2017-06-28

    Various DNA conformational changes are in correlation with biological events. In particular, DNA B-Z equilibrium showed a high correlation with translation and transcription. In this study, we developed a DNA probe containing 5-trifluoromethylcytidine or 5-trifluoromethylthymidine to detect DNA B-Z equilibrium using 19 F-NMR. Its probe enabled the quantitative detection of B-, Z-, and ss-DNA based on 19 F-NMR chemical shift change.

  8. 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.

  9. Cooperative Lamb shift and the cooperative decay rate for an initially detuned phased state

    International Nuclear Information System (INIS)

    Friedberg, Richard; Manassah, Jamal T.

    2010-01-01

    The cooperative Lamb shift (CLS) is hard to measure because in samples much larger than a resonant wavelength it is much smaller, for an initially prepared resonantly phased state, than the cooperative decay rate (CDR). We show, however, that if the phasing of the initial state is detuned so that the spatial wave vector is k 1 congruent with k 0 ±O((1/R)) (where k 0 =ω 0 /c is the resonant frequency), the CLS grows to 'giant' magnitudes making it comparable to the CDR. Moreover, for certain controlled values of detuning, the initial CDR becomes small so that the dynamical Lamb shift (DLS) can be measured over a considerable period of time.

  10. The effects of state anxiety and thermal comfort on sleep quality and eye fatigue in shift work nurses

    OpenAIRE

    Dehghan, Habibollah; Azmoon, Hiva; Souri, Shiva; Akbari, Jafar

    2014-01-01

    Psychological problems as state anxiety (SA) in the work environment has negative effect on the employees life especially shift work nurses, i.e. negative effect on mental and physical health (sleep quality, eye fatigue and comfort thermal). The purpose of this study was determination of effects of state anxiety and thermal comfort on sleep quality and eye fatigue in shift work nurses. Methods: This cross-sectional research conducted on 82 shift-work personnel of 18 nursing workstations of Is...

  11. Role of excited state solvent fluctuations on time-dependent fluorescence Stokes shift

    Energy Technology Data Exchange (ETDEWEB)

    Li, Tanping, E-mail: tanping@lsu.edu, E-mail: revatik@lsu.edu; Kumar, Revati, E-mail: tanping@lsu.edu, E-mail: revatik@lsu.edu [Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803 (United States)

    2015-11-07

    We explore the connection between the solvation dynamics of a chromophore upon photon excitation and equilibrium fluctuations of the solvent. Using molecular dynamics simulations, fluorescence Stokes shift for the tryptophan in Staphylococcus nuclease was examined using both nonequilibrium calculations and linear response theory. When the perturbed and unperturbed surfaces exhibit different solvent equilibrium fluctuations, the linear response approach on the former surface shows agreement with the nonequilibrium process. This agreement is excellent when the perturbed surface exhibits Gaussian statistics and qualitative in the case of an isomerization induced non-Gaussian statistics. However, the linear response theory on the unperturbed surface breaks down even in the presence of Gaussian fluctuations. Experiments also provide evidence of the connection between the excited state solvent fluctuations and the total fluorescence shift. These observations indicate that the equilibrium statistics on the excited state surface characterize the relaxation dynamics of the fluorescence Stokes shift. Our studies specifically analyze the Gaussian fluctuations of the solvent in the complex protein environment and further confirm the role of solvent fluctuations on the excited state surface. The results are consistent with previous investigations, found in the literature, of solutes dissolved in liquids.

  12. Proton Chemical Shift Imaging of the Brain in Pediatric and Adult Developmental Stuttering.

    Science.gov (United States)

    O'Neill, Joseph; Dong, Zhengchao; Bansal, Ravi; Ivanov, Iliyan; Hao, Xuejun; Desai, Jay; Pozzi, Elena; Peterson, Bradley S

    2017-01-01

    Developmental stuttering is a neuropsychiatric condition of incompletely understood brain origin. Our recent functional magnetic resonance imaging study indicates a possible partial basis of stuttering in circuits enacting self-regulation of motor activity, attention, and emotion. To further characterize the neurophysiology of stuttering through in vivo assay of neurometabolites in suspect brain regions. Proton chemical shift imaging of the brain was performed in a case-control study of children and adults with and without stuttering. Recruitment, assessment, and magnetic resonance imaging were performed in an academic research setting. Ratios of N-acetyl-aspartate plus N-acetyl-aspartyl-glutamate (NAA) to creatine (Cr) and choline compounds (Cho) to Cr in widespread cerebral cortical, white matter, and subcortical regions were analyzed using region of interest and data-driven voxel-based approaches. Forty-seven children and adolescents aged 5 to 17 years (22 with stuttering and 25 without) and 47 adults aged 21 to 51 years (20 with stuttering and 27 without) were recruited between June 2008 and March 2013. The mean (SD) ages of those in the stuttering and control groups were 12.2 (4.2) years and 13.4 (3.2) years, respectively, for the pediatric cohort and 31.4 (7.5) years and 30.5 (9.9) years, respectively, for the adult cohort. Region of interest-based findings included lower group mean NAA:Cr ratio in stuttering than nonstuttering participants in the right inferior frontal cortex (-7.3%; P = .02), inferior frontal white matter (-11.4%; P < .001), and caudate (-10.6%; P = .04), while the Cho:Cr ratio was higher in the bilateral superior temporal cortex (left: +10.0%; P = .03 and right: +10.8%; P = .01), superior temporal white matter (left: +14.6%; P = .003 and right: +9.5%; P = .02), and thalamus (left: +11.6%; P = .002 and right: +11.1%; P = .001). False discovery rate-corrected voxel-based findings were highly consistent

  13. 2H isotope effect on 13C chemical shifts of Nitro-Benzo-9-Crown-3

    International Nuclear Information System (INIS)

    Moghimi, A.; Rastegar, M.; Ghandi, M.; Bijanzadeh, H. R.

    2002-01-01

    Deuterium substitution on two ortho-substituted-OCH 2 fragments in Nitro-Benzo-9 Crown-3 induces low frequency shifts, positive m ''nΔC j, in all 13 C NMR resonances which is an indication of the increased shielding in this crown ether. The magnitude of these shifts vary from 15 ΔC 7=716 to 54 ΔC 3=15 ppb for C 7 and C 3 carbons directly attached to 2 H, respectively. The influences of concentration and solvent, CDCl 3 CD 3 COCD 3 , and C 6 D 6 , on mn ΔC j values were investigated. The mn ΔC j values depended more on the nature of the solvent than on the concentration. The order of induced isotope shifts is 15 Δ, 51 Δ > 24 Δ, 42 Δ> 34 Δ, 43 Δ > 56 Δ, 65 Δ> 45 Δ, 54 Δ. The isotope shifts observed are suggested to be a sum of contributions from low frequency shift due to inductive-type and negative hyperconjugation perturbations. The C-D bond, as a poorer electron acceptor than a C-H bond induced less positive charge on directly attached oxygens O 1 and O 2. This, in turn, causes shielding of C 1 and C 2 in C1O1CD 2 and C 2 0 2 CD 2 fragments. The difference in 34 ΔC 1 and 43 ΔC 2 values is attributed to the conformational dependence of the negative hyperconjugation. The C 1 and C 2, are in fact, not equally affected by the two CD 2 groups by negative hyperconjugation because of the existence of NO 2 group attached to the benzene ring

  14. 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.

  15. Sine-squared shifted pulses for recoupling interactions in solid-state NMR

    Science.gov (United States)

    Jain, Mukul G.; Rajalakshmi, G.; Equbal, Asif; Mote, Kaustubh R.; Agarwal, Vipin; Madhu, P. K.

    2017-06-01

    Rotational-Echo DOuble-Resonance (REDOR) is a versatile experiment for measuring internuclear distance between two heteronuclear spins in solid-state NMR. At slow to intermediate magic-angle spinning (MAS) frequencies, the measurement of distances between strongly coupled spins is challenging due to rapid dephasing of magnetisation. This problem can be remedied by employing the pulse-shifted version of REDOR known as Shifted-REDOR (S-REDOR) that scales down the recoupled dipolar coupling. In this study, we propose a new variant of the REDOR sequence where the positions of the π pulses are determined by a sine-squared function. This new variant has scaling properties similar to S-REDOR. We use theory, numerical simulations, and experiments to compare the dipolar recoupling efficiencies and the experimental robustness of the three REDOR schemes. The proposed variant has advantages in terms of radiofrequency field requirements at fast MAS frequencies.

  16. 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.

  17. Pressure dependence of backbone chemical shifts in the model peptides Ac-Gly-Gly-Xxx-Ala-NH{sub 2}

    Energy Technology Data Exchange (ETDEWEB)

    Erlach, Markus Beck; Koehler, Joerg [University of Regensburg, Institute of Biophysics and Physical Biochemistry and Centre of Magnetic Resonance in Chemistry and Biomedicine (Germany); Crusca, Edson [University of São Paulo, Physics Institute of São Carlos (Brazil); Kremer, Werner [University of Regensburg, Institute of Biophysics and Physical Biochemistry and Centre of Magnetic Resonance in Chemistry and Biomedicine (Germany); Munte, Claudia E. [University of São Paulo, Physics Institute of São Carlos (Brazil); Kalbitzer, Hans Robert, E-mail: hans-robert.kalbitzer@biologie.uni-regensburg.de [University of Regensburg, Institute of Biophysics and Physical Biochemistry and Centre of Magnetic Resonance in Chemistry and Biomedicine (Germany)

    2016-06-15

    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 {sup 1}H{sup α}, {sup 13}C{sup α} and {sup 13}C′ in the protected tetrapeptides Ac-Gly-Gly-Xxx-Ala-NH{sub 2} (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{sub 1} and B{sub 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.Graphical Abstract.

  18. Integrated ecological and chemical food web accumulation modeling explains PAH temporal trends during regime shifts in a shallow lake.

    Science.gov (United States)

    Kong, Xiangzhen; He, Wei; Qin, Ning; Liu, Wenxiu; Yang, Bin; Yang, Chen; Xu, Fuliu; Mooij, Wolf M; Koelmans, Albert A

    2017-08-01

    Shallow lakes can switch suddenly from a turbid situation with high concentrations of phytoplankton and other suspended solids to a vegetated state with clear water, and vice versa. These alternative stable states may have a substantial impact on the fate of hydrophobic organic compounds (HOCs). Models that are fit to simulate impacts from these complex interactions are scarce. We developed a contaminant fate model which is linked to an ecosystem model (PCLake) for shallow lakes. This integrated model was successful in simulating long-term dynamics (1953-2012) of representative polycyclic aromatic hydrocarbons (PAHs) in the main biotic and abiotic components in a large shallow lake (Chaohu in China), which has undergone regime shifts in this period. Historical records from sediment cores were used to evaluate the model. The model revealed that regime shifts in shallow lakes had a strong impact on the fate of less hydrophobic compounds due to the large storage capacity of macrophytes, which accumulated up to 55.6% of phenanthrene in the clear state. The abrupt disappearance of macrophytes after the regime shift resulted in a sudden change in phenanthrene distribution, as the sediment became the major sink. For more hydrophobic compounds such as benzo(a)pyrene, the modeled impact of the regime shift was negligible for the whole environment, yet large for biotic compartments. This study is the first to provide a full mechanistic analysis of the impact of regime shifts on the fate of PAHs in a real lake ecosystem. Copyright © 2017 Elsevier Ltd. All rights reserved.

  19. Bidirectional shifts of TRPM8 channel gating by temperature and chemical agents modulate the cold sensitivity of mammalian thermoreceptors.

    Science.gov (United States)

    Mälkiä, Annika; Madrid, Rodolfo; Meseguer, Victor; de la Peña, Elvira; Valero, María; Belmonte, Carlos; Viana, Félix

    2007-05-15

    TRPM8, a member of the melastatin subfamily of transient receptor potential (TRP) cation channels, is activated by voltage, low temperatures and cooling compounds. These properties and its restricted expression to small sensory neurons have made it the ion channel with the most advocated role in cold transduction. Recent work suggests that activation of TRPM8 by cold and menthol takes place through shifts in its voltage-activation curve, which cause the channel to open at physiological membrane potentials. By contrast, little is known about the actions of inhibitors on the function of TRPM8. We investigated the chemical and thermal modulation of TRPM8 in transfected HEK293 cells and in cold-sensitive primary sensory neurons. We show that cold-evoked TRPM8 responses are effectively suppressed by inhibitor compounds SKF96365, 4-(3-chloro-pyridin-2-yl)-piperazine-1-carboxylic acid (4-tert-butyl-phenyl)-amide (BCTC) and 1,10-phenanthroline. These antagonists exert their effect by shifting the voltage dependence of TRPM8 activation towards more positive potentials. An opposite shift towards more negative potentials is achieved by the agonist menthol. Functionally, the bidirectional shift in channel gating translates into a change in the apparent temperature threshold of TRPM8-expressing cells. Accordingly, in the presence of the antagonist compounds, the apparent response-threshold temperature of TRPM8 is displaced towards colder temperatures, whereas menthol sensitizes the response, shifting the threshold in the opposite direction. Co-application of agonists and antagonists produces predictable cancellation of these effects, suggesting the convergence on a common molecular process. The potential for half maximal activation of TRPM8 activation by cold was approximately 140 mV more negative in native channels compared to recombinant channels, with a much higher open probability at negative membrane potentials in the former. In functional terms, this difference translates

  20. Moessbauer spectroscopy-nuclear hyperfine technique for studying dynamic chemical states of iron complexes

    International Nuclear Information System (INIS)

    Maeda, Y.

    2005-01-01

    A brief introduction of Moessbauer spectroscopy will be presented, followed by a discussion of the Moessbauer parameters, isomer shifts, quadrupole splittings, and spectral shapes of complexes in the presence of relaxation of the electronic states of the iron atoms. The usefulness of Moessbauer spectroscopy to demonstrate the dynamic phenomena of electronic states will be discussed in this lecture. (1) The Moessbauer spectra of mixed valence dinuclear and trinuclear iron complexes will be discussed in connection with the chemical structure of the complexes: The values of the quadrupole splittings and isomer shifts of [Fe II Fe III (bpmp) (ppa) 2 ](BF 4 ) 2 increase on raising the temperature, where Hbpmp represents 2,6-bis[bis(2- pyridylmethyl)aminoethyl]-4-methylphenol and ppa is 3-n-phenylpropionic acid. The spectra can be accounted for by postulating intramolecular electron exchange between two energetically inequivalent vibronic states Fe A 2+ Fe B 3+ and Fe A 3+ Fe B 2+ : The apparent time averaged valence states of the iron atoms are 2.2 and 2.8 on the Moessbauer time scale at 293 K. (2) The Moessbauer spectra of iron(III) spin-crossover complexes will be discussed in connection with the spin-transition rate and chemical structure of the complexes. The Moessbauer spectra of spin-crossover iron(III) complexes with LIESST (Light Induced Electronic Spin-State Transition) and of metallomesogens will be discussed to illustrate the extension of this research area by the use of Moessbauer spectroscopy.

  1. Revisiting the chemical reactivity indices as the state function derivatives. The role of classical chemical hardness

    Energy Technology Data Exchange (ETDEWEB)

    Malek, Ali; Balawender, Robert, E-mail: rbalawender@ichf.edu.pl [Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, PL-01-224 Warsaw (Poland)

    2015-02-07

    The chemical reactivity indices as the equilibrium state-function derivatives are revisited. They are obtained in terms of the central moments (fluctuation formulas). To analyze the role of the chemical hardness introduced by Pearson [J. Am. Chem. Soc. 105, 7512 (1983)], the relations between the derivatives up to the third-order and the central moments are obtained. As shown, the chemical hardness and the chemical potential are really the principal indices of the chemical reactivity theory. It is clear from the results presented here that the chemical hardness is not the derivative of the Mulliken chemical potential (this means also not the second derivative of the energy at zero-temperature limit). The conventional quadratic dependence of energy, observed at finite temperature, reduces to linear dependence on the electron number at zero-temperature limit. The chemical hardness plays a double role in the admixture of ionic states to the reference neutral state energy: it determines the amplitude of the admixture and regulates the damping of its thermal factor.

  2. Revisiting the chemical reactivity indices as the state function derivatives. The role of classical chemical hardness

    International Nuclear Information System (INIS)

    Malek, Ali; Balawender, Robert

    2015-01-01

    The chemical reactivity indices as the equilibrium state-function derivatives are revisited. They are obtained in terms of the central moments (fluctuation formulas). To analyze the role of the chemical hardness introduced by Pearson [J. Am. Chem. Soc. 105, 7512 (1983)], the relations between the derivatives up to the third-order and the central moments are obtained. As shown, the chemical hardness and the chemical potential are really the principal indices of the chemical reactivity theory. It is clear from the results presented here that the chemical hardness is not the derivative of the Mulliken chemical potential (this means also not the second derivative of the energy at zero-temperature limit). The conventional quadratic dependence of energy, observed at finite temperature, reduces to linear dependence on the electron number at zero-temperature limit. The chemical hardness plays a double role in the admixture of ionic states to the reference neutral state energy: it determines the amplitude of the admixture and regulates the damping of its thermal factor

  3. Alternative stable states generated by ontogenetic niche shift in the presence of multiple resource use.

    Directory of Open Access Journals (Sweden)

    Takefumi Nakazawa

    2011-02-01

    Full Text Available It has been suggested that when juveniles and adults use different resources or habitats, alternative stable states (ASS may exist in systems coupled by an ontogenetic niche shift. However, mainly the simplest system, i.e., the one-consumer-two-resource system, has been studied previously, and little is known about the development of ASS existing in more complex systems. Here, I theoretically investigated the development of ASS caused by an ontogenetic niche shift in the presence of multiple resource use. I considered three independent scenarios; (i additional resources, (ii multiple habitats, and (iii interstage resource sharing. The model analyses illustrate that relative balance between the total resource availability in the juvenile and adult habitats is crucial for the development of ASS. This balance is determined by factors such as local habitat productivity, subsidy inputs, colonization area, and foraging mobility. Furthermore, it is also shown that interstage resource sharing generally suppresses ASS. These results suggest that the anthropogenic impacts of habitat modifications (e.g., fragmentation and destruction or interaction modifications (e.g., changes in ontogeny and foraging behavior propagate through space and may cause or prevent regime shifts in the regional community structure.

  4. Dimension shifting operators and null states in 2D conformally invariant field theories

    International Nuclear Information System (INIS)

    Gervais, J.L.

    1986-01-01

    We discuss the existence and properties of differential operators which transform covariant operators into covariant operators of different weights in two-dimensional conformally invariant field theories. We relate them to null states and the vanishing of the Kac determinant in representations of the conformal algebra, and to the existence of differential equations for Green functions of covariant operators. In this framework, we rederive the essential features of our earlier work on dual models with shifted intercept, which in euclidean space-time gives explicit solutions of the conformal bootstrap equations where all operators are marginal. (orig.)

  5. Chemical shift of neutron resonances and some ideas on neutron resonances and scattering theory

    International Nuclear Information System (INIS)

    Ignatovich, V.K.; )

    2002-01-01

    The dependence of positions of neutron resonances in nuclei in condensed matter on chemical environment is considered. A possibility of theoretical description of neutron resonances, different from R-matrix theory is investigated. Some contradictions of standard scattering theory are discussed and a new approach without these contradictions is formulated [ru

  6. NMR chemical shift and J coupling parameterization and quantum mechanical reference spectrum simulation for selected nerve agent degradation products in aqueous conditions.

    Science.gov (United States)

    Koskela, Harri; Anđelković, Boban

    2017-10-01

    The spectral parameters of selected nerve agent degradation products relevant to the Chemical Weapons Convention, namely, ethyl methylphosphonate, isopropyl methylphosphonate, pinacolyl methylphosphonate and methylphosphonic acid, were studied in wide range of pH conditions and selected temperatures. The pH and temperature dependence of chemical shifts and J couplings was parameterized using Henderson-Hasselbalch-based functions. The obtained parameters allowed calculation of precise chemical shifts and J coupling constants in arbitrary pH conditions and typical measurement temperatures, thus facilitating quantum mechanical simulation of reference spectra in the chosen magnetic field strength for chemical verification. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

  7. Reaction diffusion and solid state chemical kinetics handbook

    CERN Document Server

    Dybkov, V I

    2010-01-01

    This monograph deals with a physico-chemical approach to the problem of the solid-state growth of chemical compound layers and reaction-diffusion in binary heterogeneous systems formed by two solids; as well as a solid with a liquid or a gas. It is explained why the number of compound layers growing at the interface between the original phases is usually much lower than the number of chemical compounds in the phase diagram of a given binary system. For example, of the eight intermetallic compounds which exist in the aluminium-zirconium binary system, only ZrAl3 was found to grow as a separate

  8. Modeling the hyperfine state selectivity of a short lamb-shift spin-filter polarimeter

    International Nuclear Information System (INIS)

    Mendez, A.J.; Roper, C.D.; Clegg, T.B.

    1995-01-01

    An rf cavity, previously used as a spin filter in a Lamb-shift polarized ion source, is being adapted for use as a polarimeter in an atomic beam polarized hydrogen and deuterium ion source. Paramount among the design criteria is maintaining the current source performance while providing on-line beam polarization monitoring. This requires minimizing both the polarimeter system length and the coupling with the magnetic fields of the other ion source systems. Detailed computer calculations have modeled the four-level interaction involving the 2S 1/2 -2P 1/2 states of the atomic beam. These indicate that a significantly shorter spin-filter cavity and uniform axial magnetic field than used in the Lamb-shift source do not compromise the spin-state selectivity. The calculations also predict the axial magnetic field uniformity needed as well as the gains achieved from proper shaping of the cavity rf and dc fields. copyright 1995 American Institute of Physics

  9. SHIFTING WEED COMPOSITIONS AND BIOMASS PRODUCTION IN SWEET CORN FIELD TREATED WITH ORGANIC COMPOSTS AND CHEMICAL WEED CONTROLS

    Directory of Open Access Journals (Sweden)

    Marulak Simarmata

    2015-10-01

    Full Text Available The objectives of the research were to study the shift of weed compositions in sweet corn field treated with organic compost and chemical weed controls and to compare the effect of treatment combinations on weed growth, weed biomass and sweet corn biomass. The research was conducted in Bengkulu, Indonesia, from April to July 2014. Results showed that the number of weed species decreased after the trials from 14 to 13. There was a shift in weed compositions because 5 species of weeds did not emerge after the trials, but 4 new species were found. Chemical weed control used a herbiside mixture of atrazine and mesotrione applied during postemergence was the most effective method to control weeds, which was observed on decreased weed emergence and weed biomass down to 22.33 and 25.00 percent of control, respectively. Subsequently, biomass production of sweet corn increased up to 195.64 percent at the same trials. Biomass of weeds and sweet corn were also affected by the organic composts. Weed biomass was inhibited by treatment of composted empty fruith bunches of oil palm, whereas significantly increased of sweet corn biomass were observed in the plots of organic manure.

  10. A Bayesian-probability-based method for assigning protein backbone dihedral angles based on chemical shifts and local sequences

    Energy Technology Data Exchange (ETDEWEB)

    Wang Jun; Liu Haiyan [University of Science and Technology of China, Hefei National Laboratory for Physical Sciences at the Microscale, and Key Laboratory of Structural Biology, School of Life Sciences (China)], E-mail: hyliu@ustc.edu.cn

    2007-01-15

    Chemical shifts contain substantial information about protein local conformations. We present a method to assign individual protein backbone dihedral angles into specific regions on the Ramachandran map based on the amino acid sequences and the chemical shifts of backbone atoms of tripeptide segments. The method uses a scoring function derived from the Bayesian probability for the central residue of a query tripeptide segment to have a particular conformation. The Ramachandran map is partitioned into representative regions at two levels of resolution. The lower resolution partitioning is equivalent to the conventional definitions of different secondary structure regions on the map. At the higher resolution level, the {alpha} and {beta} regions are further divided into subregions. Predictions are attempted at both levels of resolution. We compared our method with TALOS using the original TALOS database, and obtained comparable results. Although TALOS may produce the best results with currently available databases which are much enlarged, the Bayesian-probability-based approach can provide a quantitative measure for the reliability of predictions.

  11. NMR Chemical Shift of a Helium Atom as a Probe for Electronic Structure of FH, F-, (FHF)-, and FH2.

    Science.gov (United States)

    Tupikina, E Yu; Efimova, A A; Denisov, G S; Tolstoy, P M

    2017-12-21

    In this work, we present the first results of outer electronic shell visualization by using a 3 He atom as a probe particle. As model objects we have chosen F - , FH, and FH 2 + species, as well as the hydrogen-bonded complex FH···F - at various H···F - distances (3.0, 2.5, 2.0, and 1.5 Å and equilibrium at ca. 1.14 Å). The interaction energy of investigated objects with helium atom (CCSD/aug-cc-pVTZ) and helium atom chemical shift (B3LYP/pcS-2) surfaces were calculated, and their topological analysis was performed. For comparison, the results of standard quantum mechanical approaches to electronic shell visualization were presented (ESP, ELF, ED, ∇ 2 ED). We show that the Laplacian of helium chemical shift, ∇ 2 δ He , is sensitive to fluorine atom lone pair localization regions, and it can be used for the visualization of the outer electronic shell, which could be used to evaluate the proton accepting ability. The sensitivity of ∇ 2 δ He to lone pairs is preserved at distances as large as 2.0-2.5 Å from the fluorine nucleus (in comparison with the distance to ESP minima, located at 1.0-1.5 Å or maxima of ELF, which are as close as 0.6 Å to the fluorine nucleus).

  12. 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.

  13. Effects of a 12-hour shift on mood states and sleepiness of Neonatal Intensive Care Unit nurses

    Directory of Open Access Journals (Sweden)

    Tadeu Sartini Ferreira

    Full Text Available Abstract OBJECTIVE To assess the effect of a 12-hour shift on mood states and sleepiness at the beginning and end of the shift. METHOD Quantitative, cross-sectional and descriptive study.It was conducted with 70 neonatal intensive care unit nurses. The Brunel Mood Scale (BRUMS, Karolinska Sleepiness Scale (KSS, and a socio-demographic profile questionnaire were administered. RESULTS When the KSS and BRUMS scores were compared at the beginning of the shift associations were found with previous sleep quality (p ≤ 0.01, and quality of life (p ≤ 0.05. Statistical significant effects on BRUMS scores were also associated with previous sleep quality, quality of life, liquid ingestion, healthy diet, marital status, and shift work stress. When the beginning and end of the shift were compared, different KSS scores were seen in the group of all nurses and in the night shift one. Significant vigor and fatigue scores were observed within shift groups. CONCLUSION A good night’s sleep has positive effects on the individual`s mood states both at the beginning and the end of the shift. The self-perception of a good quality of life also positively influenced KSS and BRUMS scores at the beginning and end of the shift. Proper liquid ingestion led to better KSS and BRUMS scores.

  14. 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

  15. Radiation-chemical aspects of solid state hot atom chemistry

    International Nuclear Information System (INIS)

    Matsuura, T.; Collins, K.E.; Collins, C.H.

    1984-01-01

    The study of nuclear hot atom chemical (NHAC) processes occurring in solids is seriously limited by the lack of adequate methods for directly studying the chemical species containing hot atoms. In the present review the effects of ionizing radiation on parent and non-parent yields from solid state targets is surveyed and qualitative interpretations are given. After a few general remarks of the relationship of radiation chemistry to solid state NHAC, a detailed description of the radiation effects is given (radiation annealing, neutron activation, changes in separable yield). (Auth.)

  16. Determination of ground and excited state dipole moments of dipolar laser dyes by solvatochromic shift method.

    Science.gov (United States)

    Patil, S K; Wari, M N; Panicker, C Yohannan; Inamdar, S R

    2014-04-05

    The absorption and fluorescence spectra of three medium sized dipolar laser dyes: coumarin 478 (C478), coumarin 519 (C519) and coumarin 523 (C523) have been recorded and studied comprehensively in various solvents at room temperature. The absorption and fluorescence spectra of C478, C519 and C523 show a bathochromic and hypsochromic shifts with increasing solvent polarity indicate that the transitions involved are π→π(∗) and n→π(∗). Onsager radii determined from ab initio calculations were used in the determination of dipole moments. The ground and excited state dipole moments were evaluated by using solvatochromic correlations. It is observed that the dipole moment values of excited states (μe) are higher than corresponding ground state values (μg) for the solvents studied. The ground and excited state dipole moments of these probes computed from ab initio calculations and those determined experimentally are compared and the results are discussed. Copyright © 2013 Elsevier B.V. All rights reserved.

  17. Chemical states of molybdenum in radioactive waste glass

    International Nuclear Information System (INIS)

    Ishiguro, Katsuhiko; Kawanishi, Nobuo; Nagaki, Hiroshi; Naito, Aritsune

    1982-01-01

    In order to confirm an expectation that the chemical state of molybdenum in glass reflects the phase separation tendency of the yellow solid from the melt of borosilicate glass, simulated waste glasses were prepared, and ESCA analysis was performed using a commercially available electron spectrometer (PHI550 E) with an excitation source consisting of Mg Kα-ray. The effects of the concentration of Mo and FE 2 O 3 and the melting atmosphere (oxidizing or reducing) in which the samples were prepared on the chemical state of Mo and the solubility of MoO 3 were examined. From the observation of Mo spectra, it was shown that Mo in waste glass had several valencies, e.g., Mo(3), Mo(4), Mo(5) and Mo(6), while Mo in the yellow solid separated from the melts exhibited hexa-valent state, the peak intensity of higher valencies increased relatively with the increase of MoO 3 concentration, but the chemical state of Mo did not change remarkably around the solubility limit of MoO 3 , the melting atmosphere influenced on the Mo state in the waste glass, the peak intensity of Mo(6) increased relatively with the increasing Fe 2 O 3 concentration, and Mo in devitrified glass exhibited hexa-valent state. (Yoshitake, I.)

  18. Chemical Shifts of the Carbohydrate Binding Domain of Galectin-3 from Magic Angle Spinning NMR and Hybrid Quantum Mechanics/Molecular Mechanics Calculations.

    Science.gov (United States)

    Kraus, Jodi; Gupta, Rupal; Yehl, Jenna; Lu, Manman; Case, David A; Gronenborn, Angela M; Akke, Mikael; Polenova, Tatyana

    2018-03-22

    Magic angle spinning NMR spectroscopy is uniquely suited to probe the structure and dynamics of insoluble proteins and protein assemblies at atomic resolution, with NMR chemical shifts containing rich information about biomolecular structure. Access to this information, however, is problematic, since accurate quantum mechanical calculation of chemical shifts in proteins remains challenging, particularly for 15 N H . Here we report on isotropic chemical shift predictions for the carbohydrate recognition domain of microcrystalline galectin-3, obtained from using hybrid quantum mechanics/molecular mechanics (QM/MM) calculations, implemented using an automated fragmentation approach, and using very high resolution (0.86 Å lactose-bound and 1.25 Å apo form) X-ray crystal structures. The resolution of the X-ray crystal structure used as an input into the AF-NMR program did not affect the accuracy of the chemical shift calculations to any significant extent. Excellent agreement between experimental and computed shifts is obtained for 13 C α , while larger scatter is observed for 15 N H chemical shifts, which are influenced to a greater extent by electrostatic interactions, hydrogen bonding, and solvation.

  19. Long-lived and largely red-shifted photoluminescence of solid-state rhodamine dyes: Molecular exciton coupling and structural effect

    International Nuclear Information System (INIS)

    Zhang, Xian-Fu; Zhang, Ya-Kui

    2015-01-01

    The optical absorption and fluorescence properties of five rhodamine dyes in solid-state are measured and show large difference from that in their gas phase or liquid solvents. All solid-state rhodamine dyes strongly absorb all light in UV and visible region, but emit only red and NIR fluorescence (680–800 nm, >100 nm red-shifted from that in solution). Further more, the absorption maxima of a solid-state rhodamine show a large red-shifted band (~100 nm) and blue-shifted peak (~125 nm) compared to that in solutions, indicating a strong molecular exciton coupling between molecules. All solid-state rhodamines still show reasonably good fluorescence quantum yield (Φ f ). In particular, solid-state Rhodamine B butyl ester and sulfonyl Rhodamine B showed a much longer emission lifetime (τ f ) than that of the corresponding molecular rhodamine, i.e. 4.12 and 4.14 ns in solid state compared to 1.61 and 2.47 ns in solution. The chemical structure of a rhodamine molecule showed dramatic effect on Φ f and τ f values for solid state rhodamine. The larger substituent in the benzene moiety favors higher Φ f and τ f values of rhodamine solids. These effects can be elucidated by the relation between structure-molecular distance and molecular exciton couplings. - Highlights: • Optical properties of solid rhodamines show large difference from that in solutions. • Solid-state rhodamine dyes emit red and NIR fluorescence (680–800 nm). • Solid-state rhodamines still show reasonably good fluorescence quantum yield. • Solid-state rhodamines have much longer fluorescence lifetimes than that in solutions

  20. Long-lived and largely red-shifted photoluminescence of solid-state rhodamine dyes: Molecular exciton coupling and structural effect

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Xian-Fu, E-mail: zhangxianfu@tsinghua.org.cn [Institute of Applied Photochemistry & Center of Analysis and Measurements, Hebei Normal University of Science and Technology, Qinhuangdao 066004, Hebei Province (China); MPC Technologies, Hamilton, ON, Canada L8S 3H4 (Canada); Zhang, Ya-Kui [Institute of Applied Photochemistry & Center of Analysis and Measurements, Hebei Normal University of Science and Technology, Qinhuangdao 066004, Hebei Province (China)

    2015-10-15

    The optical absorption and fluorescence properties of five rhodamine dyes in solid-state are measured and show large difference from that in their gas phase or liquid solvents. All solid-state rhodamine dyes strongly absorb all light in UV and visible region, but emit only red and NIR fluorescence (680–800 nm, >100 nm red-shifted from that in solution). Further more, the absorption maxima of a solid-state rhodamine show a large red-shifted band (~100 nm) and blue-shifted peak (~125 nm) compared to that in solutions, indicating a strong molecular exciton coupling between molecules. All solid-state rhodamines still show reasonably good fluorescence quantum yield (Φ{sub f}). In particular, solid-state Rhodamine B butyl ester and sulfonyl Rhodamine B showed a much longer emission lifetime (τ{sub f}) than that of the corresponding molecular rhodamine, i.e. 4.12 and 4.14 ns in solid state compared to 1.61 and 2.47 ns in solution. The chemical structure of a rhodamine molecule showed dramatic effect on Φ{sub f} and τ{sub f} values for solid state rhodamine. The larger substituent in the benzene moiety favors higher Φ{sub f} and τ{sub f} values of rhodamine solids. These effects can be elucidated by the relation between structure-molecular distance and molecular exciton couplings. - Highlights: • Optical properties of solid rhodamines show large difference from that in solutions. • Solid-state rhodamine dyes emit red and NIR fluorescence (680–800 nm). • Solid-state rhodamines still show reasonably good fluorescence quantum yield. • Solid-state rhodamines have much longer fluorescence lifetimes than that in solutions.

  1. Results of investigation of the functional state of operators involved in 8- and 12-hour shift rotations

    International Nuclear Information System (INIS)

    Chernyuk, V.I.; Zakharenko, M.I.; Nosovskij, A.V.; Lastovchenko, V.B.; Petrichenko, A.A.; Panchenko, V.I.; Lipovoj, V.V.; Pugach, A.B.

    1996-01-01

    The functional state of operators of block and central control panels of the Chernobyl NPP involved in 8- and 12-hour shift rotations was studied. Basing of the results of changes in indices of the subjective state, activation of the central nervous system, arterial pressure, heart rate, body temperature it was established that day shifts were characterized by higher functional tension whereas night shifts by mote expressed fatigue. The work with the 8-hour rotation schedule in comparison with 12-hour one appeared to be less favourable for the functional state of operators because it resulted in over excitation of the central nervous system and was characterized by more expressed fatigue in night shifts

  2. Chemical Compositions of Soils in Parts of Edo State, Southwest ...

    African Journals Online (AJOL)

    MICHAEL HORSFALL

    www.bioline.org.br/ja. Chemical Compositions of Soils in Parts of Edo State, Southwest Nigeria and their ... the soil in agriculture and engineering (Imasuen et al. 1989b). Clay mineral ..... Unpublished Ph.D. Thesis, The. University of Western ...

  3. Understanding Flood Seasonality and Its Temporal Shifts within the Contiguous United States

    Energy Technology Data Exchange (ETDEWEB)

    Ye, Sheng [Institute of Hydrology and Water Resources, School of Civil Engineering, Zhejiang University, Hangzhou, China; Li, Hong-Yi [Pacific Northwest National Laboratory, Richland, Washington; Leung, L. Ruby [Pacific Northwest National Laboratory, Richland, Washington; Guo, Jiali [College of Civil and Hydropower Engineering, China Three Gorges University, Yichang, China; State Key Laboratory of Water Resources and Hydropower Engineering Science, Wuhan University, Wuhan, China; Ran, Qihua [Institute of Hydrology and Water Resources, School of Civil Engineering, Zhejiang University, Hangzhou, China; Demissie, Yonas [Department of Civil and Environmental Engineering, Washington State University Tri-Cities, Richland, Washington; Sivapalan, Murugesu [Department of Geography and Geographic Information Science, University of Illinois at Urbana–Champaign, Champaign, Illinois; Department of Civil and Environmental Engineering, University of Illinois at Urbana–Champaign, Urbana, Illinois

    2017-07-01

    Understanding the causes of flood seasonality is critical for better flood management. This study examines the seasonality of annual maximum floods (AMF) and its changes before and after 1980 at over 250 natural catchments across the contiguous United States. Using circular statistics to define a seasonality index, our analysis focuses on the variability of the flood occurrence date. Generally, catchments with more synchronized seasonal water and energy cycles largely inherit their seasonality of AMF from that of annual maximum rainfall (AMR). In contrast, the seasonality of AMF in catchments with loosely synchronized water and energy cycles are more influenced by high antecedent storage, which is responsible for the amplification of the seasonality of AMF over that of AMR. This understanding then effectively explains a statistically significant shift of flood seasonality detected in some catchments in the recent decades. Catchments where the antecedent soil water storage has increased since 1980 exhibit increasing flood seasonality while catchments that have experienced increases in storm rainfall before the floods have shifted towards floods occurring more variably across the seasons. In the eastern catchments, a concurrent widespread increase in event rainfall magnitude and reduced soil water storage have led to a more variable timing of floods. Our findings of the role of antecedent storage and event rainfall on the flood seasonality provide useful insights for understanding future changes in flood seasonality as climate models projected changes in extreme precipitation and aridity over land.

  4. Designing molecular dynamics simulations to shift populations of the conformational states of calmodulin.

    Directory of Open Access Journals (Sweden)

    Ayse Ozlem Aykut

    Full Text Available We elucidate the mechanisms that lead to population shifts in the conformational states of calcium-loaded calmodulin (Ca(2+-CaM. We design extensive molecular dynamics simulations to classify the effects that are responsible for adopting occupied conformations available in the ensemble of NMR structures. Electrostatic interactions amongst the different regions of the protein and with its vicinal water are herein mediated by lowering the ionic strength or the pH. Amino acid E31, which is one of the few charged residues whose ionization state is highly sensitive to pH differences in the physiological range, proves to be distinctive in its control of population shifts. E31A mutation at low ionic strength results in a distinct change from an extended to a compact Ca(2+-CaM conformation within tens of nanoseconds, that otherwise occur on the time scales of microseconds. The kinked linker found in this particular compact form is observed in many of the target-bound forms of Ca(2+-CaM, increasing the binding affinity. This mutation is unique in controlling C-lobe dynamics by affecting the fluctuations between the EF-hand motif helices. We also monitor the effect of the ionic strength on the conformational multiplicity of Ca(2+-CaM. By lowering the ionic strength, the tendency of nonspecific anions in water to accumulate near the protein surface increases, especially in the vicinity of the linker. The change in the distribution of ions in the vicinal layer of water allows N- and C- lobes to span a wide variety of relative orientations that are otherwise not observed at physiological ionic strength. E31 protonation restores the conformations associated with physiological environmental conditions even at low ionic strength.

  5. Shifts in oxidation states of cerium oxide nanoparticles detected inside intact hydrated cells and organelles

    Energy Technology Data Exchange (ETDEWEB)

    Szymanski, Craig J.; Munusamy, Prabhakaran; Mihai, Cosmin; Xie, Yumei; Hu, Dehong; Gilles, Marry K.; Tyliszczak, T.; Thevuthasan, Suntharampillai; Baer, Donald R.; Orr, Galya

    2015-09-01

    Cerium oxide nanoparticles (CNPs) have been shown to induce diverse biological effects, ranging from toxic to beneficial. The beneficial effects have been attributed to the potential antioxidant activity of CNPs via certain redox reactions, depending on their oxidation state or Ce3+/Ce4+ ratio. However, this ratio is strongly dependent on the environment and age of the nanoparticles and it is unclear whether and how the complex intracellular environment impacts this ratio and the possible redox reactions of CNPs. To identify any changes in the oxidation state of CNPs in the intracellular environment and better understand their intracellular reactions, we directly quantified the oxidation states of CNPs outside and inside intact hydrated cells and organelles using correlated scanning transmission x-ray and super resolution fluorescence microscopies. By analyzing hundreds of small CNP aggregates, we detected a shift to a higher Ce3+/Ce4+ ratio in CNPs inside versus outside the cells, indicating a net reduction of CNPs in the intracellular environment. We further found a similar ratio in the cytoplasm and in the lysosomes, indicating that the net reduction occurs earlier in the internalization pathway. Together with oxidative stress and toxicity measurements, our observations identify a net reduction of CNPs in the intracellular environment, which is consistent with their involvement in potentially beneficial oxidation reactions, but also point to interactions that can negatively impact the health of cells.

  6. Quantum electrodynamics at strong electric fields. The ground state Lamb shift in hydrogenlike uranium

    Energy Technology Data Exchange (ETDEWEB)

    Gumberidze, A.; Stoehlker, T. [Gesellschaft fuer Schwerionenforschung mbH, Darmstadt (Germany)]|[Frankfurt Univ. (Germany). Inst. fuer Kernphysik; Banas, D. [Pedagogical Univ., Kielce (PL). Inst. of Phys.] [and others

    2005-05-01

    X-ray spectra following radiative recombination of free electrons with bare uranium ions (U{sup 92+}) were measured at the electron cooler of the ESR storage ring. The most intense lines observed in the spectra can be attributed to the characteristic Lyman ground-state transitions and to the recombination of free electrons into the K-shell of the ions. Our experiment was carried out by utilizing the deceleration technique which leads to a considerable reduction of the uncertainties associated with Doppler corrections. This, in combination with the 0 observation geometry, allowed us to determine the ground-state Lamb shift in hydrogen-like uranium (U{sup 91+}) from the observed X-ray lines with an accuracy of 1%. The present result is about 3 times more precise than the most accurate value available up to now and provides the most stringent test of bound-state quantum electrodynamics for one-electron systems in the strong-field regime. (orig.)

  7. Backbone and stereospecific (13)C methyl Ile (δ1), Leu and Val side-chain chemical shift assignments of Crc.

    Science.gov (United States)

    Sharma, Rakhi; Sahu, Bhubanananda; Ray, Malay K; Deshmukh, Mandar V

    2015-04-01

    Carbon catabolite repression (CCR) allows bacteria to selectively assimilate a preferred compound among a mixture of several potential carbon sources, thus boosting growth and economizing the cost of adaptability to variable nutrients in the environment. The RNA-binding catabolite repression control (Crc) protein acts as a global post-transcriptional regulator of CCR in Pseudomonas species. Crc triggers repression by inhibiting the expression of genes involved in transport and catabolism of non-preferred substrates, thus indirectly favoring assimilation of preferred one. We report here a nearly complete backbone and stereospecific (13)C methyl side-chain chemical shift assignments of Ile (δ1), Leu and Val of Crc (~ 31 kDa) from Pseudomonas syringae Lz4W.

  8. Computational Protocols for Prediction of Solute NMR Relative Chemical Shifts. A Case Study of L-Tryptophan in Aqueous Solution

    DEFF Research Database (Denmark)

    Eriksen, Janus J.; Olsen, Jógvan Magnus H.; Aidas, Kestutis

    2011-01-01

    to the results stemming from the conformations extracted from the MM conformational search in terms of replicating an experimental reference as well as in achieving the correct sequence of the NMR relative chemical shifts of L-tryptophan in aqueous solution. We find this to be due to missing conformations......In this study, we have applied two different spanning protocols for obtaining the molecular conformations of L-tryptophan in aqueous solution, namely a molecular dynamics simulation and a molecular mechanics conformational search with subsequent geometry re-optimization of the stable conformers...... using a quantum mechanically based method. These spanning protocols represent standard ways of obtaining a set of conformations on which NMR calculations may be performed. The results stemming from the solute–solvent configurations extracted from the MD simulation at 300 K are found to be inferior...

  9. Comparison of brown and white adipose tissues in infants and children with chemical-shift-encoded water-fat MRI.

    Science.gov (United States)

    Hu, Houchun H; Yin, Larry; Aggabao, Patricia C; Perkins, Thomas G; Chia, Jonathan M; Gilsanz, Vicente

    2013-10-01

    To compare fat-signal fractions (FFs) and T2* values between brown (BAT) and white (WAT) adipose tissue located within the supraclavicular fossa and subcutaneous depots, respectively. Twelve infants and 39 children were studied. Children were divided into lean and overweight/obese subgroups. Chemical-shift-encoded water-fat magnetic resonance imaging (MRI) was used to quantify FFs and T2* metrics in the supraclavicular and adjacent subcutaneous adipose tissue depots. Linear regression and t-tests were performed. Infants had lower supraclavicular FFs than children (P children exhibited lower supraclavicular FFs and T2* values than overweight children (P children, but not in infants. FFs in both depots were positively correlated with age and weight in infants (P children, they were correlated with weight and body mass index (BMI) (P children (P children, which are potentially indicative of physiological differences in adipose tissue fat content, amount, and metabolic activity. Copyright © 2013 Wiley Periodicals, Inc.

  10. Hepatic fat quantification using automated six-point Dixon: Comparison with conventional chemical shift based sequences and computed tomography.

    Science.gov (United States)

    Shimizu, Kie; Namimoto, Tomohiro; Nakagawa, Masataka; Morita, Kosuke; Oda, Seitaro; Nakaura, Takeshi; Utsunomiya, Daisuke; Yamashita, Yasuyuki

    To compare automated six-point Dixon (6-p-Dixon) MRI comparing with dual-echo chemical-shift-imaging (CSI) and CT for hepatic fat fraction in phantoms and clinical study. Phantoms and fifty-nine patients were examined both MRI and CT for quantitative fat measurements. In phantom study, linear regression between fat concentration and 6-p-Dixon showed good agreement. In clinical study, linear regression between 6-p-Dixon and dual-echo CSI showed good agreement. CT attenuation value was strongly correlated with 6-p-Dixon (R 2 =0.852; PDixon and dual-echo CSI were accurate correlation with CT attenuation value of liver parenchyma. 6-p-Dixon has the potential for automated hepatic fat quantification. Copyright © 2017 Elsevier Inc. All rights reserved.

  11. 1H, 13C and 15N chemical shift assignments of the thioredoxin from the obligate anaerobe Desulfovibrio vulgaris Hildenborough.

    Science.gov (United States)

    Garcin, Edwige B; Bornet, Olivier; Pieulle, Laetitia; Guerlesquin, Françoise; Sebban-Kreuzer, Corinne

    2011-10-01

    Thioredoxins are ubiquitous key antioxidant enzymes which play an essential role in cell defense against oxidative stress. They maintain the redox homeostasis owing to the regulation of thiol-disulfide exchange. In the present paper, we report the full resonance assignments of (1)H, (13)C and (15)N atoms for the reduced and oxidized forms of Desulfovibrio vulgaris Hildenborough thioredoxin 1 (Trx1). 2D and 3D heteronuclear NMR experiments were performed using uniformly (15)N-, (13)C-labelled Trx1. Chemical shifts of 97% of the backbone and 90% of the side chain atoms were obtained for the oxidized and reduced form (BMRB deposits with accession number 17299 and 17300, respectively).

  12. Quantitative evaluation of vertebral marrow adipose tissue in postmenopausal female using MRI chemical shift-based water–fat separation

    International Nuclear Information System (INIS)

    Li, G.-W.; Xu, Z.; Chen, Q.-W.; Tian, Y.-N.; Wang, X.-Y.; Zhou, L.; Chang, S.-X.

    2014-01-01

    Aim: To investigate the feasibility of assessing vertebral marrow adipose tissue using a magnetic resonance imaging (MRI) chemical shift-based water–fat separation technique at 3 T. Material and methods: A modified Dixon technique was performed to obtain the vertebral marrow fat fraction (FF) in a study of 58 postmenopausal females (age range 49.2–77.4 years), including 24 normal bone density, 19 osteopaenia, and 15 osteoporosis as documented with dual-energy X-ray absorptiometry. The reliability of FF measurements performed by two radiologists independently was evaluated with the intraclass correlation coefficient (ICC). Ten participants were scanned twice to assess the reproducibility of FF measurements. FF values were compared between each vertebral level and between groups. Results: The mean coefficient of variation of FF measurements was 2.1%. According to the ICC, the measurements were reliable (ICC = 0.900 for normal bone density, ICC = 0.937 for osteopaenia and ICC = 0.909 for osteoporosis, p < 0.001 for all). There was an inverse association between mean FF at L1–L4 vertebrae and lumbar spine BMD (r = −0.459, p = 0.006), which remained significant even after controlling for confounders (age, height, and body weight). FF values at different vertebral levels were significantly correlated to each other (r = 0.703–0.921, p < 0.05 for all). There was a general trend toward increased marrow adiposity for more inferior vertebral bodies. Patients with osteopaenia and osteoporosis had a higher marrow fat content compared with normal bone mass after adjusting for confounders, although no significant differences in each vertebral level and average marrow fat content were found between the osteopaenia and osteoporosis groups. Conclusion: Chemical shift-based water–fat separation enables the quantitation of vertebral marrow adiposity with excellent reproducibility, which appears to be a useful method to provide complementary information to osteoporosis

  13. Volumetric spiral chemical shift imaging of hyperpolarized [2-(13) c]pyruvate in a rat c6 glioma model.

    Science.gov (United States)

    Park, Jae Mo; Josan, Sonal; Jang, Taichang; Merchant, Milton; Watkins, Ron; Hurd, Ralph E; Recht, Lawrence D; Mayer, Dirk; Spielman, Daniel M

    2016-03-01

    MRS of hyperpolarized [2-(13)C]pyruvate can be used to assess multiple metabolic pathways within mitochondria as the (13)C label is not lost with the conversion of pyruvate to acetyl-CoA. This study presents the first MR spectroscopic imaging of hyperpolarized [2-(13)C]pyruvate in glioma-bearing brain. Spiral chemical shift imaging with spectrally undersampling scheme (1042 Hz) and a hard-pulse excitation was exploited to simultaneously image [2-(13)C]pyruvate, [2-(13)C]lactate, and [5-(13)C]glutamate, the metabolites known to be produced in brain after an injection of hyperpolarized [2-(13)C]pyruvate, without chemical shift displacement artifacts. A separate undersampling scheme (890 Hz) was also used to image [1-(13)C]acetyl-carnitine. Healthy and C6 glioma-implanted rat brains were imaged at baseline and after dichloroacetate administration, a drug that modulates pyruvate dehydrogenase kinase activity. The baseline metabolite maps showed higher lactate and lower glutamate in tumor as compared to normal-appearing brain. Dichloroacetate led to an increase in glutamate in both tumor and normal-appearing brain. Dichloroacetate-induced %-decrease of lactate/glutamate was comparable to the lactate/bicarbonate decrease from hyperpolarized [1-(13)C]pyruvate studies. Acetyl-carnitine was observed in the muscle/fat tissue surrounding the brain. Robust volumetric imaging with hyperpolarized [2-(13)C]pyruvate and downstream products was performed in glioma-bearing rat brains, demonstrating changes in mitochondrial metabolism with dichloroacetate. © 2015 Wiley Periodicals, Inc.

  14. Chemical shifts as a novel measure of interactions between two binding sites of symmetric dialkyldimethylammonium bromides to α-cyclodextrin

    International Nuclear Information System (INIS)

    Funasaki, Noriaki; Ishikawa, Seiji; Hirota, Shun

    2006-01-01

    Complex formation of α-cyclodextrin (α-CD) with decyltrimethylammonium (DeTAB), N,N-dioctyldimethylammonium (DOAB), and N,N-didecyldimethylammonium bromides (DDeAB) was investigated by proton NMR spectroscopy. Analysis of chemical shifts yielded macroscopic 1:1 and 1:2 binding constants (K 1 and K 2 ) and chemical shift differences (Δδ SD and Δδ SD2 ) for the 1:1 and 1:2 complexes of DeTAB, DOAB, and DDeAB with α-CD. The K 1 and K 2 values of DDeAB were quantitatively explained on the basis of the assumption that the microscopic 1:1 binding constant of DDeAB is identical to the observed K 1 value of DeTAB. The K 2 value of DDeAB was also explained in terms of its observed K 1 value and the independent binding of two alkyl chains. Furthermore, the Δδ SD and Δδ SD2 values for protons of DDeAB and α-CD were quantitatively explained on the basis of the assumption that the geometry of the decyl group of DDeAB in an α-CD cavity is identical to that of DeTAB. The Δδ SD value was also explicable on the basis of the same geometric assumption and the observed Δδ SD2 value for this system. Similar results were obtained for the 1:1 and 1:2 DOAB-α-CD complexes

  15. 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. Copyright © 2015 John Wiley & Sons, Ltd.

  16. Excited state electric dipole moment of 5-hydroxy indole and 5-hydroxy indole 3-acetic acid through solvatochromic shifts

    International Nuclear Information System (INIS)

    Rani, G. Neeraja; Ayachit, Narasimha H.

    2010-01-01

    The determination of excited state electric dipole moment through solvatochromic shifts is one of the easiest approaches to understand the molecular structure in the excited state. These studies have gained importance due to their application in photo science, especially if they are of biological importance. In view of this the excited state electric dipole moments of two substituted indoles which are of biological importance are determined and reported here. The fluorescence shifts have been used and the results found seem to be more consistent in comparison with the one calculated through absorption shifts. The results presented are also discussed. A qualitative estimate of the orientation of the dipole moments in ground and excited state are also presented and discussed. The method proposed by Ayachit and Neeraja Rani is used in view of the several advantages it has.

  17. 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....

  18. Indirectly detected chemical shift correlation NMR spectroscopy in solids under fast magic angle spinning

    Energy Technology Data Exchange (ETDEWEB)

    Mao, Kanmi [Iowa State Univ., Ames, IA (United States)

    2011-01-01

    The development of fast magic angle spinning (MAS) opened up an opportunity for the indirect detection of insensitive low-γ nuclei (e.g., 13C and 15N) via the sensitive high-{gamma} nuclei (e.g., 1H and 19F) in solid-state NMR, with advanced sensitivity and resolution. In this thesis, new methodology utilizing fast MAS is presented, including through-bond indirectly detected heteronuclear correlation (HETCOR) spectroscopy, which is assisted by multiple RF pulse sequences for 1H-1H homonuclear decoupling. Also presented is a simple new strategy for optimization of 1H-1H homonuclear decoupling. As applications, various classes of materials, such as catalytic nanoscale materials, biomolecules, and organic complexes, are studied by combining indirect detection and other one-dimensional (1D) and two-dimensional (2D) NMR techniques. Indirectly detected through-bond HETCOR spectroscopy utilizing refocused INEPT (INEPTR) mixing was developed under fast MAS (Chapter 2). The time performance of this approach in 1H detected 2D 1H{l_brace}13C{r_brace} spectra was significantly improved, by a factor of almost 10, compared to the traditional 13C detected experiments, as demonstrated by measuring naturally abundant organic-inorganic mesoporous hybrid materials. The through-bond scheme was demonstrated as a new analytical tool, which provides complementary structural information in solid-state systems in addition to through-space correlation. To further benefit the sensitivity of the INEPT transfer in rigid solids, the combined rotation and multiple-pulse spectroscopy (CRAMPS) was implemented for homonuclear 1H decoupling under fast MAS (Chapter 3). Several decoupling schemes (PMLG5m$\\bar{x}$, PMLG5mm$\\bar{x}$x and SAM3) were analyzed to maximize the performance of through-bond transfer based

  19. Chemical protective clothing - State of the art and the future

    International Nuclear Information System (INIS)

    Perkins, J.L.

    1990-01-01

    Clothing used to protect the skin from exposure to chemicals (CPC) is an integral part of many work-places. Only 10-15 years ago the strategy behind selecting CPC to afford this protection was to find a type of CPC which was essentially liquid-proof and would therefore protect the skin from exposure to a liquid chemical. However, in the last 10 years there has been an explosion of data in the industrial hygiene field related to the permeation of chemical protective clothing by liquid chemicals. These data indicate clearly that when CPC is exposed to a chemical, it may not disintegrate or degrade, but nevertheless, will be permeated by the chemical and the skin will be exposed. This has led to a new strategy for selecting CPC which essentially assumes that any exposure of the skin is harmful. Consequently, a worst-case scenario is assumed when selecting CPC and often the garment with the best permeation properties is selected regardless of cost. This philosophy is prompted by a lack of knowledge concerning the skin and how it is permeated by industrial chemicals in their liquid and vapor states. The interests in the last 10 years in CPC has led to new developments and an exciting future for protective clothing. Several new laminated polymeric materials are now being used in both gloves and full-body suits. These polymers are plastic rather than elastomeric and therefore do not afford good dexterity properties. However, their permeability properties are extremely good. In addition, further research on dermal penetration should give the industrial hygienist the necessary information to perform risk assessments for skin exposure. These new risk assessment strategies should negate the current need to overprotect workers. Overprotection often leads to unnecessary costs and can lead to increased stress on the worker in the form of heat stress

  20. 31P NMR Chemical Shifts of Phosphorus Probes as Reliable and Practical Acidity Scales for Solid and Liquid Catalysts.

    Science.gov (United States)

    Zheng, Anmin; Liu, Shang-Bin; Deng, Feng

    2017-10-11

    Acid-base catalytic reaction, either in heterogeneous or homogeneous systems, is one of the most important chemical reactions that has provoked a wide variety of industrial catalytic processes for production of chemicals and petrochemicals over the past few decades. In view of the fact that the catalytic performances (e.g., activity, selectivity, and reaction mechanism) of acid-catalyzed reactions over acidic catalysts are mostly dictated by detailed acidic features, viz. type (Brønsted vs Lewis acidity), amount (concentration), strength, and local environments (location) of acid sites, information on and manipulation of their structure-activity correlation are crucial for optimization of catalytic performances as well as innovative design of novel effective catalysts. This review aims to summarize recent developments on acidity characterization of solid and liquid catalysts by means of experimental 31 P nuclear magnetic resonance (NMR) spectroscopy using phosphorus probe molecules such as trialkylphosphine (TMP) and trialkylphosphine oxides (R 3 PO). In particular, correlations between the observed 31 P chemical shifts (δ 31 P) of phosphorus (P)-containing probes and acidic strengths have been established in conjuction with density functional theory (DFT) calculations, rendering practical and reliable acidity scales for Brønsted and Lewis acidities at the atomic level. As illustrated for a variety of different solid and liquid acid systems, such as microporous zeolites, mesoporous molecular sieves, and metal oxides, the 31 P NMR probe approaches were shown to provide important acid features of various catalysts, surpassing most conventional methods such as titration, pH measurement, Hammett acidity function, and some other commonly used physicochemical techniques, such as calorimetry, temperature-programmed desorption of ammonia (NH 3 -TPD), Fourier transformed infrared (FT-IR), and 1 H NMR spectroscopies.

  1. Physico-chemical studies on samarium soaps in solid state

    International Nuclear Information System (INIS)

    Mehrotra, K.N.; Chauhan, M.; Shukla, R.K.

    1989-01-01

    The physico-chemical characteristics of samarium soaps (caproate and caprate) in solid state were investigated by IR, X-ray diffraction and TGA measurements. The IR results revealed that the fatty acids exist in dimeric state through hydrogen bonding and samarium soaps possess partial ionic character. The X-ray diffraction measurements were used to calculate the long spacings and the results confirmed the double layer structure of samarium soaps. The decomposition reaction was found kinetically of zero order and the values of energy of activation for the decomposition process for caproate and caprate were found to be 8,0 and 7,8 kcal mol -1 , respectively. (Authors)

  2. State estimation of chemical engineering systems tending to multiple solutions

    Directory of Open Access Journals (Sweden)

    N. P. G. Salau

    2014-09-01

    Full Text Available A well-evaluated state covariance matrix avoids error propagation due to divergence issues and, thereby, it is crucial for a successful state estimator design. In this paper we investigate the performance of the state covariance matrices used in three unconstrained Extended Kalman Filter (EKF formulations and one constrained EKF formulation (CEKF. As benchmark case studies we have chosen: a a batch chemical reactor with reversible reactions whose system model and measurement are such that multiple states satisfy the equilibrium condition and b a CSTR with exothermic irreversible reactions and cooling jacket energy balance whose nonlinear behavior includes multiple steady-states and limit cycles. The results have shown that CEKF is in general the best choice of EKF formulations (even if they are constrained with an ad hoc clipping strategy which avoids undesired states for such case studies. Contrary to a clipped EKF formulation, CEKF incorporates constraints into an optimization problem, which minimizes the noise in a least square sense preventing a bad noise distribution. It is also shown that, although the Moving Horizon Estimation (MHE provides greater robustness to a poor guess of the initial state, converging in less steps to the actual states, it is not justified for our examples due to the high additional computational effort.

  3. Magnetic susceptibility as a direct measure of oxidation state in LiFePO4 batteries and cyclic water gas shift reactors.

    Science.gov (United States)

    Kadyk, Thomas; Eikerling, Michael

    2015-08-14

    The possibility of correlating the magnetic susceptibility to the oxidation state of the porous active mass in a chemical or electrochemical reactor was analyzed. The magnetic permeability was calculated using a hierarchical model of the reactor. This model was applied to two practical examples: LiFePO4 batteries, in which the oxidation state corresponds with the state-of-charge, and cyclic water gas shift reactors, in which the oxidation state corresponds to the depletion of the catalyst. In LiFePO4 batteries phase separation of the lithiated and delithiated phases in the LiFePO4 particles in the positive electrode gives rise to a hysteresis effect, i.e. the magnetic permeability depends on the history of the electrode. During fast charge or discharge, non-uniform lithium distributionin the electrode decreases the hysteresis effect. However, the overall sensitivity of the magnetic response to the state-of-charge lies in the range of 0.03%, which makes practical measurement challenging. In cyclic water gas shift reactors, the sensitivity is 4 orders of magnitude higher and without phase separation, no hysteresis occurs. This shows that the method is suitable for such reactors, in which large changes of the magnetic permeability of the active material occurs.

  4. NMR spectroscopy of organic compounds of selenium and tellurium. Communication 9. Chemical shifts of /sup 13/C in isological series of unsaturated ethers, sulfides, selenides and tellurides

    Energy Technology Data Exchange (ETDEWEB)

    Kalabin, G.A.; Bzhezovskii, V.M.; Kushnarev, D.F.; Proidakov, A.G. (Irkutskii Gosudarstvennyj Univ. (USSR))

    1981-06-01

    The effects of heteroatoms Eh(Eh=O, S, Se, Te) on /sup 13/C chemical shifts in eleven isological series of R/sup 1/-Eh-R/sup 2/ unsaturated compounds are compared. A linear relation between /sup 13/C nuclei screening and tEh electronegativity is observed. An assumption is suggested that both likeness of the effects of 6A and 7A group elements on /sup 13/C chemical shifts of R/sup 1/ and R/sup 2/ substituents and their difference for elements of the 4A group are caused by unbonded interactions of the substituents with unshared electron pairs of heteroatoms.

  5. State waste discharge permit application, 200-E chemical drain field

    International Nuclear Information System (INIS)

    1994-06-01

    As part of the Hanford Federal Facility Agreement and Consent Order negotiations (Ecology et al. 1994), the US Department of Energy, Richland Operations Office, the US Environmental Protection Agency, and the Washington State Department of Ecology agreed that liquid effluent discharges to the ground on the Hanford Site which affect groundwater or have the potential to affect ground would be subject to permitting under the structure of Chapter 173-216 (or 173-218 where applicable) of the Washington Administrative Code, the State Waste Discharge Permit Program. As a result of this decision, the Washington State Department of Ecology and the US Department of Energy, Richland Operations Office entered into Consent Order No. DE 91NM-177, (Ecology and DOE-RL 1991). The Consent Order No. DE 91NM-177 requires a series of permitting activities for liquid effluent discharges. This document presents the State Waste Discharge Permit (SWDP) application for the 200-E Chemical Drain Field. Waste water from the 272-E Building enters the process sewer line directly through a floor drain, while waste water from the 2703-E Building is collected in two floor drains, (north and south) that act as sumps and are discharged periodically. The 272-E and 2703-E Buildings constitute the only discharges to the process sewer line and the 200-E Chemical Drain Field

  6. State waste discharge permit application, 200-E chemical drain field

    Energy Technology Data Exchange (ETDEWEB)

    1994-06-01

    As part of the Hanford Federal Facility Agreement and Consent Order negotiations (Ecology et al. 1994), the US Department of Energy, Richland Operations Office, the US Environmental Protection Agency, and the Washington State Department of Ecology agreed that liquid effluent discharges to the ground on the Hanford Site which affect groundwater or have the potential to affect ground would be subject to permitting under the structure of Chapter 173-216 (or 173-218 where applicable) of the Washington Administrative Code, the State Waste Discharge Permit Program. As a result of this decision, the Washington State Department of Ecology and the US Department of Energy, Richland Operations Office entered into Consent Order No. DE 91NM-177, (Ecology and DOE-RL 1991). The Consent Order No. DE 91NM-177 requires a series of permitting activities for liquid effluent discharges. This document presents the State Waste Discharge Permit (SWDP) application for the 200-E Chemical Drain Field. Waste water from the 272-E Building enters the process sewer line directly through a floor drain, while waste water from the 2703-E Building is collected in two floor drains, (north and south) that act as sumps and are discharged periodically. The 272-E and 2703-E Buildings constitute the only discharges to the process sewer line and the 200-E Chemical Drain Field.

  7. 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

  8. Applicability of federal and state hazardous waste regulatory programs to waste chemical weapons and chemical warfare agents.; TOPICAL

    International Nuclear Information System (INIS)

    Haffenden, R.; Kimmell, T.

    2002-01-01

    This report reviews federal and state hazardous waste regulatory programs that govern the management of chemical weapons or chemical warfare agents. It addresses state programs in the eight states with chemical weapon storage facilities managed by the U.S. Army: Alabama, Arkansas, Colorado, Indiana, Kentucky, Maryland, Oregon, and Utah. It also includes discussions on 32 additional states or jurisdictions with known or suspected chemical weapons or chemical warfare agent presence (e.g., disposal sites containing chemical agent identification sets): Alaska, Arizona, California, Florida, Georgia, Hawaii, Idaho, Illinois, Iowa, Kansas, Louisiana, Massachusetts, Michigan, Mississippi, Missouri, Nebraska, Nevada, New Jersey, New Mexico, New York, North Carolina, Ohio, Pennsylvania, South Carolina, South Dakota, Tennessee, Texas, the U.S. Virgin Islands, Virginia, Washington, Washington, D.C., and Wyoming. Resource Conservation and Recovery Act (RCRA) hazardous waste programs are reviewed to determine whether chemical weapons or chemical warfare agents are listed hazardous wastes or otherwise defined or identified as hazardous wastes. Because the U.S. Environmental Protection Agency (EPA) military munitions rule specifically addresses the management of chemical munitions, this report also indicates whether a state has adopted the rule and whether the resulting state regulations have been authorized by EPA. Many states have adopted parts or all of the EPA munitions rule but have not yet received authorization from EPA to implement the rule. In these cases, the states may enforce the adopted munitions rule provisions under state law, but these provisions are not federally enforceable

  9. Synthesis, three-dimensional structure, conformation and correct chemical shift assignment determination of pharmaceutical molecules by NMR and molecular modeling

    Energy Technology Data Exchange (ETDEWEB)

    Azeredo, Sirlene O.F. de; Sales, Edijane M.; Figueroa-Villar, José D., E-mail: jdfv2009@gmail.com [Instituto Militar de Engenharia (IME), Rio de Janeiro, RJ (Brazil). Grupo de Ressonância Magnética Nuclear e Química Medicinal

    2017-07-01

    This work includes the synthesis of phenanthrenequinone guanylhydrazone and phenanthro[9,10-e][1,2,4]triazin-3-amine to be tested as intercalate with DNA for treatment of cancer. The other synthesized product, 2-[(4-chlorophenylamino)methylene]malononitrile, was designed for future determination of its activity against leishmaniasis. A common problem about some articles on the literature is that some previously published compounds display error of their molecular structures. In this article it is shown the application of several procedures of nuclear magnetic resonance (NMR) to determine the complete molecular structure and the non questionable chemical shift assignment of the synthesized compounds, and also their analysis by molecular modeling to confirm the NMR results. To determine the capacity of pharmacological compounds to interact with biological targets is determined by docking. This work is to motivate the application of NMR and molecular modeling on organic synthesis, being a process that is very important for the study of the prepared compounds as interactions with biological targets by NMR. (author)

  10. Synthesis, three-dimensional structure, conformation and correct chemical shift assignment determination of pharmaceutical molecules by NMR and molecular modeling

    International Nuclear Information System (INIS)

    Azeredo, Sirlene O.F. de; Sales, Edijane M.; Figueroa-Villar, José D.

    2017-01-01

    This work includes the synthesis of phenanthrenequinone guanylhydrazone and phenanthro[9,10-e][1,2,4]triazin-3-amine to be tested as intercalate with DNA for treatment of cancer. The other synthesized product, 2-[(4-chlorophenylamino)methylene]malononitrile, was designed for future determination of its activity against leishmaniasis. A common problem about some articles on the literature is that some previously published compounds display error of their molecular structures. In this article it is shown the application of several procedures of nuclear magnetic resonance (NMR) to determine the complete molecular structure and the non questionable chemical shift assignment of the synthesized compounds, and also their analysis by molecular modeling to confirm the NMR results. To determine the capacity of pharmacological compounds to interact with biological targets is determined by docking. This work is to motivate the application of NMR and molecular modeling on organic synthesis, being a process that is very important for the study of the prepared compounds as interactions with biological targets by NMR. (author)

  11. Noninvasive measurements of cardiac high-energy phosphate metabolites in dilated cardiomyopathy by using 31P spectroscopic chemical shift imaging

    International Nuclear Information System (INIS)

    Hansch, A.; Rzanny, R.; Heyne, J.-P.; Reichenbach, J.R.; Kaiser, W.A.; Leder, U.

    2005-01-01

    Dilated cardiomyopathy (DCM) is accompanied by an impaired cardiac energy metabolism. The aim of this study was to investigate metabolic ratios in patients with DCM compared to controls by using spectroscopic two-dimensional chemical shift imaging (2D-CSI). Twenty volunteers and 15 patients with severe symptoms (left ventricular ejection fraction, LVEF 30%) of DCM were investigated. Cardiac 31 P MR 2D-CSI measurements (voxel size: 40 x 40 x 100 mm 3 ) were performed with a 1.5 T whole-body scanner. Measurement time ranged from 15 min to 30 min. Peak areas and ratios of different metabolites were evaluated, including high-energy phosphates (PCr, ATP), 2,3-diphosphoglycerate (2,3-DPG) and phosphodiesters (PDE). In addition, we evaluated how PCr/ATP ratios correlate with LVEF as an established prognostic factor of heart failure. The PCr/γ-ATP ratio was significantly decreased in patients with moderate and severe DCM and showed a linear correlation with reduced LVEFs. PDE/ATP ratios were significantly increased only in patients with severe DCM as compared to volunteers. Applying 31 P MRS with commonly-available 2D-CSI sequences is a valuable technique to evaluate DCM by determining PCr/ATP ratios noninvasively. In addition to reduced PCr/ATP ratios observed in patients suffering from DCM, significantly-increased PDE/ATP ratios were found in patients with severe DCM. (orig.)

  12. Correlation of interface states/border traps and threshold voltage shift on AlGaN/GaN metal-insulator-semiconductor high-electron-mobility transistors

    Energy Technology Data Exchange (ETDEWEB)

    Wu, Tian-Li, E-mail: Tian-Li.Wu@imec.be; Groeseneken, Guido [imec, Kapeldreef 75, 3001 Leuven (Belgium); Department of Electrical Engineering, KU Leuven, Leuven (Belgium); Marcon, Denis; De Jaeger, Brice; Lin, H. C.; Franco, Jacopo; Stoffels, Steve; Van Hove, Marleen; Decoutere, Stefaan [imec, Kapeldreef 75, 3001 Leuven (Belgium); Bakeroot, Benoit [imec, Kapeldreef 75, 3001 Leuven (Belgium); Centre for Microsystems Technology, Ghent University, 9052 Gent (Belgium); Roelofs, Robin [ASM, Kapeldreef 75, 3001 Leuven (Belgium)

    2015-08-31

    In this paper, three electrical techniques (frequency dependent conductance analysis, AC transconductance (AC-g{sub m}), and positive gate bias stress) were used to evaluate three different gate dielectrics (Plasma-Enhanced Atomic Layer Deposition Si{sub 3}N{sub 4}, Rapid Thermal Chemical Vapor Deposition Si{sub 3}N{sub 4}, and Atomic Layer Deposition (ALD) Al{sub 2}O{sub 3}) for AlGaN/GaN Metal-Insulator-Semiconductor High-Electron-Mobility Transistors. From these measurements, the interface state density (D{sub it}), the amount of border traps, and the threshold voltage (V{sub TH}) shift during a positive gate bias stress can be obtained. The results show that the V{sub TH} shift during a positive gate bias stress is highly correlated to not only interface states but also border traps in the dielectric. A physical model is proposed describing that electrons can be trapped by both interface states and border traps. Therefore, in order to minimize the V{sub TH} shift during a positive gate bias stress, the gate dielectric needs to have a lower interface state density and less border traps. However, the results also show that the commonly used frequency dependent conductance analysis technique to extract D{sub it} needs to be cautiously used since the resulting value might be influenced by the border traps and, vice versa, i.e., the g{sub m} dispersion commonly attributed to border traps might be influenced by interface states.

  13. Mathematical modeling of sleep state dynamics in a rodent model of shift work

    Directory of Open Access Journals (Sweden)

    Michael J. Rempe

    2018-06-01

    Full Text Available Millions of people worldwide are required to work when their physiology is tuned for sleep. By forcing wakefulness out of the body’s normal schedule, shift workers face numerous adverse health consequences, including gastrointestinal problems, sleep problems, and higher rates of some diseases, including cancers. Recent studies have developed protocols to simulate shift work in rodents with the intention of assessing the effects of night-shift work on subsequent sleep (Grønli et al., 2017. These studies have already provided important contributions to the understanding of the metabolic consequences of shift work (Arble et al., 2015; Marti et al., 2016; Opperhuizen et al., 2015 and sleep-wake-specific impacts of night-shift work (Grønli et al., 2017. However, our understanding of the causal mechanisms underlying night-shift-related sleep disturbances is limited. In order to advance toward a mechanistic understanding of sleep disruption in shift work, we model these data with two different approaches. First we apply a simple homeostatic model to quantify differences in the rates at which sleep need, as measured by slow wave activity during slow wave sleep (SWS rises and falls. Second, we develop a simple and novel mathematical model of rodent sleep and use it to investigate the timing of sleep in a simulated shift work protocol (Grønli et al., 2017. This mathematical framework includes the circadian and homeostatic processes of the two-process model, but additionally incorporates a stochastic process to model the polyphasic nature of rodent sleep. By changing only the time at which the rodents are forced to be awake, the model reproduces some key experimental results from the previous study, including correct proportions of time spent in each stage of sleep as a function of circadian time and the differences in total wake time and SWS bout durations in the rodents representing night-shift workers and those representing day-shift workers

  14. The effects of state anxiety and thermal comfort on sleep quality and eye fatigue in shift work nurses.

    Science.gov (United States)

    Dehghan, Habibollah; Azmoon, Hiva; Souri, Shiva; Akbari, Jafar

    2014-01-01

    Psychological problems as state anxiety (SA) in the work environment has negative effect on the employees life especially shift work nurses, i.e. negative effect on mental and physical health (sleep quality, eye fatigue and comfort thermal). The purpose of this study was determination of effects of state anxiety and thermal comfort on sleep quality and eye fatigue in shift work nurses. This cross-sectional research conducted on 82 shift-work personnel of 18 nursing workstations of Isfahan hospitals in 2012. To measure the SA, sleep quality, visual fatigue and thermal comfort, Spielberger state-trait anxiety inventory, Pittsburg sleep quality index, eye fatigue questionnaire and thermal comfort questionnaire were used respectively. The data were analyzed with descriptive statistics, student test and correlation analysis. Correlation between SA and sleep quality was -0.664(P thermal comfort was -0.276(P = 0.016) and between SA and eye fatigue was 0.57 (P thermal conditions and reduce state anxiety level can be reduce eye fatigue and increase the sleep quality in shift work nurses.

  15. Chemical shift-selective snapshot FLASH MR imaging in combination with inversion-recovery T1 contrast at different field strengths

    International Nuclear Information System (INIS)

    Matthaei, D.; Haase, A.; Henrich, D.; Duhmke, E.

    1991-01-01

    With fast MR imaging, chemical shift contract becomes available to the clinician in seconds. The purpose of this paper is to evaluate the combination of chemical shift selective (CHESS) MR imaging using the snapshot FLASH MR method with the inversion-recovery technique and to obtain information concerning the signal-to-noise and chemical shift with the presaturation method at different field strengths. Investigations with volunteers and experimental animals were done at 2 and 3 T (whole body) and in a 4.7-T animal image. For the inversion-recovery experiments, saturation was done before every snapshot FLASH image. With increasing field strength due to signal-to-noise and chemical shift advantages, the method performs better. Increasing T1 values are also important at high field strengths. The combined technique is useful only for T1 water images with fat saturation. It also allows fast quantification of T1 in water-containing organs and pathologic processes. At high field strengths, fast CHESS and T1 imaging promise fast quantitative information. This is a possible argument for clinical high-field-strength MR imagining along with MR spectroscopy

  16. Automated Fragmentation Polarizable Embedding Density Functional Theory (PE-DFT) Calculations of Nuclear Magnetic Resonance (NMR) Shielding Constants of Proteins with Application to Chemical Shift Predictions

    DEFF Research Database (Denmark)

    Svendsen, Casper Steinmann; Bratholm, L.A.; Olsen, Jógvan Magnus Haugaard

    2017-01-01

    that are comparable with experiment. The introduction of a probabilistic linear regression model allows us to substantially reduce the number of snapshots that are needed to make comparisons with experiment. This approach is further improved by augmenting snapshot selection with chemical shift predictions by which we...

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

    Czech Academy of Sciences Publication Activity Database

    Vícha, J.; Marek, R.; Straka, Michal

    2016-01-01

    Roč. 55, č. 20 (2016), s. 10302-10309 ISSN 0020-1669 Institutional support: RVO:61388963 Keywords : hydrides of TlI and PbII * high-frequency 1H chemical shifts * relativistic effects Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 4.857, year: 2016

  18. High-Frequency C-13 and Si-29 NMR Chemical Shifts in Diamagnetic Low-Valence Compounds of TII and Pb-II: Decisive Role of Relativistic Effects

    Czech Academy of Sciences Publication Activity Database

    Vícha, J.; Marek, R.; Straka, Michal

    2016-01-01

    Roč. 55, č. 4 (2016), s. 1770-1781 ISSN 0020-1669 R&D Projects: GA ČR(CZ) GA14-03564S Institutional support: RVO:61388963 Keywords : high-frequency NMR chemical shifts * HALA effect * relativistic DFT calculations Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 4.857, year: 2016

  19. Differentiation of osteoporotic and neoplastic vertebral fractures by chemical shift {l_brace}in-phase and out-of phase{r_brace} MR imaging

    Energy Technology Data Exchange (ETDEWEB)

    Ragab, Yasser [Radiology Department, Faculty of Medicine, Cairo University (Egypt); Radiology Department, Dr Erfan and Bagedo General Hospital (Saudi Arabia)], E-mail: yragab61@hotmail.com; Emad, Yasser [Rheumatology and Rehabilitation Department, Faculty of Medicine, Cairo University (Egypt); Rheumatology and Rehabilitation Department, Dr Erfan and Bagedo General Hospital (Saudi Arabia)], E-mail: yasseremad68@yahoo.com; Gheita, Tamer [Rheumatology and Rehabilitation Department, Faculty of Medicine, Cairo University (Egypt)], E-mail: gheitamer@yahoo.com; Mansour, Maged [Oncology Department, Faculty of Medicine, Cairo University (Egypt); Oncology Department, Dr Erfan and Bagedo General Hospital (Saudi Arabia)], E-mail: magedmansour@yahoo.com; Abou-Zeid, A. [Public Health Department, Faculty of Medicine, Cairo University, Cairo (Egypt)], E-mail: alaabouzeid@yahoo.com; Ferrari, Serge [Division of Bone Diseases, Department of Rehabilitation and Geriatrics, and WHO, Collaborating Center for Osteoporosis Prevention, Geneva University Hospital (Switzerland)], E-mail: serge.ferrari@medecine.unige.ch; Rasker, Johannes J. [Rheumatologist University of Twente, Enschede (Netherlands)], E-mail: j.j.rasker@utwente.nl

    2009-10-15

    Objective: The objective of this study was to establish the cut-off value of the signal intensity drop on chemical shift magnetic resonance imaging (MRI) with appropriate sensitivity and specificity to differentiate osteoporotic from neoplastic wedging of the spine. Patients and methods: All patients with wedging of vertebral bodies were included consecutively between February 2006 and January 2007. A chemical shift MRI was performed and signal intensity after (in-phase and out-phase) images were obtained. A DXA was performed in all. Results: A total of 40 patients were included, 20 with osteoporotic wedging (group 1) and 20 neoplastic (group 2). They were 21 males and 19 females. Acute vertebral collapse was observed in 15 patients in group 1 and subacute collapse in another 5 patients, while in group 2, 11 patients showed acute collapse and 9 patients (45%) showed subacute vertebral collapse. On the chemical shift MRI a substantial reduction in signal intensity was found in all lesions in both groups. The proportional changes observed in signal intensity of bone marrow lesions on in-phase compared with out-of-phase images showed significant differences in both groups (P < 0.05). At a cut-off value of 35%, the observed sensitivity of out-of-phase images was 95%, specificity was 100%, positive predictive value was 100% and negative predictive value was 95.2%. Conclusion: A chemical shift MRI is useful in order to differentiate patients with vertebral collapse due to underlying osteoporosis or neoplastic process.

  20. Rapid protein fold determination using secondary chemical shifts and cross-hydrogen bond 15N-13C’ scalar couplings (3hbJNC’)

    NARCIS (Netherlands)

    Bonvin, A.M.J.J.; Houben, K.; Guenneugues, M.N.L.; Kaptein, R.; Boelens, R.

    2001-01-01

    The possibility of generating protein folds at the stage of backbone assignment using structural restraints derived from experimentally measured cross-hydrogen bond scalar couplings and secondary chemical shift information is investigated using as a test case the small alpha/beta protein

  1. H-1 chemical shift imaging of the brain in guanidino methyltransferase deficiency, a creatine deficiency syndrome; guanidinoacetate accumulation in the gray matter

    NARCIS (Netherlands)

    Sijens, PE; Verbruggen, KT; Meiners, LC; Soorani-Lunsing, RJ; Rake, JP; Oudkerk, M

    MR spectroscopy results in a mild case of guanidinoacetate methyltransferase (GAMT) deficiency are presented. The approach differs from previous MRS studies in the acquisition of a chemical shift imaging spectral map showing gray and white matter with the corresponding spectra in one overview. MR

  2. A complete set of NMR chemical shifts and spin-spin coupling constants for L-Alanyl-L-Alanine zwitterion and analysis of its conformational behavior

    Czech Academy of Sciences Publication Activity Database

    Bouř, Petr; Buděšínský, Miloš; Špirko, Vladimír; Kapitán, Josef; Šebestík, Jaroslav; Sychrovský, Vladimír

    2005-01-01

    Roč. 127, - (2005), 17079-17089 ISSN 0002-7863 R&D Projects: GA AV ČR(CZ) IAA4055104; GA ČR(CZ) GA203/05/0388 Institutional research plan: CEZ:AV0Z40550506 Keywords : NMR * chemical shifts * coupling constants Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 7.419, year: 2005

  3. Using 1H and 13C NMR chemical shifts to determine cyclic peptide conformations: a combined molecular dynamics and quantum mechanics approach.

    Science.gov (United States)

    Nguyen, Q Nhu N; Schwochert, Joshua; Tantillo, Dean J; Lokey, R Scott

    2018-05-10

    Solving conformations of cyclic peptides can provide insight into structure-activity and structure-property relationships, which can help in the design of compounds with improved bioactivity and/or ADME characteristics. The most common approaches for determining the structures of cyclic peptides are based on NMR-derived distance restraints obtained from NOESY or ROESY cross-peak intensities, and 3J-based dihedral restraints using the Karplus relationship. Unfortunately, these observables are often too weak, sparse, or degenerate to provide unequivocal, high-confidence solution structures, prompting us to investigate an alternative approach that relies only on 1H and 13C chemical shifts as experimental observables. This method, which we call conformational analysis from NMR and density-functional prediction of low-energy ensembles (CANDLE), uses molecular dynamics (MD) simulations to generate conformer families and density functional theory (DFT) calculations to predict their 1H and 13C chemical shifts. Iterative conformer searches and DFT energy calculations on a cyclic peptide-peptoid hybrid yielded Boltzmann ensembles whose predicted chemical shifts matched the experimental values better than any single conformer. For these compounds, CANDLE outperformed the classic NOE- and 3J-coupling-based approach by disambiguating similar β-turn types and also enabled the structural elucidation of the minor conformer. Through the use of chemical shifts, in conjunction with DFT and MD calculations, CANDLE can help illuminate conformational ensembles of cyclic peptides in solution.

  4. 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.

  5. Evidence for a climate-induced ecohydrological state shift in wetland ecosystems of the southern Prairie Pothole Region

    Science.gov (United States)

    McKenna, Owen; Mushet, David M.; Rosenberry, Donald O.; LaBaugh, James W.

    2017-01-01

    Changing magnitude, frequency, and timing of precipitation can influence aquatic-system hydrological, geochemical, and biological processes, in some cases resulting in system-wide shifts to an alternate state. Since the early 1990s, the southern Prairie Pothole Region has been subjected to an extended period of increased wetness resulting in marked changes to aquatic systems defining this region. We explored numerous lines of evidence to identify: (1) how the recent wet period compared to historical variability, (2) hydrological, geochemical, and biological responses, and (3) how these responses might represent a state shift in the region’s wetland ecosystems. We analyzed long-term climate records and compared how different hydrological variables responded in this wet period compared to decades before the observed shift. Additionally, we used multi-decadal records of waterfowl population and subsurface tile drain records to explore wildlife and human responses to a shifting climate. Since 1993, a novel precipitation regime corresponded with increased pond numbers, ponded-water depths, lake levels, stream flows, groundwater heights, soil-moisture, waterfowl populations, and installation of subsurface tile drains in agricultural fields. These observed changes reflect an alteration in water storage and movement across the landscape that in turn has altered solute sources and concentrations of prairie-pothole wetlands and has increased pond permanence. Combined, these changes represent significant evidence for a state shift in the ecohydrological functioning of the region’s wetland ecosystems, a shift that may require a significant refinement of the previously developed “wetland continuum” concept.

  6. Accuracy of chemical shift MR imaging in diagnosing indeterminate bone marrow lesions in the pelvis: review of a single institution's experience

    International Nuclear Information System (INIS)

    Kohl, Chad A.; Chivers, F.S.; Lorans, Roxanne; Roberts, Catherine C.; Kransdorf, Mark J.

    2014-01-01

    To re-assess the accuracy of chemical shift imaging in diagnosing indeterminate bone marrow lesions as benign or malignant. We retrospectively reviewed our experience with MR imaging of the pelvis to assess the accuracy of chemical shift imaging in distinguishing benign from malignant bone lesions. Two musculoskeletal radiologists retrospectively reviewed all osseous lesions biopsied since 2006, when chemical shift imaging was added to our routine pelvic imaging protocol. Study inclusion criteria required (1) MR imaging of an indeterminate bone marrow lesion about the pelvis and (2) subsequent histologic confirmation. The study group included 50 patients (29 male, 21 female) with an average age of 67 years (range, 41-89 years). MR imaging results were evaluated using biopsy results as the ''gold standard.'' There were 27 malignant and 23 benign lesions. Chemical shift imaging using an opposed-phase signal loss criteria of less than 20 % to indicate a malignant lesion, correctly diagnosed 27/27 malignant lesions and 14/23 benign lesions, yielding a 100 % sensitivity, 61 % specificity, 75 % PPV, 100 % NPV, and 82 % accuracy. The area under the receiver operator characteristic (ROC) curve was 0.88. The inter-rater and intra-rater agreement K values were both 1.0. Chemical shift imaging is a useful adjunct MR technique to characterize focal and diffuse marrow abnormalities on routine non-contrast pelvic imaging. It is highly sensitive in identifying malignant disease. Despite its lower specificity, the need for biopsy could be eliminated in more than 60 % of patients with benign disease. (orig.)

  7. Combining NMR ensembles and molecular dynamics simulations provides more realistic models of protein structures in solution and leads to better chemical shift prediction

    International Nuclear Information System (INIS)

    Lehtivarjo, Juuso; Tuppurainen, Kari; Hassinen, Tommi; Laatikainen, Reino; Peräkylä, Mikael

    2012-01-01

    While chemical shifts are invaluable for obtaining structural information from proteins, they also offer one of the rare ways to obtain information about protein dynamics. A necessary tool in transforming chemical shifts into structural and dynamic information is chemical shift prediction. In our previous work we developed a method for 4D prediction of protein 1 H chemical shifts in which molecular motions, the 4th dimension, were modeled using molecular dynamics (MD) simulations. Although the approach clearly improved the prediction, the X-ray structures and single NMR conformers used in the model cannot be considered fully realistic models of protein in solution. In this work, NMR ensembles (NMRE) were used to expand the conformational space of proteins (e.g. side chains, flexible loops, termini), followed by MD simulations for each conformer to map the local fluctuations. Compared with the non-dynamic model, the NMRE+MD model gave 6–17% lower root-mean-square (RMS) errors for different backbone nuclei. The improved prediction indicates that NMR ensembles with MD simulations can be used to obtain a more realistic picture of protein structures in solutions and moreover underlines the importance of short and long time-scale dynamics for the prediction. The RMS errors of the NMRE+MD model were 0.24, 0.43, 0.98, 1.03, 1.16 and 2.39 ppm for 1 Hα, 1 HN, 13 Cα, 13 Cβ, 13 CO and backbone 15 N chemical shifts, respectively. The model is implemented in the prediction program 4DSPOT, available at http://www.uef.fi/4dspothttp://www.uef.fi/4dspot.

  8. Diffusion-weighted imaging of the liver at 3 T using section-selection gradient reversal: emphasis on chemical shift artefacts and lesion conspicuity

    International Nuclear Information System (INIS)

    Lee, J.S.; Kim, Y.K.; Jeong, W.K.; Choi, D.; Lee, W.J.

    2015-01-01

    Aim: To assess the value of section-selection gradient reversal (SSGR) in liver diffusion-weighted imaging (DWI) by comparing it to conventional DWI with an emphasis on chemical shift artefacts and lesion conspicuity. Materials and methods: Forty-eight patients (29 men and 19 women; age range 33–80 years) with 48 liver lesions underwent two DWI examinations using spectral presaturation with inversion recovery fat suppression with and without SSGR at 3 T. Two reviewers evaluated each DWI (b = 100 and b = 800 image) with respect to chemical shift artefacts and liver lesion conspicuity using five-point scales and performed pairwise comparisons between the two DWIs. The signal-to-noise ratio (SNR) of the liver and the lesion and the lesion–liver contrast-to-noise ratio (CNR) were also calculated. Results: SSGR-DWI was significantly better than conventional DWI with respect to chemical shift artefacts and lesion conspicuity in both separate reviews and pairwise comparisons (p < 0.05). There were significant differences in the SNR of the liver (b = 100 and b = 800 images) and lesion (b = 800) between SSGR-DWI and conventional DWI (p < 0.05). Conclusion: Applying the SSGR method to DWI using SPIR fat suppression at 3 T could significantly reduce chemical shift artefacts without incurring additional acquisition time or SNR penalties, which leads to increased conspicuity of focal liver lesions. - Highlights: • Chemical shift artefact in liver DWI is markedly decreased by applying SSGR. • Liver lesion conspicuity is improved by applying SSGR to DWI. • In SNR of the liver, SSGR-DWI is better than conventional DWI

  9. Combining NMR ensembles and molecular dynamics simulations provides more realistic models of protein structures in solution and leads to better chemical shift prediction

    Energy Technology Data Exchange (ETDEWEB)

    Lehtivarjo, Juuso, E-mail: juuso.lehtivarjo@uef.fi; Tuppurainen, Kari; Hassinen, Tommi; Laatikainen, Reino [University of Eastern Finland, School of Pharmacy (Finland); Peraekylae, Mikael [University of Eastern Finland, Institute of Biomedicine (Finland)

    2012-03-15

    While chemical shifts are invaluable for obtaining structural information from proteins, they also offer one of the rare ways to obtain information about protein dynamics. A necessary tool in transforming chemical shifts into structural and dynamic information is chemical shift prediction. In our previous work we developed a method for 4D prediction of protein {sup 1}H chemical shifts in which molecular motions, the 4th dimension, were modeled using molecular dynamics (MD) simulations. Although the approach clearly improved the prediction, the X-ray structures and single NMR conformers used in the model cannot be considered fully realistic models of protein in solution. In this work, NMR ensembles (NMRE) were used to expand the conformational space of proteins (e.g. side chains, flexible loops, termini), followed by MD simulations for each conformer to map the local fluctuations. Compared with the non-dynamic model, the NMRE+MD model gave 6-17% lower root-mean-square (RMS) errors for different backbone nuclei. The improved prediction indicates that NMR ensembles with MD simulations can be used to obtain a more realistic picture of protein structures in solutions and moreover underlines the importance of short and long time-scale dynamics for the prediction. The RMS errors of the NMRE+MD model were 0.24, 0.43, 0.98, 1.03, 1.16 and 2.39 ppm for {sup 1}H{alpha}, {sup 1}HN, {sup 13}C{alpha}, {sup 13}C{beta}, {sup 13}CO and backbone {sup 15}N chemical shifts, respectively. The model is implemented in the prediction program 4DSPOT, available at http://www.uef.fi/4dspothttp://www.uef.fi/4dspot.

  10. Chemical modulation of electronic structure at the excited state

    Science.gov (United States)

    Li, F.; Song, C.; Gu, Y. D.; Saleem, M. S.; Pan, F.

    2017-12-01

    Spin-polarized electronic structures are the cornerstone of spintronics, and have thus attracted a significant amount of interest; in particular, researchers are looking into how to modulate the electronic structure to enable multifunctional spintronics applications, especially in half-metallic systems. However, the control of the spin polarization has only been predicted in limited two-dimensional systems with spin-polarized Dirac structures and is difficult to achieve experimentally. Here, we report the modulation of the electronic structure in the light-induced excited state in a typical half-metal, L a1 /2S r1 /2Mn O3 -δ . According to the spin-transport measurements, there appears a light-induced increase in magnetoresistance due to the enhanced spin scattering, which is closely associated with the excited spin polarization. Strikingly, the light-induced variation can be enhanced via alcohol processing and reduced by oxygen annealing. X-ray photoelectron spectroscopy measurements show that in the chemical process, a redox reaction occurs with a change in the valence of Mn. Furthermore, first-principles calculations reveal that the change in the valence of Mn alters the electronic structure and consequently modulates the spin polarization in the excited state. Our findings thus report a chemically tunable electronic structure, demonstrating interesting physics and the potential for multifunctional applications and ultrafast spintronics.

  11. Homemade chemical bomb incidents - 15 states, 2003-2011.

    Science.gov (United States)

    2013-06-21

    Homemade chemical bombs (HCBs) are made from commonly found chemicals. The volume of news reports of HCB explosions suggests they are not uncommon. To determine the number of events involving HCBs in the United States and describe the factors associated with them, the Agency for Toxic Substances and Disease Registry (ATSDR) analyzed data from its surveillance system that tracks spills and leaks of hazardous substances. This report describes the results of that analysis, which indicated that, during 2003-2011, a total of 134 events involving HCBs were reported from 15 states. Among those events, 21 (16%) resulted in adverse health effects (i.e., respiratory symptoms, burns, and skin irritation) for 53 persons. The majority (35 [66%]) of these persons were youths.HCBs are hazardous and especially dangerous if detonated in public areas. Increasing awareness of HCBs and their dangers (particularly during summer months) among first-responders, parents, school staff members and others who work with youths might help reduce injuries associated with HCBs.

  12. Determination of the bonding of alkyl monolayers to the Si(111) surface using chemical-shift, scanned-energy photoelectron diffraction

    Energy Technology Data Exchange (ETDEWEB)

    Terry, J.; Linford, M.R.; Wigren, C.; Cao, R.; Pianetta, P.; Chidsey, C.E. [Stanford University, Stanford, California 94309 (United States)

    1997-08-01

    The bonding of alkyl monolayers to Si(111) surfaces has been studied by conventional x-ray photoelectron spectroscopy (XPS) and chemical-shift, scanned-energy photoelectron diffraction (PED) using synchrotron radiation. Two very different wet-chemical methods have been used to prepare the alkyl monolayers: (i) olefin insertion into the H{endash}Si bond on the H{endash}Si(111) surface, and (ii) replacement of Cl on the Cl{endash}Si(111) surface by an alkyl group from an alkyllithium reagent. In both cases, XPS has revealed a C 1s signal chemically shifted to lower binding energy, which we have assigned to carbon bonded to silicon. PED has shown that both preparative methods result in carbon bonded in an atop site with the expected C{endash}Si bond length of 1.85{plus_minus}0.05{Angstrom}. Chemical-shift, scanned-energy photoelectron diffraction is a particularly valuable probe of local structure at surfaces that contain the same element in multiple, chemically distinct environments. {copyright} {ital 1997 American Institute of Physics.}

  13. Determination of the bonding of alkyl monolayers to the Si(111) surface using chemical-shift, scanned-energy photoelectron diffraction

    International Nuclear Information System (INIS)

    Terry, J.; Linford, M.R.; Wigren, C.; Cao, R.; Pianetta, P.; Chidsey, C.E.

    1997-01-01

    The bonding of alkyl monolayers to Si(111) surfaces has been studied by conventional x-ray photoelectron spectroscopy (XPS) and chemical-shift, scanned-energy photoelectron diffraction (PED) using synchrotron radiation. Two very different wet-chemical methods have been used to prepare the alkyl monolayers: (i) olefin insertion into the H endash Si bond on the H endash Si(111) surface, and (ii) replacement of Cl on the Cl endash Si(111) surface by an alkyl group from an alkyllithium reagent. In both cases, XPS has revealed a C 1s signal chemically shifted to lower binding energy, which we have assigned to carbon bonded to silicon. PED has shown that both preparative methods result in carbon bonded in an atop site with the expected C endash Si bond length of 1.85±0.05 Angstrom. Chemical-shift, scanned-energy photoelectron diffraction is a particularly valuable probe of local structure at surfaces that contain the same element in multiple, chemically distinct environments. copyright 1997 American Institute of Physics

  14. Variable impact of late-Quaternary megafaunal extinction in causing ecological state shifts in North and South America

    Science.gov (United States)

    Barnosky, Anthony D.; Lindsey, Emily L.; Villavicencio, Natalia A.; Bostelmann, Enrique; Hadly, Elizabeth A.; Wanket, James; Marshall, Charles R.

    2016-01-01

    Loss of megafauna, an aspect of defaunation, can precipitate many ecological changes over short time scales. We examine whether megafauna loss can also explain features of lasting ecological state shifts that occurred as the Pleistocene gave way to the Holocene. We compare ecological impacts of late-Quaternary megafauna extinction in five American regions: southwestern Patagonia, the Pampas, northeastern United States, northwestern United States, and Beringia. We find that major ecological state shifts were consistent with expectations of defaunation in North American sites but not in South American ones. The differential responses highlight two factors necessary for defaunation to trigger lasting ecological state shifts discernable in the fossil record: (i) lost megafauna need to have been effective ecosystem engineers, like proboscideans; and (ii) historical contingencies must have provided the ecosystem with plant species likely to respond to megafaunal loss. These findings help in identifying modern ecosystems that are most at risk for disappearing should current pressures on the ecosystems' large animals continue and highlight the critical role of both individual species ecologies and ecosystem context in predicting the lasting impacts of defaunation currently underway.

  15. Determination of lifetimes of nuclear excited states using the Recoil Distance Doppler Shift Method in combination with magnetic spectrometers

    Energy Technology Data Exchange (ETDEWEB)

    Doncel, M. [Universidad de Salamanca, Laboratorio de Radiaciones Ionizantes, Salamanca (Spain); Royal Institute of Technology, Department of Physics, Stockholm (Sweden); University of Liverpool, Department of Physics, Oliver Lodge Laboratory, Liverpool (United Kingdom); Gadea, A. [CSIC-University of Valencia, Istituto de Fisica Corpuscular, Valencia (Spain); Valiente-Dobon, J.J. [INFN, Laboratori Nazionali di Legnaro, Legnaro (Italy); Quintana, B. [Universidad de Salamanca, Laboratorio de Radiaciones Ionizantes, Salamanca (Spain); Modamio, V. [INFN, Laboratori Nazionali di Legnaro, Legnaro (Italy); University of Oslo, Oslo (Norway); Mengoni, D. [Dipartimento di Fisica e Astronomia, Universita di Padova, Padova (Italy); Istituto Nazionale di Fisica Nucleare, Sezione di Padova, Padova (Italy); Moeller, O.; Pietralla, N. [Technische Universitaet Darmstadt, Institut fuer Kernphysik, Darmstadt (Germany); Dewald, A. [Institut fuer Kernphysik, Universitaet Koeln (Germany)

    2017-10-15

    The current work presents the determination of lifetimes of nuclear excited states using the Recoil Distance Doppler Shift Method, in combination with spectrometers for ion identification, normalizing the intensity of the peaks by the ions detected in the spectrometer as a valid technique that produces results comparable to the ones obtained by the conventional shifted-to-unshifted peak ratio method. The technique has been validated using data measured with the γ-ray array AGATA, the PRISMA spectrometer and the Cologne plunger setup. In this paper a test performed with the AGATA-PRISMA setup at LNL and the advantages of this new approach with respect to the conventional Recoil Distance Doppler Shift Method are discussed. (orig.)

  16. Using chemical-shift MR imaging to quantify fatty degeneration within supraspinatus muscle due to supraspinatus tendon injuries

    Energy Technology Data Exchange (ETDEWEB)

    Gokalp, Gokhan; Yildirim, Nalan; Yazici, Zeynep [Uludag University Medical Faculty, Department of Radiology, Gorukle, Bursa (Turkey); Ercan, Ilker [Uludag University Medical Faculty, Department of Biostatistics, Gorukle, Bursa (Turkey)

    2010-12-15

    The objective of this study was to prospectively quantify the fatty degeneration of supraspinatus (SSP) muscle due to SSP tendon injuries by using chemical-shift magnetic resonance imaging (CS-MRI). Forty-one patients with suspected rotator cuff tear or impingement examined with MR arthrography were included in the study. The following images were obtained after injection of diluted gadolinium chelate into glenohumeral joint: fat-saturated T1-weighted spin echo in the coronal, axial, and sagittal-oblique plane; fat-saturated T2-weighted and intermediate-weighted fast spin-echo in the coronal-oblique plane; and T1-weighted spin echo in the sagittal-oblique plane. CS-MRI was performed in the coronal plane using a double-echo fast low-angle shot (FLASH) sequence. SSP tendon changes were classified as normal, tendinosis, and partial and complete tear according to MR arthrography findings. Fatty degeneration was quantified after measurement of signal intensity values within the region of interest (ROI) placed over SSP muscle. Signal intensity (SI) suppression ratio and SI index were calculated with the values obtained. Degrees of fatty degeneration depicted in normal subjects and subjects with rotator cuff injuries were compared. Median (min:max) was used as descriptive values. SI suppression ratio was -3.5% (-15.5:3.03) in normal subjects, whereas it was -13.5% (-28.55:-6.60), -30.7% (-41.5:-20.35), and -43.75% (-62:-24.90) in tendinosis, partial and complete tears, respectively. SI index was 0.75% (-6:11.5) in normal subjects. It was 10% (4.50:27), 26.5% (19.15:35.5), and 41% (23.9:57) in tendinosis, partial and complete tears, respectively. The increase in degree of fatty degeneration parallels the seriousness of tendon pathology. CS-MRI is a useful method for grading fat accumulation within SSP muscle. (orig.)

  17. High SNR Acquisitions Improve the Repeatability of Liver Fat Quantification Using Confounder-corrected Chemical Shift-encoded MR Imaging

    Science.gov (United States)

    Motosugi, Utaroh; Hernando, Diego; Wiens, Curtis; Bannas, Peter; Reeder, Scott. B

    2017-01-01

    Purpose: To determine whether high signal-to-noise ratio (SNR) acquisitions improve the repeatability of liver proton density fat fraction (PDFF) measurements using confounder-corrected chemical shift-encoded magnetic resonance (MR) imaging (CSE-MRI). Materials and Methods: Eleven fat-water phantoms were scanned with 8 different protocols with varying SNR. After repositioning the phantoms, the same scans were repeated to evaluate the test-retest repeatability. Next, an in vivo study was performed with 20 volunteers and 28 patients scheduled for liver magnetic resonance imaging (MRI). Two CSE-MRI protocols with standard- and high-SNR were repeated to assess test-retest repeatability. MR spectroscopy (MRS)-based PDFF was acquired as a standard of reference. The standard deviation (SD) of the difference (Δ) of PDFF measured in the two repeated scans was defined to ascertain repeatability. The correlation between PDFF of CSE-MRI and MRS was calculated to assess accuracy. The SD of Δ and correlation coefficients of the two protocols (standard- and high-SNR) were compared using F-test and t-test, respectively. Two reconstruction algorithms (complex-based and magnitude-based) were used for both the phantom and in vivo experiments. Results: The phantom study demonstrated that higher SNR improved the repeatability for both complex- and magnitude-based reconstruction. Similarly, the in vivo study demonstrated that the repeatability of the high-SNR protocol (SD of Δ = 0.53 for complex- and = 0.85 for magnitude-based fit) was significantly higher than using the standard-SNR protocol (0.77 for complex, P magnitude-based fit, P = 0.003). No significant difference was observed in the accuracy between standard- and high-SNR protocols. Conclusion: Higher SNR improves the repeatability of fat quantification using confounder-corrected CSE-MRI. PMID:28190853

  18. Dual-echo, chemical shift gradient-echo magnetic resonance imaging to quantify hepatic steatosis: Implications for living liver donation.

    Science.gov (United States)

    Rinella, Mary E; McCarthy, Richard; Thakrar, Kiran; Finn, John Paul; Rao, Sambasiva M; Koffron, Alan J; Abecassis, Michael; Blei, Andres T

    2003-08-01

    In living liver donation, a fatty liver poses risks for both recipient and donor. Currently, liver biopsy is the standard for assessing the presence and extent of steatosis. The goals of this study were to correlate a steatosis index derived from magnetic resonance imaging (MRI) to the histologic grade on biopsy as well as to determine the topographic distribution of steatosis within the liver. We examined the ability of dual-echo, chemical shift gradient-echo MRI to predict the degree of steatosis on liver biopsy. A total of 22 subjects received both a liver biopsy and detailed MRI evaluation. These individuals included 15 potential living donors and 7 patients with nonalcoholic fatty liver disease. MRI steatosis index was then compared with histologic grade on liver biopsy. The topographic distribution of hepatic steatosis was determined from those subjects in whom MRI detected hepatic steatosis. The steatosis index had a positive correlation with grade of steatosis on liver biopsy (correlation coefficient, 0.84). There was no significant variation in the degree of steatosis among segments. A steatosis index of >0.2 had good positive and negative predictive value for the presence of significant steatosis (>15%) on biopsy. Our quantitative MRI protocol can predict the degree of hepatic steatosis when it is minimal to moderate, and may obviate the need for liver biopsy for the purpose of quantification of steatosis in living donors. Fat saturation added to the MRI protocol may further improve diagnostic accuracy. This technique may be applicable to the larger population with hepatic steatosis.

  19. Using chemical-shift MR imaging to quantify fatty degeneration within supraspinatus muscle due to supraspinatus tendon injuries

    International Nuclear Information System (INIS)

    Gokalp, Gokhan; Yildirim, Nalan; Yazici, Zeynep; Ercan, Ilker

    2010-01-01

    The objective of this study was to prospectively quantify the fatty degeneration of supraspinatus (SSP) muscle due to SSP tendon injuries by using chemical-shift magnetic resonance imaging (CS-MRI). Forty-one patients with suspected rotator cuff tear or impingement examined with MR arthrography were included in the study. The following images were obtained after injection of diluted gadolinium chelate into glenohumeral joint: fat-saturated T1-weighted spin echo in the coronal, axial, and sagittal-oblique plane; fat-saturated T2-weighted and intermediate-weighted fast spin-echo in the coronal-oblique plane; and T1-weighted spin echo in the sagittal-oblique plane. CS-MRI was performed in the coronal plane using a double-echo fast low-angle shot (FLASH) sequence. SSP tendon changes were classified as normal, tendinosis, and partial and complete tear according to MR arthrography findings. Fatty degeneration was quantified after measurement of signal intensity values within the region of interest (ROI) placed over SSP muscle. Signal intensity (SI) suppression ratio and SI index were calculated with the values obtained. Degrees of fatty degeneration depicted in normal subjects and subjects with rotator cuff injuries were compared. Median (min:max) was used as descriptive values. SI suppression ratio was -3.5% (-15.5:3.03) in normal subjects, whereas it was -13.5% (-28.55:-6.60), -30.7% (-41.5:-20.35), and -43.75% (-62:-24.90) in tendinosis, partial and complete tears, respectively. SI index was 0.75% (-6:11.5) in normal subjects. It was 10% (4.50:27), 26.5% (19.15:35.5), and 41% (23.9:57) in tendinosis, partial and complete tears, respectively. The increase in degree of fatty degeneration parallels the seriousness of tendon pathology. CS-MRI is a useful method for grading fat accumulation within SSP muscle. (orig.)

  20. 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.

  1. Modern MRI tools for the characterization of acute demyelinating lesions: value of chemical shift and diffusion-weighted imaging

    International Nuclear Information System (INIS)

    Kueker, W.; Mehnert, F.; Mader, I.; Naegele, T.; Ruff, J.; Gaertner, S.

    2004-01-01

    Acute demyelinating lesions occur in various inflammatory disorders of the CNS. Apart from multiple sclerosis, most cases can be attributed to an overshooting immunological response to infectious agents called acute disseminated encephalomyelitis (ADEM). ADEM, which is mostly characterized by a monophasic course, has a multiphasic variant (MDEM). The early application of corticosteroids has been shown to be beneficial for the outcome; thus, an early diagnosis is highly desirable. Furthermore, the differential diagnosis ruling out neoplastic disorders may be difficult using conventional MRI alone. The potential diagnostic value of advanced MR techniques such as chemical shift imaging (CSI) and diffusion-weighted imaging (DWI) was investigated in a patient with MDEM, who had a new lesion in continuity with the initial disease manifestation. CSI was performed at 1.5 T with a long echo time of 135 ms for the evaluation of N-acetyl-aspartate (NAA) and choline (Cho) and with short TE of 30 ms for macromolecules (mm) and myo-Inositol (mI). DWI was performed using a single-shot isotropic EPI sequence. Whereas acute and chronic areas of demyelination were neither distinguishable on T2- nor on contrast-enhanced T1-weigted images, CSI and DWI revealed different metabolite concentrations and diffusion characteristics within the composite lesion, clearly separating acute from chronic areas of demyelination. In conclusion, the addition of CSI and DWI may add to the diagnostic power of MRI in the setting of demyelinating disorders by identifying areas of acute and chronic demyelination, even in the absence of contrast enhancement. (orig.)

  2. Measurement of sample temperatures under magic-angle spinning from the chemical shift and spin-lattice relaxation rate of 79Br in KBr powder.

    Science.gov (United States)

    Thurber, Kent R; Tycko, Robert

    2009-01-01

    Accurate determination of sample temperatures in solid state nuclear magnetic resonance (NMR) with magic-angle spinning (MAS) can be problematic, particularly because frictional heating and heating by radio-frequency irradiation can make the internal sample temperature significantly different from the temperature outside the MAS rotor. This paper demonstrates the use of (79)Br chemical shifts and spin-lattice relaxation rates in KBr powder as temperature-dependent parameters for the determination of internal sample temperatures. Advantages of this method include high signal-to-noise, proximity of the (79)Br NMR frequency to that of (13)C, applicability from 20 K to 320 K or higher, and simultaneity with adjustment of the MAS axis direction. We show that spin-lattice relaxation in KBr is driven by a quadrupolar mechanism. We demonstrate a simple approach to including KBr powder in hydrated samples, such as biological membrane samples, hydrated amyloid fibrils, and hydrated microcrystalline proteins, that allows direct assessment of the effects of frictional and radio-frequency heating under experimentally relevant conditions.

  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. 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.

  5. Comparison of qualitative and quantitative evaluation of diffusion-weighted MRI and chemical-shift imaging in the differentiation of benign and malignant vertebral body fractures.

    Science.gov (United States)

    Geith, Tobias; Schmidt, Gerwin; Biffar, Andreas; Dietrich, Olaf; Dürr, Hans Roland; Reiser, Maximilian; Baur-Melnyk, Andrea

    2012-11-01

    The objective of our study was to compare the diagnostic value of qualitative diffusion-weighted imaging (DWI), quantitative DWI, and chemical-shift imaging in a single prospective cohort of patients with acute osteoporotic and malignant vertebral fractures. The study group was composed of patients with 26 osteoporotic vertebral fractures (18 women, eight men; mean age, 69 years; age range, 31 years 6 months to 86 years 2 months) and 20 malignant vertebral fractures (nine women, 11 men; mean age, 63.4 years; age range, 24 years 8 months to 86 years 4 months). T1-weighted, STIR, and T2-weighted sequences were acquired at 1.5 T. A DW reverse fast imaging with steady-state free precession (PSIF) sequence at different delta values was evaluated qualitatively. A DW echo-planar imaging (EPI) sequence and a DW single-shot turbo spin-echo (TSE) sequence at different b values were evaluated qualitatively and quantitatively using the apparent diffusion coefficient. Opposed-phase sequences were used to assess signal intensity qualitatively. The signal loss between in- and opposed-phase images was determined quantitatively. Two-tailed Fisher exact test, Mann-Whitney test, and receiver operating characteristic analysis were performed. Sensitivities, specificities, and accuracies were determined. Qualitative DW-PSIF imaging (delta = 3 ms) showed the best performance for distinguishing between benign and malignant fractures (sensitivity, 100%; specificity, 88.5%; accuracy, 93.5%). Qualitative DW-EPI (b = 50 s/mm(2) [p = 1.00]; b = 250 s/mm(2) [p = 0.50]) and DW single-shot TSE imaging (b = 100 s/mm(2) [p = 1.00]; b = 250 s/mm(2) [p = 0.18]; b = 400 s/mm(2) [p = 0.18]; b = 600 s/mm(2) [p = 0.39]) did not indicate significant differences between benign and malignant fractures. DW-EPI using a b value of 500 s/mm(2) (p = 0.01) indicated significant differences between benign and malignant vertebral fractures. Quantitative DW-EPI (p = 0.09) and qualitative opposed-phase imaging (p = 0

  6. Modelling of the chemical state in groundwater infiltration systems

    International Nuclear Information System (INIS)

    Zysset, A.

    1993-01-01

    Groundwater is replenished by water stemming either from precipitations, lakes or rivers. The area where such an infiltration occurs is characterized by a change in the environmental conditions, such as a decrease of the flow velocity and an increase in the solid surface marking the boundary of the flow field. With these changes new chemical processes may become relevant to the transport behavior of contaminants. Since the rates of chemical processes usually are a function of the concentrations of several species, an understanding of infiltration sites may require a multicomponent approach. The present study aims at formulating a mathematical model together with its numerical solution for groundwater infiltration sites. Such a model should improve the understanding of groundwater quality changes related to infiltrating contaminants. The groundwater quality is of vital interest to men because at many places most of the drinking water originates from groundwater. In the first part of the present study two partial models are formulated: one accounting for the transport in a one-dimensional, homogeneous and saturated porous medium, the other accounting for chemical reactions. This second model is initially stated for general kinetic systems. Then, it is specified for two systems, namely for a system governed only by reactions which are fast compared to the transport processes and for a system with biologically mediated redox reactions of dissolved substrates. In the second part of the study a numerical solution to the model is developed. For this purpose, the two partial models are coupled. The coupling is either iterative as in the case of a system with fast reactions or sequential as in all other cases. The numerical solutions of simple test cases are compared to analytical solutions. In the third part the model is evaluated using observations of infiltration sites reported in the literature. (author) figs., tabs., 155 refs

  7. Zirconia-based solid state chemical gas sensors

    CERN Document Server

    Zhuiykov, S

    2000-01-01

    This paper presents an overview of chemical gas sensors, based on solid state technology, that are sensitive to environmental gases, such as O sub 2 , SO sub x , NO sub x , CO sub 2 and hydrocarbons. The paper is focussed on performance of electrochemical gas sensors that are based on zirconia as a solid electrolyte. The paper considers sensor structures and selection of electrode materials. Impact of interfaces on sensor performance is discussed. This paper also provides a brief overview of electrochemical properties of zirconia and their effect on sensor performance. Impact of auxiliary materials on sensors performance characteristics, such as sensitivity, selectivity, response time and recovery time, is also discussed. Dual gas sensors that can be applied for simultaneous monitoring of the concentration of both oxygen and other gas phase components, are briefly considered

  8. A retrospective cohort study of shift work and risk of cancer-specific mortality in German male chemical workers.

    Science.gov (United States)

    Yong, Mei; Nasterlack, Michael; Messerer, Peter; Oberlinner, Christoph; Lang, Stefan

    2014-02-01

    Human evidence of carcinogenicity concerning shift work is inconsistent. In a previous study, we observed no elevated risk of total mortality in shift workers followed up until the end of 2006. The present study aimed to investigate cancer-specific mortality, relative to shift work. The cohort consisted of male production workers (14,038 shift work and 17,105 day work), employed at BASF Ludwigshafen for at least 1 year between 1995 and 2005. Vital status was followed from 2000 to 2009. Cause-specific mortality was obtained from death certificates. Exposure to shift work was measured both as a dichotomous and continuous variable. While lifetime job history was not available, job duration in the company was derived from personal data, which was then categorized at the quartiles. Cox proportional hazard model was used to adjust for potential confounders, in which job duration was treated as a time-dependent covariate. Between 2000 and 2009, there were 513 and 549 deaths among rotating shift and day work employees, respectively. Risks of total and cancer-specific mortalities were marginally lower among shift workers when taking age at entry and job level into consideration and were statistically significantly lower when cigarette smoking, alcohol intake, job duration, and chronic disease prevalence at entry to follow-up were included as explanatory factors. With respect to mortality risks in relation to exposure duration, no increased risks were found in any of the exposure groups after full adjustment and there was no apparent trend suggesting an exposure-response relation with duration of shift work. The present analysis extends and confirms our previous finding of no excess risk of mortality associated with work in the shift system employed at BASF Ludwigshafen. More specifically, there is also no indication of an increased risk of mortality due to cancer.

  9. Molecular Structure and Chemical Shift Assignments of 4-(2-Methoxy-4-Methylphenoxy)Phthalonitrile (C16H12N2O2) By DFT And AB Initio HF Calculations

    International Nuclear Information System (INIS)

    Tarcan, E.

    2008-01-01

    The molecular geometry, gauge including atomic orbital (GIAO) 1 H and 13 C chemical shift values of 4-(2-Methoxy-4-methylphenoxy)phthalonitrile (C 1 6H 1 2N 2 O 2 ) in the ground state have been calculated by using the Hartree-Fock (HF) and density functional methods (B3LYP and BLYP) with 6-31G(d) basis set. The results of the optimized molecular structure are presented and compared with the experimental X-ray diffraction. The optimized bond length numbers with bond angels are in good agreement with the X-ray data

  10. Paradigm shifts and the interplay between state, business and civil sectors

    Science.gov (United States)

    Encarnação, Sara; Santos, Fernando P.; Santos, Francisco C.; Blass, Vered; Pacheco, Jorge M.; Portugali, Juval

    2016-12-01

    The recent rise of the civil sector as a main player of socio-political actions, next to public and private sectors, has largely increased the complexity underlying the interplay between different sectors of our society. From urban planning to global governance, analysis of these complex interactions requires new mathematical and computational approaches. Here, we develop a novel framework, grounded on evolutionary game theory, to envisage situations in which each of these sectors is confronted with the dilemma of deciding between maintaining a status quo scenario or shifting towards a new paradigm. We consider multisector conflicts regarding environmentally friendly policies as an example of application, but the framework developed here has a considerably broader scope. We show that the public sector is crucial in initiating the shift, and determine explicitly under which conditions the civil sector-reflecting the emergent reality of civil society organizations playing an active role in modern societies-may influence the decision-making processes accruing to other sectors, while fostering new routes towards a paradigm shift of the society as a whole. Our results are shown to be robust to a wide variety of assumptions and model parametrizations.

  11. CSSI-PRO: a method for secondary structure type editing, assignment and estimation in proteins using linear combination of backbone chemical shifts

    International Nuclear Information System (INIS)

    Swain, Monalisa; Atreya, Hanudatta S.

    2009-01-01

    Estimation of secondary structure in polypeptides is important for studying their structure, folding and dynamics. In NMR spectroscopy, such information is generally obtained after sequence specific resonance assignments are completed. We present here a new methodology for assignment of secondary structure type to spin systems in proteins directly from NMR spectra, without prior knowledge of resonance assignments. The methodology, named Combination of Shifts for Secondary Structure Identification in Proteins (CSSI-PRO), involves detection of specific linear combination of backbone 1 H α and 13 C' chemical shifts in a two-dimensional (2D) NMR experiment based on G-matrix Fourier transform (GFT) NMR spectroscopy. Such linear combinations of shifts facilitate editing of residues belonging to α-helical/β-strand regions into distinct spectral regions nearly independent of the amino acid type, thereby allowing the estimation of overall secondary structure content of the protein. Comparison of the predicted secondary structure content with those estimated based on their respective 3D structures and/or the method of Chemical Shift Index for 237 proteins gives a correlation of more than 90% and an overall rmsd of 7.0%, which is comparable to other biophysical techniques used for structural characterization of proteins. Taken together, this methodology has a wide range of applications in NMR spectroscopy such as rapid protein structure determination, monitoring conformational changes in protein-folding/ligand-binding studies and automated resonance assignment

  12. Evidence of chemical-potential shift with hole doping in Bi2Sr2CaCu2O8+δ

    International Nuclear Information System (INIS)

    Shen, Z.; Dessau, D.S.; Wells, B.O.; Olson, C.G.; Mitzi, D.B.; Lombado, L.; List, R.S.; Arko, A.J.

    1991-01-01

    We have performed photoemission studies on high-quality Bi 2 Sr 2 CaCu 2 O 8+δ samples with various δ. 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

  13. Nonsuppressing normal thymus on chemical-shift MR imaging and anterior mediastinal lymphoma. Differentiation with diffusion-weighted MR imaging by using the apparent diffusion coefficient

    International Nuclear Information System (INIS)

    Priola, Adriano Massimiliano; Priola, Sandro Massimo; Gned, Dario; Veltri, Andrea; Giraudo, Maria Teresa

    2018-01-01

    To prospectively evaluate usefulness of the apparent diffusion coefficient (ADC) in differentiating anterior mediastinal lymphoma from nonsuppressing normal thymus on chemical-shift MR, and to look at the relationship between patient age and ADC. Seventy-three young subjects (25 men, 48 women; age range, 9-29 years), who underwent chemical-shift MR and diffusion-weighted MR were divided into a normal thymus group (group A, 40 subjects), and a lymphoma group (group B, 33 patients). For group A, all subjects had normal thymus with no suppression on opposed-phase chemical-shift MR. Two readers measured the signal intensity index (SII) and ADC. Differences in SII and ADC between groups were tested using t-test. ADC was correlated with age using Pearson correlation coefficient. Mean SII±standard deviation was 2.7±1.8% for group A and 2.2±2.4% for group B, with no significant difference between groups (P=.270). Mean ADC was 2.48±0.38 x 10 -3 mm 2 /s for group A and 1.24±0.23 x 10 -3 mm 2 /s for group B. A significant difference between groups was found (P<.001), with no overlap in range. Lastly, significant correlation was found between age and ADC (r=0.935, P<.001) in group A. ADC of diffusion-weighted MR is a noninvasive and accurate parameter for differentiating lymphoma from nonsuppressing thymus on chemical-shift MR in young subjects. (orig.)

  14. Backbone and sidechain methyl Ile (δ1), Leu and Val chemical shift assignments of RDE-4 (1-243), an RNA interference initiation protein in C. elegans.

    Science.gov (United States)

    Chiliveri, Sai Chaitanya; Kumar, Sonu; Marelli, Udaya Kiran; Deshmukh, Mandar V

    2012-10-01

    The RNAi pathway of several organisms requires presence of double stranded RNA binding proteins for functioning of Dicer in gene regulation. In C. elegans, a double stranded RNA binding protein, RDE-4 (385 aa, 44 kDa) recognizes long exogenous dsRNA and initiates the RNAi pathway. We have achieved complete backbone and stereospecific methyl sidechain Ile (δ1), Leu and Val chemical shifts of first 243 amino acids of RDE-4, namely RDE-4ΔC.

  15. Structure, solvent, and relativistic effects on the NMR chemical shifts in square-planar transition-metal complexes: assessment of DFT approaches

    Czech Academy of Sciences Publication Activity Database

    Vícha, J.; Novotný, J.; Straka, Michal; Repisky, M.; Ruud, K.; Komorovsky, S.; Marek, R.

    2015-01-01

    Roč. 17, č. 38 (2015), s. 24944-24955 ISSN 1463-9076 R&D Projects: GA ČR(CZ) GA14-03564S Institutional support: RVO:61388963 Keywords : NMR chemical shifts * transition metal complexes * relativistic effects * method calibration Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 4.449, year: 2015 http://pubs.rsc.org/en/content/articlepdf/2015/cp/c5cp04214c

  16. The 1,5-H-shift in 1-butoxy: A case study in the rigorous implementation of transition state theory for a multirotamer system

    Science.gov (United States)

    Vereecken, Luc; Peeters, Jozef

    2003-09-01

    The rigorous implementation of transition state theory (TST) for a reaction system with multiple reactant rotamers and multiple transition state conformers is discussed by way of a statistical rate analysis of the 1,5-H-shift in 1-butoxy radicals, a prototype reaction for the important class of H-shift reactions in atmospheric chemistry. Several approaches for deriving a multirotamer TST expression are treated: oscillator versus (hindered) internal rotor models; distinguishable versus indistinguishable atoms; and direct count methods versus degeneracy factors calculated by (simplified) direct count methods or from symmetry numbers and number of enantiomers, where applicable. It is shown that the various treatments are fully consistent, even if the TST expressions themselves appear different. The 1-butoxy H-shift reaction is characterized quantum chemically using B3LYP-DFT; the performance of this level of theory is compared to other methods. Rigorous application of the multirotamer TST methodology in an harmonic oscillator approximation based on this data yields a rate coefficient of k(298 K,1 atm)=1.4×105 s-1, and an Arrhenius expression k(T,1 atm)=1.43×1011 exp(-8.17 kcal mol-1/RT) s-1, which both closely match the experimental recommendations in the literature. The T-dependence is substantially influenced by the multirotamer treatment, as well as by the tunneling and fall-off corrections. The present results are compared to those of simplified TST calculations based solely on the properties of the lowest energy 1-butoxy rotamer.

  17. Spin-orbit ZORA and four-component Dirac-Coulomb estimation of relativistic corrections to isotropic nuclear shieldings and chemical shifts of noble gas dimers.

    Science.gov (United States)

    Jankowska, Marzena; Kupka, Teobald; Stobiński, Leszek; Faber, Rasmus; Lacerda, Evanildo G; Sauer, Stephan P A

    2016-02-05

    Hartree-Fock and density functional theory with the hybrid B3LYP and general gradient KT2 exchange-correlation functionals were used for nonrelativistic and relativistic nuclear magnetic shielding calculations of helium, neon, argon, krypton, and xenon dimers and free atoms. Relativistic corrections were calculated with the scalar and spin-orbit zeroth-order regular approximation Hamiltonian in combination with the large Slater-type basis set QZ4P as well as with the four-component Dirac-Coulomb Hamiltonian using Dyall's acv4z basis sets. The relativistic corrections to the nuclear magnetic shieldings and chemical shifts are combined with nonrelativistic coupled cluster singles and doubles with noniterative triple excitations [CCSD(T)] calculations using the very large polarization-consistent basis sets aug-pcSseg-4 for He, Ne and Ar, aug-pcSseg-3 for Kr, and the AQZP basis set for Xe. For the dimers also, zero-point vibrational (ZPV) corrections are obtained at the CCSD(T) level with the same basis sets were added. Best estimates of the dimer chemical shifts are generated from these nuclear magnetic shieldings and the relative importance of electron correlation, ZPV, and relativistic corrections for the shieldings and chemical shifts is analyzed. © 2015 Wiley Periodicals, Inc.

  18. MR imaging of osteonecrosis using frequency selective chemical shift sequences; Neue Aspekte in der MR-Diagnostik der Osteonekrose: Selektive Fett/Wasser-Bildgebung

    Energy Technology Data Exchange (ETDEWEB)

    Duda, S H [Abt. fuer Radiologische Diagnostik, Tuebingen Univ. (Germany); Laniado, M [Abt. fuer Radiologische Diagnostik, Tuebingen Univ. (Germany); Schick, F [Inst. fuer Physik, Tuebingen Univ. (Germany)

    1994-12-31

    The MR appearance of osteonecrosis was assessed on selective fat- and water images to further evaluate the nature of double-line sign. Conventional T1- and T2-weighted SE and frequency selective chemical shift images of eight patients with avascular necrosis of the femoral head and three patients with bone infarcts were retrospectively reviewed. Eight of 11 patients showed a double-line sign on T2-weighted SE images. In these cases, correlation with selective water images revealed that a chemical shift artifact contributed to appearance and location of the hyperintense line. The authors conclude that chemical shift imaging improves our understanding of the nature of the double-line sign. (orig.) [Deutsch] Das MR-tomographische Erscheinungsbild der Osteonekrose auf selektiven Fett- und Wasserbildern wurde analysiert, um das in der Literatur beschriebene Doppellinienzeichen naeher zu untersuchen. Hierfuer wurden sowohl die herkoemmlichen T1- und T2-gewichteten Spin-Echo-Sequenzen herangezogen, als auch frequenzselektive Bilder, die aufgrund chemischer Verschiebung gewonnen wurden (1,5 T). Es wurden die Untersuchungen von acht Patienten mit avaskulaerer Hueftkopfnekrose und von drei Patienten mit Knocheninfarkten retrospektiv ausgewertet. Acht von 11 Patienten zeigten ein Doppellinienzeichen auf den T2-gewichteten Bildern. Die Korrelation mit den selektiven Wasserbildern ergab, dass durch chemische Verschiebung bedingte Artefakte das Erscheinungsbild und den Ort der hyperintensen Linie beeinflussten. Die Bildgebung mit Hilfe der chemischen Verschiebung verbessert unser Verstaendnis der MRT-Charakteristika der Osteonekrose. (orig.)

  19. Market shifting

    Energy Technology Data Exchange (ETDEWEB)

    Forst, Michael

    2013-11-01

    After years of oversupply and artificially low module pricing, market analysts believe that the solar industry will begin to stabilize by 2017. While the market activities are shifting from Europe to the Asia Pacific region and the United States, the solar shakeout continues to be in full swing including solar cell and module manufacturing. (orig.)

  20. Hadronic shift of the stable dilambda state and the existence of double hypernuclei

    International Nuclear Information System (INIS)

    Kerbikov, B.O.

    1984-01-01

    The problem of the mass of a six-quark bag with the strangeness S = -2 (the H particle) is discussed in connection with the data on double hypernuclei. It is shown that if the mass of the H particle, as predicted by the bag model, were several tens of MeV below the ΛΛ channel threshold, then the decay time of the 6 /sub LambdaLambda/He double hypernucleus in the 6 /sub LambdaLambda/He→H+α channel would be 10 -18 to 10 -20 sec. Experimentally observed double hypernuclei have the life time 10 -10 sec, which is consistent with the existence of the H particle provided that its mass is close to the ΛΛ threshold. The influence of the hadronic channels ΛΛ, NΨ and ΣΣ on the mass of the H particle is investigated. It is shown that because of coupling to hadronic channels the mass of the H particle decreases by 150--200 MeV. The existence of a large hadronic shift leads to the fact that the H particle is significantly below the ΛΛ channel threshold. Thus, with account of the hadronic shift the contradiction between the observation of double hypernuclei and the existence of the H particle is extremely acute

  1. Neurosurgery and brain shift: review of the state of the art and main contributions of robotics

    Directory of Open Access Journals (Sweden)

    Karin Correa-Arana

    2017-09-01

    Full Text Available This paper presents a review about neurosurgery, robotic assistants in this type of procedure, and the approach to the problem of brain tissue displacement, including techniques for obtaining medical images. It is especially focused on the phenomenon of brain displacement, commonly known as brain shift, which causes a loss of reference between the preoperative images and the volumes to be treated during image-guided surgery. Hypothetically, with brain shift prediction and correction for the neuronavigation system, minimal invasion trajectories could be planned and shortened. This would reduce damage to functional tissues and possibly lower the morbidity and mortality in delicate and demanding medical procedures such as the removal of a brain tumor. This paper also mentions other issues associated with neurosurgery and shows the way robotized systems have helped solve these problems. Finally, it highlights the future perspectives of neurosurgery, a branch of medicine that seeks to treat the ailments of the main organ of the human body from the perspective of many disciplines.

  2. Reproducibility and influencing factors of 31P MR spectroscopy in rabbit liver with two-dimensional chemical shift imaging

    International Nuclear Information System (INIS)

    Yu Risheng; Sun Jianzhong; Ding Wenhong; Xu Xiufang; Wang Zhikang

    2009-01-01

    Objective: To investigate the reproducibility and influencing factors of relative quantification of phosphorus metabolites with two-dimensional chemical shift imaging (2D CSI) in rabbit liver. Methods: Using 2D CSI MRS, 500 ml phosphate (NaH 2 PO 4 ) solution phantom with 0.05 mol/L concentration and one healthy rabbit were scanned 30 times respectively in one day and rescanned 30 times in the next day, and the stability of MR scanner and reproducibility of within-run and between-days in the same individual were analyzed. Each of thirty rabbits was scanned and rescanned one time respectively in different days, and the reproducibility of between-days in one group was analyzed. The data were statistically analyzed with t tests. Results: (1) Phosphate solution phantom had a good reproducibility of within-run with the coefficient variation (CV) of 4.92% and 5.12% respectively in different two days. No significant change of phosphorus metabolites was detected in between-days, which was 16.68±0.82 and 16.56± 0.85 respectively (t=0.665, P>0.05). (2) The CV of metabolites in one healthy rabbit ranged from 8.04% to 34.13%. Among the metabolites, β-ATP had the best reproducibility with the CV less than 10%. PME was 0.88±0.28 and 0.88±0.30, PDE was 4.35±0.66 and 4.35±0.66, Pi was 0.95±0.30 and 0.97±0.28, α-ATP was 5.58±0.60 and 5.61±0.61, β-ATP was 2.70±0.22 and 2.71± 0.22, γ-ATP was 2.20±0.63 and 2.18±0.44 respectively, no significant changes of metabolites were detected in between-days (P>0.05). (3) The CV of metabolites in 30 healthy rabbits ranged from 8.48% to 36.21%. Among the metabolites, β-ATP had the best reproducibility with CV less than 10%. PME was 0.84±0.30 and 0.79±0.28, PDE was 4.29±0.72 and 3.94±0.84, Pi was 0.91±0.28 and 0.92± 0.31, α-ATP was 5.65±0.66 and 5.36±0.60, β-ATP was 2.71±0.23 and 2.66±0.25, γ-ATP was 2.07±0.29 and 1.99±0.37 respectively, no significant changes of metabolites were detected in between-days (P>0

  3. Effects of a 12-hour shift on mood states and sleepiness of Neonatal Intensive Care Unit nurses.

    Science.gov (United States)

    Ferreira, Tadeu Sartini; Moreira, Clarice Zinato; Guo, James; Noce, Franco

    2017-03-09

    To assess the effect of a 12-hour shift on mood states and sleepiness at the beginning and end of the shift. Quantitative, cross-sectional and descriptive study.It was conducted with 70 neonatal intensive care unit nurses. The Brunel Mood Scale (BRUMS), Karolinska Sleepiness Scale (KSS), and a socio-demographic profile questionnaire were administered. When the KSS and BRUMS scores were compared at the beginning of the shift associations were found with previous sleep quality (p ≤ 0.01), and quality of life (p ≤ 0.05). Statistical significant effects on BRUMS scores were also associated with previous sleep quality, quality of life, liquid ingestion, healthy diet, marital status, and shift work stress. When the beginning and end of the shift were compared, different KSS scores were seen in the group of all nurses and in the night shift one. Significant vigor and fatigue scores were observed within shift groups. A good night's sleep has positive effects on the individual`s mood states both at the beginning and the end of the shift. The self-perception of a good quality of life also positively influenced KSS and BRUMS scores at the beginning and end of the shift. Proper liquid ingestion led to better KSS and BRUMS scores. Evaluar el efecto de un turno de 12 horas en estados de ánimo y somnolencia al principio y al final del turno. Estudio cuantitativo, transversal y descriptivo.Se realizó con 70 enfermeras de unidades de cuidados intensivos neonatales. Se administró la Escala de Humor Brunel (BRUMS), la Escala de Somnolencia de Karolinska (KSS) y un cuestionario de perfil sociodemográfico. Cuando se compararon las puntuaciones de KSS y BRUMS al comienzo del turno se encontraron asociaciones con calidad de sueño previa (p ≤ 0,01) y calidad de vida (p ≤ 0,05). Los efectos estadísticos significativos en las puntuaciones de BRUMS también se asociaron con la calidad previa del sueño, la calidad de vida, la ingestión de líquidos, la dieta saludable, el

  4. Optimized surface-slab excited-state muffin-tin potential and surface core level shifts

    International Nuclear Information System (INIS)

    Rundgren, J.

    2003-01-01

    An optimized muffin-tin (MT) potential for surface slabs with preassigned surface core-level shifts (SCLS's) is presented. By using the MT radii as adjustable parameters the model is able to conserve the definition of the SCLS with respect to the bulk and concurrently to generate a potential that is continuous at the MT radii. The model is conceived for elastic electron scattering in a surface slab with exchange-correlation interaction described by the local density approximation. The model employs two data bases for the self-energy of the signal electron (after Hedin and Lundqvist or Sernelius). The potential model is discussed in detail with two surface structures Be(101-bar0), for which SCLS's are available, and Cu(111)p(2x2)Cs, in which the close-packed radii of the atoms are extremely different. It is considered plausible that tensor LEED based on an optimized MT potential can be used for determining SCLS's

  5. Hadronic shift and the probability of producing the dilambda state H

    International Nuclear Information System (INIS)

    Badalyan, A.M.; Simonov, Y.A.

    1982-01-01

    The Jaffe-Low formalism and the constituent-quark bag model are used to establish a relation between the H mass in the six-quark bag and the experimental manifestations of a pole in the S matrix. The previous results of the constituent-quark bag-model analysis of the NN system are applied to the #betta##betta# system via the SU(3) flavor symmetry. The hadronic shift of the H is approx.20 MeV, that is, much smaller than was previously expected. In the case where the H is above the #betta##betta# threshold its width is large (GAMMA/Eapprox.1), which makes the experimental observation of the H very difficult. The theoretical estimate of the H-production cross section is sigma/sub H/approx.1 nb, which is much smaller than the experimental upper limit (130 nb>sigma/sup up//sub H/>30 nb)

  6. Two-loop self-energy in the Lamb shift of the ground and excited states of hydrogenlike ions

    Science.gov (United States)

    Yerokhin, V. A.

    2018-05-01

    The two-loop self-energy correction to the Lamb shift of hydrogenlike ions is calculated for the 1 s , 2 s , and 2 p1 /2 states and nuclear charge numbers Z =30 -100 . The calculation is performed to all orders in the nuclear binding strength parameter Z α . As compared to previous calculations of this correction, numerical accuracy is improved by an order of magnitude and the region of the nuclear charges is extended. An analysis of the Z dependence of the obtained results demonstrates their consistency with the known Z α -expansion coefficients.

  7. Reaction Hamiltonian and state-to-state description of chemical reactions

    International Nuclear Information System (INIS)

    Ruf, B.A.; Kresin, V.Z.; Lester, W.A. Jr.

    1985-08-01

    A chemical reaction is treated as a quantum transition from reactants to products. A specific reaction Hamiltonian (in second quantization formalism) is introduced. The approach leads to Franck-Condon-like factor, and adiabatic method in the framework of the nuclear motion problems. The influence of reagent vibrational state on the product energy distribution has been studied following the reaction Hamiltonian method. Two different cases (fixed available energy and fixed translational energy) are distinguished. Results for several biomolecular reactions are presented. 40 refs., 5 figs

  8. 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

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

    Energy Technology Data Exchange (ETDEWEB)

    Manojkumar, P.A., E-mail: manoj@igcar.gov.in [Indira Gandhi Centre for Atomic Research, Kalpakkam 603102 (India); Chirayath, V.A.; Balamurugan, A.K.; Krishna, Nanda Gopala; Ilango, S.; Kamruddin, M.; Amarendra, G.; Tyagi, A.K. [Indira Gandhi Centre for Atomic Research, Kalpakkam 603102 (India); Raj, Baldev [National Institute of Advanced Studies, Bangalore 560 012 (India)

    2016-09-15

    Highlights: • Low energy nitrogen ion implantation in titanium was studied. • Chemical and defect states were analyzed using SIMS, XPS and PAS. • SIMS and depth resolved XPS data showed good agreement. • Depth resolved defect and chemical states information were revealed. • Formation of 3 layers of defect states proposed to fit PAS results. - Abstract: Evolution of chemical states and defect structure in titanium during low energy nitrogen ion implantation by Plasma Immersion Ion Implantation (PIII) process is studied. The underlying process of chemical state evolution is investigated using secondary ion mass spectrometry and X-ray photoelectron spectroscopy. The implantation induced defect structure evolution as a function of dose is elucidated using variable energy positron annihilation Doppler broadening spectroscopy (PAS) and the results were corroborated with chemical state. Formation of 3 layers of defect state was modeled to fit PAS results.

  10. 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.

  11. Shifting characteristics of ecstasy users ages 12-34 in the United States, 2007-2014.

    Science.gov (United States)

    Palamar, Joseph J; Mauro, Pia M; Han, Benjamin H; Martins, Silvia S

    2017-12-01

    Ecstasy/MDMA has been one of the most prevalent party drugs for decades, and powder ecstasy recently increased in popularity. We examined trends in use to determine who to best target for prevention and harm reduction. Secondary analysis of the 2007-2014 National Survey on Drug Use and Health, a repeated cross-sectional, nationally representative probability sample, was conducted. Linear trends in past-year ecstasy use and trends in demographic and other past-year substance use characteristics among ecstasy users were examined among participants ages 12-34 (N=332,560). Past-year prevalence of ecstasy use was stable across years at 2% (P=0.693). Over time, the proportion of ecstasy users with a college degree increased from 11.5% in 2007/08 to 24.5% in 2013/14 (Pusers who were age 12-17 decreased, as did proportions of users who are non-Hispanic black, and reported income users (Psusers and ease of obtaining LSD increased (Psusers is growing-particularly use of otherwise rare substances such as tryptamines. Results inform prevention and harm reduction strategies in this increasingly shifting group of ecstasy users. Copyright © 2017 Elsevier B.V. All rights reserved.

  12. Long-lived, charge-shift states in heterometallic, porphyrin-based dendrimers formed via click chemistry.

    Science.gov (United States)

    Le Pleux, Loïc; Pellegrin, Yann; Blart, Errol; Odobel, Fabrice; Harriman, Anthony

    2011-05-26

    A series of multiporphyrin clusters has been synthesized and characterized in which there exists a logical gradient for either energy or electron transfer between the porphyrins. A central free-base porphyrin (FbP), for example, is equipped with peripheral zinc(II) porphyrins (ZnP) which act as ancillary light harvesters and transfer excitation energy to the FbP under visible light illumination. Additional energy-transfer steps occur at the triplet level, and the series is expanded by including magnesium(II) porphyrins and/or tin(IV) porphyrins as chromophores. Light-induced electron transfer is made possible by incorporating a gold(III) porphyrin (AuP(+)) into the array. Although interesting by themselves, these clusters serve as control compounds by which to understand the photophysical processes occurring within a three-stage dendrimer comprising an AuP(+) core, a second layer formed from four FbP units, and an outer layer containing 12 ZnP residues. Here, illumination into a peripheral ZnP leads to highly efficient electronic energy transfer to FbP, followed by charge transfer to the central AuP(+). Charge recombination within the resultant charge-shift state is intercepted by secondary hole transfer to the ZnP, which occurs with a quantum yield of around 20%. The final charge-shift state survives for some microseconds in fluid solution at room temperature.

  13. New SU(1,1) position-dependent effective mass coherent states for a generalized shifted harmonic oscillator

    International Nuclear Information System (INIS)

    Yahiaoui, Sid-Ahmed; Bentaiba, Mustapha

    2014-01-01

    A new SU(1,1) position-dependent effective mass coherent states (PDEM CS) related to the shifted harmonic oscillator (SHO) are deduced. This is accomplished by applying a similarity transformation to the generally deformed oscillator algebra (GDOA) generators for PDEM systems and a new set of operators that close the su(1,1) Lie algebra are constructed, being the PDEM CS of the basis for its unitary irreducible representation. From the Lie algebra generators, we evaluate the uncertainty relationship for a position and momentum-like operators in the PDEM CS and show that it is minimized in the sense of Barut–Girardello CS. We prove that the deduced PDEM CS preserve the same analytical form than those of Glauber states. As an illustration of our procedure, we depicted the 2D-probability density in the PDEM CS for SHO with the explicit form of the mass distribution with no singularities. (paper)

  14. 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.

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

    International Nuclear Information System (INIS)

    Min, Ji Hye; Kim, Young Kon; Lim, Sanghyeok; Jeong, Woo Kyoung; Choi, Dongil; Lee, Won Jae

    2015-01-01

    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

  16. 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. Copyright © 2013 John Wiley & Sons, Ltd.

  17. 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. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  18. Detection of fat in focal liver lesions using chemical-shift MR imaging: its significance in patients with and without hepatic cirrhosis

    International Nuclear Information System (INIS)

    Martin, J.

    1999-01-01

    To determine the utility of the chemical shift technique in MRI for the detection of fact in focal hepatic lesions and to see its significance in patients with and without hepatic cirrhosis. 159 patients with 207 hepatic lesions were studied using MRI (IT). Two groups were established: a) patients with hepatic cirrhosis (n=63 with 69 lesions) and b) patients without cirrhosis (n=96 with 138 lesions). Images were obtained in phase (P) and in opposite phase (OP) with gradient echo sequences (RG). The parameter used to differentiate the lesions with fat from those without fat was the variation percentage of the intensity of the signal (VIS) between the images in P and in OP. The statistical valuation was carried out using Student's t tests and the area under the ROC curve. The chemical shift technique detected fat in 25 lesions (12%), 10 hepatocarcinomas in the patients with cirrhosis and two angiomyolipomas and 13 nodular fat infiltrations in the patients who did not have cirrhosis. The average VIS percentage in the 10 hepatocarcinomas was 174.77% (ranging from 88.64% to 369.33%) while in the remaining 59 hepatocarcinomas it was -4.03% (ranging from 12.79% to -19.10%) (p=0.003). In the patients who did not have cirrhosis the average VIS percentage of the lesions with fat was 161.23 (ranging from 19.82 to 605.78) while in the lesions without fat it was -0.41 (ranging from -18.96 to 19.52) (p=0.003). The area under the ROC curve was 1 for the VIS parameter. The chemical shift technique allowed for fat to be detected within hepatic lesions. Based on our study, a nodule with fat in a patient with hepatic cirrhosis is suspected to have hepatocarcinomas while in patients who do not suffer from cirrhosis the existence of fat in a nodule favours its bening nature. (Author) 39 refs

  19. 1H and 13C NMR Chemical Shift Assignments and Conformational Analysis for the Two Diastereomers of the Vitamin K Epoxide Reductase Inhibitor Brodifacoum

    International Nuclear Information System (INIS)

    Cort, John R.; Cho, Herman M.

    2009-01-01

    Proton and 13C NMR chemical shift assignments and 1H-1H scalar couplings for the two diastereomers of the vitamin K epoxide reductase (VKOR) inhibitor brodifacoum have been determined from acetone solutions containing both diastereomers. Data were obtained from homo- and heteronuclear correlation spectra acquired at 1H frequencies of 750 and 900 MHz over a 268-303 K temperature range. Conformations inferred from scalar coupling and 1-D NOE measurements exhibit large differences between the diastereomers. Pacific Northwest National Laboratory is operated by Battelle for the US Department of Energy.

  20. 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)

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

    International Nuclear Information System (INIS)

    Araujo, Marcelo F. de; Vieira, Ivo J. Curcino; Braz-Filho, Raimundo; Carvalho, Mario G. de

    2012-01-01

    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 1 H, 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 1 H and 13 C NMR chemical shift assignments. (author)

  2. Hydrogen exchange rate of tyrosine hydroxyl groups in proteins as studied by the deuterium isotope effect on C(zeta) chemical shifts.

    Science.gov (United States)

    Takeda, Mitsuhiro; Jee, Jungoo; Ono, Akira Mei; Terauchi, Tsutomu; Kainosho, Masatsune

    2009-12-30

    We describe a new NMR method for monitoring the individual hydrogen exchange rates of the hydroxyl groups of tyrosine (Tyr) residues in proteins. The method utilizes (2S,3R)-[beta(2),epsilon(1,2)-(2)H(3);0,alpha,beta,zeta-(13)C(4);(15)N]-Tyr, zeta-SAIL Tyr, to detect and assign the (13)C(zeta) signals of Tyr rings efficiently, either by indirect (1)H-detection through 7-8 Hz (1)H(delta)-(13)C(zeta) spin couplings or by direct (13)C(zeta) observation. A comparison of the (13)C(zeta) chemical shifts of three Tyr residues of an 18.2 kDa protein, EPPIb, dissolved in H(2)O and D(2)O, revealed that all three (13)C(zeta) signals in D(2)O appeared at approximately 0.13 ppm ( approximately 20 Hz at 150.9 MHz) higher than those in H(2)O. In a H(2)O/D(2)O (1:1) mixture, however, one of the three signals for (13)C(zeta) appeared as a single peak at the averaged chemical shifts, and the other two appeared as double peaks at exactly the same chemical shifts in H(2)O and D(2)O, in 50 mM phosphate buffer (pH 6.6) at 40 degrees C. These three peaks were assigned to Tyr-36, Tyr-120, and Tyr-30, from the lower to higher chemical shifts, respectively. The results indicate that the hydroxyl proton of Tyr-120 exchanges faster than a few milliseconds, whereas those of Tyr-30 and Tyr-36 exchange more slowly. The exchange rate of the Tyr-30 hydroxyl proton, k(ex), under these conditions was determined by (13)C NMR exchange spectroscopy (EXSY) to be 9.2 +/- 1.1 s(-1). The Tyr-36 hydroxyl proton, however, exchanges too slowly to be determined by EXSY. These profound differences among the hydroxyl proton exchange rates are closely related to their relative solvent accessibility and the hydrogen bonds associated with the Tyr hydroxyl groups in proteins.

  3. Theory of g-shift and linewidth in CeP excited state EPR

    International Nuclear Information System (INIS)

    Yang, D.; Cooper, B.R.; Huang, C.Y.; Sugawara, K.

    1979-01-01

    The Mori-Zwanzig memory function formalism was used to analyze the observed excited state EPR mode in CeP. The mixing of the Zeeman-split crystal-field excitation by the exchange, particularly among those with degenerate frequencies, yields a normal mode determining the observed low-frequency spectrum. This is illustrated by calculation with Heisenberg exchange which yields a single peak in qualitative agreement with the experiment

  4. Shifting State Partnership Program Resources to the Asia-Pacific Region

    Science.gov (United States)

    2013-03-01

    deployed along with embedded Soldiers from their partnered states in the form of Bilateral Embedded Support Teams (BEST). In these two cases , Illinois...services, and tourism and their contributions to quality of life.38 SPP built partner capacity to deter, prevent, and prepare for threats to trade and...Bulgaria, Czech Republic, and Macedonia. SOUTHCOM SPP includes Guatamala, Uruguay, Trinidad-Tobago, Jamaica, Venezuela, Guyana, Virgin Islands, Ecuador

  5. Quantum-chemical investigation of the 1,2-proton shift in protonated five-membered aromatic heterocycles

    International Nuclear Information System (INIS)

    Abronin, I.A.; Gorb, L.G.; Litvinov, V.P.

    1985-01-01

    Calculations of the energetics of the 1,2-proton shift in protonated five-membered aromatic heterocycles - pyrrole, furan, and thiophene - have been carried out by the SCF MO LCAO method in the MINDO/3 approximation and nonempirically on the OST-3GF (OST-3GF) basis. The general features of this process, and also the influence of solvation and of taking into account the vacant d-AOs of the sulfur atom in the protonated form of thiophene on the results of the calculation are considered. The results obtained have been used for a discussion of the activity and selectivity of the heterocycles considered in aromatic electrophilic substitution reactions

  6. Structural effects on the chemical shift of exo - endo and exo - exo tetra cyclo dodecane; Efeitos estruturais sobre o deslocamento quimico de exo-endo e exo-exo tetraciclododecanos

    Energy Technology Data Exchange (ETDEWEB)

    Leal, Katia Zaccur [Universidade Federal Fluminense, Niteroi, RJ (Brazil). Dept. de Fisico-Quimica; Costa, Valentim E.U. [Rio Grande do Sul Univ., Porto Alegre, RS (Brazil). Dept. de Quimica Organica; Seidl, Peter Rudolf [Instituto Militar de Engenharia (IME), Rio de Janeiro, RJ (Brazil). Secao de Quimica

    1992-12-31

    The systematic investigation of rigid cyclic molecules has provided a basis for a number of concepts presently employed in NMR spectroscopy. Bicyclic systems of norbornyl family have been extensively studied in this respect but their tetracyclic analogs have received much less attention. The large number of peaks that into narrow chemical shift ranges and the presence of intramolecular affects that arise from groups brought into close proximity have probably been responsible for this state of affairs. As in the case of other polycyclic rings of interest, more data from model systems would be desirable. We have analysed the proton and carbon-13 spectra of endo-endo tetra cyclo [6.1.1{sup 3,6}.0{sup 2,7}] dodeca-4-en-10-ol (1A) and its analogs and found interactions between atoms that are four or more bonds away. Although these upfield {delta} and {delta}{sub E} effects could be accounted for by invoking steric interactions similar to those that give to the well-know {gamma}gauche effect, there are other discrepancies between carbon-13 chemical shifts of tetracyclic dodecanes and their bicyclic analogs that are not amenable to simple rationalizations and a look other situations where such effects may be present would be recommendable. (author) 19 refs., 8 figs., 8 tabs.

  7. Determination of chemical states of sulphur 35 obtained from the 35Cl (n, p)35S

    International Nuclear Information System (INIS)

    Rossi Filho, S.

    1980-01-01

    The chemical states of sulphur-35 obtained from the 35 Cl(n,p) 35 S reaction by the irradiation of potassium chloride without any previous treatment and with previous heating under vacuum, were determined. The influence of irradiation time and temperature after irradiation was examined. Paper electrophoresis technique was employed for the determination of the chemical states. (Author) [pt

  8. Steady State Shift Damage Localization in a Residential-Sized Wind Turbine Blade

    DEFF Research Database (Denmark)

    Markvart, Morten Kusk; Sekjær, Claus; Bull, Thomas

    2017-01-01

    methodological premise is that of mapping a model-based damage distribution to experimental vibration features from the healthy and damaged states. Damage is then localized when a postulated damage distribution yields a, under ideal conditions, perfect mapping. The S3DL method relies on a theoretical model that......, in an experimental procedure with a plate-like structure, thus the present study serves to investigate the applicability of the method for more complex structures; in this case, a residential-sized wind turbine blade, which has been designed specifically for damage identification purposes. The blade consists of two...... parts that are bolted together along the leading and trailing edges, hence enabling introduction of stiffness-related damages by untightening a number of bolts. The paper studies two damage cases: failure of the trailing edge and a mass modification....

  9. Theta and beta oscillatory dynamics in the dentate gyrus reveal a shift in network processing state during cue encounters

    Directory of Open Access Journals (Sweden)

    Lara Maria Rangel

    2015-07-01

    Full Text Available The hippocampus is an important structure for learning and memory processes, and has strong rhythmic activity. Although a large amount of research has been dedicated towards understanding the rhythmic activity in the hippocampus during exploratory behaviors, specifically in the theta (5-10 Hz frequency range, few studies have examined the temporal interplay of theta and other frequencies during the presentation of meaningful cues. We obtained in vivo electrophysiological recordings of local field potentials (LFP in the dentate gyrus (DG of the hippocampus as rats performed three different associative learning tasks. In each task, cue presentations elicited pronounced decrements in theta amplitude in conjunction with increases in beta (15-30Hz amplitude. These changes were often transient but were sustained from the onset of cue encounters until the occurrence of a reward outcome. This oscillatory profile shifted in time to precede cue encounters over the course of the session, and was not present during similar behavior in the absence of task relevant stimuli. The observed decreases in theta amplitude and increases in beta amplitude in the dentate gyrus may thus reflect a shift in processing state that occurs when encountering meaningful cues.

  10. Rapid protein fold determination using secondary chemical shifts and cross-hydrogen bond 15N-13C' scalar couplings (3hbJNC')

    Energy Technology Data Exchange (ETDEWEB)

    Bonvin, Alexandre M.J.J.; Houben, Klaartje; Guenneugues, Marc; Kaptein, Robert; Boelens, Rolf [Utrecht University, Bijvoet Center for Biomolecular Research, NMR Spectroscopy (Netherlands)

    2001-11-15

    The possibility of generating protein folds at the stage of backbone assignment using structural restraints derived from experimentally measured cross-hydrogen bond scalar couplings and secondary chemical shift information is investigated using as a test case the small {alpha}/{beta} protein chymotrypsin inhibitor 2. Dihedral angle restraints for the {phi} and {psi} angles of 32 out of 64 residues could be obtained from secondary chemical shift analysis with the TALOS program (Corneliscu et al., 1999a). This information was supplemented by 18 hydrogen-bond restraints derived from experimentally measured cross-hydrogen bond {sup 3hb}J{sub NC'} coupling constants. These experimental data were sufficient to generate structures that are as close as 1.0 A backbone rmsd from the crystal structure. The fold is, however, not uniquely defined and several solutions are generated that cannot be distinguished on the basis of violations or energetic considerations. Correct folds could be identified by combining clustering methods with knowledge-based potentials derived from structural databases.

  11. Benchmarking of density functionals for a soft but accurate prediction and assignment of (1) H and (13)C NMR chemical shifts in organic and biological molecules.

    Science.gov (United States)

    Benassi, Enrico

    2017-01-15

    A number of programs and tools that simulate 1 H and 13 C nuclear magnetic resonance (NMR) chemical shifts using empirical approaches are available. These tools are user-friendly, but they provide a very rough (and sometimes misleading) estimation of the NMR properties, especially for complex systems. Rigorous and reliable ways to predict and interpret NMR properties of simple and complex systems are available in many popular computational program packages. Nevertheless, experimentalists keep relying on these "unreliable" tools in their daily work because, to have a sufficiently high accuracy, these rigorous quantum mechanical methods need high levels of theory. An alternative, efficient, semi-empirical approach has been proposed by Bally, Rablen, Tantillo, and coworkers. This idea consists of creating linear calibrations models, on the basis of the application of different combinations of functionals and basis sets. Following this approach, the predictive capability of a wider range of popular functionals was systematically investigated and tested. The NMR chemical shifts were computed in solvated phase at density functional theory level, using 30 different functionals coupled with three different triple-ζ basis sets. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  12. 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.

  13. State and tendencies of chemical protection against ionizing radiation

    International Nuclear Information System (INIS)

    Siegel, G.; Tapp, E.; Haehn, J.; Hannig, H.; Dlaske, R.; Martinek, K.

    1977-01-01

    Papers published in 1976 in the field of chemical protection against ionizing radiation are reviewed. Protection studies in vitro and in vivo, the biochemical, pharmacological and toxic effects, the mechanisms of protection of radioprotective agents and the trends in this field of research are described. (author)

  14. State and tendencies of chemical protection against ionizing radiation

    International Nuclear Information System (INIS)

    Siegel, G.; Tapp, E.; Hannig, H.; Dlaske, R.; Haehn, J.; Martinek, K.

    1980-01-01

    Papers published in 1978 in the field of chemical protection against ionizing radiation are reviewed. Protection studies in in-vivo and model systems, the biochemical, pharmacological and toxic effects, and modes of action of radioprotective agents are described and the trends in this field of research appreciated. (author)

  15. State and tendencies of chemical protection against ionizing radiation

    International Nuclear Information System (INIS)

    Siegel, G.; Tapp, E.; Hannig, H.; Dlaske, R.; Papendieck, W.; Martinek, K.; Haehn, J.

    1982-01-01

    Papers published in 1979 and 1980 in the field of chemical protection against ionizing radiation are reviewed. Protection studies in in-vivo and model systems, the biochemical, pharmacological and toxic effects, and modes of action of radioprotective agents are described and the trends in this field of research estimated. (author)

  16. State and tendencies of chemical protection against ionizing radiation

    International Nuclear Information System (INIS)

    Siegel, G.; Tapp, E.; Haehn, J.; Hannig, H.; Dlaske, R.

    1976-03-01

    Papers published in 1974 in the field of chemical protection against ionizing radiation are reviewed. Protection studies in vitro and in vivo, the biochemical, pharmacological and toxic effects, the mechanisms of protection of radioprotective agents and the trends in this field of research are described. (author)

  17. State and tendencies of chemical protection against ionizing radiation

    International Nuclear Information System (INIS)

    Siegel, G.; Tapp, E.; Haehn, J.; Hannig, H.; Dlaske, R.; Martinek, K.

    1977-01-01

    Papers published in 1975 in the field of chemical protection against ionizing radiation are reviewed. Protection studies in vitro and in vivo, the biochemical, pharmacological and toxic effects, the mechanisms of protection of radioprotective agents and the trends in this field of research are described. (author)

  18. Driving Calmodulin Protein towards Conformational Shift by Changing Ionization States of Select Residues

    International Nuclear Information System (INIS)

    Negi, Sunita; Atilgan, Ali Rana; Atilgan, Canan

    2012-01-01

    Proteins are complex systems made up of many conformational sub-states which are mainly determined by the folded structure. External factors such as solvent type, temperature, pH and ionic strength play a very important role in the conformations sampled by proteins. Here we study the conformational multiplicity of calmodulin (CaM) which is a protein that plays an important role in calcium signaling pathways in the eukaryotic cells. CaM can bind to a variety of other proteins or small organic compounds, and mediates different physiological processes by activating various enzymes. Binding of calcium ions and proteins or small organic molecules to CaM induces large conformational changes that are distinct to each interacting partner. In particular, we discuss the effect of pH variation on the conformations of CaM. By using the pKa values of the charged residues as a basis to assign protonation states, the conformational changes induced in CaM by reducing the pH are studied by molecular dynamics simulations. Our current view suggests that at high pH, barrier crossing to the compact form is prevented by repulsive electrostatic interactions between the two lobes. At reduced pH, not only is barrier crossing facilitated by protonation of residues, but also conformations which are on average more compact are attained. The latter are in accordance with the fluorescence resonance energy transfer experiment results of other workers. The key events leading to the conformational change from the open to the compact conformation are (i) formation of a salt bridge between the N-lobe and the linker, stabilizing their relative motions, (ii) bending of the C-lobe towards the N-lobe, leading to a lowering of the interaction energy between the two-lobes, (iii) formation of a hydrophobic patch between the two lobes, further stabilizing the bent conformation by reducing the entropic cost of the compact form, (iv) sharing of a Ca +2 ion between the two lobes.

  19. Driving Calmodulin Protein towards Conformational Shift by Changing Ionization States of Select Residues

    Science.gov (United States)

    Negi, Sunita; Rana Atilgan, Ali; Atilgan, Canan

    2012-12-01

    Proteins are complex systems made up of many conformational sub-states which are mainly determined by the folded structure. External factors such as solvent type, temperature, pH and ionic strength play a very important role in the conformations sampled by proteins. Here we study the conformational multiplicity of calmodulin (CaM) which is a protein that plays an important role in calcium signaling pathways in the eukaryotic cells. CaM can bind to a variety of other proteins or small organic compounds, and mediates different physiological processes by activating various enzymes. Binding of calcium ions and proteins or small organic molecules to CaM induces large conformational changes that are distinct to each interacting partner. In particular, we discuss the effect of pH variation on the conformations of CaM. By using the pKa values of the charged residues as a basis to assign protonation states, the conformational changes induced in CaM by reducing the pH are studied by molecular dynamics simulations. Our current view suggests that at high pH, barrier crossing to the compact form is prevented by repulsive electrostatic interactions between the two lobes. At reduced pH, not only is barrier crossing facilitated by protonation of residues, but also conformations which are on average more compact are attained. The latter are in accordance with the fluorescence resonance energy transfer experiment results of other workers. The key events leading to the conformational change from the open to the compact conformation are (i) formation of a salt bridge between the N-lobe and the linker, stabilizing their relative motions, (ii) bending of the C-lobe towards the N-lobe, leading to a lowering of the interaction energy between the two-lobes, (iii) formation of a hydrophobic patch between the two lobes, further stabilizing the bent conformation by reducing the entropic cost of the compact form, (iv) sharing of a Ca+2 ion between the two lobes.

  20. Shifting stream planform state decreases stream productivity yet increases riparian animal production

    Science.gov (United States)

    Venarsky, Michael P.; Walters, David M.; Hall, Robert O.; Livers, Bridget; Wohl, Ellen

    2018-01-01

    In the Colorado Front Range (USA), disturbance history dictates stream planform. Undisturbed, old-growth streams have multiple channels and large amounts of wood and depositional habitat. Disturbed streams (wildfires and logging tested how these opposing stream states influenced organic matter, benthic macroinvertebrate secondary production, emerging aquatic insect flux, and riparian spider biomass. Organic matter and macroinvertebrate production did not differ among sites per unit area (m−2), but values were 2 ×–21 × higher in undisturbed reaches per unit of stream valley (m−1 valley) because total stream area was higher in undisturbed reaches. Insect emergence was similar among streams at the per unit area and per unit of stream valley. However, rescaling insect emergence to per meter of stream bank showed that the emerging insect biomass reaching the stream bank was lower in undisturbed sites because multi-channel reaches had 3 × more stream bank than single-channel reaches. Riparian spider biomass followed the same pattern as emerging aquatic insects, and we attribute this to bottom-up limitation caused by the multi-channeled undisturbed sites diluting prey quantity (emerging insects) reaching the stream bank (riparian spider habitat). These results show that historic landscape disturbances continue to influence stream and riparian communities in the Colorado Front Range. However, these legacy effects are only weakly influencing habitat-specific function and instead are primarily influencing stream–riparian community productivity by dictating both stream planform (total stream area, total stream bank length) and the proportional distribution of specific habitat types (pools vs riffles).

  1. Early colonizing Escherichia coli elicits remodeling of rat colonic epithelium shifting toward a new homeostatic state.

    Science.gov (United States)

    Tomas, Julie; Reygner, Julie; Mayeur, Camille; Ducroc, Robert; Bouet, Stephan; Bridonneau, Chantal; Cavin, Jean-Baptiste; Thomas, Muriel; Langella, Philippe; Cherbuy, Claire

    2015-01-01

    We investigated the effects of early colonizing bacteria on the colonic epithelium. We isolated dominant bacteria, Escherichia coli, Enterococcus faecalis, Lactobacillus intestinalis, Clostridium innocuum and a novel Fusobacterium spp., from the intestinal contents of conventional suckling rats and transferred them in different combinations into germfree (GF) adult rats. Animals were investigated after various times up to 21 days. Proliferative cell markers (Ki67, proliferating cell nuclear antigen, phospho-histone H3, cyclin A) were higher in rats monocolonized with E. coli than in GF at all time points, but not in rats monocolonized with E. faecalis. The mucin content of goblet cells declined shortly after E. coli administration whereas the mucus layer doubled in thickness. Fluorescence in situ hybridization analyses revealed that E. coli resides in this mucus layer. The epithelial mucin content progressively returned to baseline, following an increase in KLF4 and in the cell cycle arrest-related proteins p21(CIP1) and p27(KIP1). Markers of colonic differentiated cells involved in electrolyte (carbonic anhydrase II and slc26A3) and water (aquaglyceroporin3 (aqp3)) transport, and secretory responses to carbachol were modulated after E. coli inoculation suggesting that ion transport dynamics were also affected. The colonic responses to simplified microbiotas differed substantially according to whether or not E. coli was combined with the other four bacteria. Thus, proliferation markers increased substantially when E. coli was in the mix, but very much less when it was absent. This work demonstrates that a pioneer strain of E. coli elicits sequential epithelial remodeling affecting the structure, mucus layer and ionic movements and suggests this can result in a microbiota-compliant state.

  2. Click-PEGylation - A mobility shift approach to assess the redox state of cysteines in candidate proteins.

    Science.gov (United States)

    van Leeuwen, Lucie A G; Hinchy, Elizabeth C; Murphy, Michael P; Robb, Ellen L; Cochemé, Helena M

    2017-07-01

    The redox state of cysteine thiols is critical for protein function. Whereas cysteines play an important role in the maintenance of protein structure through the formation of internal disulfides, their nucleophilic thiol groups can become oxidatively modified in response to diverse redox challenges and thereby function in signalling and antioxidant defences. These oxidative modifications occur in response to a range of agents and stimuli, and can lead to the existence of multiple redox states for a given protein. To assess the role(s) of a protein in redox signalling and antioxidant defence, it is thus vital to be able to assess which of the multiple thiol redox states are present and to investigate how these alter under different conditions. While this can be done by a range of mass spectrometric-based methods, these are time-consuming, costly, and best suited to study abundant proteins or to perform an unbiased proteomic screen. One approach that can facilitate a targeted assessment of candidate proteins, as well as proteins that are low in abundance or proteomically challenging, is by electrophoretic mobility shift assays. Redox-modified cysteine residues are selectively tagged with a large group, such as a polyethylene glycol (PEG) polymer, and then the proteins are separated by electrophoresis followed by immunoblotting, which allows the inference of redox changes based on band shifts. However, the applicability of this method has been impaired by the difficulty of cleanly modifying protein thiols by large PEG reagents. To establish a more robust method for redox-selective PEGylation, we have utilised a Click chemistry approach, where free thiol groups are first labelled with a reagent modified to contain an alkyne moiety, which is subsequently Click-reacted with a PEG molecule containing a complementary azide function. This strategy can be adapted to study reversibly reduced or oxidised cysteines. Separation of the thiol labelling step from the PEG

  3. Shift Colors

    Science.gov (United States)

    Publications & News Shift Colors Pages default Sign In NPC Logo Banner : Shift Colors Search Navy Personnel Command > Reference Library > Publications & News > Shift Colors Top Link Bar Navy Personnel Library Expand Reference Library Quick Launch Shift Colors Shift Colors Archives Mailing Address How to

  4. Endocrine Disrupting Chemical Induced "Pollution of Metabolic Pathways": A Case of Shifting Paradigms With Implications for Vascular Diseases.

    Science.gov (United States)

    Janardhanan, Rajiv

    2018-05-14

    The latter half of the twentieth century has witnessed a humongous spurt in the use of synthetic chemicals in a wide variety of industrial and agricultural applications are leading to niche specific perturbations affecting every trophic level of the ecosystems due to unmitigated environmental contamination. Despite the incremental usefulness of endocrine disrupting chemicals (EDCs) such as pesticides and plasticizers, their statutory impact on environmental health is assuming worrisome proportions. The EDCs can disrupt physiological homeostasis resulting in developmental and reproductive abnormalities. Both preclinical animal experiments, as well as epidemiological studies, have correlated EDC exposure with metabolic disorders such as metabolic syndrome, type 2 diabetes as well as cardiovascular health. Here we briefly review the statutory impact of EDCs on metabolic disruption as well as their impact on environmental health. Finally, difficulties pertaining to the categorization of EDC induced metabolic diseases as risk factors for global disease burden have been addressed taking into account the complexity of such interactions. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

  5. Isotopic shifts in chemical exchange systems. 1. Large isotope effects in the complexation of Na+ isotopes by macrocyclic polyethers

    International Nuclear Information System (INIS)

    Knoechel, A.; Wilken, R.D.

    1981-01-01

    The complexation of 24 Na + and 22 Na + by 18 of the most widely used macrocyclic polyethers (crown ethers and monocyclic and bicyclic aminopolyethers) has been investigated in view of possible equilibrium isotope shifts. Solvated salts and polyether complexes were distributed differently into two phases and isotope ratios determined in both phases. Chloroform/water systems were shown to be particularly suitable to the investigations allowing favorable distribution for Na + and 13 of the 18 polyethers employed. With crown ethers 24 Na + enrichment varied from nonsignficant values (for large crown ethers) up to 3.1 +- 0.4% (18-crown-6). In the case of bicyclic aminopolyethers, ligands with cages of optimum size to accommodate Na + showed 24 Na + enrichment between O (nonsignificant) (2.2/sub B/2./sub B/) and 5.2 +- 1.8% (2.2.1). In contrast, for 2.2.2. and its derivatives, being too large for Na + , 22 Na + enrichment varying from O (nonsignificant) (2.2.2.p) up to 5.4 +- 0.5% (2.2.2.) has been observed. These values are remarkably high. They are explained by different bonding in solvate structure and polyether complex by using the theoretical approach of Bigeleisen

  6. Calculation of 125Te NMR Chemical Shifts at the Full Four-Component Relativistic Level with Taking into Account Solvent and Vibrational Corrections: A Gateway to Better Agreement with Experiment.

    Science.gov (United States)

    Rusakova, Irina L; Rusakov, Yuriy Yu; Krivdin, Leonid B

    2017-06-29

    Four-component relativistic calculations of 125 Te NMR chemical shifts were performed in the series of 13 organotellurium compounds, potential precursors of the biologically active species, at the density functional theory level under the nonrelativistic and four-component fully relativistic conditions using locally dense basis set scheme derived from relativistic Dyall's basis sets. The relativistic effects in tellurium chemical shifts were found to be of as much as 20-25% of the total calculated values. The vibrational and solvent corrections to 125 Te NMR chemical shifts are about, accordingly, 6 and 8% of their total values. The PBE0 exchange-correlation functional turned out to give the best agreement of calculated tellurium shifts with their experimental values giving the mean absolute percentage error of 4% in the range of ∼1000 ppm, provided all corrections are taken into account.

  7. Influence of short range chemical order on density of states in α-ZrNi

    International Nuclear Information System (INIS)

    Duarte Junior, J.

    1986-01-01

    Calculations of the density of electronic states for amorphous alloys of ZrNi and ZrCu with different chemical order degrees, in order to verify the effect of chemical ordering on this property, are presented. The results obtained for ZrCu shown that the density of states at Fermi level do not vary significantly with the ordering. The results for ZrNi shown that the introduction of short range chemical order can decrease significantly the density of states at Fermi level, leading to better agreement with experimental results. (M.C.K.) [pt

  8. Chemical reaction rates and non-equilibrium pressure of reacting gas mixtures in the state-to-state approach

    International Nuclear Information System (INIS)

    Kustova, Elena V.; Kremer, Gilberto M.

    2014-01-01

    Highlights: • State-to-state approach for coupled vibrational relaxation and chemical reactions. • Self-consistent model for rates of non-equilibrium reactions and energy transitions. • In viscous flows mass action law is violated. • Cross coupling between reaction rates and non-equilibrium pressure in viscous flow. • Results allow implementing the state-to-state approach for viscous flow simulations. - Abstract: Viscous gas flows with vibrational relaxation and chemical reactions in the state-to-state approach are analyzed. A modified Chapman–Enskog method is used for the determination of chemical reaction and vibrational transition rates and non-equilibrium pressure. Constitutive equations depend on the thermodynamic forces: velocity divergence and chemical reaction/transition affinity. As an application, N 2 flow with vibrational relaxation across a shock wave is investigated. Two distinct processes occur behind the shock: for small values of the distance the affinity is large and vibrational relaxation is in its initial stage; for large distances the affinity is small and the chemical reaction is in its final stage. The affinity contributes more to the transition rate than the velocity divergence and the effect of these two contributions are more important for small distances from the shock front. For the non-equilibrium pressure, the term associated with the bulk viscosity increases by a small amount the hydrostatic pressure

  9. Chemical reaction rates and non-equilibrium pressure of reacting gas mixtures in the state-to-state approach

    Energy Technology Data Exchange (ETDEWEB)

    Kustova, Elena V., E-mail: e.kustova@spbu.ru [Department of Mathematics and Mechanics, Saint Petersburg State University, 198504 Universitetskiy pr. 28, Saint Petersburg (Russian Federation); Kremer, Gilberto M., E-mail: kremer@fisica.ufpr.br [Departamento de Física, Universidade Federal do Paraná, Caixa Postal 19044, 81531-980 Curitiba (Brazil)

    2014-12-05

    Highlights: • State-to-state approach for coupled vibrational relaxation and chemical reactions. • Self-consistent model for rates of non-equilibrium reactions and energy transitions. • In viscous flows mass action law is violated. • Cross coupling between reaction rates and non-equilibrium pressure in viscous flow. • Results allow implementing the state-to-state approach for viscous flow simulations. - Abstract: Viscous gas flows with vibrational relaxation and chemical reactions in the state-to-state approach are analyzed. A modified Chapman–Enskog method is used for the determination of chemical reaction and vibrational transition rates and non-equilibrium pressure. Constitutive equations depend on the thermodynamic forces: velocity divergence and chemical reaction/transition affinity. As an application, N{sub 2} flow with vibrational relaxation across a shock wave is investigated. Two distinct processes occur behind the shock: for small values of the distance the affinity is large and vibrational relaxation is in its initial stage; for large distances the affinity is small and the chemical reaction is in its final stage. The affinity contributes more to the transition rate than the velocity divergence and the effect of these two contributions are more important for small distances from the shock front. For the non-equilibrium pressure, the term associated with the bulk viscosity increases by a small amount the hydrostatic pressure.

  10. Comparison of CT and chemical-shift MRI for differentiating thymoma from non-thymomatous conditions in myasthenia gravis: value of qualitative and quantitative assessment

    International Nuclear Information System (INIS)

    Priola, A.M.; Priola, S.M.; Gned, D.; Giraudo, M.T.; Fornari, A.; Veltri, A.

    2016-01-01

    Aim: To evaluate the usefulness of computed tomography (CT) and chemical-shift magnetic resonance imaging (MRI) in patients with myasthenia gravis (MG) for differentiating thymoma (THY) from thymic lymphoid hyperplasia (TLH) and normal thymus (NT), and to determine which technique is more accurate. Materials and methods: Eighty-three patients with generalised MG who underwent surgery were divided into the TLH/NT group (A; 65 patients) and THY group (B; 24 patients). Differences in qualitative characteristics and quantitative data (CT: radiodensity in Hounsfield units; MRI: signal intensity index [SII]) between groups were tested using Fisher's exact test and Student's t-test. Logistic regression models were estimated for both qualitative and quantitative analyses. At quantitative analysis, discrimination abilities were determined according to the area under the receiver operating characteristic (ROC) curve (AUROC) with computation of optimal cut-off points. The diagnostic accuracies of CT and MRI were compared using McNemar's test. Results: At qualitative assessment, MRI had higher accuracy than CT (96.4%, 80/83 and 86.7%, 72/83, respectively). At quantitative analysis, both the radiodensity and SII were significantly different between groups (p<0.0001). For CT, at quantitative assessment, the AUROC of the radiodensity in discriminating between groups was 0.904 (optimal cut-off point, 20 HU) with an accuracy of 77.1% (64/83). For MRI, the AUROC of the SII was 0.989 (optimal cut-off point, 7.766%) with an accuracy of 96.4% (80/83), which was significantly higher than CT (p<0.0001). By using optimal cut-off points for cases with an erroneous diagnosis at qualitative assessment, accuracy improved both for CT (89.2%, 74/83) and MRI (97.6%, 81/83). Conclusion: Quantitative analysis is useful in evaluating patients with MG and improves the diagnostic accuracy of CT and MRI based on qualitative assessment. Chemical-shift MRI is more reliable than CT in differentiating

  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. Sacrifice zones: the front lines of toxic chemical exposure in the United States

    National Research Council Canada - National Science Library

    Lerner, Steve

    2010-01-01

    ... States of America. Library of Congress Cataloging-in-Publication Data Lerner, Steve. Sacrifice zones: the front lines of toxic chemical exposure in the United States / Steve Lerner. p. cm. Includes bibliographical references and index. ISBN 978-0-262-01440-3 (hardcover : alk. paper) 1. Environmental toxicology- United States- Case studies. 2. Che...

  13. Cyanobactins from Cyanobacteria: Current Genetic and Chemical State of Knowledge.

    Science.gov (United States)

    Martins, Joana; Vasconcelos, Vitor

    2015-11-13

    Cyanobacteria are considered to be one of the most promising sources of new, natural products. Apart from non-ribosomal peptides and polyketides, ribosomally synthesized and post-translationally modified peptides (RiPPs) are one of the leading groups of bioactive compounds produced by cyanobacteria. Among these, cyanobactins have sparked attention due to their interesting bioactivities and for their potential to be prospective candidates in the development of drugs. It is assumed that the primary source of cyanobactins is cyanobacteria, although these compounds have also been isolated from marine animals such as ascidians, sponges and mollusks. The aim of this review is to update the current knowledge of cyanobactins, recognized as being produced by cyanobacteria, and to emphasize their genetic clusters and chemical structures as well as their bioactivities, ecological roles and biotechnological potential.

  14. 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.

  15. Evaluation of the Aromaticity of a Non-Planar Carbon Nano-Structure by Nucleus-Independent Chemical Shift Criterion: Aromaticity of the Nitrogen- Doped Corannulene

    Directory of Open Access Journals (Sweden)

    A. Reisi-Vanani

    2014-04-01

    Full Text Available Substitution of two or four carbon atoms by nitrogen in the corannulene molecule as a carbon nanostructure was done and the obtained structures were optimized at MP2/6-31G(d level of theory. Calculations of the nucleus-independent chemical shift (NICS were performed to analyze the aromaticity of the corannulene rings and its derivatives upon doping with N at B3LYP/6-31G(d level of theory. Results showed NICS values in six-membered and five-membered rings of two and four N atoms doped corannulene are different and very dependent to number and position of the N atoms. The values of the mean NICS of all N-doped structures are more positive than intact corannulene that show insertion of N atom to the structures causes to decreasing aromaticity of them.

  16. Chemical Weapons: FEMA and Army Must Be Proactive in Preparing States for Emergencies

    National Research Council Canada - National Science Library

    2001-01-01

    .... Such an accident could affect people in 10 different states. The Army plans to destroy its entire chemical weapons stockpile by 2007 and is taking measures to protect the public before and during the demilitarization process...

  17. 31P-MR spectroscopy of all regions of the human heart at 1.5 T with acquisition-weighted chemical shift imaging

    International Nuclear Information System (INIS)

    Koestler, H.; Beer, M.; Buchner, S.; Sandstede, J.; Pabst, T.; Kenn, W.; Hahn, D.

    2001-01-01

    Aim: Aim of this study was to show whether or not acquisition-weighted chemical shift imaging (AW-CSI) allows the determination of PCr and ATP in the lateral and posterior wall of the human heart at 1.5 T. Methods: 12 healthy volunteers were examined using a conventional chemical shift imaging (CSI) and an AW-CSI. The sequences differed only in the number of repetitions for each point in k space. A hanning function was used as filter function leading to 7 repetitions in the center of the k space and 0 in the corners. Thus, AW-CSI had the same resolution as the CSI sequence. The results for both sequences were analyzed using identically positioned voxels in the septal, anterior, lateral and posterior wall. Results: The determined averaged AW-CSI signal to noise ratios were higher for PCr by a factor of 1.3 and for ATP by 1.4 than those of CSI. The PCr/ATP ratios were higher by a factor of 1.2 - 1.3 and showed a smaller standard deviation in all locations for AW-CSI. The mean PCr/ATP ratios determined by AW-CSI of septal, lateral and posterior wall were almost identical (1.72 - 1.76), while it was higher in the anterior wall (1.9). Conclusions: The reduced contamination in AW-CSI improves the signal to noise ratio and the determination of the PCr/ATP ratio in cardiac 31 P spectroscopy compared to CSI with the same resolution. The results in volunteers indicate that AW-CSI renders 31 P spectroscopy of the lateral and posterior wall of the human heart feasible for patient studies at 1.5 T. (orig.) [de

  18. The single-particle density of states, bound states, phase-shift flip, and a resonance in the presence of an Aharonov-Bohm potential

    International Nuclear Information System (INIS)

    Moroz, A.

    1994-01-01

    Both the nonrelativistic scattering and the spectrum in the presence of the Aharonov-Bohm potential are analyzed, and the single-particle density of states for different self-adjoint extensions is calculated, which is shown to be a symmetric and periodic function of the flux depending only on the distance from the nearest integer. The Aharonov-Casher theorem on the number of zero modes is corrected for the singular field configuration. The Hall resistivity is calculated in the dilute vortex limit. The magnetic moment coupling and not the spin is shown to be the primary source for the phase-shift flip that may occur even in its absence. The total energy of the system consisting of particles and field is discussed. (author) 65 refs.; 5 figs.; 1 tab

  19. Characterization of Chemical Suicides in the United States and Its Adverse Impact on Responders and Bystanders

    Directory of Open Access Journals (Sweden)

    Ayana R. Anderson

    2016-11-01

    Full Text Available Introduction: A suicide trend that involves mixing household chemicals to produce hydrogen sulfide or hydrogen cyanide, commonly referred to as a detergent, hydrogen sulfide, or chemical suicide is a continuing problem in the United States (U.S.. Because there is not one database responsible for tracking chemical suicides, the actual number of incidents in the U.S. is unknown. To prevent morbidity and mortality associated with chemical suicides, it is important to characterize the incidents that have occurred in the U.S. Methods: The author analyzed data from 2011-2013 from state health departments participating in the Agency for Toxic Substances and Disease Registry’s National Toxic Substance Incidents Program (NTSIP. NTSIP is a web-based chemical incident surveillance system that tracks the public health consequences (e.g., morbidity, mortality from acute chemical releases. Reporting sources for NTSIP incidents typically include first responders, hospitals, state environmental agencies, and media outlets. To find chemical suicide incidents in NTSIP’s database, the author queried open text fields in the comment, synopsis, and contributing factors variables for potential incidents. Results: Five of the nine states participating in NTSIP reported a total of 22 chemical suicide incidents or attempted suicides during 2011-2013. These states reported a total of 43 victims: 15 suicide victims who died, seven people who attempted suicide but survived, eight responders, and four employees working at a coroner’s office; the remainder were members of the general public. None of the injured responders reported receiving HazMat technician-level training, and none had documented appropriate personal protective equipment. Conclusion: Chemical suicides produce lethal gases that can pose a threat to responders and bystanders. Describing the characteristics of these incidents can help raise awareness among responders and the public about the dangers of

  20. An automated system designed for large scale NMR data deposition and annotation: application to over 600 assigned chemical shift data entries to the BioMagResBank from the Riken Structural Genomics/Proteomics Initiative internal database

    International Nuclear Information System (INIS)

    Kobayashi, Naohiro; Harano, Yoko; Tochio, Naoya; Nakatani, Eiichi; Kigawa, Takanori; Yokoyama, Shigeyuki; Mading, Steve; Ulrich, Eldon L.; Markley, John L.; Akutsu, Hideo; Fujiwara, Toshimichi

    2012-01-01

    Biomolecular NMR chemical shift data are key information for the functional analysis of biomolecules and the development of new techniques for NMR studies utilizing chemical shift statistical information. Structural genomics projects are major contributors to the accumulation of protein chemical shift information. The management of the large quantities of NMR data generated by each project in a local database and the transfer of the data to the public databases are still formidable tasks because of the complicated nature of NMR data. Here we report an automated and efficient system developed for the deposition and annotation of a large number of data sets including 1 H, 13 C and 15 N resonance assignments used for the structure determination of proteins. We have demonstrated the feasibility of our system by applying it to over 600 entries from the internal database generated by the RIKEN Structural Genomics/Proteomics Initiative (RSGI) to the public database, BioMagResBank (BMRB). We have assessed the quality of the deposited chemical shifts by comparing them with those predicted from the PDB coordinate entry for the corresponding protein. The same comparison for other matched BMRB/PDB entries deposited from 2001–2011 has been carried out and the results suggest that the RSGI entries greatly improved the quality of the BMRB database. Since the entries include chemical shifts acquired under strikingly similar experimental conditions, these NMR data can be expected to be a promising resource to improve current technologies as well as to develop new NMR methods for protein studies.

  1. Ab initio/GIAO-CCSD(T) study of structures, energies, and 13C NMR chemical shifts of C4H7(+) and C5H9(+) ions: relative stability and dynamic aspects of the cyclopropylcarbinyl vs bicyclobutonium ions.

    Science.gov (United States)

    Olah, George A; Surya Prakash, G K; Rasul, Golam

    2008-07-16

    The structures and energies of the carbocations C 4H 7 (+) and C 5H 9 (+) were calculated using the ab initio method. The (13)C NMR chemical shifts of the carbocations were calculated using the GIAO-CCSD(T) method. The pisigma-delocalized bisected cyclopropylcarbinyl cation, 1 and nonclassical bicyclobutonium ion, 2 were found to be the minima for C 4H 7 (+) at the MP2/cc-pVTZ level. At the MP4(SDTQ)/cc-pVTZ//MP2/cc-pVTZ + ZPE level the structure 2 is 0.4 kcal/mol more stable than the structure 1. The (13)C NMR chemical shifts of 1 and 2 were calculated by the GIAO-CCSD(T) method. Based on relative energies and (13)C NMR chemical shift calculations, an equilibrium involving the 1 and 2 in superacid solutions is most likely responsible for the experimentally observed (13)C NMR chemical shifts, with the latter as the predominant equilibrating species. The alpha-methylcyclopropylcarbinyl cation, 4, and nonclassical bicyclobutonium ion, 5, were found to be the minima for C 5H 9 (+) at the MP2/cc-pVTZ level. At the MP4(SDTQ)/cc-pVTZ//MP2/cc-pVTZ + ZPE level ion 5 is 5.9 kcal/mol more stable than the structure 4. The calculated (13)C NMR chemical shifts of 5 agree rather well with the experimental values of C 5H 9 (+).

  2. Pionic 4f→3d transition in 181Ta, natural Re, and 209Bi and the strong interaction level shift and the strong interaction level shift and width of the pionic 3d state

    International Nuclear Information System (INIS)

    Konijn, J.; Panman, J.K.; Koch, J.H.; Doesburg, W. van; Ewan, G.T.; Johansson, T.; Tibell, G.; Fransson, K.; Tauscher, L.

    1979-01-01

    Owing to a powerful Compton-suppression technique it was possible to observe for the first time the pionic 4f→3d X-ray transition in elements heavier than A=150. The strong interaction monopole shifts epsilon 0 and widths GAMMA 0 as well as the quadrupole splitting of the 3d levels have been measured in Ta, Re and Bi. Thus in addition to the strongly shifted and broadened 5g→4f transitions, a second, strongly affected line is available for these elements. For the pionic 4f levels, standard optical potentials fit the strong interaction shifts and broadenings quite well. The now observed, deeper-lying 3d states in Ta, Re and Bi have shifts and widths that differ by a factor of 2 or more from the standard optical potential predictions. From the observed relative X-ray intensities of the pionic cascade the strong interaction widths of the 5g and 4f levels are also extracted. (Auth.)

  3. Regime shift of Indian summer monsoon rainfall to a persistent arid state: external forcing versus internal variability

    Science.gov (United States)

    Srivastava, Ankur; Pradhan, Maheswar; Goswami, B. N.; Rao, Suryachandra A.

    2017-11-01

    The high propensity of deficient monsoon rainfall over the Indian sub-continent in the recent 3 decades (seven deficient monsoons against 3 excess monsoon years) compared to the prior 3 decades has serious implications on the food and water resources in the country. Motivated by the need to understand the high occurrence of deficient monsoon during this period, we examine the change in predictability of the Indian summer monsoon (ISM) and its teleconnections with Indo-Pacific sea surface temperatures between the two periods. The shift in the tropical climate in the late 1970s appears to be one of the major reasons behind this. We find an increased predictability of the ISM in the recent 3 decades owing to reduced `internal' interannual variability (IAV) due to the high-frequency modes, while the `external' IAV arising from the low-frequency modes has remained largely the same. The Indian Ocean Dipole-ISM teleconnection has become positive during the monsoon season in the recent period thereby compensating for the weakened ENSO-ISM teleconnection. The central Pacific El-Niño and the Indian Ocean (IO) warming during the recent 3 decades are working together to realise enhanced ascending motion in the equatorial IO between 70°E and 100°E, preconditioning the Indian monsoon system prone to a deficient state.

  4. Moessbauer study of the chemical state of gold in gold ores

    International Nuclear Information System (INIS)

    Wagner, F.E.; Marion, P.H.; Regnard, J.-R.

    1986-01-01

    Information on the chemical state of gold in gold ores has been obtained by 197 Au Moessbauer spectroscopy in cases where the state of this element cannot be determined by such standard methods as optical or electron microscopy. Ore concentrates consisting mainly of pyrite or arsenopyrite and roasted ore and matte samples were studied. The results yielded directly the respective amounts of metallic and chemically bound gold. Unless the gold is metallic, its chemical state in the ores turns out to be different from that in the minerals studied so far as reference materials. The chemical processes taking place during various treatments of the ores, such as roasting or leaching, can also be followed by Moessbauer spectroscopy. It is hoped that Moessbauer spectroscopy will eventually facilitate the development of more efficient methods of gold extraction

  5. Precision measurement of the 1S ground-state Lamb shift in atomic hydrogen and deuterium by frequency comparison

    International Nuclear Information System (INIS)

    Weitz, M.; Huber, A.; Schmidt-Kaler, F.; Leibfried, D.; Vassen, W.; Zimmermann, C.; Pachucki, K.; Haensch, T.W.; Julien, L.; Biraben, F.

    1995-01-01

    We have measured the hydrogen and deuterium 1S Lamb shift by direct optical frequency comparison of the 1S-2S and 2S-4S/4D two-photon transitions. Our result of 8172.874(60) MHz for the 1S Lamb shift in hydrogen is in agreement with the theoretical value of 8172.802(40) MHz. For the 1S Lamb shift in deuterium, we obtain a value of 8183.807(78) MHz, from which we derive a deuteron matter radium of 1.945(28) fm. The precision of our value for the 1S Lamb shift has surpassed that of radio frequency measurements of the 2S-2P Lamb shift. By comparison with a recent absolute measurement of the hydrogen 1S-2S transition frequency, we deduce a value for the Rydberg constant R ∞ =109 737.315 684 9(30) cm -1

  6. 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

    of the exchanging species can be determined independently of the relaxation rates. The applicability of the approach is demonstrated by a detailed analysis of the conformational exchange processes previously observed in the reduced form of the blue copper protein, plastocyanin from the cyanobacteria Anabaena......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...... 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...

  7. Saturated amine oxides: Part 8. Hydroacridines: Part 27. Effects of N-oxidation and of N-quaternization on the 15N NMR chemical shifts of N-methylpiperidine-derived mono-, bi-, and tricycloaliphatic tertiary amines.

    Science.gov (United States)

    Potmischil, Francisc; Duddeck, Helmut; Nicolescu, Alina; Deleanu, Calin

    2007-03-01

    The (15)N chemical shifts of 13 N-methylpiperidine-derived mono-, bi- and tricycloaliphatic tertiary amines, their methiodides and their N-epimeric pairs of N-oxides were measured, and the contributions of specific structural parameters to the chemical shifts were determined by multilinear regression analysis. Within the examined compounds, the effects of N-oxidation upon the (15)N chemical shifts of the amines vary from +56 ppm to +90 ppm (deshielding), of which approx. +67.7 ppm is due to the inductive effect of the incoming N(+)--O(-) oxygen atom, whereas the rest is due to the additive shift effects of the various C-alkyl substituents of the piperidine ring. The effects of quaternization vary from -3.1 ppm to +29.3 ppm, of which approx. +8.9 ppm is due to the inductive effect of the incoming N(+)--CH(3) methyl group, and the rest is due to the additive shift effects of the various C-alkyl substituents of the piperidine ring. The shift effects of the C-alkyl substituents in the amines, the N-oxides and the methiodides are discussed. Copyright (c) 2007 John Wiley & Sons, Ltd.

  8. Nonspherical atomic ground-state densities and chemical deformation densities from x-ray scattering

    International Nuclear Information System (INIS)

    Ruedenberg, K.; Schwarz, W.H.E.

    1990-01-01

    Presuming that chemical insight can be gained from the difference between the molecular electron density and the superposition of the ground-state densities of the atoms in a molecule, it is pointed out that, for atoms with degenerate ground states, an unpromoted ''atom in a molecule'' is represented by a specific ensemble of the degenerate atomic ground-state wave functions and that this ensemble is determined by the anisotropic local surroundings. The resulting atomic density contributions are termed oriented ground state densities, and the corresponding density difference is called the chemical deformation density. The constraints implied by this conceptual approach for the atomic density contributions are formulated and a method is developed for determining them from x-ray scattering data. The electron density of the appropriate promolecule and its x-ray scattering are derived, the determination of the parameters of the promolecule is outlined, and the chemical deformation density is formulated

  9. 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.

  10. Some Considerations on the Fundamentals of Chemical Kinetics: Steady State, Quasi-Equilibrium, and Transition State Theory

    Science.gov (United States)

    Perez-Benito, Joaquin F.

    2017-01-01

    The elementary reaction sequence A ? I ? Products is the simplest mechanism for which the steady-state and quasi-equilibrium kinetic approximations can be applied. The exact integrated solutions for this chemical system allow inferring the conditions that must fulfill the rate constants for the different approximations to hold. A graphical…

  11. Creatinine and creatininium cation in water solution. Tautomerism and quantitative interpretation of the solution acidity effect on 1H, 13C and 1:4N NMR chemical shifts

    International Nuclear Information System (INIS)

    Kotsyubynskyy, D.; Molchanov, S.; Gryff-Keller, A.

    2004-01-01

    1 H, 13 C and 1 :4N NMR chemical shifts for creatinine in water solution of various acidity have been measured. Analysis of these data enabled determination of the acidity constant of creatininium cation and the chemical shifts of the neutral and protonated forms of creatinine. Molecular energies and carbon and nitrogen magnetic shielding constants for various tautomeric structures of the investigated species have been calculated using the quantum chemistry method GIAO DFT B3LYP/6-311++G(2d,p). Compilation of the available experimental and theoretical results has provided additional information on the problem of tautomerism of this important biological molecule. (author)

  12. The influence of iridium chemical oxidation state on the performance and durability of oxygen evolution catalysts in PEM electrolysis

    Science.gov (United States)

    Siracusano, S.; Baglio, V.; Grigoriev, S. A.; Merlo, L.; Fateev, V. N.; Aricò, A. S.

    2017-10-01

    Nanosized Ir-black (3 nm) and Ir-oxide (5 nm) oxygen evolution electrocatalysts showing high performance in polymer electrolyte membrane (PEM) water electrolysis based on Aquivion® short-side chain ionomer membrane are investigated to understand the role of the Ir oxidation state on the electrocatalytic activity and stability. Despite the smaller mean crystallite size, the Ir-black electrocatalyst shows significantly lower initial performance than the Ir-oxide. During operation at high current density, the Ir-black shows a decrease of cell potential with time whereas the Ir-oxide catalyst shows increasing cell potential resulting in a degradation rate of about 10 μV/h, approaching 1000 h. The unusual behaviour of the Ir-black results from the oxidation of metallic Ir to IrOx. The Ir-oxide catalyst shows instead a hydrated structure on the surface and a negative shift of about 0.5 eV for the Ir 4f binding energy after 1000 h electrolysis operation. This corresponds to the formation of a sub-stoichiometric Ir-oxide on the surface. These results indicate that a hydrated IrO2 with high oxidation state on the surface is favourable in decreasing the oxygen evolution overpotential. Modifications of the Ir chemical oxidation state during operation can affect significantly the catalytic activity and durability of the electrolysis system.

  13. Looking for chemical reaction networks exhibiting a drift along a manifold of marginally stable states.

    Science.gov (United States)

    Brogioli, Doriano

    2013-02-07

    I recently reported some examples of mass-action equations that have a continuous manifold of marginally stable stationary states [Brogioli, D., 2010. Marginally stable chemical systems as precursors of life. Phys. Rev. Lett. 105, 058102; Brogioli, D., 2011. Marginal stability in chemical systems and its relevance in the origin of life. Phys. Rev. E 84, 031931]. The corresponding chemical reaction networks show nonclassical effects, i.e. a violation of the mass-action equations, under the effect of the concentration fluctuations: the chemical system drifts along the marginally stable states. I proposed that this effect is potentially involved in abiogenesis. In the present paper, I analyze the mathematical properties of mass-action equations of marginally stable chemical reaction networks. The marginal stability implies that the mass-action equations obey some conservation law; I show that the mathematical properties of the conserved quantity characterize the motion along the marginally stable stationary state manifold, i.e. they allow to predict if the fluctuations give rise to a random walk or a drift under the effect of concentration fluctuations. Moreover, I show that the presence of the drift along the manifold of marginally stable stationary-states is a critical property, i.e. at least one of the reaction constants must be fine tuned in order to obtain the drift. Copyright © 2012 Elsevier Ltd. All rights reserved.

  14. Deuterium isotope effects on 13C and 15N chemical shifts of intramolecularly hydrogen-bonded enaminocarbonyl derivatives of Meldrum’s and Tetronic acid

    Science.gov (United States)

    Ullah, Saif; Zhang, Wei; Hansen, Poul Erik

    2010-07-01

    Secondary deuterium isotope effects on 13C and 15N nuclear shieldings in a series of cyclic enamino-diesters and enamino-esters and acyclic enaminones and enamino-esters have been examined and analysed using NMR and DFT (B3LYP/6-31G(d,p)) methods. One-dimensional and two-dimensional NMR spectra of enaminocarbonyl and their deuterated analogues were recorded in CDCl 3 and CD 2Cl 2 at variable temperatures and assigned. 1JNH coupling constants for the derivatives of Meldrum's and tetronic acids reveal that they exist at the NH-form. It was demonstrated that deuterium isotope effects, for the hydrogen bonded compounds, due to the deuterium substitution at the nitrogen nucleus lead to large one-bond isotope effects at nitrogen, 1Δ 15N(D), and two-bond isotope effects on carbon nuclei, 2ΔC(ND), respectively. A linear correlations exist between 2ΔC(ND) and 1Δ 15N(D) whereas the correlation with δNH is divided into two. A good agreement between the experimentally observed 2ΔC(ND) and calculated dσ 13C/dR NH was obtained. A very good correlation between calculated NH bond lengths and observed NH chemical shifts is found. The observed isotope effects are shown to depend strongly on Resonance Assisted Hydrogen bonding.

  15. Chemical shift assignments of the first and second RRMs of Nrd1, a fission yeast MAPK-target RNA binding protein.

    Science.gov (United States)

    Kobayashi, Ayaho; Kanaba, Teppei; Satoh, Ryosuke; Ito, Yutaka; Sugiura, Reiko; Mishima, Masaki

    2017-10-01

    Negative regulator differentiation 1 (Nrd1), a fission yeast RNA binding protein, modulates cytokinesis and sexual development and contributes to stress granule formation in response to environmental stresses. Nrd1 comprises four RRM domains and binds and stabilizes Cdc4 mRNA that encodes the myosin II light chain. Nrd1 binds the Cpc2 fission-yeast RACK1 homolog, and the interaction promotes Nrd1 localization to stress granules. Interestingly, Pmk1 mitogen-activated protein kinase phosphorylates Thr40 in the unstructured N-terminal region and Thr126 in the first RRM domain of Nrd1. Phosphorylation significantly reduces RNA-binding activity and likely modulates Nrd1 function. To reveal the relationship between the structure and function of Nrd1 and how phosphorylation affects structure, we used heteronuclear NMR techniques to investigate the three-dimensional structure of Nrd1. Here we report the 1 H, 13 C, and 15 N resonance assignments of RRM1-RRM2 (residues 108-284) comprising the first and second RRMs obtained using heteronuclear NMR techniques. Secondary structures derived from the chemical shifts are reported. These data should contribute to the understanding of the three-dimensional structure of the RRM1-RRM2 region of Nrd1 and the perturbation caused by phosphorylation.

  16. Chemical shift effect predicting lymph node status in rectal cancer using high-resolution MR imaging with node-for-node matched histopathological validation

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Hongmei; Zhang, Chongda; Ye, Feng; Liu, Yuan; Zhou, Chunwu [Chinese Academy of Medical Sciences and Peking Union Medical College, Department of Diagnostic Radiology, National Cancer Center/Cancer Hospital, ChaoYang District, Beijing (China); Zheng, Zhaoxu [Chinese Academy of Medical Sciences and Peking Union Medical College, Department of Colorectal Oncology, National Cancer Center/Cancer Hospital, ChaoYang District, Beijing (China); Zou, Shuangmei [Chinese Academy of Medical Sciences and Peking Union Medical College, Department of Pathology, National Cancer Center/Cancer Hospital, ChaoYang District, Beijing (China)

    2017-09-15

    To evaluate the value of the chemical shift effect (CSE) as well as other criteria for the prediction of lymph node status. Twenty-nine patients who underwent radical surgery of rectal cancers were studied with pre- and postoperative specimen MRI. Lymph nodes were harvested from transverse whole-mount specimens and compared with in vivo and ex vivo images to obtain a precise slice-for-section match. Preoperative MR characteristics including CSE, as well as other predictors, were evaluated by two readers independently between benign and metastatic nodes. A total of 255 benign and 35 metastatic nodes were obtained; 71.4% and 69.4% of benign nodes were detected with regular CSE for two readers, whereas 80.0% and 74.3% of metastatic nodes with absence of CSE. The CSE rendered areas under the ROC curve (AUC) of 0.879 and 0.845 for predicting nodal status for two readers. The criteria of nodal location, border, signal intensity and minimum distance to the rectal wall were also useful but with AUCs (0.629-0.743) lower than those of CSE. CSE is a reliable predictor for differentiating benign from metastatic nodes. Additional criteria should be taken into account when it is difficult to determine the nodal status by using only a single predictor. (orig.)

  17. Comparison of diffusion-weighted images using short inversion time inversion recovery or chemical shift selective pulse as fat suppression in patients with breast cancer

    International Nuclear Information System (INIS)

    Kazama, Toshiki; Nasu, Katsuhiro; Kuroki, Yoshifumi; Nawano, Shigeru; Ito, Hisao

    2009-01-01

    Fat suppression is essential for diffusion-weighted imaging (DWI) in the body. However, the chemical shift selective (CHESS) pulse often fails to suppress fat signals in the breast. The purpose of this study was to compare DWI using CHESS and DWI using short inversion time inversion recovery (STIR) in terms of fat suppression and the apparent diffusion coefficient (ADC) value. DWI using STIR, DWI using CHESS, and contrast-enhanced T1-weighted images were obtained in 32 patients with breast carcinoma. Uniformity of fat suppression, ADC, signal intensity, and visualization of the breast tumors were evaluated. In 44% (14/32) of patients there was insufficient fat suppression in the breasts on DWI using CHESS, whereas 0% was observed on DWI using STIR (P<0.0001). The ADCs obtained for DWI using STIR were 4.3% lower than those obtained for DWI using CHESS (P<0.02); there was a strong correlation of the ADC measurement (r=0.93, P<0.001). DWI using STIR may be excellent for fat suppression; and the ADC obtained in this sequence was well correlated with that obtained with DWI using CHESS. DWI using STIR may be useful when the fat suppression technique in DWI using CHESS does not work well. (author)

  18. "1H and "1"3C NMR Data on Hydroxy/methoxy Flavonoids and the Effects of Substituents on Chemical Shifts

    International Nuclear Information System (INIS)

    Yoon, Hyuk; Eom, Sung Lock; Hyun, Ji Ye; Jo, Geun Hyeong; Hwang, Do Seok; Lee, Sun Hee; Yong, Yeon Joong; Lee, Young Han; Lim, Yoong Ho; Park, Jun Cheol

    2011-01-01

    Polyphenols have recently been examined for such applications, and they are classified based on their carbon skeletons: phenolic acids with C6-C1 skeleton, hydrocinammates with C6-C_3 skeleton, stilbenes with C6-C2-C6 skeleton, and flavonoids with C6-C_3-C6 skeleton.2 Of these compounds, flavonoids are ubiquitously found in most plants. Since flavonoids belong to polyphenols, they have many hydroxy groups. From a bioavailability point of view, hydroxy groups prevent cell membrane transport, and hydroxyflavonoids can be metabolized by O-methyltransferases. However, methoxylated flavonoids may not have these problems. Hydroxylated or methoxylated flavonoids are found from natural sources. Nuclear magnetic resonance (NMR) spectroscopy is widely used to identify different compounds including hydroxylated or methoxylated flavonoids. Because the position and the number of substituted hydroxy or/and methoxy groups will change the "1H and "1"3C chemical shifts, it is important to understand these changes so that the structures of newly isolated hydroxy/methoxy-flavonoids can be easily identified

  19. Repeatability of two-dimensional chemical shift imaging multivoxel proton magnetic resonance spectroscopy for measuring human cerebral choline-containing compounds.

    Science.gov (United States)

    Puri, Basant K; Egan, Mary; Wallis, Fintan; Jakeman, Philip

    2018-03-22

    To investigate the repeatability of proton magnetic resonance spectroscopy in the in vivo measurement of human cerebral levels of choline-containing compounds (Cho). Two consecutive scans were carried out in six healthy resting subjects at a magnetic field strength of 1.5 T. On each occasion, neurospectroscopy data were collected from 64 voxels using the same 2D chemical shift imaging (CSI) sequence. The data were analyzed in the same way, using the same software, to obtain the values for each voxel of the ratio of Cho to creatine. The Wilcoxon related-samples signed-rank test, coefficient of variation (CV), repeatability coefficient (RC), and intraclass correlation coefficient (ICC) were used to assess the repeatability. The CV ranged from 2.75% to 33.99%, while the minimum RC was 5.68%. There was excellent reproducibility, as judged by significant ICC values, in 26 voxels. Just three voxels showed significant differences according to the Wilcoxon related-samples signed-rank test. It is therefore concluded that when CSI multivoxel proton neurospectroscopy is used to measure cerebral choline-containing compounds at 1.5 T, the reproducibility is highly acceptable.

  20. Hepatic steatosis assessment with {sup 1}H-spectroscopy and chemical shift imaging at 3.0 T before hepatic surgery: Reliable enough for making clinical decisions?

    Energy Technology Data Exchange (ETDEWEB)

    Koelblinger, Claus, E-mail: claus.koelblinger@meduniwien.ac.at [Department of Radiology, Medical University of Vienna (Austria); Krssak, Martin, E-mail: martin.krssak@meduniwien.ac.at [Department of Radiology, Medical University of Vienna (Austria); Maresch, Judith, E-mail: judith.maresch@meduniwien.ac.at [Department of Pathology, Medical University of Vienna (Austria); Wrba, Fritz, E-mail: fritz.wrba@meduniwien.ac.at [Department of Pathology, Medical University of Vienna (Austria); Kaczirek, Klaus, E-mail: klaus.kaczirek@meduniwien.ac.at [Department of Surgery, Medical University of Vienna (Austria); Gruenberger, Thomas, E-mail: thomas.gruenberger@meduniwien.ac.at [Department of Surgery, Medical University of Vienna (Austria); Tamandl, Dietmar, E-mail: dietmar.tamandl@meduniwien.ac.at [Department of Surgery, Medical University of Vienna (Austria); Ba-Ssalamah, Ahmed, E-mail: ahmed.ba-ssalamah@meduniwien.ac.at [Department of Radiology, Medical University of Vienna (Austria); Berger-Kulemann, Vanessa, E-mail: vanessa.berger-kulemann@meduniwien.ac.at [Department of Radiology, Medical University of Vienna (Austria); Weber, Michael, E-mail: michael.weber@meduniwien.ac.at [Department of Radiology, Medical University of Vienna (Austria); Schima, Wolfgang, E-mail: wolfgang.schima@khgh.at [Department of Radiology, KH Goettlicher Heiland and Herz-Jesu Krankenhaus, Dornbacher Strasse 20-28, 1170 Vienna (Austria)

    2012-11-15

    Purpose: To compare the accuracy of liver fat quantification using chemical shift imaging (CSI) and H1 MR-spectroscopy (MRS) at 3.0 T in patients undergoing liver resection. Methods: Totally 35 patients were included in this prospective IRB approved study. The histopathologically assessed liver fat was compared to the hepatic fat fractions calculated with CSI (with and without spleen correction) and MRS. Spearman's rank correlation and Fisher z-test were used for correlation analysis. Sensitivity and specificity regarding the detection of marked steatosis were calculated for the different modalities and compared using the McNemar test. Results: MRS (r = .85) and CSI with spleen correction (r = .85) showed a significantly better correlation (p = .03) with histology compared to CSI without spleen correction (r = .67). Sensitivity and specificity for the detection of marked steatosis was 100% (12/12) and 87% (20/23) for MRS and 92% (11/12) and 83% (19/23) for CSI with spleen correction (p > .12). Conclusion: For the assessment of hepatic steatosis both CSI with spleen correction and MRS at 3.0 T, show a good correlation with histology. CSI without spleen correction should not be used. Sensitivity and specificity for the detection of marked steatosis are high with both modalities. However, results that are scattered around the cut-off values are not reliable enough for clinical decisions.

  1. 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

  2. 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.

  3. Forensic analysis of tire rubbers based on their sulfur chemical states.

    Science.gov (United States)

    Funatsuki, Atsushi; Shiota, Kenji; Takaoka, Masaki; Tamenori, Yusuke

    2015-05-01

    The chemical states of sulfur in 11 tires were analyzed using X-ray absorption near-edge structure (XANES) in order to discriminate between various tire rubbers. All tires had peaks around 2471.5 and 2480.5eV, and the shapes and heights of these peaks differed among tires, suggesting that the sulfur chemical state could be used for discrimination between tire rubbers. Based on t-tests on the results of XANES, 43 of 55 combinations were different at a significance level of 5%. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  4. Chemical imaging and solid state analysis at compact surfaces using UV imaging

    DEFF Research Database (Denmark)

    Wu, Jian X.; Rehder, Sönke; van den Berg, Frans

    2014-01-01

    and excipients in a non-invasive way, as well as mapping the glibenclamide solid state form. An exploratory data analysis supported the critical evaluation of the mapping results and the selection of model parameters for the chemical mapping. The present study demonstrated that the multi-wavelength UV imaging......Fast non-destructive multi-wavelength UV imaging together with multivariate image analysis was utilized to visualize distribution of chemical components and their solid state form at compact surfaces. Amorphous and crystalline solid forms of the antidiabetic compound glibenclamide...

  5. Poison politics: a contentious history of consumer protection against dangerous household chemicals in the United States.

    Science.gov (United States)

    Jones, Marian Moser; Benrubi, Isidore Daniel

    2013-05-01

    The history of consumer protection against household poisons presents a key case study of the uniquely American struggle to balance public health and safety with the interests of business. By the late 19th century, package designs, warning labels, and state statutes had formed an uneven patchwork of protective mechanisms against accidental poisonings. As household chemicals proliferated in the early 20th century, physicians concerned with childhood poisonings pressured the federal government to enact legislation mandating warning labels on packaging for these substances. Manufacturers of household chemicals agreed to labeling requirements for caustic poisons but resisted broader regulation. Accidental poisonings of children continued to increase until the enactment of broad labeling and packaging legislation in the 1960s and 1970s. This history suggests that voluntary agreements between government agencies and manufacturers are inadequate to protect consumers against household poisonings and that, in the United States, protective household chemical regulation proceeds in a reactive rather than a precautionary manner.

  6. SURFACE AND LIGHTNING SOURCES OF NITROGEN OXIDES OVER THE UNITED STATES: MAGNITUDES, CHEMICAL EVOLUTION, AND OUTFLOW

    Science.gov (United States)

    We use observations from two aircraft during the ICARTT campaign over the eastern United States and North Atlantic during summer 2004, interpreted with a global 3-D model of tropospheric chemistry (GEOS-Chem) to test current understanding of regional sources, chemical evolution...

  7. Aggregate formation in a freshwater bacterial strain induced by growth state and conspecific chemical cues

    Czech Academy of Sciences Publication Activity Database

    Blom, J. F.; Horňák, Karel; Šimek, Karel; Pernthaler, J.

    2010-01-01

    Roč. 12, č. 9 (2010), s. 2486-2495 ISSN 1462-2912 R&D Projects: GA ČR(CZ) GA206/08/0015 Institutional research plan: CEZ:AV0Z60170517 Keywords : aggregate formation * Sphingobium sp. * chemical cues * growth state Subject RIV: EE - Microbiology, Virology Impact factor: 5.537, year: 2010

  8. {sup 31}P-MR spectroscopy of all regions of the human heart at 1.5 T with acquisition-weighted chemical shift imaging; P-MR-Spektroskopie aller Wandabschnitte des menschlichen Herzens bei 1,5 T mit akquisitionsgewichteter Chemical-shift-Bildgebung

    Energy Technology Data Exchange (ETDEWEB)

    Koestler, H.; Beer, M.; Buchner, S.; Sandstede, J.; Pabst, T.; Kenn, W.; Hahn, D. [Wuerzburg Univ. (Germany). Abt. fuer Roentgendiagnostik; Landschuetz, W.; Kienlin, M. von [Wuerzburg Univ. (Germany). Physikalisches Inst.; Neubauer, S. [Dept. of Cardiovascular Medicine, John Radcliffe Hospital, Oxford (United Kingdom)

    2001-12-01

    Aim: Aim of this study was to show whether or not acquisition-weighted chemical shift imaging (AW-CSI) allows the determination of PCr and ATP in the lateral and posterior wall of the human heart at 1.5 T. Methods: 12 healthy volunteers were examined using a conventional chemical shift imaging (CSI) and an AW-CSI. The sequences differed only in the number of repetitions for each point in k space. A hanning function was used as filter function leading to 7 repetitions in the center of the k space and 0 in the corners. Thus, AW-CSI had the same resolution as the CSI sequence. The results for both sequences were analyzed using identically positioned voxels in the septal, anterior, lateral and posterior wall. Results: The determined averaged AW-CSI signal to noise ratios were higher for PCr by a factor of 1.3 and for ATP by 1.4 than those of CSI. The PCr/ATP ratios were higher by a factor of 1.2 - 1.3 and showed a smaller standard deviation in all locations for AW-CSI. The mean PCr/ATP ratios determined by AW-CSI of septal, lateral and posterior wall were almost identical (1.72 - 1.76), while it was higher in the anterior wall (1.9). Conclusions: The reduced contamination in AW-CSI improves the signal to noise ratio and the determination of the PCr/ATP ratio in cardiac {sup 31}P spectroscopy compared to CSI with the same resolution. The results in volunteers indicate that AW-CSI renders {sup 31}P spectroscopy of the lateral and posterior wall of the human heart feasible for patient studies at 1.5 T. (orig.) [German] Ziel: Ziel der Arbeit war es zu untersuchen, ob die akquisitionsgewichtete Chemical-shift-Bildgebung (AW-CSI) die Bestimmung von PCr und ATP in der Seiten- und Hinterwand des menschlichen Herzens an einem klinischen 1,5 T MR-Tomographen erlaubt. Methoden: 12 gesunde Probanden wurden jeweils mit einer chemical shift imaging (CSI) und einer AW-CSI-Sequenz untersucht. Die Sequenzen unterschieden sich lediglich in der Anzahl der Wiederholungen der einzelnen

  9. Thigh muscle segmentation of chemical shift encoding-based water-fat magnetic resonance images: The reference database MyoSegmenTUM.

    Directory of Open Access Journals (Sweden)

    Sarah Schlaeger

    Full Text Available Magnetic resonance imaging (MRI can non-invasively assess muscle anatomy, exercise effects and pathologies with different underlying causes such as neuromuscular diseases (NMD. Quantitative MRI including fat fraction mapping using chemical shift encoding-based water-fat MRI has emerged for reliable determination of muscle volume and fat composition. The data analysis of water-fat images requires segmentation of the different muscles which has been mainly performed manually in the past and is a very time consuming process, currently limiting the clinical applicability. An automatization of the segmentation process would lead to a more time-efficient analysis. In the present work, the manually segmented thigh magnetic resonance imaging database MyoSegmenTUM is presented. It hosts water-fat MR images of both thighs of 15 healthy subjects and 4 patients with NMD with a voxel size of 3.2x2x4 mm3 with the corresponding segmentation masks for four functional muscle groups: quadriceps femoris, sartorius, gracilis, hamstrings. The database is freely accessible online at https://osf.io/svwa7/?view_only=c2c980c17b3a40fca35d088a3cdd83e2. The database is mainly meant as ground truth which can be used as training and test dataset for automatic muscle segmentation algorithms. The segmentation allows extraction of muscle cross sectional area (CSA and volume. Proton density fat fraction (PDFF of the defined muscle groups from the corresponding images and quadriceps muscle strength measurements/neurological muscle strength rating can be used for benchmarking purposes.

  10. Aromaticity of graphene nanoflakes in a new way: fragment analysis by combination of the nucleus-independent chemical shifts and the anisotropy of current induced density.

    Science.gov (United States)

    Li, Qing; Li, Chun-Min; Xu, Hong-Liang; Su, Zhong-Min

    2017-08-01

    A graphene nanoflake (GNF) is a polycyclic aromatic hydrocarbon (PAH) with a huge two-dimensional π-conjugated carbon material in which a central benzene ring is surrounded by identical benzene-type rings through infinite alternant method. In this paper, we explore the structure-aromaticity relationship of the GNFs and the GNFs with hollow sites (GNFHs) by combining the nucleus-independent chemical shifts (NICS) with the anisotropy of the current induced density (ACID). Firstly, the benzene is a typical aromatic molecule (NICS = -9.671 ppm), GNFs 1-6 is darned with benzene and the corresponding GNFHs 1'-6'. Secondly, the NICS values of GNFs 1-6 alternately vary: -1.214 (1) > -13.847 (2)  -14.530 (4)  -13.978 (6) ppm, the GNFs (2, 4, 6) with even fragments of annulene have larger aromaticity than that of GNFs (1, 3, 5) with odd fragments of annulene. Significantly, the NICS values of GNFs 1-6 can also be fragment analyzed by the NICS values and ACID of benzene and corresponding GNFHs 1'-6'. The NICS values for GNFs (2, 4, 6) can be roughly estimated by the NICS value of benzene minus the NICS value of the GNFHs (2', 4', 6'), respectively. The NICS values for GNFs (1, 3, 5) can be roughly estimated by the NICS value of the GNFHs (1', 3', 5') minus the NICS value of benzene, respectively. We hope that the present work can provide a simple and reliable method for the rational design of the GNF with aromaticity, which may be used to understand the origin of the graphene nanoflake aromatic properties.

  11. 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

  12. Effects of intergroup upward comparison, trait self-esteem, and identity shift on state self-esteem and affect in upward comparison with in-group members

    OpenAIRE

    Isobe, Chikae; Ura, Mitsuhiro

    2006-01-01

    The present study investigated factors that protect people low in trait self-esteem (Low-SEs), who may be less skilled at constructing information in self-enhancing manners, from threats after interpersonal upward comparison with in-group members. We hypothesized that even Low-SEs can maintain their state self-esteem under intergroup upward comparison. Furthermore, this study explored the possibility that individuals used identity-shift, a strategy to maintain their personal identity, even in...

  13. Experimental root mean square charge radii, isotope shifts, ground state magnetic dipole and electric quadrupole moments of 1≤A≤ 239 nuclei

    International Nuclear Information System (INIS)

    Antony, M.S.; Britz, J.

    1986-01-01

    A compilation of experimental root-mean square radii, isotope shifts, ground-state magnetic dipole and electric quadrupole moments of nuclei 1≤A≤239 is presented. Shell, sub-subshell closures and changes in nuclear deformations discernible from data are displayed graphically. The nuclear charge distribution, for 1≤A≤ 239 nuclei deduced from Coulomb displacement energies is shown for comparison

  14. New Aspects of Field Entropy Squeezing as an Indicator for Mixed State Entanglement in an Effective Two-Level System with Stark Shift

    Institute of Scientific and Technical Information of China (English)

    S.Abdel-Khalek; M.M.A.Ahmed; A-S F.Obada

    2011-01-01

    We present an effective two-level system in interaction through two-photon processes with a single mode quantized electromagnetic field,initially prepared in a coherent state.Field entropy squeezing as an indicator of the entanglement in a mixed state system is suggested.The temporal evolution of the negativity,Wehrl entropy,Wehrl phase distribution and field entropy squeezing are investigated.The results highlight the important roles played by both the Stark shift parameters and the mixed state setting in the dynamics of the Wehrl entropy,Wehrl phase distribution and field entropy squeezing.%We present an effective two-level system in interaction through two-photon processes with a single mode quantized electromagnetic Reid, initially prepared in a coherent state. Field entropy squeezing as an indicator of the entanglement in a mixed state system is suggested. The temporal evolution of the negativity, Wehrl entropy, Wehrl phase distribution and field entropy squeezing are investigated. The results highlight the important roles played by both the Stark shift parameters and the mixed state setting in the dynamics of the Wehrl entropy, Wehrl phase distribution and field entropy squeezing.

  15. 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…

  16. 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.

    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

  17. Conditions for extinction events in chemical reaction networks with discrete state spaces.

    Science.gov (United States)

    Johnston, Matthew D; Anderson, David F; Craciun, Gheorghe; Brijder, Robert

    2018-05-01

    We study chemical reaction networks with discrete state spaces and present sufficient conditions on the structure of the network that guarantee the system exhibits an extinction event. The conditions we derive involve creating a modified chemical reaction network called a domination-expanded reaction network and then checking properties of this network. Unlike previous results, our analysis allows algorithmic implementation via systems of equalities and inequalities and suggests sequences of reactions which may lead to extinction events. We apply the results to several networks including an EnvZ-OmpR signaling pathway in Escherichia coli.

  18. Moisture-induced solid state instabilities in α-chymotrypsin and their reduction through chemical glycosylation

    Directory of Open Access Journals (Sweden)

    Solá Ricardo J

    2010-08-01

    Full Text Available Abstract Background Protein instability remains the main factor limiting the development of protein therapeutics. The fragile nature (structurally and chemically of proteins makes them susceptible to detrimental events during processing, storage, and delivery. To overcome this, proteins are often formulated in the solid-state which combines superior stability properties with reduced operational costs. Nevertheless, solid protein pharmaceuticals can also suffer from instability problems due to moisture sorption. Chemical protein glycosylation has evolved into an important tool to overcome several instability issues associated with proteins. Herein, we employed chemical glycosylation to stabilize a solid-state protein formulation against moisture-induced deterioration in the lyophilized state. Results First, we investigated the consequences of moisture sorption on the stability and structural conformation of the model enzyme α-chymotrypsin (α-CT under controlled humidity conditions. Results showed that α-CT aggregates and inactivates as a function of increased relative humidity (RH. Furthermore, α-CT loses its native secondary and tertiary structure rapidly at increasing RH. In addition, H/D exchange studies revealed that α-CT structural dynamics increased at increasing RH. The magnitude of the structural changes in tendency parallels the solid-state instability data (i.e., formation of buffer-insoluble aggregates, inactivation, and loss of native conformation upon reconstitution. To determine if these moisture-induced instability issues could be ameliorated by chemical glycosylation we proceeded to modify our model protein with chemically activated glycans of differing lengths (lactose and dextran (10 kDa. The various glycoconjugates showed a marked decrease in aggregation and an increase in residual activity after incubation. These stabilization effects were found to be independent of the glycan size. Conclusion Water sorption leads to

  19. Radon: Chemical and physical states of radon progeny. Final technical report

    International Nuclear Information System (INIS)

    Castleman, A.W. Jr.

    1996-01-01

    The evolving chemical and physical form of radon progeny influence their transport to the bioreceptor and the extent to which that receptor can take up these species into various tissues. When first born following radioactive decay processes, the potentially deleterious radon progeny undergo various physical and chemical transformations as they transcend from a highly charged to a neutral state, and interact with various constituents of the environment. These transformations impact on the extent to which the radon progeny become associated with aerosol particles on the one hand, and their ultimate chemical form that is available for uptake in the biosystem, on the other. The program, which originally commenced in 1987, dealt with the basic chemistry and physics of radon progeny and hence impacted on several themes of importance to the DOE/OHER radon program. One of these is dose response, which is governed by the physical forms of the radon progeny, their transport to the bioreceptor and the chemical forms that govern their uptake. The second theme had to do with cellular responses, one of the major issues motivating the work. It is well known that various sizes of ions and molecules are selectively transported across cell membrane to differing degrees. This ultimately has to do with their chemical and physical forms, charge and size. The overall objective of the work was threefold: (1) quantifying the mechanisms and rates of the chemical and physical transformation; (2) ascertaining the ultimate chemical forms, and (3) determining the potential interactions of these chemical species with biological functional groups to ascertain their ultimate transport and incorporation within cells

  20. Direct Reprogramming of Fibroblasts via a Chemically Induced XEN-like State.

    Science.gov (United States)

    Li, Xiang; Liu, Defang; Ma, Yantao; Du, Xiaomin; Jing, Junzhan; Wang, Lipeng; Xie, Bingqing; Sun, Da; Sun, Shaoqiang; Jin, Xueqin; Zhang, Xu; Zhao, Ting; Guan, Jingyang; Yi, Zexuan; Lai, Weifeng; Zheng, Ping; Huang, Zhuo; Chang, Yanzhong; Chai, Zhen; Xu, Jun; Deng, Hongkui

    2017-08-03

    Direct lineage reprogramming, including with small molecules, has emerged as a promising approach for generating desired cell types. We recently found that during chemical induction of induced pluripotent stem cells (iPSCs) from mouse fibroblasts, cells pass through an extra-embryonic endoderm (XEN)-like state. Here, we show that these chemically induced XEN-like cells can also be induced to directly reprogram into functional neurons, bypassing the pluripotent state. The induced neurons possess neuron-specific expression profiles, form functional synapses in culture, and further mature after transplantation into the adult mouse brain. Using similar principles, we were also able to induce hepatocyte-like cells from the XEN-like cells. Cells in the induced XEN-like state were readily expandable over at least 20 passages and retained genome stability and lineage specification potential. Our study therefore establishes a multifunctional route for chemical lineage reprogramming and may provide a platform for generating a diverse range of cell types via application of this expandable XEN-like state. Copyright © 2017 Elsevier Inc. All rights reserved.

  1. 15 CFR 745.1 - Advance notification and annual report of all exports of Schedule 1 chemicals to other States...

    Science.gov (United States)

    2010-01-01

    ... § 745.1 Advance notification and annual report of all exports of Schedule 1 chemicals to other States... Prohibition of Chemical Weapons (OPCW) not less than 30 days in advance of every export of a Schedule 1...: “Advance Notification of Schedule 1 Chemical Export”. (3) Upon receipt of the notification, BIS will inform...

  2. Multi-GPU unsteady 2D flow simulation coupled with a state-to-state chemical kinetics

    Science.gov (United States)

    Tuttafesta, Michele; Pascazio, Giuseppe; Colonna, Gianpiero

    2016-10-01

    In this work we are presenting a GPU version of a CFD code for high enthalpy reacting flow, using the state-to-state approach. In supersonic and hypersonic flows, thermal and chemical non-equilibrium is one of the fundamental aspects that must be taken into account for the accurate characterization of the plasma and state-to-state kinetics is the most accurate approach used for this kind of problems. This model consists in writing a continuity equation for the population of each vibrational level of the molecules in the mixture, determining at the same time the species densities and the distribution of the population in internal levels. An explicit scheme is employed here to integrate the governing equations, so as to exploit the GPU structure and obtain an efficient algorithm. The best performances are obtained for reacting flows in state-to-state approach, reaching speedups of the order of 100, thanks to the use of an operator splitting scheme for the kinetics equations.

  3. Thermal hydraulic test of advanced fuel bundle with spectral shift rod (SSR) for BWR. Effect of thermal hydraulic parameters on steady state characteristics

    International Nuclear Information System (INIS)

    Kondo, Takao; Kitou, Kazuaki; Chaki, Masao; Ohga, Yukiharu; Makigami, Takeshi

    2011-01-01

    Japanese national project of next generation light water reactor (LWR) development started in 2008. Under this project, spectral shift rod (SSR) is being developed. SSR, which replaces conventional water rod (WR) of boiling water reactor (BWR) fuel bundle, was invented to enhance the BWR's merit, spectral shift effect for uranium saving. In SSR, water boils by neutron and gamma-ray direct heating and water level is formed as a boundary of the upper steam region and the lower water region. This SSR water level can be controlled by core flow rate, which amplifies the change of average core void fraction, resulting in the amplified spectral shift effect. This paper presents the steady state test results of the base geometry case in SSR thermal hydraulic test, which was conducted under the national project of next generation LWR. In the test, thermal hydraulic parameters, such as flow rate, pressure, inlet subcooling and heater rod power are changed to evaluate these effects on SSR water level and other SSR characteristics. In the test results, SSR water level rose as flow rate rose, which showed controllability of SSR water level by flow rate. The sensitivities of other thermal hydraulic parameters on SSR water level were also evaluated. The obtained data of parameter's sensitivities is various enough for the further analytical evaluation. The fluctuation of SSR water level was also measured to be small enough. As a result, it was confirmed that SSR's steady state performance was as planned and that SSR design concept is feasible. (author)

  4. Hepatic fat quantification using chemical shift MR imaging and MR spectroscopy in the presence of hepatic iron deposition: validation in phantoms and in patients with chronic liver disease.

    Science.gov (United States)

    Lee, Seung Soo; Lee, Youngjoo; Kim, Namkug; Kim, Seong Who; Byun, Jae Ho; Park, Seong Ho; Lee, Moon-Gyu; Ha, Hyun Kwon

    2011-06-01

    To compare the accuracy of four chemical shift magnetic resonance imaging (MRI) (CS-MRI) analysis methods and MR spectroscopy (MRS) with and without T2-correction in fat quantification in the presence of excess iron. CS-MRI with six opposed- and in-phase acquisitions and MRS with five-echo acquisitions (TEs of 20, 30, 40, 50, 60 msec) were performed at 1.5 T on phantoms containing various fat fractions (FFs), on phantoms containing various iron concentrations, and in 18 patients with chronic liver disease. For CS-MRI, FFs were estimated with the dual-echo method, with two T2*-correction methods (triple- and multiecho), and with multiinterference methods that corrected for both T2* and spectral interference effects. For MRS, FF was estimated without T2-correction (single-echo MRS) and with T2-correction (multiecho MRS). In the phantoms, T2*- or T2-correction methods for CS-MRI and MRS provided unbiased estimations of FFs (mean bias, -1.1% to 0.5%) regardless of iron concentration, whereas the dual-echo method (-5.5% to -8.4%) and single-echo MRS (12.1% to 37.3%) resulted in large biases in FFs. In patients, the FFs estimated with triple-echo (R = 0.98), multiecho (R = 0.99), and multiinterference (R = 0.99) methods had stronger correlations with multiecho MRS FFs than with the dual-echo method (R = 0.86; P ≤ 0.011). The FFs estimated with multiinterference method showed the closest agreement with multiecho MRS FFs (the 95% limit-of-agreement, -0.2 ± 1.1). T2*- or T2-correction methods are effective in correcting the confounding effects of iron, enabling an accurate fat quantification throughout a wide range of iron concentrations. Spectral modeling of fat may further improve the accuracy of CS-MRI in fat quantification. Copyright © 2011 Wiley-Liss, Inc.

  5. Chemical state analysis of conversion coatings by SR-XPS and TEY-XANES

    CERN Document Server

    Noro, H; Nagoshi, M

    2002-01-01

    Chromate coatings on galvanized steel have been studied by Synchrotron Radiation (SR) based techniques that include X-ray Photoelectron Spectroscopy (XPS) and Total-Electron-Yield X-ray Absorption Near Edge Structure (TEY-XANES). Non-destructive depth profiling of the coatings by SR-XPS reveals the enhancement of Cr sup 6 sup + in the outer surface. TEY-XANES spectroscopy based on simple specimen current measurement is demonstrated as an effective technique for analyzing chemical states of conversion coatings on general bulk substrates. The sampling depth of this technique, which exceeds several tens of nanometer, is determined by the penetration length of Auger electrons excited by X-ray and the inelastic mean free path of secondary electrons excited by inelastically scattered Auger electrons. The chemical states of phosphoric acid added chromate coatings are studied using this technique. The phosphoric acid is taken into the chromate coatings as partially changed into zinc and chromium phosphates, and the r...

  6. Chemical states of fission products in irradiated uranium-plutonium mixed oxide fuel

    International Nuclear Information System (INIS)

    Kurosaki, Ken; Uno, Masayoshi; Yamanaka, Shinsuke

    1999-01-01

    The chemical states of fission products (FPs) in irradiated uranium-plutonium mixed oxide (MOX) fuel for the light water reactor (LWR) were estimated by thermodynamic equilibrium calculations on system of fuel and FPs by using ChemSage program. A stoichiometric MOX containing 6.1 wt. percent PuO 2 was taken as a loading fuel. The variation of chemical states of FPs was calculated as a function of oxygen potential. Some pieces of information obtained by the calculation were compared with the results of the post-irradiation examination (PIE) of UO 2 fuel. It was confirmed that the multicomponent and multiphase thermodynamic equilibrium calculation between fuel and FPs system was an effective tool for understanding the behavior of FPs in fuel. (author)

  7. Evidence for excited-state intramolecular proton transfer in 4-chlorosalicylic acid from combined experimental and computational studies: Quantum chemical treatment of the intramolecular hydrogen bonding interaction

    Energy Technology Data Exchange (ETDEWEB)

    Paul, Bijan Kumar [Department of Chemistry, University of Calcutta, 92 Acharya Prafulla Chandra Road, Calcutta 700009 (India); Guchhait, Nikhil, E-mail: nikhil.guchhait@rediffmail.com [Department of Chemistry, University of Calcutta, 92 Acharya Prafulla Chandra Road, Calcutta 700009 (India)

    2012-07-25

    Highlights: Black-Right-Pointing-Pointer Experimental and computational studies on the photophysics of 4-chlorosalicylic acid. Black-Right-Pointing-Pointer Spectroscopically established ESIPT reaction substantiated by theoretical calculation. Black-Right-Pointing-Pointer Quantum chemical treatment of IMHB unveils strength, nature and directional nature. Black-Right-Pointing-Pointer Superiority of quantum chemical treatment of H-bond over geometric criteria. Black-Right-Pointing-Pointer Role of H-bond as a modulator of aromaticity. -- Abstract: The photophysical study of a pharmaceutically important chlorine substituted derivative of salicylic acid viz., 4-chlorosalicylic acid (4ClSA) has been carried out by steady-state absorption, emission and time-resolved emission spectroscopy. A large Stokes shifted emission band with negligible solvent polarity dependence marks the spectroscopic signature of excited-state intramolecular proton transfer (ESIPT) reaction in 4ClSA. Theoretical calculation by ab initio and Density Functional Theory methods yields results consistent with experimental findings. Theoretical potential energy surfaces predict the occurrence of proton transfer in S{sub 1}-state. Geometrical and energetic criteria, Atoms-In-Molecule topological parameters, Natural Bond Orbital population analysis have been exploited to evaluate the intramolecular hydrogen bond (IMHB) interaction and to explore its directional nature. The inter-correlation between aromaticity and resonance assisted H-bond is also discussed in this context. Our results unveil that the quantum chemical treatment is a more accurate tool to assess hydrogen bonding interaction in comparison to geometrical criteria.

  8. Rich Ground State Chemical Ordering in Nanoparticles: Exact Solution of a Model for Ag-Au Clusters

    DEFF Research Database (Denmark)

    Larsen, Peter Mahler; Jacobsen, Karsten Wedel; Schiøtz, Jakob

    2018-01-01

    We show that nanoparticles can have very rich ground state chemical order. This is illustrated by determining the chemical ordering of Ag-Au 309-atom Mackay icosahedral nanoparticles. The energy of the nanoparticles is described using a cluster expansion model, and a Mixed Integer Programming (MIP......) approach is used to find the exact ground state configurations for all stoichiometries. The chemical ordering varies widely between the different stoichiometries, and display a rich zoo of structures with non-trivial ordering....

  9. Evaluating the energy and CO2 emissions impacts of shifts in residential water heating in the United States

    International Nuclear Information System (INIS)

    Sanders, Kelly T.; Webber, Michael E.

    2015-01-01

    Water heating represented nearly 13% of 2010 residential energy consumption making it an important target for energy conservation efforts. The objective of this work is to identify spatially-resolved strategies for energy conservation, since little analysis has been done to identify how regional characteristics affect the energy consumed for water heating. We present a first-order thermodynamic analysis, utilizing ab initio calculations and regression methods, to quantify primary energy consumption and CO 2 emissions with regional specificity by considering by considering local electricity mixes, heat rates, solar radiation profiles, heating degrees days, and water heating unit sales for 27 regions of the US. Results suggest that shifting from electric towards natural gas or solar water heating offered primary energy and CO 2 emission reductions in most US regions, but these reductions varied considerably according to regional electricity mix and solar resources. We find that regions that would benefit most from technology transitions, are often least likely to switch due to limited economic incentives. Our results suggest that federal energy factor metrics, which ignore upstream losses in power generation, are insufficient in informing consumers about the energy performance of residential end use appliances. - Highlights: • US energy factor ratings for water heaters ignore upstream losses. • Switching from electric storage water heating reduces CO 2 emissions in most US regions. • Regions with greatest potential for CO 2 avoidance are least likely to shift technologies. • Benefits vary significantly according to climate and regional electricity fuel mix

  10. Congratulations, You're Pregnant! Now About Your Shifts . . . : The State of Maternity Leave Attitudes and Culture in EM.

    Science.gov (United States)

    MacVane, Casey Z; Fix, Megan L; Strout, Tania D; Zimmerman, Kate D; Bloch, Rebecca B; Hein, Christine L

    2017-08-01

    Increasing attention has been focused on parental leave, but little is known about early leave and parental experiences for male and female attending physicians. Our goal was to describe and quantify the parental leave experiences of a nationally representative sample of emergency physicians (EP). We conducted a web-based survey, distributed via emergency medicine professional organizations, discussion boards, and listservs, to address study objectives. We analyzed data from 464 respondents; 56% were women. Most experienced childbirth while employed as an EP. Fifty-three percent of women and 60% of men reported working in a setting with a formal maternity leave policy; however, 36% of women and 18% of men reported dissatisfaction with these policies. Most reported that other group members cover maternity-related shift vacancies; a minority reported that pregnant partners work extra shifts prior to leave. Leave duration and compensation varied widely, ranging from no compensated leave (18%) to 12 or more weeks at 100% salary (7%). Supportive attitudes were reported during pregnancy (53%) and, to a lesser degree (43%), during leave. Policy improvement suggestions included the development of clear, formal policies; improving leave duration and compensation; adding paternity and adoption leave; providing support for physicians working extra to cover colleagues' leave; and addressing breastfeeding issues. In this national sample of EPs, maternity leave policies varied widely. The duration and compensation during leave also had significant variation. Participants suggested formalizing policies, increasing leave duration and compensation, adding paternity leave, and changing the coverage for vacancies to relieve burden on physician colleagues.

  11. 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.

  12. Stability of racemic and chiral steady states in open and closed chemical systems

    Energy Technology Data Exchange (ETDEWEB)

    Ribo, Josep M. [Departament de Quimica Organica, Universitat de Barcelona, c. Marti i Franques 1, Barcelona (Spain); Hochberg, David [Centro de Astrobiologia (CSIC-INTA), Ctra. Ajalvir Km. 4, 28850 Torrejon de Ardoz, Madrid (Spain)], E-mail: hochbergd@inta.es

    2008-12-22

    The stability properties of models of spontaneous mirror symmetry breaking in chemistry are characterized algebraically. The models considered here all derive either from the Frank model or from autocatalysis with limited enantioselectivity. Emphasis is given to identifying the critical parameter controlling the chiral symmetry breaking transition from racemic to chiral steady-state solutions. This parameter is identified in each case, and the constraints on the chemical rate constants determined from dynamic stability are derived.

  13. Stability of racemic and chiral steady states in open and closed chemical systems

    International Nuclear Information System (INIS)

    Ribo, Josep M.; Hochberg, David

    2008-01-01

    The stability properties of models of spontaneous mirror symmetry breaking in chemistry are characterized algebraically. The models considered here all derive either from the Frank model or from autocatalysis with limited enantioselectivity. Emphasis is given to identifying the critical parameter controlling the chiral symmetry breaking transition from racemic to chiral steady-state solutions. This parameter is identified in each case, and the constraints on the chemical rate constants determined from dynamic stability are derived

  14. Trends in the chemical state of polonium-210 in the atmosphere

    International Nuclear Information System (INIS)

    Abe, M.; Abe, S.

    1980-01-01

    Trends of the chemial state of 210 Po in airborne dusts at Chiba, Japan, between 1963 and 1976 are discussed. A sublimination method is used to determine the chemical state of the 210 Po. The results show that the fraction of the component volatilizing at low temperature varies yearly in the range between 0 and 50%. If we assume the component comes from an artificial source, it may be suggested that a large fraction of 210 Po in airborne dusts comes from artificial sources. Additional reference data that show local properties of our sampling site are presented

  15. Chemical-state-selective mapping at nanometer scale using synchrotron radiation and photoelectron emission microscopy

    International Nuclear Information System (INIS)

    Hirao, Norie; Baba, Yuji; Sekiguchi, Tetsuhiro; Shimoyama, Iwao; Honda, Mitsunori

    2010-01-01

    For surface analyses of semiconductor devices and various functional materials, it has become indispensable to analyze valence states at nanometer scale due to the rapid developments of nanotechnology. Since a method for microscopic mapping dependent on the chemical bond states has not been established so far, we have developed a photoelectron emission microscopy (PEEM) system combined with synchrotron soft X-ray excitation. The samples investigated were Si/SiO x micro-patterns prepared by O 2 + ion implantation in Si(001) wafer using a mask. PEEM images excited by various photon energies around the Si K-edge were observed. The lateral spatial resolution of the system was about 41 nm. The brightness of each spot in PEEM images changed depending on the photon energy, due to the X-ray absorption intensity of the respective chemical state. Since the surface of this sample was topographically flat, it has been demonstrated that the present method can be applied to observations of the microscopic pattern, depending not on the morphology, but only on the valence states of silicon. We have also in-situ measured the changes of the PEEM images upon annealing, and elucidated the mechanism of the lateral diffusion of oxygen and valence states of silicon at the nanometer scale. (author)

  16. Chemical-state-selective mapping at nanometer scale using synchrotron radiation and photoelectron emission microscopy

    International Nuclear Information System (INIS)

    Hirao, Norie; Baba, Yuji; Sekiguchi, Tetsuhiro; Shimoyama, Iwao; Honda, Mitsunori

    2008-01-01

    For surface analyses of semiconductor devices and various functional materials, it has become indispensable to analyze the valence states at the nanometer scale due to the rapid developments of nanotechnology. Since a method for microscopic mapping dependent on the chemical bond states has not been established so far, we have developed a photoelectron emission microscopy (PEEM) system combined with synchrotron soft X-ray excitation. The samples investigated were Si/SiO x micro-patterns prepared by O 2 + ion implantation in a Si(001) wafer using a mask. PEEM images excited by various photon energies around the Si K-edge were observed. The lateral spatial resolution of the system was about 41 nm. The brightness of each spot in PEEM images changed depending on the photon energy, due to the X-ray absorption intensity of the respective chemical state. Since the surface of this sample is topographically flat, it has been demonstrated that the present method can be applied to observations of the microscopic pattern, depending not on the morphology, but only on the valence states of silicon. We have also in-situ measured the changes of PEEM images upon annealing, and elucidated the mechanism of the lateral diffusion of oxygen and valence states of silicon at the nanometer scale. (author)

  17. Quantitative chemical state XPS analysis of first row transition metals, oxides and hydroxides

    Energy Technology Data Exchange (ETDEWEB)

    Biesinger, M C; Payne, B P; McIntryre, N S [Department of Chemistry, University of Western Ontario, London, Ontario, N6A 5B7 (Canada); Hart, B R; Lau, L Wm [Surface Science Western, Room G1, Western Science Centre, University of Western Ontario, London, Ontario, N6A 5B7 (Canada); Grosvenor, A P [Department of Chemistry, Gunning/Lemieux Chemistry Centre, University of Alberta, Edmonton, Alberta, T6G 2G2 (Canada); Smart, R StC [ACeSSS, Applied Centre for Structural and Synchrotron Studies, University of South Australia, Mawson Lakes, SA 5095 (Australia)], E-mail: biesingr@uwo.ca

    2008-03-15

    Practical quantitative chemical state X-ray photoelectron spectroscopy (XPS) analysis of first row transition metals, oxides and hydroxides is challenging due to the complexity of their M 2p spectra. Complex multiplet splitting, shake-up and plasmon loss structure can play a role in the interpretation of the chemical states present. This paper will show practical curve fitting procedures for the quantitative measurement of different chemical states for metal oxides and hydroxides from a survey of transition metals. It will also discuss some of the limitations and pitfalls present as well as give practical examples of their successful use. These curve-fitting procedures are based on 1) standard spectra from quality reference samples, 2) a survey of appropriate literature databases and/or a compilation of literature references, 3) fitting of multiplet split spectra based on spectra of numerous reference materials and theoretical modelling, 4) spectral subtractions routines, again using reference spectra, and 5) specific literature references where fitting procedures are available.

  18. Quantitative chemical state XPS analysis of first row transition metals, oxides and hydroxides

    International Nuclear Information System (INIS)

    Biesinger, M C; Payne, B P; McIntryre, N S; Hart, B R; Lau, L Wm; Grosvenor, A P; Smart, R StC

    2008-01-01

    Practical quantitative chemical state X-ray photoelectron spectroscopy (XPS) analysis of first row transition metals, oxides and hydroxides is challenging due to the complexity of their M 2p spectra. Complex multiplet splitting, shake-up and plasmon loss structure can play a role in the interpretation of the chemical states present. This paper will show practical curve fitting procedures for the quantitative measurement of different chemical states for metal oxides and hydroxides from a survey of transition metals. It will also discuss some of the limitations and pitfalls present as well as give practical examples of their successful use. These curve-fitting procedures are based on 1) standard spectra from quality reference samples, 2) a survey of appropriate literature databases and/or a compilation of literature references, 3) fitting of multiplet split spectra based on spectra of numerous reference materials and theoretical modelling, 4) spectral subtractions routines, again using reference spectra, and 5) specific literature references where fitting procedures are available

  19. Soft x-ray spectroscopy for probing electronic and chemical states of battery materials

    International Nuclear Information System (INIS)

    Yang Wanli; Qiao Ruimin

    2016-01-01

    The formidable challenge of developing high-performance battery system stems from the complication of battery operations, both mechanically and electronically. In the electrodes and at the electrode–electrolyte interfaces, chemical reactions take place with evolving electron states. In addition to the extensive studies of material synthesis, electrochemical, structural, and mechanical properties, soft x-ray spectroscopy provides unique opportunities for revealing the critical electron states in batteries. This review discusses some of the recent soft x-ray spectroscopic results on battery binder, transition-metal based positive electrodes, and the solid-electrolyte-interphase. By virtue of soft x-ray’s sensitivity to electron states, the electronic property, the redox during electrochemical operations, and the chemical species of the interphases could be fingerprinted by soft x-ray spectroscopy. Understanding and innovating battery technologies need a multimodal approach, and soft x-ray spectroscopy is one of the incisive tools to probe the chemical and physical evolutions in batteries. (topical review)

  20. Chemical state of mercury and selenium in sewage sludge ash based P-fertilizers

    Energy Technology Data Exchange (ETDEWEB)

    Vogel, Christian, E-mail: cv.vogel@yahoo.de [Division 4.4 Thermochemical Residues Treatment and Resource Recovery, Bundesanstalt für Materialforschung und −prüfung (BAM), Unter den Eichen 87, 12205 Berlin (Germany); Krüger, Oliver; Herzel, Hannes [Division 4.4 Thermochemical Residues Treatment and Resource Recovery, Bundesanstalt für Materialforschung und −prüfung (BAM), Unter den Eichen 87, 12205 Berlin (Germany); Amidani, Lucia [ESRF—The European Synchrotron, 71 Avenue des Martyrs, 38000 Grenoble (France); Adam, Christian [Division 4.4 Thermochemical Residues Treatment and Resource Recovery, Bundesanstalt für Materialforschung und −prüfung (BAM), Unter den Eichen 87, 12205 Berlin (Germany)

    2016-08-05

    Highlights: • Mercury bonded to carbon/organic material was detected in some sewage sludge ashes. • After thermochemcial treatment some mercury remains stabilized in the SSA matrix. • Analysis of the chemical state of mercury and selenium in highly diluted samples. - Abstract: Phosphorus-fertilizers from secondary resources such as sewage sludge ash (SSA) will become more important in the future as they could substitute conventional fertilizers based on the nonrenewable resource phosphate rock. Thermochemical approaches were developed which remove heavy metals from SSA prior to its fertilizer application on farmlands. We analyzed the chemical state of mercury and selenium in SSA before and after thermochemical treatment under different conditions for P-fertilizer production by X-ray absorption near edge structure (XANES) spectroscopy. In some incineration plants the mercury loaded carbon adsorber from off-gas cleaning was collected together with the SSA for waste disposal. SSAs from those plants contained mercury mainly bound to carbon/organic material. The other SSAs contained inorganic mercury compounds which are most probably stabilized in the SSA matrix and were thus not evaporated during incineration. During thermochemical treatment, carbon-bound mercury was removed quantitatively. In contrast, a certain immobile fraction of inorganic mercury compounds remained in thermochemically treated SSA, which were not clearly identified. HgSe might be one of the inorganic compounds, which is supported by results of Se K-edge XANES spectroscopy. Furthermore, the chemical state of selenium in the SSAs was very sensitive to the conditions of the thermochemical treatment.

  1. Lanthanide shift reagents, binding, shift mechanisms and exchange

    International Nuclear Information System (INIS)

    Boer, J.W.M. de

    1977-01-01

    Paramagnetic lanthanide shift reagents, when added to a solution of a substrate, induce shifts in the nuclear magnetic resonance (NMR) spectrum of the substrate molecules. The induced shifts contain information about the structure of the shift reagent substrate complex. The structural information, however, may be difficult to extract because of the following effects: (1) different complexes between shift reagent and substrate may be present in solution, e.g. 1:1 and 1:2 complexes, and the shift observed is a weighed average of the shifts of the substrate nuclei in the different complexes; (2) the Fermi contact interaction, arising from the spin density at the nucleus, contributes to the induced shift; (3) chemical exchange effects may complicate the NMR spectrum. In this thesis, the results of an investigation into the influence of these effects on the NMR spectra of solutions containing a substrate and LSR are presented. The equations describing the pseudo contact and the Fermi contact shift are derived. In addition, it is shown how the modified Bloch equations describing the effect of the chemical exchange processes occurring in the systems studied can be reduced to the familiar equations for a two-site exchange case. The binding of mono- and bifunctional ethers to the shift reagent are reported. An analysis of the induced shifts is given. Finally, the results of the experiments performed to study the exchange behavior of dimethoxyethane and heptafluorodimethyloctanedionato ligands are presented

  2. 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. Copyright © 2014 John Wiley & Sons, Ltd.

  3. Easy and unambiguous sequential assignments of intrinsically disordered proteins by correlating the backbone 15N or 13C′ chemical shifts of multiple contiguous residues in highly resolved 3D spectra

    International Nuclear Information System (INIS)

    Yoshimura, Yuichi; Kulminskaya, Natalia V.; Mulder, Frans A. A.

    2015-01-01

    Sequential resonance assignment strategies are typically based on matching one or two chemical shifts of adjacent residues. However, resonance overlap often leads to ambiguity in resonance assignments in particular for intrinsically disordered proteins. We investigated the potential of establishing connectivity through the three-bond couplings between sequentially adjoining backbone carbonyl carbon nuclei, combined with semi-constant time chemical shift evolution, for resonance assignments of small folded and larger unfolded proteins. Extended sequential connectivity strongly lifts chemical shift degeneracy of the backbone nuclei in disordered proteins. We show here that 3D (H)N(COCO)NH and (HN)CO(CO)NH experiments with relaxation-optimized multiple pulse mixing correlate up to seven adjacent backbone amide nitrogen or carbonyl carbon nuclei, respectively, and connections across proline residues are also obtained straightforwardly. Multiple, recurrent long-range correlations with ultra-high resolution allow backbone 1 H N , 15 N H , and 13 C′ resonance assignments to be completed from a single pair of 3D experiments

  4. Incorporation of a Chemical Equilibrium Equation of State into LOCI-Chem

    Science.gov (United States)

    Cox, Carey F.

    2005-01-01

    Renewed interest in development of advanced high-speed transport, reentry vehicles and propulsion systems has led to a resurgence of research into high speed aerodynamics. As this flow regime is typically dominated by hot reacting gaseous flow, efficient models for the characteristic chemical activity are necessary for accurate and cost effective analysis and design of aerodynamic vehicles that transit this regime. The LOCI-Chem code recently developed by Ed Luke at Mississippi State University for NASA/MSFC and used by NASA/MSFC and SSC represents an important step in providing an accurate, efficient computational tool for the simulation of reacting flows through the use of finite-rate kinetics [3]. Finite rate chemistry however, requires the solution of an additional N-1 species mass conservation equations with source terms involving reaction kinetics that are not fully understood. In the equilibrium limit, where the reaction rates approach infinity, these equations become very stiff. Through the use of the assumption of local chemical equilibrium the set of governing equations is reduced back to the usual gas dynamic equations, and thus requires less computation, while still allowing for the inclusion of reacting flow phenomenology. The incorporation of a chemical equilibrium equation of state module into the LOCI-Chem code was the primary objective of the current research. The major goals of the project were: (1) the development of a chemical equilibrium composition solver, and (2) the incorporation of chemical equilibrium solver into LOCI-Chem. Due to time and resource constraints, code optimization was not considered unless it was important to the proper functioning of the code.

  5. Congratulations, You’re Pregnant! Now About Your Shifts . . . : The State of Maternity Leave Attitudes and Culture in EM

    Directory of Open Access Journals (Sweden)

    Casey Z. MacVane

    2017-07-01

    Full Text Available Introduction: Increasing attention has been focused on parental leave, but little is known about early leave and parental experiences for male and female attending physicians. Our goal was to describe and quantify the parental leave experiences of a nationally representative sample of emergency physicians (EP. Methods: We conducted a web-based survey, distributed via emergency medicine professional organizations, discussion boards, and listservs, to address study objectives. Results: We analyzed data from 464 respondents; 56% were women. Most experienced childbirth while employed as an EP. Fifty-three percent of women and 60% of men reported working in a setting with a formal maternity leave policy; however, 36% of women and 18% of men reported dissatisfaction with these policies. Most reported that other group members cover maternity-related shift vacancies; a minority reported that pregnant partners work extra shifts prior to leave. Leave duration and compensation varied widely, ranging from no compensated leave (18% to 12 or more weeks at 100% salary (7%. Supportive attitudes were reported during pregnancy (53% and, to a lesser degree (43%, during leave. Policy improvement suggestions included the development of clear, formal policies; improving leave duration and compensation; adding paternity and adoption leave; providing support for physicians working extra to cover colleagues’ leave; and addressing breastfeeding issues. Conclusion: In this national sample of EPs, maternity leave policies varied widely. The duration and compensation during leave also had significant variation. Participants suggested formalizing policies, increasing leave duration and compensation, adding paternity leave, and changing the coverage for vacancies to relieve burden on physician colleagues.

  6. Congratulations, You’re Pregnant! Now About Your Shifts . . . : The State of Maternity Leave Attitudes and Culture in EM

    Science.gov (United States)

    MacVane, Casey Z.; Fix, Megan L.; Strout, Tania D.; Zimmerman, Kate D.; Bloch, Rebecca B.; Hein, Christine L.

    2017-01-01

    Introduction Increasing attention has been focused on parental leave, but little is known about early leave and parental experiences for male and female attending physicians. Our goal was to describe and quantify the parental leave experiences of a nationally representative sample of emergency physicians (EP). Methods We conducted a web-based survey, distributed via emergency medicine professional organizations, discussion boards, and listservs, to address study objectives. Results We analyzed data from 464 respondents; 56% were women. Most experienced childbirth while employed as an EP. Fifty-three percent of women and 60% of men reported working in a setting with a formal maternity leave policy; however, 36% of women and 18% of men reported dissatisfaction with these policies. Most reported that other group members cover maternity-related shift vacancies; a minority reported that pregnant partners work extra shifts prior to leave. Leave duration and compensation varied widely, ranging from no compensated leave (18%) to 12 or more weeks at 100% salary (7%). Supportive attitudes were reported during pregnancy (53%) and, to a lesser degree (43%), during leave. Policy improvement suggestions included the development of clear, formal policies; improving leave duration and compensation; adding paternity and adoption leave; providing support for physicians working extra to cover colleagues’ leave; and addressing breastfeeding issues. Conclusion In this national sample of EPs, maternity leave policies varied widely. The duration and compensation during leave also had significant variation. Participants suggested formalizing policies, increasing leave duration and compensation, adding paternity leave, and changing the coverage for vacancies to relieve burden on physician colleagues. PMID:28874931

  7. Determination of Chemical States of Mercury on Activated Carbon Using XANES

    International Nuclear Information System (INIS)

    Takaoka, Masaki; Takeda, Nobuo; Oshita, Kazuyuki; Yamamoto, Takashi; Tanaka, Tsunehiro; Uruga, Tomoya

    2007-01-01

    Although the adsorption of mercury vapor onto activated carbon is a widely used technology to prevent environmental release, the adsorption mechanism is not clearly understood. In this study, we determined the chemical states of mercury on two kinds of activated carbon using X-ray absorption near-edge spectroscopy (XANES) to elucidate the adsorption mechanism. The adsorption experiments of elemental mercury onto activated carbon were conducted under air and nitrogen atmospheres at temperatures of 20 and 160 deg. C. Two types of activated carbon were prepared. X-ray absorption fine structure (XAFS) measurements were carried out on beamline BL01B1 at SPring-8. Hg-LIII edge XANES spectra suggested that chemical adsorption of elemental mercury on the activated carbon occurred in the 20-160 deg. C temperature range. According to the XANES spectra, a difference occurred in the chemical states of mercury between AC no. 1 and AC no. 2. The Hg XANES spectra on AC no. 1 were similar to those of Hg2Cl2 and HgS, and the Hg XANES spectra on AC no. 2 were similar to that of HgO, which suggested that nitric acid treatment removed sulfur from AC no. 1 and functional groups that were strong oxidizers on the surface of AC no. 2 created HgO. According to the EXAFS oscillation, a difference occurred in the chemical states of mercury on AC no. 1 between 20 and 160 deg. C. We found that impurities and oxidant functional groups on activated carbon play key roles in mercury adsorption

  8. Emergence of a super-synchronized mobbing state in a large population of coupled chemical oscillators

    Science.gov (United States)

    Ghoshal, Gourab; Muñuzuri, Alberto P.; Pérez-Mercader, Juan

    2016-01-01

    Oscillatory phenomena are ubiquitous in Nature. The ability of a large population of coupled oscillators to synchronize constitutes an important mechanism to express information and establish communication among members. To understand such phenomena, models and experimental realizations of globally coupled oscillators have proven to be invaluable in settings as varied as chemical, biological and physical systems. A variety of rich dynamical behavior has been uncovered, although usually in the context of a single state of synchronization or lack thereof. Through the experimental and numerical study of a large population of discrete chemical oscillators, here we report on the unexpected discovery of a new phenomenon revealing the existence of dynamically distinct synchronized states reflecting different degrees of communication. Specifically, we discover a novel large-amplitude super-synchronized state separated from the conventionally reported synchronized and quiescent states through an unusual sharp jump transition when sampling the strong coupling limit. Our results assume significance for further elucidating globally coherent phenomena, such as in neuropathologies, bacterial cell colonies, social systems and semiconductor lasers.

  9. Energy dependence phase shift analysis of PI4He elastic scattering and the possibility of the (PI4He) excited states existence

    International Nuclear Information System (INIS)

    Nichitiu, F.; Falomkin, I.V.; Sapozhnikov, M.G.; Shcherbakov, Yu.A.; Piragino, G.

    1981-06-01

    In the 24 MeV-260 MeV kinetic energy interval, the energy dependent phase shift analysis of π 4 He elastic scattering is done. The eneray dependence is given by the rational fraction approximants of the partial S matrix. The search for the stable S matrix zero-pole pairs in the k and √s complex plane give some proofs for the existence of the (π 4 He) excited states in the S, P and probably D partial waves. (authors)

  10. Data gaps in toxicity testing of chemicals allowed in food in the United States.

    Science.gov (United States)

    Neltner, Thomas G; Alger, Heather M; Leonard, Jack E; Maffini, Maricel V

    2013-12-01

    In the United States, chemical additives cannot be used in food without an affirmative determination that their use is safe by FDA or additive manufacturer. Feeding toxicology studies designed to estimate the amount of a chemical additive that can be eaten safely provide the most relevant information. We analyze how many chemical additives allowed in human food have feeding toxicology studies in three toxicological information sources including the U.S. Food and Drug Administration's (FDA) database. Less than 38% of FDA-regulated additives have a published feeding study. For chemicals directly added to food, 21.6% have feeding studies necessary to estimate a safe level of exposure and 6.7% have reproductive or developmental toxicity data in FDA's database. A program is needed to fill these significant knowledge gaps by using in vitro and in silico methods complemented with targeted in vivo studies to ensure public health is protected. Copyright © 2013 The Authors. Published by Elsevier Inc. All rights reserved.

  11. Novel chemically cross-linked solid state electrolyte for dye-sensitized solar cells

    International Nuclear Information System (INIS)

    Yin Xiong; Tan Weiwei; Xiang Wangchun; Lin Yuan; Zhang Jingbo; Xiao Xurui; Li Xueping; Zhou Xiaowen; Fang Shibi

    2010-01-01

    Poly(vinylpyridine-co-ethylene glycol methyl ether methacrylate) (P(VP-co-MEOMA)) and α,ω-diiodo poly(ethylene oxide-co-propylene oxide) (I[(EO) 0.8 -co-(PO) 0.2 ] y I) were synthesized and used as chemically cross-linked precursors of the electrolyte for dye-sensitized solar cells. Meanwhile, α-iodo poly(ethylene oxide-co-propylene oxide) methyl ether (CH 3 O[(EO) 0.8 -co-(PO) 0.2 ] x I) was synthesized and added into the electrolyte as an internal plasticizer. Novel polymer electrolyte resulting from chemically cross-linked precursors was obtained by the quaterisation at 90 o C for 30 min. The characteristics for this kind of electrolyte were investigated by means of ionic conductivity, thermogravimetric and photocurrent-voltage. The ambient ionic conductivity was significantly enhanced to 2.3 x 10 -4 S cm -1 after introducing plasticizer, modified-ionic liquid. The weight loss of the solid state electrolyte at 200 o C was 1.8%, and its decomposition temperature was 287 o C. Solid state dye-sensitized solar cell based on chemically cross-linked electrolyte presented an overall conversion efficiency of 2.35% under AM1.5 irradiation (100 mW cm -2 ). The as-fabricated device maintained 88% of its initial performance at room temperature even without sealing for 30 days, showing a good stability.

  12. Chemical equilibrium model for high- Tc and heavy fermion superconductors: the density of states

    International Nuclear Information System (INIS)

    Kallio, A.; Hissa, J.; Hayrynen, T.; Braysy, V.; Sakkinen, T.

    1998-01-01

    The chemical equilibrium model is based on the idea of correlated electron pairs, which in singlet state can exist as quasimolecules in the superfluid and normal states of a superconductor. These preformed pairs are bosons which can undergo a Bose-Einstein condensation in analogy with the superfluidity of 4 He+ 3 He-mixture. The bosons (B ++ ) and the fermions (h + ) are in chemical equilibrium with respect to the reaction B ++ ↔ 2h + , at any temperature. The mean densities of bosons and fermions (quasiholes) n B (T) and n h (T) are determined from the thermodynamics of the equilibrium reaction in terms of a single function f(T). By thermodynamics the function f(T) is connected to equilibrium constant φ(T) by 1-f(T) = [1 + φ(T)] -1/2 . Using a simple power law, known to be valid near T = 0, for the chemical constant φ(T) α/t 2γ , t = T/T*, the mean density of quasiholes is given in closed form. This enables one to calculate the corresponding density of states (DOS) D(E) N s /N(0), by solving an integral equation. The NIS- tunneling conductivity near T = 0, given by D(E) compares well with the most recent experiments: D(E) ∼ E γ , for small E and a finite maximum of right size, corresponding to 'finite quasiparticle lifetime'. The corresponding SIS-tunneling conductivity is obtained from a simple convolution and is also in agreement with recent break junction experiments of Hancotte et al. The position of the maximum can be used to obtain the scaling temperature T*, which comes close to the one measured by Hall coefficient in the normal state. A simple explanation for the spingap effect in NMR is given. (Copyright (1998) World Scientific Publishing Co. Pte. Ltd)

  13. All-solid-state, synchronously pumped, ultrafast BaWO4 Raman laser with long and short Raman shifts generating at 1180, 1225, and 1323 nm

    Science.gov (United States)

    Frank, Milan; Jelínek, Michal; Kubeček, Václav; Ivleva, Lyudmila I.; Zverev, Petr G.; Smetanin, Sergei

    2017-12-01

    A lot of attention is currently focused on synchronously pumped, extra-cavity crystalline Raman lasers generating one or two Stokes Raman components in KGW or diamond Raman-active crystals, and also generating additional components of stimulated polariton scattering in lithium niobate crystal having both cubic and quadratic nonlinearities. In this contribution we report on generation of more than two Stokes components of stimulated Raman scattering with different Raman shifts in the all-solid-state, synchronously pumped, extra-cavity Raman laser based on the Raman-active a-cut BaWO4 crystal excited by a mode-locked, 220 nJ, 36 ps, 150 MHz diode sidepumped Nd:GdVO4 laser generating at the wavelength of 1063 nm. Excitation by the pumping radiation polarized along the BaWO4 crystal optical axis resulted in the Raman generation with not only usual (925cm - 1), but also additional (332cm - 1) Raman shift. Besides the 1180-nm first and 1323 nm second Stokes components with the Raman shift of 925cm - 1 from the 1063nm fundamental laser wavelength, we have achieved generation of the additional 1227 nm Raman component with different Raman shift of 332cm - 1 from the 1180nm component. At the 1227 nm component the strongest 12-times pulse shortening from 36ps down to 3ps was obtained due to shorter dephasing time of this additional Raman line (3ps for the 332-cm - 1 line instead of 6.5ps for the 925cm - 1 line). It has to be also noted that the 1225 nm generation is intracavity pumped by the 1179 nm first Stokes component resulting in the strongest pulse shortening close to the 332cm -1 line dephasing time (3ps). Slope efficiency of three Stokes components generation exceeded 20%.

  14. Chimera and phase-cluster states in populations of coupled chemical oscillators

    Science.gov (United States)

    Tinsley, Mark R.; Nkomo, Simbarashe; Showalter, Kenneth

    2012-09-01

    Populations of coupled oscillators may exhibit two coexisting subpopulations, one with synchronized oscillations and the other with unsynchronized oscillations, even though all of the oscillators are coupled to each other in an equivalent manner. This phenomenon, discovered about ten years ago in theoretical studies, was then further characterized and named the chimera state after the Greek mythological creature made up of different animals. The highly counterintuitive coexistence of coherent and incoherent oscillations in populations of identical oscillators, each with an equivalent coupling structure, inspired great interest and a flurry of theoretical activity. Here we report on experimental studies of chimera states and their relation to other synchronization states in populations of coupled chemical oscillators. Our experiments with coupled Belousov-Zhabotinsky oscillators and corresponding simulations reveal chimera behaviour that differs significantly from the behaviour found in theoretical studies of phase-oscillator models.

  15. Estimation of ground and excited state dipole moment of laser dyes C504T and C521T using solvatochromic shifts of absorption and fluorescence spectra.

    Science.gov (United States)

    Basavaraja, Jana; Suresh Kumar, H M; Inamdar, S R; Wari, M N

    2016-02-05

    The absorption and fluorescence spectra of laser dyes: coumarin 504T (C504T) and coumarin 521T (C521T) have been recorded at room temperature in a series of non-polar and polar solvents. The spectra of these dyes showed bathochromic shift with increasing in solvent polarity indicating the involvement of π→π⁎ transition. Kamlet-Taft and Catalan solvent parameters were used to analyze the effect of solvents on C504T and C521T molecules. The study reveals that both general solute-solvent interactions and specific interactions are operative in these two systems. The ground state dipole moment was estimated using Guggenheim's method and also by quantum mechanical calculations. The solvatochromic data were used to determine the excited state dipole moment (μ(e)). It is observed that dipole moment value of excited state (μ(e)) is higher than that of the ground state in both the laser dyes indicating that these dyes are more polar in nature in the excited state than in the ground state. Copyright © 2015. Published by Elsevier B.V.

  16. Tough Shift

    DEFF Research Database (Denmark)

    Brewer, Robert S.; Verdezoto, Nervo; Holst, Thomas

    2015-01-01

    people to change their behavior at home. Leveraging prior research on encouraging reductions in residential energy use through game play, we introduce ShareBuddy: a casual mobile game intended to encourage players not only to reduce, but also to shift their electricity use. We conducted two field studies...... real-world resource use into a game....

  17. A phosphate-dependent shift in redox state of cerium oxide nanoparticles and its effects on catalytic properties

    Energy Technology Data Exchange (ETDEWEB)

    Singh, Sanjay; Dosani, Talib; Karakoti, Ajay S.; Kumar, Amit; Seal, Sudipta; Self, William

    2011-10-01

    Cerium oxide nanoparticles (CeNPs) have shown promise as catalytic antioxidants in cell culture and animal models as both superoxide dismutase and catalase mimetics. The reactivity of the cerium (Ce) atoms at the surface of its oxide particle is critical to such therapeutic properties, yet little is known about the potential for a protein or small molecule corona to form on these materials in vivo. Moreover Ce atoms in these active sites have the potential to interact with small molecule anions, peptides, or sugars when administered in culture or animal models. Several nanomaterials have been shown to alter or aggregate under these conditions, rendering them less useful for biomedical applications. In this work we have studied the change in catalytic properties of CeNPs when exposed to various biologically relevant conditions in vitro. We have found that CeNPs are resistant to broad changes in pH and also not altered by incubation in cell culture medium. However to our surprise phosphate anions significantly altered the characteristics of these nanomaterials and shifted the catalytic behavior due to the binding of phosphate anions to cerium. Given the abundance of phosphate in biological systems in an inorganic form, it is likely that the action of CeNPs as a catalyst may be strongly influenced by the local concentration of phosphate in the cells and/or tissues in which it has been introduced.

  18. Plasma flow reactor for steady state monitoring of physical and chemical processes at high temperatures.

    Science.gov (United States)

    Koroglu, Batikan; Mehl, Marco; Armstrong, Michael R; Crowhurst, Jonathan C; Weisz, David G; Zaug, Joseph M; Dai, Zurong; Radousky, Harry B; Chernov, Alex; Ramon, Erick; Stavrou, Elissaios; Knight, Kim; Fabris, Andrea L; Cappelli, Mark A; Rose, Timothy P

    2017-09-01

    We present the development of a steady state plasma flow reactor to investigate gas phase physical and chemical pr