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Sample records for chemical shifts scs

  1. Understanding NMR Chemical Shifts

    NASA Astrophysics Data System (ADS)

    Jameson, Cynthia J.

    1996-10-01

    The NMR chemical shift serves as a paradigm for molecular electronic properties. We consider the factors that determine the general magnitudes of the shifts, the state of the art in theoretical calculations, the nature of the shielding tensor, and the multidimensional shielding surface that describes the variation of the shielding with nuclear positions. We also examine the nature of the intermolecular shielding surface as a general example of a supermolecule property surface. The observed chemical shift in the zero-pressure limit is determined not only by the value of the shielding at the equilibrium geometry, but the dynamic average over the multidimensional shielding surface during rotation and vibration of the molecule. In the gas, solution, or adsorbed phase it is an average of the intermolecular shielding surface over all the configurations of the molecule with its neighbors. The temperature dependence of the chemical shift in the isolated molecule, the changes upon isotopic substitution, the changes with environment, are well characterized experimentally so that quantum mechanical descriptions of electronic structure and theories related to dynamics averaging of any electronic property can be subjected to stringent test.

  2. Chemical Vapor Deposited SiC (SCS-0) Fiber-Reinforced Strontium Aluminosilicate Glass-Ceramic Composites

    NASA Technical Reports Server (NTRS)

    Bansal, Narottam P.

    1997-01-01

    Unidirectional SrO Al2O3 2SiO2 glass-ceramic matrix composites reinforced with uncoated Chemical Vapor Deposited (CVD) SiC (SCS-0) fibers have been fabricated by hot-pressing under appropriate conditions using the glass-ceramic approach. Almost fully dense composites having a fiber volume fraction of 0.24 have been obtained. Monoclinic celsian, SrAl2Si2O8, was the only crystalline phase observed in the matrix by x-ray diffraction. No chemical reaction was observed between the fiber and the matrix after high temperature processing. In three-point flexure, the composite exhibited a first matrix cracking stress of approx. 231 +/- 20 MPa and an ultimate strength of 265 +/- 17 MPa. Examination of fracture surfaces revealed limited short length fiber pull-out. From fiber push-out, the fiber/matrix interfacial debonding and frictional strengths were evaluated to be approx. 17.5 +/- 2.7 MPa and 11.3 +/- 1.6 MPa, respectively. Some fibers were strongly bonded to the matrix and could not be pushed out. The micromechanical models were not useful in predicting values of the first matrix cracking stress as well as the ultimate strength of the composites.

  3. Chemical Shift Anisotropy Selective Inversion*

    PubMed Central

    Caporini, Marc. A.; Turner, Christopher. J.; Bielecki, Anthony; Griffin, Robert G.

    2009-01-01

    Magic Angle Spinning (MAS) is used in solid-state NMR to remove the broadening effects of the chemical shift anisotropy (CSA). In this work we investigate a technique that can reintroduce the CSA in order to selectively invert transverse magnetization. The technique involves an amplitude sweep of the radio frequency field through a multiple of the spinning frequency. The selectivity of this inversion mechanism is determined by the size of the CSA. We develop a theoretical framework to describe this process and demonstrate the CSA selective inversion with numerical simulations and experimental data. We combine this approach with cross polarization (CP) for potential applications in multi-dimensional MAS NMR. PMID:19648036

  4. A Short History of Three Chemical Shifts

    ERIC Educational Resources Information Center

    Nagaoka, Shin-ichi

    2007-01-01

    A short history of chemical shifts in nuclear magnetic resonance (NMR), electron spectroscopy for chemical analysis (ESCA) and Mossbauer spectroscopy, which are useful for chemical studies, is described. The term chemical shift is shown to have originated in the mistaken assumption that nuclei of a given element would all undergo resonance at the…

  5. The structural configurations of Ethylene Trithiocarbonate in the binary mixture (SCS2CH2CH2+CHCl3) investigated by polarized Raman: Experimental and quantum chemical results

    NASA Astrophysics Data System (ADS)

    Zhou, Ran; Wu, Fengqi; Zhou, Xiaoshun; Wang, Huigang; Zheng, Xuming

    2017-02-01

    The isotropic and anisotropic components of the Raman spectra of Cdbnd S stretching in Ethylene Trithiocarbonate (SCS2CH2CH2, ET) shows noncoincidence effect (NCE). The calculated absolute Raman cross-section (ARCS) of Cdbnd S stretching initially increases with the dilution of concentration to a maximum and then decreases. This unusual behavior indicates the existence of self-association. Thus we proposed aggregated model and the dimer structure were optimized with DFT/PCM to explain the NCE and ARCS behaviors. Vibrational spectra and depolarization-ratio were calculated for monomer and dimer individually, the dimer is in good accordance with the experimental data. The strong antiparallel Cdbnd S vibrational coupling in neighboring molecules accounts for the frequency shifts of the Cdbnd S stretching.

  6. Chemical shift prediction for denatured proteins.

    PubMed

    Prestegard, James H; Sahu, Sarata C; Nkari, Wendy K; Morris, Laura C; Live, David; Gruta, Christian

    2013-02-01

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

  7. Protein structure determination from NMR chemical shifts.

    PubMed

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

    2007-06-05

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

  8. NMR characterization of cellulose acetate: chemical shift assignments, substituent effects, and chemical shift additivity.

    PubMed

    Kono, Hiroyuki; Hashimoto, Hisaho; Shimizu, Yuuichi

    2015-03-15

    A series of cellulose acetates (CA) with degrees of substitution (DS) ranging from 2.92-0.92 dissolved in dimethylsulfoxide (DMSO)-d6 and cellulose dissolved in tetrabutylammonium fluoride (TBAF)/DMSO-d6 were investigated by two-dimensional NMR spectroscopy. The NMR spectroscopic analysis allowed the determination of the (1)H and (13)C NMR chemical shifts of the eight anhydroglucose units (AGUs) that contain CA: 2,3,6-tri-, 2,3-di-, 2,6-di-, 3,6-di-, 2-mono-, 3-mono-, 6-mono-, and unacetylated AGUs. A comparative analysis of the chemical shift data revealed the substituent effect of acetyl groups at the 2-, 3-, and 6-positions on the (1)H and (13)C nuclei in the same AGU. In addition, chemical shift additivity could be applied to the (1)H and (13)C chemical shifts of CA because the chemical shifts of the diacetylated and triacetylated AGUs could be almost completely explained by the acetyl substituent effects at the 2-, 3-, and 6-positions.

  9. Experimental and theoretical study of substituent effect on 13C NMR chemical shifts of 5-arylidene-2,4-thiazolidinediones

    NASA Astrophysics Data System (ADS)

    Rančić, Milica P.; Trišović, Nemanja P.; Milčić, Miloš K.; Ajaj, Ismail A.; Marinković, Aleksandar D.

    2013-10-01

    The electronic structure of 5-arylidene-2,4-thiazolidinediones has been studied by using experimental and theoretical methodology. The theoretical calculations of the investigated 5-arylidene-2,4-thiazolidinediones have been performed by the use of quantum chemical methods. The calculated 13C NMR chemical shifts and NBO atomic charges provide an insight into the influence of such a structure on the transmission of electronic substituent effects. Linear free energy relationships (LFERs) have been further applied to their 13C NMR chemical shifts. The correlation analyses for the substituent-induced chemical shifts (SCS) have been performed with σ using SSP (single substituent parameter), field (σF) and resonance (σR) parameters using DSP (dual substituent parameter), as well as the Yukawa-Tsuno model. The presented correlations account satisfactorily for the polar and resonance substituent effects operative at Cβ, and C7 carbons, while reverse substituent effect was found for Cα. The comparison of correlation results for the investigated molecules with those obtained for seven structurally related styrene series has indicated that specific cross-interaction of phenyl substituent and groups attached at Cβ carbon causes increased sensitivity of SCS Cβ to the resonance effect with increasing of electron-accepting capabilities of the group present at Cβ.

  10. Mapping of protein structural ensembles by chemical shifts.

    PubMed

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

    2010-10-01

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

  11. Using chemical shift perturbation to characterise ligand binding.

    PubMed

    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

  12. Empirical NMR Chemical Shift Correlations for Methyl and Methylene Protons.

    ERIC Educational Resources Information Center

    Friedrich, Edwin C.; Runkle, Katherine Gates

    1984-01-01

    Presents an internally consistent set of 63 substituent constants developed for use with the Schoolery Relationship to predict the chemical shifts of methylene protons of acyclic compounds. Chemical shift data used in deriving the constants were taken mainly from primary sources of HNMR (nuclear magnetic resonance) spectra. (JN)

  13. Relative Configuration of Natural Products Using NMR Chemical Shifts

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  14. An isotropic chemical shift-chemical shift anisotropic correlation experiment using discrete magic angle turning.

    PubMed

    Hu, Jian Zhi; Sears, Jesse A; Kwak, Ja Hun; Hoyt, David W; Wang, Yong; Peden, Charles H F

    2009-05-01

    An isotropic-anisotropic shift 2D correlation spectroscopy is introduced that combines the advantages of both magic angle turning (MAT) and magic angle hopping (MAH) technologies. In this new approach, denoted DMAT for "discrete magic angle turning", the sample rotates clockwise followed by an anticlockwise rotation of exactly the same amount with each rotation less or equal than 360 degrees but greater than 240 degrees , with the rotation speed being constant only for times related to the evolution dimension. This back and forth rotation is repeated and synchronized with a special radio frequency (RF) pulse sequence to produce an isotropic-anisotropic shift 2D correlation spectrum. For any spin-interaction of rank-2 such as chemical shift anisotropy, isotropic magnetic susceptibility interaction, and residual homo-nuclear dipolar interaction in biological fluid samples, the projection along the isotropic dimension is a high resolution spectrum. Since a less than 360 degrees sample rotation is involved, the design potentially allows for in situ control over physical parameters such as pressure, flow conditions, feed compositions, and temperature so that true in situ NMR investigations can be carried out.

  15. Is the Lamb shift chemically significant?

    NASA Technical Reports Server (NTRS)

    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.

  16. Bayesian inference of protein structure from chemical shift data.

    PubMed

    Bratholm, Lars A; Christensen, Anders S; Hamelryck, Thomas; Jensen, Jan H

    2015-01-01

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

  17. Counterion influence on chemical shifts in strychnine salts

    SciTech Connect

    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.

  18. 15N chemical shift referencing in solid state NMR.

    PubMed

    Bertani, Philippe; Raya, Jésus; Bechinger, Burkhard

    2014-01-01

    Solid-state NMR spectroscopy has much advanced during the last decade and provides a multitude of data that can be used for high-resolution structure determination of biomolecules, polymers, inorganic compounds or macromolecules. In some cases the chemical shift referencing has become a limiting factor to the precision of the structure calculations and we have therefore evaluated a number of methods used in proton-decoupled (15)N solid-state NMR spectroscopy. For (13)C solid-state NMR spectroscopy adamantane is generally accepted as an external standard, but to calibrate the (15)N chemical shift scale several standards are in use. As a consequence the published chemical shift values exhibit considerable differences (up to 22 ppm). In this paper we report the (15)N chemical shift of several commonly used references compounds in order to allow for comparison and recalibration of published data and future work. We show that (15)NH4Cl in its powdered form (at 39.3 ppm with respect to liquid NH3) is a suitable external reference as it produces narrow lines when compared to other reference compounds and at the same time allows for the set-up of cross-polarization NMR experiments. The compound is suitable to calibrate magic angle spinning and static NMR experiments. Finally the temperature variation of (15)NH4Cl chemical shift is reported.

  19. NMR Chemical Shifts in Hard Carbon Nitride Compounds

    SciTech Connect

    Yoon, Y.; Yoon, Y.; Pfrommer, B.G.; Pfrommer, B.G.; Louie, S.G.; Louie, S.G.; Mauri, F.

    1998-04-01

    We show that NMR chemical shift spectroscopy could help to identify the crystalline phases of hard carbon nitride compounds. To this purpose we compute the NMR chemical shifts of defect zinc-blende, cubic, {alpha}{minus} , {beta}{minus} , and graphitic C{sub 3}N{sub 4} with a newly developed {ital ab initio} method. The C shifts can be used to identify the CN bonds and to characterize C hybridization. The N shifts distinguish the {alpha}-C{sub 3}N{sub 4} from the {beta}-C{sub 3}N{sub 4} phases, and indicate the presence of the graphitic phase. {copyright} {ital 1998} {ital The American Physical Society}

  20. Protein Structure Refinement Using 13Cα Chemical Shift Tensors

    PubMed Central

    Wylie, Benjamin J.; Schwieters, Charles D.; Oldfield, Eric; Rienstra, Chad M.

    2009-01-01

    We have obtained the 13Cα chemical shift tensors for each amino acid in the protein GB1. We then developed a CST force field and incorporated this into the Xplor-NIH structure determination program. GB1 structures obtained by using CST restraints had improved precision over those obtained in the absence of CST restraints, and were also more accurate. When combined with isotropic chemical shifts, distance and vector angle restraints, the root-mean squared error with respect to existing x-ray structures was better than ~1.0 Å. These results are of broad general interest since they show that chemical shift tensors can be used in protein structure refinement, improving both structural accuracy and precision, opening up the way to accurate de novo structure determination. PMID:19123862

  1. Molecular dynamics averaging of Xe chemical shifts in liquids

    NASA Astrophysics Data System (ADS)

    Jameson, Cynthia J.; Sears, Devin N.; Murad, Sohail

    2004-11-01

    The Xe nuclear magnetic resonance chemical shift differences that afford the discrimination between various biological environments are of current interest for biosensor applications and medical diagnostic purposes. In many such environments the Xe signal appears close to that in water. We calculate average Xe chemical shifts (relative to the free Xe atom) in solution in eleven liquids: water, isobutane, perfluoro-isobutane, n-butane, n-pentane, neopentane, perfluoroneopentane, n-hexane, n-octane, n-perfluorooctane, and perfluorooctyl bromide. The latter is a liquid used for intravenous Xe delivery. We calculate quantum mechanically the Xe shielding response in Xe-molecule van der Waals complexes, from which calculations we develop Xe (atomic site) interpolating functions that reproduce the ab initio Xe shielding response in the complex. By assuming additivity, these Xe-site shielding functions can be used to calculate the shielding for any configuration of such molecules around Xe. The averaging over configurations is done via molecular dynamics (MD). The simulations were carried out using a MD technique that one of us had developed previously for the simulation of Henry's constants of gases dissolved in liquids. It is based on separating a gaseous compartment in the MD system from the solvent using a semipermeable membrane that is permeable only to the gas molecules. We reproduce the experimental trends in the Xe chemical shifts in n-alkanes with increasing number of carbons and the large chemical shift difference between Xe in water and in perfluorooctyl bromide. We also reproduce the trend for a given solvent of decreasing Xe chemical shift with increasing temperature. We predict chemical shift differences between Xe in alkanes vs their perfluoro counterparts.

  2. Chemical shift and coupling constant analysis of dibenzyloxy disulfides

    NASA Astrophysics Data System (ADS)

    Stoutenburg, Eric G.; Gryn'ova, Ganna; Coote, Michelle L.; Priefer, Ronny

    2015-02-01

    Dialkoxy disulfides have found applications in the realm of organic synthesis as an S2 or alkoxy donor, under thermal and photolytic decompositions conditions, respectively. Spectrally, dibenzyloxy disulfides possess an ABq in the 1H NMR, which can shift by over 1.1 ppm depending on the substituents present on the aromatic ring, as well as the solvent employed. The effect of the said substituents and solvent were analyzed and compared to the center of the ABq, geminal coupling, and the differences in chemical shifts of the individual doublets. Additionally, quantum-chemical calculations demonstrated the intramolecular H-bonding arrangement, found within the dibenzyloxy disulfides.

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

    NASA Astrophysics Data System (ADS)

    Chen, Fang; Yao, Guo-hua; He, Tian-jing; Chen, Dong-ming; Liu, Fan-chen

    2014-05-01

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

  4. Ligand binding analysis and screening by chemical denaturation shift.

    PubMed

    Schön, Arne; Brown, Richard K; Hutchins, Burleigh M; Freire, Ernesto

    2013-12-01

    The identification of small molecule ligands is an important first step in drug development, especially drugs that target proteins with no intrinsic activity. Toward this goal, it is important to have access to technologies that are able to measure binding affinities for a large number of potential ligands in a fast and accurate way. Because ligand binding stabilizes the protein structure in a manner dependent on concentration and binding affinity, the magnitude of the protein stabilization effect elicited by binding can be used to identify and characterize ligands. For example, the shift in protein denaturation temperature (Tm shift) has become a popular approach to identify potential ligands. However, Tm shifts cannot be readily transformed into binding affinities, and the ligand rank order obtained at denaturation temperatures (≥60°C) does not necessarily coincide with the rank order at physiological temperature. An alternative approach is the use of chemical denaturation, which can be implemented at any temperature. Chemical denaturation shifts allow accurate determination of binding affinities with a surprisingly wide dynamic range (high micromolar to sub nanomolar) and in situations where binding changes the cooperativity of the unfolding transition. In this article, we develop the basic analytical equations and provide several experimental examples.

  5. Chemical-shift MRI of exogenous lipoid pneumonia

    SciTech Connect

    Cox, J.E.; Choplin, R.H.; Chiles, C.

    1996-05-01

    Exogenous lipoid pneumonia results from the aspiration or inhalation of fatty substances, such as mineral oil found in laxatives or nasal medications containing liquid paraffin. We present standard and lipid-sensitive (chemical-shift) MR findings in a patient with histologically confirmed lipoid pneumonia. The loss of signal intensity in an area of airspace disease on opposed-phase imaging was considered specific for the presence of lipid. 14 refs., 3 figs.

  6. Heuristic overlap-exchange model of noble gas chemical shifts

    NASA Astrophysics Data System (ADS)

    Adrian, Frank J.

    2004-05-01

    It is now generally recognized that overlap-exchange interactions are the primary cause of the medium-dependent magnetic shielding (chemical shift) in all noble gases except helium, although the attractive electrostatic-dispersion (van der Waals) interactions play an indirect role in determining the penetration of the interacting species into the repulsive overlap-exchange region. The short-range nature of these overlap-exchange interactions, combined with the fact that they often can be approximated by simple functions of the overlap of the wave functions of the interacting species, suggests a useful semiempirical model of these chemical shifts. In it the total shielding is the sum of shieldings due to pairwise interactions of the noble gas atom with the individual atoms of the medium, with the "atomic" shielding terms either estimated by simple functions of the atomic overlap integrals averaged over their Boltzmann-weighted separations, or determined by fits to experimental data in systems whose complexity makes the former procedure impractical. Results for 129Xe chemical shifts in the noble gases and in a variety of molecular and condensed systems, including families of n-alkanes, straight-chain alcohols, and the endohedral compounds Xe@C60 and Xe@C70 are encouraging for the applicability of the model to systems of technical and biomedical interest.

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

    NASA Astrophysics Data System (ADS)

    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.

  8. Ultrahigh resolution protein structures using NMR chemical shift tensors

    PubMed Central

    Wylie, Benjamin J.; Sperling, Lindsay J.; Nieuwkoop, Andrew J.; Franks, W. Trent; Oldfield, Eric; Rienstra, Chad M.

    2011-01-01

    NMR chemical shift tensors (CSTs) in proteins, as well as their orientations, represent an important new restraint class for protein structure refinement and determination. Here, we present the first determination of both CST magnitudes and orientations for 13Cα and 15N (peptide backbone) groups in a protein, the β1 IgG binding domain of protein G from Streptococcus spp., GB1. Site-specific 13Cα and 15N CSTs were measured using synchronously evolved recoupling experiments in which 13C and 15N tensors were projected onto the 1H-13C and 1H-15N vectors, respectively, and onto the 15N-13C vector in the case of 13Cα. The orientations of the 13Cα CSTs to the 1H-13C and 13C-15N vectors agreed well with the results of ab initio calculations, with an rmsd of approximately 8°. In addition, the measured 15N tensors exhibited larger reduced anisotropies in α-helical versus β-sheet regions, with very limited variation (18 ± 4°) in the orientation of the z-axis of the 15N CST with respect to the 1H-15N vector. Incorporation of the 13Cα CST restraints into structure calculations, in combination with isotropic chemical shifts, transferred echo double resonance 13C-15N distances and vector angle restraints, improved the backbone rmsd to 0.16 Å (PDB ID code 2LGI) and is consistent with existing X-ray structures (0.51 Å agreement with PDB ID code 2QMT). These results demonstrate that chemical shift tensors have considerable utility in protein structure refinement, with the best structures comparable to 1.0-Å crystal structures, based upon empirical metrics such as Ramachandran geometries and χ1/χ2 distributions, providing solid-state NMR with a powerful tool for de novo structure determination. PMID:21969532

  9. Systemic bone marrow disorders: Characterization with proton chemical shift imaging

    SciTech Connect

    Gueckel, F.B.; Brix, G.; Semmler, W.; Zuna, I.; Knauf, W.; Ho, A.D.; van Kaick, G. )

    1990-07-01

    In a prospective clinical study, 26 patients (22 with malignant lymphoma and 4 with myelofibrosis) and 9 healthy volunteers were examined by conventional magnetic resonance and proton chemical shift imaging (CSI; modified Dixon method). On the basis of the CSI data, a quantitative evaluation of the relative fat and water signal fractions in regions of interest of the femur, pelvis, and spine was performed. In 16 of 17 patients with biopsy-proven bone marrow disorders, CSI revealed a significant reduction in the fat fraction of the bone marrow relative to that of normal volunteers. The visual assessment could detect only 14 of the 17 pathological cases.

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

    SciTech Connect

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

    2002-03-03

    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.

  11. Vicinal deuterium perturbations on hydrogen NMR chemical shifts in cyclohexanes.

    PubMed

    O'Leary, Daniel J; Allis, Damian G; Hudson, Bruce S; James, Shelly; Morgera, Katherine B; Baldwin, John E

    2008-10-15

    The substitution of a deuterium for a hydrogen is known to perturb the NMR chemical shift of a neighboring hydrogen atom. The magnitude of such a perturbation may depend on the specifics of bonding and stereochemical relationships within a molecule. For deuterium-labeled cyclohexanes held in a chair conformation at -80 degrees C or lower, all four possible perturbations of H by D as H-C-C-H is changed to D-C-C-H have been determined experimentally, and the variations seen, ranging from 6.9 to 10.4 ppb, have been calculated from theory and computational methods. The predominant physical origins of the NMR chemical shift perturbations in deuterium-labeled cyclohexanes have been identified and quantified. The trends defined by the Delta delta perturbation values obtained through spectroscopic experiments and by theory agree satisfactorily. They do not match the variations typically observed in vicinal J(H-H) coupling constants as a function of dihedral angles.

  12. Chemical shift-based water/fat separation in the presence of susceptibility-induced fat resonance shift

    PubMed Central

    Karampinos, Dimitrios C.; Yu, Huanzhou; Shimakawa, Ann; Link, Thomas M.; Majumdar, Sharmila

    2011-01-01

    Chemical shift-based water/fat separation methods have been emerging due to the growing clinical need for fat quantification in different body organs. Accurate quantification of proton-density fat fraction requires the assessment of many confounding factors, including the need of modeling the presence of multiple peaks in the fat spectrum. Most recent quantitative chemical shift-based water/fat separation approaches rely on a multi-peak fat spectrum with pre-calibrated peak locations and pre-calibrated or self-calibrated peak relative amplitudes. However, water/fat susceptibility differences can induce fat spectrum resonance shifts depending on the shape and orientation of the fatty inclusions. The effect is of particular interest in the skeletal muscle due to the anisotropic arrangement of extracellular lipids. In the present work, the effect of susceptibility-induced fat resonance shift on the fat fraction is characterized in a conventional complex-based chemical shift-based water/fat separation approach that does not model the susceptibility-induced fat resonance shift. A novel algorithm is then proposed in order to quantify the resonance shift in a complex-based chemical shift-based water/fat separation approach that considers the fat resonance shift in the signal model, aiming to extract information about the orientation/geometry of lipids. The technique is validated in a phantom and preliminary in vivo results are shown in the calf musculature of healthy and diabetic subjects. PMID:22247024

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

    PubMed

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

    2011-08-04

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

  14. Determination of amyloid core structure using chemical shifts.

    PubMed

    Skora, Lukasz; Zweckstetter, Markus

    2012-12-01

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

  15. A Simple and Fast Approach for Predicting 1H and 13C Chemical Shifts: Toward Chemical Shift-Guided Simulations of RNA

    PubMed Central

    2014-01-01

    We introduce a simple and fast approach for predicting RNA chemical shifts from interatomic distances that performs with an accuracy similar to existing predictors and enables the first chemical shift-restrained simulations of RNA to be carried out. Our analysis demonstrates that the applied restraints can effectively guide conformational sampling toward regions of space that are more consistent with chemical shifts than the initial coordinates used for the simulations. As such, our approach should be widely applicable in mapping the conformational landscape of RNAs via chemical shift-guided molecular dynamics simulations. The simplicity and demonstrated sensitivity to three-dimensional structure should also allow our method to be used in chemical shift-based RNA structure prediction, validation, and refinement. PMID:25255209

  16. Theoretical Modeling of 99 Tc NMR Chemical Shifts

    SciTech Connect

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

    2016-09-06

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

  17. Natural Linewidth Chemical Shift Imaging (NL-CSI)

    PubMed Central

    Bashir, Adil; Yablonskiy, Dmitriy A.

    2007-01-01

    The discrete Fourier transform (FT) is a conventional method for spatial reconstruction of chemical shifting imaging (CSI) data. Due to point spread function (PSF) effects, FT reconstruction leads to intervoxel signal leakage (Gibbs ringing). Spectral localization by imaging (SLIM) reconstruction was previously proposed to overcome this intervoxel signal contamination. However, the existence of magnetic field inhomogeneities creates an additional source of intervoxel signal leakage. It is demonstrated herein that even small field inhomogeneities substantially amplify intervoxel signal leakage in both FT and SLIM reconstruction approaches. A new CSI data acquisition strategy and reconstruction algorithm (natural linewidth (NL) CSI) is presented that eliminates effects of magnetic field inhomogeneity-induced intervoxel signal leakage and intravoxel phase dispersion on acquired data. The approach is based on acquired CSI data, high-resolution images, and magnetic field maps. The data are reconstructed based on the imaged object structure (as in the SLIM approach) and a reconstruction matrix that takes into account the inhomogeneous field distribution inside anatomically homogeneous compartments. Phantom and in vivo results show that the new method allows field inhomogeneity effects from the acquired MR signal to be removed so that the signal decay is determined only by the “natural”R2 relaxation rate constant (hence the term “natural linewidth” CSI). PMID:16721752

  18. Chemical shift assignments of the connexin37 carboxyl terminal domain.

    PubMed

    Li, Hanjun; Spagnol, Gaelle; Pontifex, Tasha K; Burt, Janis M; Sorgen, Paul L

    2017-03-01

    Connexin37 (Cx37) is a gap junction protein involved in cell-to-cell communication in the vasculature and other tissues. Cx37 suppresses proliferation of vascular cells involved in tissue development and repair in vivo, as well as tumor cells. Global deletion of Cx37 in mice leads to enhanced vasculogenesis in development, as well as collateralgenesis and angiogenesis in response to injury, which together support improved tissue remodeling and recovery following ischemic injury. Here we report the (1)H, (15)N, and (13)C resonance assignments for an important regulatory domain of Cx37, the carboxyl terminus (CT; C233-V333). The predicted secondary structure of the Cx37CT domain based on the chemical shifts is that of an intrinsically disordered protein. In the (1)H-(15)N HSQC, N-terminal residues S254-Y259 displayed a second weaker peak and residues E261-Y266 had significant line broadening. These residues are flanked by prolines (P250, P258, P260, and P268), suggesting proline cis-trans isomerization. Overall, these assignments will be useful for identifying the binding sites for intra- and inter-molecular interactions that affect Cx37 channel activity.

  19. Applications of Chemical Shift Imaging to Marine Sciences

    PubMed Central

    Lee, Haakil; Tikunov, Andrey; Stoskopf, Michael K.; Macdonald, Jeffrey M.

    2010-01-01

    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 of interest (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. PMID:20948912

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

    NASA Astrophysics Data System (ADS)

    Kumari, Amrita; Dorai, Kavita

    2013-06-01

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

  1. Tendencies of 31P chemical shifts changes in NMR spectra of nucleotide derivatives.

    PubMed Central

    Lebedev, A V; Rezvukhin, A I

    1984-01-01

    31P NMR chemical shifts of the selected mono- and oligonucleotide derivatives, including the compounds with P-N, P-C, P-S bonds and phosphite nucleotide analogues have been presented. The influence of substituents upon 31P chemical shifts has been discussed. The concrete examples of 31P chemical shifts data application in the field of nucleotide chemistry have been considered. PMID:6087290

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

    PubMed

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

    2015-11-01

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

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

    PubMed

    Harsch, Tobias; Schneider, Philipp; Kieninger, Bärbel; Donaubauer, Harald; Kalbitzer, Hans Robert

    2017-02-01

    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(δ21) and H(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.

  4. Quick Reaction Evaluation of Materials and Processes. Delivery Order 0011: Engineering Properties, Fatigue, and Crack Growth Data on SCS-6/Ti-6Al-4V Titanium Matrix Composite (16 Ply) Panels

    DTIC Science & Technology

    2009-05-01

    manufactured by Specialty Materials, Inc. The fibers were continuous monofilaments of silicon carbide ( SiC ) that was chemically deposited on a carbon...6 2.2.1 SCS-6 ( Silicon Carbide ) Fiber...SCS-6 ( Silicon Carbide ) Fiber The fibers used in manufacturing the TMC panels for testing and developing B-basis allowables were SCS-6 fibers

  5. An Improved Experiment to Illustrate the Effect of Electronegativity on Chemical Shift.

    ERIC Educational Resources Information Center

    Boggess, Robert K.

    1988-01-01

    Describes a method for using nuclear magnetic resonance to observe the effect of electronegativity on the chemical shift of protons in similar compounds. Suggests the use of 1,3-dihalopropanes as samples. Includes sample questions. (MVL)

  6. Calculation of NMR chemical shifts in organic solids: accounting for motional effects.

    PubMed

    Dumez, Jean-Nicolas; Pickard, Chris J

    2009-03-14

    NMR chemical shifts were calculated from first principles for well defined crystalline organic solids. These density functional theory calculations were carried out within the plane-wave pseudopotential framework, in which truly extended systems are implicitly considered. The influence of motional effects was assessed by averaging over vibrational modes or over snapshots taken from ab initio molecular dynamics simulations. It is observed that the zero-point correction to chemical shifts can be significant, and that thermal effects are particularly noticeable for shielding anisotropies and for a temperature-dependent chemical shift. This study provides insight into the development of highly accurate first principles calculations of chemical shifts in solids, highlighting the role of motional effects on well defined systems.

  7. A new approach to NMR chemical shift additivity parameters using simultaneous linear equation method.

    PubMed

    Shahab, Yosif A; Khalil, Rabah A

    2006-10-01

    A new approach to NMR chemical shift additivity parameters using simultaneous linear equation method has been introduced. Three general nitrogen-15 NMR chemical shift additivity parameters with physical significance for aliphatic amines in methanol and cyclohexane and their hydrochlorides in methanol have been derived. A characteristic feature of these additivity parameters is the individual equation can be applied to both open-chain and rigid systems. The factors that influence the (15)N chemical shift of these substances have been determined. A new method for evaluating conformational equilibria at nitrogen in these compounds using the derived additivity parameters has been developed. Conformational analyses of these substances have been worked out. In general, the results indicate that there are four factors affecting the (15)N chemical shift of aliphatic amines; paramagnetic term (p-character), lone pair-proton interactions, proton-proton interactions, symmetry of alkyl substituents and molecular association.

  8. AFNMR: automated fragmentation quantum mechanical calculation of NMR chemical shifts for biomolecules.

    PubMed

    Swails, Jason; Zhu, Tong; He, Xiao; Case, David A

    2015-10-01

    We evaluate the performance of the automated fragmentation quantum mechanics/molecular mechanics approach (AF-QM/MM) on the calculation of protein and nucleic acid NMR chemical shifts. The AF-QM/MM approach models solvent effects implicitly through a set of surface charges computed using the Poisson-Boltzmann equation, and it can also be combined with an explicit solvent model through the placement of water molecules in the first solvation shell around the solute; the latter substantially improves the accuracy of chemical shift prediction of protons involved in hydrogen bonding with solvent. We also compare the performance of AF-QM/MM on proteins and nucleic acids with two leading empirical chemical shift prediction programs SHIFTS and SHIFTX2. Although the empirical programs outperform AF-QM/MM in predicting chemical shifts, the differences are in some cases small, and the latter can be applied to chemical shifts on biomolecules which are outside the training set employed by the empirical programs, such as structures containing ligands, metal centers, and non-standard residues. The AF-QM/MM described here is implemented in version 5 of the SHIFTS software, and is fully automated, so that only a structure in PDB format is required as input.

  9. Density functional theory study of (13)C NMR chemical shift of chlorinated compounds.

    PubMed

    Li, Songqing; Zhou, Wenfeng; Gao, Haixiang; Zhou, Zhiqiang

    2012-02-01

    The use of the standard density functional theory (DFT) leads to an overestimation of the paramagnetic contribution and underestimation of the shielding constants, especially for chlorinated carbon nuclei. For that reason, the predictions of chlorinated compounds often yield too high chemical shift values. In this study, the WC04 functional is shown to be capable of reducing the overestimation of the chemical shift of Cl-bonded carbons in standard DFT functionals and to show a good performance in the prediction of (13)C NMR chemical shifts of chlorinated organic compounds. The capability is attributed to the minimization of the contributions that intensively increase the chemical shift in the WC04. Extensive computations and analyses were performed to search for the optimal procedure for WC04. The B3LYP and mPW1PW91 standard functionals were also used to evaluate the performance. Through detailed comparisons between the basis set effects and the solvent effects on the results, the gas-phase GIAO/WC04/6-311+G(2d,p)//B3LYP/6-31+G(d,p) was found to be specifically suitable for the prediction of (13)C NMR chemical shifts of chlorides in both chlorinated and non-chlorinated carbons. Further tests with eight molecules in the probe set sufficiently confirmed that WC04 was undoubtedly effective for accurately predicting (13) C NMR chemical shifts of chlorinated organic compounds.

  10. Errors in the Calculation of 27Al Nuclear Magnetic Resonance Chemical Shifts

    PubMed Central

    Wang, Xianlong; Wang, Chengfei; Zhao, Hui

    2012-01-01

    Computational chemistry is an important tool for signal assignment of 27Al nuclear magnetic resonance spectra in order to elucidate the species of aluminum(III) in aqueous solutions. The accuracy of the popular theoretical models for computing the 27Al chemical shifts was evaluated by comparing the calculated and experimental chemical shifts in more than one hundred aluminum(III) complexes. In order to differentiate the error due to the chemical shielding tensor calculation from that due to the inadequacy of the molecular geometry prediction, single-crystal X-ray diffraction determined structures were used to build the isolated molecule models for calculating the chemical shifts. The results were compared with those obtained using the calculated geometries at the B3LYP/6-31G(d) level. The isotropic chemical shielding constants computed at different levels have strong linear correlations even though the absolute values differ in tens of ppm. The root-mean-square difference between the experimental chemical shifts and the calculated values is approximately 5 ppm for the calculations based on the X-ray structures, but more than 10 ppm for the calculations based on the computed geometries. The result indicates that the popular theoretical models are adequate in calculating the chemical shifts while an accurate molecular geometry is more critical. PMID:23203134

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

    SciTech Connect

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

    2015-10-14

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

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

    PubMed

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

    2015-10-14

    Proton NMR spectroscopy in the solid state has recently attracted much attention owing to the significant enhancement in spectral resolution afforded by the remarkable advances in ultrafast magic angle spinning (MAS) capabilities. In particular, proton chemical shift anisotropy (CSA) has become an important tool for obtaining specific insights into inter/intra-molecular hydrogen bonding. However, even at the highest currently feasible spinning frequencies (110-120 kHz), (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

  13. Measurement of large /sup 19/F chemical shifts with the RYa-2305 spectrometer

    SciTech Connect

    Iorga, E.V.; Kucheryaev, A.G.; Lebedev, V.A.; Leont'eva, I.N.

    1985-06-01

    In order to extend the range of F-19 resonant frequencies in the RYa-2305 high-resolution NMR spectrometer, the authors have replaced the generator 9 by a tunable generator. This allows recording of the spectra together or to measure the chemical shifts exactly. The chemical shifts for MeF/sub 6/ in solutions of the hexafluorides of Mo, W, and U in organic solvents are shown, as measured at +20 degrees C. The upgrades in the RYa-2305 not only extend the range of measurable F-19 chemical shifts, but also enable one to measure large shifts with high accuracy. This principle for recording and measuring can be applied to other nuclides with the RYa2305 spectrometer.

  14. 29Si NMR Chemical Shift Calculation for Silicate Species by Gaussian Software

    NASA Astrophysics Data System (ADS)

    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).

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

    PubMed

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

    2012-01-01

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

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

    PubMed

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

    2015-10-13

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

  17. Correlation between the covalency and the thallium-205 nuclear magnetic resonance chemical shift in oxides and halides

    NASA Astrophysics Data System (ADS)

    Jouini, N.

    1986-07-01

    205Tl chemical shift measurements were carried out on thallium(I) oxides and halides. A correlation between the chemical shift and the stereochemical activity of the 6 s2 lone pair of Tl I was established; the greater this activity, the greater the absolute value of the chemical shift. For the halides, optical and chemical shift measurements gave access to the Tl- X bond ionicity via Ramsey's equation. In thallium(I) halides the absolute value of the chemical shift increases with the covalency. The work of Glaser on thallium(III) halides showed the chemical shift to decrease with increasing covalency. An explication of this difference is proposed. The hyperfine coupling constant A of the paramagnetic compound Tl 4MnI 6 was determined by the study of the chemical shift as a function of the susceptibility. This constant A is seen to be weak (-7 KG/μ B).

  18. Correlation between the covalency and the thallium-205 nuclear magnetic resonance chemical shift in oxides and halides

    SciTech Connect

    Jouini, N.

    1986-07-15

    /sup 205/Tl chemical shift measurements were carried out on thallium(I) oxides and halides. A correlation between the chemical shift and the stereochemical activity of the 6s/sup 2/ lone pair of Tl/sup I/ was established; the greater this activity, the greater the absolute value of the chemical shift. For the halides, optical and chemical shift measurements gave access to the Tl-X bond ionicity via Ramsey's equation. In thallium(I) halides the absolute value of the chemical shift increases with the covalency. The work of Glaser on thallium(III) halides showed the chemical shift to decrease with increasing covalency. An explication of this difference is proposed. The hyperfine coupling constant A of the paramagnetic compound Tl/sub 4/MnI/sub 6/ was determined by the study of the chemical shift as a function of the susceptibility. This constant A is seen to be weak (-7 KG/..mu../sub B/).

  19. Can Holo NMR Chemical Shifts be Directly Used to Resolve RNA-Ligand Poses?

    PubMed

    Frank, Aaron T

    2016-02-22

    Using a set of machine learning based predictors that are capable of predicting ligand-induced shielding effects on (1)H and (13)C nonexchangeable nuclei, it was discovered that holo NMR chemical shifts can be used to resolve RNA-ligand poses. This was accomplished by quantitatively comparing measured and predicted holo chemical shifts in conformationally diverse "decoy" pools for three test cases and then, for each, comparing the native pose to the pose in the decoy pool that exhibited the lowest error. For three test cases, the poses in the decoy pools that exhibited the best agreement between measured and predicted holo chemical shifts were within 0.28, 1.12, and 2.38 Å of the native poses. Interestingly, the predictors used in this study were trained on a database containing, only, apo RNA data. The agreement between the chemical shift-selected poses and the native NMR poses suggests that the predictors used in this study were able to "learn" general chemical shift-structure relationships from apo RNA data that could be used to account for ligand-induced shielding effects on RNA nuclei for the test cases studied.

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

    PubMed

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

    2003-01-01

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

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

    PubMed

    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.

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

    PubMed

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

    2013-01-01

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

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

    PubMed Central

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

    2013-01-01

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

  4. Modeling 15N NMR chemical shift changes in protein backbone with pressure

    NASA Astrophysics Data System (ADS)

    La Penna, Giovanni; Mori, Yoshiharu; Kitahara, Ryo; Akasaka, Kazuyuki; Okamoto, Yuko

    2016-08-01

    Nitrogen chemical shift is a useful parameter for determining the backbone three-dimensional structure of proteins. Empirical models for fast calculation of N chemical shift are improving their reliability, but there are subtle effects that cannot be easily interpreted. Among these, the effects of slight changes in hydrogen bonds, both intramolecular and with water molecules in the solvent, are particularly difficult to predict. On the other hand, these hydrogen bonds are sensitive to changes in protein environment. In this work, the change of N chemical shift with pressure for backbone segments in the protein ubiquitin is correlated with the change in the population of hydrogen bonds involving the backbone amide group. The different extent of interaction of protein backbone with the water molecules in the solvent is put in evidence.

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

    PubMed

    Hansen, Poul Erik

    2015-01-30

    The paper deals with the use of isotope effects on chemical shifts in characterizing intramolecular hydrogen bonds. Both so-called resonance-assisted (RAHB) and non-RAHB systems are treated. The importance of RAHB will be discussed. Another very important issue is the borderline between "static" and tautomeric systems. Isotope effects on chemical shifts are particularly useful in such studies. All kinds of intramolecular hydrogen bonded systems will be treated, typical hydrogen bond donors: OH, NH, SH and NH+, typical acceptors C=O, C=N, C=S C=N-. The paper will be deal with both secondary and primary isotope effects on chemical shifts. These two types of isotope effects monitor the same hydrogen bond, but from different angles.

  6. Modeling (15)N NMR chemical shift changes in protein backbone with pressure.

    PubMed

    La Penna, Giovanni; Mori, Yoshiharu; Kitahara, Ryo; Akasaka, Kazuyuki; Okamoto, Yuko

    2016-08-28

    Nitrogen chemical shift is a useful parameter for determining the backbone three-dimensional structure of proteins. Empirical models for fast calculation of N chemical shift are improving their reliability, but there are subtle effects that cannot be easily interpreted. Among these, the effects of slight changes in hydrogen bonds, both intramolecular and with water molecules in the solvent, are particularly difficult to predict. On the other hand, these hydrogen bonds are sensitive to changes in protein environment. In this work, the change of N chemical shift with pressure for backbone segments in the protein ubiquitin is correlated with the change in the population of hydrogen bonds involving the backbone amide group. The different extent of interaction of protein backbone with the water molecules in the solvent is put in evidence.

  7. (1)H chemical shift differences of Prelog-Djerassi lactone derivatives: DFT and NMR conformational studies.

    PubMed

    Aímola, Túlio J; Lima, Dimas J P; Dias, Luiz C; Tormena, Cláudio F; Ferreira, Marco A B

    2015-02-21

    This work reports an experimental and theoretical study of the conformational preferences of several Prelog-Djerassi lactone derivatives, to elucidate the (1)H NMR chemical shift differences in the lactonic core that are associated with the relative stereochemistry of these derivatives. The boat-like conformation of explains the anomalous (1)H chemical shift between H-5a and H-5b, in which the two methyl groups (C-8 and C-9) face H-5b, leading to its higher shielding effect.

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

    PubMed Central

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

    2014-01-01

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

  9. Work function shifts of catalytic metals under hydrogen gas visualized by terahertz chemical microscopy.

    PubMed

    Kiwa, Toshihiko; Hagiwara, Takafumi; Shinomiya, Mitsuhiro; Sakai, Kenji; Tsukada, Keiji

    2012-05-21

    Terahertz chemical microscopy (TCM) was applied to visualize the distribution of the work function shift of catalytic metals under hydrogen gas. TCM measures the chemical potential on the surface of a SiO(2)/Si/sapphire sensing plate without any contact with the plate. By controlling the bias voltage between an electrode on the SiO(2)/ surface and the Si layer, the relationship between the voltage and the THz amplitude from the sensing plate can be obtained. As a demonstration, two types of structures were fabricated on the sensing plate, and the work function shifts due to catalytic reactions were visualized.

  10. Grand canonical Monte Carlo simulations of the distribution and chemical shifts of xenon in the cages of zeolite NaA. I. Distribution and 129Xe chemical shifts

    NASA Astrophysics Data System (ADS)

    Jameson, Cynthia J.; Jameson, A. Keith; Baello, Bernoli I.; Lim, Hyung-Mi

    1994-04-01

    The equilibrium distribution of the Xe atoms among the alpha cages of the zeolite NaA have been measured directly by nuclear magnetic resonance (NMR) in ten samples ranging from very low xenon loading up to saturation. These distributions are simulated by a grand canonical Monte Carlo (GCMC) method which reproduces the experimental data quantitatively for all ten samples at 296 K and also at 360 K. The adsorption isotherm of the high loading samples has been determined directly from the chemical shift of the gas in equilibrium with the adsorbed xenon. The data compare favorably with the adsorption isotherms resulting from the simulations. The previously reported 129Xe chemical shifts of the individual Xen clusters and their temperature dependences in the range 188-420 K are reproduced quantitatively by the GCMC simulation which makes use of pairwise additive ab initio intermolecular shielding functions. These cluster shifts and their temperature dependence encode the distribution of configurations for a given Xen cluster in an alpha cage. Quantitative agreement with the three experimental measures of the distribution of Xe atoms in NaA (partitioning between the adsorbed phase and the gas phase, distribution of the intrazeolitic atoms among the alpha cages, and the distribution of Xe atoms within an alpha cage containing Xen) as a function of temperature has been achieved for the first time.

  11. Sequential nearest-neighbor effects on computed 13Calpha chemical shifts.

    PubMed

    Vila, Jorge A; Serrano, Pedro; Wüthrich, Kurt; Scheraga, Harold A

    2010-09-01

    To evaluate sequential nearest-neighbor effects on quantum-chemical calculations of (13)C(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 (13)C(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 (13)C(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 (13)C(alpha) chemical shifts, Delta(ca,i), for the individual residues along the sequence. This indicates that the Delta(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.

  12. SCS3 and YFT2 Link Transcription of Phospholipid Biosynthetic Genes to ER Stress and the UPR

    PubMed Central

    Moir, Robyn D.; Gross, David A.; Silver, David L.; Willis, Ian M.

    2012-01-01

    The ability to store nutrients in lipid droplets (LDs) is an ancient function that provides the primary source of metabolic energy during periods of nutrient insufficiency and between meals. The Fat storage-Inducing Transmembrane (FIT) proteins are conserved ER–resident proteins that facilitate fat storage by partitioning energy-rich triglycerides into LDs. FIT2, the ancient ortholog of the FIT gene family first identified in mammals has two homologs in Saccharomyces cerevisiae (SCS3 and YFT2) and other fungi of the Saccharomycotina lineage. Despite the coevolution of these genes for more than 170 million years and their divergence from higher eukaryotes, SCS3, YFT2, and the human FIT2 gene retain some common functions: expression of the yeast genes in a human embryonic kidney cell line promotes LD formation, and expression of human FIT2 in yeast rescues the inositol auxotrophy and chemical and genetic phenotypes of strains lacking SCS3. To better understand the function of SCS3 and YFT2, we investigated the chemical sensitivities of strains deleted for either or both genes and identified synthetic genetic interactions against the viable yeast gene-deletion collection. We show that SCS3 and YFT2 have shared and unique functions that connect major biosynthetic processes critical for cell growth. These include lipid metabolism, vesicular trafficking, transcription of phospholipid biosynthetic genes, and protein synthesis. The genetic data indicate that optimal strain fitness requires a balance between phospholipid synthesis and protein synthesis and that deletion of SCS3 and YFT2 impacts a regulatory mechanism that coordinates these processes. Part of this mechanism involves a role for SCS3 in communicating changes in the ER (e.g. due to low inositol) to Opi1-regulated transcription of phospholipid biosynthetic genes. We conclude that SCS3 and YFT2 are required for normal ER membrane biosynthesis in response to perturbations in lipid metabolism and ER stress. PMID

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

    ERIC Educational Resources Information Center

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

    2014-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Fukushima, Kenji; Hidaka, Yoshimasa

    2016-09-01

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

  15. 13C NMR chemical shifts of the triclinic and monoclinic crystal forms of valinomycin.

    PubMed

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

    2004-07-01

    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, delta(iso), for valine residue ester carbonyl carbons is predominately influenced by the intermediate component, delta(22). Additionally it was found that the smallest shift component, delta(33), for the L -lactic acid ( L -Lac) and D -alpha-hydroxyisovaleric acid ( D -Hyi) C(alpha)-O carbon was significantly displaced depending upon the nature of individual amino acid residues, and it is the delta(33) component that governs the behavior of delta(iso) in these alpha carbons.

  16. Characteristic chemical shifts of quasicrystalline Zn-Mg-Zr alloys studied by EELS and SXES

    NASA Astrophysics Data System (ADS)

    Koshiya, S.; Terauchi, M.; Ohhashi, S.; Tsai, A. P.

    2013-06-01

    Chemical shifts of the constituent atoms of primitive icosahedral quasicrystal (P-QC), face-centred icosahedral quasicrystal (F-QC) and 1/1-approximant (1/1-AP) of F-QC Zn-Mg-Zr alloys were investigated for the first time using high energy-resolution electron energy-loss spectroscopy (EELS) and soft-X-ray emission spectroscopy (SXES). Among Zn M-shell and Mg L-shell excitation EELS spectra of P-QC, F-QC and 1/1-AP alloys, only the quasicrystalline alloys showed a chemical shift towards the larger binding energy side. In Zn-L and Zr-L emission SXES spectra, the P-QC and F-QC alloys showed a chemical shift towards larger binding energy side. The magnitudes of the shifts in the Zn-L emission spectra of the quasicrystalline alloys were almost the same as for ZnO. These results strongly suggest a decrease in valence charge in quasicrystalline states. Therefore, it should be concluded that bonding in quasicrystalline states involves a characteristic increase in covalency compared with bonding in corresponding approximant and standard metal crystals.

  17. Carbon 13 chemical shift tensors in aromatic compounds. 3. Phenanthrene and triphenylene

    SciTech Connect

    Soderquist, A.; Hughes, C.D.; Horton, W.J.; Facelli, J.C.; Grant, D.M.

    1992-04-08

    Measurements of the principal values of the {sup 13}C chemical shift tensor are presented for the three carbons in triphenylene and for three different {alpha} carbons in phenanthrene. The measurements in triphenylene were made in natural abundance samples at room temperature, while the phenanthrene tensors were obtained from selectively labeled compounds (99% {sup 13}C) at low temperatures ({approx} 25 K). The principal values of the shift tensors were oriented in the molecular frame using ab initio LORG calculations. The steric compression at C{sub 4} in phenanthrene and in corresponding positions in triphenylene is manifested in sizable upfield shift in the {sigma} 33 component relative to the corresponding {sigma} 33 values at C{sub 1} and C{sub 9} in phenanthrene. The upfield shift in {sigma} 33 is mainly responsible for the well-known upfield shift of the isotropic chemical shifts of such sterically perturbed carbons. In phenanthrene c{sub 9} exhibits a unique {sigma} 22 value reflecting the greater localization of {pi}-electrons in the c{sub 9}-C{sub 10} bond. This localization of the {pi}-electrons at the C{sub 9}-C{sub 10} bond in the central ring of phenanthrene also corresponds with the most likely ordering of electrons described by the various Kekule structures in phenanthrene. The analysis of the {sup 13}C chemical shieldings of the bridgehead carbons in the triphenylene provides significant experimental information on bonding between rings in polycyclic aromatic compounds. 39 refs., 8 fig., 3 tab.

  18. Density Functional Studies of the 13C NMR Chemical Shifts in Single-Walled Carbon Nanotubes

    NASA Astrophysics Data System (ADS)

    Zurek, Eva; Autschbach, Jochen

    2007-12-01

    Density functional theory has been used to compute the electronic structure and 13C NMR chemical shifts of finite (9,0) single-walled carbon nanotubes (SWNTs) capped with fullerene hemispheres and with hydrogen atoms. The chemical shifts and HOMO-LUMO gaps were found to be dependent upon the mode of capping. The shifts of semiconducting and metallic tubes were estimated as being around 130 ppm and 141 ppm, respectively. Periodic boundary calculations on infinite zigzag (n,0) SWNTs with 7⩽n⩽17 were performed. These entities can be characterized by a family index, λ = mod(n,3), and the chemical shifts can be fitted well by a function inversely proportional to the diameter of the tube and proportional to a constant which depends on the nanotube family. Direct comparison of the molecular and periodic approaches can be made if benzene is used as the internal reference. Such a comparison indicates that capping may have a strong effect on the computed properties. Calculations on infinite zigzag (7⩽n⩽10) amine functionalized SWNTs have been performed. The functional group may react with a C-C bond which is parallel or diagonal to the tube axis and both sites have been considered. The shifts of the carbons directly attached to the group are sensitive to the bond which has been functionalized and may therefore be used to discriminate between the two products. Functionalization induces a significant line broadening of the NMR signals but it does not dramatically change the average shift of the unfunctionalized SWNT carbons.

  19. A sensitive, high resolution magic angle turning experiment for measuring chemical shift tensor principal values

    NASA Astrophysics Data System (ADS)

    Alderman, D. W.

    1998-12-01

    A sensitive, high-resolution 'FIREMAT' two-dimensional (2D) magic-angle-turning experiment is described that measures chemical shift tensor principal values in powdered solids. The spectra display spinning-sideband patterns separated by their isotropic shifts. The new method's sensitivity and high resolution in the isotropic-shift dimension result from combining the 5pi magic-angle-turning pulse sequence, an extension of the pseudo-2D sideband-suppression data rearrangement, and the TIGER protocol for processing 2D data. TPPM decoupling is used to enhance resolution. The method requires precise synchronization of the pulses and sampling to the rotor position. It is shown that the technique obtains 35 natural-abundance 13C tensors from erythromycin in 19 hours, and high quality naturalabundance 15N tensors from eight sites in potassium penicillin V in three days on a 400MHz spectrometer.

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

    PubMed

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

    2012-10-01

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

  1. Nonlinear detection of secondary isotopic chemical shifts in NMR through spin noise

    NASA Astrophysics Data System (ADS)

    Pöschko, Maria Theresia; Rodin, Victor V.; Schlagnitweit, Judith; Müller, Norbert; Desvaux, Hervé

    2017-01-01

    The detection of minor species in the presence of large amounts of similar main components remains a key challenge in analytical chemistry, for instance, to obtain isotopic fingerprints. As an alternative to the classical NMR scheme based on coherent excitation and detection, here we introduce an approach based on spin-noise detection. Chemical shifts and transverse relaxation rates are determined using only the detection circuit. Thanks to a nonlinear effect in mixtures with small chemical shift dispersion, small signals on top of a larger one can be observed with increased sensitivity as bumps on a dip; the latter being the signature of the main magnetization. Experimental observations are underpinned by an analytical theory: the coupling between the magnetization and the coil provides an amplified detection capability of both small static magnetic field inhomogeneities and small NMR signals. This is illustrated by two-bond 12C/13C isotopic measurements.

  2. Nonlinear detection of secondary isotopic chemical shifts in NMR through spin noise

    PubMed Central

    Pöschko, Maria Theresia; Rodin, Victor V.; Schlagnitweit, Judith; Müller, Norbert; Desvaux, Hervé

    2017-01-01

    The detection of minor species in the presence of large amounts of similar main components remains a key challenge in analytical chemistry, for instance, to obtain isotopic fingerprints. As an alternative to the classical NMR scheme based on coherent excitation and detection, here we introduce an approach based on spin-noise detection. Chemical shifts and transverse relaxation rates are determined using only the detection circuit. Thanks to a nonlinear effect in mixtures with small chemical shift dispersion, small signals on top of a larger one can be observed with increased sensitivity as bumps on a dip; the latter being the signature of the main magnetization. Experimental observations are underpinned by an analytical theory: the coupling between the magnetization and the coil provides an amplified detection capability of both small static magnetic field inhomogeneities and small NMR signals. This is illustrated by two-bond 12C/13C isotopic measurements. PMID:28067218

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

    PubMed

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

    2013-06-04

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

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

    NASA Astrophysics Data System (ADS)

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

    1997-06-01

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

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

    PubMed Central

    Shen, Yang; Bax, Ad

    2013-01-01

    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 (φ,ψ) torsion angles of ca 12°. TALOS-N also reports sidechain χ1 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. PMID:23728592

  6. Hydrography synthesis using LANDSAT remote sensing and the SCS models

    NASA Technical Reports Server (NTRS)

    Ragan, R. M.; Jackson, T. J.

    1976-01-01

    The land cover requirements of the Soil Conservation Service (SCS) Model used for hydrograph synthesis in urban areas were modified to be LANDSAT compatible. The Curve Numbers obtained with these alternate land cover categories compare well with those obtained in published example problems using the conventional categories. Emergency spillway hydrographs and synthetic flood frequency flows computed for a 21.1 sq. mi. test area showed excellent agreement between the conventional aerial photo-based and the Landsat-based SCS approaches.

  7. Chemical Shifts to Metabolic Pathways: Identifying Metabolic Pathways Directly from a Single 2D NMR Spectrum.

    PubMed

    Dubey, Abhinav; Rangarajan, Annapoorni; Pal, Debnath; Atreya, Hanudatta S

    2015-12-15

    Identifying cellular processes in terms of metabolic pathways is one of the avowed goals of metabolomics studies. Currently, this is done after relevant metabolites are identified to allow their mapping onto specific pathways. This task is daunting due to the complex nature of cellular processes and the difficulty in establishing the identity of individual metabolites. We propose here a new method: ChemSMP (Chemical Shifts to Metabolic Pathways), which facilitates rapid analysis by identifying the active metabolic pathways directly from chemical shifts obtained from a single two-dimensional (2D) [(13)C-(1)H] correlation NMR spectrum without the need for identification and assignment of individual metabolites. ChemSMP uses a novel indexing and scoring system comprised of a "uniqueness score" and a "coverage score". Our method is demonstrated on metabolic pathways data from the Small Molecule Pathway Database (SMPDB) and chemical shifts from the Human Metabolome Database (HMDB). Benchmarks show that ChemSMP has a positive prediction rate of >90% in the presence of decluttered data and can sustain the same at 60-70% even in the presence of noise, such as deletions of peaks and chemical shift deviations. The method tested on NMR data acquired for a mixture of 20 amino acids shows a success rate of 93% in correct recovery of pathways. When used on data obtained from the cell lysate of an unexplored oncogenic cell line, it revealed active metabolic pathways responsible for regulating energy homeostasis of cancer cells. Our unique tool is thus expected to significantly enhance analysis of NMR-based metabolomics data by reducing existing impediments.

  8. Energy landscapes of a hairpin peptide including NMR chemical shift restraints.

    PubMed

    Carr, Joanne M; Whittleston, Chris S; Wade, David C; Wales, David J

    2015-08-21

    Methods recently introduced to improve the efficiency of protein structure prediction simulations by adding a restraint potential to a molecular mechanics force field introduce additional input parameters that can affect the performance. Here we investigate the changes in the energy landscape as the relative weight of the two contributions, force field and restraint potential, is systematically altered, for restraint functions constructed from calculated nuclear magnetic resonance chemical shifts. Benchmarking calculations were performed on a 12-residue peptide, tryptophan zipper 1, which features both secondary structure (a β-hairpin) and specific packing of tryptophan sidechains. Basin-hopping global optimization was performed to assess the efficiency with which lowest-energy structures are located, and the discrete path sampling approach was employed to survey the energy landscapes between unfolded and folded structures. We find that inclusion of the chemical shift restraints improves the efficiency of structure prediction because the energy landscape becomes more funnelled and the proportion of local minima classified as native increases. However, the funnelling nature of the landscape is reduced as the relative contribution of the chemical shift restraint potential is increased past an optimal value.

  9. A predictive tool for assessing (13)C NMR chemical shifts of flavonoids.

    PubMed

    Burns, Darcy C; Ellis, David A; March, Raymond E

    2007-10-01

    Herein are presented the (1)H and (13)C NMR data for seven monohydroxyflavones (3-, 5-, 6-, 7-, 2'-, 3'-, and 4'-hydroxyflavone), five dihydroxyflavones (3,2'-, 3,3'-, 3,4'-, 3,6-, 2',3'-dihydroxyflavone), a trihydroxyflavone (apigenin; 5,7,4'-trihydroxyflavone), a tetrahydroxyflavone (luteolin; 5,7,3',4'-tetrahydroxyflavone), and three glycosylated hydroxyflavones (orientin; luteolin-6C-beta-D-glucoside, homoorientin; luteolin-8C-beta-D-glucoside, vitexin; apigenin-8C-beta-D-glucoside). When these NMR spectra are compared, it is possible to assess the impact of flavone modification and to elucidate detailed structural and electronic information for these flavonoids. A simple predictive tool for assigning flavonoid (13)C chemical shifts, which is based on the cumulative differences between the monohydroxyflavones and flavone (13)C chemical shifts, is demonstrated. The tool can be used to accurately predict (13)C flavonoid chemical shifts and it is expected to be useful for rapid assessment of flavonoid (13)C NMR spectra and for assigning substitution patterns in newly isolated flavonoids.

  10. Evaluation of cerebral 31-P chemical shift images utilizing statistical parametric mapping

    NASA Astrophysics Data System (ADS)

    Riehemann, Stefan; Gaser, Christian; Volz, Hans-Peter; Sauer, Heinrich

    1999-05-01

    We present an evaluation technique of two dimensional (2D) nuclear magnetic resonance (NMR) chemical shift images (CSI) to analyze spatial differences of metabolite distributions and/or concentrations between groups of probands. Thus, chemical shift imaging is not only used as localization technique for NMR-spectroscopy, but the information of the complete spectroscopic image is used for the evaluation process. 31P CSI of the human brain were acquired with a Philips Gyroscan ACSII whole-body scanner at 1.5 T. CSI for different phosphorus metabolites were generated, all representing the same anatomical location. For each metabolite the CSI of two groups of subjects were compared with each other using the general linear model implemented in the widely distributed SPM96 software package. With this approach, even covariates or confounding variables like age or medication can be considered. As an example for the application of this technique, variations in the distribution of the 31P metabolite phosphocreatin between unmedicated schizophrenic patients and healthy controls were visualized. To our knowledge, this is the first approach to analyze spatial variations in metabolite concentrations between groups of subjects on the basis of chemical shift images. The presented technique opens a new perspective in the evaluation of 2D NMR spectroscopic data.

  11. Investigation of 1H NMR chemical shifts of organic dye with hydrogen bonds and ring currents.

    PubMed

    Park, Sung Soo; Won, Yong Sun; Lee, Woojin; Kim, Jae Hong

    2011-04-07

    The (1)H NMR chemical shifts were theoretically computed for the organic dyes 2-(2,6-dimethyl-4H-pyran-4-ylidene)-malononitrile (1), cyano-(2,6-dimethyl-4H-pyran-4-ylidene)-acetic acid methyl ester (2), 2-(2,6-bis(4-(dimethylamino)styryl)-4H-pyran-4-ylidene)-malononitrile (3), and methyl 2-(2,6-bis(4-(dimethylamino)styryl)-4H-pyran-4-ylidene)-2-cyanoacetate (4) at the GIAO/B3LYP/6-311++G(d,p)//B3LYP/6-311++G(d,p) level of theory. Moreover, the intramolecular rotational barriers of the molecules were calculated to evaluate the internal flexibility with respect to the torsional degrees of freedom, and the nuclear-independent chemical shifts (NICS) were employed to analyze the ring currents. The difference was explained in terms of intramolecular hydrogen bonds and ring currents of the molecules. The (1)H NMR spectra were reproduced by experiments for the comparison with computationally constructed data. Our results suggest a good guideline in interpreting (1)H NMR chemical shifts using computational methods and furthermore a reliable perspective for designing molecular structures.

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

    SciTech Connect

    Martin, Bob; Autschbach, Jochen

    2015-02-07

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

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

    PubMed

    Martin, Bob; Autschbach, Jochen

    2015-02-07

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

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

    PubMed

    Kjaergaard, Magnus; Poulsen, Flemming M

    2011-06-01

    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 use random coil peptides containing glutamine instead of glycine to determine the random coil chemical shifts and the neighbor correction factors. The resulting correction factors correlate to changes in the populations of the major wells in the Ramachandran plot, which demonstrates that changes 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 the identification of small populations of transient structure in disordered proteins.

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

    PubMed

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

    2016-02-01

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

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

    PubMed

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

    2008-08-14

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

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

    PubMed

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

    2011-08-16

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

  18. Spinning sidebands from chemical shift anisotropy in 13C MAS imaging.

    PubMed

    Scheler, U; Blümich, B; Spiess, H W

    1993-07-01

    Solid state imaging by 13C MAS imaging is described. The spinning sidebands occurring at moderate spinning speeds, which disturb the images, can be suppressed by TOSS. For rigid solids the spatial resolution that can be achieved in this way is better than that of 1H images at the same spinning speed. Spatially resolved spectra with or without spinning sidebands can likewise be recorded providing information about the isotropic and the anisotropic chemical shifts which can be exploited for the study of structure, order and dynamics. The techniques are demonstrated on a phantom made with 13C-labelled glycine.

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

    NASA Technical Reports Server (NTRS)

    Grodzka, P.; Facemire, B.

    1977-01-01

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

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

    PubMed Central

    Görling, Benjamin; Bräse, Stefan; Luy, Burkhard

    2016-01-01

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

  1. Sclerosing liposarcoma of epididymis: Role of chemical shift magnetic resonance imaging

    PubMed Central

    Ramanathan, Subramaniyan; Raghu, Vineetha; Kumar, Devendra; Sempiege, Venkata R P

    2016-01-01

    Sclerosing liposarcoma of epididymis is a rare extratesticular scrotal tumor with variable prognosis. Ultrasonography is the initial imaging modality of choice for the evaluation of scrotal mass and helps to differentiate testicular and extratesticular masses, thereby narrowing down the differential diagnosis. Magnetic resonance imaging with its excellent soft tissue resolution can help in the further characterization of the nature of the tumor. In this case report, we highlight the role of chemical shift imaging in making a confident preoperative diagnosis of liposarcoma thereby guiding optimal and timely management. PMID:27857462

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

    PubMed

    Görling, Benjamin; Bräse, Stefan; Luy, Burkhard

    2016-09-02

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

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

    NASA Astrophysics Data System (ADS)

    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.

  4. Deuterium isotope effect on 13C chemical shifts of tetrabutylammonium salts of Schiff bases amino acids.

    PubMed

    Rozwadowski, Z

    2006-09-01

    Deuterium isotope effects on 13C chemical shift of tetrabutylammonium salts of Schiff bases, derivatives of amino acids (glycine, L-alanine, L-phenylalanine, L-valine, L-leucine, L-isoleucine and L-methionine) and various ortho-hydroxyaldehydes in CDCl3 have been measured. The results have shown that the tetrabutylammonium salts of the Schiff bases amino acids, being derivatives of 2-hydroxynaphthaldehyde and 3,5-dibromosalicylaldehyde, exist in the NH-form, while in the derivatives of salicylaldehyde and 5-bromosalicylaldehyde a proton transfer takes place. The interactions between COO- and NH groups stabilize the proton-transferred form through a bifurcated intramolecular hydrogen bond.

  5. Autoregressive moving average modeling for spectral parameter estimation from a multigradient echo chemical shift acquisition.

    PubMed

    Taylor, Brian A; Hwang, Ken-Pin; Hazle, John D; Stafford, R Jason

    2009-03-01

    The authors investigated the performance of the iterative Steiglitz-McBride (SM) algorithm on an autoregressive moving average (ARMA) model of signals from a fast, sparsely sampled, multiecho, chemical shift imaging (CSI) acquisition using simulation, phantom, ex vivo, and in vivo experiments with a focus on its potential usage in magnetic resonance (MR)-guided interventions. The ARMA signal model facilitated a rapid calculation of the chemical shift, apparent spin-spin relaxation time (T2*), and complex amplitudes of a multipeak system from a limited number of echoes (< or equal 16). Numerical simulations of one- and two-peak systems were used to assess the accuracy and uncertainty in the calculated spectral parameters as a function of acquisition and tissue parameters. The measured uncertainties from simulation were compared to the theoretical Cramer-Rao lower bound (CRLB) for the acquisition. Measurements made in phantoms were used to validate the T2* estimates and to validate uncertainty estimates made from the CRLB. We demonstrated application to real-time MR-guided interventions ex vivo by using the technique to monitor a percutaneous ethanol injection into a bovine liver and in vivo to monitor a laser-induced thermal therapy treatment in a canine brain. Simulation results showed that the chemical shift and amplitude uncertainties reached their respective CRLB at a signal-to-noise ratio (SNR) > or =5 for echo train lengths (ETLs) > or =4 using a fixed echo spacing of 3.3 ms. T2* estimates from the signal model possessed higher uncertainties but reached the CRLB at larger SNRs and/or ETLs. Highly accurate estimates for the chemical shift (<0.01 ppm) and amplitude (<1.0%) were obtained with > or =4 echoes and for T2*(<1.0%) with > or =7 echoes. We conclude that, over a reasonable range of SNR, the SM algorithm is a robust estimator of spectral parameters from fast CSI acquisitions that acquire < or =16 echoes for one- and two-peak systems. Preliminary ex vivo

  6. Attainable entanglement of unitary transformed thermal states in liquid-state nuclear magnetic resonance with the chemical shift

    NASA Astrophysics Data System (ADS)

    Ota, Yukihiro; Mikami, Shuji; Yoshida, Motoyuki; Ohba, Ichiro

    2007-11-01

    Yu, Brown and Chuang investigated the entanglement attainable from unitary transformed thermal states in liquid-state nuclear magnetic resonance (NMR). Their research gave insight into the role of entanglement in a liquid-state NMR quantum computer. However, they assumed that the Zeeman energy of each nuclear spin which corresponds to a qubit takes a common value for all; there is no chemical shift. In this paper, we research a model with chemical shifts and analytically derive the physical parameter region where unitary transformed thermal states are entangled, by employing the positive partial transposition (PPT) criterion with respect to any bipartition. The analysis taking account of the chemical shift reveals how the difference between quantum gates reflects on the physical parameter region where unitary transformed thermal states are entangled. In addition, we examine the distillability of unitary transformed thermal states and the effect of the chemical shifts on the boundary between the separability and the nonseparability.

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

    PubMed

    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.

  8. Noninvasive temperature mapping with MRI using chemical shift water-fat separation.

    PubMed

    Soher, Brian J; Wyatt, Cory; Reeder, Scott B; MacFall, James R

    2010-05-01

    Tissues containing both water and lipids, e.g., breast, confound standard MR proton reference frequency-shift methods for mapping temperatures due to the lack of temperature-induced frequency shift in lipid protons. Generalized Dixon chemical shift-based water-fat separation methods, such as GE's iterative decomposition of water and fat with echo asymmetry and least-squares estimation method, can result in complex water and fat images. Once separated, the phase change over time of the water signal can be used to map temperature. Phase change of the lipid signal can be used to correct for non-temperature-dependent phase changes, such as amplitude of static field drift. In this work, an image acquisition and postprocessing method, called water and fat thermal MRI, is demonstrated in phantoms containing 30:70, 50:50, and 70:30 water-to-fat by volume. Noninvasive heating was applied in an Off1-On-Off2 pattern over 50 min, using a miniannular phased radiofrequency array. Temperature changes were referenced to the first image acquisition. Four fiber optic temperature probes were placed inside the phantoms for temperature comparison. Region of interest (ROI) temperature values colocated with the probes showed excellent agreement (global mean +/- standard deviation: -0.09 +/- 0.34 degrees C) despite significant amplitude of static field drift during the experiments.

  9. Qualitative study of substituent effects on NMR (15)N and (17)O chemical shifts.

    PubMed

    Contreras, Rubén H; Llorente, Tomás; Pagola, Gabriel I; Bustamante, Manuel G; Pasqualini, Enrique E; Melo, Juan I; Tormena, Cláudio F

    2009-09-10

    A qualitative approach to analyze the electronic origin of substituent effects on the paramagnetic part of chemical shifts is described and applied to few model systems, where its potentiality can be appreciated. The formulation of this approach is based on the following grounds. The influence of different inter- or intramolecular interactions on a second-order property can be qualitatively predicted if it can be known how they affect the main virtual excitations entering into that second-order property. A set of consistent approximations are introduced in order to analyze the behavior of occupied and virtual orbitals that define some experimental trends of magnetic shielding constants. This approach is applied first to study the electronic origin of methyl-beta substituent effects on both (15)N and (17)O chemical shifts, and afterward it is applied to a couple of examples of long-range substituent effects originated in charge transfer interactions such as the conjugative effect in aromatic compounds and sigma-hyperconjugative interactions in saturated multicyclic compounds.

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

    PubMed

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

    2016-10-05

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

  11. Determination of secondary structure populations in disordered states of proteins using nuclear magnetic resonance chemical shifts.

    PubMed

    Camilloni, Carlo; De Simone, Alfonso; Vranken, Wim F; Vendruscolo, Michele

    2012-03-20

    One of the major open challenges in structural biology is to achieve effective descriptions of disordered states of proteins. This problem is difficult because these states are conformationally highly heterogeneous and cannot be represented as single structures, and therefore it is necessary to characterize their conformational properties in terms of probability distributions. Here we show that it is possible to obtain highly quantitative information about particularly important types of probability distributions, the populations of secondary structure elements (α-helix, β-strand, random coil, and polyproline II), by using the information provided by backbone chemical shifts. The application of this approach to mammalian prions indicates that for these proteins a key role in molecular recognition is played by disordered regions characterized by highly conserved polyproline II populations. We also determine the secondary structure populations of a range of other disordered proteins that are medically relevant, including p53, α-synuclein, and the Aβ peptide, as well as an oligomeric form of αB-crystallin. Because chemical shifts are the nuclear magnetic resonance parameters that can be measured under the widest variety of conditions, our approach can be used to obtain detailed information about secondary structure populations for a vast range of different protein states.

  12. Contribution of high-energy conformations to NMR chemical shifts, a DFT-BOMD study.

    PubMed

    Goursot, A; Mineva, T; Vásquez-Pérez, J M; Calaminici, P; Köster, A M; Salahub, D R

    2013-01-21

    This paper highlights the relevance of including the high-energy conformational states sampled by Born-Oppenheimer molecular dynamics (BOMD) in the calculation of time-averaged NMR chemical shifts. Our case study is the very flexible glycerol molecule that undergoes interconversion between conformers in a nonrandom way. Along the sequence of structures from one backbone conformer to another, transition states have been identified. The three (13)C NMR chemical shifts of the molecule were estimated by averaging their calculated values over a large set of BOMD snapshots. The simulation time needed to obtain a good agreement with the two signals present in the experimental spectrum is shown to be dependent on the atomic orbital basis set used for the dynamics, with a necessary longer trajectory for the most extended basis sets. The large structural deformations with respect to the optimized conformer geometries that occur along the dynamics are related to a kinetically driven conformer distribution. Calculated conformer type populations are in good agreement with experimental gas phase microwave results.

  13. The Effects of Dissolved Oxygen upon Amide Proton Relaxation and Chemical Shift in a Perdeuterated Protein

    NASA Astrophysics Data System (ADS)

    Ulmer, Tobias S.; Campbell, Iain D.; Boyd, Jonathan

    2002-08-01

    The effects of dissolved molecular oxygen upon amide proton ( 1H N) longitudinal and transverse relaxation rates and chemical shifts were studied for a small protein domain, the second type 2 module of fibronectin ( 2F2)—isotopically enriched to 99% 2H, 98% 15N. Longitudinal relaxation rate enhancements, R O 2( 1H N), of individual backbone 1H N nuclei varied up to 14 fold between a degassed and oxygenated (1 bar) solution, indicating that the oxygen distribution within the protein is inhomogeneous. On average, smaller relaxation rate enhancements were observed for 1H N nuclei associated with the core of the protein compared to 1H N nuclei closer to the surface, suggesting restricted oxygen accessibility to some regions. In agreement with an O 2- 1H N hyperfine interaction in the extreme narrowing limit, the 1H N transverse relaxation rates showed no significant change, up to an oxygen pressure of 9.5 bar (the maximum pressure used in this study). For most 1H N resonances, small Δδ O 2( 1H N) hyperfine chemical shifts could be detected between oxygen pressures of 1 bar and 9.5 bar.

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

    PubMed

    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.

  15. Cuticular hydrocarbon divergence in the jewel wasp Nasonia: Evolutionary shifts in chemical communication channels?

    PubMed Central

    Buellesbach, Jan; Gadau, Jürgen; Beukeboom, Leo W.; Echinger, Felix; Raychoudhury, Rhitoban; Werren, John H.; Schmitt, Thomas

    2013-01-01

    The evolution and maintenance of intraspecific communication channels constitutes a key feature of chemical signaling and sexual communication. However, how divergent chemical communication channels evolve while maintaining their integrity for both sender and receiver is poorly understood. In the present study, we compare male and female cuticular hydrocarbon (CHC) profiles in the jewel wasp genus Nasonia, analyze their chemical divergence, and investigate their role as species-specific sexual signaling cues. Males and females of all four Nasonia species showed unique, non-overlapping CHC profiles unambiguously separating them. Surprisingly, male and female phylogenies based on the chemical distances between their CHC profiles differed dramatically, where only male CHC divergence parallels the molecular phylogeny of Nasonia. In particular, N. giraulti female CHC profiles were the most divergent from all other species and very different from its most closely related sibling species N. oneida. Furthermore, although our behavioural assays indicate that female CHC can generally be perceived as sexual cues attracting males in Nasonia, this function has apparently been lost in the highly divergent female N. giraulti CHC profiles. Curiously, N. giraulti males are still attracted to heterospecific, but not to conspecific female CHC profiles. We suggest that this striking discrepancy has been caused by an extensive evolutionary shift in female N. giraulti CHC profiles, which are no longer used as conspecific recognition cues. Our study constitutes the first report of an apparent abandonment of a sexual recognition cue that the receiver did not adapt to. PMID:24118588

  16. Chemical potential shift in organic field-effect transistors identified by soft X-ray operando nano-spectroscopy

    SciTech Connect

    Nagamura, Naoka Kitada, Yuta; Honma, Itaru; Tsurumi, Junto; Matsui, Hiroyuki; Takeya, Jun; Horiba, Koji; Oshima, Masaharu

    2015-06-22

    A chemical potential shift in an organic field effect transistor (OFET) during operation has been revealed by soft X-ray operando nano-spectroscopy analysis performed using a three-dimensional nanoscale electron-spectroscopy chemical analysis system. OFETs were fabricated using ultrathin (3 ML or 12 nm) single-crystalline C10-DNBDT-NW films on SiO{sub 2} (200 nm)/Si substrates with a backgate electrode and top source/drain Au electrodes, and C 1s line profiles under biasing at the backgate and drain electrodes were measured. When applying −30 V to the backgate, there is C 1s core level shift of 0.1 eV; this shift can be attributed to a chemical potential shift corresponding to band bending by the field effect, resulting in p-type doping.

  17. 125Te NMR chemical-shift trends in PbTe-GeTe and PbTe-SnTe alloys.

    PubMed

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

    2013-01-01

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

  18. Relationship between nonlinear pressure-induced chemical shift changes and thermodynamic parameters.

    PubMed

    Beck Erlach, Markus; Koehler, Joerg; Moeser, Beate; Horinek, Dominik; Kremer, Werner; Kalbitzer, Hans Robert

    2014-05-29

    NMR chemical shift analysis is a powerful method to investigate local changes in the environment of the observed nuclear spin of a polypeptide that are induced by application of high hydrostatic pressure. Usually, in the fast exchange regime, the pressure dependence of chemical shifts is analyzed by a second order Taylor expansion providing the first- and second-order pressure coefficient B1 and B2. The coefficients then are interpreted in a qualitative manner. We show here that in a two-state model, the ratio of B2/B1 is related to thermodynamic parameters, namely the ratio of the difference of compressibility factors Δβ' and partial molar volumes ΔV. The analysis is applied to the random-coil model peptides Ac-Gly-Gly-Xxx-Ala-NH2, with Xxx being one of the 20 proteinogenic amino acids. The analysis gives an average Δβ'/ΔV ratio of 1.6 GPa(-1) provided the condition |ΔG(0)| ≪ 2RT holds for the difference of the Gibbs free energies (ΔG(0)) of the two states at the temperature (T0) and the pressure (p0). The amide proton and nitrogen B2/B1 of a given amino acid Xxx are strongly correlated, indicating that their pressure-dependent chemical shift changes are due to the same thermodynamic process. As a possible physical mechanism providing a two-state model, the hydrogen bonding of water with the corresponding amide protein was simulated for isoleucine in position Xxx. The obtained free energy could satisfy the relation |ΔG(0)| ≪ 2RT. The derived relation was applied to the β-amyloid peptide Aβ and the phosphocarrier protein HPr from S. carnosus. For the transition of state 1 to state 2' of Aβ, the derived relation of B2/B1 to Δβ'/ΔV can be confirmed experimentally. The HPr protein is characterized by substantially higher negative B2/B1 values than those found in the tetrapeptides with an average value of approximately -5.1 GPa(-1) (Δβ'/ΔV of 5.1 GPa(-1) provided |ΔG(0)| ≪ 2RT holds). Qualitatively, the B2/B1 ratio can be used to predict

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

    ERIC Educational Resources Information Center

    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…

  20. Identify five kinds of simple super-secondary structures with quadratic discriminant algorithm based on the chemical shifts.

    PubMed

    Kou, Gaoshan; Feng, Yonge

    2015-09-07

    The biological function of protein is largely determined by its spatial structure. The research on the relationship between structure and function is the basis of protein structure prediction. However, the prediction of super secondary structure is an important step in the prediction of protein spatial structure. Many algorithms have been proposed for the prediction of protein super secondary structure. However, the parameters used by these methods were primarily based on amino acid sequences. In this paper, we proposed a novel model for predicting five kinds of protein super secondary structures based on the chemical shifts (CSs). Firstly, we analyzed the statistical distribution of chemical shifts of six nuclei in five kinds of protein super secondary structures by using the analysis of variance (ANOVA). Secondly, we used chemical shifts of six nuclei as features, and combined with quadratic discriminant analysis (QDA) to predict five kinds of protein super secondary structures. Finally, we achieved the averaged sensitivity, specificity and the overall accuracy of 81.8%, 95.19%, 82.91%, respectively in seven-fold cross-validation. Moreover, we have performed the prediction by combining the five different chemical shifts as features, the maximum overall accuracy up to 89.87% by using the C,Cα,Cβ,N,Hα of Hα chemical shifts, which are clearly superior to that of the quadratic discriminant analysis (QDA) algorithm by using 20 amino acid compositions (AAC) as feature in the seven-fold cross-validation. These results demonstrated that chemical shifts (CSs) are indeed an outstanding parameter for the prediction of five kinds of super secondary structures. In addition, we compared the prediction of the quadratic discriminant analysis (QDA) with that of support vector machine (SVM) by using the same six CSs as features. The result suggested that the quadratic discriminant analysis method by using chemical shifts as features is a good predictor for protein super

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

    PubMed

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

    2016-09-01

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

  2. 129Xe chemical shift in human blood and pulmonary blood oxygenation measurement in humans using hyperpolarized 129Xe NMR

    PubMed Central

    Norquay, Graham; Leung, General; Stewart, Neil J.; Wolber, Jan

    2016-01-01

    Purpose To evaluate the dependency of the 129Xe‐red blood cell (RBC) chemical shift on blood oxygenation, and to use this relation for noninvasive measurement of pulmonary blood oxygenation in vivo with hyperpolarized 129Xe NMR. Methods Hyperpolarized 129Xe was equilibrated with blood samples of varying oxygenation in vitro, and NMR was performed at 1.5 T and 3 T. Dynamic in vivo NMR during breath hold apnea was performed at 3 T on two healthy volunteers following inhalation of hyperpolarized 129Xe. Results The 129Xe chemical shift in RBCs was found to increase nonlinearly with blood oxygenation at 1.5 T and 3 T. During breath hold apnea, the 129Xe chemical shift in RBCs exhibited a periodic time modulation and showed a net decrease in chemical shift of ∼1 ppm over a 35 s breath hold, corresponding to a decrease of 7–10 % in RBC oxygenation. The 129Xe‐RBC signal amplitude showed a modulation with the same frequency as the 129Xe‐RBC chemical shift. Conclusion The feasibility of using the 129Xe‐RBC chemical shift to measure pulmonary blood oxygenation in vivo has been demonstrated. Correlation between 129Xe‐RBC signal and 129Xe‐RBC chemical shift modulations in the lung warrants further investigation, with the aim to better quantify temporal blood oxygenation changes in the cardiopulmonary vascular circuit. Magn Reson Med 77:1399–1408, 2017. © 2016 The Authors Magnetic Resonance in Medicine published by Wiley Periodicals, Inc. on behalf of International Society for Magnetic Resonance in Medicine. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. PMID:27062652

  3. Experimental study of resolution of proton chemical shifts in solids: Combined multiple pulse NMR and magic-angle spinning

    SciTech Connect

    Ryan, L.M.; Taylor, R.E.; Paff, A.J.; Gerstein, B.C.

    1980-01-01

    High-resolution nuclear magnetic resonance spectra of protons in rigid, randomly oriented solids have been measured using combined homonuclear dipolar decoupling (via multiple pulse techniques) and attenuation of chemical shift anisotropies (via magic-angle sample spinning). Under those conditions, isotropic proton chemical shifts were recorded for a variety of chemical species, with individual linewidths varying from about 55 to 110 Hz (1--2 ppm). Residual line broadening was due predominately to (i) magnetic-field instability and inhomogeneity, (ii) unresolved proton--proton spin couplings, (iii) chemical shift dispersion, (iv) residual dipolar broadening, and (v) lifetime broadening under the multiple pulse sequences used. The magnitudes of those effects and the current limits of resolution for this experiment in our spectrometer have been investigated. The compounds studied included organic solids (4, 4'-dimethylbenzophenone, 2, 6-dimethylbenzoic acid, and aspirin), polymers (polystyrene and polymethylmethacrylate), and the vitrain portion of a bituminous coal.

  4. Backbone and side chain chemical shift assignments of apolipophorin III from Galleria mellonella.

    PubMed

    Crowhurst, Karin A; Horn, James V C; Weers, Paul M M

    2016-04-01

    Apolipophorin III, a 163 residue monomeric protein from the greater wax moth Galleria mellonella (abbreviated as apoLp-IIIGM), has roles in upregulating expression of antimicrobial proteins as well as binding and deforming bacterial membranes. Due to its similarity to vertebrate apolipoproteins there is interest in performing atomic resolution analysis of apoLp-IIIGM as part of an effort to better understand its mechanism of action in innate immunity. In the first step towards structural characterization of apoLp-IIIGM, 99 % of backbone and 88 % of side chain (1)H, (13)C and (15)N chemical shifts were assigned. TALOS+ analysis of the backbone resonances has predicted that the protein is composed of five long helices, which is consistent with the reported structures of apolipophorins from other insect species. The next stage in the characterization of apoLp-III from G. mellonella will be to utilize these resonance assignments in solving the solution structure of this protein.

  5. Earth field NMR with chemical shift spectral resolution: theory and proof of concept.

    PubMed

    Katz, Itai; Shtirberg, Lazar; Shakour, Gubrail; Blank, Aharon

    2012-06-01

    A new method for obtaining an NMR signal in the Earth's magnetic field (EF) is presented. The method makes use of a simple pulse sequence with only DC fields which is much less demanding than previous approaches in terms of the pulses' rise and fall times. Furthermore, it offers the possibility of obtaining NMR data with enough spectral resolution to allow retrieving high resolution molecular chemical shift (CS) information - a capability that was not considered possible in EF NMR until now. Details of the pulse sequence, the experimental system, and our specially tailored EF NMR probe are provided. The experimental results demonstrate the capability to differentiate between three types of samples made of common fluorine compounds, based on their CS data.

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

    NASA Astrophysics Data System (ADS)

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

    2014-03-01

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

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

    PubMed Central

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

    2014-01-01

    RF pulse schemes for the simultaneous acquisition of heteronuclear multi-dimensional chemical shift correlation spectra, such as {HA(CA)NH & HA(CACO)NH}, {HA(CA)NH & H(N)CAHA} and {H(N)CAHA & H(CC)NH}, that are commonly employed in the study of moderately-sized protein molecules, have been implemented using dual sequential 1H acquisitions in the direct dimension. Such an approach is not only beneficial in terms of the reduction of experimental time as compared to data collection via two separate experiments but also facilitates the unambiguous sequential linking of the backbone amino acid residues. The potential of sequential 1H data acquisition procedure in the study of RNA is also demonstrated here. PMID:24671105

  8. Protein dynamics from chemical shift and dipolar rotational spin-echo sup 15 N NMR

    SciTech Connect

    Garbow, J.R.; Jacob, G.S.; Stejskal, E.O.; Schaefer, J. )

    1989-02-07

    The partial collapse of dipolar and chemical shift tensors for peptide NH and for the amide NH at cross-link sites in cell wall peptidoglycan, of intact lyophilized cells of Aerococcus viridans, indicates NH vector root-mean-square fluctuations of 23{degree}. This result is consistent with the local mobility calculated in typical picosecond regime computer simulations of protein dynamics in the solid state. The experimental root-mean-square angular fluctuations for both types of NH vectors increase to 37{degree} for viable wet cells at 10{degree}C. The similarity in mobilities for both general protein and cell wall peptidoglycan suggests that one additional motion in wet cells involves cooperative fluctuations of segments of cell walls, attached proteins, and associated cytoplasmic proteins.

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

    SciTech Connect

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

    2011-09-21

    Cherenkov detectors employ various methods to maximize light collection at the photomultiplier tubes (PMTs). These generally involve the use of highly reflective materials lining the interior of the detector, reflective materials around the PMTs, or wavelength-shifting sheets around the PMTs. Recently, the use of water-soluble wavelength-shifters has been explored to increase the measurable light yield of Cherenkov radiation in water. These wave-shifting chemicals are capable of absorbing light in the ultravoilet and re-emitting the light in a range detectable by PMTs. Using a 250 L water Cherenkov detector, we have characterized the increase in light yield from three compounds in water: 4-Methylumbelliferone, Carbostyril-124, and Amino-G Salt. We report the gain in PMT response at a concentration of 1 ppm as: 1.88 {+-} 0.02 for 4-Methylumbelliferone, stable to within 0.5% over 50 days, 1.37 {+-} 0.03 for Carbostyril-124, and 1.20 {+-} 0.02 for Amino-G Salt. The response of 4-Methylumbelliferone was modeled, resulting in a simulated gain within 9% of the experimental gain at 1 ppm concentration. Finally, we report an increase in neutron detection performance of a large-scale (3.5 kL) gadolinium-doped water Cherenkov detector at a 4-Methylumbelliferone concentration of 1 ppm.

  10. Exploring new 129Xe chemical shift ranges in HXeY compounds: hydrogen more relativistic than xenon.

    PubMed

    Lantto, Perttu; Standara, Stanislav; Riedel, Sebastian; Vaara, Juha; Straka, Michal

    2012-08-21

    Among rare gases, xenon features an unusually broad nuclear magnetic resonance (NMR) chemical shift range in its compounds and as a non-bonded Xe atom introduced into different environments. In this work we show that (129)Xe NMR chemical shifts in the recently prepared, matrix-isolated xenon compounds appear in new, so far unexplored (129)Xe chemical shift ranges. State-of-the-art theoretical predictions of NMR chemical shifts in compounds of general formula HXeY (Y = H, F, Cl, Br, I, -CN, -NC, -CCH, -CCCCH, -CCCN, -CCXeH, -OXeH, -OH, -SH) as well as in the recently prepared ClXeCN and ClXeNC species are reported. The bonding situation of Xe in the studied compounds is rather different from the previously characterized cases as Xe appears in the electronic state corresponding to a situation with a low formal oxidation state, between I and II in these compounds. Accordingly, the predicted (129)Xe chemical shifts occur in new NMR ranges for this nucleus: ca. 500-1000 ppm (wrt Xe gas) for HXeY species and ca. 1100-1600 ppm for ClXeCN and ClXeNC. These new ranges fall between those corresponding to the weakly-bonded Xe(0) atom in guest-host systems (δ < 300 ppm) and in the hitherto characterized Xe molecules (δ > 2000 ppm). The importance of relativistic effects is discussed. Relativistic effects only slightly modulate the (129)Xe chemical shift that is obtained already at the nonrelativistic CCSD(T) level. In contrast, spin-orbit-induced shielding effects on the (1)H chemical shifts of the H1 atom directly bonded to the Xe center largely overwhelm the nonrelativistic deshielding effects. This leads to an overall negative (1)H chemical shift in the range between -5 and -25 ppm (wrt CH(4)). Thus, the relativistic effects induced by the heavy Xe atom appear considerably more important for the chemical shift of the neighbouring, light hydrogen atom than that of the Xe nucleus itself. The predicted NMR parameters facilitate an unambiguous experimental identification of

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

    NASA Astrophysics Data System (ADS)

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

    2016-09-01

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

  12. Characteristic chemical shift of quasicrystalline alloy Al53Si27Mn20 studied by EELS and SXES

    NASA Astrophysics Data System (ADS)

    Koshiya, S.; Terauchi, M.; Tsai, A. P.

    2011-06-01

    Chemical shifts of all constituent atoms for amorphous (Am), quasicrystalline (QC) and crystalline (Cryst) alloys of Al53Si27Mn20 were investigated for the first time by high energy-resolution electron energy-loss spectroscopy (EELS) and soft-X-ray emission spectroscopy (SXES). Among Al L-shell excitation EELS spectra of Am, QC and Cryst alloys, only QC alloy showed an apparent chemical shift to the larger binding energy side by 0.4 eV. In Al-Kα and Si-Kα emission SXES spectra of these alloys, only QC alloy showed a chemical shift to the larger binding energy side by 4 eV for Al-Kα and 6 eV for Si-Kα. These chemical shift values are comparable to those of corresponding metal oxides. This indicates a smaller amount of valence charge at Al and Si atomic sites in QC alloy. On the other hand, Mn-L SXES spectra did not show any chemical shift. Therefore, the decreased charge from Al and Si sites should be distributed between atomic sites, indicating the presence of covalent bonding nature for QC ordered alloy.

  13. Chemical amplification--cavity attenuated phase shift spectroscopy measurements of atmospheric peroxy radicals.

    PubMed

    Wood, Ezra C; Charest, John R

    2014-10-21

    We describe a new instrument for the quantification of atmospheric peroxy radicals (HO2, CH3O2, C2H5O2, etc.) using the chemical amplification method. Peroxy radicals are mixed with high concentrations of NO and CO, causing a chain reaction that produces a measurable increase in NO2 which is quantified by cavity attenuated phase shift (CAPS) spectroscopy, a highly sensitive spectroscopic detection technique. The instrument utilizes two identical reaction chambers, each with a dedicated CAPS NO2 sensor. Similar to all dual-channel chemical amplifiers, one reaction chamber operates in amplification or "ROx" mode and the other in background or "Ox" mode. The peroxy radical mixing ratio is determined by the difference between the two channels' NO2 readings divided by a laboratory-determined chain length. Each reaction chamber alternates between ROx and Ox mode on an anti-synchronized schedule, eliminating the effect of CAPS baseline offsets on the calculated peroxy radical concentrations. The chain length is determined by a new calibration method: peroxyacetyl and methyl peroxy radicals are produced by the photolysis of acetone and quantified as NO2 following reaction with excess NO. We demonstrate the performance of the instrument with results from ambient sampling in Amherst and several diagnostics of its precision. The detection limit while sampling ambient air at a relative humidity (RH) of 40% is 0.6 ppt (1 min average, signal-to-noise ratio =2), with an estimated accuracy of 25% (2σ).

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

    SciTech Connect

    Hartman, Joshua D.; Beran, Gregory J. O.; Monaco, Stephen; Schatschneider, Bohdan

    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.

  15. RFID - based Staff Control System (SCS) in Kazakhstan

    NASA Astrophysics Data System (ADS)

    Saparkhojayev, N.

    2015-06-01

    RFID - based Staff Control System (SCS) will allow complete hands-free access control, monitoring the whereabouts of employee and record the attendance of the employee as well. Moreover, with a help of this system, it is possible to have a nice report at the end of the month and based on the total number of worked hours, the salary will be allocated to each personnel. The access tag can be read up to 10 centimeters from the RFID reader. The proposed system is based on UHF RFID readers, supported with antennas at gate and transaction sections, and employee identification cards containing RFID-transponders which are able to electronically store information that can be read / written even without the physical contact with the help of radio medium. This system is an innovative system, which describes the benefits of applying RFID- technology in the Education System process of Republic of Kazakhstan. This paper presents the experiments conducted to set up RFID based SCS.

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

    NASA Astrophysics Data System (ADS)

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

    2012-10-01

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

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

    PubMed

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

    2013-01-24

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

  18. Correlation of Electronic Effects in N-Alkylnicotinamides with NMR Chemical Shifts and Hydride Transfer Reactivity.

    PubMed

    Burke, James R.; Frey, Perry A.

    1996-01-26

    The (13)C and (15)N NMR chemical shifts for ring atoms of a series of N-alkylnicotinamides are shown to be correlated with their reduction potentials and reactivities toward NaBH(3)CN. The nicotinamide compounds include N-ethyl-N-benzyl-N-[p-(trifluoromethyl)benzyl]-, N-(p-cyanobenzyl)-, N-(carbomethoxymethyl)-, and N-(cyanomethyl)nicotinamides. The values of delta()13(C) for all the ring carbons increase with increasing electron-withdrawing power of the N-alkyl substituent. The value for C-4 increases the most, a range of 2.4 ppm in this series, whereas those for other atoms increase on the order of 1 ppm. The value of delta()15(N) for N-1 decreases with increasing electron-withdrawing power over a range of 20 ppm. The NMR data indicate that inductive electron withdrawal by N-alkyl substituents polarizes the pi-electron system to decrease electron density on ring carbons and increase electron density on the ring nitrogen. The values of log k (second order) for reduction of these compounds by NaBH(3)CN are proportional to the values of delta()13(C) for C-4 and inversely proportional to delta()15(N) for N-1. The reduction potentials are proportional to delta()13(C). The substituent effects are qualitatively similar to the substrate-induced electrostatic effects on the nicotinamide ring of NAD(+) at the active site of UDP-galactose 4-epimerase (Burke, J. R.; Frey, P. A. Biochemistry 1993, 32, 13220-13230). However, they differ quantitatively in that the upfield perturbation at N-1 is smaller in the enzyme and the signal for C-6 is also shifted upfield. The substrate-induced enzymatic perturbation of electron density at C-4 of NAD(+) quantitatively accounts for its increase in reactivity at the active site, but the perturbation at N-1 is less closely correlated with reactivity.

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

    PubMed Central

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

    2013-01-01

    Purpose: 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. Methods: 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. Results: 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

  20. Chemical-shift-selective filter for the in vivo detection of J-coupled metabolites at 3T.

    PubMed

    Schulte, Rolf F; Trabesinger, Andreas H; Boesiger, Peter

    2005-02-01

    A chemical-shift-selective filter (CSSF) was applied to the detection of J-coupled metabolites in the human brain. This filter is an acquisition-based technique that requires the chemical shifts (CS's) of different metabolites, but not their whole multiplet structures, to be resolved. The sequence is based on the 2D constant-time spin-echo experiment, which yields pure CS spectra in the indirect dimension. Localization is achieved through point-resolved spectroscopy (PRESS). The method enables unequivocal detection of glutamate and myo-inositol, both in vitro and in vivo in the human brain, at 3T.

  1. The influence of sulfur configuration in (1) H NMR chemical shifts of diasteromeric five-membered cyclic sulfites.

    PubMed

    Obregón-Mendoza, Marco A; Sánchez-Castellanos, Mariano; Cuevas, Gabriel; Gnecco, Dino; Cassani, Julia; Poveda-Jaramillo, Juan C; Reynolds, William F; Enríquez, Raúl G

    2017-03-01

    The effect of the stereochemistry of the sulfur atom on (1) H chemical shifts of the diasteromeric pair of cyclic sulfites of 4-[methoxy(4-nitrophenyl)methyl]-5-phenyl-1,3,2-dioxathiolan-2-oxide was investigated. The complete (1) H and (13) C NMR spectral assignment was achieved by the use of one-dimensional and two-dimensional NMR techniques in combination with X-ray data. A correlation of experimental data with theoretical calculations of chemical shift tensors using density functional theory and topological theory of atoms in molecules was made. Copyright © 2016 John Wiley & Sons, Ltd.

  2. Distinct Signaling Requirements for the Establishment of ESC Pluripotency in Late-Stage EpiSCs

    PubMed Central

    Illich, Damir Jacob; Zhang, Miao; Ursu, Andrei; Osorno, Rodrigo; Kim, Kee-Pyo; Yoon, Juyong; Araúzo-Bravo, Marcos J.; Wu, Guangming; Esch, Daniel; Sabour, Davood; Colby, Douglas; Grassme, Kathrin S.; Chen, Jiayu; Greber, Boris; Höing, Susanne; Herzog, Wiebke; Ziegler, Slava; Chambers, Ian; Gao, Shaorong; Waldmann, Herbert; Schöler, Hans R.

    2016-01-01

    Summary It has previously been reported that mouse epiblast stem cell (EpiSC) lines comprise heterogeneous cell populations that are functionally equivalent to cells of either early- or late-stage postimplantation development. So far, the establishment of the embryonic stem cell (ESC) pluripotency gene regulatory network through the widely known chemical inhibition of MEK and GSK3beta has been impractical in late-stage EpiSCs. Here, we show that chemical inhibition of casein kinase 1alpha (CK1alpha) induces the conversion of recalcitrant late-stage EpiSCs into ESC pluripotency. CK1alpha inhibition directly results in the simultaneous activation of the WNT signaling pathway, together with inhibition of the TGFbeta/SMAD2 signaling pathway, mediating the rewiring of the gene regulatory network in favor of an ESC-like state. Our findings uncover a molecular mechanism that links CK1alpha to ESC pluripotency through the direct modulation of WNT and TGFbeta signaling. PMID:27149845

  3. Accurate ab initio prediction of NMR chemical shifts of nucleic acids and nucleic acids/protein complexes

    PubMed Central

    Victora, Andrea; Möller, Heiko M.; Exner, Thomas E.

    2014-01-01

    NMR chemical shift predictions based on empirical methods are nowadays indispensable tools during resonance assignment and 3D structure calculation of proteins. However, owing to the very limited statistical data basis, such methods are still in their infancy in the field of nucleic acids, especially when non-canonical structures and nucleic acid complexes are considered. Here, we present an ab initio approach for predicting proton chemical shifts of arbitrary nucleic acid structures based on state-of-the-art fragment-based quantum chemical calculations. We tested our prediction method on a diverse set of nucleic acid structures including double-stranded DNA, hairpins, DNA/protein complexes and chemically-modified DNA. Overall, our quantum chemical calculations yield highly/very accurate predictions with mean absolute deviations of 0.3–0.6 ppm and correlation coefficients (r2) usually above 0.9. This will allow for identifying misassignments and validating 3D structures. Furthermore, our calculations reveal that chemical shifts of protons involved in hydrogen bonding are predicted significantly less accurately. This is in part caused by insufficient inclusion of solvation effects. However, it also points toward shortcomings of current force fields used for structure determination of nucleic acids. Our quantum chemical calculations could therefore provide input for force field optimization. PMID:25404135

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

    PubMed

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

    2016-01-01

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

  5. Recoupling of chemical shift anisotropy by R-symmetry sequences in magic angle spinning NMR spectroscopy

    NASA Astrophysics Data System (ADS)

    Hou, Guangjin; Byeon, In-Ja L.; Ahn, Jinwoo; Gronenborn, Angela M.; Polenova, Tatyana

    2012-10-01

    13C and 15N chemical shift (CS) interaction is a sensitive probe of structure and dynamics in a wide variety of biological and inorganic systems, and in the recent years several magic angle spinning NMR approaches have emerged for residue-specific measurements of chemical shift anisotropy (CSA) tensors in uniformly and sparsely enriched proteins. All of the currently existing methods are applicable to slow and moderate magic angle spinning (MAS) regime, i.e., MAS frequencies below 20 kHz. With the advent of fast and ultrafast MAS probes capable of spinning frequencies of 40-100 kHz, and with the superior resolution and sensitivity attained at such high frequencies, development of CSA recoupling techniques working under such conditions is necessary. In this work, we present a family of R-symmetry based pulse sequences for recoupling of 13C/15N CSA interactions that work well in both natural abundance and isotopically enriched systems. We demonstrate that efficient recoupling of either first-rank (σ1) or second-rank (σ2) spatial components of CSA interaction is attained with appropriately chosen γ-encoded RNnv symmetry sequences. The advantage of these γ-encoded RNnv-symmetry based CSA (RNCSA) recoupling schemes is that they are suitable for CSA recoupling under a wide range of MAS frequencies, including fast MAS regime. Comprehensive analysis of the recoupling properties of these RNnv symmetry sequences reveals that the σ1-CSA recoupling symmetry sequences exhibit large scaling factors; however, the partial homonuclear dipolar Hamiltonian components are symmetry allowed, which makes this family of sequences suitable for CSA measurements in systems with weak homonuclear dipolar interactions. On the other hand, the γ-encoded symmetry sequences for σ2-CSA recoupling have smaller scaling factors but they efficiently suppress the homonuclear dipole-dipole interactions. Therefore, the latter family of sequences is applicable for measurements of CSA parameters in

  6. Measuring Learned Resourcefulness in College Students: Factor Structure of the Self-Control Schedule (SCS)

    ERIC Educational Resources Information Center

    McWhirter, Benedict T.; Burrow-Sanchez, Jason J.; Townsend, Katesy C.

    2008-01-01

    Rosenbaum's Self-Control Schedule (SCS) has been used as a unidimensional measure of Learned Resourcefulness (LR) in previous research. In this study we clarified the factor structure of the SCS among college students (N = 583) by conducting a principal axis factor analysis with oblique (Oblimin) rotation on the SCS. Results revealed a…

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

    NASA Astrophysics Data System (ADS)

    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.

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

    DTIC Science & Technology

    2011-07-26

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

  9. C-13 NMR chemical shifts and visible absorption spectra of unsymmetrical fluoran dye by MO calculations

    NASA Astrophysics Data System (ADS)

    Hoshiba, T.; Ida, T.; Mizuno, M.; Otsuka, T.; Takaoka, K.; Endo, K.

    2002-01-01

    An unsymmetrical fluoran dye, 3-diethylamino-6-methyl-7-chlorofluoran (DEAMCF) is one of the leuco dyes which shows the coloring-to-decoloring reversible reaction with acidity. We calculated the 13C chemical shieldings of the DEAMCF with the frame model compounds using ab initio gauge invariant atomic orbital methods, and compared it with the experimental shifts. The calculated values of the frame compounds are in good agreement with the experimental ones in the error range of -4.9-16.7 ppm. The calculated ones for the decolored-form of the DEAMCF reflected the observed ones, although the errors range from -13.4 to 23.1 ppm. Furthermore, we analyzed the UV-Visible absorption spectra of the decolored and colored forms of DEAMCF by a semiempirical ZINDO MO method. For the colored form, the observed absorption peaks at 550 and 510 nm correspond to the excitation from π-bonding HOMO (π-electrons which conjugated in xanthene ring) and π-bonding nearest HOMO (π-electrons concentrated in benzene-ring with methyl and Cl groups of xanthene) to π ∗-antibonding LUMO (π ∗-electrons of xanthene), respectively.

  10. Solid-state NMR chemical shift assignments for AL-09 VL immunoglobulin light chain fibrils.

    PubMed

    Piehl, Dennis W; Blancas-Mejía, Luis M; Ramirez-Alvarado, Marina; Rienstra, Chad M

    2017-04-01

    Light chain (AL) amyloidosis is a systemic disease characterized by the formation of immunoglobulin light-chain fibrils in critical organs of the body. The light-chain protein AL-09 presents one severe case of cardiac AL amyloidosis, which contains seven mutations in the variable domain (VL) relative to its germline counterpart, κI O18/O8 VL. Three of these mutations are non-conservative-Y87H, N34I, and K42Q-and previous work has shown that they are responsible for significantly reducing the protein's thermodynamic stability, allowing fibril formation to occur with fast kinetics and across a wide-range of pH conditions. Currently, however, there is extremely limited structural information available which explicitly describes the residues that are involved in supporting the misfolded fibril structure. Here, we assign the site-specific (15)N and (13)C chemical shifts of the rigid residues of AL-09 VL fibrils by solid-state NMR, reporting on the regions of the protein involved in the fibril as well as the extent of secondary structure.

  11. Chemical shift anisotropy and offset effects in cross polarization solid-state NMR spectroscopy.

    PubMed

    Shekar, Srinivasan C; Lee, Dong-Kuk; Ramamoorthy, A

    2002-08-01

    The effect of an offset term in the cross-polarization (CP) Hamiltonian of a heteronuclear spin-12 pair due to off-resonant radio frequency (rf) irradiation and/or chemical shift anisotropy on one of the rf channels is investigated. Analytical solutions, simulations, and experimental results are presented. Formulating the CP spin dynamics in terms of an explicit unitary evolution operator enables the CP period to be inserted as a module in a given pulse scheme regardless of the initial density matrix present. The outcome of post-CP manipulation via pulses can be calculated on the resulting density matrix as the phases and amplitudes of all coherence modes are available. Using these tools it is shown that the offset can be used to reduce the rf power on that channel and the performance is further improved by a post-CP pulse whose flip angle matches and compensates the tilt of the effective field on the offset channel. Experimental investigations on single crystalline and polycrystalline samples of peptides confirm the oscillatory nature of CP dynamics and prove the slowing down of the dynamics under offset and/or mismatch conditions.

  12. Carbon-13 chemical shift anisotropy in DNA bases from field dependence of solution NMR relaxation rates.

    PubMed

    Ying, Jinfa; Grishaev, Alexander; Bax, Ad

    2006-03-01

    Knowledge of (13)C chemical shift anisotropy (CSA) in nucleotide bases is important for the interpretation of solution-state NMR relaxation data in terms of local dynamic properties of DNA and RNA. Accurate knowledge of the CSA becomes particularly important at high magnetic fields, prerequisite for adequate spectral resolution in larger oligonucleotides. Measurement of (13)C relaxation rates of protonated carbons in the bases of the so-called Dickerson dodecamer, d(CGCGAATTCGCG)(2), at 500 and 800 MHz (1)H frequency, together with the previously characterized structure and diffusion tensor yields CSA values for C5 in C, C6 in C and T, C8 in A and G, and C2 in A that are closest to values previously reported on the basis of solid-state FIREMAT NMR measurements, and mostly larger than values obtained by in vacuo DFT calculations. Owing to the noncollinearity of dipolar and CSA interactions, interpretation of the NMR relaxation rates is particularly sensitive to anisotropy of rotational diffusion, and use of isotropic diffusion models can result in considerable errors.

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

    PubMed

    Villegas, Myriam E; Vila, Jorge A; Scheraga, Harold A

    2007-02-01

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

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

    PubMed

    Sahakyan, Aleksandr B; Vendruscolo, Michele

    2013-02-21

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

  15. Generalized k-space decomposition with chemical shift correction for non-Cartesian water-fat imaging.

    PubMed

    Brodsky, Ethan K; Holmes, James H; Yu, Huanzhou; Reeder, Scott B

    2008-05-01

    Chemical-shift artifacts associated with non-Cartesian imaging are more complex to model and less clinically acceptable than the bulk fat shift that occurs with conventional spin-warp Cartesian imaging. A novel k-space based iterative decomposition of water and fat with echo asymmetry and least-squares estimation (IDEAL) approach is introduced that decomposes multiple species while simultaneously correcting distortion of off-resonant species. The new signal model accounts for the additional phase accumulated by off-resonant spins at each point in the k-space acquisition trajectory. This phase can then be corrected by adjusting the decomposition matrix for each k-space point during the final IDEAL processing step with little increase in reconstruction time. The technique is demonstrated with water-fat decomposition using projection reconstruction (PR)/radial, spiral, and Cartesian spin-warp imaging of phantoms and human subjects, in each case achieving substantial correction of chemical-shift artifacts. Simulations of the point-spread-function (PSF) for off-resonant spins are examined to show the nature of the chemical-shift distortion for each acquisition. Also introduced is an approach to improve the signal model for species which have multiple resonant peaks. Many chemical species, including fat, have multiple resonant peaks, although such species are often approximated as a single peak. The improved multipeak decomposition is demonstrated with water-fat imaging, showing a substantial improvement in water-fat separation.

  16. Stereospecific assignment of 1H resonances through chemical shift calculation and their use in structure determination by NMR

    NASA Astrophysics Data System (ADS)

    Harvey, Timothy S.; van Gunsteren, Wilfred F.; Ikura, Mitsuhiko

    1995-04-01

    Understanding of the factors which influence proton chemical shifts in nuclear magnetic resonance (NMR) spectra of proteins has advanced steadily as the number of proteins, for which assignments in conjunction with high resolution structures have been obtained, has increased. Progress has been made in both the calculation of chemical shifts from given coordinates, both empirically for 1H (Williamson & Asakura J. Magn. Reson. (1991) 94, 557) and using ab initio approaches for calculation of 13C (De Dios et al. Science (1993) 260, 1491). Concomitantly Wishart et al. (J. Mol. Biol. (1992) 222, 311), using statistical methods have clarified the relationship between Hα chemical shift and regular secondary structure in proteins to a high degree of accuracy. We recently demonstrated the significant amount of structural information present in the Hα chemical shift through the use of chemical shift restrained molecular dynamics simulations (Harvey & van Gunsteren Techniques in Protein Chemistry IV (1993) 615, Academic Press). Here we apply a similar methodology to the stereospecific assignment of methylene and methyl proton resonances in proteins. Stereospecific assignment of such 1H resonances dramatically increases the degree of precision of ensembles of structures derived from NMR data. However, this is often a cumbersome process, requiring detailed analysis of large amounts of data. Furthermore, experimental considerations such as poor signal-to-noise ratios, spectral overlap and spin diffusion combine to make this process somewhat unreliable. We present calculations of the chemical shifts for the known structures of bovine pancreatic trypsin inhibitor (Mw 6.5 kDa) and the α-amylase inhibitor tendamistat (Mw 8 kDa), for which stereospecific assignments and high resolution structures from both NMR and crystallographic studies are available. The methods described are also applied to the ensemble of structures obtained for protein S (Mw 19 kDa) for both structure

  17. Detection of methylation, acetylation and glycosylation of protein residues by monitoring (13)C chemical-shift changes: A quantum-chemical study.

    PubMed

    Garay, Pablo G; Martin, Osvaldo A; Scheraga, Harold A; Vila, Jorge A

    2016-01-01

    Post-translational modifications of proteins expand the diversity of the proteome by several orders of magnitude and have a profound effect on several biological processes. Their detection by experimental methods is not free of limitations such as the amount of sample needed or the use of destructive procedures to obtain the sample. Certainly, new approaches are needed and, therefore, we explore here the feasibility of using (13)C chemical shifts of different nuclei to detect methylation, acetylation and glycosylation of protein residues by monitoring the deviation of the (13)C chemical shifts from the expected (mean) experimental value of the non-modified residue. As a proof-of-concept, we used (13)C chemical shifts, computed at the DFT-level of theory, to test this hypothesis. Moreover, as a validation test of this approach, we compare our theoretical computations of the (13)Cε chemical-shift values against existing experimental data, obtained from NMR spectroscopy, for methylated and acetylated lysine residues with good agreement within ∼1 ppm. Then, further use of this approach to select the most suitable (13)C-nucleus, with which to determine other modifications commonly seen, such as methylation of arginine and glycosylation of serine, asparagine and threonine, shows encouraging results.

  18. Ab initio calculations of the intermolecular chemical shift in nuclear magnetic resonance in the gas phase and for adsorbed species

    NASA Astrophysics Data System (ADS)

    Jameson, Cynthia J.; de Dios, Angel C.

    1992-07-01

    The chemical shifts observed in nuclear magnetic resonance experiments are the differences in shielding of the nuclear spin in different electronic environments. These are known to depend on intermolecular interactions as evidenced by density-dependent chemical shifts in the gas phase, gas-to-liquid shifts, and adsorption shifts on surfaces. We present the results of the first ab initio intermolecular chemical shielding function calculated for a pair of interacting atoms for a wide range of internuclear separations. We used the localized orbital local origin (LORG) approach of Hansen and Bouman and also investigated the second-order electron correlation contributions using second-order LORG (SOLO). The 39Ar shielding in Ar2 passes through zero at some very short distance, going through a minimum, and asymptotically approaches zero at larger separations. The 21Ne shielding function in Ne2 has a similar shape. The Drude model suggests a method of scaling that portion of the shielding function that is weighted most heavily by exp[-V(R)/kT]. The scaling factors, which have been verified in the comparison of 21Ne in Ne2 against 39Ar in Ar2 ab initio results, allows us to project out from the same 39Ar in Ar2 ab initio values the appropriate 129Xe shielding functions in the Xe-Ar, Xe-Kr, and Xe-Xe interacting pairs. These functions lead to temperature-dependent second virial coefficients of chemical shielding which agree with experiments in the gas phase. Ab initio calculations of 39Ar shielding in clusters of argon are used to model the observed 129Xe chemical shifts of Xe, Xe2,...,Xe8 trapped in the cages of zeolite NaA.

  19. Ab initio studies of the nuclear magnetic resonance chemical shifts of a rare gas atom in a zeolite

    NASA Astrophysics Data System (ADS)

    Jameson, Cynthia J.; Lim, Hyung-Mi

    1995-09-01

    The intermolecular chemical shift of a rare gas atom inside a zeolite cavity is calculated by ab initio analytical derivative theory using gauge-including atomic orbitals (GIAO) at the Ar atom and the atoms of selected neutral clusters each of which is a 4-, 6-, or 8-ring fragment of the zeolite cage. The Si, Al, O atoms and the charge-balancing counterions (Na+, K+, Ca2+) of the clusters (from 24 to 52 atoms) are at coordinates taken from the refined single crystal x-ray structure of the NaA, KA, and CaA zeolites. Terminating OH groups place the H atom at an appropriate O-H distance along the bond to the next Si or Al atom in the crystal. The chemical shift of the Ar atom located at various positions relative to the cluster is calculated using Boys-Bernardi counterpoise correction at each position. The dependence of the rare gas atom chemical shift on the Al/Si ratio of the clusters is investigated. The resulting shielding values are fitted to a pairwise additive form to elicit effective individual Ar-O, Ar-Na, Ar-K, Ar-Ca intermolecular shielding functions of the form σ(39Ar, Ar...Ozeol)= a6r-6+a8r-8+a10r-10+a12r -12, where r is the distance between the Ar and the O atom. A similar form is used for the counterions. The dependence of the Ar shielding on the Al/Si ratio is established (the greater the Al content, the higher the Ar chemical shift), which is in agreement with the few experimental cases where the dependence of the 129Xe chemical shift on the Al/Si ratio of the zeolite has been observed.

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

    PubMed

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

    2015-09-03

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

  1. Nickel Complexes of a Binucleating Ligand Derived from an SCS Pincer

    SciTech Connect

    Peterson, Sonja M.; Helm, Monte L.; Appel, Aaron M.

    2015-01-01

    A binucleating ligand has been prepared that contains an SCS pincer and three oxygen donor ligands in a partial crown ether loop. To enable metalation with Ni0, a bromoarene precursor was used and resulted in the formation of a nickel-bromide complex in the SCS pincer. Reaction of the nickel complex with a lithium salt yielded a heterobimetallic complex with bromide bridging the two metal centers. The solid-state structures were determined for this heterobimetallic complex and the nickel-bromide precursor, and the two complexes were characterized electrochemically to determine the influence of coordinating the second metal. This research was supported by the US Department of Energy, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences & Biosciences. MLH was supported as part of the Center for Molecular Electrocatalysis, an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science. Pacific Northwest National Laboratory (PNNL) is a multiprogram national laboratory operated for DOE by Battelle.

  2. The Relationship between NMR Chemical Shifts of Thermally Polarized and Hyperpolarized (89) Y Complexes and Their Solution Structures.

    PubMed

    Xing, Yixun; Jindal, Ashish K; Regueiro-Figueroa, Martín; Le Fur, Mariane; Kervarec, Nelly; Zhao, Piyu; Kovacs, Zoltan; Valencia, Laura; Pérez-Lourido, Paulo; Tripier, Raphaël; Esteban-Gómez, David; Platas-Iglesias, Carlos; Sherry, A Dean

    2016-11-07

    Recently developed dynamic nuclear polarization (DNP) technology offers the potential of increasing the NMR sensitivity of even rare nuclei for biological imaging applications. Hyperpolarized (89) Y is an ideal candidate because of its narrow NMR linewidth, favorable spin quantum number (I=1/2 ), and long longitudinal relaxation times (T1 ). Strong NMR signals were detected in hyperpolarized (89) Y samples of a variety of yttrium complexes. A dataset of (89) Y NMR data composed of 23 complexes with polyaminocarboxylate ligands was obtained using hyperpolarized (89) Y measurements or (1) H,(89) Y-HMQC spectroscopy. These data were used to derive an empirical equation that describes the correlation between the (89) Y chemical shift and the chemical structure of the complexes. This empirical correlation serves as a guide for the design of (89) Y sensors. Relativistic (DKH2) DFT calculations were found to predict the experimental (89) Y chemical shifts to a rather good accuracy.

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

    USGS Publications Warehouse

    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.

  4. A theoretical interpretation of the chemical shift of 29Si NMR peaks in alkali borosilicate glasses

    NASA Astrophysics Data System (ADS)

    Nanba, Tokuro; Nishimura, Mitsunori; Miura, Yoshinari

    2004-12-01

    In 29Si-NMR, it has so far been accepted that the chemical shifts of Q n species (SiO 4 units containing n bridging oxygens) were equivalent between alkali borosilicate and boron-free alkali silicate glasses. In the sodium borosilicate glasses with low sodium content, however, a contradiction was confirmed in the estimation of alkali distribution; 11B NMR suggested that Na ions were entirely distributed to borate groups to form BO 4 units, whereas a -90 ppm component was also observed in 29Si-NMR spectra, which has been attributed to Q 3 species associated with a nonbridging oxygen (NBO). Then, cluster molecular orbital calculations were performed to interpret the -90 ppm component in the borosilicate glasses. It was found that a silicon atom which had two tetrahedral borons (B4) as its second nearest neighbors was similar in atomic charge and Si2p energy to the Q 3 species in boron-free alkali silicates. Unequal distribution of electrons in Si-O-B4 bridging bonds was also found, where much electrons were localized on the Si-O bonds. It was finally concluded that the Si-O-B4 bridges with narrow bond angle were responsible for the -90 ppm 29Si component in the borosilicate glasses. There still remained another interpretation; the Q 3 species were actually present in the glasses, and NBOs in the Q 3 species were derived from the tricluster groups, such as (O 3Si)O(BO 3) 2. In the glasses with low sodium content, however, it was concluded that the tricluster groups were not so abundant to contribute to the -90 ppm component.

  5. Computed and experimental chemical shift parameters for rigid and flexible YAF peptides in the solid state.

    PubMed

    Pawlak, Tomasz; Trzeciak-Karlikowska, Katarzyna; Czernek, Jiri; Ciesielski, Wlodzimierz; Potrzebowski, Marek J

    2012-02-16

    DFT methods were employed to compute the (13)C NMR chemical shift tensor (CST) parameters for crystals of YAF peptides (Tyr-Ala-Phe) with different stereochemistry for the Ala residue. Tyr-D-Ala-Phe 1 crystallizes in the C2 space group while Tyr-L-Ala-Phe crystallizes in either the P2(1)2(1)2 space group (2a) or the P6(5) space group (2b). PISEMA MAS measurements for samples with a natural abundance of (1)H and (13)C nuclei and (2)H QUADECHO experiments for samples with deuterium labeled aromatic rings were used to analyze the geometry and time scale of the molecular motion. At ambient temperature, the tyrosine ring of sample 1 is rigid and the phenylalanine ring undergoes a π-jump, both rings in sample 2a are static, and both rings in sample 2b undergo a fast regime exchange. The theoretical values of the CST were obtained for isolated molecules (IM) and clusters employing the ONIOM approach. The experimental (13)C δ(ii) parameters for all of the samples were measured via a 2D PASS sequence. Significant scatter of the computed versus the experimental (13)C CST parameters was observed for 1 and 2b, while the observed correlation was very good for 2a. In this report, we show that the quality of the (13)C σ(ii)/(13)C δ(ii) correlations, when properly interpreted, can be a source of important information about local molecular motions.

  6. Determination of 15N chemical shift anisotropy from a membrane-bound protein by NMR spectroscopy.

    PubMed

    Pandey, Manoj Kumar; Vivekanandan, Subramanian; Ahuja, Shivani; Pichumani, Kumar; Im, Sang-Choul; Waskell, Lucy; Ramamoorthy, Ayyalusamy

    2012-06-21

    Chemical shift anisotropy (CSA) tensors are essential in the structural and dynamic studies of proteins using NMR spectroscopy. Results from relaxation studies in biomolecular solution and solid-state NMR experiments on aligned samples are routinely interpreted using well-characterized CSA tensors determined from model compounds. Since CSA tensors, particularly the (15)N CSA, highly depend on a number of parameters including secondary structure, electrostatic interaction, and the amino acid sequence, there is a need for accurately determined CSA tensors from proteins. In this study, we report the backbone amide-(15)N CSA tensors for a 16.7-kDa membrane-bound and paramagnetic-heme containing protein, rabbit Cytochrome b(5) (cytb(5)), determined using the (15)N CSA/(15)N-(1)H dipolar transverse cross-correlation rates. The mean values of (15)N CSA determined for residues in helical, sheet, and turn regions are -187.9, -166.0, and -161.1 ppm, respectively, with an overall average value of -171.7 ppm. While the average CSA value determined from this study is in good agreement with previous solution NMR experiments on small globular proteins, the CSA value determined for residues in helical conformation is slightly larger, which may be attributed to the paramagnetic effect from Fe(III) of the heme unit in cytb(5). However, like in previous solution NMR studies, the CSA values reported in this study are larger than the values measured from solid-state NMR experiments. We believe that the CSA parameters reported in this study will be useful in determining the structure, dynamics, and orientation of proteins, including membrane proteins, using NMR spectroscopy.

  7. Appointing silver and bronze standards for noncovalent interactions: A comparison of spin-component-scaled (SCS), explicitly correlated (F12), and specialized wavefunction approaches

    SciTech Connect

    Burns, Lori A.; Marshall, Michael S.; Sherrill, C. David

    2014-12-21

    A systematic examination of noncovalent interactions as modeled by wavefunction theory is presented in comparison to gold-standard quality benchmarks available for 345 interaction energies of 49 bimolecular complexes. Quantum chemical techniques examined include spin-component-scaling (SCS) variations on second-order perturbation theory (MP2) [SCS, SCS(N), SCS(MI)] and coupled cluster singles and doubles (CCSD) [SCS, SCS(MI)]; also, method combinations designed to improve dispersion contacts [DW-MP2, MP2C, MP2.5, DW-CCSD(T)-F12]; where available, explicitly correlated (F12) counterparts are also considered. Dunning basis sets augmented by diffuse functions are employed for all accessible ζ-levels; truncations of the diffuse space are also considered. After examination of both accuracy and performance for 394 model chemistries, SCS(MI)-MP2/cc-pVQZ can be recommended for general use, having good accuracy at low cost and no ill-effects such as imbalance between hydrogen-bonding and dispersion-dominated systems or non-parallelity across dissociation curves. Moreover, when benchmarking accuracy is desirable but gold-standard computations are unaffordable, this work recommends silver-standard [DW-CCSD(T**)-F12/aug-cc-pVDZ] and bronze-standard [MP2C-F12/aug-cc-pVDZ] model chemistries, which support accuracies of 0.05 and 0.16 kcal/mol and efficiencies of 97.3 and 5.5 h for adenine·thymine, respectively. Choice comparisons of wavefunction results with the best symmetry-adapted perturbation theory [T. M. Parker, L. A. Burns, R. M. Parrish, A. G. Ryno, and C. D. Sherrill, J. Chem. Phys. 140, 094106 (2014)] and density functional theory [L. A. Burns, Á. Vázquez-Mayagoitia, B. G. Sumpter, and C. D. Sherrill, J. Chem. Phys. 134, 084107 (2011)] methods previously studied for these databases are provided for readers' guidance.

  8. Appointing silver and bronze standards for noncovalent interactions: a comparison of spin-component-scaled (SCS), explicitly correlated (F12), and specialized wavefunction approaches.

    PubMed

    Burns, Lori A; Marshall, Michael S; Sherrill, C David

    2014-12-21

    A systematic examination of noncovalent interactions as modeled by wavefunction theory is presented in comparison to gold-standard quality benchmarks available for 345 interaction energies of 49 bimolecular complexes. Quantum chemical techniques examined include spin-component-scaling (SCS) variations on second-order perturbation theory (MP2) [SCS, SCS(N), SCS(MI)] and coupled cluster singles and doubles (CCSD) [SCS, SCS(MI)]; also, method combinations designed to improve dispersion contacts [DW-MP2, MP2C, MP2.5, DW-CCSD(T)-F12]; where available, explicitly correlated (F12) counterparts are also considered. Dunning basis sets augmented by diffuse functions are employed for all accessible ζ-levels; truncations of the diffuse space are also considered. After examination of both accuracy and performance for 394 model chemistries, SCS(MI)-MP2/cc-pVQZ can be recommended for general use, having good accuracy at low cost and no ill-effects such as imbalance between hydrogen-bonding and dispersion-dominated systems or non-parallelity across dissociation curves. Moreover, when benchmarking accuracy is desirable but gold-standard computations are unaffordable, this work recommends silver-standard [DW-CCSD(T**)-F12/aug-cc-pVDZ] and bronze-standard [MP2C-F12/aug-cc-pVDZ] model chemistries, which support accuracies of 0.05 and 0.16 kcal/mol and efficiencies of 97.3 and 5.5 h for adenine·thymine, respectively. Choice comparisons of wavefunction results with the best symmetry-adapted perturbation theory [T. M. Parker, L. A. Burns, R. M. Parrish, A. G. Ryno, and C. D. Sherrill, J. Chem. Phys. 140, 094106 (2014)] and density functional theory [L. A. Burns, Á. Vázquez-Mayagoitia, B. G. Sumpter, and C. D. Sherrill, J. Chem. Phys. 134, 084107 (2011)] methods previously studied for these databases are provided for readers' guidance.

  9. Appointing silver and bronze standards for noncovalent interactions: A comparison of spin-component-scaled (SCS), explicitly correlated (F12), and specialized wavefunction approaches

    NASA Astrophysics Data System (ADS)

    Burns, Lori A.; Marshall, Michael S.; Sherrill, C. David

    2014-12-01

    A systematic examination of noncovalent interactions as modeled by wavefunction theory is presented in comparison to gold-standard quality benchmarks available for 345 interaction energies of 49 bimolecular complexes. Quantum chemical techniques examined include spin-component-scaling (SCS) variations on second-order perturbation theory (MP2) [SCS, SCS(N), SCS(MI)] and coupled cluster singles and doubles (CCSD) [SCS, SCS(MI)]; also, method combinations designed to improve dispersion contacts [DW-MP2, MP2C, MP2.5, DW-CCSD(T)-F12]; where available, explicitly correlated (F12) counterparts are also considered. Dunning basis sets augmented by diffuse functions are employed for all accessible ζ-levels; truncations of the diffuse space are also considered. After examination of both accuracy and performance for 394 model chemistries, SCS(MI)-MP2/cc-pVQZ can be recommended for general use, having good accuracy at low cost and no ill-effects such as imbalance between hydrogen-bonding and dispersion-dominated systems or non-parallelity across dissociation curves. Moreover, when benchmarking accuracy is desirable but gold-standard computations are unaffordable, this work recommends silver-standard [DW-CCSD(T**)-F12/aug-cc-pVDZ] and bronze-standard [MP2C-F12/aug-cc-pVDZ] model chemistries, which support accuracies of 0.05 and 0.16 kcal/mol and efficiencies of 97.3 and 5.5 h for adenine.thymine, respectively. Choice comparisons of wavefunction results with the best symmetry-adapted perturbation theory [T. M. Parker, L. A. Burns, R. M. Parrish, A. G. Ryno, and C. D. Sherrill, J. Chem. Phys. 140, 094106 (2014)] and density functional theory [L. A. Burns, Á. Vázquez-Mayagoitia, B. G. Sumpter, and C. D. Sherrill, J. Chem. Phys. 134, 084107 (2011)] methods previously studied for these databases are provided for readers' guidance.

  10. Distribution and Xe129 NMR chemical shifts of Xen clusters in the alpha cages of zeolite AgA

    NASA Astrophysics Data System (ADS)

    Jameson, Cynthia J.; Lim, Hyung-Mi

    1997-09-01

    The distributions and 129Xe NMR chemical shifts of xenon in zeolite AgA have been measured in a series of experiments by Moudrakovski, Ratcliffe, and Ripmeester [Proc. Internat. Zeolite Conference, Quebec, 1995; unpublished]. We carry out grand canonical Monte Carlo (GCMC) simulations of xenon in a rigid zeolite AgA lattice to provide the average Xen cluster shifts, and the distributions Pn for comparison with their experiments. The GCMC results for the distributions, the fraction Pn of the alpha cages containing n Xe atoms, are compared with the experimental distributions in 12 samples and the agreement is excellent. The distributions in NaA and in AgA are very similar, as can be established from the comparison of the dispersion of the distributions, {-2}, and both are different from the idealized hypergeometric distribution, in which the component atoms occupy eight lattice sites per cage under mutual exclusion. The calculated chemical shift increments [σ(Xen)-σ(Xen-1)]AgA are in good agreement with experiment. The differences between these and the increments in zeolite NaA, {[σ(Xen)-σ(Xen-1)]AgA-[σ(Xen)-σ(Xen-1)]NaA}, are fairly small and are in good agreement with experiment. The absolute 129Xe chemical shifts of Xen in the alpha cages of AgA are nearly uniformly shifted by about 40 ppm compared to the Xen clusters in NaA. This is attributed to the Fermi contact shifts arising from the Ag0 metal atoms that form the linear Ag32+ complexes that are found within the beta cages of AgA.

  11. (1)H and (13)C NMR chemical shifts of methacrylate molecules associated with DMPC and/or DPPC liposomes.

    PubMed

    Fujisawa, Seiichiro; Ishihara, Mariko; Kadoma, Yoshinori

    2005-01-01

    In the light of recent developments, changes in (1)H and (13)C NMR chemical shifts of methacrylate molecule associated with DMPC (L-alpha dimyristoylphosphatidylcholine) or DPPC (L-alpha-dipalmitoylphosphatidylcholine) liposomes as a model for mimic native lipid bilayers were studied at 30, 37, and 52 degrees C. The chemical shifts of 3Ha, 3C, and 4C resonances in methacrylates (see Fig. 2) were greatly shifted higher field, suggesting the methacrylate molecule-lipid bilayer interaction. Comparison of the findings with methyl methacrylate (MMA), ethylene dimethacrylate (EDMA), and triethyleneglycol dimethacrylate (TEGDMA) revealed that the interaction of dimethacrylates (EDMA, TEGDMA) was greater than monomethacrylate, MMA. Their interaction with DMPC liposomes was also judged by a differential scanning calorimetry (DSC), indicating that the interaction was characterized by decreasing the enthalpy, entropy, and transition co-operativity. The evidence of the upfield NMR-shifts for methacrylate molecules was also judged by the descriptors such as the reactivity (HOMO-LUMO energy) and the electrostatic function (partial charges) between methacrylate molecules and DPPC, calculated by a PM 3 semiempirical MO method. The upfield NMR shifts were considerably well interpreted from the descriptors. NMR screening technique in methacrylates to phospholipid targets would be highly valuable in biomaterial developments. Figure 2 Changes in (1)H and (13)C NMR chemical shifts of methacrylate molecule associated with DMPC or DPPC liposomes. DMPC liposomes/MMA (1:1, molar ratio) and DMPC/TEGDMA (1:1) liposomes were measured at 30 degrees C. In DPPC liposome system, the rippled gel phase was measured at 30 degrees C, whereas the liquid crystalline phase for MMA and for both EDMA and TEGDMA were measured at 52 degrees C and 37 degrees C, respectively.

  12. Hydrophobic clustering in nonnative states of a protein: Interpretation of chemical shifts in NMR spectra of denatured states of lysozyme

    SciTech Connect

    Evans, P.A.; Topping, K.D.; Woolfson, D.N.; Dobson, C.M. )

    1991-01-01

    Chemical shifts of resonances of specific protons in the 1H NMR spectrum of thermally denatured hen lysozyme have been determined by exchange correlation with assigned native state resonances in 2D NOESY spectra obtained under conditions where the two states are interconverting. There are subtle but widespread deviations of the measured shifts from the values which would be anticipated for a random coil; in the case of side chain protons these are virtually all net upfield shifts and it is shown that this may be the averaged effect of interactions with aromatic rings in a partially collapsed denatured state. In a very few cases, notably that of two sequential tryptophan residues, it is possible to interpret these effects in terms of specific, local interresidue interactions. Generally, however, there is no correlation with either native state shift perturbations or with sequence proximity to aromatic groups. Diminution of most of the residual shift perturbations on reduction of the disulfide cross-links confirms that they are not simply effects of residues adjacent in the sequence. Similar effects of chemical denaturants, with the disulfides intact, demonstrate that the shift perturbations reflect an enhanced tendency to side chain clustering in the thermally denatured state. The temperature dependences of the shift perturbations suggest that this clustering is noncooperative and is driven by small, favorable enthalpy changes. While the extent of conformational averaging is clearly much greater than that observed for a homologous protein, alpha-lactalbumin, in its partially folded molten globule state, the results clearly show that thermally denatured lysozyme differs substantially from a random coil, principally in that it is partially hydrophobically collapsed.

  13. Assessing the accuracy of protein structures by quantum mechanical computations of 13C(alpha) chemical shifts.

    PubMed

    Vila, Jorge A; Scheraga, Harold A

    2009-10-20

    Two major techniques have been used to determine the three-dimensional structures of proteins: X-ray diffraction and NMR spectroscopy. In particular, the validation of NMR-derived protein structures is one of the most challenging problems in NMR spectroscopy. Therefore, researchers have proposed a plethora of methods to determine the accuracy and reliability of protein structures. Despite these proposals, there is a growing need for more sophisticated, physics-based structure validation methods. This approach will enable us to (a) characterize the "quality" of the NMR-derived ensemble as a whole by a single parameter, (b) unambiguously identify flaws in the sequence at a residue level, and (c) provide precise information, such as sets of backbone and side-chain torsional angles, that we can use to detect local flaws. Rather than reviewing all of the existing validation methods, this Account describes the contributions of our research group toward a solution of the long-standing problem of both global and local structure validation of NMR-derived protein structures. We emphasize a recently introduced physics-based methodology that makes use of observed and computed (13)C(alpha) chemical shifts (at the density functional theory (DFT) level of theory) for an accurate validation of protein structures in solution and in crystals. By assessing the ability of computed (13)C(alpha) chemical shifts to reproduce observed (13)C(alpha) chemical shifts of a single structure or ensemble of structures in solution and in crystals, we accomplish a global validation by using the conformationally averaged root-mean-square deviation, ca-rmsd, as a scoring function. In addition, the method enables us to provide local validation by identifying a set of individual amino acid conformations for which the computed and observed (13)C(alpha) chemical shifts do not agree within a certain error range and may represent a nonreliable fold of the protein model. Although it is computationally

  14. Prediction of carbon-13 NMR chemical shift of alkanes with rooted path vector.

    PubMed

    Zhou, L P; Sun, L L; Yu, Y; Lu, W; Li, Z L

    2006-11-01

    Systematic studies were further made on graph theory in quantitative structure-spectrum relationships (QSSR) for various areas of spectroscopies. Chemical shifts (CS) in alkanes for carbon-13 nuclear magnetic resonance (13C NMR) were well correlated with a set of novel molecular graph indices, called the rooted path vector of various lengths, as several multivariate regression equations as following:CS=3.022+5.336P1+7.356P2-1.648P3+0.83859P4+0.210P5-0.138P6-0.506P7+2.486P8-1.669P9; n=402, m=9, R=0.944, RCV=0.9413, S.D.=3.333, F=358.343, U=35833.211, Q=4355.422 for all types (primary, secondly, tertiary, quaternary as well as methane) of carbon atoms CS=0.983+6.811P1+7.584P2-2.029P3+0.809P4+0.106P5+0.043P6-0.124P7+1.715P8-1.101P9; n=374, m=9, R=0.975, RCV=0.9737, S.D.=2.303, F=773.372, U=36912.109, Q=1930.363 for primary, secondly, tertiary (including methane) carbon atoms; and CS=27.819+2.351P2+0.549P3-0.440P4+0.170P5-0.050P6; n=27, m=5, R=0.992, RCV=0.9674, S.D.=0.324, F=265.418, U=138.891, Q=2.198 for quaternary carbon atoms, respectively. Quite good estimation and prediction results were obtained from the quantitative molecular modeling and the performance of multiple linear regression (MLR) equations were tested to work well through cross-validation (CV) with the leave-one-out (LOO) procedure.

  15. NMR chemical shift pattern changed by ammonium sulfate precipitation in cyanobacterial phytochrome Cph1

    PubMed Central

    Song, Chen; Lang, Christina; Kopycki, Jakub; Hughes, Jon; Matysik, Jörg

    2015-01-01

    Phytochromes are dimeric biliprotein photoreceptors exhibiting characteristic red/far-red photocycles. Full-length cyanobacterial phytochrome Cph1 from Synechocystis 6803 is soluble initially but tends to aggregate in a concentration-dependent manner, hampering attempts to solve the structure using NMR and crystallization methods. Otherwise, the Cph1 sensory module (Cph1Δ2), photochemically indistinguishable from the native protein and used extensively in structural and other studies, can be purified to homogeneity in >10 mg amounts at mM concentrations quite easily. Bulk precipitation of full-length Cph1 by ammonium sulfate (AmS) was expected to allow us to produce samples for solid-state magic-angle spinning (MAS) NMR from dilute solutions before significant aggregation began. It was not clear, however, what effects the process of partial dehydration might have on the molecular structure. Here we test this by running solid-state MAS NMR experiments on AmS-precipitated Cph1Δ2 in its red-absorbing Pr state carrying uniformly 13C/15N-labeled phycocyanobilin (PCB) chromophore. 2D 13C–13C correlation experiments allowed a complete assignment of 13C responses of the chromophore. Upon precipitation, 13C chemical shifts for most of PCB carbons move upfield, in which we found major changes for C4 and C6 atoms associated with the A-ring positioning. Further, the broad spectral lines seen in the AmS 13C spectrum reflect primarily the extensive inhomogeneous broadening presumably due to an increase in the distribution of conformational states in the protein, in which less free water is available to partake in the hydration shells. Our data suggest that the effect of dehydration process indeed leads to changes of electronic structure of the bilin chromophore and a decrease in its mobility within the binding pocket, but not restricted to the protein surface. The extent of the changes induced differs from the freezing process of the solution samples routinely used in

  16. Backbone chemical shifts assignments, secondary structure, and ligand binding of a family GH-19 chitinase from moss, Bryum coronatum.

    PubMed

    Shinya, Shoko; Nagata, Takuya; Ohnuma, Takayuki; Taira, Toki; Nishimura, Shigenori; Fukamizo, Tamo

    2012-10-01

    Family GH19 chitinases have been recognized as important in the plant defense against fungal pathogens. However, their substrate-recognition mechanism is still unknown. We report here the first resonance assignment of NMR spectrum of a GH19 chitinase from moss, Bryum coronatum (BcChi-A). The backbone signals were nearly completely assigned, and the secondary structure was estimated based on the chemical shift values. The addition of the chitin dimer to the enzyme solution perturbed the chemical shifts of HSQC resonances of the amino acid residues forming the putative substrate-binding cleft. Further NMR analysis of the ligand binding to BcChi-A will improve understanding of the substrate-recognition mechanism of GH-19 enzymes.

  17. NMR chemical shift study of the interaction of selected peptides with liposomal and micellar models of apoptotic cells.

    PubMed

    Van Koninckxloo, Aurore; Henoumont, Céline; Laurent, Sophie; Muller, Robert N; Vander Elst, Luce

    2014-12-01

    The interaction between two peptides previously selected by phage display to target apoptotic cells and phospholipidic models of these cells (liposomes or micelles made of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) and/or 1,2-dipalmitoyl-sn-glycero-3-phospho-L-serine (DPPS, phosphatidylserine analog) was studied by the simple analysis of the changes induced on the proton NMR chemical shifts of the peptides. Our approach which does not need healthy and/or apoptotic cells for assessing the affinity of different peptides is fast and efficient and requires small amounts of peptide to determine the association constant, the interacting protons, and the number of interaction sites. The micellar model gave more reliable results than the liposomal one. The preferential interaction of the peptide with DPPS was evidenced by the change of the chemical shifts of specific amino acids of the peptides. Our micellar model is thus well suited to mimic apoptotic cells.

  18. Determination of isoleucine side-chain conformations in ground and excited states of proteins from chemical shifts.

    PubMed

    Hansen, D Flemming; Neudecker, Philipp; Kay, Lewis E

    2010-06-09

    A simple method is presented for quantifying Ile chi(2) rotamer distributions in proteins based on the measurement of Ile (13)C(delta1) chemical shifts. The methodology is well suited for applications involving very high molecular weight protein complexes, where other NMR parameters such as side-chain scalar coupling constants that report on dihedral angles cannot be measured or for studies of invisible, excited protein states, where chemical shifts are obtained from analysis of CPMG relaxation dispersion profiles. The utility of the approach is demonstrated by an application to the folding reaction of a mutant Fyn SH3 domain, where Ile side-chain structure and dynamics of an on-folding pathway intermediate state are studied.

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

    NASA Astrophysics Data System (ADS)

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

    2016-05-01

    We study by means of Nuclear Magnetic Resonance (NMR) spectroscopy the local order of water molecules in solution with lithium chloride at eutectic concentration. In particular, by measuring the proton chemical shift as a function of the temperature in the interval 203{ K}chemical shift of water solvating lithium and chlorine individually. The thermal behavior of this quantity confirms previous results about the role of the temperature in the solvation mechanisms down to about 225K. This temperature coincides with that of the so-called Widom line for water supporting the liquid-liquid transition hypothesis.

  20. Regression formulas for density functional theory calculated 1H and 13C NMR chemical shifts in toluene-d8.

    PubMed

    Konstantinov, Ivan A; Broadbelt, Linda J

    2011-11-10

    This study aimed at investigating the performance of a series of basis sets, density functional theory (DFT) functionals, and the IEF-PCM solvation model in the accurate calculation of (1)H and (13)C NMR chemical shifts in toluene-d(8). We demonstrated that, on a test set of 37 organic species with various functional moieties, linear scaling significantly improved the calculated shifts and was necessary to obtain more accurate results. Inclusion of a solvation model produced larger deviations from the experimental data as compared to the gas-phase calculations. Moreover, we did not find any evidence that very large basis sets were necessary to reproduce the experimental NMR data. Ultimately, we recommend the use of the BMK functional. For the (1)H shifts the use of the 6-311G(d) basis set gave linearly scaled mean unsigned (MU) and root-mean-square (rms) errors of 0.15 ppm and 0.21 ppm, respectively. For the calculation of the (13)C chemical shifts the 6-31G(d) basis set produced MUE of 1.82 ppm and RMSE of 3.29 ppm.

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

    PubMed

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

    2014-11-01

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

  2. Unraveling the 13C NMR chemical shifts in single-walled carbon nanotubes: dependence on diameter and electronic structure.

    PubMed

    Engtrakul, Chaiwat; Irurzun, Veronica M; Gjersing, Erica L; Holt, Josh M; Larsen, Brian A; Resasco, Daniel E; Blackburn, Jeffrey L

    2012-03-14

    The atomic specificity afforded by nuclear magnetic resonance (NMR) spectroscopy could enable detailed mechanistic information about single-walled carbon nanotube (SWCNT) functionalization as well as the noncovalent molecular interactions that dictate ground-state charge transfer and separation by electronic structure and diameter. However, to date, the polydispersity present in as-synthesized SWCNT populations has obscured the dependence of the SWCNT (13)C chemical shift on intrinsic parameters such as diameter and electronic structure, meaning that no information is gleaned for specific SWCNTs with unique chiral indices. In this article, we utilize a combination of (13)C labeling and density gradient ultracentrifugation (DGU) to produce an array of (13)C-labeled SWCNT populations with varying diameter, electronic structure, and chiral angle. We find that the SWCNT isotropic (13)C chemical shift decreases systematically with increasing diameter for semiconducting SWCNTs, in agreement with recent theoretical predictions that have heretofore gone unaddressed. Furthermore, we find that the (13)C chemical shifts for small diameter metallic and semiconducting SWCNTs differ significantly, and that the full-width of the isotropic peak for metallic SWCNTs is much larger than that of semiconducting nanotubes, irrespective of diameter.

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

    PubMed

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

    2015-10-01

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

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

    PubMed Central

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

    2015-01-01

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

  5. Space station Simulation Computer System (SCS) study for NASA/MSFC. Volume 5: Study analysis report

    NASA Technical Reports Server (NTRS)

    1989-01-01

    The Simulation Computer System (SCS) is the computer hardware, software, and workstations that will support the Payload Training Complex (PTC) at the Marshall Space Flight Center (MSFC). The PTC will train the space station payload scientists, station scientists, and ground controllers to operate the wide variety of experiments that will be on-board the Freedom Space Station. The further analysis performed on the SCS study as part of task 2-Perform Studies and Parametric Analysis-of the SCS study contract is summarized. These analyses were performed to resolve open issues remaining after the completion of task 1, and the publishing of the SCS study issues report. The results of these studies provide inputs into SCS task 3-Develop and present SCS requirements, and SCS task 4-develop SCS conceptual designs. The purpose of these studies is to resolve the issues into usable requirements given the best available information at the time of the study. A list of all the SCS study issues is given.

  6. Space station Simulation Computer System (SCS) study for NASA/MSFC. Volume 6: Study issues report

    NASA Technical Reports Server (NTRS)

    1989-01-01

    The Simulation Computer System (SCS) is the computer hardware, software, and workstations that will support the Payload Training Complex (PTC) at the Marshall Space Flight Center (MSFC). The PTC will train the space station payload specialists and mission specialists to operate the wide variety of experiments that will be on-board the Freedom Space Station. This simulation Computer System (SCS) study issues report summarizes the analysis and study done as task 1-identify and analyze the CSC study issues- of the SCS study contract.This work was performed over the first three months of the SCS study which began in August of 1988. First issues were identified from all sources. These included the NASA SOW, the TRW proposal, and working groups which focused the experience of NASA and the contractor team performing the study-TRW, Essex, and Grumman. The final list is organized into training related issues, and SCS associated development issues. To begin the analysis of the issues, a list of all the functions for which the SCS could be used was created, i.e., when the computer is turned on, what will it be doing. Analysis was continued by creating an operational functions matrix of SCS users vs. SCS functions to insure all the functions considered were valid, and to aid in identification of users as the analysis progressed. The functions will form the basis for the requirements, which are currently being developed under task 3 of the SCS study.

  7. Toward calculations of the 129Xe chemical shift in Xe@C60 at experimental conditions: relativity, correlation, and dynamics.

    PubMed

    Straka, Michal; Lantto, Perttu; Vaara, Juha

    2008-03-27

    We calculate the 129Xe chemical shift in endohedral Xe@C60 with systematic inclusion of the contributing physical effects to model the real experimental conditions. These are relativistic effects, electron correlation, the temperature-dependent dynamics, and solvent effects. The ultimate task is to obtain the right result for the right reason and to develop a physically justified methodological model for calculations and simulations of endohedral Xe fullerenes and other confined Xe systems. We use the smaller Xe...C6H6 model to calibrate density functional theory approaches against accurate correlated wave function methods. Relativistic effects as well as the coupling of relativity and electron correlation are evaluated using the leading-order Breit-Pauli perturbation theory. The dynamic effects are treated in two ways. In the first approximation, quantum dynamics of the Xe atom in a rigid cage takes advantage of the centrosymmetric potential for Xe within the thermally accessible distance range from the center of the cage. This reduces the problem of obtaining the solution of a diatomic rovibrational problem. In the second approach, first-principles classical molecular dynamics on the density functional potential energy hypersurface is used to produce the dynamical trajectory for the whole system, including the dynamic cage. Snapshots from the trajectory are used for calculations of the dynamic contribution to the absorption 129Xe chemical shift. The calculated nonrelativistic Xe shift is found to be highly sensitive to the optimized molecular structure and to the choice of the exchange-correlation functional. Relativistic and dynamic effects are significant and represent each about 10% of the nonrelativistic static shift at the minimum structure. While the role of the Xe dynamics inside of the rigid cage is negligible, the cage dynamics turns out to be responsible for most of the dynamical correction to the 129Xe shift. Solvent effects evaluated with a polarized

  8. ProCS15: a DFT-based chemical shift predictor for backbone and Cβ atoms in proteins

    PubMed Central

    Larsen, Anders S.; Bratholm, Lars A.; Christensen, Anders S.; Channir, Maher

    2015-01-01

    We present ProCS15: a program that computes the isotropic chemical shielding values of backbone and Cβ atoms given a protein structure in less than a second. ProCS15 is based on around 2.35 million OPBE/6-31G(d,p)//PM6 calculations on tripeptides and small structural models of hydrogen-bonding. The ProCS15-predicted chemical shielding values are compared to experimentally measured chemical shifts for Ubiquitin and the third IgG-binding domain of Protein G through linear regression and yield RMSD values of up to 2.2, 0.7, and 4.8 ppm for carbon, hydrogen, and nitrogen atoms. These RMSD values are very similar to corresponding RMSD values computed using OPBE/6-31G(d,p) for the entire structure for each proteins. These maximum RMSD values can be reduced by using NMR-derived structural ensembles of Ubiquitin. For example, for the largest ensemble the largest RMSD values are 1.7, 0.5, and 3.5 ppm for carbon, hydrogen, and nitrogen. The corresponding RMSD values predicted by several empirical chemical shift predictors range between 0.7–1.1, 0.2–0.4, and 1.8–2.8 ppm for carbon, hydrogen, and nitrogen atoms, respectively. PMID:26623185

  9. Spinal Cord Stimulation (SCS) with Anatomically Guided (3D) Neural Targeting Shows Superior Chronic Axial Low Back Pain Relief Compared to Traditional SCS-LUMINA Study.

    PubMed

    Veizi, Elias; Hayek, Salim M; North, James; Brent Chafin, T; Yearwood, Thomas L; Raso, Louis; Frey, Robert; Cairns, Kevin; Berg, Anthony; Brendel, John; Haider, Nameer; McCarty, Matthew; Vucetic, Henry; Sherman, Alden; Chen, Lilly; Mekel-Bobrov, Nitzan

    2017-01-20

    BACKGROUND : The aim of this study was to determine whether spinal cord stimulation (SCS) using 3D neural targeting provided sustained overall and low back pain relief in a broad routine clinical practice population.

  10. Water chemical shift in 1H NMR of red cells: effects of pH when transmembrane magnetic susceptibility differences are low.

    PubMed

    Larkin, Timothy J; Bubb, William A; Kuchel, Philip W

    2008-04-01

    The (1)H magic angle spinning (MAS) NMR spectrum of water in erythrocyte suspensions shows peaks from each of the intracellular and extracellular water pools. The splitting is a true chemical shift and is brought about by the elimination of water exchange under MAS conditions due to physical separation of the two water populations. The size of the chemical shift difference is determined by the concentration of intracellular protein affecting the average extent of hydrogen bonding of water. We present here a model of the chemical shift behavior for water in erythrocytes under normal high-resolution NMR conditions based on results from MAS experiments on these cells exposed to different pH and osmotic conditions. The model accurately predicts the chemical shift of water for a static sample, and the results demonstrate that in high-resolution NMR experiments the chemical shift of water will appear to be invariant if differences in magnetic susceptibility across the cell membrane are minimal (<10% of the magnetic susceptibility of water). Thus, changes in the shape and chemical shift of the water resonance are not due to pH changes in the physiological range. The findings are fundamental to an interpretation of the mechanism of chemical shift effects on the water resonance that may occur in functional MRI.

  11. 13C and 15N—Chemical Shift Anisotropy of Ampicillin and Penicillin-V Studied by 2D-PASS and CP/MAS NMR

    NASA Astrophysics Data System (ADS)

    Antzutkin, Oleg N.; Lee, Young K.; Levitt, Malcolm H.

    1998-11-01

    The principal values of the chemical shift tensors of all13C and15N sites in two antibiotics, ampicillin and penicillin-V, were determined by 2-dimensionalphaseadjustedspinningsideband (2D-PASS) and conventional CP/MAS experiments. The13C and15N chemical shift anisotropies (CSA), and their confidence limits, were evaluated using a Mathematica program. The CSA values suggest a revised assignment of the 2-methyl13C sites in the case of ampicillin. We speculate on a relationship between the chemical shift principal values of many of the13C and15N sites and the β-lactam ring conformation.

  12. Phenylboronic acid-based (19)F MRI probe for the detection and imaging of hydrogen peroxide utilizing its large chemical-shift change.

    PubMed

    Nonaka, Hiroshi; An, Qi; Sugihara, Fuminori; Doura, Tomohiro; Tsuchiya, Akira; Yoshioka, Yoshichika; Sando, Shinsuke

    2015-01-01

    Herein, we report on a new (19)F MRI probe for the detection and imaging of H2O2. Our designed 2-fluorophenylboronic acid-based (19)F probe promptly reacted with H2O2 to produce 2-fluorophenol via boronic acid oxidation. The accompanying (19)F chemical-shift change reached 31 ppm under our experimental conditions. Such a large chemical-shift change allowed for the imaging of H2O2 by (19)F chemical-shift-selective MRI.

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

    PubMed

    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.

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

    PubMed

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

    2014-06-14

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

  15. Evolution of the SCS curve number method and its applications to continuous runoff simulation

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The Natural Resources Conservation Service (NRCS) [previously Soil Conservation Service (SCS)] developed the SCS runoff curve-number (CN) method for estimating direct runoff from storm rainfall. The NRCS uses the CN method for designing structures and for evaluating their effectiveness. Structural...

  16. Influence of the chemical shift artifact on measurements of compact bone thickness in equine distal limb MR images.

    PubMed

    Dimock, Abigail N; Spriet, Mathieu

    2010-01-01

    The effect of the chemical shift artifact, resulting from misregistration or phase cancellation at the interface between compact and trabecular bone, on apparent bone thickness was quantified in six isolated equine limbs. Sagittal T1-weighted spin echo (SE) and in-phase three-dimensional spoiled gradient echo (SPGR) images were acquired twice with a 1.5 T magnetic resonance (MR) unit, switching the frequency encoding direction between acquisitions. Out-of-phase SPGR images were also obtained. MR images with different frequency encoding directions were compared with each other and to radiographs made from corresponding 3-mm-bone sections. Compact bone thickness was significantly different when comparing images acquired with different frequency encoding directions for both SE and SPGR sequences. Significant differences were identified in the frequency but not the phase encoding direction when measurements of compact bone in MR images were compared with measurements obtained from thin section radiographs for the majority of surfaces studied (P < 0.05). Correction of MR measurements with the calculated chemical shift abolished these differences (P > 0.05). Measurements of compact bone from out-of-phase SPGR sequences were significantly different than from in-phase sequences (P < 0.001) with out-of-phase measurements greater than in-phase measurements by an average of 0.38mm. These results indicate that the chemical shift artifact results in errors in MR evaluation of compact bone thickness when measurements are performed in the frequency encoding direction or in out-of-phase images. For better accuracy, measurements should be performed parallel to the phase encoding direction and avoiding out-of-phase gradient echo sequences.

  17. Effects of hydrogen bonding on amide-proton chemical shift anisotropy in a proline-containing model peptide

    NASA Astrophysics Data System (ADS)

    Pichumani, Kumar; George, Gijo; Hebbar, Sankeerth; Chatterjee, Bhaswati; Raghothama, Srinivasarao

    2015-05-01

    Longitudinal relaxation due to cross-correlation between dipolar (1HN-1Hα) and amide-proton chemical shift anisotropy (1HN CSA) has been measured in a model tripeptide Piv-LPro-LPro-LPhe-OMe. The peptide bond across diproline segment is known to undergo cis/trans isomerization and only in the cis form does the lone Phe amide-proton become involved in intramolecular hydrogen bonding. The strength of the cross correlated relaxation interference is found to be significantly different between cis and trans forms, and this difference is shown as an influence of intramolecular hydrogen bonding on the amide-proton CSA.

  18. Host response. Inflammation-induced disruption of SCS macrophages impairs B cell responses to secondary infection.

    PubMed

    Gaya, Mauro; Castello, Angelo; Montaner, Beatriz; Rogers, Neil; Reis e Sousa, Caetano; Bruckbauer, Andreas; Batista, Facundo D

    2015-02-06

    The layer of macrophages at the subcapsular sinus (SCS) captures pathogens entering the lymph node, preventing their global dissemination and triggering an immune response. However, how infection affects SCS macrophages remains largely unexplored. Here we show that infection and inflammation disrupt the organization of SCS macrophages in a manner that involves the migration of mature dendritic cells to the lymph node. This disrupted organization reduces the capacity of SCS macrophages to retain and present antigen in a subsequent secondary infection, resulting in diminished B cell responses. Thus, the SCS macrophage layer may act as a sensor or valve during infection to temporarily shut down the lymph node to further antigenic challenge. This shutdown may increase an organism's susceptibility to secondary infections.

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

    PubMed

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

    2016-04-14

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

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

    PubMed

    Van den Heuvel, Willem; Soncini, Alessandro

    2013-02-07

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

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

    PubMed Central

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

    2015-01-01

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

  2. Ab initio and DFT study of 31P-NMR chemical shifts of sphingomyelin and dihydrosphingomyelin lipid molecule

    NASA Astrophysics Data System (ADS)

    Sugimori, K.; Kawabe, H.; Nagao, H.; Nishikawa, K.

    One of the phospholipids, sphingomyelin (SM, N-acyl-sphingosine-1-phosphorylcholine) is the most abundant component of mammalian membranes in brain, nervous tissues, and human ocular lens. It plays an important role for apoptosis, aging, and signal transduction. Recently, Yappert and coworkers have shown that human lens sphingomyelin and its hydrogenated derivative, dihydrosphingomyelin (DHSM) are interacted with Ca2+ ions to develop human cataracts. Previously, we have investigated conformational differences between an isolated SM/DHSM molecule and Ca2+-coordinated form by using density functional theory (DFT) for geometry optimization and normal mode analysis. As a result, one of stable conformers of SMs has a hydrogen bonding between hydroxyl group and phosphate group, whereas another conformer has a hydrogen bonding between hydroxyl and phosphate amide group. In this study, 31P-Nuclear Magnetic Resonance (NMR) shielding constants of the obtained conformers are investigated by using ab initio and DFT with NMR-gauge invariant atomic orbitals (NMR-GIAO) calculations. The experimental 31P-NMR chemical shifts of SMs and DHSMs have significant small value around 0.1 ppm. We consider the relative conformational changes between SMs and DHSMs affect the slight deviations of 31P-NMR chemical shifts, and discuss intramolecular hydrogen bondings and the solvent effect in relation to NMR experimental reference.

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

    PubMed

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

    2015-11-17

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

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

    SciTech Connect

    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.

  5. Quantitative analysis of deuterium using the isotopic effect on quaternary (13)C NMR chemical shifts.

    PubMed

    Darwish, Tamim A; Yepuri, Nageshwar Rao; Holden, Peter J; James, Michael

    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 (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 D2O, one of the most convenient deuteration methods. In this study, deuterium-induced NMR isotope shifts of quaternary (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 (13)C NMR signals while decoupling both proton and deuterium nuclei, it is possible to resolve (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 ((1)H, (2)H) resolves closely separated quaternary (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.

  6. Suppression of sodium nuclear magnetic resonance double-quantum coherence by chemical shift and relaxation reagents

    NASA Astrophysics Data System (ADS)

    Hutchison, Robert B.; Huntley, James J. A.; Jin, Haoran; Shapiro, Joseph I.

    1992-12-01

    An investigation into the signal suppression behavior of the paramagnetic shift and relaxation reagents, Dy(P3O10)27- and Gd(P3O10)27-, with regard to their use in the nuclear magnetic resonance spectroscopic study of sodium has been performed. Measurements of T1 and T2 relaxation time constants of sodium in normal saline, Krebs-Henseleit buffer, and human blood serum, as a function of concentration of these reagents showed that, although closely coupled in the saline and K-H buffer environments, in plasma T1 and T2 become decoupled, transverse relaxation dominating in comparison to longitudinal relaxation. Linewidth measurements further suggest that relaxation in the plasma milieu is controlled primarily by inherent T2 relaxation, rather than by field inhomogeneity or diffusion effects. Quantitative single-quantum (1Q) and double-quantum (2Q) intensity measurements, biexponential T2 relaxation measurements, and parametric studies of the preparation time of the 2Q pulse sequence, were obtained in suspensions of bovine serum albumin and human erythrocytes. The observed suppression of sodium 2Q coherence by paramagnetic shift and relaxation reagents was found to exhibit a complex behavior in albumin solutions, involving the biexponential T2 decay to be expected during the preparation time of the 2Q filter pulse sequence, as well as the optimum preparation time for production of the double-quantum coherence itself. The controlling factor for both of these effects is the biexponential amplitude function in the expression for the transverse magnetization observed following application of the 2Q pulse sequence. This in turn is determined entirely by the values for the slow and fast components of biexponential relaxation in sodium, which themselves depend upon the concentration of the macromolecular binding sites for quadrupolar interaction. A similar behavior has been observed in suspensions of human erythrocytes.

  7. Demystifying fluorine chemical shifts: electronic structure calculations address origins of seemingly anomalous (19)F-NMR spectra of fluorohistidine isomers and analogues.

    PubMed

    Kasireddy, Chandana; Bann, James G; Mitchell-Koch, Katie R

    2015-11-11

    Fluorine NMR spectroscopy is a powerful tool for studying biomolecular structure, dynamics, and ligand binding, yet the origins of (19)F chemical shifts are not well understood. Herein, we use electronic structure calculations to describe the changes in (19)F chemical shifts of 2F- and 4F-histidine/(5-methyl)-imidazole upon acid titration. While the protonation of the 2F species results in a deshielded chemical shift, protonation of the 4F isomer results in an opposite, shielded chemical shift. The deshielding of 2F-histidine/(5-methyl)-imidazole upon protonation can be rationalized by concomitant decreases in charge density on fluorine and a reduced dipole moment. These correlations do not hold for 4F-histidine/(5-methyl)-imidazole, however. Molecular orbital calculations reveal that for the 4F species, there are no lone pair electrons on the fluorine until protonation. Analysis of a series of 4F-imidazole analogues, all with delocalized fluorine electron density, indicates that the deshielding of (19)F chemical shifts through substituent effects correlates with increased C-F bond polarity. In summary, the delocalization of fluorine electrons in the neutral 4F species, with gain of a lone pair upon protonation may help explain the difficulty in developing a predictive framework for fluorine chemical shifts. Ideas debated by chemists over 40 years ago, regarding fluorine's complex electronic effects, are shown to have relevance for understanding and predicting fluorine NMR spectra.

  8. NMR chemical shift perturbation mapping of DNA binding by a zinc-finger domain from the yeast transcription factor ADR1.

    PubMed Central

    Schmiedeskamp, M.; Rajagopal, P.; Klevit, R. E.

    1997-01-01

    Mutagenesis studies have revealed that the minimal DNA-binding domain of the yeast transcription factor ADR1 consists of two Cys2-His2 zinc fingers plus an additional 20 residues proximal and N-terminal to the fingers. We have assigned NMR 1H, 15N, and 13C chemical shifts for the entire minimal DNA-binding domain of ADR1 both free and bound to specific DNA. 1H chemical shift values suggest little structural difference between the zinc fingers in this construct and in single-finger constructs, and 13C alpha chemical shift index analysis indicates little change in finger structure upon DNA binding. 1H chemical shift perturbations upon DNA binding are observed, however, and these are mapped to define the protein-DNA interface. The two zinc fingers appear to bind DNA with different orientations, as the entire helix of finger 1 is perturbed, while only the extreme N-terminus of the finger 2 helix is affected. Furthermore, residues N-terminal to the first finger undergo large chemical shift changes upon DNA binding suggesting a role at the protein-DNA interface. A striking correspondence is observed between the protein-DNA interface mapped by chemical shift changes and that previously mapped by mutagenesis. PMID:9300483

  9. Position dependence of the 13C chemical shifts of α-helical model peptides. Fingerprint of the 20 naturally occurring amino acids

    PubMed Central

    Vila, Jorge A.; Baldoni, Héctor A.; Scheraga, Harold A.

    2004-01-01

    The position dependence of the 13C chemical shifts was investigated at the density functional level for α-helical model peptides represented by the sequence Ac-(Ala)i-X-(Ala)j-NH2, where X represents any of the 20 naturally occurring amino acids, with 0 ≤ i ≤ 8 and i + j = 8. Adoption of the locally dense basis approach for the quantum chemical calculations enabled us to reduce the length of the chemical-shift calculations while maintaining good accuracy of the results. For the 20 naturally occurring amino acids in α-helices, there is (1) significant variability of the computed 13C shielding as a function of both the guest residue (X) and the position along the sequence; for example, at the N terminus, the 13Cα and 13Cβ shieldings exhibit a uniform pattern of variation with respect to both the central or the C-terminal positions; (2) good agreement between computed and observed 13Cα and 13Cβ chemical shifts in the interior of the helix, with correlation coefficients of 0.98 and 0.99, respectively; for 13Cα chemical shifts, computed in the middle of the helix, only five residues, namely Asn, Asp, Ser, Thr, and Leu, exhibit chemical shifts beyond the observed standard deviation; and (3) better agreement for four of these residues (Asn, Asp, Ser, and Thr) only for the computed values of the 13Cα chemical shifts at the N terminus. The results indicate that 13Cβ, but not 13Cβ, chemical shifts are sensitive enough to reflect the propensities of some amino acids for specific positions within an α-helix, relative to the N and C termini of peptides and proteins. PMID:15498939

  10. Chemical potential shift and gap-state formation in SrTiO3-δ revealed by photoemission spectroscopy

    NASA Astrophysics Data System (ADS)

    Pal, Prabir; Kumar, Pramod; Aswin, V.; Dogra, Anjana; Joshi, Amish G.

    2014-08-01

    In this study, we report on investigations of the electronic structure of SrTiO3 annealed at temperature ranging between 550 and 840 °C in an ultrahigh vacuum. Annealing induced oxygen vacancies (Ovac) impart considerable changes in the electronic structure of SrTiO3. Using core-level photoemission spectroscopy, we have studied the chemical potential shift (Δμ) as a function of annealing temperature. The result shows that the chemical potential monotonously increases with electron doping in SrTiO3-δ. The monotonous increase of the chemical potential rules out the existence of electronic phase separation in the sample. Using valence band photoemission, we have demonstrated the formation of a low density of states at the near Fermi level electronic spectrum of SrTiO3-δ. The gap-states were observed by spectral weight transfer over a large energy scale of the stoichiometric band gap of SrTiO3 system leading finally to an insulator-metal transition. We have interpreted our results from the point of structural distortions induced by oxygen vacancies.

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

    PubMed

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

    2014-04-28

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

  12. 1H, 13C and 15N chemical shift assignments of the thioredoxin from the obligate anaerobe Desulfovibrio vulgaris Hildenborough.

    PubMed

    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).

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

    PubMed

    Raya, Jésus; Perrone, Barbara; Hirschinger, Jérôme

    2013-02-01

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

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

    NASA Astrophysics Data System (ADS)

    Raya, Jésus; Perrone, Barbara; Hirschinger, Jérôme

    2013-02-01

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

  15. Non-invasive localization of thymol accumulation in Carum copticum (Apiaceae) fruits by chemical shift selective magnetic resonance imaging.

    PubMed

    Gersbach, P V; Reddy, N

    2002-08-01

    Magnetic resonance imaging was used to localize the site of essential oil accumulation in fruit of Carum copticum L. (Apiaceae). A chemical shift method is described that utilized the spectral properties of the aromatic monoterpene thymol, the major component of the essential oil, to image thymol selectively. The presence of essential oil secretory structures in the fruit and an essential oil containing a high proportion of thymol were confirmed with optical microscopy and gas chromatography-mass spectrometry, respectively. Selective imaging of whole C. copticum fruits showed that thymol accumulation was localized to the secretory structures (canals) situated in the fruit wall. The technique was considered non-invasive as the seeds used in the imaging experiments remained intact and viable.

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

    PubMed

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

    2016-08-07

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

  17. Robust algorithms for automated chemical shift calibration of 1D 1H NMR spectra of blood serum.

    PubMed

    Pearce, Jake T M; Athersuch, Toby J; Ebbels, Timothy M D; Lindon, John C; Nicholson, Jeremy K; Keun, Hector C

    2008-09-15

    In biofluid NMR spectroscopy, the frequency of each resonance is typically calibrated by addition of a reference compound such as 3-(trimethylsilyl)-propionic acid- d 4 (TSP) to the sample. However biofluids such as serum cannot be referenced to TSP, due to shifts resonance caused by binding to macromolecules in solution. In order to overcome this limitation we have developed algorithms, based on analysis of derivative spectra, to locate and calibrate (1)H NMR spectra to the alpha-glucose anomeric doublet. We successfully used these algorithms to calibrate 77 serum (1)H NMR spectra and demonstrate the greater reproducibility of the calculated chemical-shift corrections ( r = 0.97) than those generated by manual alignment ( r = 0.8-0.88). Hence we show that these algorithms provide robust and reproducible methods of calibrating (1)H NMR of serum, plasma, or any biofluid in which glucose is abundant. Precise automated calibration of complex biofluid NMR spectra is an important tool in large-scale metabonomic or metabolomic studies, where hundreds or even thousands of spectra may be analyzed in high-resolution by pattern recognition analysis.

  18. Space station Simulation Computer System (SCS) study for NASA/MSFC. Volume 2: Concept document

    NASA Technical Reports Server (NTRS)

    1989-01-01

    The Simulation Computer System (SCS) concept document describes and establishes requirements for the functional performance of the SCS system, including interface, logistic, and qualification requirements. The SCS is the computational communications and display segment of the Marshall Space Flight Center (MSFC) Payload Training Complex (PTC). The PTC is the MSFC facility that will train onboard and ground operations personnel to operate the payloads and experiments on board the international Space Station Freedom. The requirements to be satisfied by the system implementation are identified here. The SCS concept document defines the requirements to be satisfied through the implementation of the system capability. The information provides the operational basis for defining the requirements to be allocated to the system components and enables the system organization to assess whether or not the completed system complies with the requirements of the system.

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

    PubMed

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

    2016-08-31

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

  20. A Magic-Angle Spinning NMR Method for the Site-Specific Measurement of Proton Chemical-Shift Anisotropy in Biological and Organic Solids

    PubMed Central

    Hou, Guangjin; Gupta, Rupal; Polenova, Tatyana; Vega, Alexander J.

    2014-01-01

    Proton chemical shifts are a rich probe of structure and hydrogen bonding environments in organic and biological molecules. Until recently, measurements of 1H chemical shift tensors have been restricted to either solid systems with sparse proton sites or were based on the indirect determination of anisotropic tensor components from cross-relaxation and liquid-crystal experiments. We have introduced an MAS approach that permits site-resolved determination of CSA tensors of protons forming chemical bonds with labeled spin-1/2 nuclei in fully protonated solids with multiple sites, including organic molecules and proteins. This approach, originally introduced for the measurements of chemical shift tensors of amide protons, is based on three RN-symmetry based experiments, from which the principal components of the 1H CS tensor can be reliably extracted by simultaneous triple fit of the data. In this article, we expand our approach to a much more challenging system involving aliphatic and aromatic protons. We start with a review of the prior work on experimental-NMR and computational-quantum-chemical approaches for the measurements of 1H chemical shift tensors and for relating these to the electronic structures. We then present our experimental results on U-13C,15N-labeled histdine demonstrating that 1H chemical shift tensors can be reliably determined for the 1H15N and 1H13C spin pairs in cationic and neutral forms of histidine. Finally, we demonstrate that the experimental 1H(C) and 1H(N) chemical shift tensors are in agreement with Density Functional Theory calculations, therefore establishing the usefulness of our method for characterization of structure and hydrogen bonding environment in organic and biological solids. PMID:25484446

  1. 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.

    PubMed

    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.

  2. SLUDGE PARTICLE SEPAPATION EFFICIENCIES DURING SETTLER TANK RETRIEVAL INTO SCS-CON-230

    SciTech Connect

    DEARING JI; EPSTEIN M; PLYS MG

    2009-07-16

    The purpose of this document is to release, into the Hanford Document Control System, FA1/0991, Sludge Particle Separation Efficiencies for the Rectangular SCS-CON-230 Container, by M. Epstein and M. G. Plys, Fauske & Associates, LLC, June 2009. The Sludge Treatment Project (STP) will retrieve sludge from the 105-K West Integrated Water Treatment System (IWTS) Settler Tanks and transfer it to container SCS-CON-230 using the Settler Tank Retrieval System (STRS). The sludge will enter the container through two distributors. The container will have a filtration system that is designed to minimize the overflow of sludge fines from the container to the basin. FAI/09-91 was performed to quantify the effect of the STRS on sludge distribution inside of and overflow out of SCS-CON-230. Selected results of the analysis and a system description are discussed. The principal result of the analysis is that the STRS filtration system reduces the overflow of sludge from SCS-CON-230 to the basin by roughly a factor of 10. Some turbidity can be expected in the center bay where the container is located. The exact amount of overflow and subsequent turbidity is dependent on the density of the sludge (which will vary with location in the Settler Tanks) and the thermal gradient between the SCS-CON-230 and the basin. Attachment A presents the full analytical results. These results are applicable specifically to SCS-CON-230 and the STRS filtration system's expected operating duty cycles.

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

    PubMed

    Vícha, Jan; Marek, Radek; Straka, Michal

    2016-10-17

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

  4. Development of multicomponent hybrid density functional theory with polarizable continuum model for the analysis of nuclear quantum effect and solvent effect on NMR chemical shift

    SciTech Connect

    Kanematsu, Yusuke; Tachikawa, Masanori

    2014-04-28

    We have developed the multicomponent hybrid density functional theory [MC-(HF+DFT)] method with polarizable continuum model (PCM) for the analysis of molecular properties including both nuclear quantum effect and solvent effect. The chemical shifts and H/D isotope shifts of the picolinic acid N-oxide (PANO) molecule in chloroform and acetonitrile solvents are applied by B3LYP electron exchange-correlation functional for our MC-(HF+DFT) method with PCM (MC-B3LYP/PCM). Our MC-B3LYP/PCM results for PANO are in reasonable agreement with the corresponding experimental chemical shifts and isotope shifts. We further investigated the applicability of our method for acetylacetone in several solvents.

  5. Simple quantitative structure-property relationship (QSPR) modeling of 17O carbonyl chemical shifts in substituted benzaldehydes compared to DFT and empirical approaches.

    PubMed

    Kiralj, Rudolf; Ferreira, Márcia M C

    2008-07-10

    The geometry of 50 substituted benzaldehydes was optimized at the semiempirical PM3 level, and various electronic and steric descriptors accounting for properties of the benzene ring, aldehyde group, and their connecting carbon-carbon bond were calculated. Quantitative structure-property relationships (QSPR) between (17)O carbonyl chemical shifts and these descriptors were established using partial least-squares regression and principal component regression. These two parsimonious QSPR models were comparable with the literature empirical model and DFT (density functional theory) and capable of predicting (17)O chemical shifts for 10 benzaldehydes. Principal component analysis, hierarchical cluster analysis, and crystal structure data retrieved from the Cambridge Structural Database were additional methods for chemical verification of the regression models. The QSPR models are recommended as being more reliable than and superior to the empirical and DFT models due to the results of all validations, simplicity, and short time that regressions need for (17)O shift prediction.

  6. Geometries and tautomerism of OHN hydrogen bonds in aprotic solution probed by H/D isotope effects on (13)C NMR chemical shifts.

    PubMed

    Tolstoy, Peter M; Guo, Jing; Koeppe, Benjamin; Golubev, Nikolai S; Denisov, Gleb S; Smirnov, Sergei N; Limbach, Hans-Heinrich

    2010-10-14

    The (1)H and (13)C NMR spectra of 17 OHN hydrogen-bonded complexes formed by CH(3)(13)COOH(D) with 14 substituted pyridines, 2 amines, and N-methylimidazole have been measured in the temperature region between 110 and 150 K using CDF(3)/CDF(2)Cl mixture as solvent. The slow proton and hydrogen bond exchange regime was reached, and the H/D isotope effects on the (13)C chemical shifts of the carboxyl group were measured. In combination with the analysis of the corresponding (1)H chemical shifts, it was possible to distinguish between OHN hydrogen bonds exhibiting a single proton position and those exhibiting a fast proton tautomerism between molecular and zwitterionic forms. Using H-bond correlations, we relate the H/D isotope effects on the (13)C chemical shifts of the carboxyl group with the OHN hydrogen bond geometries.

  7. Brain temperature and pH measured by (1)H chemical shift imaging of a thulium agent.

    PubMed

    Coman, Daniel; Trubel, Hubert K; Rycyna, Robert E; Hyder, Fahmeed

    2009-02-01

    Temperature and pH are two of the most important physiological parameters and are believed to be tightly regulated because they are intricately related to energy metabolism in living organisms. Temperature and/or pH data in mammalian brain are scarce, however, mainly because of lack of precise and non-invasive methods. At 11.7 T, we demonstrate that a thulium-based macrocyclic complex infused through the bloodstream can be used to obtain temperature and pH maps of rat brain in vivo by (1)H chemical shift imaging (CSI) of the sensor itself in conjunction with a multi-parametric model that depends on several proton resonances of the sensor. Accuracies of temperature and pH determination with the thulium sensor - which has a predominantly extracellular presence - depend on stable signals during the course of the CSI experiment as well as redundancy for temperature and pH sensitivities contained within the observed signals. The thulium-based method compared well with other methods for temperature ((1)H MRS of N-acetylaspartate and water; copper-constantan thermocouple wire) and pH ((31)P MRS of inorganic phosphate and phosphocreatine) assessment, as established by in vitro and in vivo studies. In vitro studies in phantoms with two compartments of different pH value observed under different ambient temperature conditions generated precise temperature and pH distribution maps. In vivo studies in alpha-chloralose-anesthetized and renal-ligated rats revealed temperature (33-34 degrees C) and pH (7.3-7.4) distributions in the cerebral cortex that are in agreement with observations by other methods. These results show that the thulium sensor can be used to measure temperature and pH distributions in rat brain in vivo simultaneously and accurately using Biosensor Imaging of Redundant Deviation in Shifts (BIRDS).

  8. Novel use of chemical shift in NMR as molecular descriptor: a first report on modeling carbonic anhydrase inhibitory activity and related parameters.

    PubMed

    Khadikar, Padmakar V; Sharma, Vimukta; Karmarkar, Sneha; Supuran, Claudiu T

    2005-02-15

    A novel use of NMR chemical shift of the SO(2)NH(2) protons (in dioxane as solvent) as a molecular descriptor is described for modeling the inhibition constant for benzene sulfonamides against the zinc enzyme carbonic anhydrase (CA, EC 4.2.1.1). The methodology is extended to model diuretic activity and lipophilicity of benzene sulfonamide derivatives. The regression analysis of the data has shown that the NMR chemical shift is incapable of modeling lipophilicity. However, it is quite useful for modeling the diuretic activity of these derivatives. The results are compared with those obtained using distance-based topological indices: Wiener (W)-, Szeged (Sz)-, and PI (Padmakar-Ivan) indices.

  9. 1H and 13C NMR chemical shift assignments of spiro-cycloalkylidenehomo- and methanofullerenes by the DFT-GIAO method.

    PubMed

    Khalilov, L M; Tulyabaev, A R; Yanybin, V M; Tuktarov, A R

    2011-06-01

    The (1)H and (13)C NMR chemical shifts of spiro-cycloalkylidene[60]fullerenes were assigned using experimental NMR data and the Density Functional Theory (DFT)-Gauge Independence Of Atomic Orbitals method (GAIO) calculation method in the Perdew Burke Ernzerhof (PBE)/3z approach. The calculated values of the (13)C NMR chemical shifts adequately reproduce the experimental values at this quantum chemistry approach. Similar assignments will be helpful for (13)C NMR spectral analysis of homo- and methano[60]fullerene derivatives for structure elucidation and to determine the influence of fullerene frames on substituents and the influence of substituents on fullerene cores.

  10. MRI chemical shift imaging of the fat content of the pancreas and liver of patients with type 2 diabetes mellitus.

    PubMed

    Chai, Jun; Liu, Peng; Jin, Erhu; Su, Tianhao; Zhang, Jie; Shi, Kaining; Hong, X U; Yin, Jie; Yu, Hengchi

    2016-02-01

    The present study aimed to investigate the association between the content and distribution of fat in the pancreas and liver in patients with type 2 diabetes mellitus (T2DM). A total of 70 patients newly diagnosed with T2DM (T2DM group) and 30 healthy volunteers (normal control group) were enrolled in the present study. Dual-echo magnetic resonance (MR) chemical shift imaging was used to measure the fat content of the liver and the head, body and tail regions of the pancreas. In addition, the distribution of fat in the various regions of the pancreas, as well as the average fat content of the pancreas versus the liver, were compared. The fat content of the pancreatic head, body and tail regions of the T2DM group were 5.59±4.70, 4.80±3.75 and 4.89±3.86%, respectively. The fat content of these regions in the normal control group were 3.89±2.47, 3.30±2.11 and 3.23±2.23%, respectively. The average fat content of the pancreas was 5.19±3.75% for the T2DM group and 3.47±2.00% for the normal control group. The average fat content of the liver was 9.87±3.19% for the T2DM group and 7.24±2.38% for the normal control group. Therefore, the results from MR chemical shift imaging suggested that there were no significant differences in the distribution of fat between the pancreas of patients newly diagnosed with T2DM and that from the healthy population; however, the average fat content in the pancreas of the T2DM group was significantly higher (F=3.597; P<0.05), as compared with the normal control group. In addition, there was no correlation between the fat contents in the pancreas and liver in patients newly diagnosed with T2DM and the healthy population.

  11. Space station Simulation Computer System (SCS) study for NASA/MSFC. Volume 3: Refined conceptual design report

    NASA Technical Reports Server (NTRS)

    1989-01-01

    The results of the refined conceptual design phase (task 5) of the Simulation Computer System (SCS) study are reported. The SCS is the computational portion of the Payload Training Complex (PTC) providing simulation based training on payload operations of the Space Station Freedom (SSF). In task 4 of the SCS study, the range of architectures suitable for the SCS was explored. Identified system architectures, along with their relative advantages and disadvantages for SCS, were presented in the Conceptual Design Report. Six integrated designs-combining the most promising features from the architectural formulations-were additionally identified in the report. The six integrated designs were evaluated further to distinguish the more viable designs to be refined as conceptual designs. The three designs that were selected represent distinct approaches to achieving a capable and cost effective SCS configuration for the PTC. Here, the results of task 4 (input to this task) are briefly reviewed. Then, prior to describing individual conceptual designs, the PTC facility configuration and the SSF systems architecture that must be supported by the SCS are reviewed. Next, basic features of SCS implementation that have been incorporated into all selected SCS designs are considered. The details of the individual SCS designs are then presented before making a final comparison of the three designs.

  12. Shifts in controls on the temporal coherence of throughfall chemical flux in Acadia National Park, Maine, USA

    USGS Publications Warehouse

    Nelson, Sarah J.; Webster, Katherine E.; Loftin, Cynthia S.; Weathers, Kathleen C.

    2013-01-01

    Major ion and mercury (Hg) inputs to terrestrial ecosystems include both wet and dry deposition (total deposition). Estimating total deposition to sensitive receptor sites is hampered by limited information regarding its spatial heterogeneity and seasonality. We used measurements of throughfall flux, which includes atmospheric inputs to forests and the net effects of canopy leaching or uptake, for ten major ions and Hg collected during 35 time periods in 1999–2005 at over 70 sites within Acadia National Park, Maine to (1) quantify coherence in temporal dynamics of seasonal throughfall deposition and (2) examine controls on these patterns at multiple scales. We quantified temporal coherence as the correlation between all possible site pairs for each solute on a seasonal basis. In the summer growing season and autumn, coherence among pairs of sites with similar vegetation was stronger than for site-pairs that differed in vegetation suggesting that interaction with the canopy and leaching of solutes differed in coniferous, deciduous, mixed, and shrub or open canopy sites. The spatial pattern in throughfall hydrologic inputs across Acadia National Park was more variable during the winter snow season, suggesting that snow re-distribution affects net hydrologic input, which consequently affects chemical flux. Sea-salt corrected calcium concentrations identified a shift in air mass sources from maritime in winter to the continental industrial corridor in summer. Our results suggest that the spatial pattern of throughfall hydrologic flux, dominant seasonal air mass source, and relationship with vegetation in winter differ from the spatial pattern of throughfall flux in these solutes in summer and autumn. The coherence approach applied here made clear the strong influence of spatial heterogeneity in throughfall hydrologic inputs and a maritime air mass source on winter patterns of throughfall flux. By contrast, vegetation type was the most important influence on

  13. 10-kHz High-Frequency SCS Therapy: A Clinical Summary

    PubMed Central

    Russo, Marc; Van Buyten, Jean-Pierre

    2015-01-01

    Objective Chronic pain remains a serious public health problem worldwide. A spinal cord stimulation (SCS) therapy called HF10 SCS uses 10-kHz high-frequency stimulation to provide pain relief without paresthesia. In this article, we describe the therapy, device, and the methods of implant and then review the safety and effectiveness data for this therapy. Results HF10 SCS uses a charge-balanced stimulation waveform that has been shown to be safe in both animal and human studies. Data from a multicenter, prospective clinical trial shows that the therapy provides substantial back and leg pain relief. Numerous additional reports suggest improved pain relief in other body areas and for complex pain patterns, even for patients who have previously failed other neuromodulation therapies. Conclusions The clinical experience reported in this article supports the efficacy and pain relief provided by HF10 SCS therapy. Clinical studies have also concluded that HF10 SCS does not generate paresthesia nor was it necessary to provide adequate coverage for pain relief. As clinical evidence accumulates and technological innovation improves patient outcomes, neuromodulatory techniques will be sought earlier in the treatment continuum to reduce the suffering for the many with otherwise intractable chronic pain. PMID:25377278

  14. Determination of the Chemical-Shift Difference between the Lactate Multiplets and Its pH Dependence

    NASA Astrophysics Data System (ADS)

    Bunse, Michael; Jung, Wulf-Ingo; Dietze, Günther; Lutz, Otto

    1996-09-01

    A volume-selective NMR method is presented for very exact determination of the difference of the Larmor frequencies between the coupled resonances of homonuclear AX3spin systems, as, for example, lactate. The frequency difference can be determined with an accuracy of 0.003 ppm even if only the doublet of the spin system can be detected. The method is based on the effects of homonuclear polarization transfer which occurs in localized double-spin-echo spectroscopy. It is used for determination of the chemical-shift difference of the lactate multiplets, which depends on the degree of dissociation and consequently on pH. Measurements were performed with a 1.5 T Siemens Magnetom SP 63 whole-body imager on solutions of lactate and acetic acid in physiological sodium chloride solution with pH from 1 to 11. As a consequence of these measurements, conclusions are possible for the optimum echo time for PRESS measurements which avoid signal losses from polarization transfer. Furthermore, the possibility of localized pH determination by this effect is discussed.

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

    PubMed

    Toy, Mehmet; Tanak, Hasan

    2016-01-05

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

  16. 13C-detected NMR experiments for measuring chemical shifts and coupling constants in nucleic acid bases.

    PubMed

    Fiala, Radovan; Sklenár, Vladimír

    2007-10-01

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

  17. An artificially evolved albumin binding module facilitates chemical shift epitope mapping of GA domain interactions with phylogenetically diverse albumins.

    PubMed

    He, Yanan; Chen, Yihong; Rozak, David A; Bryan, Philip N; Orban, John

    2007-07-01

    Protein G-related albumin-binding (GA) modules occur on the surface of numerous Gram-positive bacterial pathogens and their presence may promote bacterial growth and virulence in mammalian hosts. We recently used phage display selection to evolve a GA domain, PSD-1 (phage selected domain-1), which tightly bound phylogenetically diverse albumins. With respect to PSD-1's broad albumin binding specificity, it remained unclear how the evolved binding epitope compared to those of naturally occurring GA domains and whether PSD-1's binding mode was the same for different albumins. We investigate these questions here using chemical shift perturbation measurements of PSD-1 with rabbit serum albumin (RSA) and human serum albumin (HSA) and put the results in the context of previous work on structure and dynamics of GA domains. Combined, these data provide insights into the requirements for broad binding specificity in GA-albumin interactions. Moreover, we note that using the phage-optimized PSD-1 protein significantly diminishes the effects of exchange broadening at the binding interface between GA modules and albumin, presumably through stabilization of a ligand-bound conformation. The employment of artificially evolved domains may be generally useful in NMR structural studies of other protein-protein complexes.

  18. Water Solvent Effect on Theoretical Evaluation of (1)H NMR Chemical Shifts: o-Methyl-Inositol Isomer.

    PubMed

    Dos Santos, Hélio F; Chagas, Marcelo A; De Souza, Leonardo A; Rocha, Willian R; De Almeida, Mauro V; Anconi, Cleber P A; De Almeida, Wagner B

    2017-04-13

    In this paper, density functional theory calculations of nuclear magnetic resonance (NMR) chemical shifts for l-quebrachitol isomer, previously studied in our group, are reported with the aim of investigating in more detail the water solvent effect on the prediction of (1)H NMR spectra. In order to include explicit water molecules, 20 water-l-quebrachitol configurations obtained from Monte Carlo simulation were selected to perform geometry optimizations using the effective fragment potential method encompassing 60 water molecules around the solute. The solvated solute optimized geometries were then used in B3LYP/6-311+G(2d,p) NMR calculations with PCM-water. The inclusion of explicit solvent in the B3LYP NMR calculations resulted in large changes in the (1)H NMR profiles. We found a remarkable improvement in the agreement with experimental NMR profiles when the explicit hydrated l-quebrachitol structure is used in B3LYP (1)H NMR calculations, yielding a mean absolute error (MAE) of only 0.07 ppm, much lower than reported previously for the gas phase optimized structure (MAE = 0.11 ppm). In addition, a very improved match between theoretical and experimental (1)H NMR spectrum measured in D2O was achieved with the new hydrated optimized l-quebrachitol structure, showing that a fine-tuning of the theoretical NMR spectra can be accomplished once solvent effects are properly considered.

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

    NASA Astrophysics Data System (ADS)

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

    2014-03-01

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

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

    PubMed

    Jose, K V Jovan; Raghavachari, Krishnan

    2017-03-14

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

  1. Quantum-chemical analysis of paramagnetic 13C NMR shifts of iron-bound cyanide ions in heme-protein environments

    NASA Astrophysics Data System (ADS)

    Yamaki, Daisuke; Hada, Masahiko

    2012-12-01

    Paramagnetic 13C NMR chemical shifts of iron-bound cyanide ions located in biological environments such as heme-proteins are significantly sensitive to the environments. These chemical shifts are due to negative spin density at 13C induced by the open-shell iron center. In order to examine the environments effects on the electronic states around heme parts, ab initio calculations were performed for model systems of heme-proteins. The proximal residues in proteinparts of cytochrome c, hemoglobin, myoglobin and horseradish peroxidase were included in the model systems with the common active site (cyanide imidazole porphyrinato iron(III)) to take account of the environments effects. The calculated paramagnetic shifts of model systems reproduce the experimental trend of corresponding heme-proteins. It is found that the effects of proximal residues on the electronic states of the heme-parts are significant for these hemeproteins. In this abstract we focused on the calculations and analysis of cytochrome c.

  2. Elucidation of the resting state of a rhodium NNN-pincer hydrogenation catalyst that features a remarkably upfield hydride (1)H NMR chemical shift.

    PubMed

    Hänninen, Mikko M; Zamora, Matthew T; MacNeil, Connor S; Knott, Jackson P; Hayes, Paul G

    2016-01-11

    Rhodium(I) alkene complexes of an NNN-pincer ligand catalyze the hydrogenation of alkenes, including ethylene. The terminal or resting state of the catalyst, which exhibits an unprecedentedly upfield Rh-hydride (1)H NMR chemical shift, has been isolated and a synthetic cycle for regenerating the catalytically active species has been established.

  3. High accuracy NMR chemical shift corrected for bulk magnetization as a tool for structural elucidation of microemulsions. Part 2 - Anionic and nonionic dilutable microemulsions.

    PubMed

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

    2016-02-01

    In our previous report we suggested a new analytical tool, high accuracy NMR chemical shift corrected for bulk magnetization as a supplementary tool to study structural transitions and droplet size and shape of dilutable microemulsions. The aim of this study was to show the generality of this technique and to demonstrate that in almost any type of microemulsion this technique provides additional valuable structural information. The analysis made by the technique adds to the elucidation of some structural aspects that could not be clearly determined by other classical techniques. Therefore, in this part we are extending the study to three additional systems differing in the type of oil phase (toluene and cyclohexane), the nature of the surfactants (anionic and nonionic), and other microemulsion characteristics. We studied sodium dodecyl sulfate (SDS)-based anionic microemulsions with different oils and a nonionic microemulsion based on Tween 20 as the surfactant and toluene as the oil phase. All the microemulsions were fully dilutable with water. We found that the change in the slope of chemical shift against dilution reflects phase transition points of the microemulsion (O/W, bicontinuous, W/O). Chemical shift changes were clearly observed with the transition between spherical and non-spherical (wormlike, etc.) droplet shapes. We compared the interaction of cyclohexane and toluene and used the anisotropic effect of toluene's ring current to determine its preferred orientation relative to SDS. Chemical shifts of the microemulsion components are therefore a useful addition to the arsenal of techniques for characterizing microemulsions.

  4. Space Station Simulation Computer System (SCS) study for NASA/MSFC. Volume 1: Baseline architecture report

    NASA Technical Reports Server (NTRS)

    1990-01-01

    NASA's Space Station Freedom Program (SSFP) planning efforts have identified a need for a payload training simulator system to serve as both a training facility and as a demonstrator to validate operational concepts. The envisioned MSFC Payload Training Complex (PTC) required to meet this need will train the Space Station payload scientists, station scientists, and ground controllers to operate the wide variety of experiments that will be onboard the Space Station Freedom. The Simulation Computer System (SCS) is made up of the computer hardware, software, and workstations that will support the Payload Training Complex at MSFC. The purpose of this SCS Study is to investigate issues related to the SCS, alternative requirements, simulator approaches, and state-of-the-art technologies to develop candidate concepts and designs.

  5. Space Station Simulation Computer System (SCS) study for NASA/MSFC. Operations concept report

    NASA Technical Reports Server (NTRS)

    1990-01-01

    NASA's Space Station Freedom Program (SSFP) planning efforts have identified a need for a payload training simulator system to serve as both a training facility and as a demonstrator to validate operational concepts. The envisioned MSFC Payload Training Complex (PTC) required to meet this need will train the Space Station payload scientists, station scientists, and ground controllers to operate the wide variety of experiments that will be onboard the Space Station Freedom. The Simulation Computer System (SCS) is made up of computer hardware, software, and workstations that will support the Payload Training Complex at MSFC. The purpose of this SCS Study is to investigate issues related to the SCS, alternative requirements, simulator approaches, and state-of-the-art technologies to develop candidate concepts and designs.

  6. Space Station Simulation Computer System (SCS) study for NASA/MSFC. Volume 2: Baseline architecture report

    NASA Technical Reports Server (NTRS)

    1990-01-01

    NASA's Space Station Freedom Program (SSFP) planning efforts have identified a need for a payload training simulator system to serve as both a training facility and as a demonstrator to validate operational concepts. The envisioned MSFC Payload Training Complex (PTC) required to meet this need will train the Space Station payload scientists, station scientists, and ground controllers to operate the wide variety of experiments that will be onboard the Space Station Freedom. The Simulation Computer System (SCS) is the computer hardware, software, and workstations that will support the Payload Training Complex at MSFC. The purpose of this SCS Study is to investigate issues related to the SCS, alternative requirements, simulator approaches, and state-of-the-art technologies to develop candidate concepts and designs.

  7. Space Station Simulation Computer System (SCS) study for NASA/MSFC. Phased development plan

    NASA Technical Reports Server (NTRS)

    1990-01-01

    NASA's Space Station Freedom Program (SSFP) planning efforts have identified a need for a payload training simulator system to serve as both a training facility and as a demonstrator to validate operational concepts. The envisioned MSFC Payload Training Complex (PTC) required to meet this need will train the Space Station payload scientists, station scientists and ground controllers to operate the wide variety of experiments that will be onboard the Space Station Freedom. The Simulation Computer System (SCS) is made up of computer hardware, software, and workstations that will support the Payload Training Complex at MSFC. The purpose of this SCS Study is to investigate issues related to the SCS, alternative requirements, simulator approaches, and state-of-the-art technologies to develop candidate concepts and designs.

  8. Determination of individual side-chain conformations, tertiary conformations, and molecular topography of tyrocidine A from scalar coupling constants and chemical shifts.

    PubMed

    Kuo, M C; Gibbons, W A

    1979-12-25

    We report for the decapeptide tyrocidine A: (a) H alpha and H beta chemical shifts and scalar coupling constants for most residues of tyrocidine A in methanol-d4 and dimethyl-d6 sulfoxide (Me2so-d6) and the H alpha and H beta chemical shifts for other residues; (b) scalar coupling constants 3J alpha beta for nine side chains in methanol-d4 but only seven side chains in Me2SO-d6, due to chemical shift degeneracy; the Gln9 and Tyr10 side chains in methanol-d4 were only approximately analyzed; (c) a total spin-spin analysis of Pro5 in Me2SO-d6 and, partly by comparison, also in methanol-d4; (d) conversion of 3J alpha beta values to side-chain conformations for all residues in methanol-d4; comparisons, where possible, led to the conclusion that side-chain conformations are similar in methanol-d4 and Me2SO-d6; (e) an absolute conformational analysis of Pro5 from 3J values and a method of assigning all pro-R,S protons; Pro5 has a Ramachandran B, C2-Cexo-Cendo conformation; (f) chi 1, chi 2 conformations of several aromatic residues based upon proton-chromophore distance measurement from anomalous chemical shifts and Johnson-Bovey diagrams; (g) pro-R and pro-S assignments of H beta's from anomalous chemical shifts, high-temperature dependence of anomalous chemical shifts, and backbone side-chain nuclear Overhauser effects; (h) most tertiary conformations of the whole tyrocidine A molecule possessing residues 4--8 and 10 in highly preferred (ca. 90%) chi 1 conformations, but residues 1--3 and 9 having at least two chi 1 rotamers; (2) description of three topographical regions of the molecule--a hydrophobic region, a flat hydrophilic surface on the other side of the molecule, and a hydrophilic region consisting of two peptide backbone units and the side chains of Asn8, Gln9, and Tyr10; (j) proposed side chain, beta-turn, and beta-pleated sheet conformations that readily account for all "normal" and anomalous chemical shifts.

  9. Fully adiabatic 31P 2D-CSI with reduced chemical shift displacement error at 7 T--GOIA-1D-ISIS/2D-CSI.

    PubMed

    Chmelík, M; Kukurová, I Just; Gruber, S; Krššák, M; Valkovič, L; Trattnig, S; Bogner, W

    2013-05-01

    A fully adiabatic phosphorus (31P) two-dimensional (2D) chemical shift spectroscopic imaging sequence with reduced chemical shift displacement error for 7 T, based on 1D-image-selected in vivo spectroscopy, combined with 2D-chemical shift spectroscopic imaging selection, was developed. Slice-selective excitation was achieved by a spatially selective broadband GOIA-W(16,4) inversion pulse with an interleaved subtraction scheme before nonselective adiabatic excitation, and followed by 2D phase encoding. The use of GOIA-W(16,4) pulses (bandwidth 4.3-21.6 kHz for 10-50 mm slices) reduced the chemical shift displacement error in the slice direction ∼1.5-7.7 fold, compared to conventional 2D-chemical shift spectroscopic imaging with Sinc3 selective pulses (2.8 kHz). This reduction was experimentally demonstrated with measurements of an MR spectroscopy localization phantom and with experimental evaluation of pulse profiles. In vivo experiments in clinically acceptable measurement times were demonstrated in the calf muscle (nominal voxel volume, 5.65 ml in 6 min 53 s), brain (10 ml, 6 min 32 s), and liver (8.33 ml, 8 min 14 s) of healthy volunteers at 7 T. High reproducibility was found in the calf muscle at 7 T. In combination with adiabatic excitation, this sequence is insensitive to the B1 inhomogeneities associated with surface coils. This sequence, which is termed GOIA-1D-ISIS/2D-CSI (goISICS), has the potential to be applied in both clinical research and in the clinical routine.

  10. Space Station Simulation Computer System (SCS) study for NASA/MSFC. Concept document

    NASA Technical Reports Server (NTRS)

    1990-01-01

    NASA's Space Station Freedom Program (SSFP) planning efforts have identified a need for a payload training simulator system to serve as both a training facility and as a demonstrator to validate operational concepts. The envisioned MSFC Payload Training Complex (PTC) required to meet this need will train the Space Station Payload of experiments that will be onboard the Space Station Freedom. The simulation will support the Payload Training Complex at MSFC. The purpose of this SCS Study is to investigate issues related to the SCS, alternative requirements, simulator approaches, and state-of-the-art technologies to develop candidate concepts and designs.

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

    PubMed

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

    2011-06-09

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

  12. Space station Simulation Computer System (SCS) study for NASA/MSFC. Volume 4: Conceptual design report

    NASA Technical Reports Server (NTRS)

    1989-01-01

    The Simulation Computer System (SCS) is the computer hardware, software, and workstations that will support the Payload Training Complex (PTC) at Marshall Space Flight Center (MSFC). The PTC will train the space station payload scientists, station scientists, and ground controllers to operate the wide variety of experiments that will be onboard the Space Station Freedom. In the first step of this task, a methodology was developed to ensure that all relevant design dimensions were addressed, and that all feasible designs could be considered. The development effort yielded the following method for generating and comparing designs in task 4: (1) Extract SCS system requirements (functions) from the system specification; (2) Develop design evaluation criteria; (3) Identify system architectural dimensions relevant to SCS system designs; (4) Develop conceptual designs based on the system requirements and architectural dimensions identified in step 1 and step 3 above; (5) Evaluate the designs with respect to the design evaluation criteria developed in step 2 above. The results of the method detailed in the above 5 steps are discussed. The results of the task 4 work provide the set of designs which two or three candidate designs are to be selected by MSFC as input to task 5-refine SCS conceptual designs. The designs selected for refinement will be developed to a lower level of detail, and further analyses will be done to begin to determine the size and speed of the components required to implement these designs.

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

    PubMed

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

    2016-01-01

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

  14. NMR-based structural modeling of graphite oxide using multidimensional 13C solid-state NMR and ab initio chemical shift calculations.

    PubMed

    Casabianca, Leah B; Shaibat, Medhat A; Cai, Weiwei W; Park, Sungjin; Piner, Richard; Ruoff, Rodney S; Ishii, Yoshitaka

    2010-04-28

    Chemically modified graphenes and other graphite-based materials have attracted growing interest for their unique potential as lightweight electronic and structural nanomaterials. It is an important challenge to construct structural models of noncrystalline graphite-based materials on the basis of NMR or other spectroscopic data. To address this challenge, a solid-state NMR (SSNMR)-based structural modeling approach is presented on graphite oxide (GO), which is a prominent precursor and interesting benchmark system of modified graphene. An experimental 2D (13)C double-quantum/single-quantum correlation SSNMR spectrum of (13)C-labeled GO was compared with spectra simulated for different structural models using ab initio geometry optimization and chemical shift calculations. The results show that the spectral features of the GO sample are best reproduced by a geometry-optimized structural model that is based on the Lerf-Klinowski model (Lerf, A. et al. Phys. Chem. B 1998, 102, 4477); this model is composed of interconnected sp(2), 1,2-epoxide, and COH carbons. This study also convincingly excludes the possibility of other previously proposed models, including the highly oxidized structures involving 1,3-epoxide carbons (Szabo, I. et al. Chem. Mater. 2006, 18, 2740). (13)C chemical shift anisotropy (CSA) patterns measured by a 2D (13)C CSA/isotropic shift correlation SSNMR were well reproduced by the chemical shift tensor obtained by the ab initio calculation for the former model. The approach presented here is likely to be applicable to other chemically modified graphenes and graphite-based systems.

  15. Imaging Mantle Discontinuities Beneath North America Using ScS Reverberations

    NASA Astrophysics Data System (ADS)

    Griebel, K. A.; Schmerr, N. C.; Courtier, A. M.; Lekic, V.

    2015-12-01

    Seismic discontinuities are rapid changes in velocity and density over depth that arise from mechanisms such as changes in mineralogy, major element composition, melt content, volatile abundance, anisotropy, or a combination of the above. Seismic imaging of discontinuities complements information provided by seismic tomography and is important for understanding the dynamics and the structure of the mantle. For example, imaging variations in the depth and sharpness of discontinuities can trace underlying variations in temperature and composition in the mantle. We use ScSScS precursors and ScS postcursors (ScS reverberations) to map the depth and sharpness of upper- and mid- mantle discontinuities beneath North America. To observe the reverberations, we collected broadband data recordings of earthquakes with depth > 300 km, source moment magnitude ≥ 5.5, and location < 60 degrees of EarthScope USArray stations. Two primary source regions met our qualifications: earthquakes from the subduction of the Nazca plate beneath South America, and earthquakes from the subduction of the Pacific plate beneath the Sea of Okhotsk. Our dataset consists of ~15 deep focus earthquakes that have well defined ScS and ScSScS arrivals. We use array processing to generate vespagrams for detecting the ScS reverberations. Seismic energy falling at the appropriate slowness and travel time for reflections from upper- and mid- mantle discontinuities is migrated to depth. We use the resulting ScS reverberation derived reflectivity profiles to obtain estimates for discontinuity depth and impedance contrast in the regions falling between the source and array. We can use this information to image parts of the mantle under North America. Preliminary results indicate presence of multiple discontinuities in the upper mantle, including the 410 km discontinuity, a complex 660 km discontinuity, and intermittent mid-mantle discontinuities at 800-900 km depth.

  16. Beyond the SCS-CN method: A theoretical framework for spatially lumped rainfall-runoff response

    NASA Astrophysics Data System (ADS)

    Bartlett, M. S.; Parolari, A. J.; McDonnell, J. J.; Porporato, A.

    2016-06-01

    Since its introduction in 1954, the Soil Conservation Service curve number (SCS-CN) method has become the standard tool, in practice, for estimating an event-based rainfall-runoff response. However, because of its empirical origins, the SCS-CN method is restricted to certain geographic regions and land use types. Moreover, it does not describe the spatial variability of runoff. To move beyond these limitations, we present a new theoretical framework for spatially lumped, event-based rainfall-runoff modeling. In this framework, we describe the spatially lumped runoff model as a point description of runoff that is upscaled to a watershed area based on probability distributions that are representative of watershed heterogeneities. The framework accommodates different runoff concepts and distributions of heterogeneities, and in doing so, it provides an implicit spatial description of runoff variability. Heterogeneity in storage capacity and soil moisture are the basis for upscaling a point runoff response and linking ecohydrological processes to runoff modeling. For the framework, we consider two different runoff responses for fractions of the watershed area: "prethreshold" and "threshold-excess" runoff. These occur before and after infiltration exceeds a storage capacity threshold. Our application of the framework results in a new model (called SCS-CNx) that extends the SCS-CN method with the prethreshold and threshold-excess runoff mechanisms and an implicit spatial description of runoff. We show proof of concept in four forested watersheds and further that the resulting model may better represent geographic regions and site types that previously have been beyond the scope of the traditional SCS-CN method.

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

    PubMed

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

    2014-04-21

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

  18. 1H NMR spectra of alcohols and diols in chloroform: DFT/GIAO calculation of chemical shifts.

    PubMed

    Lomas, John S

    2014-12-01

    Proton nuclear magnetic resonance (NMR) shifts of aliphatic alcohols in chloroform have been computed on the basis of density functional theory, the solvent being included by the integral-equation-formalism polarisable continuum model of Gaussian 09. Relative energies of all conformers are calculated at the Perdew, Burke and Ernzerhof (PBE)0/6-311+G(d,p) level, and NMR shifts by the gauge-including atomic orbital method with the PBE0/6-311+G(d,p) geometry and the cc-pVTZ basis set. The 208 computed CH proton NMR shifts for 34 alcohols correlate very well with the experimental values, with a gradient of 1.00 ± 0.01 and intercept close to zero; the overall root mean square difference (RMSD) is 0.08 ppm. Shifts for CH protons of diols in chloroform are well correlated with the theoretical values for (isotropic) benzene, with similar gradient and intercept (1.02 ± 0.01, -0.13 ppm), but the overall RMSD is slightly higher, 0.12 ppm. This approach generally gives slightly better results than the CHARGE model of Abraham et al. The shifts of unsaturated alcohols in benzene have been re-examined with Gaussian 09, but the overall fit for CH protons is not improved, and OH proton shifts are worse. Shifts of vinyl protons in alkenols are systematically overestimated, and the correlation of computed shifts against the experimental data for unsaturated alcohols follows a quadratic equation. Splitting the 20 compounds studied into two sets, and applying empirical scaling based on the quadratic for the first set to the second set, gives an RMSD of 0.10 ppm. A multi-standard approach gives a similar result.

  19. Exploiting the phase of NMR signals to carry useful information. Application to the measurement of chemical shifts in aliased 2D spectra.

    PubMed

    Ramírez-Gualito, Karla; Jeannerat, Damien

    2015-11-01

    Taking advantage of the phase of nuclear magnetic resonance (NMR) signals to encode NMR information is not easy because of their low precision and their sensitivity to nearby signals. We nevertheless demonstrated that the phase in indirect dimension of (1) H-(13) C heteronuclear single quantum coherence (HSQC) signals could provide carbon chemical shifts at low, but sufficient precision to resolve the ambiguities of the chemical shifts in aliased spectra. This approach, we called phase-encoding of the aliasing order Na (PHANA), only requires inserting a constant delay during the t1 evolution time to obtain spectra where signals with mixed phases can be decoded at the processing to reconstruct full spectra with a 15-fold increase in resolution.

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

    NASA Astrophysics Data System (ADS)

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

    2012-03-01

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

  1. Quantification of the push-pull Effect in disubstituted alkynes - Application of occupation quotients π*/π and 13C chemical shift differences ΔδCtbnd C

    NASA Astrophysics Data System (ADS)

    Kleinpeter, Erich; Klaumünzer, Ute

    2014-09-01

    Structures, 13C chemical shifts, and the occupation quotients of anti-bonding π* and bonding π orbitals of the Ctbnd C triple bond along a series of push-pull alkynes (p)Xsbnd C6H4sbnd C(O)sbnd Ctbnd Csbnd NHsbnd C6H4sbnd Y(p) (X,Y = H, Me, OMe, NMe2, NO2, COMe, COOMe, F, Cl, Br) were computed at the DFT level (B3LYP/6-311G**) of theory. Both the stereochemistry (cis/trans-isomers) by steric twist and the push-pull character by both 13C chemical shift differences (ΔδCtbnd C) and the occupation quotient (π*Ctbnd C/πCtbnd C) were studied; the latter two parameters can be readily employed to precisely quantify the push-pull effect in alkynes.

  2. Use of chemical shift encoded magnetic resonance imaging (CSE-MRI) for high resolution fat-suppressed imaging of the brachial and lumbosacral plexuses

    PubMed Central

    Grayev, Allison; Reeder, Scott; Hanna, Amgad

    2016-01-01

    Purpose In the era of increasingly complex surgical techniques for peripheral nerve repair, there is a need for high spatial resolution imaging of the neural plexuses in the body. We describe our experience with chemical shift encoded MRI and its implications for patient management. Materials and methods IDEAL water-fat separation is a chemical shift based method of homogeneously suppressing signal from fat, while maintaining adequate signal. This technique was used in clinical practice and the patient images reviewed. Results IDEAL water-fat separation was shown to improve visualization of the brachial and lumbosacral plexuses with good fat suppression and high signal to noise ratio. Conclusion IDEAL water − fat separation is an excellent technique to use in the imaging of the brachial and lumbosacral plexuses as it balances the need for homogeneous fat suppression with maintenance of excellent signal to noise ratio. PMID:27161071

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

    SciTech Connect

    Taylor, J.S.; Vigneron, D.B.; Murphy-Boesch, J.; Nelson, S.J.; Kessler, H.B.; Coia, L.; Curran, W.; Brown, T.R. )

    1991-08-01

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

  4. The covariance of the differences between experimental and theoretical chemical shifts as an aid for assigning two-dimensional heteronuclear correlation solid-state NMR spectra

    NASA Astrophysics Data System (ADS)

    Czernek, Jiří; Brus, Jiří

    2014-07-01

    A robust method for the assignment of two-dimensional heteronuclear correlations in the solid-state NMR spectra is described. It statistically evaluates the differences between measured and theoretical (obtained from first-principles calculations of the NMR chemical shielding property of periodic materials) chemical shifts. The values of the covariance of these differences, and of the standard deviations of the respective linear correlations, are elucidative for the spectral assignment process. The efficacy of the method is demonstrated for three crystalline systems: L-tyrosine hydrochloride, L-tyrosine ansolvate, and the polymorphic form I of o-acetylsalicylic acid.

  5. The RAMANITA method for non-destructive and in situ semi-quantitative chemical analysis of mineral solid-solutions by multidimensional calibration of Raman wavenumber shifts.

    PubMed

    Smith, David C

    2005-08-01

    The "RAMANITA" method, for semi-quantitative chemical analysis of mineral solid-solutions by multidimensional calibration of Raman wavenumber shifts and mathematical calculation by simultaneous equations, is published here in detail in English for the first time. It was conceived by the present writer 20 years ago for binary and ternary pyroxene and garnet systems. The mathematical description was set out in 1989, but in an abstract in an obscure French special publication. Detailed "step-by-step" calibration of two garnet ternaries, followed by their linking, in the early 1990s provided a hexary garnet database. Much later, using this garnet database, which forms part of his personal database called RAMANITA, the present writer began to develop the method by improving the terminology, automating the calculations, discussing problems and experimenting with different real chemical problems in archaeometry. Although this RAMANITA method has been very briefly mentioned in two recent books, the necessary full mathematical explanation is given only here. The method will find application in any study which requires obtaining a non-destructive semi-quantitative chemical analysis from mineral solid solutions that cannot be analysed by any destructive analytical method, in particular for archaeological, geological or extraterrestrial research projects, e.g. Recently some other workers have begun deducing chemical compositions from Raman wavenumber shifts in multivariate chemical space, but the philosophical approach is quite different.

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

    PubMed

    Mananga, Eugene Stephane

    2013-01-01

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

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

    PubMed

    Vícha, Jan; Novotný, Jan; Straka, Michal; Repisky, Michal; Ruud, Kenneth; Komorovsky, Stanislav; Marek, Radek

    2015-10-14

    The role of various factors (structure, solvent, and relativistic treatment) was evaluated for square-planar 4d and 5d transition-metal complexes. The DFT method for calculating the structures was calibrated using a cluster approach and compared to X-ray geometries, with the PBE0 functional (def2-TZVPP basis set) providing the best results, followed closely by the hybrid TPSSH and the MN12SX functionals. Calculations of the NMR chemical shifts using the two-component (2c, Zeroth-Order Regular Approximation as implemented in the ADF package) and four-component (4c, Dirac-Coulomb as implemented in the ReSpect code) relativistic approaches were performed to analyze and demonstrate the importance of solvent corrections (2c) as well as a proper treatment of relativistic effects (4c). The importance of increased exact-exchange admixture in the functional (here PBE0) for reproducing the experimental data using the current implementation of the 2c approach is partly rationalized as a compensation for the missing exchange-correlation response kernel. The kernel contribution was identified to be about 15-20% of the spin-orbit-induced NMR chemical shift, ΔδSO, which roughly corresponds to an increase in ΔδSO introduced by the artificially increased exact-exchange admixture in the functional. Finally, the role of individual effects (geometry, solvent, relativity) in the NMR chemical shift is discussed in selected complexes. Although a fully relativistic DFT approach is still awaiting the implementation of GIAOs for hybrid functionals and an implicit solvent model, it nevertheless provides reliable NMR chemical shift data at an affordable computational cost. It is expected to outperform the 2c approach, in particular for the calculation of NMR parameters in heavy-element compounds.

  8. 1H, 15N, and 13C chemical shift assignments of cyanobacteriochrome NpR6012g4 in the red-absorbing dark state.

    PubMed

    Yu, Qinhong; Lim, Sunghyuk; Rockwell, Nathan C; Martin, Shelley S; Clark Lagarias, J; Ames, James B

    2016-04-01

    Cyanobacteriochrome (CBCR) photosensory proteins are phytochrome homologs using bilin chromophores for light sensing across the visible spectrum. NpR6012g4 is a CBCR from Nostoc punctiforme that serves as a model for a widespread CBCR subfamily with red/green photocycles. We report NMR chemical shift assignments for both the protein backbone and side-chain resonances of the red-absorbing dark state of NpR6012g4 (BMRB no. 26582).

  9. Progress in Spin Dynamics Solid-State Nuclear Magnetic Resonance with the Application of Floquet-Magnus Expansion to Chemical Shift Anisotropy

    PubMed Central

    Mananga, Eugene Stephane

    2013-01-01

    The purpose of this article is to present an historical overview of theoretical approaches used for describing spin dynamics under static or rotating experiments in solid state nuclear magnetic resonance. The article gives a brief historical overview for major theories in nuclear magnetic resonance and the promising theories. We present the first application of Floquet-Magnus expansion to chemical shift anisotropy when irradiated by BABA pulse sequence. PMID:23711337

  10. Design of a hyperpolarized (15)N NMR probe that induces a large chemical-shift change upon binding of calcium ions.

    PubMed

    Hata, Ryunosuke; Nonaka, Hiroshi; Takakusagi, Yoichi; Ichikawa, Kazuhiro; Sando, Shinsuke

    2015-08-07

    Ca(2+) is a fundamental metal ion for physiological functioning. Therefore, molecular probes for Ca(2+) analysis are required. Recently, a hyperpolarized NMR probe has emerged as a promising tool. Here, we report a new design of a hyperpolarized NMR probe for Ca(2+), which showed a large chemical shift change upon binding to Ca(2+) and was applied for Ca(2+) sensing in a hyperpolarized state.

  11. (1)H NMR spectra of alcohols in hydrogen bonding solvents: DFT/GIAO calculations of chemical shifts.

    PubMed

    Lomas, John S

    2016-01-01

    Proton nuclear magnetic resonance (NMR) shifts of aliphatic alcohols in hydrogen bonding solvents have been computed on the basis of density functional theory by applying the gauge-including atomic orbital method to geometry-optimized alcohol/solvent complexes. The OH proton shifts and hydrogen bond distances for methanol or ethanol complexed with pyridine depend very much on the functional employed and very little on the basis set, provided it is sufficiently large to give the correct quasi-linear hydrogen bond geometry. The CH proton shifts are insensitive to both the functional and the basis set. NMR shifts for all protons in several alcohol/pyridine complexes are calculated at the Perdew, Burke and Ernzerhof PBE0/cc-pVTZ//PBE0/6-311 + G(d,p) level in the gas phase. The results correlate with the shifts for the pyridine-complexed alcohols, determined by analysing data from the NMR titration of alcohols against pyridine. More pragmatically, computed shifts for a wider range of alcohols correlate with experimental shifts in neat pyridine. Shifts for alcohols in dimethylsulfoxide, based on the corresponding complexes in the gas phase, correlate well with the experimental values, but the overall root mean square difference is high (0.23 ppm), shifts for the OH, CHOH and other CH protons being systematically overestimated, by averages of 0.42, 0.21 and 0.06 ppm, respectively. If the computed shifts are corrected accordingly, a very good correlation is obtained with a gradient of 1.00 ± 0.01, an intercept of 0.00 ± 0.02 ppm and a root mean square difference of 0.09 ppm. This is a modest improvement on the result of applying the CHARGE programme to a slightly different set of alcohols. Some alcohol complexes with acetone and acetonitrile were investigated both in the gas phase and in a continuum of the relevant solvent.

  12. NMR chemical shifts as a tool to analyze first principles molecular dynamics simulations in condensed phases: the case of liquid water.

    PubMed

    Banyai, Douglas R; Murakhtina, Tatiana; Sebastiani, Daniel

    2010-12-01

    We present (1)H NMR chemical shift calculations of liquid water based on first principles molecular dynamics simulations under periodic boundary conditions. We focus on the impact of computational parameters on the structural and spectroscopic data, which is an important question for understanding how sensitive the computed (1)H NMR resonances are upon variation of the simulation setup. In particular, we discuss the influence of the exchange-correlation functional and the size of the basis set, the choice for the fictitious electronic mass and the use of pseudopotentials for the nuclear magnetic resonance (NMR) calculation on one hand and the underlying Car-Parrinello-type molecular dynamics simulations on the other hand. Our findings show that the direct effect of these parameters on (1)H shifts is not big, whereas the indirect dependence via the structural data is more important. The (1)H NMR chemical shifts clearly reflect the induced structural changes, illustrating once again the sensitivity of (1)H NMR observables on small changes in the local chemical structure of complex hydrogen-bonded liquids.

  13. Chemical shift and diffusion-weighted magnetic resonance imaging of the anterior mediastinum in oncology: Current clinical applications in qualitative and quantitative assessment.

    PubMed

    Priola, Adriano Massimiliano; Gned, Dario; Veltri, Andrea; Priola, Sandro Massimo

    2016-02-01

    Recently, the use of magnetic resonance (MR) in clinical practice for the evaluation of the anterior mediastinum has considerably increased due to technological improvements and standardization of thoracic protocols. Currently, MR imaging is increasingly seen as a useful problem-solving modality, especially in equivocal cases at computed tomography, with the advantage of a higher contrast resolution and no radiation exposure. Chemical shift and diffusion-weighted MR are helpful in tissue characterization and present advantages over conventional MR imaging, first in providing quantitative data, without the need for the administration of contrast medium. By detecting microscopic fat in tissue, chemical shift imaging is useful for differentiating normal thymus and rebound hyperplasia from cancer tissue at diagnosis and after chemotherapy in oncologic patients, and for distinguishing lymphoid hyperplasia from thymoma in autoimmune diseases such as myasthenia gravis. Diffusion-weighted MR reflects diffusivity of water molecules within tissue and is increasingly used as a cancer biomarker, even in the thorax, for the detection and characterization of tumors, for their differentiation from benign conditions, and for monitoring treatment response. In this review, based on the current literature, technical considerations about image acquisition and data analysis of chemical shift and diffusion-weighted MR are discussed along with clinical applications in the field of benign and malignant disease of the anterior mediastinum.

  14. A device for the measurement of residual chemical shift anisotropy and residual dipolar coupling in soluble and membrane-associated proteins

    PubMed Central

    Liu, Yizhou

    2010-01-01

    Residual dipolar coupling (RDC) and residual chemical shift anisotropy (RCSA) report on orientational properties of a dipolar bond vector and a chemical shift anisotropy principal axis system, respectively. They can be highly complementary in the analysis of backbone structure and dynamics in proteins as RCSAs generally include a report on vectors out of a peptide plane while RDCs usually report on in-plane vectors. Both RDC and RCSA average to zero in isotropic solutions and require partial orientation in a magnetic field to become observable. While the alignment and measurement of RDC has become routine, that of RCSA is less common. This is partly due to difficulties in providing a suitable isotopic reference spectrum for the measurement of the small chemical shift offsets coming from RCSA. Here we introduce a device (modified NMR tube) specifically designed for accurate measurement of reference and aligned spectra for RCSA measurements, but with a capacity for RDC measurements as well. Applications to both soluble and membrane anchored proteins are illustrated. PMID:20506033

  15. Effects of dose shift on line width, line edge roughness, and stochastic defect generation in chemically amplified extreme ultraviolet resist with photodecomposable quencher

    NASA Astrophysics Data System (ADS)

    Kozawa, Takahiro

    2015-01-01

    In chemically amplified resists used for high-volume production of semiconductor devices, the control of acid catalytic reaction is essential for fine patterning. A basic compound, called a quencher, plays an important role in the control of acid catalytic reaction. In particular, the photodecomposable quencher is effective for the enhancement of the chemical gradient. In this study, the effects of photodecomposable quenchers on the dose shift (the deviation from the sizing dose) dependences of line width, line edge roughness (LER), and stochastic defect generation were investigated, assuming line-and-space patterns with 11 nm half-pitch. The exposure latitude of line width in a chemically amplified resist with photodecomposable quenchers was larger than that in a chemically amplified resist with conventional non-photodecomposable quenchers at sizing doses >20 mJ cm-2. By using photodecomposable quenchers, LER and the probability of stochastic defect generation were decreased, while the dose shift dependences of LER and stochastic defect generation did not significantly differ, compared with those observed using conventional non-photodecomposable quenchers.

  16. Calculation of the {sup 13}C NMR chemical shift of ether linkages in lignin derived geopolymers: Constraints on the preservation of lignin primary structure with diagenesis

    SciTech Connect

    Cody, G.D.; Saghi-Szabo, G.

    1999-01-01

    Methodology for the calculation of {sup 13}C NMR shielding on molecular organic fragments, representative of monomers in a type 3 kerogen, is presented. Geometry optimization of each molecular fragment was carried out using Density Functional Theory employing the generalized gradient approximation. NMR shieldings were calculated using the Individual Gauge for Localized orbital Method. Convincing agreement was obtained between calculated and experimentally derived isotropic chemical shielding values over a broad frequency range. Shielding calculations employing the localized orbitals/local origin method resulted in nearly identical results. NMR chemical shift static powder patterns also exhibit excellent agreement with experimental values. These quantum mechanical calculations were applied to determine the extent of lignin primary structure preservation with diagenesis. Specifically, the calculations were used to assess whether inhomogeneous spectral broadening due to both functional group variation and local configurational variability may inhibit the detection of otherwise significant quantities of alkyl-aryl ethers in lignin derived geopolymers. Determination of the chemical-shielding tensor principle axis values reveals a strong correlation between anisotropy and asymmetry with local configuration effects such as dihedral rotation, phenyl group rotation, and bond angle variation. These results indicate that a range of 9 ppm in the isotropic chemical shift can be ascribed to local configuration. Consequently, an upper limit of 5% alkyl-aryl-linkages may go undetected using NMR spectroscopy on lignin-derived geopolymers at the liginite-sub-bituminous transition. It is concluded that the primary structure of lignin does not persist in kerogens even at relatively low thermal maturities.

  17. Calculation of the 13C NMR chemical shift of ether linkages in lignin derived geopolymers: . Constraints on the preservation of lignin primary structure with diagenesis

    NASA Astrophysics Data System (ADS)

    Cody, G. D.; Sághi-Szabó, G.

    1999-01-01

    Methodology for the calculation of 13C NMR shieldings on molecular organic fragments, representative of monomers in a type III kerogen, is presented. Geometry optimization of each molecular fragment was carried out using Density Functional Theory employing the generalized gradient approximation. NMR shieldings were calculated using the Individual Gauge for Localized Orbital Method. Convincing agreement was obtained between calculated and experimentally derived isotropic chemical shielding values over a broad frequency range. Shielding calculations employing the localized orbitals/local origin method resulted in nearly identical results. NMR chemical shift static powder patterns also exhibit excellent agreement with experimental values. These quantum mechanical calculations were applied to determine the extent of lignin primary structure preservation with diagenesis. Specifically, the calculations were used to assess whether inhomogeneous spectral broadening due to both functional group variation and local configurational variability may inhibit the detection of otherwise significant quantities of alkyl-aryl ethers in lignin derived geopolymers. Determination of the chemical-shielding tensor principle axis values reveals a strong correlation between anisotropy and asymmetry with local configuration effects such as dihedral rotation, phenyl group rotation, and bond angle variation. These results indicate that a range of 9 ppm in the isotropic chemical shift can be ascribed to local configuration. Consequently, an upper limit of 5% alkyl-aryl-linkages may go undetected using NMR spectroscopy on lignin-derived geopolymers at the liginite-sub-bituminous transition. It is concluded that the primary structure of lignin does not persist in kerogens even at relatively low thermal maturities.

  18. SCS macrophages suppress melanoma by restricting tumor-derived vesicle-B cell interactions.

    PubMed

    Pucci, Ferdinando; Garris, Christopher; Lai, Charles P; Newton, Andita; Pfirschke, Christina; Engblom, Camilla; Alvarez, David; Sprachman, Melissa; Evavold, Charles; Magnuson, Angela; von Andrian, Ulrich H; Glatz, Katharina; Breakefield, Xandra O; Mempel, Thorsten R; Weissleder, Ralph; Pittet, Mikael J

    2016-04-08

    Tumor-derived extracellular vesicles (tEVs) are important signals in tumor-host cell communication, yet it remains unclear how endogenously produced tEVs affect the host in different areas of the body. We combined imaging and genetic analysis to track melanoma-derived vesicles at organismal, cellular, and molecular scales to show that endogenous tEVs efficiently disseminate via lymphatics and preferentially bind subcapsular sinus (SCS) CD169(+) macrophages in tumor-draining lymph nodes (tdLNs) in mice and humans. The CD169(+) macrophage layer physically blocks tEV dissemination but is undermined during tumor progression and by therapeutic agents. A disrupted SCS macrophage barrier enables tEVs to enter the lymph node cortex, interact with B cells, and foster tumor-promoting humoral immunity. Thus, CD169(+) macrophages may act as tumor suppressors by containing tEV spread and ensuing cancer-enhancing immunity.

  19. A Relativistic Quantum-Chemical Analysis of the trans Influence on (1)H NMR Hydride Shifts in Square-Planar Platinum(II) Complexes.

    PubMed

    Greif, Anja H; Hrobárik, Peter; Hrobáriková, Veronika; Arbuznikov, Alexei V; Autschbach, Jochen; Kaupp, Martin

    2015-08-03

    Empirical correlations between characteristic (1)H NMR shifts in Pt(II) hydrides with trans ligand influence series, Pt-H distances, and (195)Pt shifts are analyzed at various levels of including relativistic effects into density-functional calculations. A close examination of the trans ligand effects on hydride NMR shifts is shown to be dominated by spin-orbit shielding σ(SO). A rather complete understanding of the trends has been obtained by detailed molecular orbital (MO)-by-MO and localized MO analyses of the paramagnetic and spin-orbit (SO) contributions to the chemical shifts, noting that it is the perpendicular shift-tensor components that determine the trend of the (1)H hydride shifts. In contrast to previous assumptions, the change of the Pt-H distance in given complexes does not allow correlations between hydride shifts and metal-hydrogen bond length to be understood. Instead, variations in the polarization of metal 5d orbitals by the trans ligand affects the SO (and partly paramagnetic) shift contributions, as well as the Pt-H distances and the covalency of the metal-hydrogen bond (quantified, e.g., by natural atomic charges and delocalization indices from quantum theory atoms-in-molecules), resulting in a reasonable correlation of these structural/electronic quantities with hydride σ(SO) shieldings. Our analysis also shows that specific σ(p)- and σ(SO)-active MOs are not equally important across the entire series. This explains some outliers in the correlation for limited ranges of trans-influence ligands. Additionally, SO effects from heavy-halide ligands may further complicate trends, indicating some limitations of the simple one-parameter correlations. Strikingly, σ-donating/π-accepting ligands with a very strong trans influence are shown to invert the sign of the usually shielding σ(SO) contribution to the (1)H shifts, by a substantial reduction of the metal 5d orbital involvement in Pt-H bonding, and by involvement of metal 6p-type orbitals

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

    PubMed

    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.

  1. U.S.-Vietnamese Security Cooperation for Access to the SCS

    DTIC Science & Technology

    2015-06-16

    of the claimants to islands in the SCS, China has more Coast Guard/MLE vessels than Japan, Indonesia , Malaysia, and the Philippines combined.7...economic collapse of the 1980s and fall of the Soviet Union. Vietnam’s leadership revamped its socialist market economy and enacted reforms in order...previously contested Paracel Islands). China sent approximately 80 vessels to escort the rig, including navy, MLE (Coast Guard), and fishing boats

  2. Space station Simulation Computer System (SCS) study for NASA/MSFC. Volume 1: Overview and summary

    NASA Technical Reports Server (NTRS)

    1989-01-01

    NASA's Space Station Freedom Program (SSFP) planning efforts have identified a need for a payload training simulator system to serve as both a training facility and as a demonstrator to validate operational concepts. The envisioned Marshall Space Flight Center (MSFC) Payload Training Complex (PTC) required to meet this need will train the space station payload scientists, station scientists, and ground controllers to operate the wide variety of experiments that will be onboard the Space Station Freedom. The Simulation Computer System (SCS) is the computer hardware, software, and workstations that will support the Payload Training Complex at MSFC. The purpose of this SCS study is to investigate issues related to the SCS, alternative requirements, simulator approaches, and state-of-the-art technologies to develop candidate concepts and designs. This study was performed August 1988 to October 1989. Thus, the results are based on the SSFP August 1989 baseline, i.e., pre-Langley configuration/budget review (C/BR) baseline. Some terms, e.g., combined trainer, are being redefined. An overview of the study activities and a summary of study results are given here.

  3. An Alternative Scheme for 13C Chemical-Shift Imaging via Inverse Detection of Protons through an MILS (or Inverse SLIM) Technique

    PubMed

    Lee; Tzou; Chiou; Yeung

    1998-01-01

    An alternative scheme in acquiring 13C spectroscopic images using inverse detection via polarization transfer through protons was proposed and experimentally verified by a phantom using a heteronuclear multiple-quantum coherence technique. This scheme has some features that, in special circumstances, can be exploited to one's advantages. These features are: (1) signal enhancement, a feat realizable under favorable conditions; (2) spectroscopic encoding via constant time; and (3) improvement of the time efficiency of the constant-time method via optimization by singular-value decomposition analysis. Features (1) and (2) can, in some cases, yield better sensitivity than the conventional 3DFT technique without sacrificing the most important attribute of 13C, the enormity of the chemical shifts. Such is the case because spectroscopic images acquired by the technique proposed are based on the chemical shifts of carbon, in contrast to the other more prevalent inverse-detection schemes. Feature (2) can also offer higher spatial resolution by shifting the emphasis of signal encoding from a spectral-resolution-first viewpoint to one that favors spatial resolution. Feature (3) was adopted from a method previously known as MILS (metabolite imaging of lines in a spectrum), or the inverse of SLIM, an economical scheme originally proposed by Hu et al. (1988, Magn. Reson. Med. 8, 314) for obtaining a compartmentalized NMR spectrum. Copyright 1998 Academic Press. Copyright 1998 Academic Press

  4. Hydrogen bonding between acetate-based ionic liquids and water: Three types of IR absorption peaks and NMR chemical shifts change upon dilution

    NASA Astrophysics Data System (ADS)

    Chen, Yu; Cao, Yuanyuan; Zhang, Yuwei; Mu, Tiancheng

    2014-01-01

    The hydrogen-bonding interaction between acetate-based ionic liquids (AcIL) and water was investigated by attenuated total reflection infrared (ATR-IR) and 1H NMR. Interestingly, the relative change of chemical shift δ of 1H NMR upon dilution could be divided into three regions. All the H show an upfield shift in Regions 1 and 2 while a different tendency in Region 3 (upfield, no, and downfield shift classified as Types 1, 2, 3, respectively). For ATR-IR, the red, no, or blue shift of νOD (IR absorption peak of OD in D2O) and ν± (IR absorption peak of AcILs) also have three types, respectively. Two-Times Explosion Mechanism (TTEM) was proposed to interpret the dynamic processes of AcILs upon dilution macroscopically, meanwhile an Inferior Spring Model (ISM) was proposed to help to understand the TTEM microscopically, All those indicate that AcILs present the state of network, sub-network, cluster, sub-cluster, ion pairs and sub-ion pairs in sequence upon dilution by water and the elongation of hydrogen bonding between AcILs-water, between cation-anion of AcILs is plastic deformation rather than elastic deformation.

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

    NASA Technical Reports Server (NTRS)

    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.

  6. Hydrogen Atomic Positions of O-H···O Hydrogen Bonds in Solution and in the Solid State: The Synergy of Quantum Chemical Calculations with ¹H-NMR Chemical Shifts and X-ray Diffraction Methods.

    PubMed

    Siskos, Michael G; Choudhary, M Iqbal; Gerothanassis, Ioannis P

    2017-03-07

    The exact knowledge of hydrogen atomic positions of O-H···O hydrogen bonds in solution and in the solid state has been a major challenge in structural and physical organic chemistry. The objective of this review article is to summarize recent developments in the refinement of labile hydrogen positions with the use of: (i) density functional theory (DFT) calculations after a structure has been determined by X-ray from single crystals or from powders; (ii) ¹H-NMR chemical shifts as constraints in DFT calculations, and (iii) use of root-mean-square deviation between experimentally determined and DFT calculated ¹H-NMR chemical shifts considering the great sensitivity of ¹H-NMR shielding to hydrogen bonding properties.

  7. Shift of optical absorption edge in SnO2 films with high concentrations of nitrogen grown by chemical vapor deposition

    NASA Astrophysics Data System (ADS)

    Jiang, Jie; Lu, Yinmei; Meyer, Bruno K.; Hofmann, Detlev M.; Eickhoff, Martin

    2016-06-01

    The optical and electrical properties of n-type SnO2 films with high concentrations of nitrogen (SnO2:N) grown by chemical vapor deposition are studied. The carrier concentration increases from 4.1 × 1018 to 3.9 × 1019 cm-3 and the absorption edge shifts from 4.26 to 4.08 eV with increasing NH3 flow rate. Typical Urbach tails were observed from the absorption spectra and the Urbach energy increases from 0.321 to 0.526 eV with increasing NH3 flow rate. An "effective" absorption edge of about 4.61 eV was obtained for all investigated samples from fitting the extrapolations of the Urbach tails. Burstein-Moss effect, electron-impurity, and electron-electron interactions are shown to play a minor role for the shift of the absorption edges in SnO2:N thin films.

  8. The HSP90 binding mode of a radicicol-like E-oxime from docking, binding free energy estimations, and NMR 15N chemical shifts

    PubMed Central

    Spichty, Martin; Taly, Antoine; Hagn, Franz; Kessler, Horst; Barluenga, Sofia; Winssinger, Nicolas; Karplus, Martin

    2009-01-01

    We determine the binding mode of a macrocyclic radicicol-like oxime to yeast HSP90 by combining computer simulations and experimental measurements. We sample the macrocyclic scaffold of the unbound ligand by parallel tempering simulations and dock the most populated conformations to yeast HSP90. Docking poses are then evaluated by the use of binding free energy estimations with the linear interaction energy method. Comparison of QM/MM-calculated NMR chemical shifts with experimental shift data for a selective subset of back-bone 15N provides an additional evaluation criteria. As a last test we check the binding modes against available structure-activity-relationships. We find that the most likely binding mode of the oxime to yeast HSP90 is very similar to the known structure of the radicicol-HSP90 complex. PMID:19482409

  9. The RAMANITA © method for non-destructive and in situ semi-quantitative chemical analysis of mineral solid-solutions by multidimensional calibration of Raman wavenumber shifts

    NASA Astrophysics Data System (ADS)

    Smith, David C.

    2005-08-01

    The "RAMANITA ©" method, for semi-quantitative chemical analysis of mineral solid-solutions by multidimensional calibration of Raman wavenumber shifts and mathematical calculation by simultaneous equations, is published here in detail in English for the first time. It was conceived by the present writer 20 years ago for binary and ternary pyroxene and garnet systems. The mathematical description was set out in 1989, but in an abstract in an obscure French special publication. Detailed "step-by-step" calibration of two garnet ternaries, followed by their linking, by M. Pinet and D.C. Smith in the early 1990s provided a hexary garnet database. Much later, using this garnet database, which forms part of his personal database called RAMANITA ©, the present writer began to develop the method by improving the terminology, automating the calculations, discussing problems and experimenting with different real chemical problems in archaeometry. Although this RAMANITA © method has been very briefly mentioned in two recent books, the necessary full mathematical explanation is given only here. The method will find application in any study which requires obtaining a non-destructive semi-quantitative chemical analysis from mineral solid solutions that cannot be analysed by any destructive analytical method, in particular for archaeological, geological or extraterrestrial research projects, e.g. from gemstones or other crystalline artworks of the cultural heritage (especially by Mobile Raman Microscopy (MRM)) in situ in museums or at archaeological sites, including under water for subaquatic archaeometry; from scientifically precious mineral microinclusions (such as garnet or pyroxene within diamond); from minerals in rocks analysed in situ on planetary bodies by a rover (especially "at distance" by telescopy). Recently some other workers have begun deducing chemical compositions from Raman wavenumber shifts in multivariate chemical space, but the philosophical approach is

  10. 1H and 13C NMR Chemical Shift Assignments and Conformational Analysis for the Two Diastereomers of the Vitamin K Epoxide Reductase Inhibitor Brodifacoum

    SciTech Connect

    Cort, John R.; Cho, Herman M.

    2009-10-01

    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.

  11. The Saccharomyces cerevisiae suppressor of choline sensitivity (SCS2) gene is a multicopy Suppressor of mec1 telomeric silencing defects.

    PubMed Central

    Craven, R J; Petes, T D

    2001-01-01

    Mec1p is a cell cycle checkpoint protein related to the ATM protein kinase family. Certain mec1 mutations or overexpression of Mec1p lead to shortened telomeres and loss of telomeric silencing. We conducted a multicopy suppressor screen for genes that suppress the loss of silencing in strains overexpressing Mec1p. We identified SCS2 (suppressor of choline sensitivity), a gene previously isolated as a suppressor of defects in inositol synthesis. Deletion of SCS2 resulted in decreased telomeric silencing, and the scs2 mutation increased the rate of cellular senescence observed for mec1-21 tel1 double mutant cells. Genetic analysis revealed that Scs2p probably acts through a different telomeric silencing pathway from that affected by Mec1p. PMID:11333225

  12. Structural and Functional Characterization of ScsC, a Periplasmic Thioredoxin-Like Protein from Salmonella enterica Serovar Typhimurium

    PubMed Central

    Shepherd, Mark; Heras, Begoña; Achard, Maud E. S.; King, Gordon J.; Argente, M. Pilar; Kurth, Fabian; Taylor, Samantha L.; Howard, Mark J.; King, Nathan P.

    2013-01-01

    Abstract Aims: The prototypical protein disulfide bond (Dsb) formation and protein refolding pathways in the bacterial periplasm involving Dsb proteins have been most comprehensively defined in Escherichia coli. However, genomic analysis has revealed several distinct Dsb-like systems in bacteria, including the pathogen Salmonella enterica serovar Typhimurium. This includes the scsABCD locus, which encodes a system that has been shown via genetic analysis to confer copper tolerance, but whose biochemical properties at the protein level are not defined. The aim of this study was to provide functional insights into the soluble ScsC protein through structural, biochemical, and genetic analyses. Results: Here we describe the structural and biochemical characterization of ScsC, the soluble DsbA-like component of this system. Our crystal structure of ScsC reveals a similar overall fold to DsbA, although the topology of β-sheets and α-helices in the thioredoxin domains differ. The midpoint reduction potential of the CXXC active site in ScsC was determined to be −132 mV versus normal hydrogen electrode. The reactive site cysteine has a low pKa, typical of the nucleophilic cysteines found in DsbA-like proteins. Deletion of scsC from S. Typhimurium elicits sensitivity to copper (II) ions, suggesting a potential involvement for ScsC in disulfide folding under conditions of copper stress. Innovation and Conclusion: ScsC is a novel disulfide oxidoreductase involved in protection against copper ion toxicity. Antioxid. Redox Signal. 19, 1494–1506. PMID:23642141

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

    PubMed

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

    2016-01-01

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

  14. Solvatochromic shift of donor-acceptor substituted bithiophene in solvents of different polarity: quantum chemical and molecular dynamics simulations.

    PubMed

    Meng, Suci; Ma, Jing

    2008-04-10

    The dependence of excitation energies of the solvatochromic dye, 5-dimethylamino-5'-nitro-2,2'-bithiophene (Me(2)N-2T-NO(2)) on the solvent polarity is demonstrated by time-dependent density functional theory (TD-DFT) calculations in combination with molecular dynamics (MD) simulations. Three kinds of solvation models, namely, the continuum dielectric model, the discrete approach, and the combined discrete/continuum strategy, are employed to calculate the lowest dipole-allowed excitation energies of Me(2)N-2T-NO(2) in seven solvents with the dielectric constant, epsilon, ranging from 2.23 to 111.00. Our calculations demonstrate the limitations of the continuum dielectric model in predicting the solvatochromic shift of Me(2)N-2T-NO(2) in very polar solvents with epsilon > 35. The accuracy of the explicit solvent model is largely limited by the size of supermolecular cluster. The combined discrete/continuum solvent model gives a satisfactory description of the bathochromic shift of Me(2)N-2T-NO(2) with increasing solvent polarity, in agreement with the experimental observations.

  15. Validation of SCS CN Method for Runoff Estimation with Field Observed Regression Analysis Results in Venna Basin, Central India.

    NASA Astrophysics Data System (ADS)

    Katpatal, Y. B.; Paranjpe, S. V.; Kadu, M.

    2014-12-01

    Effective Watershed management requires authentic data of surface runoff potential for which several methods and models are in use. Generally, non availability of field data calls for techniques based on remote observations. Soil Conservation Services Curve Number (SCS CN) method is an important method which utilizes information generated from remote sensing for estimation of runoff. Several attempts have been made to validate the runoff values generated from SCS CN method by comparing the results obtained from other methods. In the present study, runoff estimation through SCS CN method has been performed using IRS LISS IV data for the Venna Basin situated in the Central India. The field data was available for Venna Basin. The Land use/land cover and soil layers have been generated for the entire watershed using the satellite data and Geographic Information System (GIS). The Venna basin have been divided into intercepted catchment and free catchment. Run off values have been estimated using field data through regression analysis. The runoff values estimated using SCS CN method have been compared with yield values generated using data collected from the tank gauge stations and data from the discharge stations. The correlation helps in validation of the results obtained from the SCS CN method and its applicability in Indian conditions. Key Words: SCS CN Method, Regression Analysis, Land Use / Land cover, Runoff, Remote Sensing, GIS.

  16. The yeast VAP homolog Scs2p has a phosphoinositide-binding ability that is correlated with its activity

    SciTech Connect

    Kagiwada, Satoshi Hashimoto, Misa

    2007-12-28

    The yeast VAMP-associated protein (VAP) homolog Scs2p is an endoplasmic reticulum (ER)/nuclear membrane protein that binds to an FFAT (diphenylalanine in an acidic tract) motif found in various lipid-metabolic proteins, including Opi1p, a negative regulator of phospholipid biosynthesis. Here, we show that Scs2p is a novel phosphoinositide-binding protein that can bind to phosphatidylinositol monophosphates and bisphosphates in vitro. The phosphoinositide-binding domain was assigned to the N-terminal major sperm protein (MSP) domain which also contains the FFAT-binding domain. When several lysine residues in the MSP domain were substituted for alanine, the resulting mutant Scs2 proteins lost the phosphoinositide-binding ability and failed to complement the inositol auxotrophy of an scs2 deletion strain. However, the mutant proteins still localized in the ER/nuclear membrane, in a similar manner to wild-type Scs2p. These results suggest the possibility that Scs2p activity is regulated by phosphoinositides to coordinate phospholipid biosynthesis in response to changes in phospholipid composition.

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

    PubMed

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

    1994-01-01

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

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

    PubMed

    Goudarzi, Nasser

    2016-04-05

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

  19. Triosephosphate isomerase: 15N and 13C chemical shift assignments and conformational change upon ligand binding by magic-angle spinning solid-state NMR spectroscopy.

    PubMed

    Xu, Yimin; Lorieau, Justin; McDermott, Ann E

    2010-03-19

    Microcrystalline uniformly (13)C,(15)N-enriched yeast triosephosphate isomerase (TIM) is sequentially assigned by high-resolution solid-state NMR (SSNMR). Assignments are based on intraresidue and interresidue correlations, using dipolar polarization transfer methods, and guided by solution NMR assignments of the same protein. We obtained information on most of the active-site residues involved in chemistry, including some that were not reported in a previous solution NMR study, such as the side-chain carbons of His95. Chemical shift differences comparing the microcrystalline environment to the aqueous environment appear to be mainly due to crystal packing interactions. Site-specific perturbations of the enzyme's chemical shifts upon ligand binding are studied by SSNMR for the first time. These changes monitor proteinwide conformational adjustment upon ligand binding, including many of the sites probed by solution NMR and X-ray studies. Changes in Gln119, Ala163, and Gly210 were observed in our SSNMR studies, but were not reported in solution NMR studies (chicken or yeast). These studies identify a number of new sites with particularly clear markers for ligand binding, paving the way for future studies of triosephosphate isomerase dynamics and mechanism.

  20. Unified Electrostatic Understanding on the Solvation-Induced Changes in the CN Stretching Frequency and the NMR Chemical Shifts of a Nitrile.

    PubMed

    Torii, Hajime

    2016-09-15

    Understanding on the spectroscopic properties of a functional group is essential to use it to detect changes in the structural and/or dynamical properties through the situations of intermolecular interactions. The present study is devoted to elucidating the factors that control the solvation-induced changes in the C≡N stretching frequency and the (13)C and (15)N NMR chemical shifts of the nitrile group. It is shown that the nonelectrostatic contribution of the hydration-induced changes in the C≡N stretching frequency as previously thought, as well as the specific effect of hydrogen bonding on the (13)C and (15)N chemical shifts, actually originate from the spatially inhomogeneous nature of the electrostatic situation generated by the hydrogen-bond donating water molecule, especially by the OH bond dipole. On this basis, a unified electrostatic interaction model that encompasses the cases of both hydration and dipolar solvation is constructed. The responses of electrons in these two cases are also discussed.

  1. Understanding Chemical versus Electrostatic Shifts in X-ray Photoelectron Spectra of Organic Self-Assembled Monolayers

    PubMed Central

    2016-01-01

    The focus of the present article is on understanding the insight that X-ray photoelectron spectroscopy (XPS) measurements can provide when studying self-assembled monolayers. Comparing density functional theory calculations to experimental data on deliberately chosen model systems, we show that both the chemical environment and electrostatic effects arising from a superposition of molecular dipoles influence the measured core-level binding energies to a significant degree. The crucial role of the often overlooked electrostatic effects in polar self-assembled monolayers (SAMs) is unambiguously demonstrated by changing the dipole density through varying the SAM coverage. As a consequence of this effect, care has to be taken when extracting chemical information from the XP spectra of ordered organic adsorbate layers. Our results, furthermore, imply that XPS is a powerful tool for probing local variations in the electrostatic energy in nanoscopic systems, especially in SAMs. PMID:26937264

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

    SciTech Connect

    Smith, Kenneth F.

    2006-07-26

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

  3. In-phase thermomechanical fatigue mechanisms in an unidirectional SCS-6/Ti 15-3 MMC

    NASA Technical Reports Server (NTRS)

    Newaz, Golam M.; Majumdar, Bhaskar S.

    1995-01-01

    The objective of this investigation was to identify the inelastic deformation and damage mechanisms under in-phase (IP) thermomechanical fatigue (TMF) in a unidirectional SCS-6/Ti 15-3 metal matrix composite (MMC). Load-controlled IP TMF tests were conducted at 300-538 C at various stress ranges in high-purity argon. A major emphasis of this work was to identify damage mechanism well before final fracture of specimens, rather than to generate life diagrams, to aid development of a realistic deformation/damage and life model.

  4. Theoretical investigations of the γ- gauche effect on the 13C chemical shifts produced by oxygen atoms at the γ position by quantum chemistry calculations

    NASA Astrophysics Data System (ADS)

    Suzuki, Shinji; Horii, Fumitaka; Kurosu, Hiromichi

    2009-02-01

    The γ- gauche effect on 13C chemical shifts that is produced by the O atoms located at the γ positions has been evaluated by quantum chemistry calculations based on the GAIO-CHF procedure. The γ- gauche effects produced by the O and Cl atoms in n-propanol and n-propyl chloride are found to be, respectively, +1.4 and -0.7 ppm, whereas that due to the C atom in n-butane is -3.0 ppm in good agreement of the values previously calculated. The apparent cause of such a difference in the γ- gauche effect is mainly relatively higher shielding of the CH 3 carbon in the trans conformation for the n-propanol and n-propyl chloride. Extending the n-propanol chain at both ends causes no significant change in the γ- gauche effect produced by the O atom. In 2-butanol and 2-methyl-2-butanol as examples of secondarily and tertiarily substituted compounds, the γ- gauche effects produced by the γ-OH groups are estimated to be -7 to -9 ppm. In addition, the γ- gauche effect due to the C atom is found to increase in n-butane, secondary, and tertiary butanols in this order. The γ- gauche effect produced by the O atom in hydroxyethylcyclohexane is as negligibly small as -0.7 ppm, whereas that produced by the C atom in ethylcyclohexane is about -5 ppm. These results suggest that the γ- gauche effect, including downfield shift, produced by the O atom in a compound greatly depends on its chemical structure, whereas upfield shifts of -3 to -7 ppm are induced in all examined compounds as the γ- gauche effect due to the C atom.

  5. Chemical reaction optimization for solving shortest common supersequence problem.

    PubMed

    Khaled Saifullah, C M; Rafiqul Islam, Md

    2016-10-01

    Shortest common supersequence (SCS) is a classical NP-hard problem, where a string to be constructed that is the supersequence of a given string set. The SCS problem has an enormous application of data compression, query optimization in the database and different bioinformatics activities. Due to NP-hardness, the exact algorithms fail to compute SCS for larger instances. Many heuristics and meta-heuristics approaches were proposed to solve this problem. In this paper, we propose a meta-heuristics approach based on chemical reaction optimization, CRO_SCS that is designed inspired by the nature of the chemical reactions. For different optimization problems like 0-1 knapsack, quadratic assignment, global numeric optimization problems CRO algorithm shows very good performance. We have redesigned the reaction operators and a new reform function to solve the SCS problem. The outcomes of the proposed CRO_SCS algorithm are compared with those of the enhanced beam search (IBS_SCS), deposition and reduction (DR), ant colony optimization (ACO) and artificial bee colony (ABC) algorithms. The length of supersequence, execution time and standard deviation of all related algorithms show that CRO_SCS gives better results on the average than all other algorithms.

  6. Theory of pure short S--c--S and S--c--N microjunctions

    SciTech Connect

    Zaitsev, A.V.

    1980-01-01

    A theory is developed for the nonstationary Josephson effect in pure S--c--S junctions (mean free path l much larger than the constriction radius a), and the current-voltage characteristic (CVC) of such a junction is obtained. The model considered for the construction was an opening of small radius a<<(xi/sup -1/(0)+l/sup -1/)/sup -1/ in a thin impermeable partition (Kulik and Omel'yanchuk, Sov. J. Low Temp. Phys. 3, 459 (1977); Omel'yanchuk, Kulik, and Shekhter, JETP Lett. 25, 437 (1977)). A linear response from an S--c--S junction was obtained with a direct current smaller than the critical value, and the resistive regime was investigated in the voltage region V<<..delta.. near T/sub c/ and in the region V>>..delta.. at arbitrary temperatures. In the case of the S--c--N junction, the CVC was obtained for arbitrary V and T. The results differ not only quantitatively but also qualitatively from those obtained by Artemenko, Volkov, and Zaitsev (Soviet Phys. JETP 49, 924 (1979); Solid State Commun. 30, 771 (1979)) for dirty short constrictions.

  7. Chemical potential shift and gap-state formation in SrTiO{sub 3−δ} revealed by photoemission spectroscopy

    SciTech Connect

    Pal, Prabir Kumar, Pramod; Aswin, V.; Dogra, Anjana; Joshi, Amish G.

    2014-08-07

    In this study, we report on investigations of the electronic structure of SrTiO{sub 3} annealed at temperature ranging between 550 and 840 °C in an ultrahigh vacuum. Annealing induced oxygen vacancies (O{sub vac}) impart considerable changes in the electronic structure of SrTiO{sub 3}. Using core-level photoemission spectroscopy, we have studied the chemical potential shift (Δμ) as a function of annealing temperature. The result shows that the chemical potential monotonously increases with electron doping in SrTiO{sub 3−δ}. The monotonous increase of the chemical potential rules out the existence of electronic phase separation in the sample. Using valence band photoemission, we have demonstrated the formation of a low density of states at the near Fermi level electronic spectrum of SrTiO{sub 3−δ}. The gap-states were observed by spectral weight transfer over a large energy scale of the stoichiometric band gap of SrTiO{sub 3} system leading finally to an insulator-metal transition. We have interpreted our results from the point of structural distortions induced by oxygen vacancies.

  8. Mapping of the C3d ligand binding site on complement receptor 2 (CR2/CD21) using nuclear magnetic resonance and chemical shift analysis.

    PubMed

    Kovacs, James M; Hannan, Jonathan P; Eisenmesser, Elan Z; Holers, V Michael

    2009-04-03

    Complement receptor 2 (CR2, CD21) is a cell membrane protein, with 15 or 16 extracellular short consensus repeats (SCRs), that promotes B lymphocyte responses and bridges innate and acquired immunity. The most distally located SCRs (SCR1-2) mediate the interaction of CR2 with its four known ligands (C3d, Epstein-Barr virus gp350, interferon-alpha, and CD23). Inhibitory monoclonal antibodies against SCR1-2 block binding of all ligands. To develop ligand-specific inhibitors that would also assist in identifying residues unique to each receptor-ligand interaction, phage were selected from randomly generated libraries by panning with recombinant SCR1-2, followed by specific ligand-driven elution. Derived peptides were tested by competition ELISA. One peptide, C3dp1 (APQHLSSQYSRT) exhibited ligand-specific inhibition at midmicromolar IC(50). C3d was titrated into (15)N-labeled SCR1-2, which revealed chemical shift changes indicative of specific intermolecular interactions. With backbone assignments made, the chemical shift changes were mapped onto the crystal structure of SCR1-2. With regard to C3d, the binding surface includes regions of SCR1, SCR2, and the inter-SCR linker, specifically residues Arg(13), Tyr(16), Arg(28), Tyr(29), Ser(32), Thr(34), Lys(48), Asp(56), Lys(57), Tyr(68), Arg(83), Gly(84), Asn(101), Asn(105), and Ser(109). SCR1 and SCR2 demonstrated distinct binding modes. The CR2 binding surface incorporating SCR1 is inconsistent with a previous x-ray CR2-C3d co-crystal analysis but consistent with mutagenesis, x-ray neutron scattering, and inhibitory monoclonal antibody epitope mapping. Titration with C3dp1 yielded chemical shift changes (Arg(13), Tyr(16), Thr(34), Lys(48), Asp(56), Lys(57), Tyr(68), Arg(83), Gly(84), Asn(105), and Ser(109)) overlapping with C3d, indicating that C3dp1 interacts at the same CR2 site as C3d.

  9. Relative importance of first and second derivatives of nuclear magnetic resonance chemical shifts and spin-spin coupling constants for vibrational averaging.

    PubMed

    Dracínský, Martin; Kaminský, Jakub; Bour, Petr

    2009-03-07

    Relative importance of anharmonic corrections to molecular vibrational energies, nuclear magnetic resonance (NMR) chemical shifts, and J-coupling constants was assessed for a model set of methane derivatives, differently charged alanine forms, and sugar models. Molecular quartic force fields and NMR parameter derivatives were obtained quantum mechanically by a numerical differentiation. In most cases the harmonic vibrational function combined with the property second derivatives provided the largest correction of the equilibrium values, while anharmonic corrections (third and fourth energy derivatives) were found less important. The most computationally expensive off-diagonal quartic energy derivatives involving four different coordinates provided a negligible contribution. The vibrational corrections of NMR shifts were small and yielded a convincing improvement only for very accurate wave function calculations. For the indirect spin-spin coupling constants the averaging significantly improved already the equilibrium values obtained at the density functional theory level. Both first and complete second shielding derivatives were found important for the shift corrections, while for the J-coupling constants the vibrational parts were dominated by the diagonal second derivatives. The vibrational corrections were also applied to some isotopic effects, where the corrected values reasonably well reproduced the experiment, but only if a full second-order expansion of the NMR parameters was included. Contributions of individual vibrational modes for the averaging are discussed. Similar behavior was found for the methane derivatives, and for the larger and polar molecules. The vibrational averaging thus facilitates interpretation of previous experimental results and suggests that it can make future molecular structural studies more reliable. Because of the lengthy numerical differentiation required to compute the NMR parameter derivatives their analytical implementation in

  10. 1H chemical shift imaging of the brain in guanidino methyltransferase deficiency, a creatine deficiency syndrome; guanidinoacetate accumulation in the gray matter.

    PubMed

    Sijens, P E; Verbruggen, K T; Meiners, L C; Soorani-Lunsing, R J; Rake, J P; Oudkerk, M

    2005-09-01

    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 spectroscopy revealed guanidinoacetate (GAA) in the absence of creatine. New is that GAA signals are more prominent in gray matter than in white. In the prevailing view, that enzyme deficiency is localized in liver and pancreas and that all GAA is transported into the brain from the blood and the cerebrospinal fluid, this would be compatible with a more limited uptake and/or better clearance of GAA from the white matter compared to the grey matter.

  11. Structural elucidation of dioxa-cage compounds from tetrahydroisobenzofuran-1(3H)-one: analysis of NMR data and GIAO chemical shifts calculations.

    PubMed

    da Costa Resende, Gabriela; Alvarenga, Elson Santiago

    2016-12-01

    The polycyclic compounds, especially the dioxa-cages, have attracted considerable attention in recent years. In our work, a series of 9β-substituted 3-oxo-4,11-dioxatetracyclo[5.2.1.1(5,8) .0(2,6) ]undecane compounds were unexpectedly isolated during bromination, chlorination and epoxidation reactions of the 3-hydroxy-3a,4,7,7a-tetrahydro-4,7-methanoisobenzofuran-1(3H)-one. After careful analysis of the NMR data, the chemical shifts of the isolated and the expected products were predicted by theoretical calculations using density functional theory and gauge including atomic orbitals. The best correlation between calculated and experimental data was evaluated by comparing mean absolute errors and applying DP4 probability methodology. Results from both approaches indicated a correct structural elucidation. Copyright © 2016 John Wiley & Sons, Ltd.

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

    PubMed

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

    2015-09-21

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

  13. Fatigue-life behavior and matrix fatigue crack spacing in unnotched SCS-6/Timetal 21S metal matrix composites

    NASA Technical Reports Server (NTRS)

    Ward, G. T.; Herrmann, D. J.; Hillberry, B. M.

    1993-01-01

    Fatigue tests of the SCS-6/Timetal 21S composite system were performed to characterize the fatigue behavior for unnotched conditions. The stress-life behavior of the unnotched (9/90)2s laminates was investigated for stress ratios of R = 0.1 and R = 0.3. The occurrence of matrix cracking was also examined in these specimens. This revealed multiple matrix crack initiation sites throughout the composite, as well as evenly spaced surface cracks along the length of the specimens. No difference in fatigue lives were observed for stress ratios of R = 0.1 and R = 0.3 when compared on a stress range basis. The unnotched SCS-6/Timetal 21S composites had shorter fatigue lives than the SCS-6/Ti-15-3 composites, however the neat Timetal 21S matrix material had a longer fatigue life than the neat Ti-15-3.

  14. Radial variation of elastic properties of SCS-6 silicon carbide fiber

    NASA Technical Reports Server (NTRS)

    Sathish, Shamachary; Cantrell, John H.; Yost, William T.

    1994-01-01

    The upper and lower bounds of the bulk, shear, and Young's moduli are calculated point-by-point along the radius of SCS-6 silicon carbide fibers using the Hashin-Shtrikman equations from considerations of the Auger spectra along the fiber radius. The calculated values are in agreement with measurements of the average Young modulus obtained over relatively large radial regions of the fiber using scanning acoustic microscopy (SAM). The validity of the Hashin-Shtrikman bounds calculations is enhanced by the agreement found between experimental SAM V(z) curves for fixed z along the fiber radius and the theoretical bounds of such curves obtained from the bounds of the calculated bulk and shear moduli.

  15. Radial Variation of Elastic Properties of SCS-6 Silicon Carbide Fiber

    NASA Technical Reports Server (NTRS)

    Sathish, Shamachary; Cantrell, John H.; Yost, William T.

    1994-01-01

    The upper and lower bounds of the bulk, shear, and Young's moduli are calculated point-by-point along the radius of SCS-6 silicon carbide fibers using the Hashin-Shtrikman equations from considerations of the Auger spectra along the fiber radius. The calculated values are in agreement with measurements of the average Young modulus obtained over relatively large radial regions of the fiber using scanning acoustic microscopy (SAM). The validity of the Hashin-Shtrikman bounds calculations is enhanced by the agreement found between experimental SAM V(z) curves for fixed z along the fiber radius and the theoretical bounds of such curves obtained from the bounds of the calculated bulk and shear moduli.

  16. Fatigue crack growth study of SCS6/Ti-15-3 composite

    NASA Technical Reports Server (NTRS)

    Kantzos, P.; Telesman, J.

    1990-01-01

    A study was performed to determine the fatigue crack growth (FCG) behavior and the associated fatigue damage processes in a (0)8- and (90)8-oriented SCS6/Ti-15-3 composite. Companion testing was also done on identically processed Ti-15-3 unreinforced material. The active fatigue crack growth failure processes were very similar for both composite orientations tested. For both orientations, fatigue crack growth was along the fiber direction. It was found that the composite constituent most susceptible to fatigue damage was the interface region and, in particular, the carbon coating surrounding the fiber. The failure of the interface region led to crack initiation and also strongly influenced the FCG behavior in this composite. The failure of the interface region was apparently driven by normal stresses perpendicular to the fiber direction. The FCG rates were considerably higher for the (90)8-oriented CT specimens in comparison to the unreinforced material.

  17. Improved Algorithm of SCS-CN Model Parameters in Typical Inland River Basin in Central Asia

    NASA Astrophysics Data System (ADS)

    Wang, Jin J.; Ding, Jian L.; Zhang, Zhe; Chen, Wen Q.

    2017-02-01

    Rainfall-runoff relationship is the most important factor for hydrological structures, social and economic development on the background of global warmer, especially in arid regions. The aim of this paper is find the suitable method to simulate the runoff in arid area. The Soil Conservation Service Curve Number (SCS-CN) is the most popular and widely applied model for direct runoff estimation. In this paper, we will focus on Wen-quan Basin in source regions of Boertala River. It is a typical valley of inland in Central Asia. First time to use the 16m resolution remote sensing image about high-definition earth observation satellite “Gaofen-1” to provide a high degree accuracy data for land use classification determine the curve number. Use surface temperature/vegetation index (TS/VI) construct 2D scatter plot combine with the soil moisture absorption balance principle calculate the moisture-holding capacity of soil. Using original and parameter algorithm improved SCS-CN model respectively to simulation the runoff. The simulation results show that the improved model is better than original model. Both of them in calibration and validation periods Nash-Sutcliffe efficiency were 0.79, 0.71 and 0.66,038. And relative error were3%, 12% and 17%, 27%. It shows that the simulation accuracy should be further improved and using remote sensing information technology to improve the basic geographic data for the hydrological model has the following advantages: 1) Remote sensing data having a planar characteristic, comprehensive and representative. 2) To get around the bottleneck about lack of data, provide reference to simulation the runoff in similar basin conditions and data-lacking regions.

  18. Spinal Cord Stimulation (SCS)—The Implantable Systems Performance Registry (ISPR)

    PubMed Central

    Schultz, David M.; Calodney, Aaron K.; Mogilner, Alon Y.; Weaver, Todd W.; Wells, Michelle D.; Stromberg, E. Katherine; Roediger, Mollie P.; Sasaki, John T.

    2016-01-01

    Objectives The Implantable Systems Performance Registry (ISPR) was created to monitor the product performance of Medtronic Spinal Cord Stimulation (SCS) and implanted intrathecal drug infusion systems available in the United States. Materials and Methods Data were collected on 2605 patients from 44 centers from various geographic regions across the United States implanting and following patients with SCS systems between June 25, 2004 and January 31, 2014. Actuarial life table methods are used to estimate device performance over time. Of the 2605 patients, 1490 (57.2%) were female, 1098 (42.1%) were male and 17 (0.7%) did not provide gender data. The average age at enrollment was 56.3 years (range: 4–97, SD = 14.3) and average follow‐up time was 20.1 months (SD = 22.5). Results Currently the estimates of device survival from neurostimulator‐related events exceed 97% for all neurostimulator models across the applicable follow‐up time points and all applicable extension models had greater than 95% survival from extension events. The majority of product performance events were lead‐related. At 5 years of follow‐up, all applicable lead families, with the exception of the Pisces‐Quad LZ family, had greater than 75% survival from lead events. Conclusions The ISPR is designed to serve as an ongoing source of system and device‐related information with a focus on “real‐world” safety and product performance. ISPR data continue to be used to guide future product development efforts aimed at improving product reliability and quality. PMID:27730706

  19. FTIR and 1H MAS NMR investigations on the correlation between the frequency of stretching vibration and the chemical shift of surface OH groups of solids

    NASA Astrophysics Data System (ADS)

    Brunner, Eike; Karge, H. G.; Pfeifer, H.

    1992-03-01

    The study of surface hydroxyl groups of solids, especially of zeolites, belongs to the 'classical' topics of IR spectroscopy since physico-chemical information may be derived from the wavenumber (nu) OH of the stretching vibration of the different hydroxyls. On the other hand, the last decade has seen the development of high resolution solid-state NMR spectroscopy and through the use of the so-called magic-angle-spinning technique (MAS) the signals of different hydroxyl species can be resolved in the 1H NMR spectra of solids. The chemical shift (delta) H describing the position of these lines may be used as well as (nu) OH to characterize quantitatively the strength of acidity of surface OH groups of solids. In a first comparison of (nu) OH with (delta) H for several types of surface OH groups, a linear correlation between them could be found. The aim of this paper was to prove the validity of this correlation for a wide variety of hydroxyls. The IR measurements were carried out on a Perkin-Elmer FTIR spectrometer 1800 at the Fritz Haber Institute of the Max Planck Society, Berlin, and the 1H MAS NMR spectra were recorded on a Bruker MSL- 300 at the University of Leipzig.

  20. Catchment area-based evaluation of the AMC-dependent SCS-CN-based rainfall-runoff models

    NASA Astrophysics Data System (ADS)

    Mishra, S. K.; Jain, M. K.; Pandey, R. P.; Singh, V. P.

    2005-09-01

    Using a large set of rainfall-runoff data from 234 watersheds in the USA, a catchment area-based evaluation of the modified version of the Mishra and Singh (2002a) model was performed. The model is based on the Soil Conservation Service Curve Number (SCS-CN) methodology and incorporates the antecedent moisture in computation of direct surface runoff. Comparison with the existing SCS-CN method showed that the modified version performed better than did the existing one on the data of all seven area-based groups of watersheds ranging from 0.01 to 310.3 km2.

  1. Fatigue crack propagation parallel to fibers in unidirectionally reinforced SCS-6/Timetal{reg_sign}21S

    SciTech Connect

    John, R.; Lackey, A.F.; Ashbaugh, N.E.

    1996-09-15

    The primary weakness of a component made of unidirectionally reinforced SCS-6/Timetal{reg_sign}21S is its susceptibility to transverse loads. The strength of the component in the transverse direction is significantly lower than that in the longitudinal direction under monotonic, sustained and fatigue loading conditions. The previous investigations did not investigate the effect of applied stress ratio on the crack growth behavior of the composite. This paper describes extensive characterization of the fatigue crack growth parallel to fibers in unidirectional SCS-6/Timetal{reg_sign}21S using two geometries, three applied stress ratios and closure measurements.

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

    SciTech Connect

    Zhang, Rongchun; Ramamoorthy, Ayyalusamy

    2015-05-28

    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 {sup 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 {sup 1}H/{sup 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.

  3. Ring current effects in crystals. Evidence from 13C chemical shift tensors for intermolecular shielding in 4,7-di-t-butylacenaphthene versus 4,7-di-t-butylacenaphthylene.

    PubMed

    Ma, Zhiru; Halling, Merrill D; Solum, Mark S; Harper, James K; Orendt, Anita M; Facelli, Julio C; Pugmire, Ronald J; Grant, David M; Amick, Aaron W; Scott, Lawrence T

    2007-03-15

    13C chemical shift tensor data from 2D FIREMAT spectra are reported for 4,7-di-t-butylacenaphthene and 4,7-di-t-butylacenaphthylene. In addition, calculations of the chemical shielding tensors were completed at the B3LYP/6-311G** level of theory. While the experimental tensor data on 4,7-di-t-butylacenaphthylene are in agreement with theory and with previous data on polycyclic aromatic hydrocarbons, the experimental and theoretical data on 4,7-di-t-butylacenaphthene lack agreement. Instead, larger than usual differences are observed between the experimental chemical shift components and the chemical shielding tensor components calculated on a single molecule of 4,7-di-t-butylacenaphthene, with a root mean square (rms) error of +/-7.0 ppm. The greatest deviation is concentrated in the component perpendicular to the aromatic plane, with the largest value being a 23 ppm difference between experiment and theory for the 13CH2 carbon delta11 component. These differences are attributed to an intermolecular chemical shift that arises from the graphitelike, stacked arrangement of molecules found in the crystal structure of 4,7-di-t-butylacenaphthene. This conclusion is supported by a calculation on a trimer of molecules, which improves the agreement between experiment and theory for this component by 14 ppm and reduces the overall rms error between experiment and theory to 4.0 ppm. This intermolecular effect may be modeled with the use of nuclei independent chemical shieldings (NICS) calculations and is also observed in the isotropic 1H chemical shift of the CH2 protons as a 4.2 ppm difference between the solution value and the solid-state chemical shift measured via a 13C-1H heteronuclear correlation experiment.

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

    NASA Astrophysics Data System (ADS)

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

    2000-12-01

    The magnitudes and orientations of the principal elements of the 13C chemical shift anisotropy (CSA) tensor in the molecular frame of the formate ion in β-calcium formate is determined using one-dimensional dipolar-shift spectroscopy. The magnitudes of the principal elements of the 13C CSA tensor are σ11C=104 ppm, σ22C=179 ppm, and σ33C=233 ppm. The least shielding element of the 13C CSA tensor, σ33C, is found to be collinear with the C-H bond. The temperature dependence of the 13C CSA and the 2H quadrupole coupling tensors in β-calcium formate are analyzed for a wide range of temperature (173-373 K). It was found that the span of the 13C CSA and the magnitude of the 2H quadrupole coupling interactions are averaged with the increasing temperature. The experimental results also show that the 2H quadrupole coupling tensor becomes more asymmetric with increasing temperature. A librational motion about the σ22C axis of the 13C CSA tensor is used to model the temperature dependence of the 13C CSA tensor. The temperature dependence of the mean-square amplitude of the librational motion is found to be <α2>=2.6×10-4(T) rad2 K-1. The same librational motion also accounts for the temperature-dependence of the 2H quadrupole coupling tensor after the relative orientation of the 13C CSA and 2H electric field gradient tensors are taken into account. Reconsideration of the results of a previous study found that the librational motion, not the vibrational motion, accounts for an asymmetry in the 1H-13C dipolar coupling tensor of α-calcium formate at room temperature.

  5. 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.

    PubMed

    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.

  6. Regime shift of the South China Sea SST in the late 1990s

    NASA Astrophysics Data System (ADS)

    Thompson, Bijoy; Tkalich, Pavel; Malanotte-Rizzoli, Paola

    2017-03-01

    Decadal variability of the South China Sea (SCS) sea surface temperature (SST) during 1982-2014 is investigated using observations and ocean reanalysis datasets. The SCS SST shows an abrupt transition from a cold-to-warm regime in the late 1990s. Based on the long-term SST variability two epochs are defined, 1982-1996 and 2000-2014 as cold and warm regimes respectively, spanning on either side of the 1997-1999 SCS warming. Despite the occurrence of strong El Nino induced warming events, the SST anomalies tend to be negative in the cold regime. Conversely during the warm regime, the positive SST anomalies have dominated over the La Nina driven cooling events. The cold (warm) SST regime is marked by net heat gain (loss) by the SCS. The long-term variations of net surface heat flux are mainly driven by the latent heat flux anomalies while the short wave flux plays a secondary role. Low-frequency variability of the South China Sea throughflow (SCSTF) appears to be closely related to the SCS SST regime shift. The SCSTF shows reversing trends during the cold and warm epochs. The weakened SCSTF in the warm regime has promoted the SCS warming by limiting the outward flow of warm water from the SCS. Meanwhile, enhanced SCSTF during the cold regime acts as a cooling mechanism and lead to persistent negative SST anomalies. The change in trend of the SCSTF and SST regime shift coincides with the switching of pacific decadal oscillation from a warm to cold phase in the late 1990s.

  7. Internucleotide J-couplings and chemical shifts of the N-H···N hydrogen-bonds in the radiation-damaged guanine-cytosine base pairs.

    PubMed

    Li, Huifang; Zhang, Laibin; Han, Li; Sun, Wenming; Bu, Yuxiang

    2011-04-30

    Internucleotide (2h)J(NN) spin-spin couplings and chemical shifts (δ((1)H) and Δδ((15)N)) of N-H···N H-bond units in the natural and radiation-damaged G-C base pairs were predicted using the appropriate density functional theory calculations with a large basis set. Four possible series of the damaged G-C pairs (viz., dehydrogenated and deprotonated G-C pairs, GC(•-) and GC(•+) radicals) were discussed carefully in this work. Computational NMR results show that radicalization and anionization of the base pairs can yield strong effect on their (2h)J(NN) spin scalar coupling constants and the corresponding chemical shifts. Thus, variations of the NMR parameters associated with the N-H···N H-bonds may be taken as an important criterion for prejudging whether the natural G-C pair is radiation-damaged or not. Analysis shows that (2h)J(NN) couplings are strongly interrelated with the energy gaps (ΔE(LP→σ*)) and the second-order interaction energies (E(2)) between the donor N lone-pair (LP(N)) and the acceptor σ*(N-H) localized NBO orbitals, and also are sensitive to the electron density distributions over the σ*(N-H) orbital, indicating that (2h)J(NN) couplings across the N-H···N H-bonds are charge-transfer-controlled. This is well supported by variation of the electrostatic potential surfaces and corresponding charge transfer amount between G and C moieties. It should be noted that although the NMR spectra for the damaged G-C pair radicals are unavailable now and the states of the radicals are usually detected by the electron spin resonance, this study provides a correlation of the properties of the damaged DNA species with some of the electronic parameters associated with the NMR spectra for the understanding of the different state character of the damaged DNA bases.

  8. Zonation of flood production potential in Kabutar Ali Chai watershed using SCS model

    NASA Astrophysics Data System (ADS)

    Jananeh, Keristineh

    2015-04-01

    Kabutar Ali Chai watershed is located on the southern hillsides of Mishow mountains, 75 km northwest of Tabriz, NW Iran. This watershed is confined to 1390 and 3230 m elevation levels, where the general dip is from north to south. The watershed area is 67.46 km2 and the length of the main stream is about 24.5 km. This is one of the flood basins in the region and considering the availability of precipitation data for the 20 year interval and the possibility of flood occurrence threatening the downstream villages, the flood production investigations in order to prioritize the sub-basins regarding their flood-potential were carried out using the SCS method. In this regard, the watershed area was divided into 4 sections based on physiographic and topographic characteristics and the existing stream network: A1 (the southern and the low-height end of the watershed), A2 (the mid-western half), A3 (the mid-eastern half) and A4 (the northern and highest part). The precipitation data for 20 year interval were gathered from the nearby weather stations of Tabriz, Sahand, Marand and Sharafkhaneh based on which, the average annual precipitation is about 294 mm, with the highest amounts of 415 to 450 mm in A4 sub-basin and the lowest value of 253 mm in the southern A1 sub-basin. According to the time of concentration estimates based on the stream lengths and the elevation differences, this parameter is highest in A1 sub-basin with the rate of 1.64 h and lowest at A3 sub-basin with the rate of 0.35 h. This parameter has negative correlation with the flood production potential. The runoff height is estimated using the SCS method. In order to determine the CN curve Number, the maps of hydrologic groups of soil, land use and vegetation were prepared and combined with each other and then, by taking into account the area of each homogeneous unit, the CN number was calculated for the watershed and the related CN map was prepared. The peak discharge of the hydrologic units across the

  9. High resolution spectroscopy and chemical shift imaging of hyperpolarized 129Xe dissolved in the human brain in vivo at 1.5 tesla

    PubMed Central

    Rao, Madhwesha; Stewart, Neil J.; Norquay, Graham; Griffiths, Paul D.

    2016-01-01

    Purpose Upon inhalation, xenon diffuses into the bloodstream and is transported to the brain, where it dissolves in various compartments of the brain. Although up to five chemically distinct peaks have been previously observed in 129Xe rat head spectra, to date only three peaks have been reported in the human head. This study demonstrates high resolution spectroscopy and chemical shift imaging (CSI) of 129Xe dissolved in the human head at 1.5 Tesla. Methods A 129Xe radiofrequency coil was built in‐house and 129Xe gas was polarized using spin‐exchange optical pumping. Following the inhalation of 129Xe gas, NMR spectroscopy was performed with spectral resolution of 0.033 ppm. Two‐dimensional CSI in all three anatomical planes was performed with spectral resolution of 2.1 ppm and voxel size 20 mm × 20 mm. Results Spectra of hyperpolarized 129Xe dissolved in the human head showed five distinct peaks at 188 ppm, 192 ppm, 196 ppm, 200 ppm, and 217 ppm. Assignment of these peaks was consistent with earlier studies. Conclusion High resolution spectroscopy and CSI of hyperpolarized 129Xe dissolved in the human head has been demonstrated. For the first time, five distinct NMR peaks have been observed in 129Xe spectra from the human head in vivo. Magn Reson Med 75:2227–2234, 2016. © 2016 The Authors Magnetic Resonance in Medicine published by Wiley Periodicals, Inc. on behalf of International Society for Magnetic Resonance in Medicine. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. PMID:27080441

  10. Correlation between ¹⁹⁵Pt chemical shifts and the electronic transitions among d orbitals in pincer NCN Pt(II) complexes: A theoretical study and application of Ramsey's equation.

    PubMed

    Hashemi, Majid

    2015-12-05

    The chemical potentials for two series of [PtCl(NCN-Z-4)] (NCN=2,6-bis[(dimethylamino)methyl]phenyl, Z=H, CHO, COOH, NH2, OH, NO2, SiMe3, I, t-Bu) and [PtCl(NCN-4-CHN-C6H4-Z'-4')] (Z'=NMe2, Me, H, Cl, CN) were calculated. The energies of platinum d orbitals were calculated by NBO analysis. Good correlations were obtained between (195)Pt chemical shifts and the spectral parameters obtained from the energies of electronic transitions between Pt d orbitals in these complexes. The correlations between (195)Pt chemical shifts and the chemical potentials were also good. The correlations were discussed based on Ramsey's equation.

  11. Understanding the effect of watershed characteristic on the runoff using SCS curve number

    NASA Astrophysics Data System (ADS)

    Damayanti, Frieta; Schneider, Karl

    2015-04-01

    Runoff modeling is a key component in watershed management. The temporal course and amount of runoff is a complex function of a multitude of parameters such as climate, soil, topography, land use, and water management. Against the background of the current rapid environmental change, which is due to both i) man-made changes (e.g. urban development, land use change, water management) as well as ii) changes in the natural systems (e.g. climate change), understanding and predicting the impacts of these changes upon the runoff is very important and affects the wellbeing of many people living in the watershed. A main tool for predictions is hydrologic models. Particularly process based models are the method of choice to assess the impact of land use and climate change. However, many regions which experience large changes in the watersheds can be described as rather data poor, which limits the applicability of such models. This is particularly also true for the Telomoyo Watershed (545 km2) which is located in southern part of Central Java province. The average annual rainfall of the study area reaches 2971 mm. Irrigated paddy field are the dominating land use (35%), followed by built-up area and dry land agriculture. The only available soil map is the FAO soil digital map of the world, which provides rather general soil information. A field survey accompanied by a lab analysis 65 soil samples of was carried out to provide more detailed soil texture information. The soil texture map is a key input in the SCS method to define hydrological soil groups. In the frame of our study on 'Integrated Analysis on Flood Risk of Telomoyo Watershed in Response to the Climate and Land Use Change' funded by the German Academic Exchange service (DAAD) we analyzed the sensitivity of the modeled runoff upon the choice of the method to estimate the CN values using the SCS-CN method. The goal of this study is to analyze the impact of different data sources on the curve numbers and the

  12. 129Xe NMR chemical shift in Xe@C60 calculated at experimental conditions: essential role of the relativity, dynamics, and explicit solvent.

    PubMed

    Standara, Stanislav; Kulhánek, Petr; Marek, Radek; Straka, Michal

    2013-08-15

    The isotropic (129)Xe nuclear magnetic resonance (NMR) chemical shift (CS) in Xe@C60 dissolved in liquid benzene was calculated by piecewise approximation to faithfully simulate the experimental conditions and to evaluate the role of different physical factors influencing the (129)Xe NMR CS. The (129)Xe shielding constant was obtained by averaging the (129)Xe nuclear magnetic shieldings calculated for snapshots obtained from the molecular dynamics trajectory of the Xe@C60 system embedded in a periodic box of benzene molecules. Relativistic corrections were added at the Breit-Pauli perturbation theory (BPPT) level, included the solvent, and were dynamically averaged. It is demonstrated that the contribution of internal dynamics of the Xe@C60 system represents about 8% of the total nonrelativistic NMR CS, whereas the effects of dynamical solvent add another 8%. The dynamically averaged relativistic effects contribute by 9% to the total calculated (129)Xe NMR CS. The final theoretical value of 172.7 ppm corresponds well to the experimental (129)Xe CS of 179.2 ppm and lies within the estimated errors of the model. The presented computational protocol serves as a prototype for calculations of (129)Xe NMR parameters in different Xe atom guest-host systems.

  13. ¹³C solid-state NMR analysis of the most common pharmaceutical excipients used in solid drug formulations, Part I: Chemical shifts assignment.

    PubMed

    Pisklak, Dariusz Maciej; Zielińska-Pisklak, Monika Agnieszka; Szeleszczuk, Łukasz; Wawer, Iwona

    2016-04-15

    Solid-state NMR is an excellent and useful method for analyzing solid-state forms of drugs. In the (13)C CP/MAS NMR spectra of the solid dosage forms many of the signals originate from the excipients and should be distinguished from those of active pharmaceutical ingredient (API). In this work the most common pharmaceutical excipients used in the solid drug formulations: anhydrous α-lactose, α-lactose monohydrate, mannitol, sucrose, sorbitol, sodium starch glycolate type A and B, starch of different origin, microcrystalline cellulose, hypromellose, ethylcellulose, methylcellulose, hydroxyethylcellulose, sodium alginate, magnesium stearate, sodium laurilsulfate and Kollidon(®) were analyzed. Their (13)C CP/MAS NMR spectra were recorded and the signals were assigned, employing the results (R(2): 0.948-0.998) of GIPAW calculations and theoretical chemical shifts. The (13)C ssNMR spectra for some of the studied excipients have not been published before while for the other signals in the spectra they were not properly assigned or the assignments were not correct. The results summarize and complement the data on the (13)C ssNMR analysis of the most common pharmaceutical excipients and are essential for further NMR studies of API-excipient interactions in the pharmaceutical formulations.

  14. Linear-scaling method for calculating nuclear magnetic resonance chemical shifts using gauge-including atomic orbitals within Hartree-Fock and density-functional theory.

    PubMed

    Kussmann, Jörg; Ochsenfeld, Christian

    2007-08-07

    Details of a new density matrix-based formulation for calculating nuclear magnetic resonance chemical shifts at both Hartree-Fock and density functional theory levels are presented. For systems with a nonvanishing highest occupied molecular orbital-lowest unoccupied molecular orbital gap, the method allows us to reduce the asymptotic scaling order of the computational effort from cubic to linear, so that molecular systems with 1000 and more atoms can be tackled with today's computers. The key feature is a reformulation of the coupled-perturbed self-consistent field (CPSCF) theory in terms of the one-particle density matrix (D-CPSCF), which avoids entirely the use of canonical MOs. By means of a direct solution for the required perturbed density matrices and the adaptation of linear-scaling integral contraction schemes, the overall scaling of the computational effort is reduced to linear. A particular focus of our formulation is to ensure numerical stability when sparse-algebra routines are used to obtain an overall linear-scaling behavior.

  15. Chemical shift assignments of the first and second RRMs of Nrd1, a fission yeast MAPK-target RNA binding protein.

    PubMed

    Kobayashi, Ayaho; Kanaba, Teppei; Satoh, Ryosuke; Ito, Yutaka; Sugiura, Reiko; Mishima, Masaki

    2017-03-11

    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. Hydrogen bond geometries and proton tautomerism of homoconjugated anions of carboxylic acids studied via H/D isotope effects on 13C NMR chemical shifts.

    PubMed

    Guo, Jing; Tolstoy, Peter M; Koeppe, Benjamin; Golubev, Nikolai S; Denisov, Gleb S; Smirnov, Sergei N; Limbach, Hans-Heinrich

    2012-11-26

    Ten formally symmetric anionic OHO hydrogen bonded complexes, modeling Asp/Glu amino acid side chain interactions in nonaqueous environment (CDF(3)/CDF(2)Cl solution, 200-110 K) have been studied by (1)H, (2)H, and (13)C NMR spectroscopy, i.e. intermolecularly H-bonded homoconjugated anions of acetic, chloroacetic, dichloroacetic, trifluoroacetic, trimethylacetic, and isobutyric acids, and intramolecularly H-bonded hydrogen succinate, hydrogen rac-dimethylsuccinate, hydrogen maleate, and hydrogen phthalate. In particular, primary H/D isotope effects on the hydrogen bond proton signals as well as secondary H/D isotope effects on the (13)C signals of the carboxylic groups are reported and analyzed. We demonstrate that in most of the studied systems there is a degenerate proton tautomerism between O-H···O(-) and O(-)···H-O structures which is fast in the NMR time scale. The stronger is the proton donating ability of the acid, the shorter and more symmetric are the H-bonds in each tautomer of the homoconjugate. For the maleate and phthalate anions exhibiting intramolecular hydrogen bonds, evidence for symmetric single well potentials is obtained. We propose a correlation between H/D isotope effects on carboxylic carbon chemical shifts and the proton transfer coordinate, q(1) = ½(r(OH) - r(HO)), which allows us to estimate the desired OHO hydrogen bond geometries from the observed (13)C NMR parameters, taking into account the degenerate proton tautomerism.

  17. 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

    PubMed Central

    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

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

    SciTech Connect

    Brothers, Michael C; Nesbitt, Anna E; Hallock, Michael J; Rupasinghe, Sanjeewa; Tang, Ming; Harris, Jason B; Baudry, Jerome Y; Schuler, Mary A; Rienstra, Chad M

    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.

  19. Determination of NH proton chemical shift anisotropy with 14N-1H heteronuclear decoupling using ultrafast magic angle spinning solid-state NMR

    NASA Astrophysics Data System (ADS)

    Pandey, Manoj Kumar; Nishiyama, Yusuke

    2015-12-01

    The extraction of chemical shift anisotropy (CSA) tensors of protons either directly bonded to 14N nuclei (I = 1) or lying in their vicinity using rotor-synchronous recoupling pulse sequence is always fraught with difficulty due to simultaneous recoupling of 14N-1H heteronuclear dipolar couplings and the lack of methods to efficiently decouple these interactions. This difficulty mainly arises from the presence of large 14N quadrupolar interactions in comparison to the rf field that can practically be achieved. In the present work it is demonstrated that the application of on-resonance 14N-1H decoupling with rf field strength ∼30 times weaker than the 14N quadrupolar coupling during 1H CSA recoupling under ultrafast MAS (90 kHz) results in CSA lineshapes that are free from any distortions from recoupled 14N-1H interactions. With the use of extensive numerical simulations we have shown the applicability of our proposed method on a naturally abundant L-Histidine HCl·H2O sample.

  20. Chemical-shift X-ray standing wavefield determination of the local structure of methanethiolate phases on Ni( 1 1 1 )

    NASA Astrophysics Data System (ADS)

    Fisher, C. J.; Woodruff, D. P.; Jones, R. G.; Cowie, B. C. C.; Formoso, V.

    2002-01-01

    By monitoring the X-ray absorption through the chemically-shifted components of the S 1s photoemission signal, normal-incidence X-ray standing wavefield absorption at the (1 1 1) and ( 1¯ 1 1) scatterer planes has been used to determine the local adsorption geometry of the two distinct methanethiolate (CH 3S-) species which occur on Ni(1 1 1) following exposure to methanethiol. The species which is favoured at low temperatures is found to occupy either mixed hollow or bridge sites on a non-reconstructed Ni(1 1 1) surface, whereas that seen at higher temperatures is shown to involve Ni surface layer reconstruction and the data are consistent with hollow site adsorption on a reduced density outermost Ni layer. The relative merits of alternative reconstruction models based on that which occurs due to methanethiolate adsorption on Cu(1 1 1), or the (5√3×2)rect. phase formed by atomic S on Ni(1 1 1), are discussed. Both of these models are based on local square or `pseudo-(1 0 0)' outermost Ni layers. Co-adsorbed atomic sulphur, to which the methanethiolate species decompose at higher temperatures, appears to occupy mainly fcc hollow sites at low temperatures, but is partially converted to the local geometry of the ordered reconstructed (5√3×2)rect.-S phase after higher temperature annealing.

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

    NASA Astrophysics Data System (ADS)

    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 79Br 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 79Br NMR frequency to that of 13C, 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.

  2. Backbone chemical shift assignments for Xanthomonas campestris peroxiredoxin Q in the reduced and oxidized states: a dramatic change in backbone dynamics.

    PubMed

    Buchko, Garry W; Perkins, Arden; Parsonage, Derek; Poole, Leslie B; Karplus, P Andrew

    2016-04-01

    Peroxiredoxins (Prx) are ubiquitous enzymes that reduce peroxides as part of antioxidant defenses and redox signaling. While Prx catalytic activity and sensitivity to hyperoxidative inactivation depend on their dynamic properties, there are few examples where their dynamics has been characterized by NMR spectroscopy. Here, we provide a foundation for studies of the solution properties of peroxiredoxin Q from the plant pathogen Xanthomonas campestris (XcPrxQ) by assigning the observable (1)H(N), (15)N, (13)C(α), (13)C(β), and (13)C' chemical shifts for both the reduced (dithiol) and oxidized (disulfide) states. In the reduced state, most of the backbone amide resonances (149/152, 98 %) can be assigned in the XcPrxQ (1)H-(15)N HSQC spectrum. In contrast, a remarkable 51 % (77) of these amide resonances are not visible in the (1)H-(15)N HSQC spectrum of the disulfide state of the enzyme, indicating a substantial change in backbone dynamics associated with the formation of an intramolecular C48-C84 disulfide bond.

  3. pH-dependent random coil (1)H, (13)C, and (15)N chemical shifts of the ionizable amino acids: a guide for protein pK a measurements.

    PubMed

    Platzer, Gerald; Okon, Mark; McIntosh, Lawrence P

    2014-11-01

    The pK a values and charge states of ionizable residues in polypeptides and proteins are frequently determined via NMR-monitored pH titrations. To aid the interpretation of the resulting titration data, we have measured the pH-dependent chemical shifts of nearly all the (1)H, (13)C, and (15)N nuclei in the seven common ionizable amino acids (X = Asp, Glu, His, Cys, Tyr, Lys, and Arg) within the context of a blocked tripeptide, acetyl-Gly-X-Gly-amide. Alanine amide and N-acetyl alanine were used as models of the N- and C-termini, respectively. Together, this study provides an essentially complete set of pH-dependent intra-residue and nearest-neighbor reference chemical shifts to help guide protein pK a measurements. These data should also facilitate pH-dependent corrections in algorithms used to predict the chemical shifts of random coil polypeptides. In parallel, deuterium isotope shifts for the side chain (15)N nuclei of His, Lys, and Arg in their positively-charged and neutral states were also measured. Along with previously published results for Asp, Glu, Cys, and Tyr, these deuterium isotope shifts can provide complementary experimental evidence for defining the ionization states of protein residues.

  4. Fatigue Crack Growth and Crack Bridging in SCS-6/Ti-24-11

    NASA Technical Reports Server (NTRS)

    Ghosn, Louis J.; Kantzos, Pete; Telesman, Jack

    1995-01-01

    Interfacial damage induced by relative fiber/matrix sliding was found to occur in the bridged zone of unidirectional SCS-6/Ti-24Al-11Nb intermetallic matrix composite specimens subjected to fatigue crack growth conditions. The degree of interfacial damage was not uniform along the bridged crack wake. Higher damage zones were observed near the machined notch in comparison to the crack tip. The interfacial friction shear strength tau(sub f) measured in the crack wake using pushout testing revealed lower values than the as-received interface. Interfacial wear also reduced the strength of the bridging fibers. The reduction in fiber strength is thought to be a function of the magnitude of relative fiber/matrix displacements ind the degree of interfacial damage. Furthermore, two different fiber bridging models were used to predict the influence of bridging on the fatigue crack driving force. The shear lag model required a variable tau(sub f) in the crack wake (reflecting the degradation of the interface) before its predictions agreed with trends exhibited by the experimental data. The fiber pressure model did an excellent job in predicting both the FCG data and the DeltaCOD in the bridged zone even though it does not require a knowledge of tau(sub f).

  5. Characterization of unnotched SCS-6/Ti-15-3 metal matrix composites at 650 C

    NASA Technical Reports Server (NTRS)

    Pollock, W. D.; Johnson, W. Steven

    1990-01-01

    Ti-15-3 reinforced with SCS-6 silicon carbide fibers, in five different layups, was tested at 650 C to determine monotonic and fatigue strengths, basic mechanical properties, and damage initiation and progression. The elevated temperature results were compared to those obtained at room temperature. Analytical predictions were made of the monotonic stress-strain response as well as cyclic stress-strain hysteresis. The fiber reinforcement was found to significantly increase the static and fatigue strengths of the laminates over that of the matrix material at elevated temperature while the increase was insignificant at room temperature. Initial damage, in either the fibers or the matrix, was partitioned as a function of the life and applied strain range in the constituents. High strains and short lives resulted in multiple fiber failure with no signs of matrix fatigue cracking. Low strains and long lives resulted in extensive matrix cracking and no fiber breaks away from the fracture surface. At 650 C the matrix was too weak to cause fiber-matrix interface failure prior to matrix yielding. Laminate fatigue lives were hypothesized to be a function of the 0 deg fiber stress. More scatter was found in the 0 deg fiber stress vs. high temperature fatigue life data than for the room temperature data. An initial unloading modulus that was greater than the initial loading modulus was observed in the elevated temperature fatigue tests.

  6. Origins of non-stoichiometry in compounds: vacancy-ordering in ScS

    NASA Astrophysics Data System (ADS)

    Hart, Gus L. W.; Zunger, Alex

    2001-03-01

    While most stable compounds have fixed Daltonian ratios of their constituents (e.g., 1:1 ratio in ZnS, NaCl, GaAs), some materials exhibit significant nonstoichiometry even at low temperatures. Examples include some NaCl-structure transition-metal monochalcogenides such as HfS, ZrSe, and YS. The prototype system ScS exhibits this peculiar property of preferring the presence of vacancies (up to 30%) over a purely stoichiometric structure. Moreover, these vacancies order spatially in unusual structures. We consider Sc_1-xBox _xS as a binary alloy (where Box denotes a vacancy) and express the energy E_MBCE(σ) of any of the 2^N configurations σ in a ``mixed-basis cluster expansion'' (MBCE) obtained from ab initio calculations of ~ 30 ordered structures. A ground state search of all possible configurations reveals that indeed an ordered array of vacancies has the lowest energy. We show systematic features in the electronic structure that help explain the preference for vacancies.

  7. Runoff Potentiality of a Watershed through SCS and Functional Data Analysis Technique

    PubMed Central

    Adham, M. I.; Shirazi, S. M.; Othman, F.; Rahman, S.; Yusop, Z.; Ismail, Z.

    2014-01-01

    Runoff potentiality of a watershed was assessed based on identifying curve number (CN), soil conservation service (SCS), and functional data analysis (FDA) techniques. Daily discrete rainfall data were collected from weather stations in the study area and analyzed through lowess method for smoothing curve. As runoff data represents a periodic pattern in each watershed, Fourier series was introduced to fit the smooth curve of eight watersheds. Seven terms of Fourier series were introduced for the watersheds 5 and 8, while 8 terms of Fourier series were used for the rest of the watersheds for the best fit of data. Bootstrapping smooth curve analysis reveals that watersheds 1, 2, 3, 6, 7, and 8 are with monthly mean runoffs of 29, 24, 22, 23, 26, and 27 mm, respectively, and these watersheds would likely contribute to surface runoff in the study area. The purpose of this study was to transform runoff data into a smooth curve for representing the surface runoff pattern and mean runoff of each watershed through statistical method. This study provides information of runoff potentiality of each watershed and also provides input data for hydrological modeling. PMID:25152911

  8. Fatigue crack growth study of SCS6/Ti-15-3 composite

    NASA Technical Reports Server (NTRS)

    Kantzos, Peter; Telesman, Jack

    1989-01-01

    A study was performed to determine the fatigue crack growth (FCG) behavior and the associated fatigue damage processes in a (0)(8) and (90)(8) oriented SCS(6)/Ti-15-3 composite. Companion testing (CT) was also done on identically processed Ti-15-3 unreinforced material. The active fatigue crack growth failure processes were very similar for both composite orientations tested. For both orientations, fatigue crack growth was along the fiber direction. It was found that the composite constituent most susceptible to fatigue damage was the interface region and in particular the carbon coating surrounding the fiber. The failure of the interface region lead to crack initiation and also strongly influenced the FCG behavior in this composite. The failure of the interface region was apparently driven by normal stresses perpendicular to the fiber direction. The FCG rates were considerably higher for the (90)(8) oriented CT specimens in comparison to the unreinforced material. This is consistent with the scenario in which the interface has lower fatigue resistance than the matrix, causing lower composite fatigue resistance. The FCG rates of the (0)(8) composite could not be directly compared to the (90)(8) composite but were shown to increase with an increase in the crack length.

  9. Inelastic deformation mechanisms in SCS-6/Ti 15-3 MMC lamina under compression

    NASA Technical Reports Server (NTRS)

    Newaz, Golam M.; Majumdar, Bhaskar S.

    1993-01-01

    An investigation was undertaken to study the inelastic deformation mechanisms in (0)(sub 8) and (90)(sub 8) Ti 15-3/SCS-6 lamina subjected to pure compression. Monotonic tests were conducted at room temperature (RT), 538 C and 650 C. Results indicate that mechanical response and deformation characteristics were different in monotonic tension and compression loading whereas some of those differences could be attributed to residual stress effects. There were other differences because of changes in damage and failure modes. The inelastic deformation in the (0)(sub 8) lamina under compression was controlled primarily by matrix plasticity, although some evidence of fiber-matrix debonding was observed. Failure of the specimen in compression was due to fiber buckling in a macroscopic shear zone (the failure plane). The inelastic deformation mechanisms under compression in (90)(sub 8) lamina were controlled by radial fiber fracture, matrix plasticity, and fiber-matrix debonding. The radial fiber fracture was a new damage mode observed for MMC's. Constitutive response was predicted for both the (0)(sub 8) and (90)(sub 8) laminae, using AGLPLY, METCAN, and Battelle's Unit Cell FEA model. Results from the analyses were encouraging.

  10. Shifting Attention

    ERIC Educational Resources Information Center

    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…

  11. Muscle metabolism and activation heterogeneity by combined 31P chemical shift and T2 imaging, and pulmonary O2 uptake during incremental knee-extensor exercise.

    PubMed

    Cannon, Daniel T; Howe, Franklyn A; Whipp, Brian J; Ward, Susan A; McIntyre, Dominick J; Ladroue, Christophe; Griffiths, John R; Kemp, Graham J; Rossiter, Harry B

    2013-09-01

    The integration of skeletal muscle substrate depletion, metabolite accumulation, and fatigue during large muscle-mass exercise is not well understood. Measurement of intramuscular energy store degradation and metabolite accumulation is confounded by muscle heterogeneity. Therefore, to characterize regional metabolic distribution in the locomotor muscles, we combined 31P magnetic resonance spectroscopy, chemical shift imaging, and T2-weighted imaging with pulmonary oxygen uptake during bilateral knee-extension exercise to intolerance. Six men completed incremental tests for the following: (1) unlocalized 31P magnetic resonance spectroscopy; and (2) spatial determination of 31P metabolism and activation. The relationship of pulmonary oxygen uptake to whole quadriceps phosphocreatine concentration ([PCr]) was inversely linear, and three of four knee-extensor muscles showed activation as assessed by change in T2. The largest changes in [PCr], [inorganic phosphate] ([Pi]) and pH occurred in rectus femoris, but no voxel (72 cm3) showed complete PCr depletion at exercise cessation. The most metabolically active voxel reached 11 ± 9 mM [PCr] (resting, 29 ± 1 mM), 23 ± 11 mM [Pi] (resting, 7 ± 1 mM), and a pH of 6.64 ± 0.29 (resting, 7.08 ± 0.03). However, the distribution of 31P metabolites and pH varied widely between voxels, and the intervoxel coefficient of variation increased between rest (∼10%) and exercise intolerance (∼30-60%). Therefore, the limit of tolerance was attained with wide heterogeneity in substrate depletion and fatigue-related metabolite accumulation, with extreme metabolic perturbation isolated to only a small volume of active muscle (<5%). Regional intramuscular disturbances are thus likely an important requisite for exercise intolerance. How these signals integrate to limit muscle power production, while regional "recruitable muscle" energy stores are presumably still available, remains uncertain.

  12. An optimized method for NMR-based plant seed metabolomic analysis with maximized polar metabolite extraction efficiency, signal-to-noise ratio, and chemical shift consistency.

    PubMed

    Wu, Xiangyu; Li, Ning; Li, Hongde; Tang, Huiru

    2014-04-07

    Plant metabolomic analysis has become an essential part of functional genomics and systems biology and requires effective extraction of both primary and secondary metabolites from plant cells. To establish an optimized extraction method for the NMR-based analysis, we used the seeds of mungbean (Vigna radiata cv. Elü no. 1) as a model and systematically investigated the dependence of the metabolite composition in plant extracts on various extraction parameters including cell-breaking methods, extraction solvents, number of extraction repeats, tissue-to-solvent ratio, and extract-to-buffer ratio (for final NMR analysis). We also compared two NMR approaches for quantitative metabolomic analysis from completely relaxed spectra directly and from partially relaxed spectra calculated with T1. By maximizing the extraction efficiency and signal-to-noise ratio but minimizing inter-sample chemical-shift variations and metabolite degradations, we established a parameter-optimized protocol for NMR-based plant seed metabolomic analysis. We concluded that aqueous methanol was the best extraction solvent with an optimal tissue-to-solvent ratio of about 1 : 10-1 : 15 (mg per μL). The combination of tissuelyser homogenization with ultrasonication was the choice of cell-breaking method with three repeated extractions being necessary. For NMR analysis, the optimal extract-to-solvent was around 5-8 mg mL(-1) and completely relaxed spectra were ideal for intrinsically quantitative metabolomic analysis although partially relaxed spectra were employable for comparative metabolomics. This optimized method will offer ensured data quality for high-throughput and reliable plant metabolomics studies.

  13. Comparison of accelerated 3-D spiral chemical shift imaging and single-voxel spectroscopy at 3T in the pediatric age group.

    PubMed

    Yazbek, Sandrine; Prabhu, Sanjay P; Connaughton, Pauline; Grant, Patricia E; Gagoski, Borjan

    2015-08-01

    Single-voxel spectroscopy (SVS) is usually used in the pediatric population when a short acquisition time is crucial. To overcome the long acquisition time of 3-D phase-encoded chemical shift imaging (CSI) and lack of spatial coverage of single-voxel spectroscopy, efficient encoding schemes using spiral k-space trajectories have been successfully deployed, enabling acquisition of volumetric CSI in <5 min. We assessed feasibility of using 3-D spiral CSI sequence routinely in pediatric clinical settings by comparing its reconstructed spectra against SVS spectra. Volumetric spiral CSI obtained spectra from 2-cc isotropic voxels over a 16×16×10-cm region. SVS acquisition encoded a 3.4-cc (1.5-mm) isotropic voxel. Acquisition time was 3 min for every technique. Data were gathered prospectively from 11 random pediatric patients. Spectra from left basal ganglia were obtained using both techniques and were processed with post-processing software. The following metabolite ratios were calculated: N-acetylaspartate/creatine (NAA/Cr), choline/creatine (Cho/Cr), lactate/creatine (Lac/Cr) and N-acetylapartate/choline (NAA/Cho). We collected data on 11 children ages 4 days to 10 years. In 10/11 cases, spectral quality of both methods was acceptable. Considering 10/11 cases, we found a statistically significant difference between SVS and 3-D spiral CSI for all three ratios. However, this difference was fixed and was probably caused by a fixed bias. This means that 3-D spiral CSI can be used instead of SVS by removing the mean difference between the methods for each ratio. Accelerated 3-D CSI is feasible in pediatric patients and can potentially substitute for SVS.

  14. Multiple ScS travel times in the western pacific: Implications for mantle heterogeneity

    SciTech Connect

    Sipkin, S.A.; Jordan, T.H.

    1980-02-10

    Multiple ScS travel times have been obtained by wave form cross correlation from seismograms digitally recorded by the High Gain Long Period (HGLP) and Seismic Research Observatory (SRO) networks. The surface projections of the paths corresponding to these data cross the western Pacific on oceanic crust greater than 100 m.y. old or traverse continental regions. The difference between the median ScS/sub n/--ScS/sub n-1/ residuals for all western Pacific paths and all continental paths is +5.2 s, in agreement with our World Wide Standardized Seismograph Network (WWSSN) data (Sipkin and Jordan, 1976). These results support the hypothesis that the average mantle shear velocity of old ocean basins is significantly less than that of old continental nuclei. The medians of both the oceanic and continental residuals for the HGLP and SRO data are more positive than those for the higher-frequency WWSSN data by amounts consistent with attenuative dispersion, which we take to be direct evidence for such dispersion. The residuals for paths crossing China have a median 2 s greater than the median for all continental paths, supporting the inference from dispersion studies that the upper mantle beneath China is characterized by anomalously low shear velocities. The residuals for western Pacific paths show lateral variations of 5 s or more not correlated in any systematic way with crustal ages along the paths. An analysis of these variations suggests that for horizontal scale lengths of the order of 10/sup 3/ km the amplitude of lateral variability is greater along a SW-NE axis than along a SE-NW axis. Mesoscale heterogeneity in the western Pacific may thus consist of predominantly NW trending structures.

  15. Electrostatic shape control of single crystal silicon (SCS), free standing, thin plate deformable mirrors

    NASA Astrophysics Data System (ADS)

    Tidwell, Terry L.

    This research involved the creation and investigation of a low cost design for a MEMS platform capable of controlled shape morphing using very simple mechanical design and manufacturing processes. The platform is made of single crystal silicon and loaded with multiple in-plane forces and moments from three fixed positions on the plate boundary, and with distributed electrostatic forces across the platform surface. This work is important because such a platform could be used as a deformable mirror for adaptive optics systems used in laser communications, vision science, precision beam shaping, and many other important applications. The work involved the development and experimental validation of analytical models that can map the displacement field of a thin flat SCS plate subject to complex loading on the boundary and distributed electrostatic forces. The achievement of these goals included experimentally mapping the platform surface after deformation into three-dimensional geometries defined by the Zernike polynomials. These are relatively large elastic deflections requiring a highly nonlinear analysis. The current analysis applies to circular plates supported on buckled flexures, which have been designed based an model results, fabricated using common microelectronic fabrication processes, and characterized using optical and interference microscopy. Of special interest is the investigation of post-buckling behavior which enhances the range and robustness of operation of the device by providing local upward motion for some modes. The prototypes have been tested and the results compared well with the theoretical results. The first 15 Zernike modes were examined with successful mode shape generation of 13, and fitting errors less than unity were achieved for all 15. From continued analysis of the experimental results the models can be further enhanced to create a commercially viable real time control algorithm for the device.

  16. Characterization Data Package for Containerized Sludge Samples Collected from Engineered Container SCS-CON-210

    SciTech Connect

    Fountain, Matthew S.; Fiskum, Sandra K.; Baldwin, David L.; Daniel, Richard C.; Bos, Stanley J.; Burns, Carolyn A.; Carlson, Clark D.; Coffey, Deborah S.; Delegard, Calvin H.; Edwards, Matthew K.; Greenwood, Lawrence R.; Neiner, Doinita; Oliver, Brian M.; Pool, Karl N.; Schmidt, Andrew J.; Shimskey, Rick W.; Sinkov, Sergey I.; Snow, Lanee A.; Soderquist, Chuck Z.; Thompson, Christopher J.; Trang-Le, Truc LT; Urie, Michael W.

    2013-09-10

    This data package contains the K Basin sludge characterization results obtained by Pacific Northwest National Laboratory during processing and analysis of four sludge core samples collected from Engineered Container SCS-CON-210 in 2010 as requested by CH2M Hill Plateau Remediation Company. Sample processing requirements, analytes of interest, detection limits, and quality control sample requirements are defined in the KBC-33786, Rev. 2. The core processing scope included reconstitution of a sludge core sample distributed among four to six 4-L polypropylene bottles into a single container. The reconstituted core sample was then mixed and subsampled to support a variety of characterization activities. Additional core sludge subsamples were combined to prepare a container composite. The container composite was fractionated by wet sieving through a 2,000 micron mesh and a 500-micron mesh sieve. Each sieve fraction was sampled to support a suite of analyses. The core composite analysis scope included density determination, radioisotope analysis, and metals analysis, including the Waste Isolation Pilot Plant Hazardous Waste Facility Permit metals (with the exception of mercury). The container composite analysis included most of the core composite analysis scope plus particle size distribution, particle density, rheology, and crystalline phase identification. A summary of the received samples, core sample reconstitution and subsampling activities, container composite preparation and subsampling activities, physical properties, and analytical results are presented. Supporting data and documentation are provided in the appendices. There were no cases of sample or data loss and all of the available samples and data are reported as required by the Quality Assurance Project Plan/Sampling and Analysis Plan.

  17. Nucleotide sequence and phylogeny of a chloramphenicol acetyltransferase encoded by the plasmid pSCS7 from Staphylococcus aureus.

    PubMed

    Schwarz, S; Cardoso, M

    1991-08-01

    The nucleotide sequence of the chloramphenicol acetyltransferase gene (cat) and its regulatory region, encoded by the plasmid pSCS7 from Staphylococcus aureus, was determined. The structural cat gene encoded a protein of 209 amino acids, which represented one monomer of the enzyme chloramphenicol acetyltransferase (CAT). Comparisons between the amino acid sequences of the pSCS7-encoded CAT from S. aureus and the previously sequenced CAT variants from S. aureus, Staphylococcus intermedius, Staphylococcus haemolyticus, Bacillus pumilis, Clostridium difficile, Clostridium perfringens, Escherichia coli, Shigella flexneri, and Proteus mirabilis were performed. An alignment of CAT amino acid sequences demonstrated the presence of 34 conserved amino acids among all CAT variants. These conserved residues were considered for their possible roles in the structure and function of CAT. On the basis of the alignment, a phylogenetic tree was constructed. It demonstrated relatively large evolutionary distances between the CAT variants of enteric bacteria, Clostridium, Bacillus, and Staphylococcus species.

  18. The Seasonal Circulation and Dynamics of the South China Sea (SCS) and the Indonesian Throughflow (ITF) Region

    NASA Astrophysics Data System (ADS)

    Xu, D.; Rizzoli, P. M.

    2013-12-01

    The upper layer, wind-driven circulation of the South China Sea (SCS) and the Indonesian Throughflow (ITF) are simulated using a high resolution model, FVCOM (Finite Volume Coastal Ocean Model) in a regional domain comprising the Maritime Continent. The seasonal variability of the wind-driven circulation produced by the monsoon system is realistically simulated. In the SCS the dominant driving force is the monsoon wind and the surface circulation reverses accordingly, with a net cyclonic tendency in winter and anticyclonic in summer. The SCS circulation in the 90s is weaker than in the 60s because of the weaker monsoon system in the 90s. In the upper 50 m the interaction between the SCSTF and ITF is very important. The southward ITF can be blocked by the SCSTF at the Makassar Strait during winter. In summer, part of the ITF feeds the SCSTF flowing into the SCS through the Karimata Strait. The ITF is primarily controlled by the sea level difference between the western Pacific and eastern Indian Ocean. The ITF flow, consistently southwestward below the surface layer, is stronger in the 90s. The volume transports for winter, summer and yearly are estimated from the simulation through all the interocean straits. On the annual average, there is a ~ 5.6 Sv of western Pacific water entering the SCS through the Luzon Strait and ~ 1.4 Sv exiting through the Karimata Strait into the Java Sea. Also, ~ 2 Sv of SCS water enters the Sulu Sea through the Mindoro Strait, while ~ 2.9 Sv flow southwards through the Sibutu Strait merging into the ITF. The ITF inflow occurs through the Makassar Strait (up to ~ 62%) and the Lifamatola Strait ( ~ 38% ). The annual average volume transport of the ITF inflow from the simulation is ~ 15 Sv in the 60s and ~ 16.6 Sv in the 90s, very close to the long term observations. The transport estimates of the simulation at all the straits are in rather good agreement with the observational estimates. We analyze the thermal structure of the domain in

  19. Theoretical studies of the low-lying states of ScO, ScS, VO, and VS

    NASA Technical Reports Server (NTRS)

    Bauschlicher, Charles W., Jr.; Langhoff, Stephen R.

    1986-01-01

    Bonding in the low-lying states of ScO, ScS, VO, and VS is theoretically studied. Excellent agreement is obtained with experimental spectroscopic constants for the low-lying states of ScO and VO. The results for VS and ScS show that the bonding in the oxides and sulfides is similar, but that the smaller electronegativity in S leads to a smaller ionic component in the bonding. The computed D0 of the sulfides are about 86 percent of the corresponding oxides, and the low-lying excited states are lower in the sulfides than in the corresponding oxides. The CPF method is shown to be an accurate and cost-effective method for obtaining reliable spectroscopic constants for these systems.

  20. The MC-DFT approach including the SCS-MP2 energies to the new Minnesota-type functionals.

    PubMed

    Liu, Po-Chun; Hu, Wei-Ping

    2014-08-05

    We have applied the multicoefficient density functional theory (MC-DFT) to four recent Minnesota functionals, including M06-2X, M08-HX, M11, and MN12-SX on the performance of thermochemical kinetics. The results indicated that the accuracy can be improved significantly using more than one basis set. We further included the SCS-MP2 energies into MC-DFT, and the resulting mean unsigned errors (MUEs) decreased by approximately 0.3 kcal/mol for the most accurate basis set combinations. The M06-2X functional with the simple [6-311+G(d,p)/6-311+G(2d,2p)] combination gave the best performance/cost ratios for the MC-DFT and MC-SCS-MP2|MC-DFT methods with MUE of 1.58 and 1.22 kcal/mol, respectively.

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

    PubMed

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

    2012-04-01

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

  2. Human cord blood-derived multipotent stem cells (CB-SCs) treated with all-trans-retinoic acid (ATRA) give rise to dopamine neurons.

    PubMed

    Li, Xiaohong; Li, Heng; Bi, Jianfen; Chen, Yana; Jain, Sumit; Zhao, Yong

    2012-03-02

    Parkinson's disease (PD) results from the chronic degeneration of dopaminergic neurons. A replacement for these neurons has the potential to provide a clinical cure and/or lasting treatment for symptoms of the disease. Human cord blood-derived multipotent stem cells (CB-SCs) display embryonic stem cell characteristics, including multi-potential differentiation. To explore their therapeutic potential in PD, we examined whether CB-SCs could be induced to differentiate into dopamine neurons in the presence of all-trans retinoic acid (ATRA). Prior to treatment, CB-SCs expressed mRNA and protein for the key dopaminergic transcription factors Nurr1, Wnt1, and En1. Following treatment with 10 μM ATRA for 12 days, CB-SCs displayed elongated neuronal-like morphologies. Immunocytochemistry revealed that 48 ± 11% of ATRA-treated cells were positive for tyrosine hydroxylase (TH), and 36 ± 9% of cells were positive for dopamine transporter (DAT). In contrast, control CB-SCs (culture medium only) expressed only background levels of TH and DAT. Finally, ATRA-treated CB-SCs challenged with potassium released increased levels of dopamine compared to control. These data demonstrate that ATRA induces differentiation of CB-SCs into dopaminergic neurons. This finding may lead to the development of an alternative approach to stem cell therapy for Parkinson's disease.

  3. Application of the PJ and NPS evaporation duct models over the South China Sea (SCS) in winter

    PubMed Central

    Yang, Shaobo; Li, Xingfei; Wu, Chao; He, Xin; Zhong, Ying

    2017-01-01

    The detection of duct height has a significant effect on marine radar or wireless apparatus applications. The paper presents two models to verify the adaptation of evaporation duct models in the SCS in winter. A meteorological gradient instrument used to measure evaporation ducts was fabricated using hydrological and meteorological sensors at different heights. An experiment on the adaptive characteristics of evaporation duct models was carried out over the SCS. The heights of the evaporation ducts were measured by means of log-linear fit, Paulus-Jeske (PJ) and Naval Postgraduate School (NPS) models. The results showed that NPS model offered significant advantages in stability compared with the PJ model. According the collected data computed by the NPS model, the mean deviation (MD) was -1.7 m, and the Standard Deviation (STD) of the MD was 0.8 m compared with the true value. The NPS model may be more suitable for estimating the evaporation duct height in the SCS in winter due to its simpler system characteristics compared with meteorological gradient instruments. PMID:28273113

  4. Application of the PJ and NPS evaporation duct models over the South China Sea (SCS) in winter.

    PubMed

    Yang, Shaobo; Li, Xingfei; Wu, Chao; He, Xin; Zhong, Ying

    2017-01-01

    The detection of duct height has a significant effect on marine radar or wireless apparatus applications. The paper presents two models to verify the adaptation of evaporation duct models in the SCS in winter. A meteorological gradient instrument used to measure evaporation ducts was fabricated using hydrological and meteorological sensors at different heights. An experiment on the adaptive characteristics of evaporation duct models was carried out over the SCS. The heights of the evaporation ducts were measured by means of log-linear fit, Paulus-Jeske (PJ) and Naval Postgraduate School (NPS) models. The results showed that NPS model offered significant advantages in stability compared with the PJ model. According the collected data computed by the NPS model, the mean deviation (MD) was -1.7 m, and the Standard Deviation (STD) of the MD was 0.8 m compared with the true value. The NPS model may be more suitable for estimating the evaporation duct height in the SCS in winter due to its simpler system characteristics compared with meteorological gradient instruments.

  5. The analysis of SCS return momentum effects on the RCS water level during mid-loop operations

    SciTech Connect

    swang Seo, J.; Young Yang, J.; Tack Hwang, S.

    1995-09-01

    An accurate prediction of Reactor Coolant System (RCS) water levels is of importance in the determination of allowable operating range to ensure the safety during the mid-loop operations. However, complex hydraulic phenomena induced by Shutdown Cooling System (SCS) return momentum cause different water levels from those in the loop where the water level indicators are located. This was apparantly observed at the pre-core cold hydro test of the Younggwang Nuclear Unit 3 (YGN 3) in Korea. In this study, in order to analytically understand the effect of the SCS return momentum on the RCS water level and its general trend, a model using one-dimensional momentum equation, hydraulic jump, Bernoulli equation, flow resistance coefficient, and total water volume conservation has been developed to predict the RCS water levels at various RCS locations during the mid-loop conditions and the simulation results were compared with the test data. The analysis shows that the hydraulic jump in the operating cold legs in conjunction with the momentum loss throughout the RCS is the main cause creating the water level differences at various RCS locations. The prediction results provide good explanations for the test data and show the significant effect of the SCS return momentum on the RCS water levels.

  6. Electrochemical Characterization of a Novel Exoelectrogenic Bacterium Strain SCS5, Isolated from a Mediator-Less Microbial Fuel Cell and Phylogenetically Related to Aeromonas jandaei

    PubMed Central

    Sharma, Subed Chandra Dev; Feng, Cuijie; Li, Jiangwei; Hu, Anyi; Wang, Han; Qin, Dan; Yu, Chang-Ping

    2016-01-01

    A facultative anaerobic bacterium, designated as strain SCS5, was isolated from the anodic biofilm of a mediator-less microbial fuel cell using acetate as the electron donor and α-FeOOH as the electron acceptor. The isolate was Gram-negative, motile, and shaped as short rods (0.9–1.3 μm in length and 0.4–0.5 μm in width). A phylogenetic analysis of the 16S rRNA, gyrB, and rpoD genes suggested that strain SCS5 belonged to the Aeromonas genus in the Aeromonadaceae family and exhibited the highest 16S rRNA gene sequence similarity (99.45%) with Aeromonas jandaei ATCC 49568. However, phenotypic, cellular fatty acid profile, and DNA G+C content analyses revealed that there were some distinctions between strain SCS5 and the type strain A. jandaei ATCC 49568. The optimum growth temperature, pH, and NaCl (%) for strain SCS5 were 35°C, 7.0, and 0.5% respectively. The DNA G+C content of strain SCS5 was 59.18%. The isolate SCS5 was capable of reducing insoluble iron oxide (α-FeOOH) and transferring electrons to extracellular material (the carbon electrode). The electrochemical activity of strain SCS5 was corroborated by cyclic voltammetry and a Raman spectroscopic analysis. The cyclic voltammogram of strain SCS5 revealed two pairs of oxidation-reduction peaks under anaerobic and aerobic conditions. In contrast, no redox pair was observed for A. jandaei ATCC 49568. Thus, isolated strain SCS5 is a novel exoelectrogenic bacterium phylogenetically related to A. jandaei, but shows distinct electrochemical activity from its close relative A. jandaei ATCC 49568. PMID:27396922

  7. Cardiac High-Energy Phosphate Metabolism Alters with Age as Studied in 196 Healthy Males with the Help of 31-Phosphorus 2-Dimensional Chemical Shift Imaging

    PubMed Central

    Esterhammer, Regina; Klug, Gert; Wolf, Christian; Mayr, Agnes; Reinstadler, Sebastian; Feistritzer, Hans-Josef; Metzler, Bernhard; Schocke, Michael F. H.

    2014-01-01

    Recently published studies have elucidated alterations of mitochondrial oxidative metabolism during ageing. The intention of the present study was to evaluate the impact of ageing on cardiac high-energy phosphate metabolism and cardiac function in healthy humans. 31-phosphorus 2-dimensional chemical shift imaging (31P 2D CSI) and echocardiography were performed in 196 healthy male volunteers divided into groups of 20 to 40 years (I, n = 43), 40 to 60 years (II, n = 123) and >60 years (III, n = 27) of age. Left ventricular PCr/β-ATP ratio, myocardial mass (MM), ejection fraction and E/A ratio were assessed. Mean PCr/β-ATP ratios were significantly different among the three groups of volunteers (I, 2.10±0.37; II, 1.77±0.37; III, 1.45±0.28; all p<0.001). PCr/β-ATP ratios were inversely related to age (r2 = −0.25; p<0.001) with a decrease from 2.65 by 0.02 per year of ageing. PCr/β-ATP ratios further correlated with MM (r = −0.371; p<0.001) and E/A ratios (r = 0.213; p<0.02). Moreover, E/A ratios (r = −0.502, p<0.001), MM (r = 0.304, p<0.001), glucose-levels (r = 0.157, p<0.05) and systolic blood pressure (r = 0.224, p<0.005) showed significant correlations with age. The ejection fraction did not significantly differ between the groups. This study shows that cardiac PCr/β-ATP ratios decrease moderately with age indicating an impairment of mitochondrial oxidative metabolism due to age. Furthermore, MM increases, and E/A ratio decreases with age. Both correlate with left-ventricular PCr/β-ATP ratios. The findings of the present study confirm numerous experimental studies showing an impairment of cardiac mitochondrial function with age. PMID:24940736

  8. Ethanol-induced fatty liver in the rat examined by in vivo 1H chemical shift selective magnetic resonance imaging and localized spectroscopic methods.

    PubMed

    Ling, M; Brauer, M

    1992-01-01

    In vivo 1H magnetic resonance imaging (MRI), chemical shift selective imaging (CSI), and localized (VOSY) 1H magnetic resonance spectroscopy (MRS) were used to study fatty infiltration in the livers of rats chronically fed an ethanol-containing all-liquid DeCarli-Lieber diet. Conventional total proton MRI showed a somewhat hyperintense liver for ethanol-fed rats, compared with pair-fed controls. CSI showed a dramatic increase in the fat signal intensity for ethanol-treated rats that was fairly homogeneous throughout the liver. However, CSI also showed a substantial decrease in the water signal intensity for the ethanol-treated rats compared to pair-fed control rats. 1H VOSY MR spectra also showed a 5.5-fold increase in the methylene resonance (1.3 ppm) of fat and a 50-70% decrease in the water resonance (4.8 ppm). Relative in vivo proton T1 and T2 relaxation times for the water resonance separate from the fat resonance, determined from modified VOSY experiments, were found to tend to increase and decrease, respectively, for ethanol-treated rat livers compared with controls. The decrease in hepatic water signal intensity could be accounted for by the decrease in T2 and decrease in water density due to the presence of accumulated hepatic fat (approximately 25 mg/g wet weight of liver). When ethanol was withdrawn from the chronically treated rats, fatty infiltration was observed by both CSI and VOSY spectra to revert toward control values with a half-life of 2-4 days. By day 16, however, the signal intensity for hepatic fat was still significantly higher than control levels. In vitro 1H MRS studies of chloroform-methanol extracts confirmed the 5.5-fold increase in total hepatic fat induced by the chronic ethanol treatment, and showed further that triacylglycerols were increased 7.7-fold, cholesterol was increased fourfold, and phospholipids were increased 3.3-fold, compared with liver extracts from pair-fed control rats.

  9. Mapping lithosphere thickness beneath China with ScS reverberation data: what controls the intraplate seismicity in Mainland China

    NASA Astrophysics Data System (ADS)

    Niu, F.

    2011-12-01

    China is a country with high levels of seismic activity, and has a history of strong earthquakes that caused great loss in both life and property. While it is generally believed that the high seismicity is the result of the prolonged collision between India and Eurasia plates in the west, and the continuous rollback of the Pacific subduction in the east, there are, however, no quantitative explanations on the distribution of the observed seismicity. In this study, we intend to seek a possible relationship between the seismicity and lithospheric structure at large scale (~100km). We developed a new method that uses ScS reverberation data from deep earthquakes to image the lithosphere and asthenosphere boundary (LAB). More specifically, we used more than 600 CEArray records (The CEArray consists of 31 regional networks operated by the China Earthquake Administration (CEA)) from a large deep earthquake occurring beneath the Sea of Okhotsk on July 5 of 2008. Multiple reflections of SH waves between the free surface and the core-mantle boundary (ScS1, ScS2, ScS3) can be clearly identified from all the individual records. We used the upperside reflections at the LAB (ScSm_SdS), which arrive after the main ScS multiples (ScSm), to estimate the depth of the boundary. We employed a common-reflection-point (CRP) stacking technique to the ScS reverberation data to enhance the signal-to-noise ratio (SNR) of the LAB reflections. At an assuming LAB depth, d, for each source-receiver pair, we first computed the reflection points of ScSm_SdS and the time moveouts of the ScSm_SdS with respect to ScSm by ray tracing the iasp91 velocity model. We further included corrections computed from 3D crustal and mantle velocity models. We divided the study area (18°N to 54°N, 75°E to 134°E) into meshed grid of 1° by 1°, and used a circular cap with a radius of 1 degree for gathering the ScS reverberations. We then summed all the reverberation data within a 0.5 s window centered on the

  10. Synthesis, NMR spectroscopic characterization and structure of a divinyldisilazane-(triphenylphosphine)platinum(0) complex: observation of isotope-induced chemical shifts (1)Δ(12/13)C((195)Pt).

    PubMed

    Wrackmeyer, Bernd; Klimkina, Elena V; Schmalz, Thomas; Milius, Wolfgang

    2013-05-01

    Tetramethyldivinyldisilazane-(triphenylphosphine)platinum(0) was prepared, characterized in solid state by X-ray crystallography and in solution by multinuclear magnetic resonance spectroscopy ((1)H, (13)C, (15)N, (29)Si, (31)P and (195)Pt NMR). Numerous signs of spin-spin coupling constants were determined by two-dimensional heteronuclear shift correlations (HETCOR) and two-dimensional (1)H/(1)H COSY experiments. Isotope-induced chemical shifts (1)Δ(12/13)C((195)Pt) were measured from (195)Pt NMR spectra of the title compound as well as of other Pt(0), Pt(II) and Pt(IV) compounds for comparison. In contrast to other heavy nuclei such as (199)Hg or (207)Pb, the "normal" shifts of the heavy isotopomers to low frequencies are found, covering a range of >500 ppb.

  11. Fluid Shifts

    NASA Technical Reports Server (NTRS)

    Stenger, M. B.; Hargens, A.; Dulchavsky, S.; Ebert, D.; Lee, S.; Laurie, S.; Garcia, K.; Sargsyan, A.; Martin, D.; Lui, J.; Macias, B.; Arbeille, P.; Danielson, R.; Chang, D.; Gunga, H.; Johnston, S.; Westby, C.; Ribeiro, L.; Ploutz-Snyder, R.; Smith, S.

    2015-01-01

    INTRODUCTION: Mechanisms responsible for the ocular structural and functional changes that characterize the visual impairment and intracranial pressure (ICP) syndrome (VIIP) are unclear, but hypothesized to be secondary to the cephalad fluid shift experienced in spaceflight. This study will relate the fluid distribution and compartmentalization associated with long-duration spaceflight with VIIP symptoms. We also seek to determine whether the magnitude of fluid shifts during spaceflight, as well as the VIIP-related effects of those shifts, can be predicted preflight with acute hemodynamic manipulations, and also if lower body negative pressure (LBNP) can reverse the VIIP effects. METHODS: Physiologic variables will be examined pre-, in- and post-flight in 10 International Space Station crewmembers including: fluid compartmentalization (D2O and NaBr dilution); interstitial tissue thickness (ultrasound); vascular dimensions and dynamics (ultrasound and MRI (including cerebrospinal fluid pulsatility)); ocular measures (optical coherence tomography, intraocular pressure, ultrasound); and ICP measures (tympanic membrane displacement, otoacoustic emissions). Pre- and post-flight measures will be assessed while upright, supine and during 15 deg head-down tilt (HDT). In-flight measures will occur early and late during 6 or 12 month missions. LBNP will be evaluated as a countermeasure during HDT and during spaceflight. RESULTS: The first two crewmembers are in the preflight testing phase. Preliminary results characterize the acute fluid shifts experienced from upright, to supine and HDT postures (increased stroke volume, jugular dimensions and measures of ICP) which are reversed with 25 millimeters Hg LBNP. DISCUSSION: Initial results indicate that acute cephalad fluid shifts may be related to VIIP symptoms, but also may be reversible by LBNP. The effect of a chronic fluid shift has yet to be evaluated. Learning Objectives: Current spaceflight VIIP research is described

  12. Determination of pKa values of tenoxicam from 1H NMR chemical shifts and of oxicams from electrophoretic mobilities (CZE) with the aid of programs SQUAD and HYPNMR.

    PubMed

    Rodríguez-Barrientos, Damaris; Rojas-Hernández, Alberto; Gutiérrez, Atilano; Moya-Hernández, Rosario; Gómez-Balderas, Rodolfo; Ramírez-Silva, María Teresa

    2009-12-15

    In this work it is explained, by the first time, the application of programs SQUAD and HYPNMR to refine equilibrium constant values through the fit of electrophoretic mobilities determined by capillary zone electrophoresis experiments, due to the mathematical isomorphism of UV-vis absorptivity coefficients, NMR chemical shifts and electrophoretic mobilities as a function of pH. Then, the pK(a) values of tenoxicam in H(2)O/DMSO 1:4 (v/v) have been obtained from (1)H NMR chemical shifts, as well as of oxicams in aqueous solution from electrophoretic mobilities determined by CZE, at 25 degrees C. These values are in very good agreement with those reported by spectrophotometric and potentiometric measurements.

  13. Arginine Interactions with Anatase TiO2 (100) Surface and the Perturbation of 49Ti NMR Chemical Shifts - A DFT Investigation: Relevance to Renu-Seeram Bio Solar Cell

    SciTech Connect

    Koch, Rainer; Lipton, Andrew S.; Filipek, S.; Renugopalakrishnan, Venkatesan M.

    2011-06-01

    Density functional theoretical calculations have been utilized to investigate the interaction of the amino acid arginine with the (100) surface of anatase and the reproduction of experimentally measured 49Ti NMR chemical shifts of anatase. Significant binding of arginine through electrostatic interaction and hydrogen bonds of the arginine guanidinium protons to the TiO2 surface oxygen atoms is observed, allowing attachment of proteins to titania surfaces in the construction of bio-sensitized solar cells. GIAO-B3LYP/6-31G(d) NMR calculation of a three-layer model based on the experimental structure of this TiO2 modification gives an excellent reproduction of the experimental value (-927 ppm) within +/- 7 ppm, however, the change in relative chemical shifts, EFGs and CSA suggest that the effect of the electrostatic arginine binding might be too small for experimental detection.

  14. Application of ChemDraw NMR Tool: Correlation of Program-Generated (Super 13)C Chemical Shifts and pK[subscript a] Values of Para-Substituted Benzoic Acids

    ERIC Educational Resources Information Center

    Hongyi Wang

    2005-01-01

    A study uses the ChemDraw nuclear magnetic resonance spectroscopy (NMR) tool to process 15 para-substituted benzoic acids and generate (super 13)C NMR chemical shifts of C1 through C5. The data were plotted against their pK[subscript a] value and a fairly good linear fit was found for pK[subscript a] versus delta[subscript c1].

  15. Proton Resonance Frequency Chemical Shift Thermometry: Experimental Design and Validation Towards High-Resolution Non-Invasive Temperature Monitoring, and in vivo Experience in a Non-human Primate Model of Acute Ischemic Stroke

    PubMed Central

    Dehkharghani, Seena; Mao, Hui; Howell, Leonard; Zhang, Xiaodong; Pate, K S; Magrath, P R; Tong, Frank; Wei, L; Qiu, D; Fleischer, C; Oshinski, J N

    2016-01-01

    BACKGROUND AND PURPOSE Applications for non-invasive biological temperature monitoring are widespread in biomedicine, and of particular interest in the context of brain temperature regulation, where traditionally costly and invasive monitoring schemes limit their applicability in many settings. Brain thermal regulation therefore remains controversial, motivating the development of non-invasive approaches such as temperature-sensitive NMR phenomena. The purpose of this work was to compare the utility of competing approaches to MR thermometry (MRT) employing proton resonance frequency chemical shift. Three methodologies were tested, hypothesizing the feasibility of a fast and accurate approach to chemical shift thermometry, in a phantom study at 3.0 Tesla. MATERIALS AND METHODS A conventional, paired approach (DIFF-1), an accelerated single-scan approach (DIFF-2), and a new, further accelerated strategy (DIFF-3) were tested. Phantom temperatures were modulated during real-time fiber optic temperature monitoring, with MRT derived simultaneously from temperature-sensitive changes in the water proton chemical shift (~0.01 ppm/°C). MRT was subsequently performed in a series of in vivo non-human primate experiments under physiologic and ischemic conditions testing its reproducibility and overall performance. RESULTS Chemical shift thermometry demonstrated excellent agreement with phantom temperatures for all three approaches (DIFF-1 linear regression R2=0.994, p<0.001, acquisition time 4 min 40 s; DIFF-2 R2=0.996, p<0.001, acquisition time 4 min; DIFF-3 R2=0.998, p<0.001, acquisition time 40 s). CONCLUSION These findings confirm the comparability in performance of three competing approaches MRT, and present in vivo applications under physiologic and ischemic conditions in a primate stroke model. PMID:25655874

  16. 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).

    PubMed

    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.

  17. Fluid Shifts

    NASA Technical Reports Server (NTRS)

    Stenger, M.; Hargens, A.; Dulchavsky, S.; Ebert, D.; Lee, S.; Lauriie, S.; Garcia, K.; Sargsyan, A.; Martin, D.; Ribeiro, L.; Lui, J.; Macias, B.; Arbeille, P.; Danielson, R.; Chang, D.; Johnston, S.; Ploutz-Snyder, R.; Smith, S.

    2016-01-01

    NASA is focusing on long-duration missions on the International Space Station (ISS) and future exploration-class missions beyond low-Earth orbit. Visual acuity changes observed after short-duration missions were largely transient, but more than 50% of ISS astronauts experienced more profound, chronic changes with objective structural and functional findings such as papilledema and choroidal folds. Globe flattening, optic nerve sheath dilation, and optic nerve tortuosity also are apparent. This pattern is referred to as the visual impairment and intracranial pressure (VIIP) syndrome. VIIP signs and symptoms, as well as postflight lumbar puncture data, suggest that elevated intracranial pressure (ICP) may be associated with the spaceflight-induced cephalad fluid shifts, but this hypothesis has not been tested. The purpose of this study is to characterize fluid distribution and compartmentalization associated with long-duration spaceflight, and to correlate these findings with vision changes and other elements of the VIIP syndrome. We also seek to determine whether the magnitude of fluid shifts during spaceflight, as well as the VIIP-related effects of those shifts, is predicted by the crewmember's preflight conditions and responses to acute hemodynamic manipulations (such as head-down tilt). Lastly, we will evaluate the patterns of fluid distribution in ISS astronauts during acute reversal of fluid shifts through application of lower body negative pressure (LBNP) interventions to characterize and explain general and individual responses. METHODS: We will examine a variety of physiologic variables in 10 long-duration ISS crewmembers using the test conditions and timeline presented in the Figure below. Measures include: (1) fluid compartmentalization (total body water by D2O, extracellular fluid by NaBr, intracellular fluid by calculation, plasma volume by CO rebreathe, interstitial fluid by calculation); (2) forehead/eyelids, tibia, calcaneus tissue thickness (by

  18. A Series of Diamagnetic Pyridine Monoimine Rhenium Complexes with Different Degrees of Metal-to-Ligand Charge Transfer: Correlating (13) C NMR Chemical Shifts with Bond Lengths in Redox-Active Ligands.

    PubMed

    Sieh, Daniel; Kubiak, Clifford P

    2016-07-18

    A set of pyridine monoimine (PMI) rhenium(I) tricarbonyl chlorido complexes with substituents of different steric and electronic properties was synthesized and fully characterized. Spectroscopic (NMR and IR) and single-crystal X-ray diffraction analyses of these complexes showed that the redox-active PMI ligands are neutral and that the overall electronic structure is little affected by the choices of the substituent at the ligand backbone. One- and two-electron reduction products were prepared from selected starting compounds and could also be characterized by multiple spectroscopic methods and X-ray diffraction. The final product of a one-electron reduction in THF is a diamagnetic metal-metal-bonded dimer after loss of the chlorido ligand. Bond lengths in and NMR chemical shifts of the PMI ligand backbone indicate partial electron transfer to the ligand. Two-electron reduction in THF also leads to the loss of the chlorido ligand and a pentacoordinate complex is obtained. The comparison with reported bond lengths and (13) C NMR chemical shifts of doubly reduced free pyridine monoaldimine ligands indicates that both redox equivalents in the doubly reduced rhenium complex investigated here are located in the PMI ligand. With diamagnetic complexes varying over three formal reduction stages at the PMI ligand we were, for the first time, able to establish correlations of the (13) C NMR chemical shifts with the relevant bond lengths in redox-active ligands over a full redox series.

  19. Yet1p-Yet3p interacts with Scs2p-Opi1p to regulate ER localization of the Opi1p repressor.

    PubMed

    Wilson, Joshua D; Thompson, Sarah L; Barlowe, Charles

    2011-05-01

    Lipid sensing mechanisms at the endoplasmic reticulum (ER) coordinate an array of biosynthetic pathways. A major phospholipid regulatory circuit in yeast is controlled by Scs2p, an ER membrane protein that binds the transcriptional repressor protein Opi1p. Cells grown in the absence of inositol sequester Scs2p-Opi1p at the ER and derepress target genes including INO1. We recently reported that Yet1p and Yet3p, the yeast homologues of BAP29 and BAP31, are required for normal growth in the absence of inositol. Here we show that the Yet1p-Yet3p complex acts in derepression of INO1 through physical association with Scs2p-Opi1p. Yet complex binding to Scs2p-Opi1p was enhanced by inositol starvation, although the interaction between Scs2p and Opi1p was not influenced by YET1 or YET3 deletion. Interestingly, live-cell imaging analysis indicated that Opi1p does not efficiently relocalize to the ER during inositol starvation in yet3Δ cells. Together our data demonstrate that a physical association between the Yet complex and Scs2p-Opi1p is required for proper localization of the Opi1p repressor to ER membranes and subsequent INO1 derepression.

  20. Crystal structure and anomalous chemical shift of 10-(prop-1-yn-1-yl)-10H-phenothiazine 5,5-dioxide: Intramolecular S⋯N transannular effect

    NASA Astrophysics Data System (ADS)

    Umezono, Satoru; Okuno, Tsunehisa

    2013-10-01

    The novel ynamine compounds, 10-(prop-1-yn-1-yl)-10H-phenothiazine 5-oxide (2) and 10-(prop-1-yn-1-yl)-10H-phenothiazine 5,5-dioxide (3), were prepared by MCPBA oxidation of 10-(prop-1-yn-1-yl)-10H-phenothiazine (1). These compounds were characterized successfully by crystallographical analyses, 1H and 13C NMR. The 1H NMR signals of 2 showed downfield shifts compared with 1 as expected. However two kinds of signals, methyl and 1,9-position of 3, indicated upfield shifts compared with 2. These anomalous upfield shifts were reasonably explained by trans-annular S⋯N interaction and by increase of electron density on the nitrogen atom.

  1. {sup 13}C chemical shift anisotropies for carbonate ions in cement minerals and the use of {sup 13}C, {sup 27}Al and {sup 29}Si MAS NMR in studies of Portland cement including limestone additions

    SciTech Connect

    Sevelsted, Tine F.; Herfort, Duncan

    2013-10-15

    {sup 13}C isotropic chemical shifts and chemical shift anisotropy parameters have been determined for a number of inorganic carbonates relevant in cement chemistry from slow-speed {sup 13}C MAS or {sup 13}C({sup 1}H) CP/MAS NMR spectra (9.4 T or 14.1 T) for {sup 13}C in natural abundance. The variation in the {sup 13}C chemical shift parameters is relatively small, raising some doubts that different carbonate species in Portland cement-based materials may not be sufficiently resolved in {sup 13}C MAS NMR spectra. However, it is shown that by combining {sup 13}C MAS and {sup 13}C({sup 1}H) CP/MAS NMR carbonate anions in anhydrous and hydrated phases can be distinguished, thereby providing valuable information about the reactivity of limestone in cement blends. This is illustrated for three cement pastes prepared from an ordinary Portland cement, including 0, 16, and 25 wt.% limestone, and following the hydration for up to one year. For these blends {sup 29}Si MAS NMR reveals that the limestone filler accelerates the hydration for alite and also results in a smaller fraction of tetrahedrally coordinated Al incorporated in the C-S-H phase. The latter result is more clearly observed in {sup 27}Al MAS NMR spectra of the cement–limestone blends and suggests that dissolved aluminate species in the cement–limestone blends readily react with carbonate ions from the limestone filler, forming calcium monocarboaluminate hydrate. -- Highlights: •{sup 13}C chemical shift anisotropies for inorganic carbonates from {sup 13}C MAS NMR. •Narrow {sup 13}C NMR chemical shift range (163–171 ppm) for inorganic carbonates. •Anhydrous and hydrated carbonate species by {sup 13}C MAS and {sup 13}C({sup 1}H) CP/MAS NMR. •Limestone accelerates the hydration for alite in Portland – limestone cements. •Limestone reduces the amount of aluminium incorporated in the C-S-H phase.

  2. [Genetic polymorphism of the IL8 gene and its associations with milk traits and SCS in Chinese Holstein].

    PubMed

    Chen, Ren-Jin; Yang, Zhang-Ping; Mao, Yong-Jiang; Chen, Ying; Chang, Ling-Ling; Ji, De-Jun; Wu, Hai-Tao; Li, Yun-Long; Li, Rui

    2010-12-01

    The polymorphism of Interleukin-8 (IL8) gene were investigated for 610 Chinese Holstein cows of 30 bull families from a dairy farm in Shanghai using Polymerase Chain Reaction-Single Strand Conformation Polymorphism (PCR-SSCP) technique with a mixed animal model to verify the effects of the polymorphisms on some milk productive performance, tested day milk yield, tested day fat percentage, tested day milk protein percentage, 305 d corrected milk yield, 305 d milk fat yield, 305 d milk protein yield, and somatic cell score (SCS). The aim was to explore the significant molecular marker in practical dairy production. Three genotypes were identified and the genotypic frequencies of KK, KA, and AA were 0.187, 0.451, and 0.362, respectively. The gene frequencies of K and A were 0.412 and 0.588. The results showed highly significant (P < 0.01) association of IL8 mutations with tested day milk yield, 305 d milk protein yield, 305 d corrected milk yield and 305 d milk fat yield, SCS and tested day milk protein percentage (P < 0.05). However, no association (P > 0.05) with tested day milk fat percentage was recorded. The cows with KK genotype had higher tested day milk yield, 305 d milk protein yield, 305 d corrected milk yield and 305 d milk fat yield than those with AA and KA genotypes (P < 0.01). The least square mean of SCS for KK was significantly lower than that with AA and KA genotypes (P < 0.01). AA genotype was significant lower in tested day milk protein percentage than KK and KA genotypes (P < 0.05). The IL8 gene genetic diversity has a great genetic effect on milk traits and mastitis resistance and could be a useful genetic marker for Chinese Holstein breeding.

  3. Framework for event-based semidistributed modeling that unifies the SCS-CN method, VIC, PDM, and TOPMODEL

    NASA Astrophysics Data System (ADS)

    Bartlett, M. S.; Parolari, A. J.; McDonnell, J. J.; Porporato, A.

    2016-09-01

    Hydrologists and engineers may choose from a range of semidistributed rainfall-runoff models such as VIC, PDM, and TOPMODEL, all of which predict runoff from a distribution of watershed properties. However, these models are not easily compared to event-based data and are missing ready-to-use analytical expressions that are analogous to the SCS-CN method. The SCS-CN method is an event-based model that describes the runoff response with a rainfall-runoff curve that is a function of the cumulative storm rainfall and antecedent wetness condition. Here we develop an event-based probabilistic storage framework and distill semidistributed models into analytical, event-based expressions for describing the rainfall-runoff response. The event-based versions called VICx, PDMx, and TOPMODELx also are extended with a spatial description of the runoff concept of "prethreshold" and "threshold-excess" runoff, which occur, respectively, before and after infiltration exceeds a storage capacity threshold. For total storm rainfall and antecedent wetness conditions, the resulting ready-to-use analytical expressions define the source areas (fraction of the watershed) that produce runoff by each mechanism. They also define the probability density function (PDF) representing the spatial variability of runoff depths that are cumulative values for the storm duration, and the average unit area runoff, which describes the so-called runoff curve. These new event-based semidistributed models and the traditional SCS-CN method are unified by the same general expression for the runoff curve. Since the general runoff curve may incorporate different model distributions, it may ease the way for relating such distributions to land use, climate, topography, ecology, geology, and other characteristics.

  4. Catalytic Y-tailed amphiphilic homopolymers – aqueous nanoreactors for high activity, low loading SCS pincer catalysts

    PubMed Central

    Patterson, Joseph P.; Cotanda, Pepa; Kelley, Elizabeth G.; Moughton, Adam O.; Lu, Annhelen; Epps, Thomas H.; O’Reilly, Rachel K.

    2013-01-01

    A new amphiphilic homopolymer bearing an SCS pincer palladium complex has been synthesized by reversible addition fragmentation chain transfer polymerization. The amphiphile has been shown to form spherical and worm-like micelles in water by cryogenic transmission electron microscopy and small angle neutron scattering. Segregation of reactive components within the palladium containing core results in increased catalytic activity of the pincer compound compared to small molecule analogues. This allows carbon-carbon bond forming reactions to be performed in water with reduced catalyst loadings and enhanced activity. PMID:23539324

  5. Prediction of (195) Pt NMR chemical shifts of dissolution products of H2 [Pt(OH)6 ] in nitric acid solutions by DFT methods: how important are the counter-ion effects?

    PubMed

    Tsipis, Athanassios C; Karapetsas, Ioannis N

    2016-08-01

    (195) Pt NMR chemical shifts of octahedral Pt(IV) complexes with general formula [Pt(NO3 )n (OH)6 - n ](2-) , [Pt(NO3 )n (OH2 )6 - n ](4 - n) (n = 1-6), and [Pt(NO3 )6 - n  - m (OH)m (OH2 )n ](-2 + n - m) formed by dissolution of platinic acid, H2 [Pt(OH)6 ], in aqueous nitric acid solutions are calculated employing density functional theory methods. Particularly, the gauge-including atomic orbitals (GIAO)-PBE0/segmented all-electron relativistically contracted-zeroth-order regular approximation (SARC-ZORA)(Pt) ∪ 6-31G(d,p)(E)/Polarizable Continuum Model computational protocol performs the best. Excellent second-order polynomial plots of δcalcd ((195) Pt) versus δexptl ((195) Pt) chemical shifts and δcalcd ((195) Pt) versus the natural atomic charge QPt are obtained. Despite of neglecting relativistic and spin orbit effects the good agreement of the calculated δ (195) Pt chemical shifts with experimental values is probably because of the fact that the contribution of relativistic and spin orbit effects to computed σ(iso) (195) Pt magnetic shielding of Pt(IV) coordination compounds is effectively cancelled in the computed δ (195) Pt chemical shifts, because the relativistic corrections are expected to be similar in the complexes and the proper reference standard used. To probe the counter-ion effects on the (195) Pt NMR chemical shifts of the anionic [Pt(NO3 )n (OH)6 - n ](2-) and cationic [Pt(NO3 )n (OH2 )6 - n ](4 - n) (n = 0-3) complexes we calculated the (195) Pt NMR chemical shifts of the neutral (PyH)2 [Pt(NO3 )n (OH)6 - n ] (n = 1-6; PyH = pyridinium cation, C5 H5 NH(+) ) and [Pt(NO3 )n (H2 O)6 - n ](NO3 )4 - n (n = 0-3) complexes. Counter-anion effects are very important for the accurate prediction of the (195) Pt NMR chemical shifts of the cationic [Pt(NO3 )n (OH2 )6 - n ](4 - n) complexes, while counter-cation effects are less important for the anionic [Pt(NO3 )n (OH)6

  6. Fluid Shifts

    NASA Technical Reports Server (NTRS)

    Stenger, Michael; Hargens, A.; Dulchavsky, S.; Ebert, D.; Lee, S.; Sargsyan, A.; Martin, D.; Lui, J.; Macias, B.; Arbeille, P.; Platts, S.

    2014-01-01

    NASA is focusing on long-duration missions on the International Space Station (ISS) and future exploration-class missions beyond low Earth orbit. Visual acuity changes observed after short-duration missions were largely transient, but more than 30% of ISS astronauts experience more profound, chronic changes with objective structural and functional findings such as papilledema and choroidal folds. Globe flattening, optic nerve sheath dilation, and optic nerve tortuosity also are apparent. This pattern is referred to as the visual impairment and intracranial pressure (VIIP) syndrome. VIIP signs and symptoms, as well as postflight lumbar puncture data, suggest that elevated intracranial pressure (ICP) may be associated with the space flight-induced cephalad fluid shifts, but this hypothesis has not been tested. The purpose of this study is to characterize fluid distribution and compartmentalization associated with long-duration space flight, and to correlate these findings with vision changes and other elements of the VIIP syndrome. We also seek to determine whether the magnitude of fluid shifts during space flight, as well as the VIIP-related effects of those shifts, is predicted by the crewmember's pre-flight condition and responses to acute hemodynamic manipulations (such as head-down tilt). Lastly, we will evaluate the patterns of fluid distribution in ISS astronauts during acute reversal of fluid shifts through application of lower body negative pressure (LBNP) interventions to characterize and explain general and individual responses. We will examine a variety of physiologic variables in 10 long-duration ISS crewmembers using the test conditions and timeline presented in the Figure below. Measures include: (1) fluid compartmentalization (total body water by D2O, extracellular fluid by NaBr, intracellular fluid by calculation, plasma volume by CO rebreathe, interstitial fluid by calculation); (2) forehead/eyelids, tibia, calcaneus tissue thickness (by ultrasound

  7. Validation of the Spanish versions of the long (26 items) and short (12 items) forms of the Self-Compassion Scale (SCS)

    PubMed Central

    2014-01-01

    Background Self-compassion is a key psychological construct for assessing clinical outcomes in mindfulness-based interventions. The aim of this study was to validate the Spanish versions of the long (26 item) and short (12 item) forms of the Self-Compassion Scale (SCS). Methods The translated Spanish versions of both subscales were administered to two independent samples: Sample 1 was comprised of university students (n = 268) who were recruited to validate the long form, and Sample 2 was comprised of Aragon Health Service workers (n = 271) who were recruited to validate the short form. In addition to SCS, the Mindful Attention Awareness Scale (MAAS), the State-Trait Anxiety Inventory–Trait (STAI-T), the Beck Depression Inventory (BDI) and the Perceived Stress Questionnaire (PSQ) were administered. Construct validity, internal consistency, test-retest reliability and convergent validity were tested. Results The Confirmatory Factor Analysis (CFA) of the long and short forms of the SCS confirmed the original six-factor model in both scales, showing goodness of fit. Cronbach’s α for the 26 item SCS was 0.87 (95% CI = 0.85-0.90) and ranged between 0.72 and 0.79 for the 6 subscales. Cronbach’s α for the 12-item SCS was 0.85 (95% CI = 0.81-0.88) and ranged between 0.71 and 0.77 for the 6 subscales. The long (26-item) form of the SCS showed a test-retest coefficient of 0.92 (95% CI = 0.89–0.94). The Intraclass Correlation (ICC) for the 6 subscales ranged from 0.84 to 0.93. The short (12-item) form of the SCS showed a test-retest coefficient of 0.89 (95% CI: 0.87-0.93). The ICC for the 6 subscales ranged from 0.79 to 0.91. The long and short forms of the SCS exhibited a significant negative correlation with the BDI, the STAI and the PSQ, and a significant positive correlation with the MAAS. The correlation between the total score of the long and short SCS form was r = 0.92. Conclusion The Spanish versions of the long (26-item) and short

  8. Full-Quantum chemical calculation of the absorption maximum of bacteriorhodopsin: a comprehensive analysis of the amino acid residues contributing to the opsin shift

    PubMed Central

    Hayashi, Tomohiko; Matsuura, Azuma; Sato, Hiroyuki; Sakurai, Minoru

    2012-01-01

    Herein, the absorption maximum of bacteriorhodopsin (bR) is calculated using our recently developed method in which the whole protein can be treated quantum mechanically at the level of INDO/S-CIS//ONIOM (B3LYP/6-31G(d,p): AMBER). The full quantum mechanical calculation is shown to reproduce the so-called opsin shift of bR with an error of less than 0.04 eV. We also apply the same calculation for 226 different bR mutants, each of which was constructed by replacing any one of the amino acid residues of the wild-type bR with Gly. This substitution makes it possible to elucidate the extent to which each amino acid contributes to the opsin shift and to estimate the inter-residue synergistic effect. It was found that one of the most important contributions to the opsin shift is the electron transfer from Tyr185 to the chromophore upon excitation. We also indicate that some aromatic (Trp86, Trp182) and polar (Ser141, Thr142) residues, located in the vicinity of the retinal polyene chain and the β-ionone ring, respectively, play an important role in compensating for the large blue-shift induced by both the counterion residues (Asp85, Asp212) and an internal water molecule (W402) located near the Schiff base linkage. In particular, the effect of Trp86 is comparable to that of Tyr185. In addition, Ser141 and Thr142 were found to contribute to an increase in the dipole moment of bR in the excited state. Finally, we provide a complete energy diagram for the opsin shift together with the contribution of the chromophore-protein steric interaction. PMID:27493528

  9. High-Frequency (13)C and (29)Si NMR Chemical Shifts in Diamagnetic Low-Valence Compounds of Tl(I) and Pb(II): Decisive Role of Relativistic Effects.

    PubMed

    Vícha, Jan; Marek, Radek; Straka, Michal

    2016-02-15

    The (13)C and (29)Si NMR signals of ligand atoms directly bonded to Tl(I) or Pb(II) heavy-element centers are predicted to resonate at very high frequencies, up to 400 ppm for (13)C and over 1000 ppm for (29)Si, outside the typical experimental NMR chemical-shift ranges for a given type of nuclei. The large (13)C and (29)Si NMR chemical shifts are ascribed to sizable relativistic spin-orbit effects, which can amount to more than 200 ppm for (13)C and more than 1000 ppm for (29)Si, values unexpected for diamagnetic compounds of the main group elements. The origin of the vast spin-orbit contributions to the (13)C and (29)Si NMR shifts is traced to the highly efficient 6p → 6p* metal-based orbital magnetic couplings and related to the 6p orbital-based bonding together with the low-energy gaps between the occupied and virtual orbital subspaces in the subvalent Tl(I) and Pb(II) compounds. New NMR spectral regions for these compounds are suggested based on the fully relativistic density functional theory calculations in the Dirac-Coulomb framework carefully calibrated on the experimentally known NMR data for Tl(I) and Pb(II) complexes.

  10. Fluid Shifts

    NASA Technical Reports Server (NTRS)

    Stenger, M. B.; Hargens, A. R.; Dulchavsky, S. A.; Arbeille, P.; Danielson, R. W.; Ebert, D. J.; Garcia, K. M.; Johnston, S. L.; Laurie, S. S.; Lee, S. M. C.; Liu, J.; Macias, B.; Martin, D. S.; Minkoff, L.; Ploutz-Snyder, R.; Ribeiro, L. C.; Sargsyan, A.; Smith, S. M.

    2017-01-01

    Introduction. NASA's Human Research Program is focused on addressing health risks associated with long-duration missions on the International Space Station (ISS) and future exploration-class missions beyond low Earth orbit. Visual acuity changes observed after short-duration missions were largely transient, but now more than 50 percent of ISS astronauts have experienced more profound, chronic changes with objective structural findings such as optic disc edema, globe flattening and choroidal folds. These structural and functional changes are referred to as the visual impairment and intracranial pressure (VIIP) syndrome. Development of VIIP symptoms may be related to elevated intracranial pressure (ICP) secondary to spaceflight-induced cephalad fluid shifts, but this hypothesis has not been tested. The purpose of this study is to characterize fluid distribution and compartmentalization associated with long-duration spaceflight and to determine if a relation exists with vision changes and other elements of the VIIP syndrome. We also seek to determine whether the magnitude of fluid shifts during spaceflight, as well as any VIIP-related effects of those shifts, are predicted by the crewmember's pre-flight status and responses to acute hemodynamic manipulations, specifically posture changes and lower body negative pressure. Methods. We will examine a variety of physiologic variables in 10 long-duration ISS crewmembers using the test conditions and timeline presented in the figure below. Measures include: (1) fluid compartmentalization (total body water by D2O, extracellular fluid by NaBr, intracellular fluid by calculation, plasma volume by CO rebreathe, interstitial fluid by calculation); (2) forehead/eyelids, tibia, and calcaneus tissue thickness (by ultrasound); (3) vascular dimensions by ultrasound (jugular veins, cerebral and carotid arteries, vertebral arteries and veins, portal vein); (4) vascular dynamics by MRI (head/neck blood flow, cerebrospinal fluid

  11. An analytical solution of Richards' equation providing the physical basis of SCS curve number method and its proportionality relationship

    NASA Astrophysics Data System (ADS)

    Hooshyar, Milad; Wang, Dingbao

    2016-08-01

    The empirical proportionality relationship, which indicates that the ratio of cumulative surface runoff and infiltration to their corresponding potentials are equal, is the basis of the extensively used Soil Conservation Service Curve Number (SCS-CN) method. The objective of this paper is to provide the physical basis of the SCS-CN method and its proportionality hypothesis from the infiltration excess runoff generation perspective. To achieve this purpose, an analytical solution of Richards' equation is derived for ponded infiltration in shallow water table environment under the following boundary conditions: (1) the soil is saturated at the land surface; and (2) there is a no-flux boundary which moves downward. The solution is established based on the assumptions of negligible gravitational effect, constant soil water diffusivity, and hydrostatic soil moisture profile between the no-flux boundary and water table. Based on the derived analytical solution, the proportionality hypothesis is a reasonable approximation for rainfall partitioning at the early stage of ponded infiltration in areas with a shallow water table for coarse textured soils.

  12. Theoretical Study of the Electrostatic and Steric Effects on the Spectroscopic Characteristics of the Metal-Ligand Unit of Heme Proteins. 2. C-O Vibrational Frequencies, 17O Isotropic Chemical Shifts, and Nuclear Quadrupole Coupling Constants

    PubMed Central

    Kushkuley, Boris; Stavrov, Solomon S.

    1997-01-01

    The quantum chemical calculations, vibronic theory of activation, and London-Pople approach are used to study the dependence of the C-O vibrational frequency, 17O isotropic chemical shift, and nuclear quadrupole coupling constant on the distortion of the porphyrin ring and geometry of the CO coordination, changes in the iron-carbon and iron-imidazole distances, magnitude of the iron displacement out of the porphyrin plane, and presence of the charged groups in the heme environment. It is shown that only the electrostatic interactions can cause the variation of all these parameters experimentally observed in different heme proteins, and the heme distortions could modulate this variation. The correlations between the theoretically calculated parameters are shown to be close to the experimentally observed ones. The study of the effect of the electric field of the distal histidine shows that the presence of the four C-O vibrational bands in the infrared absorption spectra of the carbon monoxide complexes of different myoglobins and hemoglobins can be caused by the different orientations of the different tautomeric forms of the distal histidine. The dependence of the 17O isotropic chemical shift and nuclear quadrupole coupling constant on pH and the distal histidine substitution can be also explained from the same point of view. PMID:9017215

  13. Nuclear magnetic resonance studies of phosphorus(v) pesticides. Part I. Chemical shifts of protons as a means of identification of pesticides

    USGS Publications Warehouse

    Babad, H.; Herbert, W.; Goldberg, M.C.

    1968-01-01

    Correlations of structural and proton chemical-hift data for 40 commercial phosphorus(V) pesticides are reported. Correlations of structure with the phosphorus coupling constants are discussed, and general trends are noted which aid in the use of NMR as a tool for identification and analysis of phosphorus(V) compounds. ?? 1968.

  14. Shifting sugars and shifting paradigms.

    PubMed

    Siegal, Mark L

    2015-02-01

    No organism lives in a constant environment. Based on classical studies in molecular biology, many have viewed microbes as following strict rules for shifting their metabolic activities when prevailing conditions change. For example, students learn that the bacterium Escherichia coli makes proteins for digesting lactose only when lactose is available and glucose, a better sugar, is not. However, recent studies, including three PLOS Biology papers examining sugar utilization in the budding yeast Saccharomyces cerevisiae, show that considerable heterogeneity in response to complex environments exists within and between populations. These results join similar recent results in other organisms that suggest that microbial populations anticipate predictable environmental changes and hedge their bets against unpredictable ones. The classical view therefore represents but one special case in a range of evolutionary adaptations to environmental changes that all organisms face.

  15. High intensity low temperature (HILT) performance of space concentrator GaInP/GaInAs/Ge MJ SCs

    SciTech Connect

    Shvarts, Maxim Z. Kalyuzhnyy, Nikolay A.; Mintairov, Sergey A.; Soluyanov, Andrei A.; Timoshina, Nailya Kh.; Gudovskikh, Alexander S.; Luque, Antonio

    2014-09-26

    In the work, the results of an investigation of GaInP/GaInAs/Ge MJ SCs intended for converting concentrated solar radiation, when operating at low temperatures (down to −190 °C) are presented. A kink of the cell I-V characteristic has been observed in the region close to V{sub oc} starting from −20°C at operation under concentrated sunlight. The causes for its occurrence have been analyzed and the reasons for formation of a built-in potential barrier for majority charge carriers at the n-GaInP/n-Ge isotype hetero-interface are discussed. The effect of charge carrier transport in n-GaInP/n-pGe heterostructures on MJ SC output characteristics at low temperatures has been studied including EL technique.

  16. Interface-controlled fatigue cracking of SCS-6/Ti-22Al-23Nb orthorhombic titanium aluminide composite

    SciTech Connect

    Her, Y.C.; Wang, P.C.; Yang, J.M.

    1998-11-01

    The effect of aging at elevated temperature on interfacial stability and fatigue behavior of a SCS-6/Ti-22Al-23Nb orthorhombic (O) titanium aluminide composite is investigated. The composite was heat treated in vacuum at 900 C for up to 250 hours to change the microstructural characteristics. The stability of the matrix alloy and interfacial reaction zone after extended thermal exposure was analyzed. The effect of interface on fatigue behavior, including stiffness degradation, evolution of fatigue damage, and crack growth rates, was characterized. Finally, a modified shear-lag model was used to predict the saturated matrix crack spacing in the composite under fatigue loading. The results demonstrate that aging at elevated temperature affects the stability of the interfacial reaction zone, which, in turn, degrades the fatigue properties of the composite. However, fatigue crack will not developed from the ruptured interfacial reaction layer until the thickness of the reaction zone or the maximum applied stress exceeds a critical value.

  17. Prediction of stress-strain response of SCS-6/Timetal-21S subjected to a hypersonic flight profile

    NASA Technical Reports Server (NTRS)

    Mirdamadi, Massoud; Johnson, W. Steven

    1994-01-01

    Thermomechanical response of a cross-ply SCS-6/Timetal-21S composite subjected to a generic hypersonic flight profile with the temperature ranging from -130 C to 816 C was evaluated experimentally and analytically. A two dimensional micromechanical anlaysis, VISCOPLY, was used to predict the stress-strain response of the laminate and of the constituents in each ply during thermomechanical loading conditions. In the analysis, the fiber was modeled as elastic with transverse orthotropic and temperature dependent properties and the matrix was modeled using a thermoviscoplastic constitutive relation. The fiber transverse modulus was reduced in the analysis to simulate fiber-matrix interface failure. Reasonable agreement was found between measured and predicted laminate stress-strain response when fiber-matrix debonding was modeled.

  18. Surface runoff estimation from various land use in Mapili Watershed using SCS Curve Number and Geographic Information System

    NASA Astrophysics Data System (ADS)

    Malahayati Yusuf, Sri; Guluda, David; Jayanegara, Trisumitra

    2017-01-01

    Mapili watershed which is located in West Sulawesi is dominated by secondary forest and agriculture land. The condition of the watershed is affected by land use and soil type. Land use is a form of interaction between man and land in order to meet their needs. Soil is function from organism, climate, topographic, material, and time. This information then will affect the hydrological condition in the watershed, especially surface runoff. The objective of study is to analyze the surface runoff in Mapili watershed. SCS curve number method that integrates with geographic information system was used in the analysis. The highest surface runoff value is about 887.6 mm and the highest of surface runoff coefficient is about 0.31.

  19. Investigation of fatigue damage mechanisms in SCS-6/Ti-15-3 metal matrix composite at elevated temperature

    NASA Astrophysics Data System (ADS)

    Mall, S.; Portner, B. D.

    A study was conducted to study the fatigue behavior of cross-ply, (0/90)2s, laminate of silicon fiber reinforced titanium matrix composite, SCS-6/Ti-15-3 at an elevated temperature of 427 C. Two sets of tests, at frequencies 0.02 and 2 Hz, were run at different stress levels which were either below or above the static first ply failure strength of laminate. Crack initiation locations and growth patterns were dependent on to specific test conditions of frequency and stress level. Also, microscopic analysis of the fatigued specimens revealed matrix failure mechanisms ranging from ductile failure to cleavage fracture. The results of this study clearly showed that temperature, frequency as well as stress levels are important design considerations for this composite in fatigue loading applications.

  20. A combined DFT - NMR study of cyclic 1,2-diones and methyl ethers of their enols: The power and limitations of the method based on theoretical predictions of 13C NMR chemical shifts

    NASA Astrophysics Data System (ADS)

    Kubicki, Dominik; Gryff-Keller, Adam; Szczeciński, Przemysław

    2012-08-01

    A series of cyclic 1,2-diones and methyl ethers of their enols were investigated by a combined 13C NMR/computational DFT method to establish their preferred solution structures. The optimum molecular geometries and magnetic shielding constants of carbon nuclei were calculated with GIAO DFT [PBE1PBE/6-311++G(2d,p) PCM] method for the investigated molecules allowing for enolization and dynamic conformational equilibriums occurring in the solutions. These compounds served simultaneously as model compounds for testing the effectiveness and limitations of the exploited method of investigating molecular structures based on comparison of the theoretically calculated magnetic shielding constants and experimental 13C NMR chemical shifts. Generally, a very good agreement between experimental and theoretical data was obtained for the investigated group of compounds, which proved the applied level of theory and used methodology to be adequate and should ensure a high accuracy of the 13C NMR chemical shift predictions. Some divergences between the experiment and theory could be interpreted as the results of insufficiencies of the molecular modelling and the effects of neglecting vibrational/librational molecular motions. Furthermore, we report herein an observation of an unexpected 1H NMR spectral pattern for 2,3-dimethoxycyclodeca-1,3-diene (diether of cyclodecadione dienol), which was interpreted to be caused by the slow (in NMR time scale) enantiomerization of this molecule which preferentially assumes a chiral conformation.

  1. Hash: a Program to Accurately Predict Protein Hα Shifts from Neighboring Backbone Shifts3

    PubMed Central

    Zeng, Jianyang; Zhou, Pei; Donald, Bruce Randall

    2012-01-01

    Chemical shifts provide not only peak identities for analyzing NMR data, but also an important source of conformational information for studying protein structures. Current structural studies requiring Hα chemical shifts suffer from the following limitations. (1) For large proteins, the Hα chemical shifts can be difficult to assign using conventional NMR triple-resonance experiments, mainly due to the fast transverse relaxation rate of Cα that restricts the signal sensitivity. (2) Previous chemical shift prediction approaches either require homologous models with high sequence similarity or rely heavily on accurate backbone and side-chain structural coordinates. When neither sequence homologues nor structural coordinates are available, we must resort to other information to predict Hα chemical shifts. Predicting accurate Hα chemical shifts using other obtainable information, such as the chemical shifts of nearby backbone atoms (i.e., adjacent atoms in the sequence), can remedy the above dilemmas, and hence advance NMR-based structural studies of proteins. By specifically exploiting the dependencies on chemical shifts of nearby backbone atoms, we propose a novel machine learning algorithm, called Hash, to predict Hα chemical shifts. Hash combines a new fragment-based chemical shift search approach with a non-parametric regression model, called the generalized additive model, to effectively solve the prediction problem. We demonstrate that the chemical shifts of nearby backbone atoms provide a reliable source of information for predicting accurate Hα chemical shifts. Our testing results on different possible combinations of input data indicate that Hash has a wide rage of potential NMR applications in structural and biological studies of proteins. PMID:23242797

  2. Computation provides chemical insight into the diverse hydride NMR chemical shifts of [Ru(NHC)4(L)H](0/+) species (NHC = N-heterocyclic carbene; L = vacant, H2, N2, CO, MeCN, O2, P4, SO2, H(-), F(-) and Cl(-)) and their [Ru(R2PCH2CH2PR2)2(L)H](+) congeners.

    PubMed

    Häller, L Jonas L; Mas-Marzá, Elena; Cybulski, Mateusz K; Sanguramath, Rajashekharayya A; Macgregor, Stuart A; Mahon, Mary F; Raynaud, Christophe; Russell, Christopher A; Whittlesey, Michael K

    2017-02-28

    Relativistic density functional theory calculations, both with and without the effects of spin-orbit coupling, have been employed to model hydride NMR chemical shifts for a series of [Ru(NHC)4(L)H](0/+) species (NHC = N-heterocyclic carbene; L = vacant, H2, N2, CO, MeCN, O2, P4, SO2, H(-), F(-) and Cl(-)), as well as selected phosphine analogues [Ru(R2PCH2CH2PR2)2(L)H](+) (R = (i)Pr, Cy; L = vacant, O2). Inclusion of spin-orbit coupling provides good agreement with the experimental data. For the NHC systems large variations in hydride chemical shift are shown to arise from the paramagnetic term, with high net shielding (L = vacant, Cl(-), F(-)) being reinforced by the contribution from spin-orbit coupling. Natural chemical shift analysis highlights the major orbital contributions to the paramagnetic term and rationalizes trends via changes in the energies of the occupied Ru dπ orbitals and the unoccupied σ*Ru-H orbital. In [Ru(NHC)4(η(2)-O2)H](+) a δ-interaction with the O2 ligand results in a low-lying LUMO of dπ character. As a result this orbital can no longer contribute to the paramagnetic shielding, but instead provides additional deshielding via overlap with the remaining (occupied) dπ orbital under the Lz angular momentum operator. These two effects account for the unusual hydride chemical shift of +4.8 ppm observed experimentally for this species. Calculations reproduce hydride chemical shift data observed for [Ru((i)Pr2PCH2CH2P(i)Pr2)2(η(2)-O2)H](+) (δ = -6.2 ppm) and [Ru(R2PCH2CH2PR2)2H](+) (ca. -32 ppm, R = (i)Pr, Cy). For the latter, the presence of a weak agostic interaction trans to the hydride ligand is significant, as in its absence (R = Me) calculations predict a chemical shift of -41 ppm, similar to the [Ru(NHC)4H](+) analogues. Depending on the strength of the agostic interaction a variation of up to 18 ppm in hydride chemical shift is possible and this factor (that is not necessarily readily detected experimentally) can aid in the

  3. Suppressors (scsl-scs7) of CSG2, a Gene Required by Saccharomyces cerevisiae for Growth in Media Containing 10 mMCa(2+), Identify Genes Required for Sphingolipid Biosynthesis

    DTIC Science & Technology

    1994-07-01

    activity and requires phytosphingosine or dihydrosphingarune for growth indicating that SCSI encodes serine palmitoyltransferase. This enzyme... phytosphingosine on the growth rate of scsI csg2, scsI CSG2, scsI::LEUZ’ CSGZ, SCSI csgZ and SCSI CSGZ. 87 20. Acid titration of wild·type and scsI-I cells. 21...ceramide) and a polar head group. The ceramide consists of a long-chain base (sphingosine in animals, phytosphingosine (PHS) in fungi and plants) and a

  4. 1H, 13C NMR spectral and single crystal structural studies of toxaphene congeners. Quantum chemical calculations for preferred conformers of 2,5- endo,6- exo,8,9,9,10,10-octachloro-2-bornene and their DFT/GIAO 13C chemical shifts

    NASA Astrophysics Data System (ADS)

    Laihia, K.; Valkonen, A.; Kolehmainen, E.; Suontamo, R.; Nissinen, M.; Nikiforov, V.; Selivanov, S.

    2005-11-01

    The 1H and 13C NMR chemical shifts for six toxaphene congeners: 2- exo,3- endo,6- exo,8,9,10-hexachloro- ( 1), 2- exo,3- endo,5- exo,9,9,10,10-heptachloro- ( 2), 2- exo,3- endo,6- exo,8,9,10,10-heptachloro- ( 3), 2- exo,3- endo,5- exo,6- endo,8,9,10-heptachloro- ( 4), 2- exo,3- endo,5- exo,6- endo,8,9,9,10-octachlorobornane ( 5) and 2,5- endo,6- exo,8,9,9,10,10-octachloro-2-bornene ( 6) are reported. Their chemical shift assignments have been obtained by means of Pulsed Field Gradient (PFG) Double Quantum Filtered (DQF) 1H, 1H correlation spectroscopy (COSY), PFG 1H, 13C Heteronuclear Multiple Quantum Coherence (HMQC) and PFG 1H, 13C Heteronuclear Multiple Bond Correlation (HMBC) experiments. A single crystal X-ray structural analysis was made for compounds 1, 3, 4 and 6. The prevalences of two octachlorobornene rotamers ( 6 a, 6 b) were elucidated by ab initio MO method and single point DFT/GIAO calculations for 13C chemical shifts. Theoretical calculations proved that the single crystal structure of 6 corresponds its most stable conformer in solution.

  5. Synthesis, antimicrobial evaluation and theoretical prediction of NMR chemical shifts of thiazole and selenazole derivatives with high antifungal activity against Candida spp.

    NASA Astrophysics Data System (ADS)

    Łączkowski, Krzysztof Z.; Motylewska, Katarzyna; Baranowska-Łączkowska, Angelika; Biernasiuk, Anna; Misiura, Konrad; Malm, Anna; Fernández, Berta

    2016-03-01

    Synthesis and investigation of antimicrobial activities of novel thiazoles and selenazoles is presented. Their structures were determined using NMR, FAB(+)-MS, HRMS and elemental analyses. To support the experiment, theoretical calculations of the 1H NMR shifts were carried out for representative systems within the DFT B3LYP/6-311++G** approximation which additionally confirmed the structure of investigated compounds. Among the derivatives, compounds 4b, 4h, 4j and 4l had very strong activity against reference strains of Candida albicans ATCC and Candida parapsilosis ATCC 22019 with MIC = 0.49-7.81 μg/ml. In the case of compounds 4b, 4c, 4h - 4j and 4l, the activity was very strong against of Candida spp. isolated from clinical materials, i.e. C. albicans, Candida krusei, Candida inconspicua, Candida famata, Candida lusitaniae, Candida sake, C. parapsilosis and Candida dubliniensis with MIC = 0.24-15.62 μg/ml. The activity of several of these was similar to the activity of commonly used antifungal agent fluconazole. Additionally, compounds 4m - 4s were found to be active against Gram-positive bacteria, both pathogenic staphylococci Staphylococcus aureus ATCC with MIC = 31.25-125 μg/ml and opportunistic bacteria, such as Staphylococcus epidermidis ATCC 12228 and Micrococcus luteus ATCC 10240 with MIC = 7.81-31.25 μg/ml.

  6. Unusual Physical and Chemical Properties of Ni in Ce1-xNixO2-y Oxides: Structural Characterization and Catalytic Activity for the Water Gas Shift Reaction

    SciTech Connect

    Rodriguez, J.A.; Barrio, L.; Kubacka, A.; Zhou, G.; Estrella, M.; Martınez-Arias, A.; Hanson, J.C.; Fernandez-Garcıa, M.

    2010-07-29

    The structural and electronic properties of Ce{sub 1-x}Ni{sub x}O{sub 2-y} nanosystems prepared by a reverse microemulsion method were characterized with synchrotron-based X-ray diffraction, X-ray absorption spectroscopy, Raman spectroscopy, and density functional calculations. The Ce{sub 1-x}Ni{sub x}O{sub 2-y} systems adopt a lattice with a fluorite-type structure with an acute local order where Ni displays a strongly distorted (oxygen) nearest-neighbor coordination and the presence of Ni atoms as first cation distances, pointing to the existence of Ni-O-Ni entities embedded into the ceria lattice. A Ni {leftrightarrow} Ce exchange within the CeO{sub 2} leads to a charge redistribution and the appearance of O vacancies. The Ni?O bonds in Ce{sub 1-x}Ni{sub x}O{sub 2-y} are more difficult to reduce than the bonds in pure NiO. The specific structural configuration of Ni inside the mixed-metal oxide leads to a unique catalyst with a high activity for the water gas shift (CO + H{sub 2}O {yields} H{sub 2} + CO{sub 2}) reaction and a simultaneous reduction of the methanation activity of nickel. Characterization results indicate that small particles of metallic Ni at the interface position of a ceria network may be the key for high WGS activity and that the formate?carbonate route is operative for the production of hydrogen.

  7. Unusual Physical and Chemical Properties of Ni in Ce1-xNixO2-y Oxides: Structural Characterization and Catalytic Activity for the Water Gas Shift Reaction

    SciTech Connect

    Barrio, L.; Kubacka, A; Zhou, G; Estrella, M; Martinez-Arias, A; Hanson, J; Fernandez-Garcia, M; Rodriguez, J

    2010-01-01

    The structural and electronic properties of Ce{sub 1-x}Ni{sub x}O{sub 2-y} nanosystems prepared by a reverse microemulsion method were characterized with synchrotron-based X-ray diffraction, X-ray absorption spectroscopy, Raman spectroscopy, and density functional calculations. The Ce{sub 1-x}Ni{sub x}O{sub 2-y} systems adopt a lattice with a fluorite-type structure with an acute local order where Ni displays a strongly distorted (oxygen) nearest-neighbor coordination and the presence of Ni atoms as first cation distances, pointing to the existence of Ni-O-Ni entities embedded into the ceria lattice. A Ni {leftrightarrow} Ce exchange within the CeO{sub 2} leads to a charge redistribution and the appearance of O vacancies. The Ni-O bonds in Ce{sub 1-x}Ni{sub x}O{sub 2-y} are more difficult to reduce than the bonds in pure NiO. The specific structural configuration of Ni inside the mixed-metal oxide leads to a unique catalyst with a high activity for the water gas shift (CO + H{sub 2}O {yields} H{sub 2} + CO{sub 2}) reaction and a simultaneous reduction of the methanation activity of nickel. Characterization results indicate that small particles of metallic Ni at the interface position of a ceria network may be the key for high WGS activity and that the formate-carbonate route is operative for the production of hydrogen.

  8. Self-Compassion Scale (SCS): Psychometric Properties of The French Translation and Its Relations with Psychological Well-Being, Affect and Depression

    PubMed Central

    Kotsou, Ilios; Leys, Christophe

    2016-01-01

    Over the past few years, the topic of self-compassion has attracted increasing attention from both scientific and clinical fields. The Self-Compassion Scale (SCS) was created to specifically capture this way of being kind and understanding towards oneself in moments of turmoil. In this article, we present a French adaptation of the SCS. We first explore the psychometric properties of this adaptation and then investigate its relation to psychological well-being. As in the original version of the SCS, the French adaptation has a strong 6-factor structure but a weaker hierarchical second order structure. However the bi-factor model yields a good omega index suggesting the relevance of a single score accounting for self-compassion. Moreover, there was a relation between the SCS and classical outcomes such as a positive relation with psychological well-being and negative relation with depressive symptoms. We then hypothesized that self-compassion would have a moderating role on the relation between affect and depression. This hypothesis was confirmed: expressing negative affect is correlated with depressive symptoms; however, being kind with oneself lowers depressive symptoms even when expressing negative affect. In conclusion, this research presents a valid self-compassion measure for French-speaking researchers and clinicians and outlines the need for further research on the concept of self-compassion. PMID:27078886

  9. Self-Compassion Scale (SCS): Psychometric Properties of The French Translation and Its Relations with Psychological Well-Being, Affect and Depression.

    PubMed

    Kotsou, Ilios; Leys, Christophe

    2016-01-01

    Over the past few years, the topic of self-compassion has attracted increasing attention from both scientific and clinical fields. The Self-Compassion Scale (SCS) was created to specifically capture this way of being kind and understanding towards oneself in moments of turmoil. In this article, we present a French adaptation of the SCS. We first explore the psychometric properties of this adaptation and then investigate its relation to psychological well-being. As in the original version of the SCS, the French adaptation has a strong 6-factor structure but a weaker hierarchical second order structure. However the bi-factor model yields a good omega index suggesting the relevance of a single score accounting for self-compassion. Moreover, there was a relation between the SCS and classical outcomes such as a positive relation with psychological well-being and negative relation with depressive symptoms. We then hypothesized that self-compassion would have a moderating role on the relation between affect and depression. This hypothesis was confirmed: expressing negative affect is correlated with depressive symptoms; however, being kind with oneself lowers depressive symptoms even when expressing negative affect. In conclusion, this research presents a valid self-compassion measure for French-speaking researchers and clinicians and outlines the need for further research on the concept of self-compassion.

  10. Fatigue damage evolution and property degradation of a SCS-6/Ti-22Al-23Nb orthorhombic titanium aluminide composite

    SciTech Connect

    Wang, P.C.; Jeng, S.M.; Yang, J.M.; Russ, S.M.

    1996-08-01

    The fatigue damage evolution and property degradation of a SCS-6/Ti-22Al-23Nb orthorhombic titanium aluminide composite under low cycle fatigue loading at room temperature was investigated. The fatigue test was conducted under a load-controlled mode with a load ratio (R) of 0.1, a frequency of 10 Hz, and a maximum applied stress ranging from 600 to 945 MPa. The stiffness reduction as well as the evolution of microstructural damage which includes matrix crack length, matrix crack density and interfacial debonding length as a function of fatigue cycles, and applied stresses were measured. An analytical model and a computer simulation were also developed to predict the residual stiffness and the post-fatigued tensile strength as a function of microstructural damage. Finally, a steady-state crack growth model proposed by Marshall et al. was used to predict the interfacial frictional stress and the critical crack length. Correlation between the theoretical predictions and experimental results were also discussed.

  11. Thermomechanical testing techniques for high-temparature composites: TMF behavior of SiC(SCS-6)/Ti-15-3

    NASA Technical Reports Server (NTRS)

    Castelli, Michael G.; Ellis, J. Rodney; Bartolotta, Paul A.

    1990-01-01

    Thermomechanical testing techniques recently developed for monolithic structural alloys were successfully extended to continuous fiber reinforced composite materials in plate form. The success of this adaptation was verified on a model metal matrix composite (MMC) material, namely SiC(SCS-6)/Ti-15V-3Cr-3Al-3Sn. Effects of heating system type and specimen preparation are also addressed. Cyclic lives determined under full thermo-mechanical conditions were shown to be significantly reduced from those obtained under comparable isothermal and in-phase bi-thermal conditions. Fractography and metallography from specimens subjected to isothermal, out-of-phase and in-phase conditions reveal distinct differences in damage-failure modes. Isothermal metallography revealed extensive matrix cracking associated with fiber damage throughout the entire cross-section of the specimen. Out-of-phase metallography revealed extensive matrix damage associated with minimal (if any) fiber cracking. However, the damage was located exclusively at surface and near-surface locations. In-phase conditions produced extensive fiber cracking throughout the entire cross-section, associated with minimal (if any) matrix damage.

  12. SiC (SCS-6) Fiber Reinforced-Reaction Formed SiC Matrix Composites: Microstructure and Interfacial Properties

    NASA Technical Reports Server (NTRS)

    Singh, M.; Dickerson, R. M.; Olmstead, Forrest A.; Eldridge, J. I.

    1997-01-01

    Microstructural and interfacial characterization of unidirectional SiC (SCS-6) fiber reinforced-reaction formed SiC (RFSC) composites has been carried out. Silicon-1.7 at.% molybdenum alloy was used as the melt infiltrant, instead of pure silicon, to reduce the activity of silicon in the melt as well as to reduce the amount of free silicon in the matrix. Electron microprobe analysis was used to evaluate the microstructure and phase distribution in these composites. The matrix is SiC with a bi-modal grain-size distribution and small amounts of MoSi2, silicon, and carbon. Fiber push-outs tests on these composites showed that a desirably low interfacial shear strength was achieved. The average debond shear stress at room temperature varied with specimen thickness from 29 to 64 MPa, with higher values observed for thinner specimens. Initial frictional sliding stresses showed little thickness dependence with values generally close to 30 MPa. Push-out test results showed very little change when the test temperature was increased to 800 C from room temperature, indicating an absence of significant residual stresses in the composite.

  13. Pressure and temperature effects on 2H spin-lattice relaxation times and 1H chemical shifts in tert-butyl alcohol- and urea-D2O solutions

    NASA Astrophysics Data System (ADS)

    Yoshida, Koji; Ibuki, Kazuyasu; Ueno, Masakatsu

    1998-01-01

    The pressure and temperature effects of hydrophobic hydration were studied by NMR spectroscopy. The 1H chemical shifts (δ) were measured at 7.7, 29.9, and 48.4 °C under high pressure up to 294 MPa for HDO contained as impurity in neat D2O, 1 mol kg-1 tert-butyl alcohol (TBA)-D2O, and 1 mol kg-1 urea-D2O solutions, for the methyl group of TBA in the TBA-D2O solution, and for the amino group of urea in the urea-D2O solution. The 2H spin-lattice relaxation times (T1) were measured under the same conditions as the chemical shift measurements for D2O in neat D2O, TBA-D2O and urea-D2O solutions with organic contents up to 8 mol%. The following features are observed for the pressure effect on δ (HDO) and 2H-T1 in TBA-D2O solutions: (1) The δ (HDO) exhibits a downfield shift relative to that in neat D2O, and the difference of δ (HDO) between TBA solution and neat D2O becomes larger with increasing pressure at lower temperature. (2) The decrement of the rotational correlation time of water in the hydration shell of TBA (τcs) relative to the value at atmospheric pressure is smaller than that in the bulk (τc0). (3) The pressure coefficients of T1 are positive in dilute solutions but are negative in more than 4 to 5 mol% solutions. These results suggest that the hydrophobic hydration shell of TBA is different than the open structure of water present in bulk, and resists pressure more strongly than the open structure of water in the bulk. In solutions of 4 to 5 mol%, the hydration shell collapses. On the other hand, the τcs in the hydration shell of urea is slightly larger than that in bulk water at lower pressure, but is obviously larger at higher pressure. In view of the rotational motion of water molecules, urea seems to strengthen the water structure slightly rather than weaken it, although δ (HDO) approaches that in the bulk with pressure. It is difficult to classify urea into a structure maker or a breaker.

  14. The seasonal variation of the upper layers of the South China Sea (SCS) circulation and the Indonesian through flow (ITF): An ocean model study

    NASA Astrophysics Data System (ADS)

    Xu, Danya; Malanotte-Rizzoli, Paola

    2013-09-01

    The upper layer, wind-driven circulation of the South China Sea (SCS), its through-flow (SCSTF) and the Indonesian through flow (ITF) are simulated using a high resolution model, FVCOM (finite volume coastal ocean model) in a regional domain comprising the Maritime Continent. The regional model is embedded in the MIT global ocean general circulation model (ogcm) which provides surface forcing and boundary conditions of all the oceanographic variables at the lateral open boundaries in the Pacific and Indian oceans. A five decade long simulation is available from the MITgcm and we choose to investigate and compare the climatologies of two decades, 1960-1969 and 1990-1999. The seasonal variability of the wind-driven circulation produced by the monsoon system is realistically simulated. In the SCS the dominant driving force is the monsoon wind and the surface circulation reverses accordingly, with a net cyclonic tendency in winter and anticyclonic in summer. The SCS circulation in the 90s is weaker than in the 60s because of the weaker monsoon system in the 90s. In the upper 50 m the interaction between the SCSTF and ITF is very important. The southward ITF can be blocked by the SCSTF at the Makassar Strait during winter. In summer, part of the ITF feeds the SCSTF flowing into the SCS through the Karimata Strait. Differently from the SCS, the ITF is primarily controlled by the sea level difference between the western Pacific and eastern Indian Ocean. The ITF flow, consistently southwestward below the surface layer, is stronger in the 90s. The volume transports for winter, summer and yearly are estimated from the simulation through all the interocean straits. On the annual average, there is a ∼5.6 Sv of western Pacific water entering the SCS through the Luzon Strait and ∼1.4 Sv exiting through the Karimata Strait into the Java Sea. Also, ∼2 Sv of SCS water enters the Sulu Sea through the Mindoro Strait, while ∼2.9 Sv flow southwards through the Sibutu Strait

  15. Materials characterization of silicon carbide reinforced titanium (Ti/SCS-6) metal matrix composites: Part I. Tensile and fatigue behavior

    NASA Astrophysics Data System (ADS)

    Liaw, P. K.; Diaz, E. S.; Chiang, K. T.; Loh, D. H.

    1995-12-01

    Flexural fatigue behavior was investigated on titanium (Ti-15V-3Cr) metal matrix composites reinforced with cross-ply, continuous silicon carbide (SiC) fibers. The titanium composites had an eightply (0, 90, +45, -45 deg) symmetric layup. Fatigue life was found to be sensitive to fiber layup sequence. Increasing the test temperature from 24 °C to 427 °C decreased fatigue life. Interface debonding and matrix and fiber fracture were characteristic of tensile behavior regardless of test temperature. In the tensile fracture process, interface debonding between SiC and the graphite coating and between the graphite coating and the carbon core could occur. A greater amount of coating degradation at 427 °C than at 24 °C reduced the Ti/SiC interface bonding integrity, which resulted in lower tensile properties at 427 °C. During tensile testing, a crack could initiate from the debonded Ti/SiC interface and extend to the debonded interface of the neighboring fiber. The crack tended to propagate through the matrix and the interface. Dimpled fracture was the prime mode of matrix fracture. During fatigue testing, four stages of flexural deflection behavior were observed. The deflection at stage I increased slightly with fatigue cycling, while that at stage II increased significantly with cycling. Interestingly, the deflection at stage III increased negligibly with fatigue cycling. Stage IV was associated with final failure, and the deflection increased abruptly. Interface debonding, matrix cracking, and fiber bridging were identified as the prime modes of fatigue mechanisms. To a lesser extent, fiber fracture was observed during fatigue. However, fiber fracture was believed to occur near the final stage of fatigue failure. In fatigued specimens, facet-type fracture appearance was characteristic of matrix fracture morphology. Theoretical modeling of the fatigue behavior of Ti/SCS-6 composites is presented in Part II of this series of articles.

  16. Impact damage resistance and residual property assessment of (0/+/-45/90)s SCS-6/Timetal 21S

    NASA Technical Reports Server (NTRS)

    Miller, Jennifer L.; Portanova, Marc A.; Johnson, W. Steven

    1995-01-01

    The impact damage resistance and residual mechanical properties of (0/ +/- 45/90)s SCS-6/Timetal 21S composites were evaluated. Both quasi-static indentation and drop-weight impact tests were used to investigate the impact behavior at two nominal energy levels (5.5 and 8.4 J) and determine the onset of internal damage. Through x-ray inspection, the extent of internal damage was characterized non-destructively. The composite strength and constant amplitude fatigue response were evaluated to assess the effects of the sustained damage. Scanning electron microscopy was used to characterize internal damage from impact in comparison to damage that occurs during mechanical loading alone. The effect of stacking sequence was examined by using specimens with the long dimension of the specimen both parallel (longitudinal) and perpendicular (transverse) to the 0 deg fiber direction. Damage in the form of longitudinal and transverse cracking occurred in all longitudinal specimens tested at energies greater than 6.3 J. Similar results occurred in the transverse specimens tested above 5.4 J. Initial load drop, characteristic of the onset of damage, occurred on average at 6.3 J in longitudinal specimens and at 5.0 J in transverse specimens. X-ray analysis showed broken fibers in the impacted region in specimens tested at the higher impact energies. At low impact energies, visible matrix cracking may occur, but broken fibers may not. Matrix cracking was noted along fiber swims and it appeared to depend on the surface quality of composite. At low impact energies, little damage has been incurred by the composite and the residual strength and residual life is not greatly reduced as compared to an undamaged composite. At higher impact energies, more damage occurred and a greater effect of the impact damage was observed.

  17. The limits of ray theory when measuring shear wave splitting in the lowermost mantle with ScS waves

    NASA Astrophysics Data System (ADS)

    Nowacki, Andy; Wookey, James

    2016-12-01

    Observations of shear wave splitting provide unambiguous evidence of the presence of anisotropy in the Earth's lowermost mantle, a region known as D″. Much recent work has attempted to use these observations to place constraints on strain above the core-mantle boundary (CMB), as this may help map flow throughout the mantle. Previously, this interpretation has relied on the assumption that waves can be modelled as infinite-frequency rays, or that the Earth is radially symmetric. Due to computational constraints it has not been possible to test these approximations until now. We use fully 3-D, generally anisotropic simulations of ScS waves at the frequencies of the observations to show that ray methods are sometimes inadequate to interpret the signals seen. We test simple, uniform models, and for a D″ layer as thin as 50 km, significant splitting may be produced, and we find that recovered fast orientations usually reflect the imposed fast orientation above the CMB. Ray theory in these cases provides useful results, though there are occasional, notable differences between forward methods. Isotropic models do not generate apparent splitting. We also test more complex models, including ones based on our current understanding of mineral plasticity and elasticity in D″. The results show that variations of anisotropy over even several hundred kilometres cause the ray-theoretical and finite-frequency calculations to differ greatly. Importantly, models with extreme mineral alignment in D″ yield splitting times not dissimilar to observations (δt ≤ 3 s), suggesting that anisotropy in the lowermost mantle is probably much stronger than previously thought-potentially ˜10 per cent shear wave anisotropy or more. We show that if the base of the mantle is as complicated as we believe, future studies of lowermost mantle anisotropy will have to incorporate finite-frequency effects to fully interpret observations of shear wave splitting.

  18. Thermomechanical Fatigue Damage/Failure Mechanisms in SCS-6/Timetal 21S [0/90](Sub S) Composite

    NASA Technical Reports Server (NTRS)

    Castelli, Michael G.

    1994-01-01

    The thermomechanical fatigue (TMF) deformation, damage, and life behaviors of SCS6/Timetal 21S (0/90)s were investigated under zero-tension conditions. In-phase (IP) and out-of-phase (OP) loadings were investigated with a temperature cycle from 150 to 650 deg C. An advanced TMF test technique was used to quantify mechanically damage progression. The technique incorporated explicit measurements of the macroscopic (1) isothermal static moduli at the temperature extremes of the TMF cycle and (2) coefficient of thermal expansion (CTE) as functions of the TMF cycles. The importance of thermal property degradation and its relevance to accurate post-test data analysis and interpretation is briefly addressed. Extensive fractography and metallography were conducted on specimens from failed and interrupted tests to characterize the extent of damage at the microstructure level. Fatigue life results indicated trends analogous to those established for similar unidirectional(0) reinforced titanium matrix composite systems. High stress IP and mid to low stress OP loading conditions were life-limiting in comparison to maximum temperature isothermal conditions. Dominant damage mechanisms changed with cycle type. Damage resulting from IP TMF conditions produced measurable decreases in static moduli but only minimal changes in the CTE. Metallography on interrupted and failed specimens revealed extensive (0) fiber cracking with sparse matrix damage. No surface initiated matrix cracks were present. Comparable OP TMF conditions initiated environment enhanced surface cracking and matrix cracking initiated at (90) fiber/matrix (F/M) interfaces. Notable static moduli and CTE degradations were measured. Fractography and metallography revealed that the transverse cracks originating from the surface and (90) F/M interfaces tended to converge and coalesce at the (0) fibers.

  19. Vibrational frequency scaling factors for correlation consistent basis sets and the methods CC2 and MP2 and their spin-scaled SCS and SOS variants

    SciTech Connect

    Friese, Daniel H.; Törk, Lisa; Hättig, Christof

    2014-11-21

    We present scaling factors for vibrational frequencies calculated within the harmonic approximation and the correlated wave-function methods coupled cluster singles and doubles model (CC2) and Møller-Plesset perturbation theory (MP2) with and without a spin-component scaling (SCS or spin-opposite scaling (SOS)). Frequency scaling factors and the remaining deviations from the reference data are evaluated for several non-augmented basis sets of the cc-pVXZ family of generally contracted correlation-consistent basis sets as well as for the segmented contracted TZVPP basis. We find that the SCS and SOS variants of CC2 and MP2 lead to a slightly better accuracy for the scaled vibrational frequencies. The determined frequency scaling factors can also be used for vibrational frequencies calculated for excited states through response theory with CC2 and the algebraic diagrammatic construction through second order and their spin-component scaled variants.

  20. Identification of Two Suppressors of CSG2 Calcium Sensitivity, SCS7 and SUR2, as Genes Encoding Hydroxylases of the Sphingolipid Biosynthetic Pathway of Saccharomyces cerevisiae

    DTIC Science & Technology

    1997-12-10

    the aliphatic chains is provided by a long chain base, (LCB; phytosphingosine in Figure 1), and the other is in amide linkage with the LCB. Ceramide...the ceramide structure they are the first three carbon positions ofthe ceramide long chain base, ( phytosphingosine as drawn). Sphingosine differs from...biosyn- thesis, the condensation ofserine and palmitoyl-CoA to form 3-ketosphinganine. There- fore the scsI mutant was tested for phytosphingosine

  1. Speeding up spin-component-scaled third-order pertubation theory with the chain of spheres approximation: the COSX-SCS-MP3 method

    NASA Astrophysics Data System (ADS)

    Izsák, Róbert; Neese, Frank

    2013-07-01

    The 'chain of spheres' approximation, developed earlier for the efficient evaluation of the self-consistent field exchange term, is introduced here into the evaluation of the external exchange term of higher order correlation methods. Its performance is studied in the specific case of the spin-component-scaled third-order Møller--Plesset perturbation (SCS-MP3) theory. The results indicate that the approximation performs excellently in terms of both computer time and achievable accuracy. Significant speedups over a conventional method are obtained for larger systems and basis sets. Owing to this development, SCS-MP3 calculations on molecules of the size of penicillin (42 atoms) with a polarised triple-zeta basis set can be performed in ∼3 hours using 16 cores of an Intel Xeon E7-8837 processor with a 2.67 GHz clock speed, which represents a speedup by a factor of 8-9 compared to the previously most efficient algorithm. Thus, the increased accuracy offered by SCS-MP3 can now be explored for at least medium-sized molecules.

  2. Chemical characterization of synthetic cannabinoids by electrospray ionization FT-ICR mass spectrometry.

    PubMed

    Kill, Jade B; Oliveira, Izabela F; Tose, Lilian V; Costa, Helber B; Kuster, Ricardo M; Machado, Leandro F; Correia, Radigya M; Rodrigues, Rayza R T; Vasconcellos, Géssica A; Vaz, Boniek G; Romão, Wanderson

    2016-09-01

    The synthetic cannabinoids (SCs) represent the most recent advent of the new psychotropic substances (NPS) and has become popularly known to mitigate the effects of the Δ(9)-THC. The SCs are dissolved in organic solvents and sprayed in a dry herbal blend. However, little information is reported on active ingredients of SCs as well as the excipients or diluents added to the herbal blend. In this work, the direct infusion electrospray ionization Fourier transform ion cyclotron mass spectrometry technique (ESI-FT-ICR MS) was applied to explore the chemical composition of nine samples of herbal extract blends, where a total of 11 SCs (UR-144, JWH-073, XLR-11, JWH-250, JWH-122, AM-2201, AKB48, JWH-210, JWH-081, MAM-2201 and 5F-AKB48) were identified in the positive ionization mode, ESI(+), and other 44 chemical species (saturated and unsaturated fatty acids, sugars, flavonoids, etc.) were detected in the negative ionization mode, ESI(-). Additionally, CID experiments were performed, and fragmentation pathways were proposed to identify the connectivity of SCs. Thus, the direct infusion ESI-FT-ICR MS technique is a powerful tool in forensic chemistry that enables the rapid and unequivocal way for the determination of molecular formula, the degree of unsaturation (DBE-double bond equivalent) and exact mass (<1ppm) of a total of 55 chemical species without the prior separation step.

  3. Psychopathology of Shift Work.

    ERIC Educational Resources Information Center

    Akinnawo, Ebenezer Olutope

    1989-01-01

    Examined incidence and nature of general psychopathology among Nigerian shift workers (N=320). Found shift workers more significantly psychopathological than non-shift workers (p<0.001). Prominent disorders among shift workers were intellectual, sleep, mood, and general somatic disorders. No significant difference could be attributed to gender…

  4. Structure, Vibrational Spectra and (11)B-NMR Chemical Shift of Na8[AlSiO4]6(B(OH)4)2: Comparison of Theory and Experiment.

    PubMed

    Schneider, Alexander G; Schomborg, Lars; Ulpe, Anna C; Rüscher, Claus H; Bredow, Thomas

    2016-09-29

    Density functional theory (DFT) calculations at generalized gradient approximation (GGA) level were performed to interpret experimental IR and Raman vibrational spectra, to assign (11)B-NMR chemical shifts, and to calculate the structure of the tetrahydroxyborate sodalite Na8[AlSiO4]6(B(OH)4)2. Full optimization of the intercalated compound gave the following structural parameters of B(OH)4(-): B-O-B (105.3-115.3°) and B-O-H (111.5-115.4°) angles, B-O (1.476 Å, 1.491 Å) and O-H (0.98 Å) distances. The calculated normal modes were assigned to experimental IR and Raman spectra. In general, close agreement between theory and experiment was obtained. The mean absolute deviation (MAD) is below 11 cm(-1). We also calculate the thermodynamical stability of Na8[AlSiO4]6(B(OH)4)2 with respect to Na8[AlSiO4]6(BH4)2 in the context of the tetrahydroborate hydration reaction.

  5. 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.

    PubMed

    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.

  6. Modeling the impact of soil and water conservation on surface and ground water based on the SCS and Visual MODFLOW.

    PubMed

    Wang, Hong; Gao, Jian-en; Zhang, Shao-long; Zhang, Meng-jie; Li, Xing-hua

    2013-01-01

    Soil and water conservation measures can impact hydrological cycle, but quantitative analysis of this impact is still difficult in a watershed scale. To assess the effect quantitatively, a three-dimensional finite-difference groundwater flow model (MODFLOW) with a surface runoff model-the Soil Conservation Service (SCS) were calibrated and applied based on the artificial rainfall experiments. Then, three soil and water conservation scenarios were simulated on the sand-box model to assess the effect of bare slope changing to grass land and straw mulching on water volume, hydraulic head, runoff process of groundwater and surface water. Under the 120 mm rainfall, 60 mm/h rainfall intensity, 5 m(2) area, 3° slope conditions, the comparative results indicated that the trend was decrease in surface runoff and increase in subsurface runoff coincided with the land-use converted from bare slope to grass land and straw mulching. The simulated mean surface runoff modulus was 3.64×10(-2) m(3)/m(2)/h in the bare slope scenario, while the observed values were 1.54×10(-2) m(3)/m(2)/h and 0.12×10(-2) m(3)/m(2)/h in the lawn and straw mulching scenarios respectively. Compared to the bare slope, the benefits of surface water reduction were 57.8% and 92.4% correspondingly. At the end of simulation period (T = 396 min), the simulated mean groundwater runoff modulus was 2.82×10(-2) m(3)/m(2)/h in the bare slope scenario, while the observed volumes were 3.46×10(-2) m(3)/m(2)/h and 4.91×10(-2) m(3)/m(2)/h in the lawn and straw mulching scenarios respectively. So the benefits of groundwater increase were 22.7% and 60.4% correspondingly. It was concluded that the soil and water conservation played an important role in weakening the surface runoff and strengthening the underground runoff. Meanwhile the quantitative analysis using a modeling approach could provide a thought for the study in a watershed scale to help decision-makers manage water resources.

  7. Modeling the Impact of Soil and Water Conservation on Surface and Ground Water Based on the SCS and Visual Modflow

    PubMed Central

    Wang, Hong; Gao, Jian-en; Zhang, Shao-long; Zhang, Meng-jie; Li, Xing-hua

    2013-01-01

    Soil and water conservation measures can impact hydrological cycle, but quantitative analysis of this impact is still difficult in a watershed scale. To assess the effect quantitatively, a three-dimensional finite-difference groundwater flow model (MODFLOW) with a surface runoff model–the Soil Conservation Service (SCS) were calibrated and applied based on the artificial rainfall experiments. Then, three soil and water conservation scenarios were simulated on the sand-box model to assess the effect of bare slope changing to grass land and straw mulching on water volume, hydraulic head, runoff process of groundwater and surface water. Under the 120 mm rainfall, 60 mm/h rainfall intensity, 5 m2 area, 3° slope conditions, the comparative results indicated that the trend was decrease in surface runoff and increase in subsurface runoff coincided with the land-use converted from bare slope to grass land and straw mulching. The simulated mean surface runoff modulus was 3.64×10−2 m3/m2/h in the bare slope scenario, while the observed values were 1.54×10−2 m3/m2/h and 0.12×10−2 m3/m2/h in the lawn and straw mulching scenarios respectively. Compared to the bare slope, the benefits of surface water reduction were 57.8% and 92.4% correspondingly. At the end of simulation period (T = 396 min), the simulated mean groundwater runoff modulus was 2.82×10−2 m3/m2/h in the bare slope scenario, while the observed volumes were 3.46×10−2 m3/m2/h and 4.91×10−2 m3/m2/h in the lawn and straw mulching scenarios respectively. So the benefits of groundwater increase were 22.7% and 60.4% correspondingly. It was concluded that the soil and water conservation played an important role in weakening the surface runoff and strengthening the underground runoff. Meanwhile the quantitative analysis using a modeling approach could provide a thought for the study in a watershed scale to help decision-makers manage water resources. PMID:24244427

  8. Gear shift control mechanism

    SciTech Connect

    Janson, D.A.

    1987-03-10

    A gear shift control mechanism is described comprising: multiple shift rods directed substantially parallel to one another, each rod carrying a shift fork for axial movement; a shift lever supported for pivotal movement about a first axis directed parallel to the axes of the shift rods and for pivotal movement about a second axis directed substantially perpendicular to the axes of the shift rods. The lever is moveable about the first axis and the second axis into engagement with a selected shift fork; interlock means located on each lateral side of the shift lever and mounted for pivotal movement about the first axis for blocking engagement with the shift forks; detent means for holding the shift lever in multiple predetermined angular positions about the second axis; and spring means located on a lateral side of the shift lever and mounted for pivotal movement about the first axis into interference contact with the shift forks for producing a force tending to resiliently bias the shift lever out of engagement with the selected shift fork.

  9. High-throughput backbone resonance assignment of small 13C, 15N-labeled proteins by a triple-resonance experiment with four sequential connectivity pathways using chemical shift-dependent, apparent 1J ( 1H, 13C): HNCACB codedHAHB

    NASA Astrophysics Data System (ADS)

    Pegan, Scott; Kwiatkowski, Witek; Choe, Senyon; Riek, Roland

    2003-12-01

    The proposed three-dimensional triple-resonance experiment HNCACB codedHAHB correlates sequential 15N, 1H moieties via the chemical shifts of 13C α, 13C β, 1H α, and 1H β. The four sequential correlation pathways are achieved by the incorporation of the concept of chemical shift-coding [J. Biomol. NMR 25 (2003) 281] to the TROSY-HNCACB experiment. The monitored 1H α and 1H β chemical shifts are then coded in the line shape of the cross-peaks of 13C α, 13C β along the 13C dimension through an apparent residual scalar coupling, the size of which depends on the attached hydrogen chemical shift. The information of four sequential correlation pathways enables a rapid backbone assignment. The HNCACB codedHAHB experiment was applied to ˜85% labeled 13C, 15N-labeled amino-terminal fragment of Vaccinia virus DNA topoisomerase I comprising residues 1-77. After one day of measurement on a Bruker Avance 700 MHz spectrometer and 8 h of manual analysis of the spectrum 93% of the backbone assignment was achieved.

  10. Host shifts and evolutionary radiations of butterflies.

    PubMed

    Fordyce, James A

    2010-12-22

    Ehrlich and Raven proposed a model of coevolution where major host plant shifts of butterflies facilitate a burst of diversification driven by their arrival to a new adaptive zone. One prediction of this model is that reconstructions of historical diversification of butterflies should indicate an increase in diversification rate following major host shifts. Using reconstructed histories of 15 butterfly groups, I tested this prediction and found general agreement with Ehrlich and Raven's model. Butterfly lineages with an inferred major historical host shift showed evidence of diversification rate variation, with a significant acceleration following the host shift. Lineages without an inferred major host shift generally agreed with a constant-rate model of diversification. These results are consistent with the view that host plant associations have played a profound role in the evolutionary history of butterflies, and show that major shifts to chemically distinct plant groups leave a historical footprint that remains detectable today.

  11. Surface Runoff Variability on two Slope Positions and Land Use in Koupendri Catchment, Benin, West Africa: Observation and Modeling using SCS_CN Approach

    NASA Astrophysics Data System (ADS)

    Azuka, C. V.; Diekkrüger, B.; Igué, A. M.; Bossa, A. Y.

    2015-12-01

    Surface runoff contributes significantly to soil erosion by water which is a serious worldwide problem causing decline in water resources quality, agricultural and forest land productivity, alongside environmental and ecological degradations. A field experiment was carried out on two hillslope (2-7 %) positions (downslope (2.3%), upslope (5.8%)) and two land use types; maize-beans intercrop (MB); fallow shrub-grassland (SG) in Koupendri catchment in north-western part of Benin, West Africa using microplots. The objective was to evaluate the influence of slope positions and land use on surface runoff and their variability, and the ability of Soil Conservation Service Curve Number (SCS-CN) approach to simulate the measured runoff on both slope positions and land use types in Koupendri catchment. Six microplots (1m x 1m) were installed at 0.5m spacing, and on the same soil type in each slope positions and land use giving a total of 24 microplots. Surface runoff was measured after each rain event from September - October, 2014 and major runoff producing rain events were selected for analysis. The data obtained was subjected to analysis of variance (ANOVA) in RCBD. The results showed a very low variability (CV= 9%) for measured surface runoff on both slope positions and land use respectively. The surface runoff measured was significantly (p < 0.05) influenced by the land use with a total surface runoff of 340.1 mm in MB as against 250.3 mm in SG. However, the higher surface runoff depth obtained at the downslope (299.9 mm) compared to the upslope (290.5 mm) was due to shallow soil depth and saturation of the soil downslope but not slope position. Thus, land use must be given greater priority in future surface runoff and soil erosion related studies in the catchment or region. A good simulation (R2= 0.92 - 0.97) of the measured runoff depth was obtained using the SCS-CN approach on both slopes and land use types. A better simulation was obtained under the cultivated plot

  12. Metabolites with Gram-negative bacteria quorum sensing inhibitory activity from the marine animal endogenic fungus Penicillium sp. SCS-KFD08.

    PubMed

    Kong, Fan Dong; Zhou, Li Man; Ma, Qing Yun; Huang, Sheng Zhuo; Wang, Pei; Dai, Hao Fu; Zhao, You Xing

    2017-01-01

    Three new compounds named penicitor A, aculene E and penicitor B, as well as four known compounds, were isolated from the fermentation broth of Penicillium sp. SCS-KFD08 associated with a marine animal Sipunculus nudus from the Haikou bay of China. Their planar structures and absolute configurations were unambiguously elucidated by spectroscopic data, Mosher's method, CD spectrum analysis along with quantum ECD calculation. Among them, compounds 2-7 showed quorum sensing inhibitory activity against Chromobacterium violaceum CV026, and could significantly reduce violacein production in N-hexanoyl-l-homoserine lactone (C6-HSL) induced C. violaceum CV026 cultures at sub-inhibitory concentrations.

  13. Making Shifts toward Proficiency

    ERIC Educational Resources Information Center

    McGatha, Maggie B.; Bay-Williams, Jennifer M.

    2013-01-01

    The Leading for Mathematical Proficiency (LMP) Framework (Bay-Williams et al.) has three components: (1) The Standards for Mathematical Practice; (2) Shifts in classroom practice; and (3) Teaching skills. This article briefly describes each component of the LMP framework and then focuses more in depth on the second component, the shifts in…

  14. Shifting scintillator neutron detector

    DOEpatents

    Clonts, Lloyd G; Cooper, Ronald G; Crow, Jr., Morris Lowell; Hannah, Bruce W; Hodges, Jason P; Richards, John D; Riedel, Richard A

    2014-03-04

    Provided are sensors and methods for detecting thermal neutrons. Provided is an apparatus having a scintillator for absorbing a neutron, the scintillator having a back side for discharging a scintillation light of a first wavelength in response to the absorbed neutron, an array of wavelength-shifting fibers proximate to the back side of the scintillator for shifting the scintillation light of the first wavelength to light of a second wavelength, the wavelength-shifting fibers being disposed in a two-dimensional pattern and defining a plurality of scattering plane pixels where the wavelength-shifting fibers overlap, a plurality of photomultiplier tubes, in coded optical communication with the wavelength-shifting fibers, for converting the light of the second wavelength to an electronic signal, and a processor for processing the electronic signal to identify one of the plurality of scattering plane pixels as indicative of a position within the scintillator where the neutron was absorbed.

  15. A Long-Gap Peripheral Nerve Injury Therapy Using Human Skeletal Muscle-Derived Stem Cells (Sk-SCs): An Achievement of Significant Morphological, Numerical and Functional Recovery

    PubMed Central

    Hirata, Maki; Nakajima, Nobuyuki; Saito, Kosuke; Hashimoto, Hiroyuki; Soeda, Shuichi; Uchiyama, Yoshiyasu; Watanabe, Masahiko

    2016-01-01

    Losses in vital functions of the somatic motor and sensory nervous system are induced by severe long-gap peripheral nerve transection injury. In such cases, autologous nerve grafts are the gold standard treatment, despite the unavoidable sacrifice of other healthy functions, whereas the prognosis is not always favorable. Here, we use human skeletal muscle-derived stem cells (Sk-SCs) to reconstitute the function after long nerve-gap injury. Muscles samples were obtained from the amputated legs from 9 patients following unforeseen accidents. The Sk-SCs were isolated using conditioned collagenase solution, and sorted as CD34+/45- (Sk-34) and CD34-/45-/29+ (Sk-DN/29+) cells. Cells were separately cultured/expanded under optimal conditions for 2 weeks, then injected into the athymic nude mice sciatic nerve long-gap model (7-mm) bridging an acellular conduit. After 8–12 weeks, active cell engraftment was observed only in the Sk-34 cell transplanted group, showing preferential differentiation into Schwann cells and perineurial/endoneurial cells, as well as formation of the myelin sheath and perineurium/endoneurium surrounding regenerated axons, resulted in 87% of numerical recovery. Differentiation into vascular cell lineage (pericyte and endothelial cells) were also observed. A significant tetanic tension recovery (over 90%) of downstream muscles following electrical stimulation of the sciatic nerve (at upper portion of the gap) was also achieved. In contrast, Sk-DN/29+ cells were completely eliminated during the first 4 weeks, but relatively higher numerical (83% vs. 41% in axon) and functional (80% vs. 60% in tetanus) recovery than control were observed. Noteworthy, significant increase in the formation of vascular networks in the conduit during the early stage (first 2 weeks) of recovery was observed in both groups with the expression of key factors (mRNA and protein levels), suggesting the paracrine effects to angiogenesis. These results suggested that the human Sk-SCs

  16. Protein structure prediction using global optimization by basin-hopping with NMR shift restraints

    NASA Astrophysics Data System (ADS)

    Hoffmann, Falk; Strodel, Birgit

    2013-01-01

    Computational methods that utilize chemical shifts to produce protein structures at atomic resolution have recently been introduced. In the current work, we exploit chemical shifts by combining the basin-hopping approach to global optimization with chemical shift restraints using a penalty function. For three peptides, we demonstrate that this approach allows us to find near-native structures from fully extended structures within 10 000 basin-hopping steps. The effect of adding chemical shift restraints is that the α and β secondary structure elements form within 1000 basin-hopping steps, after which the orientation of the secondary structure elements, which produces the tertiary contacts, is driven by the underlying protein force field. We further show that our chemical shift-restraint BH approach also works for incomplete chemical shift assignments, where the information from only one chemical shift type is considered. For the proper implementation of chemical shift restraints in the basin-hopping approach, we determined the optimal weight of the chemical shift penalty energy with respect to the CHARMM force field in conjunction with the FACTS solvation model employed in this study. In order to speed up the local energy minimization procedure, we developed a function, which continuously decreases the width of the chemical shift penalty function as the minimization progresses. We conclude that the basin-hopping approach with chemical shift restraints is a promising method for protein structure prediction.

  17. Instantaneous phase shifting deflectometry.

    PubMed

    Trumper, Isaac; Choi, Heejoo; Kim, Dae Wook

    2016-11-28

    An instantaneous phase shifting deflectometry measurement method is presented and implemented by measuring a time varying deformable mirror with an iPhone ® 6. The instantaneous method is based on multiplexing phase shifted fringe patterns with color, and decomposing them in x and y using Fourier techniques. Along with experimental data showing the capabilities of the instantaneous deflectometry system, a quantitative comparison with the Fourier transform profilometry method, which is a distinct phase measuring method from the phase shifting approach, is presented. Sources of error, nonlinear color-multiplexing induced error correction, and hardware limitations are discussed.

  18. Improved feedback shift register

    NASA Technical Reports Server (NTRS)

    Perlman, M.

    1972-01-01

    Design of feedback shift register with three tap feedback decoding scheme is described. Application for obtaining sequence synchronization patterns is examined. Operation of the circuitry is described and drawings of the systems are included.

  19. Shape-Shifting Plastic

    SciTech Connect

    2015-05-20

    A new plastic developed by ORNL and Washington State University transforms from its original shape through a series of temporary shapes and returns to its initial form. The shape-shifting process is controlled through changes in temperature

  20. Our World: Fluid Shift

    NASA Video Gallery

    Learn about the circulatory system and how gravity aids blood flow in our bodies here on Earth. Find out how NASA flight surgeons help the astronauts deal with the fluid shift that happens during s...

  1. Shift Verification and Validation

    SciTech Connect

    Pandya, Tara M.; Evans, Thomas M.; Davidson, Gregory G; Johnson, Seth R.; Godfrey, Andrew T.

    2016-09-07

    This documentation outlines the verification and validation of Shift for the Consortium for Advanced Simulation of Light Water Reactors (CASL). Five main types of problems were used for validation: small criticality benchmark problems; full-core reactor benchmarks for light water reactors; fixed-source coupled neutron-photon dosimetry benchmarks; depletion/burnup benchmarks; and full-core reactor performance benchmarks. We compared Shift results to measured data and other simulated Monte Carlo radiation transport code results, and found very good agreement in a variety of comparison measures. These include prediction of critical eigenvalue, radial and axial pin power distributions, rod worth, leakage spectra, and nuclide inventories over a burn cycle. Based on this validation of Shift, we are confident in Shift to provide reference results for CASL benchmarking.

  2. Straddling a paradigm shift

    SciTech Connect

    Landgren, D.

    1995-05-01

    Paul Meagher made a big mistake when he asked me about my speech. I asked him what I should talk about. He reiterated the title of the conference {open_quotes}Forecasting and DSM: Organizing for Success,{close_quotes} and said that whatever issues I wanted to cover were fine with him. As a result I will cover those areas I`ve been thinking about recently. It is hard for me to extract either Forecasting or Demand-Side Management out from the broader issues unwinding in the industry today. I`ve been around long enough to be involved in two major shifts in the industry. I call these paradigm shifts because as a planner I tend to build models in my mind to represent business or regulatory structure. Since a paradigm is defined as a clear model of something, I tend to talk about structural shifts in the industry as paradigm shifts. The first paradigm shift was brought about by the rapid escalation of energy prices in the 1970s. The second paradigm shift, brought about in part because of the first and because of growing concerns about the environment, ushered in the era of utility conservation and load management programs (components of a broader DSM concept - unfortunately today many people limit DSM to only these two pieces). The third paradigm shift is just starting, driven by partial deregulation and the subsequent increase in competition. My talk today will focus on issues related to the second paradigm, particularly in terms of utility planners getting more organized to deal with the synergies in the fields of forecasting, demand-side planning, and evaluation. I will also reflect on two new issues within the existing paradigm that influence these functional areas, namely beneficial electrification and integration of DSM into T&D planning. Finally I will talk about what I see coming as we go through another paradigm shift, particularly as it impacts forecasting and DSM.

  3. Molecular Electronic Shift Registers

    NASA Technical Reports Server (NTRS)

    Beratan, David N.; Onuchic, Jose N.

    1990-01-01

    Molecular-scale shift registers eventually constructed as parts of high-density integrated memory circuits. In principle, variety of organic molecules makes possible large number of different configurations and modes of operation for such shift-register devices. Several classes of devices and implementations in some specific types of molecules proposed. All based on transfer of electrons or holes along chains of repeating molecular units.

  4. Development of an extended Kalman Filter on the Oise river's watershed : application to the hydrological model HYDRABV-SCS at Hirson

    NASA Astrophysics Data System (ADS)

    Laborie, Vanessya; Hissel, François; Sergent, Philippe; Fayet, Laurence; de Bruyn, Bertrand; Le Pelletier, Thierry

    2014-05-01

    Operational flood forecasting nowadays usually makes use of hydraulic numerical models fed by hydrological (rainfall-runoff) models. Those latter, which allow to obtain discharges to inject at the input of hydraulic numerical models, are very often calibrated once and for all only for specific events. In other hydrological situations, their results significantly differ from measurements at hydrometric stations of the watershed. The use of data assimilation methods may then be useful to "incorporate" available observations during an event as they become available and therefore to "readjust" the forecasts of the model by bringing them back as close as possible to the reality. A numerical flood forecasting model has been developed for the Service in charge of flood forecasting for Oise and Aisne watersheds. It is divided into two models : the first model is a hydrological numerical model which provides discharges at each station of the watersheds of the Oise and Aisne rivers. It is based on the software HYDRABV-SCS-PQ developed by HYDRATEC and feeds a numerical hydraulic model with the input discharges at different points (Hirson for the Oise river, Verrières and Amblaincourt on the Aisne river), as well as the discharges of the main tributaries.CEREMA has developed an extended Kalman filter based on the hydrological model SCS-PQ which aim is to assimilate available discharges data at several hydrometric stations of the watershed and, by this way, improve flood forecasts. While this method often relies on assumptions about the differentiability of the underlying model, special techniques were applied here to account for the numerous thresholds where the hydrological model is not differentiable. The object of the presentation is to explain the methodology used and describe several results obtained for two periods (2007-2008 and 2009-2010) for the station of Hirson on the Oise river. For these two periods, Nash coefficients have been significantly improved using Kalman

  5. Trophic shift, not collapse

    USGS Publications Warehouse

    Madenjian, Charles P.; Rutherford, Edward S.; Stow, Craig A.; Roseman, Edward F.; He, Ji X.

    2013-01-01

    scientists who are closely monitoring Lake Huron’s food web, we believe that the ongoing changes are more accurately characterized as a trophic shift in which benthic pathways have become more prominent. While decreases in abundance have occurred for some species, others are experiencing improved reproduction resulting in the restoration of several important native species.

  6. Eluding catastrophic shifts.

    PubMed

    Villa Martín, Paula; Bonachela, Juan A; Levin, Simon A; Muñoz, Miguel A

    2015-04-14

    Transitions between regimes with radically different properties are ubiquitous in nature. Such transitions can occur either smoothly or in an abrupt and catastrophic fashion. Important examples of the latter can be found in ecology, climate sciences, and economics, to name a few, where regime shifts have catastrophic consequences that are mostly irreversible (e.g., desertification, coral reef collapses, and market crashes). Predicting and preventing these abrupt transitions remains a challenging and important task. Usually, simple deterministic equations are used to model and rationalize these complex situations. However, stochastic effects might have a profound effect. Here we use 1D and 2D spatially explicit models to show that intrinsic (demographic) stochasticity can alter deterministic predictions dramatically, especially in the presence of other realistic features such as limited mobility or spatial heterogeneity. In particular, these ingredients can alter the possibility of catastrophic shifts by giving rise to much smoother and easily reversible continuous ones. The ideas presented here can help further understand catastrophic shifts and contribute to the discussion about the possibility of preventing such shifts to minimize their disruptive ecological, economic, and societal consequences.

  7. Eluding catastrophic shifts

    PubMed Central

    Villa Martín, Paula; Bonachela, Juan A.; Levin, Simon A.; Muñoz, Miguel A.

    2015-01-01

    Transitions between regimes with radically different properties are ubiquitous in nature. Such transitions can occur either smoothly or in an abrupt and catastrophic fashion. Important examples of the latter can be found in ecology, climate sciences, and economics, to name a few, where regime shifts have catastrophic consequences that are mostly irreversible (e.g., desertification, coral reef collapses, and market crashes). Predicting and preventing these abrupt transitions remains a challenging and important task. Usually, simple deterministic equations are used to model and rationalize these complex situations. However, stochastic effects might have a profound effect. Here we use 1D and 2D spatially explicit models to show that intrinsic (demographic) stochasticity can alter deterministic predictions dramatically, especially in the presence of other realistic features such as limited mobility or spatial heterogeneity. In particular, these ingredients can alter the possibility of catastrophic shifts by giving rise to much smoother and easily reversible continuous ones. The ideas presented here can help further understand catastrophic shifts and contribute to the discussion about the possibility of preventing such shifts to minimize their disruptive ecological, economic, and societal consequences. PMID:25825772

  8. Problematic chemical shifts of a fluorine-labeled surfactant and oil in some microemulsion systems. [Soap is potassium 11-(2,2,2-trifluoroethoxy)undecanoate oil is 1-(2,2,2-trifluoroethoxy)hexane or a mixture of this material with heptane

    SciTech Connect

    Muller, N.

    1982-05-27

    Fluorine chemical shifts are reported for water/oil/soap/butanol microemulsions in which the soap is potassium 11-(2,2,2-trifluoroethoxy)undecanoate and the oil is 1-(2,2,2-trifluoroethoxy)hexane or a mixture of this material with heptane. In many of the solutions the two fluorinated compounds appear to have identical microenvironments. This reinforces arguments presented recently by others to the effect that microemulsions do not always contain distinct oil-rich and water-rich domains separated by a well-defined interfacial layer.

  9. Inefficiency in macromolecular transport of SCS-based microcapsules affects viability of primary human mesenchymal stem cells but not of immortalized cells.

    PubMed

    Sanz-Nogués, Clara; Horan, Jason; Thompson, Kerry; Howard, Linda; Ryan, Gerard; Kassem, Moustapha; O'Brien, Timothy

    2015-11-01

    Microcapsules made of sodium cellulose sulphate (SCS) and poly-diallyl-dimethyl-ammonium chloride (pDADMAC) have been employed to encapsulate a wide range of established cell lines for several applications. However, little is known about the encapsulation of primary cells including human mesenchymal stem cells (hMSCs). Human MSCs are of interest in regenerative medicine applications due to pro-angiogenic, anti-inflammatory and immunomodulatory properties, which result from paracrine effects of this cell type. In the present work we have encapsulated primary hMSCs and hMSC-TERT immortalized cells and compared their behavior and in vitro angiogenic potential. We found that, although both cell types were able to secret angiogenic factors such as VEGF, there was a marked reduction of primary hMSC viability compared to hMSC-TERT cells when cultured in these microcapsules. Moreover, this applied to other primary cell cultures such as primary human fibroblasts but not to other cell lines such as human embryonic kidney 293 (HEK293) cells. We found that the microcapsule membrane had a molecular weight cut-off below a critical size, which caused impairment in the diffusion of essential nutrients and had a more detrimental effect on the viability of primary cell cultures compared to cell lines and immortalized cells.

  10. SCS-CN and GIS-based approach for identifying potential water harvesting sites in the Kali Watershed, Mahi River Basin, India

    NASA Astrophysics Data System (ADS)

    Ramakrishnan, D.; Bandyopadhyay, A.; Kusuma, K. N.

    2009-08-01

    The Kali sub-watershed is situated in the semi-arid region of Gujarat, India and forms a part of the Mahi River Watershed. This watershed receives an average annual rainfall of 900mm mainly between July and September. Due to high runoff potential, evapo-transpiration and poor infiltration, drought like situation prevails in this area from December to June almost every year. In this paper, augmentation of water resource is proposed by construction of runoff harvesting structures like check dam, percolation pond, farm pond, well and subsurface dyke. The site suitability for different water harvesting structures is determined by considering spatially varying parameters like runoff potential, slope, fracture pattern and micro-watershed area. GIS is utilised as a tool to store, analyse and integrate spatial and attribute information pertaining to runoff, slope, drainage and fracture. The runoff derived by SCS-CN method is a function of runoff potential which can be expressed in terms of runoff coefficient (ratio between the runoff and rainfall) which can be classified into three classes, viz., high (>40%), moderate (20-40%) and low (<20%). In addition to IMSD, FAO specifications for water harvesting/recharging structures, parameters such as effective storage, rock mass permeability are herein considered to augment effective storage. Using the overlay and decision tree concepts in GIS, potential water harvesting sites are identified. The derived sites are field investigated for suitability and implementation. In all, the accuracy of the site selection at implementation level varies from 80-100%.

  11. Isothermal Damage and Fatigue Behavior of SCS-6/Timetal 21S [0/90](Sub S) Composite at 650 Deg C

    NASA Technical Reports Server (NTRS)

    Castelli, Michael G.

    1994-01-01

    The isothermal fatigue damage and life behaviors of SCS-6/Timetal 21S (0/90)s were investigated at 650 C. Strain ratcheting and degradation of the composite's static elastic modulus were carefully monitored as functions of cycles to indicate damage progression. Extensive fractographic and metallographic analyses were conducted to determine damage/failure mechanisms. Resulting fatigue lives show considerable reductions in comparison to (0) reinforced titanium matrix composites subjected to comparable conditions. Notable stiffness degradations were found to occur after the first cycle of loading, even at relatively low maximum stress levels, where cyclic lives are greater than 25,000 cycles. This was attributed to the extremely weak fiber/matrix bond which fails under relatively low transverse loads. Stiffness degradations incurred on first cycle loadings and degradations thereafter were found to increase with increasing maximum stress. Environmental effects associated with oxidation of the (90) fiber interfaces clearly played a role in the damage mechanisms as fracture surfaces revealed environment assisted matrix cracking along the (90) fibers. Metallographic analysis indicated that all observable matrix fatigue cracks initiated at the (90) fiber/matrix interfaces. Global de-bonding in the loading direction was found along the (90) fibers. No surface initiated cracks were evident and minimal if any (0) fiber cracking was visible.

  12. Chrodrimanins K-N and Related Meroterpenoids from the Fungus Penicillium sp. SCS-KFD09 Isolated from a Marine Worm, Sipunculus nudus.

    PubMed

    Kong, Fan-Dong; Ma, Qing-Yun; Huang, Sheng-Zhuo; Wang, Pei; Wang, Jun-Feng; Zhou, Li-Man; Yuan, Jing-Zhe; Dai, Hao-Fu; Zhao, You-Xing

    2017-02-17

    Six new meroterpenoids, chrodrimanins K-N (1-4), including two uncommon chlorinated ones (1 and 2), and verruculides B2 (5) and B3 (6), as well as seven known ones (7-13), were isolated from the fermentation broth of Penicillium sp. SCS-KFD09 isolated from a marine worm, Sipunculus nudus, from Haikou Bay, China. The structures including the absolute configurations of the new compounds were unambiguously elucidated by spectroscopic data, X-ray diffraction analysis, and ECD spectra analysis along with quantum ECD calculations. In addition, the X-ray crystal structures and absolute configurations of two previously reported meroterpenoids, chrodrimanins F (9) and A (11), are described for the first time. Compounds 1, 4, and 7 displayed anti-H1N1 activity with IC50 values of 74, 58, and 34 μM, respectively, while compound 5 showed weak inhibitory activity against Staphylococcus aureus with an MIC of 32 μg/mL.

  13. Label-free surface-enhanced infrared spectro-electro-chemical analysis of the Redox potential shift of cytochrome c complexed with a cardiolipin-containing lipid membrane of varied composition

    NASA Astrophysics Data System (ADS)

    Liu, Li; Wu, Lie; Zeng, Li; Jiang, Xiu-E.

    2015-12-01

    In this study, a lipid membrane was fabricated by fusing cardiolipin-phosphatidylcholine (CL_PC, 1:4) vesicles onto a hydrophobic surface of 1-dodecanethiol (DT) preadsorbed on a nanostructured gold film. By changing the concentration of the DT adsorption solution, we constructed a series of CL_PC-DT bilayers with different hydrophobicity to study the effects of lipid membrane characteristics on the adsorption conformation of cytochrome c (Cyt c). Electrochemical analysis showed that the formal potential is 0.24 V for Cyt c-CL_PC-DT(10), 0.2 V for Cyt c-CL_PC-DT(20), and 0.16 V for Cyt c-CL_PC-DT(40) — a gradual positive shift with the decreasing DT concentration — relative to the potential of native cyt c (0.02 V). Potential-induced surface-enhanced infrared adsorption difference spectroscopy revealed that the gradual positive shift of the formal potential of CL-bound cyt c is determined by the environment with the gradually lowered dielectric constant for the heme cofactor in CL-bound cyt c (Fe3+). Project supported by the National Natural Science Foundation of China (Grant Nos. 91227114, 21322510, and 21105097), the China Postdoctoral Science Foundation (Grant No. 2013M530998), the Natural Science Foundation of Jilin Province, China (Grant No. 201215092), and the President Funds of the Chinese Academy of Sciences.

  14. New shifted hybrid inflation

    NASA Astrophysics Data System (ADS)

    Jeannerot, Rachel; Khalil, Shaaban; Lazarides, George

    2002-07-01

    A new shifted hybrid inflationary scenario is introduced which, in contrast to the older one, relies only on renormalizable superpotential terms. This scenario is automatically realized in a concrete extension of the `minimal' supersymmetric Pati-Salam model which naturally leads to a moderate violation of Yukawa unification so that, for μ>0, the predicted b-quark mass is acceptable even with universal boundary conditions. It is shown that this extended model possesses a classically flat `shifted' trajectory which acquires a slope via one-loop radiative corrections and can be used as inflationary path. The constraints from the cosmic background explorer can be met with natural values of the relevant parameters. Also, there is no disastrous production of magnetic monopoles after inflation since the Pati-Salam gauge group is already broken on the `shifted' path. The relevant part of inflation takes place at values of the inflaton field which are not much smaller than the `reduced' Planck scale and, thus, supergravity corrections could easily invalidate inflation. It is, however, shown that inflation can be kept intact provided that an extra gauge singlet with a superheavy vacuum expectation value, which originates from D-terms, is introduced and a specific form of the Kähler potential is used. Moreover, it is found that, although the supergravity corrections are sizable, the constraints from the cosmic background explorer can again be met by readjusting the values of the parameters which were obtained with global supersymmetry.

  15. Final results for the EPRI-DOE-SCS Chiyoda Thoroughbred CT-121 clean coal project at Georgia Power`s Plant Yates

    SciTech Connect

    Burford, D.P.

    1997-12-31

    The Yates Clean Coal Project was a co-funded Clean Coal Technology effort, sponsored by the US Department of Energy, the Electric Power Research Institute and Southern Company Services (EPRI-DOE-SCS) to evaluate a retrofit wet-limestone-based, sulfur dioxide (SO{sub 2}) scrubbing system in treating the hot flue gases of a coal-fired, 110MW electric utility boiler. This Project tested the operational limits of Chiyoda`s CT-121 Jet Bubbling Reactor System (JBR ) at Georgia Power`s Plant Yates from 1992 through 1994. Although the original test plan called for a very conservative assessment, the CT-121 system proved robust, so it was tested at widely varying conditions. Fuel sulfur content was varied between 1.5% to 4.3%, various limestone sources at several grind sizes were used, particulate removal and air toxics performance were measured and by-product gypsum soil amendment experimentation was conducted. In all cases, the CT-121 system gave encouraging results with predictably high SO{sub 2} removals (95--99%) and particulate removals (99+%) at all conditions with high reliability. Closed loop operations (no liquids treated, none discharged) called for the extensive application of corrosion impervious, fiberglass reinforced plastics (FRP) that was also very successful. Gypsum by-product proved to be significant as a soil enhancement and was granted a plant food license by the State of Georgia. So far, the Yates Project has received several awards from industry and environmental groups for its performance including Power Plant of the Year in 1994 from Power magazine.

  16. Computational Study of (13)C NMR Chemical Shift Anisotropy Patterns in C20H10 and [C20H10](4-). Insights into Their Variation upon Planarization and Formation of Concentric Aromatic Species in the Smaller Isolated-Pentagon Structural Motif.

    PubMed

    Muñoz-Castro, Alvaro; Caimanque-Aguilar, Wilson; Morales-Verdejo, Cesar

    2017-04-06

    Corannulene, C20H10, exhibits a concave surface in the ground state that is able to experience a bowl-to-bowl inversion through a planar conformation. Such a structure is the smaller example resembling an isolated-pentagon motif, as a relevant fragment in fullerene chemistry. Here, we explored the differences between bowl and planar conformations involving both energetic and (13)C NMR properties, for the neutral and tetraanionic species by using density functional theory (DFT) methods. This allows us to understand the variation of the chemical environment at the carbon atoms upon planarization of this representive motif. Our results reveal that the variation of the chemical shift comes about from the variation of different main components of the shielding tensor, according to the relative position of the carbon atoms in the structure (i.e., rim, hub, and protonated), which is more relevant for both hub and protonated sites, in contrast to the rim carbon remaining almost unshifted. Interestingly, the planar transition state exhibits a more favorable bonding situation than the bowl-shaped conformation; however, the higher strain is enough to overcome this extra stabilization. Upon reduction to the tetraanionic counterpart (C20H10(4-)), a lesser strain in the planar conformation is observed, decreasing the inversion barrier. In addition, the formation of the concentric aromatic ring systems in C20H10(4-), results in a more axially symmetric chemical shift anisotropy (CSA) tensor for the hub carbons, accounting in a local manner, for the concentric aromatic behavior in such structure in contrast to the neutral parent. These observations can be useful to evaluate the aromatic behavior of teh isolated-pentagon rule (IPR) motif in fullerene cages.

  17. Transmission shift control assembly

    SciTech Connect

    Dzioba, D.L.

    1989-04-18

    This patent describes a transmission shift control assembly mounted on a steering column having a longitudinal axis comprising: bracket means secured to the steering column; transmission shift cable means having a portion secured to the bracket means and a portion linearly movable relative to the secured portion; mounting means on the bracket cable drive arm means having an axis and being rotatably mounted on the rotary axis on the mounting means oblique to the longitudinal axis and including a cable connecting portion secured to the movable portion of the cable means and lever mounting means adjacent the mounting means; operator control means including lever means, pin means for pivotally mounting the lever means on the lever mounting means on an axis substantially perpendicular to the rotary axis and positioning arm means formed on the lever means and extending from the pin means; and detent gate means disposed on the bracket means in position to abut the positioning arm means for limiting the extent of pivotal movement of the lever means.

  18. Shift Work: Improving Daytime Sleep

    MedlinePlus

    Healthy Lifestyle Adult health I just started working the night shift, and I'm having trouble sleeping during ... as long as you work the shift. Make healthy lifestyle choices. Eat a healthy diet and include physical ...

  19. Phase shifting diffraction interferometer

    DOEpatents

    Sommargren, G.E.

    1996-08-29

    An interferometer which has the capability of measuring optical elements and systems with an accuracy of {lambda}/1000 where {lambda} is the wavelength of visible light. Whereas current interferometers employ a reference surface, which inherently limits the accuracy of the measurement to about {lambda}/50, this interferometer uses an essentially perfect spherical reference wavefront generated by the fundamental process of diffraction. This interferometer is adjustable to give unity fringe visibility, which maximizes the signal-to-noise, and has the means to introduce a controlled prescribed relative phase shift between the reference wavefront and the wavefront from the optics under test, which permits analysis of the interference fringe pattern using standard phase extraction algorithms. 8 figs.

  20. Phase shifting interferometer

    DOEpatents

    Sommargren, Gary E.

    1999-01-01

    An interferometer which has the capability of measuring optical elements and systems with an accuracy of .lambda./1000 where .lambda. is the wavelength of visible light. Whereas current interferometers employ a reference surface, which inherently limits the accuracy of the measurement to about .lambda./50, this interferometer uses an essentially perfect spherical reference wavefront generated by the fundamental process of diffraction. Whereas current interferometers illuminate the optic to be tested with an aberrated wavefront which also limits the accuracy of the measurement, this interferometer uses an essentially perfect spherical measurement wavefront generated by the fundamental process of diffraction. This interferometer is adjustable to give unity fringe visibility, which maximizes the signal-to-noise, and has the means to introduce a controlled prescribed relative phase shift between the reference wavefront and the wavefront from the optics under test, which permits analysis of the interference fringe pattern using standard phase extraction algorithms.

  1. Phase shifting diffraction interferometer

    DOEpatents

    Sommargren, Gary E.

    1996-01-01

    An interferometer which has the capability of measuring optical elements and systems with an accuracy of .lambda./1000 where .lambda. is the wavelength of visible light. Whereas current interferometers employ a reference surface, which inherently limits the accuracy of the measurement to about .lambda./50, this interferometer uses an essentially perfect spherical reference wavefront generated by the fundamental process of diffraction. This interferometer is adjustable to give unity fringe visibility, which maximizes the signal-to-noise, and has the means to introduce a controlled prescribed relative phase shift between the reference wavefront and the wavefront from the optics under test, which permits analysis of the interference fringe pattern using standard phase extraction algorithms.

  2. Phase shifting interferometer

    DOEpatents

    Sommargren, G.E.

    1999-08-03

    An interferometer is disclosed which has the capability of measuring optical elements and systems with an accuracy of {lambda}/1000 where {lambda} is the wavelength of visible light. Whereas current interferometers employ a reference surface, which inherently limits the accuracy of the measurement to about {lambda}/50, this interferometer uses an essentially perfect spherical reference wavefront generated by the fundamental process of diffraction. Whereas current interferometers illuminate the optic to be tested with an aberrated wavefront which also limits the accuracy of the measurement, this interferometer uses an essentially perfect spherical measurement wavefront generated by the fundamental process of diffraction. This interferometer is adjustable to give unity fringe visibility, which maximizes the signal-to-noise, and has the means to introduce a controlled prescribed relative phase shift between the reference wavefront and the wavefront from the optics under test, which permits analysis of the interference fringe pattern using standard phase extraction algorithms. 11 figs.

  3. Shift work in a security environment

    SciTech Connect

    Longhouser, G.A. Jr.

    1993-12-31

    Human beings are diurnal species, normally active by day and asleep by night. Yet over thirty million Americans struggle with work schedules that include an off-normal work effort. The railroads, law enforcement, health services, Department of Defense, factory workers, chemical plants and public services, communications and utility workers must provide some form of around-the-clock effort. Shift work has been around since the advent of recorded history. There has always been a need for some type of off-normal service and assistance. The impact of shift work is replete with tales and factual evidence of an increased personnel error rate; disorders, both personal and family, and of course, increased accident events. In recent memory, the Three Mile Island Nuclear Plant incident, Union Carbide`s explosion in Bhopal, and the Chernobyl Nuclear Plant catastrophe all occurred during off-normal working hours. Yet management overall has done little to correct the production-driven twelve hour, seven day week shift mentality of the nineteenth century. Most schedules in use today are nothing more than cosmetic variations of the old production schedules. This could be driven by a management consideration of the worker`s response to change coupled with a reluctant buy-in of responsibility for the effects of change. Florida Power Corporation has developed for its nuclear security force, a unique work schedule which attempts to employ the sound principles of circadian rhythms coupled with a comprehensive training program to counter the problems associated with shift work. The results over the last four years have seen a marked reduction in the generic problems of personnel errors, absenteeism, unscheduled overtime and turnover rates. Utilization and understanding of this scheduling process for rotational shift work needs to be assessed to determine if the benefits are site specific or provide an expected response to the problems of shift work.

  4. Hydraulically actuated well shifting tool

    SciTech Connect

    Roth, B.A.

    1992-10-20

    This patent describes a hydraulically actuated shifting tool for actuating a sliding member in a well tool. It comprises: a housing having a hydraulic fluid bore therein; shifting dog means positioned on the housing for movement away and toward the housing; locking dog means positioned on the housing for movement away and toward the body; shifting dog hydraulic actuating means in fluid communication with the bore for causing engagement of the shifting dogs with the sliding member; locking dog hydraulic actuating means in communication with the bore for causing engagement of the locking dogs with the locking means; and hydraulic shifting means in communication with the bore for causing relative movement between the shifting dog means and the locking dog means for shifting the sliding sleeve.

  5. Pyridazine-based Schiff base ligands with N4OxS2 (x=2, 4) donor set atoms: synthesis, characterization, spectral studies and 13C chemical shifts computed by the GIAO-DFT and CSGT-DFT methodologies.

    PubMed

    Khanmohammadi, Hamid; Erfantalab, Malihe

    2010-01-01

    Six pyridazine-based Schiff base ligands, H(2)L(n) (n=1-5) and H(4)L, with N(4)O(2)S(2) and N(4)O(4)S(2) donor set atoms, respectively, were prepared by condensation reaction of 3,6-bis-((2-aminoethyl)thio)pyridazine with various salicyladehyde derivatives in ethanol and under solvent-free polyphosphate ester catalyzed conditions. The acid-base properties of H(2)L(2) and H(2)L(3) in DMSO/water (1:1) solution have been studied by spectrophotometric method at 25 degrees C. Optimized geometries of all compounds were also obtained at the B3LYP level of theory. Additionally, the (13)C chemical shielding of gas phase H(2)L(1) and H(2)L(2) were studied by the gauge independent atomic orbital (GIAO) and continuous set of gauge transformations (CSGT) methods at the level of density functional theory (DFT). The 6-311++G* basis set was utilized for all of the atoms.

  6. Pyridazine-based Schiff base ligands with N 4O xS 2 ( x = 2, 4) donor set atoms: Synthesis, characterization, spectral studies and 13C chemical shifts computed by the GIAO-DFT and CSGT-DFT methodologies

    NASA Astrophysics Data System (ADS)

    Khanmohammadi, Hamid; Erfantalab, Malihe

    2010-01-01

    Six pyridazine-based Schiff base ligands, H 2L n ( n = 1-5) and H 4L, with N 4O 2S 2 and N 4O 4S 2 donor set atoms, respectively, were prepared by condensation reaction of 3,6-bis-((2-aminoethyl)thio)pyridazine with various salicyladehyde derivatives in ethanol and under solvent-free polyphosphate ester catalyzed conditions. The acid-base properties of H 2L 2 and H 2L 3 in DMSO/water (1:1) solution have been studied by spectrophotometric method at 25 °C. Optimized geometries of all compounds were also obtained at the B3LYP level of theory. Additionally, the 13C chemical shielding of gas phase H 2L 1 and H 2L 2 were studied by the gauge independent atomic orbital (GIAO) and continuous set of gauge transformations (CSGT) methods at the level of density functional theory (DFT). The 6-311++G* basis set was utilized for all of the atoms.

  7. 1H, 13C, and 15N backbone, side-chain, and heme chemical shift assignments for oxidized and reduced forms of the monoheme c-type cytochrome ApcA isolated from the acidophilic metal-reducing bacterium Acidiphilium cryptum.

    SciTech Connect

    Cort, John R.; Swenson, Michael; Magnuson, Timothy S.

    2011-03-04

    We report the 1H, 13C, and 15N chemical shift assignments of both oxidized and reduced forms of an abundant periplasmic c-type cytochrome, designated ApcA, from the acidophilic gram-negative facultatively anaerobic metal-reducing alpha-proteobacterium Acidiphilium cryptum. These resonance assignments prove that ApcA is a monoheme cytochrome c2 and the product of the Acry_2099 gene. An absence of resonance peaks in the NMR spectra for the 21 N-terminal residues suggests that a predicted N-terminal signal sequence is cleaved. We also describe the preparation and purification of the protein in labeled form from laboratory cultures of A. cryptum growing on 13C- and 15N- labeled substrates.

  8. A study of fiber volume fraction effects in notched unidirectional SCS-6/Ti-15V-3Cr-3Al-3Sn composite. Ph.D. Thesis Final Report

    NASA Technical Reports Server (NTRS)

    Covey, Steven J.

    1993-01-01

    Notched unidirectional SCS-6/Ti-15-3 composite of three different fiber volume fractions (vf = 0.15, 0.37, and 0.41) was investigated for various room temperature microstructural and material properties including: fatigue crack initiation, fatigue crack growth, and fracture toughness. While the matrix hardness is similar for all fiber volume fractions, the fiber/matrix interfacial shear strength and matrix residual stress increases with fiber volume fraction. The composite fatigue crack initiation stress is shown to be matrix controlled and occurs when the net maximum matrix stress approaches the endurance limit stress of the matrix. A model is presented which includes residual stresses and presents the composite initiation stress as a function of fiber volume fraction. This model predicts a maximum composite initiation stress at vf approximately 0.15 which agrees with the experimental data. The applied composite stress levels were increased as necessary for continued crack growth. The applied Delta(K) values at crack arrest increase with fiber volume fraction by an amount better approximated using an energy based formulation rather than when scaled linear with modulus. After crack arrest, the crack growth rate exponents for vf37 and vf41 were much lower and toughness much higher, when compared to the unreinforced matrix, because of the bridged region which parades with the propagating fatigue crack. However, the vf15 material exhibited a higher crack growth rate exponent and lower toughness than the unreinforced matrix because once the bridged fibers nearest the crack mouth broke, the stress redistribution broke all bridged fibers, leaving an unbridged crack. Degraded, unbridged behavior is modeled using the residual stress state in the matrix ahead of the crack tip. Plastic zone sizes were directly measured using a metallographic technique and allow prediction of an effective matrix stress intensity which agrees with the fiber pressure model if residual stresses

  9. High salt diets dose-dependently promote gastric chemical carcinogenesis in Helicobacter pylori-infected Mongolian gerbils associated with a shift in mucin production from glandular to surface mucous cells.

    PubMed

    Kato, Sosuke; Tsukamoto, Tetsuya; Mizoshita, Tsutomu; Tanaka, Harunari; Kumagai, Toshiko; Ota, Hiroyoshi; Katsuyama, Tsutomu; Asaka, Masahiro; Tatematsu, Masae

    2006-10-01

    Intake of salt and salty food is known as a risk factor for gastric carcinogenesis. To examine the dose-dependence and the mechanisms underlying enhancing effects, Mongolian gerbils were treated with N-methyl-N-nitrosourea (MNU), Helicobacter pylori and food containing various concentrations of salt, and were sacrificed after 50 weeks. Among gerbils treated with MNU and H. pylori, the incidences of glandular stomach cancers were 15% in the normal diet group and 33%, 36% and 63% in the 2.5%, 5% and 10% NaCl diet groups, showing dose-dependent increase (p < 0.01). Intermittent intragastric injection of saturated NaCl solution, in contrast, did not promote gastric carcinogenesis. In gerbils infected with H. pylori, a high salt diet was associated with elevation of anti-H. pylori antibody titers, serum gastrin levels and inflammatory cell infiltration in a dose-dependent fashion. Ten percent NaCl diet upregulated the amount of surface mucous cell mucin (p < 0.05), suitable for H. pylori colonization, despite no increment of MUC5AC mRNA, while H. pylori infection itself had an opposing effect, stimulating transcription of MUC6 and increasing the amount of gland mucous cell mucin (GMCM). High salt diet, in turn, decreased the amount of GMCM, which acts against H. pylori infection. In conclusion, the present study demonstrated dose-dependent enhancing effects of salt in gastric chemical carcinogenesis in H. pylori-infected Mongolian gerbils associated with alteration of the mucous microenvironment. Reduction of salt intake could thus be one of the most important chemopreventive methods for human gastric carcinogenesis.

  10. Antiretroviral therapy: Shifting sands

    PubMed Central

    Sashindran, V.K.; Chauhan, Rajeev

    2016-01-01

    HIV/AIDS has been an extremely difficult pandemic to control. However, with the advent of antiretroviral therapy (ART), HIV has now been transformed into a chronic illness in patients who have continued treatment access and excellent long-term adherence. Existing indications for ART initiation in asymptomatic patients were based on CD4 levels; however, recent evidence has broken the shackles of CD4 levels. Early initiation of ART in HIV patients irrespective of CD4 counts can have profound positive impact on morbidity and mortality. Early initiation of ART has been found not only beneficial for patients but also to community as it reduces the risk of transmission. There have been few financial concerns about providing ART to all HIV-positive people but various studies have proven that early initiation of ART not only proves to be cost-effective but also contributes to economic and social growth of community. A novel multidisciplinary approach with early initiation and availability of ART at its heart can turn the tide in our favor in future. Effective preexposure prophylaxis and postexposure prophylaxis can also lower transmission risk of HIV in community. New understanding of HIV pathogenesis is opening new vistas to cure and prevention. Various promising candidate vaccines and drugs are undergoing aggressive clinical trials, raising optimism for an ever-elusive cure for HIV. This review describes various facets of tectonic shift in management of HIV. PMID:26900224

  11. Shape-shifting colloids via stimulated dewetting

    PubMed Central

    Youssef, Mena; Hueckel, Theodore; Yi, Gi-Ra; Sacanna, Stefano

    2016-01-01

    The ability to reconfigure elementary building blocks from one structure to another is key to many biological systems. Bringing the intrinsic adaptability of biological systems to traditional synthetic materials is currently one of the biggest scientific challenges in material engineering. Here we introduce a new design concept for the experimental realization of self-assembling systems with built-in shape-shifting elements. We demonstrate that dewetting forces between an oil phase and solid colloidal substrates can be exploited to engineer shape-shifting particles whose geometry can be changed on demand by a chemical or optical signal. We find this approach to be quite general and applicable to a broad spectrum of materials, including polymers, semiconductors and magnetic materials. This synthetic methodology can be further adopted as a new experimental platform for designing and rapidly prototyping functional colloids, such as reconfigurable micro swimmers, colloidal surfactants and switchable building blocks for self-assembly. PMID:27426418

  12. Shape-shifting colloids via stimulated dewetting

    NASA Astrophysics Data System (ADS)

    Youssef, Mena; Hueckel, Theodore; Yi, Gi-Ra; Sacanna, Stefano

    2016-07-01

    The ability to reconfigure elementary building blocks from one structure to another is key to many biological systems. Bringing the intrinsic adaptability of biological systems to traditional synthetic materials is currently one of the biggest scientific challenges in material engineering. Here we introduce a new design concept for the experimental realization of self-assembling systems with built-in shape-shifting elements. We demonstrate that dewetting forces between an oil phase and solid colloidal substrates can be exploited to engineer shape-shifting particles whose geometry can be changed on demand by a chemical or optical signal. We find this approach to be quite general and applicable to a broad spectrum of materials, including polymers, semiconductors and magnetic materials. This synthetic methodology can be further adopted as a new experimental platform for designing and rapidly prototyping functional colloids, such as reconfigurable micro swimmers, colloidal surfactants and switchable building blocks for self-assembly.

  13. Phase-shift coherence holography.

    PubMed

    Naik, Dinesh N; Ezawa, Takahiro; Miyamoto, Yoko; Takeda, Mitsuo

    2010-05-15

    We propose and experimentally demonstrate a new reconstruction scheme for coherence holography using computer-generated phase-shift coherence holograms. A 3D object encoded into the spatial coherence function is reconstructed directly from a set of incoherently illuminated computer-generated holograms with numerically introduced phase shifts. Although a rotating ground glass is used to introduce spatially incoherent illumination, the phase-shifting portion of the system is simple and free from mechanically moving components.

  14. Zero-shifted accelerometer outputs

    NASA Astrophysics Data System (ADS)

    Galef, Arnold

    1986-08-01

    It is claimed that the commonly appearing zero-shift in pyroshock data is usually a symptom of a malfunctioning measurement system, so that the data can not be repaired (by high-pass filtering or equivalent) unless tests can be devised that permit the demonstration that the system is operating in a linear mode in all respects other than the shift. The likely cause of the zero-shift and its prevention are discussed.

  15. Quantized beam shifts in graphene

    SciTech Connect

    de Melo Kort-Kamp, Wilton Junior; Sinitsyn, Nikolai; Dalvit, Diego Alejandro Roberto

    2015-10-08

    We predict the existence of quantized Imbert-Fedorov, Goos-Hanchen, and photonic spin Hall shifts for light beams impinging on a graphene-on-substrate system in an external magnetic field. In the quantum Hall regime the Imbert-Fedorov and photonic spin Hall shifts are quantized in integer multiples of the fine structure constant α, while the Goos-Hanchen ones in multiples of α2. We investigate the influence on these shifts of magnetic field, temperature, and material dispersion and dissipation. An experimental demonstration of quantized beam shifts could be achieved at terahertz frequencies for moderate values of the magnetic field.

  16. Thermochromic shifts in supercritical fluids

    SciTech Connect

    Yonker, C.R.; Smith, R.D. )

    1989-02-23

    Thermochromic shifts of organic solute molecules in supercritical CO{sub 2} under conditions of both constant pressure and density are compared to previous studies of solvatochromic shifts at isothermal conditions. Similar solvatochromic and thermochromic shifts are seen as a function of density for supercritical CO{sub 2}. At constant density a small thermochromic shift ({approx}400 cm{sup {minus}1}) for supercritical CO{sub 2} was seen for both 2-nitroanisole and 4-ethylnitrobenzene. The excited-state dipole moments for 2-nitroanisole, as calculated from the thermochromic and solvatochromic data, were in agreement.

  17. Shifts in fisheries management: adapting to regime shifts

    PubMed Central

    King, Jacquelynne R.; McFarlane, Gordon A.; Punt, André E.

    2015-01-01

    For many years, fisheries management was based on optimizing yield and maintaining a target biomass, with little regard given to low-frequency environmental forcing. However, this policy was often unsuccessful. In the last two to three decades, fisheries science and management have undergone a shift towards balancing sustainable yield with conservation, with the goal of including ecosystem considerations in decision-making frameworks. Scientific understanding of low-frequency climate–ocean variability, which is manifested as ecosystem regime shifts and states, has led to attempts to incorporate these shifts and states into fisheries assessment and management. To date, operationalizing these attempts to provide tactical advice has met with limited success. We review efforts to incorporate regime shifts and states into the assessment and management of fisheries resources, propose directions for future investigation and outline a potential framework to include regime shifts and changes in ecosystem states into fisheries management.

  18. Metabolic impact of shift work.

    PubMed

    Zimberg, Ioná Zalcman; Fernandes Junior, Silvio A; Crispim, Cibele Aparecida; Tufik, Sergio; de Mello, Marco Tulio

    2012-01-01

    In developing countries, shift work represents a considerable contingent workforce. Recently, studies have shown that overweight and obesity are more prevalent in shift workers than day workers. In addition, shift work has been associated with a higher propensity for the development of many metabolic disorders, such as insulin resistance, diabetes, dislipidemias and metabolic syndrome. Recent data have pointed that decrease of the sleep time, desynchronization of circadian rhythm and alteration of environmental aspects are the main factors related to such problems. Shortened or disturbed sleep is among the most common health-related effects of shift work. The plausible physiological and biological mechanisms are related to the activation of the autonomic nervous system, inflammation, changes in lipid and glucose metabolism, and related changes in the risk for atherosclerosis, metabolic syndrome, and type II diabetes. The present review will discuss the impact of shift work on obesity and metabolic disorders and how disruption of sleep and circadian misalignment may contribute to these metabolic dysfunctions.

  19. A Shifted Double-Diamond Titania Scaffold.

    PubMed

    Li, Hong; Liu, Ye; Cao, Xin; Han, Lu; Jiang, Chun; Che, Shunai

    2017-01-16

    Photonic crystals are expected to be metamaterials because of their potential to control the propagation of light in the linear and nonlinear regimes. Biological single-network, triply periodic constant mean curvature surface structures are considered excellent candidates owing to their large complete band gap. However, the chemical construction of these relevant structures is rare and developing new structures from thermodynamically stable double-network self-organizing systems is challenging. Herein, we reveal that the shifted double-diamond titania scaffold can achieve a complete band gap. The largest (7.71 %) band gap is theoretically obtained by shifting 0.332 c with the dielectric contrast of titania (6.25). A titania scaffold with similar shifted double-diamond structure was fabricated using a reverse core-shell microphase-templating system with an amphiphilic diblock copolymer and a titania source in a mixture of tetrahydrofuran and water, which could result in a 2.05-3.78 % gap.

  20. Is there a shift to "active nanostructures"?

    NASA Astrophysics Data System (ADS)

    Subramanian, Vrishali; Youtie, Jan; Porter, Alan L.; Shapira, Philip

    2010-01-01

    It has been suggested that an important transition in the long-run trajectory of nanotechnology development is a shift from passive to active nanostructures. Such a shift could present different or increased societal impacts and require new approaches for risk assessment. An active nanostructure "changes or evolves its state during its operation," according to the National Science Foundation's (2006) Active Nanostructures and Nanosystems grant solicitation. Active nanostructure examples include nanoelectromechanical systems (NEMS), nanomachines, self-healing materials, targeted drugs and chemicals, energy storage devices, and sensors. This article considers two questions: (a) Is there a "shift" to active nanostructures? (b) How can we characterize the prototypical areas into which active nanostructures may emerge? We build upon the NSF definition of active nanostructures to develop a research publication search strategy, with a particular intent to distinguish between passive and active nanotechnologies. We perform bibliometric analyses and describe the main publication trends from 1995 to 2008. We then describe the prototypes of research that emerge based on reading the abstracts and review papers encountered in our search. Preliminary results suggest that there is a sharp rise in active nanostructures publications in 2006, and this rise is maintained in 2007 and through to early 2008. We present a typology that can be used to describe the kind of active nanostructures that may be commercialized and regulated in the future.

  1. Health Effects of Shift Work

    PubMed Central

    LaDou, Joseph

    1982-01-01

    More than 13.5 million American workers, close to 20 percent of the work force, are assigned to evening or night shifts. In some industries such as automobile, petrochemical and textile manufacturing the proportion of shift workers is greater than 50 percent. As the popularity of shift work and other “alternative work schedules” grows, concern is increasing over the disturbance created in the lives of workers and their families by these economically and socially useful innovations. Twenty percent of workers are unable to tolerate shift work. Daily physiologic variations termed circadian rhythms are interactive and require a high degree of phase relationship to produce subjective feelings of wellbeing. Disturbance of these activities, circadian desynchronization, whether from passage over time zones or from shift rotation, results in health effects such as disturbance of the quantity and quality of sleep, disturbance of gastrointestinal and other organ system activities, and aggravation of diseases such as diabetes mellitus, epilepsy and thyrotoxicosis. Worker selection can reduce the number of health problems resulting from shift work. The periodic examination of shift workers is recommended. PMID:6962577

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

    PubMed Central

    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

  3. Red-Shifting versus Blue-Shifting Hydrogen Bonds: Perspective from Ab Initio Valence Bond Theory.

    PubMed

    Chang, Xin; Zhang, Yang; Weng, Xinzhen; Su, Peifeng; Wu, Wei; Mo, Yirong

    2016-05-05

    Both proper, red-shifting and improper, blue-shifting hydrogen bonds have been well-recognized with enormous experimental and computational studies. The current consensus is that there is no difference in nature between these two kinds of hydrogen bonds, where the electrostatic interaction dominates. Since most if not all the computational studies are based on molecular orbital theory, it would be interesting to gain insight into the hydrogen bonds with modern valence bond (VB) theory. In this work, we performed ab initio VBSCF computations on a series of hydrogen-bonding systems, where the sole hydrogen bond donor CF3H interacts with ten hydrogen bond acceptors Y (═NH2CH3, NH3, NH2Cl, OH(-), H2O, CH3OH, (CH3)2O, F(-), HF, or CH3F). This series includes four red-shifting and six blue-shifting hydrogen bonds. Consistent with existing findings in literature, VB-based energy decomposition analyses show that electrostatic interaction plays the dominating role and polarization plays the secondary role in all these hydrogen-bonding systems, and the charge transfer interaction, which denotes the hyperconjugation effect, contributes only slightly to the total interaction energy. As VB theory describes any real chemical bond in terms of pure covalent and ionic structures, our fragment interaction analysis reveals that with the approaching of a hydrogen bond acceptor Y, the covalent state of the F3C-H bond tends to blue-shift, due to the strong repulsion between the hydrogen atom and Y. In contrast, the ionic state F3C(-) H(+) leads to the red-shifting of the C-H vibrational frequency, owing to the attraction between the proton and Y. Thus, the relative weights of the covalent and ionic structures essentially determine the direction of frequency change. Indeed, we find the correlation between the structural weights and vibrational frequency changes.

  4. Refining the shifted topological vertex

    SciTech Connect

    Drissi, L. B.; Jehjouh, H.; Saidi, E. H.

    2009-01-15

    We study aspects of the refining and shifting properties of the 3d MacMahon function C{sub 3}(q) used in topological string theory and BKP hierarchy. We derive the explicit expressions of the shifted topological vertex S{sub {lambda}}{sub {mu}}{sub {nu}}(q) and its refined version T{sub {lambda}}{sub {mu}}{sub {nu}}(q,t). These vertices complete results in literature.

  5. Goos-Hänchen shift.

    PubMed

    Snyder, A W; Love, J D

    1976-01-01

    An extremely simple derivation of the Goos-Hänchen shift is presented for total internal reflection at a plane interface between two semiinfinite dielectric media, as well as for optical waveguides of plane arid circular cross section. The derivation is based on energy considerations, requires knowledge of Fresnel's equation only, and shows explicitly that the shift is due to the flow of energy across the dielectric boundary.

  6. Electronic structure and isomer shifts of neptunium compounds

    NASA Astrophysics Data System (ADS)

    Svane, A.; Petit, L.; Temmerman, W. M.; Szotek, Z.

    2002-08-01

    The electronic structures of αNp metal and 28 Np compounds are calculated with the generalized gradient approximation to density-functional theory, implemented with the full-potential linear-muffin-tin-orbital method. The calculations are compared to experimental isomer shifts providing a calibration of the 237Np isomeric transition with a value of Δ=(-40.1+/-1.3)×10- 3 fm2 for the difference in nuclear radius between the excited isomeric level and the ground state. The isomer shift is primarily determined by the chemical environment. Decreasing the volume, either by external or chemical pressure, causes an f-->s+d charge transfer on Np, which leads to a higher electron contact density. The possible f-electron localization in Np compounds is discussed using self-interaction corrections, and it is concluded that f-electron localization has only a minor influence on the isomer shift.

  7. Distal and proximal ligand interactions in heme proteins: Correlations between C-O and Fe-C vibrational frequencies, oxygen-17 and carbon-13 nuclear magnetic resonance chemical shifts, and oxygen-17 nuclear quadrupole coupling constants in C sup 17 O- and sup 13 CO-labeled species

    SciTech Connect

    Ki Deok Park; Guo, K.; Adebodun, F.; Chiu, M.L.; Sligar, S.G.; Oldfield, E. )

    1991-03-05

    The authors have obtained the oxygen-17 nuclear magnetic resonance (NMR) spectra of a variety of C{sup 17}O-labeled heme proteins, including sperm whale (Physeter catodon) myoglobin, two synthetic sperm whale myoglobin mutants (His E7 {yields} Val E7; His E7 {yields} Phe E7), adult human hemoglobin, rabbit (Oryctolagus cuniculus) hemoglobin, horseradish (Cochlearia armoracia) peroxidase isoenzymes A and C, and Caldariomyces fumago chloroperoxidase, in some cases as a function of pH, and have determined their isotropic {sup 17}O NMR chemical shifts, {delta}{sub i}, and spin-lattice relaxation times, T{sub 1}. They have also obtained similar results on a picket fence prophyrin. The results show an excellent correlation between the infrared C-O vibrational frequencies, {nu}(C-O), and {delta}{sub i}, between {nu}(C-O) and the {sup 17}O nuclear quadrupole coupling constant, and as expected between e{sup 2}qQ/h and {delta}{sub i}. The results suggest the IR and NMR measurements reflect the same interaction, which is thought to be primarily the degree of {pi}-back-bonding from Fe d to CO {pi}* orbitals, as outlined previously.

  8. B1 Mapping by Bloch-Siegert Shift

    PubMed Central

    Sacolick, Laura I.; Wiesinger, Florian; Hancu, Ileana; Vogel, Mika W.

    2010-01-01

    A novel method for B1+ field mapping based on the Bloch-Siegert shift is presented. Unlike conventionally applied double-angle or other signal magnitude-based methods it encodes the B1 information into signal phase, resulting in important advantages in terms of acquisition speed, accuracy and robustness. The Bloch Siegert frequency shift is caused by irradiating with an off-resonance RF pulse following conventional spin excitation. When applying the off-resonance RF in the kHz range, spin nutation can be neglected and the primarily observed effect is a spin precession frequency shift. This shift is proportional to the square of the RF field magnitude B12. Adding gradient image encoding following the off-resonance pulse allows one to acquire spatially resolved B1 maps. The frequency shift from the Bloch-Siegert effect gives a phase shift in the image that is proportional to B12. The phase difference of two acquisitions, with the RF pulse applied at two frequencies symmetrically around the water resonance is used to eliminate undesired off-resonance effects due to B0 inhomogeneity and chemical shift. In-vivo Bloch Siegert B1 mapping with 25 seconds / slice is demonstrated to be quantitatively comparable to a 21 minute double-angle map. As such this method enables robust, high resolution B1+ mapping in a clinically acceptable time frame. PMID:20432302

  9. Analysis of the interaction of phytoestrogens and synthetic chemicals: an in vitro/in vivo comparison.

    PubMed

    Charles, Grantley D; Gennings, Chris; Tornesi, Belen; Kan, H Lynn; Zacharewski, Timothy R; Bhaskar Gollapudi, B; Carney, Edward W

    2007-02-01

    In the evaluation of chemical mixture toxicity, it is desirable to develop an evaluation paradigm which incorporates some critical attributes of real world exposures, particularly low dose levels, larger numbers of chemicals, and chemicals from synthetic and natural sources. This study evaluated the impact of low level exposure to a mixture of six synthetic chemicals (SC) under conditions of co-exposure to various levels of plant-derived phytoestrogen (PE) compounds. Estrogenic activity was evaluated using an in vitro human estrogen receptor (ER) transcriptional activation assay and an in vivo immature rat uterotrophic assay. Initially, dose-response curves were characterized for each of the six SCs (methoxyclor, o,p-DDT, octylphenol, bisphenol A, beta-hexachlorocyclohexane,