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Sample records for 2d exchange nmr

  1. Liquid Disordered-Liquid Ordered Phase Coexistence in Lipid/Cholesterol Mixtures: A Deuterium 2D NMR Exchange Study.

    PubMed

    Schmidt, Miranda L; Davis, James H

    2017-02-28

    Model membranes composed of two types of long chain phospholipids, one unsaturated and one saturated, along with cholesterol can exhibit two coexisting fluid phases (liquid disordered ([Formula: see text]) and liquid ordered ([Formula: see text])) at various temperatures and compositions. Here we used 1D and 2D (2)H NMR to compare the behavior of multilamellar dispersions, magnetically oriented bicelles, and mechanically aligned bilayers on glass plates, all of which contain the same proportions of dipalmitoleoylphosphatidylcholine (DPoPC), dimyristoylphosphatidylcholine (DMPC), and cholesterol. We found that multilamellar dispersions and bilayers aligned on glass plates behave very similarly. These samples were close to a critical composition and exhibit exchange of the lipids between the two fluid phases at temperatures near the [Formula: see text] to [Formula: see text]-[Formula: see text] phase boundary. On the other hand, when a short chain lipid is added to the ternary long chain lipid/cholesterol mixture to form bicelles, the phase behavior is changed significantly and the [Formula: see text] phase occurs at a higher than expected temperature. In addition, there was no evidence of exchange of lipids between the [Formula: see text] and [Formula: see text] phases or critical fluctuations at the temperature where the bulk of the sample enters the two-phase region for these bicelles. It appears that the addition of the short chain lipid results in these samples no longer being near a critical composition.

  2. Quantitative 2D liquid-state NMR.

    PubMed

    Giraudeau, Patrick

    2014-06-01

    Two-dimensional (2D) liquid-state NMR has a very high potential to simultaneously determine the absolute concentration of small molecules in complex mixtures, thanks to its capacity to separate overlapping resonances. However, it suffers from two main drawbacks that probably explain its relatively late development. First, the 2D NMR signal is strongly molecule-dependent and site-dependent; second, the long duration of 2D NMR experiments prevents its general use for high-throughput quantitative applications and affects its quantitative performance. Fortunately, the last 10 years has witnessed an increasing number of contributions where quantitative approaches based on 2D NMR were developed and applied to solve real analytical issues. This review aims at presenting these recent efforts to reach a high trueness and precision in quantitative measurements by 2D NMR. After highlighting the interest of 2D NMR for quantitative analysis, the different strategies to determine the absolute concentrations from 2D NMR spectra are described and illustrated by recent applications. The last part of the manuscript concerns the recent development of fast quantitative 2D NMR approaches, aiming at reducing the experiment duration while preserving - or even increasing - the analytical performance. We hope that this comprehensive review will help readers to apprehend the current landscape of quantitative 2D NMR, as well as the perspectives that may arise from it.

  3. Hierarchical folding mechanism of apomyoglobin revealed by ultra-fast H/D exchange coupled with 2D NMR.

    PubMed

    Uzawa, Takanori; Nishimura, Chiaki; Akiyama, Shuji; Ishimori, Koichiro; Takahashi, Satoshi; Dyson, H Jane; Wright, Peter E

    2008-09-16

    The earliest steps in the folding of proteins are complete on an extremely rapid time scale that is difficult to access experimentally. We have used rapid-mixing quench-flow methods to extend the time resolution of folding studies on apomyoglobin and elucidate the structural and dynamic features of members of the ensemble of intermediate states that are populated on a submillisecond time scale during this process. The picture that emerges is of a continuum of rapidly interconverting states. Even after only 0.4 ms of refolding time a compact state is formed that contains major parts of the A, G, and H helices, which are sufficiently well folded to protect amides from exchange. The B, C, and E helix regions fold more slowly and fluctuate rapidly between open and closed states as they search docking sites on this core; the secondary structure in these regions becomes stabilized as the refolding time is increased from 0.4 to 6 ms. No further stabilization occurs in the A, G, H core at 6 ms of folding time. These studies begin to time-resolve a progression of compact states between the fully unfolded and native folded states and confirm the presence an ensemble of intermediates that interconvert in a hierarchical sequence as the protein searches conformational space on its folding trajectory.

  4. NMR Analysis of Unknowns: An Introduction to 2D NMR Spectroscopy

    ERIC Educational Resources Information Center

    Alonso, David E.; Warren, Steven E.

    2005-01-01

    A study combined 1D (one-dimensional) and 2D (two-dimensional) NMR spectroscopy to solve structural organic problems of three unknowns, which include 2-, 3-, and 4-heptanone. Results showed [to the first power]H NMR and [to the thirteenth power]C NMR signal assignments for 2- and 3-heptanone were more challenging than for 4-heptanone owing to the…

  5. Characterization of heroin samples by 1H NMR and 2D DOSY 1H NMR.

    PubMed

    Balayssac, Stéphane; Retailleau, Emmanuel; Bertrand, Geneviève; Escot, Marie-Pierre; Martino, Robert; Malet-Martino, Myriam; Gilard, Véronique

    2014-01-01

    Twenty-four samples of heroin from different illicit drug seizures were analyzed using proton Nuclear Magnetic Resonance ((1)H NMR) and two-dimensional diffusion-ordered spectroscopy (2D DOSY) (1)H NMR. A careful assignment and quantification of (1)H signals enabled a comprehensive characterization of the substances present in the samples investigated: heroin, its main related impurities (6-acetylmorphine, acetylcodeine, morphine, noscapine and papaverine) and cutting agents (caffeine and acetaminophen in nearly all samples as well as lactose, lidocaine, mannitol, piracetam in one sample only), and hence to establish their spectral signatures. The good agreement between the amounts of heroin, noscapine, caffeine and acetaminophen determined by (1)H NMR and gas chromatography, the reference method in forensic laboratories, demonstrates the validity of the (1)H NMR technique. In this paper, 2D DOSY (1)H NMR offers a new approach for a whole characterization of the various components of these complex mixtures.

  6. 2D NMR-spectroscopic screening reveals polyketides in ladybugs.

    PubMed

    Deyrup, Stephen T; Eckman, Laura E; McCarthy, Patrick H; Smedley, Scott R; Meinwald, Jerrold; Schroeder, Frank C

    2011-06-14

    Small molecules of biological origin continue to yield the most promising leads for drug design, but systematic approaches for exploring nature's cache of structural diversity are lacking. Here, we demonstrate the use of 2D NMR spectroscopy to screen a library of biorationally selected insect metabolite samples for partial structures indicating the presence of new chemical entities. This NMR-spectroscopic survey enabled detection of novel compounds in complex metabolite mixtures without prior fractionation or isolation. Our screen led to discovery and subsequent isolation of two families of tricyclic pyrones in Delphastus catalinae, a tiny ladybird beetle that is employed commercially as a biological pest control agent. The D. catalinae pyrones are based on 23-carbon polyketide chains forming 1,11-dioxo-2,6,10-trioxaanthracene and 4,8-dioxo-1,9,13-trioxaanthracene derivatives, representing ring systems not previously found in nature. This study highlights the utility of 2D NMR-spectroscopic screening for exploring nature's structure space and suggests that insect metabolomes remain vastly underexplored.

  7. 2D NMR-spectroscopic screening reveals polyketides in ladybugs

    PubMed Central

    Deyrup, Stephen T.; Eckman, Laura E.; McCarthy, Patrick H.; Smedley, Scott R.; Meinwald, Jerrold; Schroeder, Frank C.

    2011-01-01

    Small molecules of biological origin continue to yield the most promising leads for drug design, but systematic approaches for exploring nature’s cache of structural diversity are lacking. Here, we demonstrate the use of 2D NMR spectroscopy to screen a library of biorationally selected insect metabolite samples for partial structures indicating the presence of new chemical entities. This NMR-spectroscopic survey enabled detection of novel compounds in complex metabolite mixtures without prior fractionation or isolation. Our screen led to discovery and subsequent isolation of two families of tricyclic pyrones in Delphastus catalinae, a tiny ladybird beetle that is employed commercially as a biological pest control agent. The D. catalinae pyrones are based on 23-carbon polyketide chains forming 1,11-dioxo-2,6,10-trioxaanthracene and 4,8-dioxo-1,9,13-trioxaanthracene derivatives, representing ring systems not previously found in nature. This study highlights the utility of 2D NMR-spectroscopic screening for exploring nature’s structure space and suggests that insect metabolomes remain vastly underexplored. PMID:21646540

  8. Optimizing water hyperpolarization and dissolution for sensitivity-enhanced 2D biomolecular NMR

    NASA Astrophysics Data System (ADS)

    Olsen, Greg; Markhasin, Evgeny; Szekely, Or; Bretschneider, Christian; Frydman, Lucio

    2016-03-01

    A recent study explored the use of hyperpolarized water, to enhance the sensitivity of nuclei in biomolecules thanks to rapid proton exchanges with labile amide backbone and sidechain groups. Further optimizations of this approach have now allowed us to achieve proton polarizations approaching 25% in the water transferred into the NMR spectrometer, effective water T1 times approaching 40 s, and a reduction in the dilution demanded for the cryogenic dissolution process. Further hardware developments have allowed us to perform these experiments, repeatedly and reliably, in 5 mm NMR tubes. All these ingredients - particularly the ⩾3000× 1H polarization enhancements over 11.7 T thermal counterparts, long T1 times and a compatibility with high-resolution biomolecular NMR setups - augur well for hyperpolarized 2D NMR studies of peptides, unfolded proteins and intrinsically disordered systems undergoing fast exchanges of their protons with the solvent. This hypothesis is here explored by detailing the provisions that lead to these significant improvements over previous reports, and demonstrating 1D coherence transfer experiments and 2D biomolecular HMQC acquisitions delivering NMR spectral enhancements of 100-500× over their optimized, thermally-polarized, counterparts.

  9. Peak width issues with generalised 2D correlation NMR spectroscopy

    NASA Astrophysics Data System (ADS)

    Kirwan, Gemma M.; Adams, Michael J.

    2008-12-01

    Two-dimensional spectral correlation analysis is shown to be sensitive to fluctuations in spectral peak width as a function of perturbation variable. This is particularly significant where peak width fluctuations are of similar order of magnitude as the peak width values themselves and where changes in peak width are not random but are, for example, proportional to intensity. In such cases these trends appear in the asynchronous matrix as false peaks that serve to interfere with interpretation of the data. Complex, narrow band spectra such as provided by 1H NMR spectroscopy are demonstrated to be prone to such interference. 2D correlation analysis was applied to a series of NMR spectra corresponding to a commercial wine fermentation, in which the samples collected over a period of several days exhibit dramatic changes in concentration of minor and major components. The interference due to changing peak width effects is eliminated by synthesizing the recorded spectra using a constant peak width value prior to performing 2D correlation analysis.

  10. T2-Filtered T2 - T2 Exchange NMR

    NASA Astrophysics Data System (ADS)

    d'Eurydice, Marcel Nogueira; Montrazi, Elton Tadeu; Fortulan, Carlos Alberto; Bonagamba, Tito José

    2016-05-01

    This work introduces an alternative way to perform the T2 - T2 Exchange NMR experiment. Rather than varying the number of π pulses in the first CPMG cycle of the T2 - T2 Exchange NMR pulse sequence, as used to obtain the 2D correlation maps, it is fixed and small enough to act as a short T2-filter. By varying the storage time, a set of 1D measurements of T2 distributions can be obtained to reveal the effects of the migration dynamics combined with relaxation effects. This significantly reduces the required time to perform the experiment, allowing a more in-depth study of exchange dynamics and relaxation processes with improved signal-to-noise ratio. These aspects stand as basis of this novel experiment, T2-Filtered T2 - T2 Exchange NMR or simply T2 F-TREx.

  11. Fast, accurate 2D-MR relaxation exchange spectroscopy (REXSY): Beyond compressed sensing

    NASA Astrophysics Data System (ADS)

    Bai, Ruiliang; Benjamini, Dan; Cheng, Jian; Basser, Peter J.

    2016-10-01

    Previously, we showed that compressive or compressed sensing (CS) can be used to reduce significantly the data required to obtain 2D-NMR relaxation and diffusion spectra when they are sparse or well localized. In some cases, an order of magnitude fewer uniformly sampled data were required to reconstruct 2D-MR spectra of comparable quality. Nonetheless, this acceleration may still not be sufficient to make 2D-MR spectroscopy practicable for many important applications, such as studying time-varying exchange processes in swelling gels or drying paints, in living tissue in response to various biological or biochemical challenges, and particularly for in vivo MRI applications. A recently introduced framework, marginal distributions constrained optimization (MADCO), tremendously accelerates such 2D acquisitions by using a priori obtained 1D marginal distribution as powerful constraints when 2D spectra are reconstructed. Here we exploit one important intrinsic property of the 2D-MR relaxation exchange spectra: the fact that the 1D marginal distributions of each 2D-MR relaxation exchange spectrum in both dimensions are equal and can be rapidly estimated from a single Carr-Purcell-Meiboom-Gill (CPMG) or inversion recovery prepared CPMG measurement. We extend the MADCO framework by further proposing to use the 1D marginal distributions to inform the subsequent 2D data-sampling scheme, concentrating measurements where spectral peaks are present and reducing them where they are not. In this way we achieve compression or acceleration that is an order of magnitude greater than that in our previous CS method while providing data in reconstructed 2D-MR spectral maps of comparable quality, demonstrated using several simulated and real 2D T2 - T2 experimental data. This method, which can be called "informed compressed sensing," is extendable to other 2D- and even ND-MR exchange spectroscopy.

  12. Characterization of Secondary Amide Peptide Bonds Isomerization: Thermodynamics and Kinetics from 2D NMR Spectroscopy

    PubMed Central

    Zhang, Jin; Germann, Markus W.

    2011-01-01

    Secondary amide cis peptide bonds are of even lower abundance than the cis tertiary amide bonds of prolines, yet they are of biochemical importance. Using 2D NMR exchange spectroscopy we investigated the formation of cis peptide bonds in several oligopeptides: Ac-G-G-G-NH2, Ac-I-G-G-NH2, Ac-I-G-G-N-NH2 and its cyclic form: I-G-G-N in DMSO. From the NMR studies, using the amide protons as monitors, an occurrenc.e of 0.13% – 0.23% of cis bonds was obtained at 296 K. The rate constants for the trans to cis conversion determined from 2D EXSY spectroscopy were 4–9·10−3 s−1. Multiple minor conformations were detected for most peptide bonds. From their thermodynamic and kinetic properties the cis isomers are distinguished from minor trans isomers that appear because of an adjacent cis peptide bond. Solvent and sequence effects were investigated utilizing N-methylacetamide and various peptides, which revealed an unique enthalpy profile in DMSO. The cyclization of a tetrapeptide resulted in greatly lowered cis populations and slower isomerization rate compared to its linear counterpart, further highlighting the impact of structural constraints. PMID:21538331

  13. Isolation and 2D NMR Studies of Alkaloids from Comptonella sessilifoliola1.

    PubMed

    Pusset, J; Lopez, J L; Pais, M; Neirabeyeh, M A; Veillon, J M

    1991-04-01

    Six known furanoquinoline alkaloids have been isolated from the wood and trunk bark of COMPTONELLA SESSILIFOLIOLA (Guillaumin) Hartley (Rutaceae). 2D NMR experiments gave the assignment of all the signals for both (1)H- and (13)C-NMR spectra. Pteleine and kokusaginine were used as models. The two-dimensional carbon-proton correlation experiments, performed for the first time on furanoquinoline alkaloids, led us to correct (13)C-NMR assignments previously described in the literature.

  14. Deuterium Exchange Kinetics by NMR.

    ERIC Educational Resources Information Center

    Roper, G. C.

    1985-01-01

    Describes a physical chemistry experiment which allows such concepts as kinetics, catalysis, isotope shifts, coupling constants, and the use of nuclear magnetic resonance (NMR) for quantitative work to be covered in the same exercise. Background information, experimental procedures used, and typical results obtained are included. (JN)

  15. Dynamic UltraFast 2D EXchange SpectroscopY (UF-EXSY) of hyperpolarized substrates

    PubMed Central

    Swisher, Christine Leon; Koelsch, Bertram; Sukumar, Subramianam; Sriram, Renuka; Santos, Romelyn Delos; Wang, Zhen Jane; Kurhanewicz, John; Vigneron, Daniel; Larson, Peder

    2015-01-01

    In this work, we present a new ultrafast method for acquiring dynamic 2D EXchange SpectroscopY (EXSY) within a single acquisition. This technique reconstructs two-dimensional EXSY spectra from one-dimensional spectra based on the phase accrual during echo times. The Ultrafast-EXSY acquisition overcomes long acquisition times typically needed to acquire 2D NMR data by utilizing sparsity and phase dependence to dramatically undersample in the indirect time dimension. This allows for the acquisition of the 2D spectrum within a single shot. We have validated this method in simulations and hyperpolarized enzyme assay experiments separating the dehydration of pyruvate and lactate-to-pyruvate conversion. In a renal cell carcinoma cell (RCC) line, bidirectional exchange was observed. This new technique revealed decreased conversion of lactate-to-pyruvate with high expression of monocarboxylate transporter 4 (MCT4), known to correlate with aggressive cancer phenotypes. We also showed feasibility of this technique in vivo in a RCC model where bidirectional exchange was observed for pyruvate–lactate, pyruvate–alanine, and pyruvate–hydrate and were resolved in time. Broadly, the technique is well suited to investigate the dynamics of multiple exchange pathways and applicable to hyperpolarized substrates where chemical exchange has shown great promise across a range of disciplines. PMID:26117655

  16. Dynamic UltraFast 2D EXchange SpectroscopY (UF-EXSY) of hyperpolarized substrates

    NASA Astrophysics Data System (ADS)

    Leon Swisher, Christine; Koelsch, Bertram; Sukumar, Subramianam; Sriram, Renuka; Santos, Romelyn Delos; Wang, Zhen Jane; Kurhanewicz, John; Vigneron, Daniel; Larson, Peder

    2015-08-01

    In this work, we present a new ultrafast method for acquiring dynamic 2D EXchange SpectroscopY (EXSY) within a single acquisition. This technique reconstructs two-dimensional EXSY spectra from one-dimensional spectra based on the phase accrual during echo times. The Ultrafast-EXSY acquisition overcomes long acquisition times typically needed to acquire 2D NMR data by utilizing sparsity and phase dependence to dramatically undersample in the indirect time dimension. This allows for the acquisition of the 2D spectrum within a single shot. We have validated this method in simulations and hyperpolarized enzyme assay experiments separating the dehydration of pyruvate and lactate-to-pyruvate conversion. In a renal cell carcinoma cell (RCC) line, bidirectional exchange was observed. This new technique revealed decreased conversion of lactate-to-pyruvate with high expression of monocarboxylate transporter 4 (MCT4), known to correlate with aggressive cancer phenotypes. We also showed feasibility of this technique in vivo in a RCC model where bidirectional exchange was observed for pyruvate-lactate, pyruvate-alanine, and pyruvate-hydrate and were resolved in time. Broadly, the technique is well suited to investigate the dynamics of multiple exchange pathways and applicable to hyperpolarized substrates where chemical exchange has shown great promise across a range of disciplines.

  17. Single-scan 2D NMR: An Emerging Tool in Analytical Spectroscopy

    PubMed Central

    Giraudeau, Patrick; Frydman, Lucio

    2016-01-01

    Two-dimensional Nuclear Magnetic Resonance (2D NMR) spectroscopy is widely used in chemical and biochemical analyses. Multidimensional NMR is also witnessing an increased use in quantitative and metabolic screening applications. Conventional 2D NMR experiments, however, are affected by inherently long acquisition durations, arising from their need to sample the frequencies involved along their indirect domains in an incremented, scan-by-scan nature. A decade ago a so-called “ultrafast” (UF) approach was proposed, capable to deliver arbitrary 2D NMR spectra involving any kind of homo- or hetero-nuclear correlations, in a single scan. During the intervening years the performance of this sub-second 2D NMR methodology has been greatly improved, and UF 2D NMR is rapidly becoming a powerful analytical tool witnessing an expanded scope of applications. The present reviews summarizes the principles and the main developments which have contributed to the success of this approach, and focuses on applications which have been recently demonstrated in various areas of analytical chemistry –from the real time monitoring of chemical and biochemical processes, to extensions in hyphenated techniques and in quantitative applications. PMID:25014342

  18. 1D and 2D NMR of nanocellulose in aqueous colloidal suspensions.

    PubMed

    Jiang, Feng; Dallas, Jerry L; Ahn, B Kollbe; Hsieh, You-Lo

    2014-09-22

    This is the first report on surface structural elucidation of individual nanocellulose as colloidal suspensions by 1D 1H, 2D heteronuclear single quantum coherence (HSQC) as well as 13C nuclear magnetic resonance (NMR). 1H NMR of rice straw CNCs (4.7 nm thick, 143 nm long, 0.04 sulfate per AG or 19.0% surface hydroxyl to sulfate conversion) resembled that of homogeneous cellulose solution. Conventional 2D HSQC NMR of CNC, CNF 1.5 (2-14 nm thick, several micrometers long, 0.10 COOH per AG) and CNF10 (2.0 nm thick, up to 1 μm long, 0.28 COOH per AG) gave H1:H2 ratios of 1.08:1, 0.97:1 and 0.94:1, respectively, all close to the theoretical 1:1 value for cellulose. The H1:H6 ratios determined from 2D HSQC NMR for CNCs, CNF1.5 and CNF10 were 1:1.47, 1:0.88 and 1:0.14, respectively, and corresponded to 26%, 56% and 93% C6 primary hydroxyl conversion to sulfate and carboxyl groups, consistent with, but more sensitive than those by conductometric titration and X-ray diffraction. Both 1H and 2D HSQC NMR data confirm that solution-state NMR detects nanocellulose surface carbons and protons primarily, validating this technique for direct surface characterization of nanocellulose in aqueous colloidal suspensions, presenting a sensitive and meaningful NMR tool for direct characterizing individual nanocellulose surfaces in never-dried state.

  19. Structural investigations on betacyanin pigments by LC NMR and 2D NMR spectroscopy.

    PubMed

    Stintzing, Florian C; Conrad, Jürgen; Klaiber, Iris; Beifuss, Uwe; Carle, Reinhold

    2004-02-01

    Four betacyanin pigments were analysed by LC NMR and subjected to extensive NMR characterisation after isolation. Previously, low pH values were applied for NMR investigations of betalains resulting in rapid degradation of the purified substances thus preventing extensive NMR studies. Consequently, up to now only one single (13)C NMR spectrum of a betalain pigment, namely that of neobetanin (=14,15-dehydrobetanin), was available. Because of its sufficient stability under highly acidic conditions otherwise detrimental for betacyanins, this pigment remained an exemption. Since betalains are most stable in the pH range of 5-7, a new solvent system has been developed allowing improved data acquisition through improved pigment stability at near neutral pH. Thus, not only (1)H, but for the first time also partial (13)C data of betanin, isobetanin, phyllocactin and hylocerenin isolated from red-purple pitaya [Hylocereus polyrhizus (Weber) Britton & Rose, Cactaceae] could be indirectly obtained by gHSQC- and gHMQC-NMR experiments.

  20. In situ fluid typing and quantification with 1D and 2D NMR logging.

    PubMed

    Sun, Boqin

    2007-05-01

    In situ nuclear magnetic resonance (NMR) fluid typing has recently gained momentum due to data acquisition and inversion algorithm enhancement of NMR logging tools. T(2) distributions derived from NMR logging contain information on bulk fluids and pore size distributions. However, the accuracy of fluid typing is greatly overshadowed by the overlap between T(2) peaks arising from different fluids with similar apparent T(2) relaxation times. Nevertheless, the shapes of T(2) distributions from different fluid components are often different and can be predetermined. Inversion with predetermined T(2) distributions allows us to perform fluid component decomposition to yield individual fluid volume ratios. Another effective method for in situ fluid typing is two-dimensional (2D) NMR logging, which results in proton population distribution as a function of T(2) relaxation time and fluid diffusion coefficient (or T(1) relaxation time). Since diffusion coefficients (or T(1) relaxation time) for different fluid components can be very different, it is relatively easy to separate oil (especially heavy oil) from water signal in a 2D NMR map and to perform accurate fluid typing. Combining NMR logging with resistivity and/or neutron/density logs provides a third method for in situ fluid typing. We shall describe these techniques with field examples.

  1. 2D multinuclear NMR, hyperpolarized xenon and gas storage in organosilica nanochannels with crystalline order in the walls.

    PubMed

    Comotti, Angiolina; Bracco, Silvia; Valsesia, Patrizia; Ferretti, Lisa; Sozzani, Piero

    2007-07-11

    The combination of 2D 1H-13C and 1H-29Si solid state NMR, hyperpolarized 129Xe NMR, synchrotron X-ray diffraction, together with adsorption measurements of vapors and gases for environmental and energetic relevance, was used to investigate the structure and the properties of periodic mesoporous hybrid p-phenylenesilica endowed with crystalline order in the walls. The interplay of 1H, 13C, and 29Si in the 2D heteronuclear correlation NMR measurements, together with the application of Lee-Goldburg homonuclear decoupling, revealed the spatial relationships (<5 angstroms) among various spin-active nuclei of the framework. Indeed, the through-space correlations in the 2D experiments evidenced, for the first time, the interfaces of the matrix walls with guest molecules confined in the nanochannels. Organic-inorganic and organic-organic heterogeneous interfaces between the matrix and the guests were identified. The open-pore structure and the easy accessibility of the nanochannels to the gas phase have been demonstrated by highly sensitive hyperpolarized (HP) xenon NMR, under extreme xenon dilution. Two-dimensional exchange experiments showed the exchange time to be as short as 2 ms. Through variable-temperature HP 129Xe NMR experiments we were able to achieve an unprecedented description of the nanochannel space and surface, a physisorption energy of 13.9 kJ mol-1, and the chemical shift value of xenon probing the internal surfaces. These results prompted us to measure the high storage capacity of the matrix towards benzene, hexafluorobenzene, ethanol, and carbon dioxide. Both host-guest, CH...pi, and OH...pi interactions contribute to the stabilization of the aromatic guests (benzene and hexafluorobenzene) on the extended surfaces. The full carbon dioxide loading in the channels could be detected by synchrotron radiation X-ray diffraction experiments. The selective adsorption of carbon dioxide (ca. 90 wt %) vs that of oxygen and hydrogen, together with the permanent

  2. Quenched Hydrogen Exchange NMR of Amyloid Fibrils.

    PubMed

    Alexandrescu, Andrei T

    2016-01-01

    Amyloid fibrils are associated with a number of human diseases. These aggregatively misfolded intermolecular β-sheet assemblies constitute some of the most challenging targets in structural biology because to their complexity, size, and insolubility. Here, protocols and controls are described for experiments designed to study hydrogen-bonding in amyloid fibrils indirectly, by transferring information about amide proton occupancy in the fibrils to the dimethyl sulfoxide-denatured state. Since the denatured state is amenable to solution NMR spectroscopy, the method can provide residue-level-resolution data on hydrogen exchange for the monomers that make up the fibrils.

  3. GEL-STATE NMR OF BALL-MILLED WHOLE CELL WALLS IN DMSO-d6 USING 2D SOLUTION-STATE NMR SPECTROSCOPY

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Plant cell walls were used for obtaining 2D solution-state NMR spectra without actual solubilization or structural modification. Ball-milled whole cell walls were swelled directly in the NMR tube with DMSO-d6 where they formed a gel. There are relatively few gel-state NMR studies. Most have involved...

  4. Well-defined azazirconacyclopropane complexes supported on silica structurally determined by 2D NMR comparative elucidation.

    PubMed

    El Eter, Mohamad; Hamzaoui, Bilel; Abou-Hamad, Edy; Pelletier, Jérémie D A; Basset, Jean-Marie

    2013-05-21

    Grafting of Zr(NMe2)4 on mesoporous silica SBA-15 afforded selectively well-defined surface species [triple bond, length as m-dash]SiOZr(NMe2)(η2NMeCH2). 2D solid-state NMR ((1)H-(13)C HETCOR, Multiple Quantum) experiments have shown a unique structural rearrangement occurring on the immobilised zirconium bis methylamido ligand.

  5. Fast acquisition of high-resolution 2D NMR spectroscopy in inhomogeneous magnetic fields

    NASA Astrophysics Data System (ADS)

    Lin, Liangjie; Wei, Zhiliang; Zeng, Qing; Yang, Jian; Lin, Yanqin; Chen, Zhong

    2016-05-01

    High-resolution nuclear magnetic resonance (NMR) spectroscopy plays an important role in chemical and biological analyses. In this study, we combine the J-coupling coherence transfer module with the echo-train acquisition technique for fast acquisition of high-resolution 2D NMR spectra in magnetic fields with unknown spatial variations. The proposed method shows satisfactory performance on a 5 mM ethyl 3-bromopropionate sample, under a 5-kHz (10 ppm at 11.7 T) B0 inhomogeneous field, as well as under varying degrees of pulse-flip-angle deviations. Moreover, a simulative ex situ NMR measurement is also conducted to show the effectiveness of the proposed pulse sequence.

  6. Non-linear effects in quantitative 2D NMR of polysaccharides: pitfalls and how to avoid them.

    PubMed

    Martineau, Estelle; El Khantache, Kamel; Pupier, Marion; Sepulcri, Patricia; Akoka, Serge; Giraudeau, Patrick

    2015-04-10

    Quantitative 2D NMR is a powerful analytical tool which is widely used to determine the concentration of small molecules in complex samples. Due to the site-specific response of the 2D NMR signal, the determination of absolute concentrations requires the use of a calibration or standard addition approach, where the analyte acts as its own reference. Standard addition methods, where the targeted sample is gradually spiked with known amounts of the targeted analyte, are particularly well-suited for quantitative 2D NMR of small molecules. This paper explores the potential of such quantitative 2D NMR approaches for the quantitative analysis of a high molecular weight polysaccharide. The results highlight that the standard addition method leads to a strong under-estimation of the target concentration, whatever the 2D NMR pulse sequence. Diffusion measurements show that a change in the macromolecular organization of the studied polysaccharide is the most probable hypothesis to explain the non-linear evolution of the 2D NMR signal with concentration. In spite of this non-linearity--the detailed explanation of which is out of the scope of this paper--we demonstrate that accurate quantitative results can still be obtained provided that an external calibration is performed with a wide range of concentrations surrounding the target value. This study opens the way to a number of studies where 2D NMR is needed for the quantitative analysis of macromolecules.

  7. Sodium ion effect on silk fibroin conformation characterized by solid-state NMR and generalized 2D NMR NMR correlation

    NASA Astrophysics Data System (ADS)

    Ruan, Qing-Xia; Zhou, Ping

    2008-07-01

    In the present work, we investigated Na + ion effect on the silk fibroin (SF) conformation. Samples are Na +-involved regenerated silk fibroin films. 13C CP-MAS NMR demonstrates that as added [Na +] increases, partial silk fibroin conformation transit from helix-form to β-form at certain Na + ion concentration which is much higher than that in Bombyx mori silkworm gland. The generalized two-dimensional NMR-NMR correlation analysis reveals that silk fibroin undergoes several intermediate states during its conformation transition process as [Na +] increase. The appearance order of the intermediates is followed as: helix and/or random coil → helix-like → β-sheet-like → β-sheet, which is the same as that produced by pH decrease from 6.8 to 4.8 in the resultant regenerated silk fibroin films. The binding sites of Na + to silk fibroin might involve the carbonyl oxygen atom of certain amino acids sequence which could promote the formation of β-sheet conformation. Since the Na +sbnd O bond is weak, the ability of Na + inducing the secondary structure transition is weaker than those of Ca 2+, Cu 2+ and even K +. It is maybe a reason why the sodium content is much lower than potassium in the silkworm gland.

  8. Analysis of pyruvylated beta-carrageenan by 2D NMR spectroscopy and reductive partial hydrolysis.

    PubMed

    Falshaw, Ruth; Furneaux, Richard H; Wong, Herbert

    2003-06-23

    A polysaccharide rich in 4',6'-O-(1-carboxyethylidene)-substituted (i.e., pyruvylated) beta-carrageenan has been prepared by solvolytic desulfation of a polysaccharide containing predominantly pyruvylated alpha-carrageenan, which was extracted from the red seaweed, Callophycus tridentifer. The 13C and 1H NMR chemical shifts of pyruvylated beta-carrageenan have been fully assigned using 2D NMR spectroscopic techniques. The 4',6'-O-(1-methoxycarbonylethylidene) group, generated during chemical methylation of the polysaccharide, has been shown to survive under the conditions of acidic hydrolysis that cleave the 3,6-anhydro-alpha-D-galactosidic bonds in permethylated samples of both pyruvylated beta- and pyruvylated alpha-carrageenans. As a result, two novel pyruvylated carrabiitol derivatives have been prepared.

  9. The inversion of 2D NMR relaxometry data using L1 regularization

    NASA Astrophysics Data System (ADS)

    Zhou, Xiaolong; Su, Guanqun; Wang, Lijia; Nie, Shengdong; Ge, Xinmin

    2017-02-01

    NMR relaxometry has been used as a powerful tool to study molecular dynamics. Many algorithms have been developed for the inversion of 2D NMR relaxometry data. Unlike traditional algorithms implementing L2 regularization, high order Tikhonov regularization or iterative regularization, L1 penalty term is involved to constrain the sparsity of resultant spectra in this paper. Then fast iterative shrinkage-thresholding algorithm (FISTA) is proposed to solve the L1 regularization problem. The effectiveness, noise vulnerability and practical utility of the proposed algorithm are analyzed by simulations and experiments. The results demonstrate that the proposed algorithm has a more excellent capability to reveal narrow peaks than traditional inversion algorithms. The L1 regularization implemented by our algorithm can be a useful complementary to the existing algorithms.

  10. 1D and 2D NMR studies of isobornyl acrylate - Methyl methacrylate copolymers

    NASA Astrophysics Data System (ADS)

    Khandelwal, Deepika; Hooda, Sunita; Brar, A. S.; Shankar, Ravi

    2011-10-01

    Isobornyl acrylate - methyl methacrylate (B/M) copolymers of different compositions were synthesized by atom transfer radical polymerization (ATRP) using methyl-2-bromopropionate as an initiator and PMDETA copper complex as catalyst under nitrogen atmosphere at 70 °C. 1H NMR spectrum was used to determine the compositions of copolymer. The copolymer compositions were then used to determine the reactivity ratios of monomers. Reactivity ratios of co-monomers in B/M copolymer, determined from linear Kelen-Tudos method (KT) and non linear Error-in-Variable Method (EVM), are rB = 0.41 ± 0.11, rM = 1.11 ± 0.33 and rB = 0.52, rM = 1.31 respectively. The complete resonance assignments of 1H and 13C{ 1H} NMR spectra were carried out with the help of Distortion less Enhancement by Polarization Transfer (DEPT), two-dimensional Heteronuclear Single Quantum Coherence (HSQC). 2D HSQC assignments were further confirmed by 2D Total Correlation Spectroscopy (TOCSY). The carbonyl carbon of B and M units and methyl carbon of M unit were assigned up to triad compositional and configurational sequences whereas β-methylene carbons were assigned up to tetrad compositional and configurational sequences. Similarly the methine carbon of B unit was assigned up to pentad level. 1,3 and 1,4 bond order couplings of carbonyl carbon and quaternary carbon resonances with methine, methylene and methyl protons were studied in detail using 2D Hetero Nuclear Multiple Bond Correlation (HMBC) spectra.

  11. Measuring JHH values with a selective constant-time 2D NMR protocol

    NASA Astrophysics Data System (ADS)

    Lin, Liangjie; Wei, Zhiliang; Lin, Yanqin; Chen, Zhong

    2016-11-01

    Proton-proton scalar couplings play important roles in molecule structure elucidation. However, measurements of JHH values in complex coupled spin systems remain challenging. In this study, we develop a selective constant-time (SECT) 2D NMR protocol with which scalar coupling networks involving chosen protons can be revealed, and corresponding JHH values can be measured through doublets along the F1 dimension. All JHH values within a network of n fully coupled protons can be separately determined with (n - 1) SECT experiments. Additionally, the proposed pulse sequence possesses satisfactory sensitivity and handy implementation. Therefore, it will interest scientists who intend to address structural analyzes of molecules with overcrowded spectra, and may greatly facilitate the applications of scalar-coupling constants in molecule structure studies.

  12. Ionic Liquid–Solute Interactions Studied by 2D NOE NMR Spectroscopy

    SciTech Connect

    Khatun, Sufia; Castner, Edward W.

    2014-11-26

    Intermolecular interactions between a Ru²⁺(bpy)₃ solute and the anions and cations of four different ionic liquids (ILs) are investigated by 2D NMR nuclear Overhauser effect (NOE) techniques, including {¹H-¹⁹F} HOESY and {¹H-¹H} ROESY. Four ILs are studied, each having the same bis(trifluoromethylsulfonyl)amide anion in common. Two of the ILs have aliphatic 1-alkyl-1-methylpyrrolidinium cations, while the other two ILs have aromatic 1-alkyl-3-methylimidazolium cations. ILs with both shorter (butyl) and longer (octyl or decyl) cationic alkyl substituents are studied. NOE NMR results suggest that the local environment of IL anions and cations near the Ru²⁺(bpy)₃ solute is rather different from the bulk IL structure. The solute-anion and solute-cation interactions are significantly different both for ILs with short vs long alkyl tails and for ILs with aliphatic vs aromatic cation polar head groups. In particular, the solute-anion interactions are observed to be about 3 times stronger for the cations with shorter alkyl tails relative to the ILs with longer alkyl tails. The Ru²⁺(bpy)₃ solute interacts with both the polar head and the nonpolar tail groups of the 1- butyl-1-methylpyrrolidinium cation but only with the nonpolar tail groups of the 1-decyl-1-methylpyrrolidinium cation.

  13. Ionic Liquid–Solute Interactions Studied by 2D NOE NMR Spectroscopy

    DOE PAGES

    Khatun, Sufia; Castner, Edward W.

    2014-11-26

    Intermolecular interactions between a Ru²⁺(bpy)₃ solute and the anions and cations of four different ionic liquids (ILs) are investigated by 2D NMR nuclear Overhauser effect (NOE) techniques, including {¹H-¹⁹F} HOESY and {¹H-¹H} ROESY. Four ILs are studied, each having the same bis(trifluoromethylsulfonyl)amide anion in common. Two of the ILs have aliphatic 1-alkyl-1-methylpyrrolidinium cations, while the other two ILs have aromatic 1-alkyl-3-methylimidazolium cations. ILs with both shorter (butyl) and longer (octyl or decyl) cationic alkyl substituents are studied. NOE NMR results suggest that the local environment of IL anions and cations near the Ru²⁺(bpy)₃ solute is rather different from the bulkmore » IL structure. The solute-anion and solute-cation interactions are significantly different both for ILs with short vs long alkyl tails and for ILs with aliphatic vs aromatic cation polar head groups. In particular, the solute-anion interactions are observed to be about 3 times stronger for the cations with shorter alkyl tails relative to the ILs with longer alkyl tails. The Ru²⁺(bpy)₃ solute interacts with both the polar head and the nonpolar tail groups of the 1- butyl-1-methylpyrrolidinium cation but only with the nonpolar tail groups of the 1-decyl-1-methylpyrrolidinium cation.« less

  14. 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.

  15. Hierarchical alignment and full resolution pattern recognition of 2D NMR spectra: application to nematode chemical ecology.

    PubMed

    Robinette, Steven L; Ajredini, Ramadan; Rasheed, Hasan; Zeinomar, Abdulrahman; Schroeder, Frank C; Dossey, Aaron T; Edison, Arthur S

    2011-03-01

    Nuclear magnetic resonance (NMR) is the most widely used nondestructive technique in analytical chemistry. In recent years, it has been applied to metabolic profiling due to its high reproducibility, capacity for relative and absolute quantification, atomic resolution, and ability to detect a broad range of compounds in an untargeted manner. While one-dimensional (1D) (1)H NMR experiments are popular in metabolic profiling due to their simplicity and fast acquisition times, two-dimensional (2D) NMR spectra offer increased spectral resolution as well as atomic correlations, which aid in the assignment of known small molecules and the structural elucidation of novel compounds. Given the small number of statistical analysis methods for 2D NMR spectra, we developed a new approach for the analysis, information recovery, and display of 2D NMR spectral data. We present a native 2D peak alignment algorithm we term HATS, for hierarchical alignment of two-dimensional spectra, enabling pattern recognition (PR) using full-resolution spectra. Principle component analysis (PCA) and partial least squares (PLS) regression of full resolution total correlation spectroscopy (TOCSY) spectra greatly aid the assignment and interpretation of statistical pattern recognition results by producing back-scaled loading plots that look like traditional TOCSY spectra but incorporate qualitative and quantitative biological information of the resonances. The HATS-PR methodology is demonstrated here using multiple 2D TOCSY spectra of the exudates from two nematode species: Pristionchus pacificus and Panagrellus redivivus. We show the utility of this integrated approach with the rapid, semiautomated assignment of small molecules differentiating the two species and the identification of spectral regions suggesting the presence of species-specific compounds. These results demonstrate that the combination of 2D NMR spectra with full-resolution statistical analysis provides a platform for chemical and

  16. Quantitative 2D HSQC NMR determination of polymer structures by selecting suitable internal standard references.

    PubMed

    Zhang, Liming; Gellerstedt, Göran

    2007-01-01

    A new analytical method based on the 2D HSQC NMR sequence is presented, which can be applied for quantitative structural determination of complicated polymers. The influence of T1 and T2 relaxations, off-resonance effects, coupling constants and homonuclear couplings are discussed. It was found that the T2 values measured on polymeric samples with the conventional HSQC-CPMG sequence could not be used to correct the errors caused by T2 relaxations during the polarization transfer delay. A unique way of selecting the proper internal standard reference signal(s) is therefore proposed to eliminate the major errors caused by T2 relaxations, resonance offsets, coupling constant deviations and homonuclear couplings. Two polymer samples, a cellulose triacetate and an acetylated lignin, have been used to illustrate the principles. The methodology developed in this work is robust to instrument miss-setting and it can find wide-spread applications in areas where a quantitative analysis of structurally complicated polymers is necessary.

  17. The use of spin desalting columns in DMSO-quenched H/D-exchange NMR experiments.

    PubMed

    Chandak, Mahesh S; Nakamura, Takashi; Takenaka, Toshio; Chaudhuri, Tapan K; Yagi-Utsumi, Maho; Chen, Jin; Kato, Koichi; Kuwajima, Kunihiro

    2013-04-01

    Dimethylsulfoxide (DMSO)-quenched hydrogen/deuterium (H/D)-exchange is a powerful method to characterize the H/D-exchange behaviors of proteins and protein assemblies, and it is potentially useful for investigating non-protected fast-exchanging amide protons in the unfolded state. However, the method has not been used for studies on fully unfolded proteins in a concentrated denaturant or protein solutions at high salt concentrations. In all of the current DMSO-quenched H/D-exchange studies of proteins so far reported, lyophilization was used to remove D2 O from the protein solution, and the lyophilized protein was dissolved in the DMSO solution to quench the H/D exchange reactions and to measure the amide proton signals by two-dimensional nuclear magnetic resonance (2D NMR) spectra. The denaturants or salts remaining after lyophilization thus prevent the measurement of good NMR spectra. In this article, we report that the use of spin desalting columns is a very effective alternative to lyophilization for the medium exchange from the D2 O buffer to the DMSO solution. We show that the medium exchange by a spin desalting column takes only about 10 min in contrast to an overnight length of time required for lyophilization, and that the use of spin desalting columns has made it possible to monitor the H/D-exchange behavior of a fully unfolded protein in a concentrated denaturant. We report the results of unfolded ubiquitin in 6.0M guanidinium chloride.

  18. Monolignol acylation and lignin structure in some nonwoody plants: a 2D NMR study.

    PubMed

    Martínez, Angel T; Rencoret, Jorge; Marques, Gisela; Gutiérrez, Ana; Ibarra, David; Jiménez-Barbero, Jesús; del Río, José C

    2008-11-01

    Lignins from three nonwoody angiosperms were analyzed by 2D NMR revealing important differences in their molecular structures. The Musa textilis milled-wood-lignin (MWL), with a syringyl-to-guaiacyl (S/G) ratio of 9, was strongly acylated (near 85% of side-chains) at the gamma-carbon by both acetates and p-coumarates, as estimated from (1)H-(13)C correlations in C(gamma)-esterified and C(gamma)-OH units. The p-coumarate H(3,5)-C(3,5) correlation signal was completely displaced by acetylation, and disappeared after alkali treatment, indicating that p-coumaric acid was esterified maintaining its free phenolic group. By contrast, the Cannabis sativa MWL (S/G approximately 0.8) was free of acylating groups, and the Agave sisalana MWL (S/G approximately 4) showed high acylation degree (near 80%) but exclusively with acetates. Extensive C(gamma)-acylation results in the absence (in M. textilis lignin) or low abundance (4% in A. sisalana lignin) of beta-beta' resinol linkages, which require free C(gamma)-OH to form the double tetrahydrofuran ring. However, minor signals revealed unusual acylated beta-beta' structures confirming that acylation is produced at the monolignol level, in agreement with chromatographic identification of gamma-acetylated sinapyl alcohol among the plant extractives. In contrast, resinol substructures involved 22% side-chains in the C.sativa MWL. The ratio between beta-beta' and beta-O-4' side-chains in these and other MWL varied from 0.32 in C.sativa MWL to 0.02 in M. textilis MWL, and was inversely correlated with the degree of acylation. The opposite was observed for the S/G ratio that was directly correlated with the acylation degree. Monolignol acylation is discussed as a mechanism potentially involved in the control of lignin structure.

  19. Simultaneous acquisition of 2D and 3D solid-state NMR experiments for sequential assignment of oriented membrane protein samples.

    PubMed

    Gopinath, T; Mote, Kaustubh R; Veglia, Gianluigi

    2015-05-01

    We present a new method called DAISY (Dual Acquisition orIented ssNMR spectroScopY) for the simultaneous acquisition of 2D and 3D oriented solid-state NMR experiments for membrane proteins reconstituted in mechanically or magnetically aligned lipid bilayers. DAISY utilizes dual acquisition of sine and cosine dipolar or chemical shift coherences and long living (15)N longitudinal polarization to obtain two multi-dimensional spectra, simultaneously. In these new experiments, the first acquisition gives the polarization inversion spin exchange at the magic angle (PISEMA) or heteronuclear correlation (HETCOR) spectra, the second acquisition gives PISEMA-mixing or HETCOR-mixing spectra, where the mixing element enables inter-residue correlations through (15)N-(15)N homonuclear polarization transfer. The analysis of the two 2D spectra (first and second acquisitions) enables one to distinguish (15)N-(15)N inter-residue correlations for sequential assignment of membrane proteins. DAISY can be implemented in 3D experiments that include the polarization inversion spin exchange at magic angle via I spin coherence (PISEMAI) sequence, as we show for the simultaneous acquisition of 3D PISEMAI-HETCOR and 3D PISEMAI-HETCOR-mixing experiments.

  20. A constraint-based assignment system for automating long side chain assignments in protein 2D NMR spectra

    SciTech Connect

    Leishman, S.; Gray, P.; Fothergill, J.E.

    1995-12-31

    The sequential assignment of protein 2D NMR data has been tackled by many automated and semi-automated systems. One area that these systems have not tackled is the searching of the TOCSY spectrum looking for cross peaks and chemical shift values for hydrogen nuclei that are at the end of long side chains. This paper describes our system for solving this problem using constraint logic programming and compares our constraint satisfaction algorithm to a standard backtracking version.

  1. 2D fluorescence spectroscopy for monitoring ion-exchange membrane based technologies - Reverse electrodialysis (RED).

    PubMed

    Pawlowski, Sylwin; Galinha, Claudia F; Crespo, João G; Velizarov, Svetlozar

    2016-01-01

    Reverse electrodialysis (RED) is one of the emerging, membrane-based technologies for harvesting salinity gradient energy. In RED process, fouling is an undesirable operation constraint since it leads to a decrease of the obtainable net power density due to increasing stack electric resistance and pressure drop. Therefore, early fouling detection is one of the main challenges for successful RED technology implementation. In the present study, two-dimensional (2D) fluorescence spectroscopy was used, for the first time, as a tool for fouling monitoring in RED. Fluorescence excitation-emission matrices (EEMs) of ion-exchange membrane surfaces and of natural aqueous streams were acquired during one month of a RED stack operation. Fouling evolvement on the ion-exchange membrane surfaces was successfully followed by 2D fluorescence spectroscopy and quantified using principal components analysis (PCA). Additionally, the efficiency of cleaning strategy was assessed by measuring the membrane fluorescence emission intensity before and after cleaning. The anion-exchange membrane (AEM) surface in contact with river water showed to be significantly affected due to fouling by humic compounds, which were found to cross through the membrane from the lower salinity (river water) to higher salinity (sea water) stream. The results obtained show that the combined approach of using 2D fluorescence spectroscopy and PCA has a high potential for studying fouling development and membrane cleaning efficiency in ion exchange membrane processes.

  2. An inversion method of 2D NMR relaxation spectra in low fields based on LSQR and L-curve

    NASA Astrophysics Data System (ADS)

    Su, Guanqun; Zhou, Xiaolong; Wang, Lijia; Wang, Yuanjun; Nie, Shengdong

    2016-04-01

    The low-field nuclear magnetic resonance (NMR) inversion method based on traditional least-squares QR decomposition (LSQR) always produces some oscillating spectra. Moreover, the solution obtained by traditional LSQR algorithm often cannot reflect the true distribution of all the components. Hence, a good solution requires some manual intervention, for especially low signal-to-noise ratio (SNR) data. An approach based on the LSQR algorithm and L-curve is presented to solve this problem. The L-curve method is applied to obtain an improved initial optimal solution by balancing the residual and the complexity of the solutions instead of manually adjusting the smoothing parameters. First, the traditional LSQR algorithm is used on 2D NMR T1-T2 data to obtain its resultant spectra and corresponding residuals, whose norms are utilized to plot the L-curve. Second, the corner of the L-curve as the initial optimal solution for the non-negative constraint is located. Finally, a 2D map is corrected and calculated iteratively based on the initial optimal solution. The proposed approach is tested on both simulated and measured data. The results show that this algorithm is robust, accurate and promising for the NMR analysis.

  3. Isotope-Labeled Amyloids via Synthesis, Expression, and Chemical Ligation for Use in FTIR, 2D IR, and NMR Studies.

    PubMed

    Zhang, Tianqi O; Grechko, Maksim; Moran, Sean D; Zanni, Martin T

    2016-01-01

    This chapter provides protocols for isotope-labeling the human islet amyloid polypeptide (hIAPP or amylin) involved in type II diabetes and γD-crystallin involved in cataract formation. Because isotope labeling improves the structural resolution, these protocols are useful for experiments using Fourier transform infrared (FTIR), two-dimensional infrared (2D IR), and NMR spectroscopies. Our research group specializes in using 2D IR spectroscopy and isotope labeling. 2D IR spectroscopy provides structural information by measuring solvation from 2D diagonal lineshapes and vibrational couplings from cross peaks. Infrared spectroscopy can be used to study kinetics, membrane proteins, and aggregated proteins. Isotope labeling provides greater certainty in the spectral assignment, which enables new structural insights that are difficult to obtain with other methods. For amylin, we provide a protocol for (13)C/(18)O labeling backbone carbonyls at one or more desired amino acids in order to obtain residue-specific structural resolution. We also provide a protocol for expressing and purifying amylin from E. coli, which enables uniform (13)C or (13)C/(15)N labeling. Uniform labeling is useful for measuring the monomer infrared spectrum in an amyloid oligomer or fiber as well as amyloid protein bound to another polypeptide or protein, such as a chaperone or an inhibitor. In addition, our expression protocol results in 2-2.5 mg of amylin peptide per 1 L cell culture, which is a high enough yield to straightforwardly obtain the 2-10 mg needed for high resolution and solid-state NMR experiments. Finally, we provide a protocol to isotope-label either of the two domains of γD-crystallin using expressed protein ligation. Domain labeling makes it possible to resolve the structures of the two halves of the protein in FTIR and 2D IR spectra. With modifications, these strategies and protocols for isotope labeling can be applied to other amyloid polypeptides and proteins.

  4. Preparation and characterization of CdSe colloidal quantum dots by pptical spectroscopy and 2D DOSY NMR

    NASA Astrophysics Data System (ADS)

    Geru, I.; Bordian, O.; Culeac, I.; Turta, C.; Verlan, V.; Barba, A.

    2015-02-01

    We present experimental results on preparation and characterization of colloidal CdSe quantum dots (QD) in organic solvent. CdSe QDs were synthesized following a modified literature method and have been characterized by UV-Vis absorption and photoluminescent (PL) spectroscopy, as well as by 2D Diffusion Ordered Spectroscopy (DOSY) NMR. The average CdSe particles size estimated from the UV-Vis absorption spectra was found to be in the range 2.28 - 2.92 nm, which correlates very well with the results obtained from NMR measurements. The PL spectrum for CdSe nanodots can be characterized by a narrow emission band with the peak maximum shifting from 508 to 566 nm in dependence of the CdSe nanoparticle size. The PL is dominated by a near-band-edge emission, accompanied by a weak broad band in the near IR, related to the surface shallow trap emission.

  5. Positional isotope exchange studies on enzyme using NMR spectroscopy

    SciTech Connect

    Matsunaga, T.O.

    1987-01-01

    The isotopically enriched compounds, /sup 18/O-..beta..,..gamma..-ATP and /sup 18/O bridge-labeled pyrophosphate, synthesized previously in this laboratory, were used to investigate and measure the exchange vs. turnover of substrates and products from their central complexes in four selected enzyme systems. Using hi-field /sup 31/P NMR, we were able to differentiate between /sup 18/O labeled in the bridge vs. the non-bridge positions by virtue of the isotope shift upon the phosphorus nuclei. The bridge to non-bridge scrambling of the label was quantitated and the exchange vs. turnover ratios under a variety of conditions was determined. Using the substrate inhibitor carboxycreatinine, PIX experiments with /sup 18/O-..beta..,..gamma..-ATP and creatine kinase were conducted. It was shown that carboxycreatinine and creatine kinase promoted exchange of the /sup 18/O label as determined by NMR. We have concluded that carboxycreatinine is either a substrate that catalyzes very slow turnover or it catalyzes exchange by a dissociative (SN/sub 1//sub P/) type of mechanism

  6. Adsorption mechanism at the molecular level between polymers and uremic octapeptide by the 2D 1H NMR Technique.

    PubMed

    Li, Guohua; Li, Jihong; Wang, Wei; Yang, Mei; Zhang, Yuanwei; Sun, Pingchuan; Yuan, Zhi; He, Binglin; Yu, Yaoting

    2006-06-01

    To remove uremic octapeptide from the blood stream of uremic patients, various modified polyacylamide cross-linked absorbents were prepared. Adsorption experiments showed these absorbents have significant differences in adsorption capacity to the target peptide. In this paper, two-dimension proton nuclear magnetic resonance (2D 1H NMR) spectroscopy was used to investigate the interaction mechanism between the peptide and the adsorbents. Because of the insolubility of the absorbent, some soluble linear polymers with the same functional groups as the absorbents were employed as the model adsorbents in 2D 1H NMR. The preferred binding site for the peptide and polymers was identified to be at the C-terminal carboxyl group of the octapeptide via chemical shift perturbation effects. In this study, we found that hydrogen bonding, electrostatic, and hydrophobic interactions all play a role in the interaction force but had different contributions. Especially, the great chemical shift changes of the aromatic amino acid residues (Trp) during the interaction between butyl-modified polyacrylamide and octapeptide suggested the hydrophobic interaction, incorporated with the electrostatic force, played an important role in the binding reaction in aqueous solutions. This information not only rationally explained the results of the adsorption experiments, but also identified the effective binding site and mechanism, and shall provide a structural basis for designing better affinity-type adsorbents for the target peptide.

  7. Cannibalism Affects Core Metabolic Processes in Helicoverpa armigera Larvae—A 2D NMR Metabolomics Study

    PubMed Central

    Vergara, Fredd; Shino, Amiu; Kikuchi, Jun

    2016-01-01

    Cannibalism is known in many insect species, yet its impact on insect metabolism has not been investigated in detail. This study assessed the effects of cannibalism on the metabolism of fourth-instar larvae of the non-predatory insect Helicoverpa armigera (Lepidotera: Noctuidea). Two groups of larvae were analyzed: one group fed with fourth-instar larvae of H. armigera (cannibal), the other group fed with an artificial plant diet. Water-soluble small organic compounds present in the larvae were analyzed using two-dimensional nuclear magnetic resonance (NMR) and principal component analysis (PCA). Cannibalism negatively affected larval growth. PCA of NMR spectra showed that the metabolic profiles of cannibal and herbivore larvae were statistically different with monomeric sugars, fatty acid- and amino acid-related metabolites as the most variable compounds. Quantitation of 1H-13C HSQC (Heteronuclear Single Quantum Coherence) signals revealed that the concentrations of glucose, glucono-1,5-lactone, glycerol phosphate, glutamine, glycine, leucine, isoleucine, lysine, ornithine, proline, threonine and valine were higher in the herbivore larvae. PMID:27598144

  8. Kinetics of Neuraminidase Action on Glycoproteins by 1D and 2D NMR

    PubMed Central

    Barb, Adam W.; Glushka, John N.; Prestegard, James H.

    2011-01-01

    The surfaces of mammalian cells are coated with complex carbohydrates, many terminated with a negatively charged N-acetylneuraminic acid residue. This motif is specifically targeted by pathogens, including influenza viruses and many pathogenic bacteria, to gain entry into the cell. A necessary step in the influenza virus life cycle is the release of viral particles from the cell surface; this is achieved by cleaving N-acetylneuraminic acid from cell surface glycans with a virally-produced neuraminidase. Here we present a laboratory exercise to model this process using a glycoprotein as a glycan carrier and using real time nuclear magnetic resonance (NMR) spectroscopy to monitor N-acetylneuraminic acid release as catalyzed by neuraminidase. A time-resolved two dimensional data processing technique, statistical total correlation spectroscopy (STOCSY), enhances the resolution of the complicated 1D glycoprotein spectrum and isolates characteristic peaks corresponding to substrates and products. This exercise is relatively straightforward and leads students through a wide range of biologically and chemically relevant procedures, including use of NMR spectroscopy, enzymology and data processing techniques. PMID:22058570

  9. Kinetics of Neuraminidase Action on Glycoproteins by 1D and 2D NMR.

    PubMed

    Barb, Adam W; Glushka, John N; Prestegard, James H

    2011-01-01

    The surfaces of mammalian cells are coated with complex carbohydrates, many terminated with a negatively charged N-acetylneuraminic acid residue. This motif is specifically targeted by pathogens, including influenza viruses and many pathogenic bacteria, to gain entry into the cell. A necessary step in the influenza virus life cycle is the release of viral particles from the cell surface; this is achieved by cleaving N-acetylneuraminic acid from cell surface glycans with a virally-produced neuraminidase. Here we present a laboratory exercise to model this process using a glycoprotein as a glycan carrier and using real time nuclear magnetic resonance (NMR) spectroscopy to monitor N-acetylneuraminic acid release as catalyzed by neuraminidase. A time-resolved two dimensional data processing technique, statistical total correlation spectroscopy (STOCSY), enhances the resolution of the complicated 1D glycoprotein spectrum and isolates characteristic peaks corresponding to substrates and products. This exercise is relatively straightforward and leads students through a wide range of biologically and chemically relevant procedures, including use of NMR spectroscopy, enzymology and data processing techniques.

  10. Structural study of synthetic mica montmorillonite by means of 2D MAS NMR experiments

    NASA Astrophysics Data System (ADS)

    Alba, M. D.; Castro, M. A.; Chain, P.; Naranjo, M.; Perdigón, A. C.

    2005-07-01

    Syn-1, is a synthetic mica montmorillonite interstratified mineral that forms one of the standard clay samples in the Clay Minerals Society Source Clays Project. However, there are still controversies regarding some structural aspects such as the interlayer composition or the location of the extra-aluminium determined by chemical analysis. The main objective of this paper is to shed light on those structural aspects that affect the reactivity of the interstratified minerals. For this purpose, we have used 1 H 29 Si and 1 H 27Al HETCOR MAS NMR to show that it is likely that the interlayer space of the beidellite part is composed of ammonium ions whereas ammonium and aluminium ions are responsible for the charge balance in the mica type layer.

  11. Structure elucidation of organic compounds from natural sources using 1D and 2D NMR techniques

    NASA Astrophysics Data System (ADS)

    Topcu, Gulacti; Ulubelen, Ayhan

    2007-05-01

    In our continuing studies on Lamiaceae family plants including Salvia, Teucrium, Ajuga, Sideritis, Nepeta and Lavandula growing in Anatolia, many terpenoids, consisting of over 50 distinct triterpenoids and steroids, and over 200 diterpenoids, several sesterterpenoids and sesquiterpenoids along with many flavonoids and other phenolic compounds have been isolated. For Salvia species abietanes, for Teucrium and Ajuga species neo-clerodanes for Sideritis species ent-kaurane diterpenes are characteristic while nepetalactones are specific for Nepeta species. In this review article, only some interesting and different type of skeleton having constituents, namely rearranged, nor- or rare diterpenes, isolated from these species will be presented. For structure elucidation of these natural diterpenoids intensive one- and two-dimensional NMR techniques ( 1H, 13C, APT, DEPT, NOE/NOESY, 1H- 1H COSY, HETCOR, COLOC, HMQC/HSQC, HMBC, SINEPT) were used besides mass and some other spectroscopic methods.

  12. Nanoscale Catalysts for NMR Signal Enhancement by Reversible Exchange

    PubMed Central

    2015-01-01

    Two types of nanoscale catalysts were created to explore NMR signal enhancement via reversible exchange (SABRE) at the interface between heterogeneous and homogeneous conditions. Nanoparticle and polymer comb variants were synthesized by covalently tethering Ir-based organometallic catalysts to support materials composed of TiO2/PMAA (poly(methacrylic acid)) and PVP (polyvinylpyridine), respectively, and characterized by AAS, NMR, and DLS. Following parahydrogen (pH2) gas delivery to mixtures containing one type of “nano-SABRE” catalyst particle, a target substrate, and ethanol, up to ∼(−)40-fold and ∼(−)7-fold 1H NMR signal enhancements were observed for pyridine substrates using the nanoparticle and polymer comb catalysts, respectively, following transfer to high field (9.4 T). These enhancements appear to result from intact particles and not from any catalyst molecules leaching from their supports; unlike the case with homogeneous SABRE catalysts, high-field (in situ) SABRE effects were generally not observed with the nanoscale catalysts. The potential for separation and reuse of such catalyst particles is also demonstrated. Taken together, these results support the potential utility of rational design at molecular, mesoscopic, and macroscopic/engineering levels for improving SABRE and HET-SABRE (heterogeneous-SABRE) for applications varying from fundamental studies of catalysis to biomedical imaging. PMID:26185545

  13. How to face the low intrinsic sensitivity of 2D heteronuclear NMR with fast repetition techniques: go faster to go higher !

    PubMed

    Farjon, Jonathan

    2017-04-13

    Nuclear Magnetic Resonance (NMR) is one of the most widely used analytical techniques in numerous domains where molecules are objects of investigation. However, major limitations of multidimensional NMR experiments come from their low sensitivity and from the long times needed for their acquisition. In order to overcome such limitations, fast repetition NMR techniques allowed for the reduction of 2D experimental time and for the conversion of the gained time into a higher number of scans leading to a better sensitivity. Thus, fast repetition 2D heteronuclear NMR techniques have allowed new advances in NMR, especially to access infomation on low abundant nuclei, to enhance the detection of low concentrated compounds and to probe weak interactions like hydrogen bonds at natural abundance.

  14. NMR resonance splitting of urea in stretched hydrogels: proton exchange and (1)H/(2)H isotopologues.

    PubMed

    Kuchel, Philip W; Naumann, Christoph; Chapman, Bogdan E; Shishmarev, Dmitry; Håkansson, Pär; Bacskay, George; Hush, Noel S

    2014-10-01

    Urea at ∼12 M in concentrated gelatin gel, that was stretched, gave (1)H and (2)H NMR spectral splitting patterns that varied in a predictable way with changes in the relative proportions of (1)H2O and (2)H2O in the medium. This required consideration of the combinatorics of the two amide groups in urea that have a total of four protonation/deuteration sites giving rise to 16 different isotopologues, if all the atoms were separately identifiable. The rate constant that characterized the exchange of the protons with water was estimated by back-transformation analysis of 2D-EXSY spectra. There was no (1)H NMR spectral evidence that the chiral gelatin medium had caused in-equivalence in the protons bonded to each amide nitrogen atom. The spectral splitting patterns in (1)H and (2)H NMR spectra were accounted for by intra-molecular scalar and dipolar interactions, and quadrupolar interactions with the electric field gradients of the gelatin matrix, respectively.

  15. HIFI-C: a robust and fast method for determining NMR couplings from adaptive 3D to 2D projections.

    PubMed

    Cornilescu, Gabriel; Bahrami, Arash; Tonelli, Marco; Markley, John L; Eghbalnia, Hamid R

    2007-08-01

    We describe a novel method for the robust, rapid, and reliable determination of J couplings in multi-dimensional NMR coupling data, including small couplings from larger proteins. The method, "High-resolution Iterative Frequency Identification of Couplings" (HIFI-C) is an extension of the adaptive and intelligent data collection approach introduced earlier in HIFI-NMR. HIFI-C collects one or more optimally tilted two-dimensional (2D) planes of a 3D experiment, identifies peaks, and determines couplings with high resolution and precision. The HIFI-C approach, demonstrated here for the 3D quantitative J method, offers vital features that advance the goal of rapid and robust collection of NMR coupling data. (1) Tilted plane residual dipolar couplings (RDC) data are collected adaptively in order to offer an intelligent trade off between data collection time and accuracy. (2) Data from independent planes can provide a statistical measure of reliability for each measured coupling. (3) Fast data collection enables measurements in cases where sample stability is a limiting factor (for example in the presence of an orienting medium required for residual dipolar coupling measurements). (4) For samples that are stable, or in experiments involving relatively stronger couplings, robust data collection enables more reliable determinations of couplings in shorter time, particularly for larger biomolecules. As a proof of principle, we have applied the HIFI-C approach to the 3D quantitative J experiment to determine N-C' RDC values for three proteins ranging from 56 to 159 residues (including a homodimer with 111 residues in each subunit). A number of factors influence the robustness and speed of data collection. These factors include the size of the protein, the experimental set up, and the coupling being measured, among others. To exhibit a lower bound on robustness and the potential for time saving, the measurement of dipolar couplings for the N-C' vector represents a realistic

  16. Effects of equilibrium exchange on diffusion-weighted NMR signals: the diffusigraphic "shutter-speed".

    PubMed

    Lee, Jing-Huei; Springer, Charles S

    2003-03-01

    A general picture is presented of the implications for diffusion-weighted NMR signals of the parsimonious two-site-exchange (2SX) paradigm. In particular, it is shown that the diffusigraphic "shutter-speed," tau(-1) identical with |q(2)(D(A) - D(B))|, is a useful concept. The "wave-number" q has its standard definition (given in the text), and D(A) and D(B) are the apparent diffusion coefficients (ADCs) of molecules in the two "sites," A and B, if there is no exchange between them. At low gradient strengths (center of q-space), tau(-1) is less than rate constants for intercompartmental water molecule exchange in most tissue cases. Thus, the exchange reaction appears fast. However, q is increased during the course of most experiments and, as it is, the shutter-speed becomes "faster" and the exchange reaction, the kinetics of which do not change, appears to slow down. This causes a multiexponential behavior in the diffusion-weighting dimension, b, which also has its standard definition. This picture is found to be in substantial agreement with a number of different experimental observations. It is applied here to literature (1)H(2)O data from a yeast cell suspension and from the human and the rat brain. Since the equilibrium transcytolemmal water exchange reaction appears to be in the fast-exchange-limit at small b, the initial slope represents the weighted-average of the ADCs of intra- and extracellular water. Of course, in tissue the former is in the significant majority. Furthermore, a consideration of reasonable values for the other 2SX parameters suggests that, for resting brain tissue, the intracellular water ADC may be larger than the extracellular water ADC. There are some independent inferences of this, which would have ramifications for many applications of diffusion-weighted MRI.

  17. [Interactions between proteins and cation exchange adsorbents analyzed by NMR and hydrogen/deuterium exchange technique].

    PubMed

    Wang, Kang; Hao, Dongxia; Qi, Shuting; Ma, Guanghui

    2014-09-01

    In silico acquirement of the accurate residue details of protein on chromatographic media is a bottleneck in protein chromatography separation and purification. Here we developed a novel approach by coupling with H/D exchange and nuclear magnetic resonance to observe hen egg white lysozyme (HEWL) unfolding behavior adsorbed on cation exchange media (SP Sepharose FF). Analysis of 1D 1H-NMR shows that protein unfolding accelerated H/D exchange rate, leading to more loss of signal of amide hydrogen owing to exposure of residues and the more unfolding of protein. Analysis of two-dimensional hydrogen-hydrogen total correlation spectroscopy shows that lysozyme lost more signals and experienced great unfolding during its adsorption on media surface. However, for several distinct fragments, the protection degrees varied, the adsorbed lysozyme lost more signal intensity and was less protected at disorder structures (coil, bend, and turn), but was comparatively more protected against exchange at secondary structure domains (α-helix, β-sheet). Finally, the binding site was determined by electrostatic calculations using computer simulation methods in conjunction with hydrogen deuterium labeled protein and NMR. This study would help deeply understand the microscopic mechanism of protein chromatography and guide the purposely design of chromatographic process and media. Moreover, it also provide an effective tool to study the protein and biomaterials interaction in other applications.

  18. Detailed temporally resolved 2-D Velocity Measurements in a Novel Heat Exchanger Surface

    NASA Astrophysics Data System (ADS)

    Guezennec, Yann G.; Ko, Jang-Hyok; Choi, Woong-Chul

    1998-11-01

    Using flow visualization as a primary tool, a novel, high-performance heat transfer surface for compact heat exchangers was designed, specifically for low Reynolds number applications. This geometry was specifically created to enhance or generate strong three-dimensional transport even at low Reynolds number. It consists of a staggered array of "pin" mounted normal to the fins. A 15:1 model of this heat exchanger surface core was built out of Plexiglas to provide optical access and this model was placed in a 1'x1' water channel. The flow speed was adjusted to match the Reynolds based on the hydraulic diameter based on the fin pitch. The flow was seeded with small polystyrene particles and illuminated by a laser sheet from an Argon Ion laser. The fluid motion was recorded using a CCD camera and an S-VHS video recorder. In post-processing, the video records were automatically digitized and processed using a cinematographic PIV technique. The temporal evolution of the 2-D flow field (side view) clearly shows the presence of unsteady, shed vortical regions behind the pins, modulated by the spatially-periodic acceleration/deceleration and meandering of the mean flow between the periodic array of staggered pins. In the perpendicular view (top view), the results show the presence of two strong cross-stream transport mechanisms, mainly the horse-shoe vortex near the pin-fin junctions and the very strong spanwise transport in the separated wake region of the pins. This transport is most likely associated with the strong interaction of the longitudinal vortices (emanating form the horseshoe) and the spanwise vortices from the pin wake. This vortex interaction sets up a strong spanwise pressure gradient inducing large cross-stream transport from the fin to the core flow. Animation of the results illustrating these effects will be presented.

  19. Effects of various types of molecular dynamics on 1D and 2D (2)H NMR studied by random walk simulations

    PubMed

    Vogel; Rossler

    2000-11-01

    By carrying out random walk simulations we systematically study the effects of various types of complex molecular dynamics on (2)H NMR experiments in solids. More precisely, we calculate one-dimensional (1D) (2)H NMR spectra and the results of two dimensional (2D) (2)H NMR experiments in time domain, taking into account isotropic as well as highly restricted motions which involve rotational jumps about different finite angles. Although the dynamical models are chosen to mimic the primary and secondary relaxation in supercooled liquids and glasses, we do not intend to describe experimental results quantitatively but rather to show general effects appearing for complex reorientations. We carefully investigate whether 2D (2)H NMR in time domain, which was originally designed to measure correlation times of ultraslow motions (tau >/= 1 ms), can be used to obtain shorter tau, too. It is demonstrated that an extension of the time window to tau >/= 10 &mgr;s is possible when dealing with exponential relaxation, but that it will fail if there is a distribution of correlation times G(lgtau). Vice versa, we show that 1D (2)H NMR spectra, usually recorded to look at dynamics with tau in the microsecond regime, are also applicable for studying ultraslow motions provided that the loss of correlation is achieved step by step. Therefore, it is useful to carry out 1D and 2D NMR experiments simultaneously in order to reveal the mechanism of complex molecular motions. In addition, we demonstrate that highly restricted dynamics can be clearly observed in 1D spectra and in 2D NMR in time domain if long solid-echo delays and large evolution times are applied, respectively. Finally, unexpected observations are described which appear in the latter experiment when considering very broad distributions G(lgtau). Because of these effects, time scale and geometry of a considered motion cannot be extracted from a straightforward analysis of experimental results. Copyright 2000 Academic Press.

  20. 2D NMR-based metabolomics uncovers interactions between conserved biochemical pathways in the model organism Caenorhabditis elegans.

    PubMed

    Izrayelit, Yevgeniy; Robinette, Steven L; Bose, Neelanjan; von Reuss, Stephan H; Schroeder, Frank C

    2013-02-15

    Ascarosides are small-molecule signals that play a central role in C. elegans biology, including dauer formation, aging, and social behaviors, but many aspects of their biosynthesis remain unknown. Using automated 2D NMR-based comparative metabolomics, we identified ascaroside ethanolamides as shunt metabolites in C. elegans mutants of daf-22, a gene with homology to mammalian 3-ketoacyl-CoA thiolases predicted to function in conserved peroxisomal lipid β-oxidation. Two groups of ethanolamides feature β-keto functionalization confirming the predicted role of daf-22 in ascaroside biosynthesis, whereas α-methyl substitution points to unexpected inclusion of methylmalonate at a late stage in the biosynthesis of long-chain fatty acids in C. elegans. We show that ascaroside ethanolamide formation in response to defects in daf-22 and other peroxisomal genes is associated with severe depletion of endocannabinoid pools. These results indicate unexpected interaction between peroxisomal lipid β-oxidation and the biosynthesis of endocannabinoids, which are major regulators of lifespan in C. elegans. Our study demonstrates the utility of unbiased comparative metabolomics for investigating biochemical networks in metazoans.

  1. 2D NMR-based metabolomics uncovers interactions between conserved biochemical pathways in the model organism Caenorhabditis elegans

    PubMed Central

    Izrayelit, Yevgeniy; Robinette, Steven L.; Bose, Neelanjan; von Reuss, Stephan H.; Schroeder, Frank C.

    2012-01-01

    Ascarosides are small-molecule signals that play a central role in C. elegans biology, including dauer formation, aging, and social behaviors, but many aspects of their biosynthesis remain unknown. Using automated 2D NMR-based comparative metabolomics, we identified ascaroside ethanolamides as shunt metabolites in C. elegans mutants of daf-22, a gene with homology to mammalian 3-ketoacyl-CoA thiolases predicted to function in conserved peroxisomal lipid β-oxidation. Two groups of ethanolamides feature β-keto functionalization confirming the predicted role of daf-22 in ascaroside biosynthesis, whereas α-methyl substitution points to unexpected inclusion of methylmalonte at a late stage in the biosynthesis of long-chain fatty acids in C. elegans. We show that ascaroside ethanolamide formation in response to defects in daf-22 and other peroxisomal genes is associated with severe depletion of endocannabinoid pools. These results indicate unexpected interaction between peroxisomal lipid β-oxidation and the biosynthesis of endocannabinoids, which are major regulators of lifespan in C. elegans. Our study demonstrates the utility of unbiased comparative metabolomics for investigating biochemical networks in metazoans. PMID:23163760

  2. Analysis of amorphous solid dispersions using 2D solid-state NMR and (1)H T(1) relaxation measurements.

    PubMed

    Pham, Tran N; Watson, Simon A; Edwards, Andrew J; Chavda, Manisha; Clawson, Jacalyn S; Strohmeier, Mark; Vogt, Frederick G

    2010-10-04

    Solid-state NMR (SSNMR) can provide detailed structural information about amorphous solid dispersions of pharmaceutical small molecules. In this study, the ability of SSNMR experiments based on dipolar correlation, spin diffusion, and relaxation measurements to characterize the structure of solid dispersions is explored. Observation of spin diffusion effects using the 2D (1)H-(13)C cross-polarization heteronuclear correlation (CP-HETCOR) experiment is shown to be a useful probe of association between the amorphous drug and polymer that is capable of directly proving glass solution formation. Dispersions of acetaminophen and indomethacin in different polymers are examined using this approach, as well as (1)H double-quantum correlation experiments to probe additional structural features. (1)H-(19)F CP-HETCOR serves a similar role for fluorinated drug molecules such as diflunisal in dispersions, providing a rapid means to prove the formation of a glass solution. Phase separation is detected using (13)C, (19)F, and (23)Na-detected (1)H T(1) experiments in crystalline and amorphous solid dispersions that contain small domains. (1)H T(1) measurements of amorphous nanosuspensions of trehalose and dextran illustrate the ability of SSNMR to detect domain size effects in dispersions that are not glass solutions via spin diffusion effects. Two previously unreported amorphous solid dispersions involving up to three components and containing voriconazole and telithromycin are analyzed using these experiments to demonstrate the general applicability of the approach.

  3. Temperature dependence of the rate coefficient for charge exchange of metastable O/+//2D/ with N2. [in atmosphere

    NASA Technical Reports Server (NTRS)

    Torr, M. R.; Torr, D. G.

    1980-01-01

    Using a data base of aeronomical parameters measured on board the Atmosphere Explorer-C satellite, temperature dependence of the reaction rate coefficient is deduced for the charge exchange of O(+)(2D) with N2. The results indicate the Explorer values determined over the temperature range from 700 to 1900 K are not in conflict with laboratory measurements made at higher temperatures.

  4. Mixed micelles of polyethylene glycol (23) lauryl ether with ionic surfactants studied by proton 1D and 2D NMR.

    PubMed

    Gao, Hong-Chang; Zhao, Sui; Mao, Shi-Zhen; Yuan, Han-Zhen; Yu, Jia-Yong; Shen, Lian-Fang; Du, You-Ru

    2002-05-01

    (1)H NMR chemical shift, spin-lattice relaxation time, spin-spin relaxation time, self-diffusion coefficient, and two-dimensional nuclear Overhauser enhancement (2D NOESY) measurements have been used to study the nonionic-ionic surfactant mixed micelles. Cetyl trimethyl ammonium bromide (CTAB) and sodium dodecyl sulfate (SDS) were used as the ionic surfactants and polyethylene glycol (23) lauryl ether (Brij-35) as the nonionic surfactant. The two systems are both with varying molar ratios of CTAB/Brij-35 (C/B) and SDS/Brij-35 (S/B) ranging from 0.5 to 2, respectively, at a constant concentration of 6 mM for Brij-35 in aqueous solutions. Results give information about the relative arrangement of the surfactant molecules in the mixed micelles. In the former system, the trimethyl groups attached to the polar heads of the CTAB molecules are located between the first oxy-ethylene groups next to the hydrophobic chains of Brij-35 molecules. These oxy-ethylene groups gradually move outward from the hydrophobic core of the mixed micelle with an increase in C/B in the mixed solution. In contrast to the case of the CTAB/Triton X-100 system, the long flexible hydrophilic poly oxy-ethylene chains, which are in the exterior part of the mixed micelles, remain coiled, but looser, surrounding the hydrophobic core. There is almost no variation in conformation of the hydrophilic chains of Brij-35 molecules in the mixed micelles of the SDS/Brij-35 system as the S/B increases. The hydrophobic chains of both CTAB and SDS are co-aggregated with Brij-35, respectively, in their mixed micellar cores.

  5. Finite element modeling of 129Xe diffusive gas exchange NMR in the human alveoli

    NASA Astrophysics Data System (ADS)

    Stewart, Neil J.; Parra-Robles, Juan; Wild, Jim M.

    2016-10-01

    Existing models of 129Xe diffusive exchange for lung microstructural modeling with time-resolved MR spectroscopy data have considered analytical solutions to one-dimensional, homogeneous models of the lungs with specific assumptions about the alveolar geometry. In order to establish a model system for simulating the effects of physiologically-realistic changes in physical and microstructural parameters on 129Xe exchange NMR, we have developed a 3D alveolar capillary model for finite element analysis. To account for the heterogeneity of the alveolar geometry across the lungs, we have derived realistic geometries for finite element analysis based on 2D histological samples and 3D micro-CT image volumes obtained from ex vivo biopsies of lung tissue from normal subjects and patients with interstitial lung disease. The 3D alveolar capillary model permits investigation of the impact of alveolar geometrical parameters and diffusion and perfusion coefficients on the in vivo measured 129Xe CSSR signal response. The heterogeneity of alveolar microstructure that is accounted for in image-based models resulted in considerable alterations to the shape of the 129Xe diffusive uptake curve when compared to 1D models. Our findings have important implications for the future design and optimization of 129Xe MR experiments and in the interpretation of lung microstructural changes from this data.

  6. Irreversible Catalyst Activation Enables Hyperpolarization and Water Solubility for NMR Signal Amplification by Reversible Exchange

    DTIC Science & Technology

    2016-09-12

    Irreversible Catalyst Activation Enables Hyperpolarization and Water Solubility for NMR Signal Amplification by Reversible Exchange Milton L. Truong...Supporting Information ABSTRACT: Activation of a catalyst [IrCl(COD)(IMes)] (IMes = 1,3-bis(2,4,6-trimethylphenyl)imidazol-2-ylidene; COD = cyclooctadiene...for signal amplification by reversible exchange (SABRE) was monitored by in situ hyperpolarized proton NMR at 9.4 T. During the catalyst -activation

  7. Solution behavior and complete sup 1 H and sup 13 C NMR assignments of the coenzyme B sub 12 derivative (5 prime -deoxyadenosyl)cobinamide using modern 2D NMR experiments, including 600-MHz sup 1 H NMR data

    SciTech Connect

    Pagano, T.G.; Yohannes, P.G.; Marzilli, L.G. ); Hay, B.P.; Scott, J.R.; Finke, R.G. )

    1989-02-15

    Two-dimensional (2D) NMR methods have been used to assign completely the {sup 1}H and {sup 13}C NMR spectra of the (5{prime}-deoxyadenosyl)cobinamide cation (AdoCbi{sup +}) in D{sub 2}O. Most of the {sup 1}H spectral assignments were made by using 2D homonuclear shift correlation spectroscopy (COSY), homonuclear Hartmann-Hahn spectroscopy (HOHAHA), absorption-mode (phase sensitive) 2D nuclear Overhauser effect (NOE) spectroscopy, and spin-locked NOE spectroscopy (also called ROESY, for rotating-frame Overhauser enhancement spectroscopy). Most of the protonated carbon resonances were assigned by using {sup 1}H-detected heteronuclear multiple-quantum coherence (HMQC) spectroscopy. The nonprotonated carbon resonances, as well as the remaining unassigned {sup 1}H and {sup 13}C NMR signals, were assigned from long-range {sup 1}H-{sup 13}C connectivities determined from {sup 1}H-detected multiple-bond heteronuclear multiple-quantum coherence spectroscopy (HMBC). Comparison of the {sup 13}C chemical shifts and {sup 1}H NOEs of AdoCbi{sup +} with those of coenzyme B{sup 12} ((5{prime}-deoxyadenosyl)cobalamin) and its benzimidazole-protonated, base-off form indicates that the electronic properties and structure of AdoCbi{sup +} are similar to that of coenzyme B{sup 12} in the protonated, base-off form. The {sup 13}C chemical shifts of most of the carbons of AdoCbi{sup +} do not vary significantly from those of base-off, benzimidazole-protonated coenzyme B{sup 12}, indicating that the electronic environment of the corrin ring is also similar in both compounds. However, significant differences in the chemical shifts of some of the corresponding carbons of the b, d, e, and f corrin side chains in AdoCbi{sup +} and in base-off, benzimidazole-protonated coenzyme B{sub 12} indicate that the positions of these side chains may be different in AdoCbi{sup +} compared to base-off coenzyme B{sup 12}.

  8. Elucidating structural characteristics of biomass using solution-state 2 D NMR with a mixture of deuterated dimethylsulfoxide and hexamethylphosphoramide

    DOE PAGES

    Pu, Yunqiao; Ragauskas, Arthur J.; Yoo, Chang Geun; ...

    2016-04-26

    In recent developments of NMR methods for characterization of lignocellulosic biomass allow improved understanding of plant cell-wall structures with minimal deconstruction and modification of biomass. This study introduces a new NMR solvent system composed of dimethylsulfoxide (DMSO-d6) and hexamethylphosphoramide (HMPA-d18). HMPA as a co-solvent enhanced swelling and mobility of the biomass samples; thereby it allowed enhancing signals of NMR spectra. Moreover, the structural information of biomass was successfully analyzed by the proposed NMR solvent system (DMSO-d6/HMPA-d18; 4:1, v/v) with different biomass. The proposed bi-solvent system does not require derivatization or isolation of biomass, facilitating a facile sample preparation and involvingmore » with no signals overlapping with biomass peaks. Furthermore, it also allows analyzing biomass with a room-temperature NMR probe instead of cryo-probes, which are traditionally used for enhancing signal intensities.« less

  9. High-resolution 2D NMR spectra in inhomogeneous fields based on intermolecular multiple-quantum coherences with efficient acquisition schemes

    NASA Astrophysics Data System (ADS)

    Lin, Meijin; Huang, Yuqing; Chen, Xi; Cai, Shuhui; Chen, Zhong

    2011-01-01

    High-resolution 2D NMR spectra in inhomogeneous fields can be achieved by the use of intermolecular multiple-quantum coherences and shearing reconstruction of 3D data. However, the long acquisition time of 3D spectral data is generally unbearable for invivo applications. To overcome this problem, two pulse sequences dubbed as iDH-COSY and iDH-JRES were proposed in this paper. Although 3D acquisition is still required for the new sequences, the high-resolution 2D spectra can be obtained with a relatively short scanning time utilizing the manipulation of indirect evolution period and sparse sampling. The intermolecular multiple-quantum coherence treatment combined with the raising and lowering operators was applied to derive analytical signal expressions for the new sequences. And the experimental observations agree with the theoretical predictions. Our results show that the new sequences possess bright perspective in the applications on invivo localized NMR spectroscopy.

  10. Measuring the equation of state for a 2D colloidal membrane: A microfluidic approach to buffer exchange

    NASA Astrophysics Data System (ADS)

    Balchunas, Andrew; Cabanas, Rafael; Fraden, Seth; Dogic, Zvonimir

    Previous work has shown that monodisperse rod-like colloidal particles, such as a filamentous bacteriophage, self assemble into a 2D monolayer smectic in the presence of a non-adsorbing depleting polymer. These structures have the same functional form of bending rigidity and lateral compressibility as conventional lipid bi-layers, so we name the monolayer smectic a colloidal membrane. We have developed a microfluidic device such that the osmotic pressure acting on a colloidal membrane may be controlled via a full in situ buffer exchange. Rod density within individual colloidal membranes was measured as a function of osmotic pressure and a first order phase transition, from 2D fluid to 2D solid, was observed. kon and koff rates of rod to membrane binding were measured by lowering the osmotic pressure until membrane evaporation occurred.

  11. Microwave assisted regioselective synthesis and 2D-NMR studies of novel azoles and azoloazines utilizing fluorine-containing building blocks

    NASA Astrophysics Data System (ADS)

    Al-Bogami, Abdullah S.; Saleh, Tamer S.; Mekky, Ahmed E. M.; Shaaban, Mohamed R.

    2016-10-01

    An efficient regioselective synthesis of novel azoles containing a trifluoromethyl moiety via the 1,3-dipolar cycloaddition reaction under microwave irradiation, using fluorine-containing building blocks methodology was achieved. Furthermore, these novel azoles scaffolds have been employed as the starting material in the synthesis of new azoloazines containing a trifluoromethyl group. An unambiguous structural assignment of the obtained regioisomers was determined using the 2D HMBC NMR techniques as a valuable tool.

  12. Hepatitis B virus direct repeat sequence: imino proton exchange rates and distance and torsion angle restraints from NMR.

    PubMed

    Bishop, K D; Blocker, F J; Egan, W; James, T L

    1994-01-18

    Structural features of a trisdecamer duplex, [d(GGCAGAGGTGAAA).d(TTTCACCTCTGCC)], in solution are being investigated by proton one-dimensional (1D) and two-dimensional (2D) NMR spectroscopy. This DNA sequence is comprised of the 11-base-pair direct repeat sequence found in the hepatitis B viral genome with an additional base pair from the genome included on each end to minimize end effects on the 11-bp sequence of interest. The direct repeat sequence occurs twice in the viral genome; both are essential for initiation of DNA synthesis. The critical nature of this sequence suggests it may be a target to control replication of the virus. Elucidation of the structure of the direct repeat sequence could prove to be beneficial in targeting efforts. Structural determination via restrained molecular dynamics requires experimentally derived distance restraints. The ability to determine solution structures of biomolecules by NMR spectroscopy is limited by the quality and quantity of distance and torsion angle restraints that can be extracted from the NMR data. Techniques used to establish these restraints are constantly evolving and improving. Modifications in procedure are applied to the trisdecamer duplex to yield improvements in the determination of sugar conformations from COSY data and a substantial increase in the number of distance restraints typically garnered from 2D NOE intensity data. This increase in the number of distance restraints normally obtained from 2D NOE intensities was accomplished by utilizing a new version of the iterative complete relaxation matrix program MARDIGRAS with intensities extracted from a 2D NOE data set acquired in 90% H2O. The exchange rate of the imino and amino protons with the solvent water protons can now be included in the relaxation matrix calculations, thereby providing more accurate distances when utilizing the 2D NOE cross-peaks involving at least one exchangeable proton. In this lab, analysis of two-quantum-filtered correlation

  13. Elucidating structural characteristics of biomass using solution-state 2 D NMR with a mixture of deuterated dimethylsulfoxide and hexamethylphosphoramide

    SciTech Connect

    Pu, Yunqiao; Ragauskas, Arthur J.; Yoo, Chang Geun; Li, Mi

    2016-04-26

    In recent developments of NMR methods for characterization of lignocellulosic biomass allow improved understanding of plant cell-wall structures with minimal deconstruction and modification of biomass. This study introduces a new NMR solvent system composed of dimethylsulfoxide (DMSO-d6) and hexamethylphosphoramide (HMPA-d18). HMPA as a co-solvent enhanced swelling and mobility of the biomass samples; thereby it allowed enhancing signals of NMR spectra. Moreover, the structural information of biomass was successfully analyzed by the proposed NMR solvent system (DMSO-d6/HMPA-d18; 4:1, v/v) with different biomass. The proposed bi-solvent system does not require derivatization or isolation of biomass, facilitating a facile sample preparation and involving with no signals overlapping with biomass peaks. Furthermore, it also allows analyzing biomass with a room-temperature NMR probe instead of cryo-probes, which are traditionally used for enhancing signal intensities.

  14. Suppressing exchange effects in diffusion-ordered NMR spectroscopy.

    PubMed

    Aguilar, Juan A; Adams, Ralph W; Nilsson, Mathias; Morris, Gareth A

    2014-01-01

    In diffusion-ordered spectroscopy (DOSY) the aim is to separate signals from different molecular species according to their different diffusion coefficients. Each species has its individual diffusion coefficient (that may accidentally coincide with that of another species, e.g. if they are of very similar size). In exchanging systems, however, there is a serious complication in that the apparent diffusion coefficient of an exchanging signal will be a compromise that depends, among other factors, on the diffusion coefficients of the exchange partners and the rate of exchange between them. The DOSY spectrum will be much harder to interpret and can often give the appearance of extra (spurious) components in the mixture. Here a new and surprisingly simple experiment is described that suppresses the effects of exchange on apparent diffusion coefficients, restoring the simplicity of interpretation enjoyed by non-exchanging systems.

  15. Ultrafast 2D-IR and simulation investigations of preferential solvation and cosolvent exchange dynamics.

    PubMed

    Dunbar, Josef A; Arthur, Evan J; White, Aaron M; Kubarych, Kevin J

    2015-05-21

    Using a derivative of the vitamin biotin labeled with a transition-metal carbonyl vibrational probe in a series of aqueous N,N-dimethylformamide (DMF) solutions, we observe a striking slowdown in spectral diffusion dynamics with decreased DMF concentration. Equilibrium solvation dynamics, measured with the rapidly acquired spectral diffusion (RASD) technique, a variant of heterodyne-detected photon-echo peak shift experiments, range from 1 ps in neat DMF to ∼3 ps in 0.07 mole fraction DMF/water solution. Molecular dynamics simulations of the biotin-metal carbonyl solute in explicit aqueous DMF solutions show marked preferential solvation by DMF, which becomes more pronounced at lower DMF concentrations. The simulations and the experimental data are consistent with an interpretation where the slowdown in spectral diffusion is due to solvent exchange involving distinct cosolvent species. A simple two-component model reproduces the observed spectral dynamics as well as the DMF concentration dependence, enabling the extraction of the solvent exchange time scale of 8 ps. This time scale corresponds to the diffusive motion of a few Å, consistent with a solvent-exchange mechanism. Unlike most previous studies of solvation dynamics in binary mixtures of polar solvents, our work highlights the ability of vibrational probes to sense solvent exchange as a new, slow component in the spectral diffusion dynamics.

  16. Orphan spin operators enable the acquisition of multiple 2D and 3D magic angle spinning solid-state NMR spectra

    NASA Astrophysics Data System (ADS)

    Gopinath, T.; Veglia, Gianluigi

    2013-05-01

    We propose a general method that enables the acquisition of multiple 2D and 3D solid-state NMR spectra for U-13C, 15N-labeled proteins. This method, called MEIOSIS (Multiple ExperIments via Orphan SpIn operatorS), makes it possible to detect four coherence transfer pathways simultaneously, utilizing orphan (i.e., neglected) spin operators of nuclear spin polarization generated during 15N-13C cross polarization (CP). In the MEIOSIS experiments, two phase-encoded free-induction decays are decoded into independent nuclear polarization pathways using Hadamard transformations. As a proof of principle, we show the acquisition of multiple 2D and 3D spectra of U-13C, 15N-labeled microcrystalline ubiquitin. Hadamard decoding of CP coherences into multiple independent spin operators is a new concept in solid-state NMR and is extendable to many other multidimensional experiments. The MEIOSIS method will increase the throughput of solid-state NMR techniques for microcrystalline proteins, membrane proteins, and protein fibrils.

  17. Coupled folding and binding with 2D Window-Exchange Umbrella Sampling

    PubMed Central

    Dickson, Alex; Ahlstrom, Logan S.

    2015-01-01

    Intrinsically disordered regions of proteins can gain structure by binding to a partner. This process, of coupled folding and binding, is a fundamental part of many important biological processes. Structure-based models have proven themselves capable of revealing fundamental aspects of how coupled folding and binding occurs, however typical methods to enhance the sampling of these transitions, such as replica exchange, do not adequately sample the transition state region of this extremely rare process. Here we use a variant of Umbrella Sampling to enforce sampling of the transition states of coupled folding and binding of HdeA monomers at neutral pH, an extremely rare process that occurs over timescales ranging from seconds to hours. Using high resolution sampling in the transition state region we cluster states along the principal transition path to obtain a detailed description of coupled binding and folding for the HdeA dimer, revealing new insight into the ensemble of states that are accessible to client recognition. We then demonstrate that exchanges between umbrella sampling windows, as done in previous work, significantly improve relaxation in variables orthogonal to the restraints used. Altogether, these results show that Window Exchange Umbrella Sampling (WEUS) is a promising approach for systems that exhibit flexible binding, and can reveal transition state ensembles of these systems in high detail. PMID:26250657

  18. Theorization on ion-exchange equilibria: activity of species in 2-D phases.

    PubMed

    Tamura, Hiroki

    2004-11-01

    Ion-exchange reactions are naturally occurring at soil and sediment/water interphases, determining soil fertility and water quality. These ion-exchange reactions with inorganic and organic exchangers are applied to chemical analysis, recovery of useful ions from low-grade ores (potentially from sea water), water purification including the preparation of "ultrapure" water, production of foods and medicines, therapy, and other uses. It is important to theorize about or to model ion-exchange reactions for quantitative explanations of ion-exchange phenomena and for efficient operation of ion-exchange processes. This paper describes the modeling of ion-exchange equilibria for hydroxyl sites on metal oxides and carboxyl sites in resins with monovalent cations (alkali metal ions), a monovalent anion (nitrate ion), and divalent heavy metal ions. The procedure of modeling is as follows: the stoichiometry and material balance equations of the respective ion-exchange reactions were established based on findings here and by others. The equilibrium conditions were given by the Frumkin equation, where the mass-action relation is modified with lateral interactions between species at the interphase. The model equations were fitted to the measured data and model parameter values were determined by nonlinear regression analysis. The formation of bonds between ions and exchanger sites was evaluated by the equilibrium constant and the suppression of bond formation by electrostatic, geometric, and other lateral interactions was evaluated by the interaction constant. It was established that the properties of ions are determined by the valence, size, and hydration state of the ions. Monovalent ions (anions and cations) react with oxide surface hydroxyl and resin carboxyl sites as hydrated ions and form loose ion-site pairs by a weak electrostatic bond (nonspecific adsorption). However, the lateral interactions are large because of a large polarization of the ion-site pairs. When the

  19. Spin Saturation Transfer Difference NMR (SSTD NMR): A New Tool to Obtain Kinetic Parameters of Chemical Exchange Processes

    PubMed Central

    Quirós, María Teresa; Macdonald, Colin; Angulo, Jesús; Muñoz, María Paz

    2016-01-01

    This detailed protocol describes the new Spin Saturation Transfer Difference Nuclear Magnetic Resonance protocol (SSTD NMR), recently developed in our group to study processes of mutual-site chemical exchange that are difficult to analyze by traditional methods. As the name suggests, this method combines the Spin Saturation Transfer method used for small molecules, with the Saturation Transfer Difference (STD) NMR method employed for the study of protein-ligand interactions, by measuring transient spin saturation transfer along increasing saturation times (build-up curves) in small organic and organometallic molecules undergoing chemical exchange. Advantages of this method over existing ones are: there is no need to reach coalescence of the exchanging signals; the method can be applied as long as one signal of the exchanging sites is isolated; there is no need to measure T1 or reach steady state saturation; rate constant values are measured directly, and T1 values are obtained in the same experiment, using only one set of experiments. To test the method, we have studied the dynamics of the hindered rotation of N,N-dimethylamides, for which much data is available for comparison. The thermodynamic parameters obtained using SSTD are very similar to the reported ones (spin-saturation transfer techniques and line-shape analysis). The method can be applied to more challenging substrates that cannot be studied by previous methods. We envisage that the simple experimental set up and the wide applicability of the method to a great variety of substrates will make this a common technique amongst organic and organometallic chemists without extensive expertise in NMR. PMID:27911361

  20. Contribution of NAD 2D-NMR in liquid crystals to the determination of hydrogen isotope profile of methyl groups in miliacin

    NASA Astrophysics Data System (ADS)

    Berdagué, Philippe; Lesot, Philippe; Jacob, Jérémy; Terwilliger, Valery J.; Le Milbeau, Claude

    2016-01-01

    The hydrogen isotopic composition (δD or (D/H) value) of molecular biomarkers preserved in sedimentary archives is increasingly used to provide clues about the evolution of past climatic conditions. The rationale is that intact biomarkers retain isotopic information related to the climatic conditions that prevailed at the time of their synthesis. Some of these biomarkers may be degraded during diagenesis, however. The extent to which these degradations alter the original δD value of the source biomarker is presently debated and the capacity to resolve this question by determination of compound-specific δD values alone is limited. The "bulk" or "global" δD value of any molecule is in fact a composite of δD values at each site within this molecule (δDi or (D/H)i with i = number of hydrogen/deuterium atoms in the considered molecule). Determination of this site-specific δDi value in biomarkers could not only yield outstanding paleoenvironmental information but also help forecast the impacts of diagenesis and define essential steps in biosynthetic pathways. This task is analytically challenging. Here, we examined the capabilities of natural abundance deuterium 2D-NMR (NAD 2D-NMR) using homopolypeptide liquid crystals as an NMR solvent to: (i) analyze the NAD spectra of biomakers; (ii) determine the site-specific distribution of hydrogen in the nine methyl groups (δDMei with i = 23-31) of miliacin, a pentacyclic triterpene of the amyrin family and key biomarker for broomcorn millet in sedimentary archives. Relative (D/H)Mei values were established by anisotropic NAD 2D-NMR. Then absolute δDMei values were obtained by determining δDMei value of the methoxy group of miliacin using two independent approaches: isotropic NAD NMR (SNIF-NMR™) and GC-irMS. The resulting isotope profile for miliacin shows, for the first time, large variations in δDMei values that can directly be explained by biosynthetic processes. This approach has also the potential to permit

  1. Solid-solid phase transformations induced through cation exchange and strain in 2D heterostructured copper sulfide nanocrystals.

    PubMed

    Ha, Don-Hyung; Caldwell, Andrew H; Ward, Matthew J; Honrao, Shreyas; Mathew, Kiran; Hovden, Robert; Koker, Margaret K A; Muller, David A; Hennig, Richard G; Robinson, Richard D

    2014-12-10

    We demonstrate dual interface formation in nanocrystals (NCs) through cation exchange, creating epitaxial heterostructures within spherical NCs. The thickness of the inner-disk layer can be tuned to form two-dimensional (2D), single atomic layers (<1 nm). During the cation exchange reaction from copper sulfide to zinc sulfide (ZnS), we observe a solid-solid phase transformation of the copper sulfide phase in heterostructured NCs. As the cation exchange reaction is initiated, Cu ions replaced by Zn ions at the interfaces are accommodated in intrinsic Cu vacancy sites present in the initial roxbyite (Cu1.81S) phase of copper sulfide, inducing a full phase transition to djurleite (Cu1.94S)/low chalcocite (Cu2S), a more thermodynamically stable phase than roxbyite. As the reaction proceeds and reduces the size of the copper sulfide layer, the epitaxial strain at the interfaces between copper sulfide and ZnS increases and is maximized for a copper sulfide disk ∼ 5 nm thick. To minimize this strain energy, a second phase transformation occurs back to the roxbyite phase, which shares a similar sulfur sublattice to wurtzite ZnS. The observation of a solid-solid phase transformation in our unique heterostructured NCs provides a new pathway to control desired phases and an insight into the influence of cation exchange on nanoscale phase transitions in heterostructured materials.

  2. A 2-D oscillating flow analysis in Stirling engine heat exchangers

    NASA Technical Reports Server (NTRS)

    Ahn, Kyung H.; Ibrahim, Mounir B.

    1991-01-01

    A two dimensional oscillating flow analysis was conducted, simulating the gas flow inside Stirling heat exchangers. Both laminar and turbulent oscillating pipe flow were investigated numerically for Re(max) = 1920 (Va = 80), 10800 (Va = 272), 19300 (Va = 272), and 60800 (Va = 126). The results are compared with experimental results of previous investigators. Also, predictions of the flow regime on present oscillating flow conditions were checked by comparing velocity amplitudes and phase differences with those from laminar theory and quasi-steady profile. A high Reynolds number k-epsilon turbulence model was used for turbulent oscillating pipe flow. Finally, performance evaluation of the K-epsilon model was made to explore the applicability of quasi-steady turbulent models to unsteady oscillating flow analysis.

  3. Mechanism of dilute-spin-exchange in solid-state NMR

    SciTech Connect

    Lu, George J.; Opella, Stanley J.

    2014-03-28

    In the stationary, aligned samples used in oriented sample (OS) solid-state NMR, {sup 1}H-{sup 1}H homonuclear dipolar couplings are not attenuated as they are in magic angle spinning solid-state NMR; consequently, they are available for participation in dipolar coupling-based spin-exchange processes. Here we describe analytically the pathways of {sup 15}N-{sup 15}N spin-exchange mediated by {sup 1}H-{sup 1}H homonuclear dipolar couplings. The mixed-order proton-relay mechanism can be differentiated from the third spin assisted recoupling mechanism by setting the {sup 1}H to an off-resonance frequency so that it is at the “magic angle” during the spin-exchange interval in the experiment, since the “magic angle” irradiation nearly quenches the former but only slightly attenuates the latter. Experimental spectra from a single crystal of N-acetyl leucine confirm that this proton-relay mechanism plays the dominant role in {sup 15}N-{sup 15}N dilute-spin-exchange in OS solid-state NMR in crystalline samples. Remarkably, the “forbidden” spin-exchange condition under “magic angle” irradiation results in {sup 15}N-{sup 15}N cross-peaks intensities that are comparable to those observed with on-resonance irradiation in applications to proteins. The mechanism of the proton relay in dilute-spin-exchange is crucial for the design of polarization transfer experiments.

  4. NMR and IR spectroscopic study of proton exchange between o-nitrophenol and methanol in CCl/sub 4/

    SciTech Connect

    Bureiko, S.F.; Golubev, N.S.; Lange, I.Y.

    1982-08-01

    The kinetics of proton exchange in solution between o-nitrophenol and methanol have been studied by dynamic NMR and IR spectroscopy, and a method has been developed for the simultaneous determination of the rate constants for H-H, H-D, and D-H exchange from /sup 1/H NMR spectra.

  5. Ultrasensitive anion detection by NMR spectroscopy: a supramolecular strategy based on modulation of chemical exchange rate.

    PubMed

    Perruchoud, Loïse H; Hadzovic, Alen; Zhang, Xiao-An

    2015-06-08

    NMR spectroscopy is a powerful tool for monitoring molecular interactions and is widely used to characterize supramolecular systems at the atomic level. NMR is limited for sensing purposes, however, due to low sensitivity. Dynamic processes such as conformational changes or binding events can induce drastic effects on NMR spectra in response to variations in chemical exchange (CE) rate, which can lead to new strategies in the design of supramolecular sensors through the control and monitoring of CE rate. Here, we present an indirect NMR anion sensing technique in which increased CE rate, due to anion-induced conformational flexibility of a relatively rigid structure of a novel sensor, allows ultrasensitive anion detection as low as 120 nM.

  6. Characterization of the isomeric configuration and impurities of (Z)-endoxifen by 2D NMR, high resolution LC⬜MS, and quantitative HPLC analysis.

    PubMed

    Elkins, Phyllis; Coleman, Donna; Burgess, Jason; Gardner, Michael; Hines, John; Scott, Brendan; Kroenke, Michelle; Larson, Jami; Lightner, Melissa; Turner, Gregory; White, Jonathan; Liu, Paul

    2014-01-01

    (Z)-Endoxifen (4-hydroxy-N-desmethyltamoxifen), an active metabolite generated via actions of CYP3A4/5 and CYP2D6, is a more potent selective estrogen receptor modulator (SERM) than tamoxifen. In the MCF-7 human mammary tumor xenograft model with female athymic mice, (Z)-endoxifen, at an oral dose of 4⬜8 mg/kg, significantly inhibits tumor growth. (Z)-Endoxifen's potential as an alternative therapeutic agent independent of CYP2D6 activities, which can vary widely in ER+ breast cancer patients, is being actively evaluated. This paper describes confirmation of the configuration of the active (Z)-isomer through 2D NMR experiments, including NOE (ROESY) to establish spatial proton⬜proton correlations, and identification of the major impurity as the (E)-isomer in endoxifen drug substance by HPLC/HRMS (HPLC/MS-TOF). Stability of NMR solutions was confirmed by HPLC/UV analysis. For pre-clinical studies, a reverse-phase HPLC⬜UV method, with methanol/water mobile phases containing 10 mM ammonium formate at pH 4.3, was developed and validated for the accurate quantitation and impurity profiling of drug substance and drug product. Validation included demonstration of linearity, method precision, accuracy, and specificity in the presence of impurities, excipients (for the drug product), and degradation products. Ruggedness and reproducibility of the method were confirmed by collaborative studies between two independent laboratories. The method is being applied for quality control of the API and oral drug product. Kinetic parameters of Z- to E-isomerization were also delineated in drug substance and in aqueous formulation, showing conversion at temperatures above 25 °C.

  7. Characterization of the isomeric configuration and impurities of (Z)-endoxifen by 2D NMR, high resolution LC–MS, and quantitative HPLC analysis

    PubMed Central

    Elkins, Phyllis; Coleman, Donna; Burgess, Jason; Gardner, Michael; Hines, John; Scott, Brendan; Kroenke, Michelle; Larson, Jami; Lightner, Melissa; Turner, Gregory; White, Jonathan; Liu, Paul

    2014-01-01

    (Z)-Endoxifen (4-hydroxy-N-desmethyltamoxifen), an active metabolite generated via actions of CYP3A4/5 and CYP2D6, is a more potent selective estrogen receptor modulator (SERM) than tamoxifen. In the MCF-7 human mammary tumor xenograft model with female athymic mice, (Z)-endoxifen, at an oral dose of 4– 8 mg/kg, significantly inhibits tumor growth. (Z)-Endoxifen's potential as an alternative therapeutic agent independent of CYP2D6 activities, which can vary widely in ER+ breast cancer patients, is being actively evaluated. This paper describes confirmation of the configuration of the active (Z)-isomer through 2D NMR experiments, including NOE (ROESY) to establish spatial proton–proton correlations, and identification of the major impurity as the (E)-isomer in endoxifen drug substance by HPLC/HRMS (HPLC/MS-TOF). Stability of NMR solutions was confirmed by HPLC/UV analysis. For pre-clinical studies, a reverse-phase HPLC–UV method, with methanol/water mobile phases containing 10 mM ammonium formate at pH 4.3, was developed and validated for the accurate quantitation and impurity profiling of drug substance and drug product. Validation included demonstration of linearity, method precision, accuracy, and specificity in the presence of impurities, excipients (for the drug product), and degradation products. Ruggedness and reproducibility of the method were confirmed by collaborative studies between two independent laboratories. The method is being applied for quality control of the API and oral drug product. Kinetic parameters of Z- to E-isomerization were also delineated in drug substance and in aqueous formulation, showing conversion at temperatures above 25 °C. PMID:24055701

  8. 2D 31P solid state NMR spectroscopy, electronic structure and thermochemistry of PbP7

    NASA Astrophysics Data System (ADS)

    Benndorf, Christopher; Hohmann, Andrea; Schmidt, Peer; Eckert, Hellmut; Johrendt, Dirk; Schäfer, Konrad; Pöttgen, Rainer

    2016-03-01

    Phase pure polycrystalline PbP7 was prepared from the elements via a lead flux. Crystalline pieces with edge-lengths up to 1 mm were obtained. The assignment of the previously published 31P solid state NMR spectrum to the seven distinct crystallographic sites was accomplished by radio-frequency driven dipolar recoupling (RFDR) experiments. As commonly found in other solid polyphosphides there is no obvious correlation between the 31P chemical shift and structural parameters. PbP7 decomposes incongruently under release of phosphorus forming liquid lead as remainder. The thermal decomposition starts at T>550 K with a vapor pressure almost similar to that of red phosphorus. Electronic structure calculations reveal PbP7 as a semiconductor according to the Zintl description and clearly shows the stereo-active Pb-6s2 lone pairs in the electron localization function ELF.

  9. Water exchange in plant tissue studied by proton NMR in the presence of paramagnetic centers.

    PubMed

    Bacić, G; Ratković, S

    1984-04-01

    The proton NMR relaxation of water in maize roots in the presence of paramagnetic centers, Mn2+, Mn- EDTA2 -, and dextran-magnetite was measured. It was shown that the NMR method of Conlon and Outhred (1972, Biochem. Biophys. Acta. 288:354-361) can be applied to a heterogenous multicellular system, and the water exchange time between cortical cells and the extracellular space can be calculated. The water exchange is presumably controlled by the intracellular unstirred layers. The Mn- EDTA2 - complex is a suitable paramagnetic compound for complex tissue, while the application of dextran-magnetite is probably restricted to studies of water exchange in cell suspensions. The water free space of the root and viscosity of the cells cytoplasm was estimated with the use of Mn- EDTA2 -. The convenience of proton NMR for studying the multiphase uptake of paramagnetic ions by plant root as well as their transport to leaves is demonstrated. A simple and rapid NMR technique (spin-echo recovery) for continuous measurement of the uptake process is presented.

  10. 2D-NMR investigation and in vitro evaluation of antioxidant, antigenotoxic and estrogenic/antiestrogenic activities of strawberry grape.

    PubMed

    D'Abrosca, Brigida; Lavorgna, Margherita; Scognamiglio, Monica; Russo, Chiara; Graziani, Vittoria; Piscitelli, Concetta; Fiorentino, Antonio; Isidori, Marina

    2017-03-27

    Strawberry grape is considered beneficial due to its extensive phytochemical properties. To expand the knowledge about the chemical constituents and the biological activities of the whole plant, 2D-NMR investigation has been carried out on pulp, peel, seeds, stalks and leaves. Catechin and epicatechin were identified as the main constituents of the seed extract, quercetin and ferulic acid were detected in the leaves and malvidin and cyanidin glucopyranoside in the peels. The leaf, stalk and seed extracts were found to be very rich in phytochemicals and were tested for their ability to reduce the mutagenicity and genotoxicity of standard agents via Salmonella mutagenicity assay and SOS chromotest, respectively. Moreover, the estrogen/antiestrogen-like activity was evaluated on the MCF-7 estrogen-responsive cells. Seed and stalk extracts had an elevated antimutagenic/antigenotoxic activity. Stalk extracts highly reduced the proliferative effect of natural estrogen, 17β-estradiol.

  11. Constant-time 2D and 3D through-bond correlation NMR spectroscopy of solids under 60 kHz MAS

    SciTech Connect

    Zhang, Rongchun; Ramamoorthy, Ayyalusamy

    2016-01-21

    Establishing connectivity and proximity of nuclei is an important step in elucidating the structure and dynamics of molecules in solids using magic angle spinning (MAS) NMR spectroscopy. Although recent studies have successfully demonstrated the feasibility of proton-detected multidimensional solid-state NMR experiments under ultrafast-MAS frequencies and obtaining high-resolution spectral lines of protons, assignment of proton resonances is a major challenge. In this study, we first re-visit and demonstrate the feasibility of 2D constant-time uniform-sign cross-peak correlation (CTUC-COSY) NMR experiment on rigid solids under ultrafast-MAS conditions, where the sensitivity of the experiment is enhanced by the reduced spin-spin relaxation rate and the use of low radio-frequency power for heteronuclear decoupling during the evolution intervals of the pulse sequence. In addition, we experimentally demonstrate the performance of a proton-detected pulse sequence to obtain a 3D {sup 1}H/{sup 13}C/{sup 1}H chemical shift correlation spectrum by incorporating an additional cross-polarization period in the CTUC-COSY pulse sequence to enable proton chemical shift evolution and proton detection in the incrementable t{sub 1} and t{sub 3} periods, respectively. In addition to through-space and through-bond {sup 13}C/{sup 1}H and {sup 13}C/{sup 13}C chemical shift correlations, the 3D {sup 1}H/{sup 13}C/{sup 1}H experiment also provides a COSY-type {sup 1}H/{sup 1}H chemical shift correlation spectrum, where only the chemical shifts of those protons, which are bonded to two neighboring carbons, are correlated. By extracting 2D F1/F3 slices ({sup 1}H/{sup 1}H chemical shift correlation spectrum) at different {sup 13}C chemical shift frequencies from the 3D {sup 1}H/{sup 13}C/{sup 1}H spectrum, resonances of proton atoms located close to a specific carbon atom can be identified. Overall, the through-bond and through-space homonuclear/heteronuclear proximities determined from the

  12. Constant-time 2D and 3D through-bond correlation NMR spectroscopy of solids under 60 kHz MAS

    PubMed Central

    Zhang, Rongchun; Ramamoorthy, Ayyalusamy

    2016-01-01

    Establishing connectivity and proximity of nuclei is an important step in elucidating the structure and dynamics of molecules in solids using magic angle spinning (MAS) NMR spectroscopy. Although recent studies have successfully demonstrated the feasibility of proton-detected multidimensional solid-state NMR experiments under ultrafast-MAS frequencies and obtaining high-resolution spectral lines of protons, assignment of proton resonances is a major challenge. In this study, we first re-visit and demonstrate the feasibility of 2D constant-time uniform-sign cross-peak correlation (CTUC-COSY) NMR experiment on rigid solids under ultrafast-MAS conditions, where the sensitivity of the experiment is enhanced by the reduced spin-spin relaxation rate and the use of low radio-frequency power for heteronuclear decoupling during the evolution intervals of the pulse sequence. In addition, we experimentally demonstrate the performance of a proton-detected pulse sequence to obtain a 3D 1H/13C/1H chemical shift correlation spectrum by incorporating an additional cross-polarization period in the CTUC-COSY pulse sequence to enable proton chemical shift evolution and proton detection in the incrementable t1 and t3 periods, respectively. In addition to through-space and through-bond 13C/1H and 13C/13C chemical shift correlations, the 3D 1H/13C/1H experiment also provides a COSY-type 1H/1H chemical shift correlation spectrum, where only the chemical shifts of those protons, which are bonded to two neighboring carbons, are correlated. By extracting 2D F1/F3 slices (1H/1H chemical shift correlation spectrum) at different 13C chemical shift frequencies from the 3D 1H/13C/1H spectrum, resonances of proton atoms located close to a specific carbon atom can be identified. Overall, the through-bond and through-space homonuclear/heteronuclear proximities determined from the 3D 1H/13C/1H experiment would be useful to study the structure and dynamics of a variety of chemical and biological

  13. Chemical exchange spectroscopy based on carbon-13 NMR. Applications to enzymology and protein folding

    NASA Astrophysics Data System (ADS)

    Alexandrescu, Andrei T.; Loh, Stewart N.; Markley, John L.

    We explore how 13C-based two-dimensional chemical exchange spectroscopy (EXSY) can be used to investigate exchange processes that are slow on the NMR time scale. Results are shown for the mutarotase-catalyzed α →← β isomerization of [1- 13C]glucose using experiments that detect carbon spins: homonuclear 13C exchange spectroscopy [ 13C { 13C} EXSY] and heteronuclear exchange spectroscopy [ 13C { 1H} EXSY]; and inverse experiments that select for proton spins attached to 13C: 1H- 13C single-bond correlation exchange spectroscopy [ 1H { 13C} SBC-EXSY] and 13C-filtered 1H exchange spectroscopy [ 1H{ 1H}- 13Cƒ- EXSY] . The main advantage of 13C-based exchange experiments is the simplification of complex spectra afforded by incorporation of selective labels. The inherent power of this approach is illustrated with a 1H { 13C} SBC-EXSY spectrum showing the native →← denatured interconversion of [ 13Cδ1] Trp-staphylococcal nuclease. Certain 13C-based EXSY experiments are useful for discriminating exchange connectivities from dipole-dipole connectivities.

  14. A spectroscopic study of nicotine analogue 2-phenylpyrrolidine (PPD) using resonant two-photon ionization (R2PI), microwave, and 2D NMR techniques.

    PubMed

    Martin, Danielle E; Robertson, Evan G; MacLellan, Jonathan G; Godfrey, Peter D; Thompson, Christopher D; Morrison, Richard J S

    2009-02-25

    Conformational preferences of the nicotine analogue 2-phenylpyrrolidine (PPD) have been studied in both gaseous and solution phases. Theoretical calculations at the MP2 and B3LYP levels point to 5-6 stable conformers which differ in three degrees of conformational freedom; torsion between the two rings, inversion at the pyrrolidine (PY) amine, and PY ring puckering, characterized using the Cremer-Pople definition for pseudorotation. Only one conformer has a trans arrangement between the amino hydrogen and the phenyl substituent. It is 6-8 kJ mol(-1) more stable than the cis conformers, has a perpendicular ring arrangement, and puckers at the nitrogen atom--similar to structures reported for nicotine. Resonant two-photon ionization (R2PI) data, including hole burn spectra, indicate only one conformer is present in the free jet expansion, and band contour analysis suggests assignment to the trans conformer. Confirmation was provided by microwave spectroscopy. Fifty-seven lines measured in the 48-72 GHz region were assigned to 206 b-type transitions and fitted to yield rotational constants within 2 MHz of MP2 values predicted for the trans conformer. The solution-phase conformers of PPD were studied using 1D and 2D (1)H NMR spectroscopy and solvent-based theoretical calculations. In marked contrast to the gas phase, NMR data reveals only cis conformers present in solution. Calculations confirm increased stability for these conformers when placed in simulated chloroform or water environments. Solvent molecules are believed to disrupt a crucial N...H(ortho) stabilizing interaction present within the trans conformer.

  15. Cellulose Structural Polymorphism in Plant Primary Cell Walls Investigated by High-Field 2D Solid-State NMR Spectroscopy and Density Functional Theory Calculations.

    PubMed

    Wang, Tuo; Yang, Hui; Kubicki, James D; Hong, Mei

    2016-06-13

    The native cellulose of bacterial, algal, and animal origins has been well studied structurally using X-ray and neutron diffraction and solid-state NMR spectroscopy, and is known to consist of varying proportions of two allomorphs, Iα and Iβ, which differ in hydrogen bonding, chain packing, and local conformation. In comparison, cellulose structure in plant primary cell walls is much less understood because plant cellulose has lower crystallinity and extensive interactions with matrix polysaccharides. Here we have combined two-dimensional magic-angle-spinning (MAS) solid-state nuclear magnetic resonance (solid-state NMR) spectroscopy at high magnetic fields with density functional theory (DFT) calculations to obtain detailed information about the structural polymorphism and spatial distributions of plant primary-wall cellulose. 2D (13)C-(13)C correlation spectra of uniformly (13)C-labeled cell walls of several model plants resolved seven sets of cellulose chemical shifts. Among these, five sets (denoted a-e) belong to cellulose in the interior of the microfibril while two sets (f and g) can be assigned to surface cellulose. Importantly, most of the interior cellulose (13)C chemical shifts differ significantly from the (13)C chemical shifts of the Iα and Iβ allomorphs, indicating that plant primary-wall cellulose has different conformations, packing, and hydrogen bonding from celluloses of other organisms. 2D (13)C-(13)C correlation experiments with long mixing times and with water polarization transfer revealed the spatial distributions and matrix-polysaccharide interactions of these cellulose structures. Celluloses f and g are well mixed chains on the microfibril surface, celluloses a and b are interior chains that are in molecular contact with the surface chains, while cellulose c resides in the core of the microfibril, outside spin diffusion contact with the surface. Interestingly, cellulose d, whose chemical shifts differ most significantly from those of

  16. Cellulose Structural Polymorphism in Plant Primary Cell Walls Investigated by High-Field 2D Solid-State NMR Spectroscopy and Density Functional Theory Calculations

    PubMed Central

    Wang, Tuo; Yang, Hui; Kubicki, James D.; Hong, Mei

    2017-01-01

    The native cellulose of bacterial, algal, and animal origins has been well studied structurally using X-ray and neutron diffraction and solid-state NMR spectroscopy, and is known to consist of varying proportions of two allomorphs, Iα and Iβ, which differ in hydrogen bonding, chain packing, and local conformation. In comparison, cellulose structure in plant primary cell walls is much less understood because plant cellulose has lower crystallinity and extensive interactions with matrix polysaccharides. Here we have combined two-dimensional magic-angle-spinning (MAS) solid-state nuclear magnetic resonance (solid-state NMR) spectroscopy at high magnetic fields with density functional theory (DFT) calculations to obtain detailed information about the structural polymorphism and spatial distributions of plant primary-wall cellulose. 2D 13C-13C correlation spectra of uniformly 13C-labeled cell walls of several model plants resolved seven sets of cellulose chemical shifts. Among these, five sets (denoted a-e) belong to cellulose in the interior of the microfibril while two sets (f and g) can be assigned to surface cellulose. Importantly, most of the interior cellulose 13C chemical shifts differ significantly from the 13C chemical shifts of the Iα and Iβ allomorphs, indicating that plant primary-wall cellulose has different conformations, packing and hydrogen bonding from celluloses of other organisms. 2D 13C-13C correlation experiments with long mixing times and with water polarization transfer revealed the spatial distributions and matrix-polysaccharide interactions of these cellulose structures. Cellulose f and g are well mixed chains on the microfibril surface, cellulose a and b are interior chains that are in molecular contact with the surface chains, while cellulose c resides in the core of the microfibril, outside spin diffusion contact with the surface. Interestingly, cellulose d, whose chemical shifts differ most significantly from those of bacterial, algal

  17. Conformation states of gramicidin A along the pathway to the formation of channels in model membranes determined by 2D NMR and circular dichroism spectroscopy.

    PubMed

    Abdul-Manan, N; Hinton, J F

    1994-06-07

    Gramicidin A incorporated into SDS (sodium dodecyl sulfate) micelles exists as a right-handed, N-to-N-terminal beta 6.3 helical dimer [Lomize, A. L., Orechov, V. Yu., & Arseniev, A.S. (1992) Bioorg. Khim. 18, 182-189]. In the incorporation procedure to achieve the ion channel state of gramicidin A in SDS micelles, trifluoroethanol (TFE) is used to solubilize the hydrophobic peptide before addition to the aqueous/micelle solution. The conformational transition of gramicidin A to form ion channels in SDS micelles, i.e., in TFE and 10% TFE/water, has been investigated using 2D NMR and CD spectroscopy. In neat TFE, gramicidin A was found to be monomeric and may possibly exist in an equilibrium of rapidly interconverting conformers of at least three different forms believed to be left- and/or right-handed alpha and beta 4.4 helices. It was found that the interconversion between these conformers was slowed down in 55% TFE as evident by the observation of at least three different sets of d alpha N COSY peaks although CD gave a net spectrum similar to that in neat TFE. In 10% TFE gramicidin A spontaneously forms a precipitate. The precipitated species were isolated and solubilized in dioxane where gramicidin conformers undergo very slow interconversion and could be characterized by NMR. At least seven different gramicidin A conformations were found in 10% TFE. Four of thes are the same types of double helices as previously found in ethanol (i.e., a symmetric left-handed parallel beta 5.6 double helix, an unsymmetric left-handed parallel beta 5.6 double helix, a symmetric left-handed antiparallel beta 5.6 double helix, a symmetric right-handed parallel beta 5.6 double helix); the fifth is possibly a symmetric right-handed antiparallel beta 5.6 double helix. There is also evidence for the presence of at least one form of monomeric species. Previous observation on the solvent history dependence in the ease of channel incorporation may be explained by the presence of several

  18. NOVEL CONTINUOUS PH/SALT GRADIENT AND PEPTIDE SCORE FOR STRONG CATION EXCHANGE CHROMATOGRAPHY IN 2D-NANO-LC/MSMS PEPTIDE IDENTIFICATION FOR PROTEOMICS

    EPA Science Inventory

    Tryptic digests of human serum albumin (HSA) and human lung epithelial cell lysates were used as test samples in a novel proteomics study. Peptides were separated and analyzed using 2D-nano-LC/MSMS with strong cation exchange (SCX) and reverse phase (RP) chromatography and contin...

  19. Alternating zinc fingers in the human male associated protein ZFY: 2D NMR structure of an even finger and implications for jumping-linker DNA recognition

    SciTech Connect

    Kochoyan, M.; Havel, T.F.; Dahl, C.E. ); Nguyen, D.T.; Keutmann, H.T. ); Weiss, M.A. Massachusetts General Hospital, Boston )

    1991-04-09

    ZFY, a sex-related Zn-finger protein encoded by the human Y chromosome, is distinguished from the general class of Zn-finger proteins by the presence of a two-finger repeat. Whereas odd-numbered domains and linkers fit a general consensus, even-numbered domains and linkers exhibit systematic differences. Because this alternation may have fundamental implications for the mechanism of protein-DNA recognition, the authors have undertaken biochemical and structural studies of fragments of ZFY. They describe here the solution structure of a representative nonconsensus (even-numbered) Zn finger based on 2D NMR studies of a 30-residue peptide. Structural modeling by distance geometry and simulated annealing (DG/SA) demonstrates that this peptide folds as a miniglobular domain containing a C-terminal {beta}-hairpin and N-terminal {alpha}-helix ({beta}{beta}{alpha} motif). These features are similar to (but not identical with) those previously described in consensus-type Zn fingers (derived from ADR1 and Xfin); the similarities suggest that even and odd ZFY domains bind DNA by a common mechanism. A model of the protein-DNA complex (designated the jumping-linker model) is presented and discussed in terms of the ZFY two-finger repeat. In this model every other linker is proposed to cross the minor groove by means of a putative finger/linker submotif HX{sub 4}HX{sub 3}-hydrophobic residue-X{sub 3}.

  20. Understanding API-polymer proximities in amorphous stabilized composite drug products using fluorine-carbon 2D HETCOR solid-state NMR.

    PubMed

    Abraham, Anuji; Crull, George

    2014-10-06

    A simple and robust method for obtaining fluorine-carbon proximities was established using a (19)F-(13)C heteronuclear correlation (HETCOR) two-dimensional (2D) solid-state nuclear magnetic resonance (ssNMR) experiment under magic-angle spinning (MAS). The method was applied to study a crystalline active pharmaceutical ingredient (API), avagacestat, containing two types of fluorine atoms and its API-polymer composite drug product. These results provide insight into the molecular structure, aid with assigning the carbon resonances, and probe API-polymer proximities in amorphous spray dried dispersions (SDD). This method has an advantage over the commonly used (1)H-(13)C HETCOR because of the large chemical shift dispersion in the fluorine dimension. In the present study, fluorine-carbon distances up to 8 Å were probed, giving insight into the API structure, crystal packing, and assignments. Most importantly, the study demonstrates a method for probing an intimate molecular level contact between an amorphous API and a polymer in an SDD, giving insights into molecular association and understanding of the role of the polymer in API stability (such as recrystallization, degradation, etc.) in such novel composite drug products.

  1. Probing exchange kinetics and atomic resolution dynamics in high-molecular-weight complexes using dark-state exchange saturation transfer NMR spectroscopy.

    PubMed

    Fawzi, Nicolas L; Ying, Jinfa; Torchia, Dennis A; Clore, G Marius

    2012-07-19

    We present the protocol for the measurement and analysis of dark-state exchange saturation transfer (DEST), a novel solution NMR method for characterizing, at atomic resolution, the interaction between an NMR-'visible' free species and an NMR-'invisible' species transiently bound to a very high-molecular-weight (>1 MDa) macromolecular entity. The reduced rate of reorientational motion in the bound state that precludes characterization by traditional NMR methods permits the observation of DEST. (15)N-DEST profiles are measured on a sample comprising the dark state in exchange with an NMR-visible species; in addition, the difference (ΔR(2)) in (15)N transverse relaxation rates between this sample and a control sample comprising only the NMR-visible species is also obtained. The (15)N-DEST and ΔR(2) data for all residues are then fitted simultaneously to the McConnell equations for various exchange models describing the residue-specific dynamics in the bound state(s) and the interconversion rate constants. Although the length of the experiments depends strongly on sample conditions, approximately 1 week of NMR spectrometer time was sufficient for full characterization of samples of amyloid-β (Aβ) at concentrations of ~100 μM.

  2. Catalysis of H(2)/D(2) scrambling and other H/D exchange processes by [Fe]-hydrogenase model complexes.

    PubMed

    Zhao, Xuan; Georgakaki, Irene P; Miller, Matthew L; Mejia-Rodriguez, Rosario; Chiang, Chao-Yi; Darensbourg, Marcetta Y

    2002-07-29

    Protonation of the [Fe]-hydrogenase model complex (mu-pdt)[Fe(CO)(2)(PMe(3))](2) (pdt = SCH(2)CH(2)CH(2)S) produces a species with a high field (1)H NMR resonance, isolated as the stable [(mu-H)(mu-pdt)[Fe(CO)(2)(PMe(3))](2)](+)[PF(6)](-) salt. Structural characterization found little difference in the 2Fe2S butterfly cores, with Fe.Fe distances of 2.555(2) and 2.578(1) A for the Fe-Fe bonded neutral species and the bridging hydride species, respectively (Zhao, X.; Georgakaki, I. P.; Miller, M. L.; Yarbrough, J. C.; Darensbourg, M. Y. J. Am. Chem. Soc. 2001, 123, 9710). Both are similar to the average Fe.Fe distance found in structures of three Fe-only hydrogenase active site 2Fe2S clusters: 2.6 A. A series of similar complexes (mu-edt)-, (mu-o-xyldt)-, and (mu-SEt)(2)[Fe(CO)(2)(PMe(3))](2) (edt = SCH(2)CH(2)S; o-xyldt = SCH(2)C(6)H(4)CH(2)S), (mu-pdt)[Fe(CO)(2)(PMe(2)Ph)](2), and their protonated derivatives likewise show uniformity in the Fe-Fe bond lengths of the neutral complexes and Fe.Fe distances in the cationic bridging hydrides. The positions of the PMe(3) and PMe(2)Ph ligands are dictated by the orientation of the S-C bonds in the (mu-SRS) or (mu-SR)(2) bridges and the subsequent steric hindrance of R. The Fe(II)(mu-H)Fe(II) complexes were compared for their ability to facilitate H/D exchange reactions, as have been used as assays of H(2)ase activity. In a reaction that is promoted by light but inhibited by CO, the [(mu-H)(mu-pdt)[Fe(CO)(2)(PMe(3))](2)](+) complex shows H/D exchange activity with D(2), producing [(mu-D)(mu-pdt)[Fe(CO)(2)(PMe(3))](2)](+) in CH(2)Cl(2) and in acetone, but not in CH(3)CN. In the presence of light, H/D scrambling between D(2)O and H(2) is also promoted by the Fe(II)(mu-H)Fe(II) catalyst. The requirement of an open site suggests that the key step in the reactions involves D(2) or H(2) binding to Fe(II) followed by deprotonation by the internal hydride base, or by external water. As indicated by similar catalytic efficiencies

  3. In situ (1)H and (13)C MAS NMR kinetic study of the mechanism of H/D exchange for propane on zeolite H-ZSM-5.

    PubMed

    Arzumanov, Sergei S; Reshetnikov, Sergei I; Stepanov, Alexander G; Parmon, Valentin N; Freude, Dieter

    2005-10-27

    The kinetics of hydrogen (H/D) exchange between Brønsted acid sites of zeolite H-ZSM-5 and variously deuterated propanes (propane-d(8), propane-1,1,1,3,3,3-d(6), propane-2,2-d(2)) have been monitored in situ by (1)H MAS NMR spectroscopy within the temperature range of 503-556 K. The contribution of intramolecular hydrogen transfer to the H/D exchange in the adsorbed propane was estimated by monitoring the kinetics of (13)C-labeled carbon scrambling in propane-2-(13)C in situ with (13)C MAS NMR at 543-573 K. Possible mechanisms of the exchange have been verified on the basis of the analysis of the variation of protium concentration in both the methyl and the methylene groups of propane in dependence of the reaction time. The main route of the exchange consists of a direct exchange of the acidic OH groups of the zeolite with either the methyl groups or the methylene group presumably with a pentacoordinated carbonium ion intermediate. The assumption that the intramolecular H scrambling between the methyl groups and the methylene group of propane via carbenium-ion-type intermediates is the fastest process among the other possible routes does not account for the experimental kinetics of H/D exchange for propanes with different initial contents and locations of deuterium in a propane molecule. The rate constant (k(3)) for intramolecular H/D exchange between the methyl and the methylene groups is 4-5 times lower compared to those of the direct exchange of both the methyl (k(1)) and the methylene (k(2)) groups with Brønsted acid sites of the zeolite, the k(1) being ca. 1.5 times higher than k(2). At lower temperature (473 K), the exchange is slower, and the expected difference between k(1) and k(2) is more essential, k(1) = 3k(2). This accounts for earlier observed regioselectivity of the exchange for propane on H-ZSM-5 at 473 K. Faster direct exchange with the methyl groups compared to that with the methylene groups was attributed to a possible, more spatial

  4. Measurement of laser heating in spin exchange optical pumping by NMR diffusion sensitization gradients

    SciTech Connect

    Parnell, Steven R.; Deppe, Martin H.; Ajraoui, Salma; Parra-Robles, Juan; Wild, Jim M.; Boag, Stephen

    2010-05-15

    This paper details pulsed gradient NMR measurements of the {sup 3}He diffusion coefficient in sealed cells during spin exchange optical pumping. The potential of ultra low field magnetic resonance imgaing (MRI) and NMR for noninvasive measurement of cell pressure is demonstrated. Diffusion sensitization gradients allow measurement of the {sup 3}He diffusion coefficient from which the pressure and/or temperature of the gas can be determined during optical pumping. The pressure measurements were compared with neutron time of flight transmission measurements. Good agreement was observed between the temperature/pressure measurements and predictions based on Chapman-Enskog theory. The technique had sufficient sensitivity to observe the diffusion coefficient increasing with temperature in a sealed cell. With this method, evidence for laser heating of the {sup 3}He during optical pumping was found. The results show that NMR diffusion measurements allow noninvasive measurement of the cell temperature and/or pressure in an optical pumping setup. The method can be expanded using MRI to probe the spatial distribution of the diffusion coefficient. These techniques can be applied to the further investigation of polarization limiting effects such as laser heating.

  5. Direct evidence for a two-state protein unfolding transition from hydrogen-deuterium exchange, mass spectrometry, and NMR.

    PubMed Central

    Yi, Q.; Baker, D.

    1996-01-01

    We use mass spectrometry in conjunction with hydrogen-deuterium exchange and NMR to characterize the conformational dynamics of the 62-residue IgG binding domain of protein L under conditions in which the native state is marginally stable. Mass spectra of protein L after short incubations in D2O reveal the presence of two distinct populations containing different numbers of protected protons. NMR experiments indicate that protons in the hydrophobic core are protected in one population, whereas all protons are exchanged for deuterons in the other. As the exchange period is increased, molecules are transferred from the former population to the latter. The absence of molecules with a subset of the core protons protected suggests that exchange occurs in part via a highly concerted transition to an excited state in which all protons exchange rapidly with deuterons. A steady increase in the molecular weight of the population with protected protons, and variation in the exchange rates of the individual protected protons indicates the presence of an additional exchange mechanism. A simple model in which exchange results from rapid (> 10(5)/s) local fluctuations around the native state superimposed upon transitions to an unfolded excited state at approximately 0.06/s is supported by qualitative agreement between the observed mass spectra and the mass spectra simulated according to the model using NMR-derived estimates of the proton exchange rates. PMID:8762137

  6. Fast proton exchange in histidine: measurement of rate constants through indirect detection by NMR spectroscopy.

    PubMed

    Sehgal, Akansha Ashvani; Duma, Luminita; Bodenhausen, Geoffrey; Pelupessy, Philippe

    2014-05-19

    Owing to its imidazole side chain, histidine participates in various processes such as enzyme catalysis, pH regulation, metal binding, and phosphorylation. The determination of exchange rates of labile protons for such a system is important for understanding its functions. However, these rates are too fast to be measured directly in an aqueous solution by using NMR spectroscopy. We have obtained the exchange rates of the NH3(+) amino protons and the labile NH(ε2) and NH(δ1) protons of the imidazole ring by indirect detection through nitrogen-15 as a function of temperature (272 KExchange rates up to 8.5×10(4) s(-1) could be determined (i.e., lifetimes as short as 12 μs). The three chemical shifts δH(i) of the invisible exchanging protons H(i) and the three one-bond scalar coupling constants (1)J(N,H(i)) could also be determined accurately.

  7. The 2D method for determining the temperatures field of the gas flow at the outlet of a multi-channel heat exchanger

    NASA Astrophysics Data System (ADS)

    Slesareva, E. Yu; Elistratov, S. L.; Ovchinnikov, V. V.

    2016-10-01

    The method for experimental determination of energy efficiency in the multichannel heat exchanger was tested. The visualization of a temperatures field has been performed to determine the thermal structure of gas flows with the use of fast-response fine- meshed wire. Thermograms of the temperature fields of the multi-channels assembly at the outlet were registered by thermal imaging camera. Results show that the 2D method provides a sufficient time resolution for the temperature field for the steady-state gas flow regime, heat generation, and nonsteady regime. The 2D method allows us to determine the gas stream parameters at the channel outlet in real time, which are necessary for determining the efficiency of the heat exchanger. Qualitative and quantitative characters of temperature changes in the thermograms are consistent with modern physical understanding of the gas flow in channels.

  8. 1H and 15N NMR Analyses on Heparin, Heparan Sulfates and Related Monosaccharides Concerning the Chemical Exchange Regime of the N-Sulfo-Glucosamine Sulfamate Proton

    PubMed Central

    Pomin, Vitor H.

    2016-01-01

    Heparin and heparan sulfate are structurally related glycosaminoglycans (GAGs). Both GAGs present, although in different concentrations, N-sulfo-glucosamine (GlcNS) as one of their various composing units. The conditional fast exchange property of the GlcNS sulfamate proton in these GAGs has been pointed as the main barrier to its signal detection via NMR experiments, especially 1H-15N HSQC. Here, a series of NMR spectra is collected on heparin, heparan sulfate and related monosaccharides. The N-acetyl glucosamine-linked uronic acid types of these GAGs were properly assigned in the 1H-15N HSQC spectra. Dynamic nuclear polarization (DNP) was employed in order to facilitate 1D spectral acquisition of the sulfamate 15N signal of free GlcNS. Analyses on the multiplet pattern of scalar couplings of GlcNS 15N has helped to understand the chemical properties of the sulfamate proton in solution. The singlet peak observed for GlcNS happens due to fast chemical exchange of the GlcNS sulfamate proton in solution. Analyses on kinetics of alpha-beta anomeric mutarotation via 1H NMR spectra have been performed in GlcNS as well as other glucose-based monosaccharides. 1D 1H and 2D 1H-15N HSQC spectra recorded at low temperature for free GlcNS dissolved in a proton-rich solution showed signals from all exchangeable protons, including those belonging to the sulfamate group. This work suits well to the current grand celebration of one-century-anniversary of the discovery of heparin. PMID:27618066

  9. Cryogenic sample exchange NMR probe for magic angle spinning dynamic nuclear polarization

    PubMed Central

    Barnes, Alexander B.; Mak-Jurkauskas, Melody L.; Matsuki, Yoh; Bajaj, Vikram S.; van der Wel, Patrick C. A.; DeRocher, Ronald; Bryant, Jeffrey; Sirigiri, Jagadishwar R.; Temkin, Richard J.; Lugtenburg, Johan; Herzfeld, Judith; Griffin, Robert G.

    2009-01-01

    We describe a cryogenic sample exchange system that dramatically improves the efficiency of magic angle spinning (MAS) dynamic nuclear polarization (DNP) experiments by reducing the time required to change samples and by improving long-term instrument stability. Changing samples in conventional cryogenic MAS DNP/NMR experiments involves warming the probe to room temperature, detaching all cryogenic, RF, and microwave connections, removing the probe from the magnet, replacing the sample, and reversing all the previous steps, with the entire cycle requiring a few hours. The sample exchange system described here — which relies on an eject pipe attached to the front of the MAS stator and a vacuum jacketed dewar with a bellowed hole — circumvents these procedures. To demonstrate the excellent sensitivity, resolution, and stability achieved with this quadruple resonance sample exchange probe, we have performed high precision distance measurements on the active site of the membrane protein bacteriorhodopsin. We also include a spectrum of the tripeptide N-f-MLF-OH at 100 K which shows 30 Hz linewidths. PMID:19356957

  10. Cryogenic sample exchange NMR probe for magic angle spinning dynamic nuclear polarization.

    PubMed

    Barnes, Alexander B; Mak-Jurkauskas, Melody L; Matsuki, Yoh; Bajaj, Vikram S; van der Wel, Patrick C A; Derocher, Ronald; Bryant, Jeffrey; Sirigiri, Jagadishwar R; Temkin, Richard J; Lugtenburg, Johan; Herzfeld, Judith; Griffin, Robert G

    2009-06-01

    We describe a cryogenic sample exchange system that dramatically improves the efficiency of magic angle spinning (MAS) dynamic nuclear polarization (DNP) experiments by reducing the time required to change samples and by improving long-term instrument stability. Changing samples in conventional cryogenic MAS DNP/NMR experiments involves warming the probe to room temperature, detaching all cryogenic, RF, and microwave connections, removing the probe from the magnet, replacing the sample, and reversing all the previous steps, with the entire cycle requiring a few hours. The sample exchange system described here-which relies on an eject pipe attached to the front of the MAS stator and a vacuum jacketed dewar with a bellowed hole-circumvents these procedures. To demonstrate the excellent sensitivity, resolution, and stability achieved with this quadruple resonance sample exchange probe, we have performed high precision distance measurements on the active site of the membrane protein bacteriorhodopsin. We also include a spectrum of the tripeptide N-f-MLF-OH at 100K which shows 30 Hz linewidths.

  11. Synthesis and Resolution of the Atropisomeric 1,1'-Bi-2-Naphthol: An Experiment in Organic Synthesis and 2-D NMR Spectroscopy

    ERIC Educational Resources Information Center

    Mak, Kendrew K. W.

    2004-01-01

    NMR spectroscopy is presented. It is seen that the experiment regarding the synthesis and resolution of 1,1'-Bi-2-naphtol presents a good experiment for teaching organic synthesis and NMR spectroscopy and provides a strategy for obtaining enantiopure compounds from achiral starting materials.

  12. Implications of using approximate Bloch-McConnell equations in NMR analyses of chemically exchanging systems: application to the electron self-exchange of plastocyanin.

    PubMed

    Hansen, D Flemming; Led, Jens J

    2003-08-01

    The validity of a series of approximate solutions of the Bloch-McConnell equations normally applied in the analyses of chemically exchanging systems is evaluated, using the electron self-exchange (ESE) in the blue copper protein plastocyanin from Anabaena variabilis as an example. The evaluation is based on a comparison with the results of a complete analysis of the NMR signals of chemically exchanging nuclei that allows an independent and accurate determination of all the involved parameters. The complete analysis is based on the general solution of the Bloch-McConnell equations. It includes a simultaneous analysis of the chemical shift, and the transverse and longitudinal relaxation rates of the observed nuclei as well as the variation of these parameters with the molar fractions of the exchanging species and the rate of the chemical exchange process. The linear prediction model method was used in the data analysis to achieve the highest possible precision. Surprisingly, it is found that the fast exchange condition may not be fulfilled even in cases where a single exchange-averaged NMR signal is observed, and the Larmor frequency and relaxation rates depend linearly on the molar fractions of the exchanging species. In such cases the use of approximate solutions in the analysis of the transverse relaxation rates and the pseudo-contact shifts can lead to erroneous results. In limiting cases close to the fast exchange and slow exchange regimes correct values of some of the parameters can be obtained using the second order approximate solution of the Bloch-McConnell equations. In contrast, the complete analysis of the NMR signals results in an accurate determination of the exchange rates and the NMR parameters of the exchanging sites. This, in turn, can provide information about the structure and function of a protein undergoing chemically exchange. For the investigated plastocyanin the complete analysis results in an accurate determination of the paramagnetic

  13. Rapid Determination of Fast Protein Dynamics from NMR Chemical Exchange Saturation Transfer Data.

    PubMed

    Gu, Yina; Hansen, Alexandar L; Peng, Yu; Brüschweiler, Rafael

    2016-02-24

    Functional motions of (15)N-labeled proteins can be monitored by solution NMR spin relaxation experiments over a broad range of timescales. These experiments however typically take of the order of several days to a week per protein. Recently, NMR chemical exchange saturation transfer (CEST) experiments have emerged to probe slow millisecond motions complementing R1ρ and CPMG-type experiments. CEST also simultaneously reports on site-specific R1 and R2 parameters. It is shown here how CEST-derived R1 and R2 relaxation parameters can be measured within a few hours at an accuracy comparable to traditional relaxation experiments. Using a "lean" version of the model-free approach S(2) order parameters can be determined that match those from the standard model-free approach applied to (15)N R1, R2 , and {(1)H}-(15)N NOE data. The new methodology, which is demonstrated for ubiquitin and arginine kinase (42 kDa), should serve as an effective screening tool of protein dynamics from picosecond-to-millisecond timescales.

  14. Dynamic NMR of Intramolecular Exchange Processes in EDTA Complexes of Sc[superscript 3+], Y[superscript 3+], and La[superscript 3+

    ERIC Educational Resources Information Center

    Ba, Yong; Han, Steven; Ni, Lily; Su, Tony; Garcia, Andres

    2006-01-01

    Dynamic NMR makes use of the effect of chemical exchanges on NMR spectra to study kinetics and thermodynamics. An advanced physical chemistry lab experiment was developed to study the intramolecular exchange processes of EDTA (the disodium salt of ethylenediaminetetraacetic acid) metal complexes. EDTA is an important chelating agent, used in…

  15. Effects of island-edge exchange barrier on 2D pattern formation in surfactant-mediated epitaxy

    NASA Astrophysics Data System (ADS)

    Wang, Dai-mu; Sun, Xia; Wu, Zi-qin

    2001-11-01

    The nucleation and growth of two-dimensional islands in a surfactant-mediated epitaxy system have been studied by computer simulation. To improve the recent results published in the literature, we use a configuration-dependent energy barrier for the exchange process at the island edge in our model. The simulations produce fractal islands at high temperatures or low deposition fluxes and a transition to regular compact islands occurs at lower temperatures or higher fluxes, in good agreement with the recent experimental results. The barrier for the island-edge exchange has quite a strong effect on the island density as a function of temperature and flux. A small change of the island-edge exchange barrier induces a large variation of the island density in the low-temperature or high-flux region. The flux-dependent island density shows a clear scaling-law behaviour in the intermediate-flux region. The scaling exponent increases evidently as the island-edge exchange barrier increases.

  16. Synthesizing 2D MoS2 Nanofins on carbon nanospheres as catalyst support for Proton Exchange Membrane Fuel Cells

    NASA Astrophysics Data System (ADS)

    Hu, Yan; Chua, Daniel H. C.

    2016-06-01

    Highly dense 2D MoS2 fin-like nanostructures on carbon nanospheres were fabricated and formed the main catalyst support structure in the oxygen reduction reaction (ORR) for polymer electrolyte membrane (PEM) fuel cells. These nanofins were observed growing perpendicular to the carbon nanosphere surface in random orientations and high resolution transmission electron microscope confirmed 2D layers. The PEM fuel cell test showed enhanced electrochemical activity with good stability, generating over 8.5 W.mgPt‑1 as compared to standard carbon black of 7.4 W.mgPt‑1 under normal operating conditions. Electrochemical Impedance Spectroscopy confirmed that the performance improvement is highly due to the excellent water management of the MoS2 lamellar network, which facilitates water retention at low current density and flood prevention at high current density. Reliability test further demonstrated that these nanofins are highly stable in the electrochemical reaction and is an excellent ORR catalyst support.

  17. Synthesizing 2D MoS2 Nanofins on carbon nanospheres as catalyst support for Proton Exchange Membrane Fuel Cells

    PubMed Central

    Hu, Yan; Chua, Daniel H. C.

    2016-01-01

    Highly dense 2D MoS2 fin-like nanostructures on carbon nanospheres were fabricated and formed the main catalyst support structure in the oxygen reduction reaction (ORR) for polymer electrolyte membrane (PEM) fuel cells. These nanofins were observed growing perpendicular to the carbon nanosphere surface in random orientations and high resolution transmission electron microscope confirmed 2D layers. The PEM fuel cell test showed enhanced electrochemical activity with good stability, generating over 8.5 W.mgPt−1 as compared to standard carbon black of 7.4 W.mgPt−1 under normal operating conditions. Electrochemical Impedance Spectroscopy confirmed that the performance improvement is highly due to the excellent water management of the MoS2 lamellar network, which facilitates water retention at low current density and flood prevention at high current density. Reliability test further demonstrated that these nanofins are highly stable in the electrochemical reaction and is an excellent ORR catalyst support. PMID:27302135

  18. The effect of N2/+/ recombination on the aeronomic determination of the charge exchange rate coefficient of O/+//2D/ with N2

    NASA Technical Reports Server (NTRS)

    Torr, D. G.; Orsini, N.

    1978-01-01

    The Atmosphere Explorer (AE) data are reexamined in the light of new laboratory measurements of the N2(+) recombination rate coefficient alpha. The new measurements support earlier measurements which yielded values of alpha significantly lower than the AE values. It is found that the values for alpha determined from the satellite data can be reconciled with the laboratory measurements, if the charge exchange rate coefficient for O(+)(2D) with N2 is less than one-quarter of that derived in the laboratory by Rutherford and Vroom (1971).

  19. NMR study of the exchange coupling in the trinuclear cluster of the multicopper oxidase Fet3p

    PubMed Central

    Zaballa, María-Eugenia; Ziegler, Lynn; Kosman, Daniel J.; Vila, Alejandro J.

    2010-01-01

    Fet3p from Saccharomyces cerevisiae is a multicopper oxidase (MCO) which oxidizes Fe2+ to Fe3+. The electronic structure of the different copper centers in this family of enzymes has been extensively studied and discussed for years with a particular focus on the exchange coupling regime in the trinuclear cluster (TNC). Using NMR spectroscopy we have quantified the exchange coupling constant in the type 3 center in a fully metallated oxidase; this value in Fet3p is significantly higher than that reported for proteins containing isolated type 3 centers as in tyrosinase. We also provide evidence of exchange coupling between the type 2 and the type 3 Cu2+ ions, which supports the crystallographic evidence of dioxygen binding to the TNC. This work provides the foundation for the application of NMR to these complex systems. PMID:20698686

  20. Characterizing mixed phosphonic acid ligand capping on CdSe/ZnS quantum dots using ligand exchange and NMR spectroscopy.

    PubMed

    Davidowski, Stephen K; Lisowski, Carmen E; Yarger, Jeffery L

    2016-03-01

    The ligand capping of phosphonic acid functionalized CdSe/ZnS core-shell quantum dots (QDs) was investigated with a combination of solution and solid-state (31) P nuclear magnetic resonance (NMR) spectroscopy. Two phosphonic acid ligands were used in the synthesis of the QDs, tetradecylphosphonic acid and ethylphosphonic acid. Both alkyl phosphonic acids showed broad liquid and solid-state (31) P NMR resonances for the bound ligands, indicative of heterogeneous binding to the QD surface. In order to quantify the two ligand populations on the surface, ligand exchange facilitated by phenylphosphonic acid resulted in the displacement of the ethylphosphonic acid and tetradecylphosphonic acid and allowed for quantification of the free ligands using (31) P liquid-state NMR. After washing away the free ligand, two broad resonances were observed in the liquids' (31) P NMR corresponding to the alkyl and aromatic phosphonic acids. The washed samples were analyzed via solid-state (31) P NMR, which confirmed the ligand populations on the surface following the ligand exchange process. Copyright © 2015 John Wiley & Sons, Ltd.

  1. Hyporheic Exchange: Analysis of Aquifer Heterogeneity, Channel Morphology and Bedforms- 2D and 3D Simulations Using MODFLOW and MODPATH

    NASA Astrophysics Data System (ADS)

    Matos, J. R.; Welty, C.; Packman, A.

    2005-12-01

    The main purpose of the simulations in this research is the analysis of three-dimensional surface-groundwater interchange in heterogeneous systems. The effects of channel pattern, bed forms and aquifer heterogeneity on flow interactions between stream and groundwater systems are examined in order to contribute for a better understanding of the hyporheic process. A two-dimensional approach was also adopted to allow comparisons with the three-dimensional results. The grid was designed using the correlation scales of the heterogeneous fields and the scale of the stream meanders. MODFLOW and MODPATH were used to evaluate magnitude, direction and spatial distribution of the exchange flow. PMWIN and PMPATH were used as pre and post-processors during the construction of the models and analysis of results. Gaining and losing streams as well as parallel flow and flow across streams were simulated as idealized cases intended to describe how properties of the streambed and aquifer in low-gradient lowland streams contribute to hyporheic exchange. At first a straight river was analyzed then meandering streams were created with a sine curve and variations on wavelength and amplitude. Bed forms were simulated assuming a sinusoidal distribution of pressure head in the bed surface. Aspects of the influence of bedforms on mechanisms such as "pumping" and "turnover" are expected to be addressed with simulations. Flow velocities between 20 and 40 cm/s in the channel were tested with the objective of showing the influence of river morphology and natural bed forms on the flow exchange in the hyporheic zone. Several meander cycles and four levels of hydraulic conductivity variance were analyzed. Results of flow variances along the cross-sections and wetted perimeter show the increasing on hyporheic exchange as the degree of heterogeneity increases. Particle tracking was performed to define hyporheic residence time distributions. When comparing the homogeneous fields with all degrees of

  2. Mass-dependent dynamics of the luminescent exchange reactions C+(2P), P+(3P) + H2, D2, HD

    NASA Astrophysics Data System (ADS)

    Glenewinkel-Meyer, Th; Hoppe, U.; Kowalski, A.; Ottinger, Ch; Rabenda, D.

    1995-06-01

    Chemiluminescent ion/molecule reactions of ground state C+ and P+ ions with H2, D2 and HD have been studied in an ion beam/target gas cell arrangement. Emission spectra of CH+, CD+ (A 1II) and of PH+, PD+ (A 2[Delta]) were observed with up to 1 Å FWHM resolution and at collision energies from threshold ([approximate] 3 eV) to 8 eVc.m. (centre-of-mass) and 15eVc.m., respectively. Very detailed computer simulations of the spectral contours were done, including ab initio transition moments and, in the case of PH+/PD+, the effects of predissociation. In simulating the spectra obtained with HD, the overlapped hydride and deuteride product ion spectra could be isolated by varying the respective weighting factors to achieve an optimum overall fit. In the case of C+ + HD, the two components were found to have very similar rovibrational distributions as with the products from C+ + H2 and C+ + D2. In the P+ case, however, the rotational, although not the vibrational, distributions were found to be significantly different for the isotopically mixed and the pure reactions. The cross-sections showed an intermolecular isotope effect only for C+ + H2 vs. C+ + D2 at high energies. However, both with C+ + HD and P+ + HD, a very strong intramolecular isotope effect, i.e. an energy-dependent branching ratio, was observed: at low energies deuteride formation prevails, at high energies hydride. This behaviour is discussed in terms of an impulsive collision model, assuming the "pairwise" relative kinetic energy between the reacting atoms to be the determining factor. On the basis of the measured cross-section curves for the H2 and D2 reactions, the energy-dependent hydride/deuteride ratio in the HD reaction can then be predicted. The agreement with the experimental results is excellent in the P+ case, but only moderate for the C+ reactions. Even the P+ reaction, however, does not occur via the spectator stripping mechanisms. The spectra show an energy-independent vibrational excitation

  3. NMR longitudinal relaxation enhancement in metal halides by heteronuclear polarization exchange during magic-angle spinning.

    PubMed

    Shmyreva, Anna A; Safdari, Majid; Furó, István; Dvinskikh, Sergey V

    2016-06-14

    Orders of magnitude decrease of (207)Pb and (199)Hg NMR longitudinal relaxation times T1 upon magic-angle-spinning (MAS) are observed and systematically investigated in solid lead and mercury halides MeX2 (Me = Pb, Hg and X = Cl, Br, I). In lead(ii) halides, the most dramatic decrease of T1 relative to that in a static sample is in PbI2, while it is smaller but still significant in PbBr2, and not detectable in PbCl2. The effect is magnetic-field dependent but independent of the spinning speed in the range 200-15 000 Hz. The observed relaxation enhancement is explained by laboratory-frame heteronuclear polarization exchange due to crossing between energy levels of spin-1/2 metal nuclei and adjacent quadrupolar-spin halogen nuclei. The enhancement effect is also present in lead-containing organometal halide perovskites. Our results demonstrate that in affected samples, it is the relaxation data recorded under non-spinning conditions that characterize the local properties at the metal sites. A practical advantage of fast relaxation at slow MAS is that spectral shapes with orientational chemical shift anisotropy information well retained can be acquired within a shorter experimental time.

  4. NMR longitudinal relaxation enhancement in metal halides by heteronuclear polarization exchange during magic-angle spinning

    NASA Astrophysics Data System (ADS)

    Shmyreva, Anna A.; Safdari, Majid; Furó, István; Dvinskikh, Sergey V.

    2016-06-01

    Orders of magnitude decrease of 207Pb and 199Hg NMR longitudinal relaxation times T1 upon magic-angle-spinning (MAS) are observed and systematically investigated in solid lead and mercury halides MeX2 (Me = Pb, Hg and X = Cl, Br, I). In lead(ii) halides, the most dramatic decrease of T1 relative to that in a static sample is in PbI2, while it is smaller but still significant in PbBr2, and not detectable in PbCl2. The effect is magnetic-field dependent but independent of the spinning speed in the range 200-15 000 Hz. The observed relaxation enhancement is explained by laboratory-frame heteronuclear polarization exchange due to crossing between energy levels of spin-1/2 metal nuclei and adjacent quadrupolar-spin halogen nuclei. The enhancement effect is also present in lead-containing organometal halide perovskites. Our results demonstrate that in affected samples, it is the relaxation data recorded under non-spinning conditions that characterize the local properties at the metal sites. A practical advantage of fast relaxation at slow MAS is that spectral shapes with orientational chemical shift anisotropy information well retained can be acquired within a shorter experimental time.

  5. Molecular Engineering of Liquid Crystal Polymers by Living Polymerization. 17. Characterization of Poly(10-((4-Cyano-4’-Biphenyl)oxy) decanyl Vinyl Ether)s by 1-D and 2-D H-NMR Spectroscopy

    DTIC Science & Technology

    1991-10-30

    Spectroscopy by Virril Percec and Myongsoo Lee Department of Macromolecular Science Case Western Reserve University Cleveland, OH 44106-2699 and Peter L ...AUTHOrZ(S) Virgil Percec, Myongsoo Lee, Peter L . Rinaldi and Vincent E. Litman l3a TYPE OF REPORT 1131) TIME COVERED 14. DATE OF REPORT (Year. Afot? Dy I...with CF3SO 3 H/S(CH 3)2 in CH2Cl2 at 0OC and termninated by ammoniacal methanol, by 1 -D and 2-D (COSY) 300 MHz IH-NMR spectroscopy is presented. The

  6. Structure and Metabolic-Flow Analysis of Molecular Complexity in a (13) C-Labeled Tree by 2D and 3D NMR.

    PubMed

    Komatsu, Takanori; Ohishi, Risa; Shino, Amiu; Kikuchi, Jun

    2016-05-10

    Improved signal identification for biological small molecules (BSMs) in a mixture was demonstrated by using multidimensional NMR on samples from (13) C-enriched Rhododendron japonicum (59.5 atom%) cultivated in air containing (13) C-labeled carbon dioxide for 14 weeks. The resonance assignment of 386 carbon atoms and 380 hydrogen atoms in the mixture was achieved. 42 BSMs, including eight that were unlisted in the spectral databases, were identified. Comparisons between the experimental values and the (13) C chemical shift values calculated by density functional theory supported the identifications of unlisted BSMs. Tracing the (13) C/(12) C ratio by multidimensional NMR spectra revealed faster and slower turnover ratios of BSMs involved in central metabolism and those categorized as secondary metabolites, respectively. The identification of BSMs and subsequent flow analysis provided insight into the metabolic systems of the plant.

  7. 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.

  8. WHNMR--a universal NMR application package.

    PubMed

    Xiaodong, Z; Hongbin, H; Nian, H; Lianfang, S; Chaohui, Y

    1996-06-01

    A PC-based NMR off-line data processing system is developed and described in detail. With this software system, one-dimensional (1D), two-dimensional (2D), and NMR imaging (MRI) data can be processed easily, and give reliable results. By the applications of this system, a versatile software interface is set up to achieve data exchanging and integrated usage with other PC application software and aids the PC to become an effective and powerful workstation.

  9. Amide proton exchange rates of a bound pepsin inhibitor determined by isotope-edited proton NMR experiments

    SciTech Connect

    Fesik, S.W.; Luly, J.R.; Stein, H.H.; BaMaung, N.

    1987-09-30

    From a series of isotope-edited proton NMR spectra, amide proton exchange rates were measured at 20 C, 30 C, and 40/sup 0/C for a tightly bound /sup 15/N-labeled tripeptide inhibitor of porcine pepsin (IC50 = 1.7 X 10(-) M). Markedly different NH exchange rates were observed for the three amide protons of the bound inhibitor. The P1 NH exchanged much more slowly than the P2 NH and P3 NH. These results are discussed in terms of the relative solvent accessibility in the active site and the role of the NH protons of the inhibitor for hydrogen bonding to the enzyme. In this study a useful approach is demonstrated for obtaining NH exchange rates on ligands bound to biomacromolecules, the knowledge of which could be of potential utility in the design of therapeutically useful nonpeptide enzyme inhibitors from peptide leads.

  10. Quenched hydrogen-deuterium exchange NMR of a disease-relevant Aβ(1-42) amyloid polymorph

    PubMed Central

    Wälti, Marielle Aulikki; Orts, Julien; Riek, Roland

    2017-01-01

    Alzheimer’s disease is associated with the aggregation into amyloid fibrils of Aβ(1–42) and Aβ(1–40) peptides. Interestingly, these fibrils often do not obtain one single structure but rather show different morphologies, so-called polymorphs. Here, we compare quenched hydrogen-deuterium (H/D) exchange of a disease-relevant Aβ(1–42) fibril for which the 3D structure has been determined by solid-state NMR with H/D exchange previously determined on another structural polymorph. This comparison reveals secondary structural differences between the two polymorphs suggesting that the two polymorphisms can be classified as segmental polymorphs. PMID:28319116

  11. Efficient 2D MRI relaxometry using compressed sensing

    NASA Astrophysics Data System (ADS)

    Bai, Ruiliang; Cloninger, Alexander; Czaja, Wojciech; Basser, Peter J.

    2015-06-01

    Potential applications of 2D relaxation spectrum NMR and MRI to characterize complex water dynamics (e.g., compartmental exchange) in biology and other disciplines have increased in recent years. However, the large amount of data and long MR acquisition times required for conventional 2D MR relaxometry limits its applicability for in vivo preclinical and clinical MRI. We present a new MR pipeline for 2D relaxometry that incorporates compressed sensing (CS) as a means to vastly reduce the amount of 2D relaxation data needed for material and tissue characterization without compromising data quality. Unlike the conventional CS reconstruction in the Fourier space (k-space), the proposed CS algorithm is directly applied onto the Laplace space (the joint 2D relaxation data) without compressing k-space to reduce the amount of data required for 2D relaxation spectra. This framework is validated using synthetic data, with NMR data acquired in a well-characterized urea/water phantom, and on fixed porcine spinal cord tissue. The quality of the CS-reconstructed spectra was comparable to that of the conventional 2D relaxation spectra, as assessed using global correlation, local contrast between peaks, peak amplitude and relaxation parameters, etc. This result brings this important type of contrast closer to being realized in preclinical, clinical, and other applications.

  12. Resolution-optimized NMR measurement of (1)D(CH), (1)D(CC) and (2)D(CH) residual dipolar couplings in nucleic acid bases.

    PubMed

    Boisbouvier, Jérôme; Bryce, David L; O'neil-Cabello, Erin; Nikonowicz, Edward P; Bax, Ad

    2004-11-01

    New methods are described for accurate measurement of multiple residual dipolar couplings in nucleic acid bases. The methods use TROSY-type pulse sequences for optimizing resolution and sensitivity, and rely on the E.COSY principle to measure the relatively small two-bond (2)D(CH) couplings at high precision. Measurements are demonstrated for a 24-nt stem-loop RNA sequence, uniformly enriched in (13)C, and aligned in Pf1. The recently described pseudo-3D method is used to provide homonuclear (1)H-(1)H decoupling, which minimizes cross-correlation effects and optimizes resolution. Up to seven (1)H-(13)C and (13)C-(13)C couplings are measured for pyrimidines (U and C), including (1)D(C5H5), (1)D(C6H6), (2)D(C5H6), (2)D(C6H5), (1)D(C5C4), (1)D(C5C6), and (2)D(C4H5). For adenine, four base couplings ((1)D(C2H2), (1)D(C8H8), (1)D(C4C5), and (1)D(C5C6)) are readily measured whereas for guanine only three couplings are accessible at high relative accuracy ((1)D(C8H8), (1)D(C4C5), and (1)D(C5C6)). Only three dipolar couplings are linearly independent in planar structures such as nucleic acid bases, permitting cross validation of the data and evaluation of their accuracies. For the vast majority of dipolar couplings, the error is found to be less than +/-3% of their possible range, indicating that the measurement accuracy is not limiting when using these couplings as restraints in structure calculations. Reported isotropic values of the one- and two-bond J couplings cluster very tightly for each type of nucleotide.

  13. Solution structure of the 45-residue MgATP-binding peptide of adenylate kinase as examined by 2-D NMR, FTIR, and CD spectroscopy.

    PubMed

    Fry, D C; Byler, D M; Susi, H; Brown, E M; Kuby, S A; Mildvan, A S

    1988-05-17

    The structure of a synthetic peptide corresponding to residues 1-45 of rabbit muscle adenylate kinase has been studied in aqueous solution by two-dimensional NMR, FTIR, and CD spectroscopy. This peptide, which binds MgATP and is believed to represent most of the MgATP-binding site of the enzyme [Fry, D.C., Kuby, S.A., & Mildvan, A.S. (1985) Biochemistry 24, 4680-4694], appears to maintain a conformation similar to that of residues 1-45 in the X-ray structure of intact porcine adenylate kinase [Sachsenheimer, W., & Schulz, G.E. (1977) J. Mol. Biol. 114, 23-26], with 42% of the residues of the peptide showing NOEs indicative of phi and psi angles corresponding to those found in the protein. The NMR studies suggest that the peptide is composed of two helical regions of residues 4-7 and 23-29, and three stretches of beta-strand at residues 8-15, 30-32, and 35-40, yielding an overall secondary structure consisting of 24% alpha-helix, 38% beta-structure, and 38% aperiodic. Although the resolution-enhanced amide I band of the peptide FTIR spectrum is broad and rather featureless, possibly due to disorder, it can be fit by using methods developed on well-characterized globular proteins. On this basis, the peptide consists of 35 +/- 10% beta-structure, 60 +/- 12% turns and aperiodic structure, and not more than 10% alpha-helix. The CD spectrum is best fit by assuming the presence of at most 13% alpha-helix in the peptide, 24 +/- 2% beta-structure, and 66 +/- 4% aperiodic. The inability of the high-frequency FTIR and CD methods to detect helices in the amount found by NMR may result from the short helical lengths as well as from static and dynamic disorder in the peptide. Upon binding of MgATP, numerous conformational changes in the backbone of the peptide are detected by NMR, with smaller alterations in the overall secondary structure as assessed by CD. Detailed assignments of resonances in the peptide spectrum and intermolecular NOEs between protons of bound MgATP and

  14. Novel stilbene-based Fischer base analog of leuco-TAM - (2E,2'Z)-{2-(4-(E)-styrylphenyl)propane-1,3-diylidene}bis(1,3,3-trimethylindoline) - derivatives: synthesis and structural consideration by 1D NMR and 2D NMR spectroscopy.

    PubMed

    Keum, Sam-Rok; Lim, Hyun-Woo

    2016-02-01

    We report the synthesis of a series of novel stilbene-based (St) Fischer base analogs of leuco-triarylmethane (LTAM) dyes by treating Fischer base with (E)-4-styrylbenzaldehyde derivatives. All St-LTAM molecules examined herein are characterized by 1D and 2D NMR. They were found to exhibit ZE configuration and isomerize to their diastereomers EE and ZZ in 2-3 h. They exhibit type I behavior of diastereomeric isomerization.

  15. (13)CHD2-CEST NMR spectroscopy provides an avenue for studies of conformational exchange in high molecular weight proteins.

    PubMed

    Rennella, Enrico; Huang, Rui; Velyvis, Algirdas; Kay, Lewis E

    2015-10-01

    An NMR experiment for quantifying slow (millisecond) time-scale exchange processes involving the interconversion between visible ground state and invisible, conformationally excited state conformers is presented. The approach exploits chemical exchange saturation transfer (CEST) and makes use of (13)CHD2 methyl group probes that can be readily incorporated into otherwise highly deuterated proteins. The methodology is validated with an application to a G48A Fyn SH3 domain that exchanges between a folded conformation and a sparsely populated and transiently formed unfolded ensemble. Experiments on a number of different protein systems, including a 360 kDa half-proteasome, establish that the sensitivity of this (13)CHD2 (13)C-CEST technique can be upwards of a factor of 5 times higher than for a previously published (13)CH3 (13)C-CEST approach (Bouvignies and Kay in J Biomol NMR 53:303-310, 2012), suggesting that the methodology will be powerful for studies of conformational exchange in high molecular weight proteins.

  16. Fluorine detected 2D NMR experiments for the practical determination of size and sign of homonuclear F-F and heteronuclear C-F multiple bond J-coupling constants in multiple fluorinated compounds.

    PubMed

    Aspers, Ruud L E G; Ampt, Kirsten A M; Dvortsak, Peter; Jaeger, Martin; Wijmenga, Sybren S

    2013-06-01

    The use of fluorine in molecules obtained from chemical synthesis has become increasingly important within the pharmaceutical and agricultural industry. NMR characterization of these compounds is of great value with respect to their structure elucidation, their screening in metabolomics investigations and binding studies. The favorable NMR properties of the fluorine nucleus make NMR with fluorine detection of great value in this respect. A suite of NMR 2D F-F- and F-C-correlation experiments with fluorine detection was applied to the assignment of resonances, (n)J(CF)- and (n)J(FF)-couplings as well as the determination of their size and sign. The utilization of this experiment suite was exemplarily demonstrated for a highly fluorinated vinyl alkyl ether. Especially F-C HSQC and J-scaled F-C HMBC experiments allowed determining the size of the J-couplings of this compound. The relative sign of its homo- and heteronuclear couplings was achieved by different combinations of 2D NMR experiments, including non-selective and F2-selective F-C XLOC, F2-selective F-C HMQC, and F-F COSY. The F2-one/two-site selective F-C XLOC versions were found highly useful, as they led to simplifications of the common E.COSY patterns and resulted in a higher confidence level of the assignment by using selective excitation. The combination of F2-one/two-site selective F-C XLOC experiments with a F2-one-site selective F-C HMQC experiment provided the signs of all (n)J(CF)- and (n)J(FF)-couplings in the vinyl moiety of the test compound. Other combinations of experiments were found useful as well for special purposes when focusing for example on homonuclear couplings a combination of F-F COSY-10 with a F2-one-site selective F-C HMQC could be used. The E.COSY patterns in the spectra demonstrated were analyzed by use of the spin-selective displacement vectors, and in case of the XLOC also by use of the DQ- and ZQ-displacement vectors. The variety of experiments presented shall contribute to

  17. 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.

  18. 31P NMR 2D Mapping of Creatine Kinase Forward Flux Rate in Hearts with Postinfarction Left Ventricular Remodeling in Response to Cell Therapy

    PubMed Central

    Gao, Ling; Cui, Weina; Zhang, Pengyuan; Jang, Albert; Zhu, Wuqiang; Zhang, Jianyi

    2016-01-01

    Utilizing a fast 31P magnetic resonance spectroscopy (MRS) 2-dimensional chemical shift imaging (2D-CSI) method, this study examined the heterogeneity of creatine kinase (CK) forward flux rate of hearts with postinfarction left ventricular (LV) remodeling. Immunosuppressed Yorkshire pigs were assigned to 4 groups: 1) A sham-operated normal group (SHAM, n = 6); 2) A 60 minutes distal left anterior descending coronary artery ligation and reperfusion (MI, n = 6); 3) Open patch group; ligation injury plus open fibrin patch over the site of injury (Patch, n = 6); and 4) Cell group, hiPSCs-cardiomyocytes, -endothelial cells, and -smooth muscle cells (2 million, each) were injected into the injured myocardium pass through a fibrin patch (Cell+Patch, n = 5). At 4 weeks, the creatine phosphate (PCr)/ATP ratio, CK forward flux rate (Flux PCr→ATP), and k constant of CK forward flux rate (kPCr→ATP) were severely decreased at border zone myocardium (BZ) adjacent to MI. Cell treatment results in significantly increase of PCr/ATP ratio and improve the value of kPCr→ATP and Flux PCr→ATP in BZ myocardium. Moreover, the BZ myocardial CK total activity and protein expression of CK mitochondria isozyme and CK myocardial isozyme were significantly reduced, but recovered in response to cell treatment. Thus, cell therapy results in improvement of BZ bioenergetic abnormality in hearts with postinfarction LV remodeling, which is accompanied by significantly improvements in BZ CK activity and CK isozyme expression. The fast 2D 31P MR CSI mapping can reliably measure the heterogeneity of bioenergetics in hearts with post infarction LV remodeling. PMID:27606901

  19. Analysis of local molecular motions of aromatic sidechains in proteins by 2D and 3D fast MAS NMR spectroscopy and quantum mechanical calculations.

    PubMed

    Paluch, Piotr; Pawlak, Tomasz; Jeziorna, Agata; Trébosc, Julien; Hou, Guangjin; Vega, Alexander J; Amoureux, Jean-Paul; Dracinsky, Martin; Polenova, Tatyana; Potrzebowski, Marek J

    2015-11-21

    We report a new multidimensional magic angle spinning NMR methodology, which provides an accurate and detailed probe of molecular motions occurring on timescales of nano- to microseconds, in sidechains of proteins. The approach is based on a 3D CPVC-RFDR correlation experiment recorded under fast MAS conditions (ν(R) = 62 kHz), where (13)C-(1)H CPVC dipolar lineshapes are recorded in a chemical shift resolved manner. The power of the technique is demonstrated in model tripeptide Tyr-(d)Ala-Phe and two nanocrystalline proteins, GB1 and LC8. We demonstrate that, through numerical simulations of dipolar lineshapes of aromatic sidechains, their detailed dynamic profile, i.e., the motional modes, is obtained. In GB1 and LC8 the results unequivocally indicate that a number of aromatic residues are dynamic, and using quantum mechanical calculations, we correlate the molecular motions of aromatic groups to their local environment in the crystal lattice. The approach presented here is general and can be readily extended to other biological systems.

  20. Magnetic structure and domain conversion of the quasi-2D frustrated antiferromagnet CuCrO{sub 2} probed by NMR

    SciTech Connect

    Sakhratov, Yu. A.; Svistov, L. E.; Kuhns, P. L.; Zhou, H. D.; Reyes, A. P.

    2014-11-15

    We have carried out {sup 63,65}Cu NMR spectra measurements in a magnetic field up to about 15.5 T on a single crystal of the multiferroic triangular-lattice antiferromagnet CuCrO{sub 2}. The measurements were performed for perpendicular and parallel orientations of the magnetic field with respect to the c axis of the crystal, and the detailed angle dependence of the spectra on the magnetic field direction in the ab plane was studied. The shape of the spectra can be well described in the model of spiral spin structure proposed by recent neutron diffraction experiments. When the field is rotated perpendicular to the crystal c axis, we observed, directly for the first time, a remarkable reorientation of the spin plane simultaneous with rotation of the incommensurate wavevector, by quantitatively deducing the conversion of the energetically less favorable domain to a more favorable one. At high enough fields parallel to the c axis, the data are consistent with either a field-induced commensurate spiral magnetic structure or an incommensurate spiral magnetic structure with a disorder in the c direction, suggesting that high fields may have influence on interplanar ordering.

  1. 2D-NMR, X-ray crystallography and theoretical studies of the reaction mechanism for the synthesis of 1,5-benzodiazepines from dehydroacetic acid derivatives and o-phenylenediamines

    NASA Astrophysics Data System (ADS)

    Rabahi, Amal; Hamdi, Safouane M.; Rachedi, Yahia; Hamdi, Maamar; Talhi, Oualid; Almeida Paz, Filipe A.; Silva, Artur S. M.; Fadila, Balegroune; Malika, Hamadène; Kamel, Taïbi

    2014-03-01

    The synthesis of 1,5-benzodiazepines by the reaction of o-phenylenediamines (o-PDAs) with dehydroacetic acid DHAA [3-acetyl-4-hydroxy-6-methyl-2H-pyran-2-one] or conjugate analogues is largely reported in the literature, but still with uncontrolled stereochemistry. In this work, a comprehensive mechanistic study on the formation of some synthesized 1,5-benzodiazepine models following different organic routes is established based on liquid-state 2D NMR, single-crystal X-ray diffraction and theoretical calculations allowing the classification of two prototropic forms A (enaminopyran-2,4-dione) and B (imino-4-hydroxypyran-2-one). Evidences are presented to show that most of the reported 1,5-benzodiazepine structures arising from DHAA and derivatives preferentially adopt the (E)-enaminopyran-2,4-diones A.

  2. A high-throughput 2D-analytical technique to obtain single protein parameters from complex cell lysates for in silico process development of ion exchange chromatography.

    PubMed

    Kröner, Frieder; Elsäßer, Dennis; Hubbuch, Jürgen

    2013-11-29

    The accelerating growth of the market for biopharmaceutical proteins, the market entry of biosimilars and the growing interest in new, more complex molecules constantly pose new challenges for bioseparation process development. In the presented work we demonstrate the application of a multidimensional, analytical separation approach to obtain the relevant physicochemical parameters of single proteins in a complex mixture for in silico chromatographic process development. A complete cell lysate containing a low titre target protein was first fractionated by multiple linear salt gradient anion exchange chromatography (AEC) with varying gradient length. The collected fractions were subsequently analysed by high-throughput capillary gel electrophoresis (HT-CGE) after being desalted and concentrated. From the obtained data of the 2D-separation the retention-volumes and the concentration of the single proteins were determined. The retention-volumes of the single proteins were used to calculate the related steric-mass action model parameters. In a final evaluation experiment the received parameters were successfully applied to predict the retention behaviour of the single proteins in salt gradient AEC.

  3. The origin of anomalous 3rd neighbor exchange in 2D triangular magnets (NiGa2S4 and others)

    NASA Astrophysics Data System (ADS)

    Mazin, Igor

    2008-03-01

    2D magnetic materials with triangular lattices have been attracting much interest. Among them one finds the parent compound of an exotic superconductor, NaxCoO2.yH2O, A-type antiferromagnets like NaNiO2, in-plane antiferromagnetism (LiCrO2), spin-liquid type materials (NiGa2S4), charge-order (AgNiO2). The main structural motif in all of them is the AB2 plane, where A is a transition metal and B is oxygen or sulfur. Experiments and calculations inevitably find anomalously strong 3rd neighbor exchange coupling in all these triangular planes, despite different band fillings and different magnetic ground states. I will explain why this happens, why this effect is so universal, and why it can be understood entirely on a one-electron level. I will use as an example NiGa2S4, with a reference to NaxCoO2 as well.

  4. Effect of molecular exchange on water droplet size analysis in W/O emulsions as determined by diffusion NMR.

    PubMed

    Vermeir, Lien; Sabatino, Paolo; Balcaen, Mathieu; Declerck, Arnout; Dewettinck, Koen; Martins, José C; Van der Meeren, Paul

    2016-02-01

    Using NMR diffusometry, the diffusion of water and tetramethylammonium chloride was recorded in order to determine the water droplet size distribution in W/O emulsions. This study aimed at evaluating the effect of extradroplet diffusion of water on the estimated droplet size distribution upon comparison to the real droplet size distribution. The latter originated from the diffusion behavior of the tetramethylammonium cation (TMA+), which is known to have a much lower permeability through the oil phase as compared to water. Whereas both low-resolution and high-resolution pulsed field gradient NMR revealed that the water droplet size overestimation could be reduced selecting either a lower measurement temperature during diffusion analysis, or a smaller diffusion delay value Δ, still comparison to TMA+ diffusion indicated that artefacts were unavoidable even at low Δ and temperature. In order to correct for this extradroplet water diffusion phenomenon, different data analysis methods were evaluated. The previously described Pfeuffer exchange model could only partly compensate for the effect of extradroplet diffusion on the water droplet size determination. On the other hand, accurate water droplet size analysis results were obtained by correcting the experimentally determined diffusion distances based on Einstein's diffusion law. As such, reliable data could be obtained by low resolution NMR based on water diffusion at or even above room temperature.

  5. Molecular interactions in the ionic liquid emim acetate and water binary mixtures probed via NMR spin relaxation and exchange spectroscopy.

    PubMed

    Allen, Jesse J; Bowser, Sage R; Damodaran, Krishnan

    2014-05-07

    Interactions of ionic liquids (ILs) with water are of great interest for many potential IL applications. 1-Ethyl-3-methylimidazolium (emim) acetate, in particular, has shown interesting interactions with water including hydrogen bonding and even chemical exchange. Previous studies have shown the unusual behavior of emim acetate when in the presence of 0.43 mole fraction of water, and a combination of NMR techniques is used herein to investigate the emim acetate-water system and the unusual behavior at 0.43 mole fraction of water. NMR relaxometry techniques are used to describe the effects of water on the molecular motion and interactions of emim acetate with water. A discontinuity is seen in nuclear relaxation behavior at the concentration of 0.43 mole fraction of water, and this is attributed to the formation of a hydrogen bonded network. EXSY measurements are used to determine the exchange rates between the H2 emim proton and water, which show a complex dependence on the concentration of the mixture. The findings support and expand our previous results, which suggested the presence of an extended hydrogen bonding network in the emim acetate-water system at concentrations close to 0.50 mole fraction of H2O.

  6. Lead exchange into zeolite and clay minerals: A [sup 29]Si, [sub 27]Al, [sup 23]Na solid-state NMR study

    SciTech Connect

    Liang, J.J.; Sherriff, B.L. )

    1993-08-01

    Chabazite, vermiculite, montmorillonite, hectorite, and kaolinite were used to remove Pb, through ion exchange, from 0.01 M aqueous Pb(NO[sub 3])[sub 2] solutions. These minerals contained 27 (Na-chabazite), 16, 9, 9, and 0.5 wt % of Pb, respectively, after equilibration with the solutions. Ion exchange reached equilibrium within 24 h for Na-chabazite and vermiculite, but in less than 5 min for montmorillonite and hectorite. Na-chabazite took up more Pb than natural (Ca, Na)-chabazite (7 wt % Pb), whereas no such difference was observed in different cation forms of the clay minerals. Calcite impurities, associated with the clay minerals, effectively removed Pb from the aqueous solutions by the precipitation of cerussite (PbCO[sub 3]). [sup 29]Si, [sup 27]Al, and [sup 23]Na magic angle spinning (MAS) nuclear magnetic resonance (NMR), [sup 23]Na double rotation (DOR) NMR, and [sup 23]Na variable-temperature MAS NMR were used to study the ion exchange mechanisms. In Na-chabazite, cations in all three possible sites take part in the fast chemical exchange. The chemical exchange passes from the fast exchange regime to the slow regime at [minus]80 to [minus]100[degrees]C. One site contains a relatively low population of exchangeable cations. The other two more shielded sites contain most of the exchangeable cation. The exchangeable cations in chabazite and vermiculite were found to be close to the SiO[sub 4] and AlO[sub 4] tetrahedra, while those in the other clay minerals were more distant. Two sites (or groups of sites) for exchangeable cations were observed in hectorite. Lead tended to occupy the one which corresponds to the [minus]8 ppM peak on the [sup 23]Na MAS NMR spectrum. The behavior of the exchangeable cations in the interlayer sites was similar in all the clay minerals studied. 27 refs., 7 figs., 4 tabs.

  7. Beryllium fluoride exchange rate accelerated by Mg²⁺ as discovered by ¹⁹F NMR.

    PubMed

    Liu, Yixiang; Mao, Xi-an; Liu, Maili; Jiang, Ling

    2015-01-08

    Beryllium fluoride is widely used as a phosphoryl analogue in macromolecular studies, which are not only fluoride-sensitive but also magnesium-dependent. The beryllium fluorides are a mixture of different species including BeF3(-) and BeF4(2-) exchanging under thermodynamic equilibrium in neutral aqueous solutions. In the cases of mimicking phosphate group transfer, both beryllium fluoride and the magnesium ion are generally needed. However, the impact of magnesium on the bioactivity of beryllium fluoride is not clear. We have found by (19)F NMR spectroscopy that Mg(2+) can severely affect the chemical exchange kinetics between BeF3(-) and BeF4(2-). When the F(-) concentration is relatively low, the presence of 10.0 mM Mg(2+) can accelerate the exchange rate 3-4 fold. However, when the F(-) concentration is relatively high, the Mg(2+) effect on the chemical exchange vanishes. On the basis of these findings, we proposed a possible mechanism that BeF4(2-) and Mg(2+) form an ion pair that affects the distribution of beryllium fluoride species and thus the activity in the solution.

  8. NMR analysis of t‐butyl‐catalyzed deuterium exchange at unactivated arene localities

    PubMed Central

    Eastman, Rachel

    2016-01-01

    Regioselective labelling of arene rings via electrophilic exchange is often dictated by the electronic environment caused by substituents present on the aromatic system. Previously, we observed the presence of a t‐butyl group, either covalently bond or added as an external reagent, could impart deuterium exchange to the unactivated, C1‐position of estrone. Here, we provide nuclear magnetic resonance analysis of this exchange in a solvent system composed of 50:50 trifluoroacetic acid and D2O with either 2‐t‐butylestrone or estrone in the presence of t‐butyl alcohol has shed insights into the mechanism of this t‐butyl‐catalyzed exchange. Fast exchange of the t‐butyl group concurrent with the gradual reduction of the H1 proton signal in both systems suggest a mechanism involving ipso attack of the t‐butyl position by deuterium. The reversible addition/elimination of the t‐butyl group activates the H1 proton towards exchange by a mechanism of t‐butyl incorporation, H1 activation and exchange, followed by eventual t‐butyl elimination. Density functional calculations are consistent with the observation of fast t‐butyl exchange concurrent with slower H1 exchange. The σ‐complex resulting from ipso attack of deuterium at the t‐butyl carbon was 6.6 kcal/mol lower in energy than that of the σ‐complex resulting from deuterium attack at C1. A better understanding of the t‐butyl‐catalyzed exchange could help in the design of labelling recipes for other phenolic metabolites. PMID:27645832

  9. Residue-specific NH exchange rates studied by NMR diffusion experiments

    NASA Astrophysics Data System (ADS)

    Brand, Torsten; Cabrita, Eurico J.; Morris, Gareth A.; Günther, Robert; Hofmann, Hans-Jörg; Berger, Stefan

    2007-07-01

    We present a novel approach to the investigation of rapid (>2 s -1) NH exchange rates in proteins, based on residue-specific diffusion measurements. 1H, 15N-DOSY-HSQC spectra are recorded in order to observe resolved amide proton signals for most residues of the protein. Human ubiquitin was used to demonstrate the proposed method. Exchange rates are derived directly from the decay data of the diffusion experiment by applying a model deduced from the assumption of a two-site exchange with water and the "pure" diffusion coefficients of water and protein. The "pure" diffusion coefficient of the protein is determined in an experiment with selective excitation of the amide protons in order to suppress the influence of magnetization transfer from water to amide protons on the decay data. For rapidly exchanging residues a comparison of our results with the exchange rates obtained in a MEXICO experiment showed good agreement. Molecular dynamics (MD) and quantum mechanical calculations were performed to find molecular parameters correlating with the exchangeability of the NH protons. The RMS fluctuations of the amide protons, obtained from the MD simulations, together with the NH coupling constants provide a bilinear model which shows a good correlation with the experimental NH exchange rates.

  10. Comparison of Kinetic Models for Analysis of Pyruvate-to-Lactate Exchange by Hyperpolarized 13C NMR

    PubMed Central

    Harrison, Crystal; Yang, Chendong; Jindal, Ashish; DeBerardinis, Ralph J.; Hooshyar, M.A.; Merritt, Matthew; Sherry, A. Dean; Malloy, Craig R.

    2012-01-01

    The activity of specific enzyme-catalyzed reactions may be detected in vivo by 13C NMR of hyperpolarized (HP) substrates. The signal from HP substrates and products, acquired over time, have been fit to a number of different mathematical models to determine fluxes, but these models have not been critically compared. In this study, two-pool and three-pool first-order models were constructed to measure flux through lactate dehydrogenase in isolated glioblastoma cells by NMR detection of lactate and pyruvate following addition of hyperpolarized [1-13C]pyruvate. Mass spectrometry (MS) was used to independently monitor 13C enrichment in intra- and extracellular lactate. Six models were evaluated using time dependent pyruvate C2 and lactate C1 HP NMR data acquired by use of selective excitation pulses plus 13C enrichment data from intracellular and extracellular lactate measured by MS. A three-pool bi-directional model provided the most accurate description of pyruvate metabolism in these cells. With computed values for the T1 of pyruvate and lactate as well as the effect of pulsing, the initial flux through lactate dehydrogenase (LDH) was well-determined by both the two-pool bidirectional and unidirectional models when only HP data was available. The three-pool model was necessary to fit the combined data from both MS and HP, but the simpler two-pool exchange model was sufficient to determine the 13C lactate concentration when the lactate appearance was measured only by HP. PMID:22451442

  11. NMR relaxation and exchange in metal-organic frameworks for surface area screening

    SciTech Connect

    Chen, JJ; Mason, JA; Bloch, ED; Gygi, D; Long, JR; Reimer, JA

    2015-03-15

    We describe a robust screening technique that correlates the surface area of metal organic frameworks to the proton T-2 relaxation behavior of imbibed solvent at low field (13 MHz). In frameworks with small pore sizes (<1 nm) or strong solvent-framework interactions, diffusional exchange between the pore-confined and inter-particle solvent populations remains slow compared to the T-2 of the pore-confined solvent, allowing for a direct porosity analysis of the T-2 spectrum obtained from Laplace inversions. Increases in framework pore-size (>1 nm) lead to corresponding increases in the rate of solvent exchange, as confirmed by T-2 relaxation exchange (REXSY) experiments; increases in the pore size also increases the T-2 of the pore-confined solvent. The combination of these two effects results in comparable rates of relaxation and exchange, which precludes the direct analysis of Laplace inversions. Thus, two- and three-site kinetics models were applied to extract porosity from relaxation decays, thereby improving the utility of the porosity screening tool. (C) 2014 Elsevier Inc. All rights reserved.

  12. Changes in Lignin and Polysaccharide Components in 13 Cultivars of Rice Straw following Dilute Acid Pretreatment as Studied by Solution-State 2D 1H-13C NMR

    PubMed Central

    Teramura, Hiroshi; Sasaki, Kengo; Oshima, Tomoko; Aikawa, Shimpei; Matsuda, Fumio; Okamoto, Mami; Shirai, Tomokazu; Kawaguchi, Hideo; Ogino, Chiaki; Yamasaki, Masanori; Kikuchi, Jun; Kondo, Akihiko

    2015-01-01

    A renewable raw material, rice straw is pretreated for biorefinery usage. Solution-state two-dimensional (2D) 1H-13 C hetero-nuclear single quantum coherence (HSQC) nuclear magnetic resonance (NMR) spectroscopy, was used to analyze 13 cultivars of rice straw before and after dilute acid pretreatment, to characterize general changes in the lignin and polysaccharide components. Intensities of most (15 of 16) peaks related to lignin aromatic regions, such as p-coumarate, guaiacyl, syringyl, p-hydroxyphenyl, and cinnamyl alcohol, and methoxyl, increased or remained unchanged after pretreatment. In contrast, intensities of most (11 of 13) peaks related to lignin aliphatic linkages or ferulate decreased. Decreased heterogeneity in the intensities of three peaks related to cellulose components in acid-insoluble residues resulted in similar glucose yield (0.45–0.59 g/g-dry biomass). Starch-derived components showed positive correlations (r = 0.71 to 0.96) with glucose, 5-hydroxymethylfurfural (5-HMF), and formate concentrations in the liquid hydrolysates, and negative correlations (r = –0.95 to –0.97) with xylose concentration and acid-insoluble residue yield. These results showed the fate of lignin and polysaccharide components by pretreatment, suggesting that lignin aromatic regions and cellulose components were retained in the acid insoluble residues and starch-derived components were transformed into glucose, 5-HMF, and formate in the liquid hydrolysate. PMID:26083431

  13. NMR imaging of fluid exchange between macropores and matrix in eogenetic karst

    USGS Publications Warehouse

    Florea, L.J.; Cunningham, K.J.; Altobelli, S.

    2009-01-01

    Sequential time-step images acquired using nuclear magnetic resonance (NMR) show the displacement of deuterated water (D2O) by fresh water within two limestone samples characterized by a porous and permeable limestone matrix of peloids and ooids. These samples were selected because they have a macropore system representative of some parts of the eogenetic karst limestone of the Biscayne Aquifer in southeastern Florida. The macroporosity, created by the trace fossil Ophiomorpha, is principally well connected and of centimeter scale. These macropores occur in broadly continuous stratiform zones that create preferential flow layers within the hydrogeologic units of the Biscayne. This arrangement of porosity is important because in coastal areas, it could produce a preferential pathway for salt water intrusion. Two experiments were conducted in which samples saturated with D2O were placed in acrylic chambers filled with fresh water and examined with NMR. Results reveal a substantial flux of fresh water into the matrix porosity with a simultaneous loss of D 2O. Specifically, we measured rates upward of 0.001 mL/h/g of sample in static conditions, and perhaps as great as 0.07 mL/h/g of sample when fresh water continuously flows past a sample at velocities less than those found within stressed areas of the Biscayne. These experiments illustrate how fresh water and D2O, with different chemical properties, migrate within one type of matrix porosity found in the Biscayne. Furthermore, these experiments are a comparative exercise in the displacement of sea water by fresh water in the matrix of a coastal, karst aquifer since D2O has a greater density than fresh water. ?? 2008 National Ground Water Association.

  14. Study of H/D exchange rates to derive the strength of intramolecular hydrogen bonds in halo substituted organic building blocks: An NMR spectroscopic investigation

    NASA Astrophysics Data System (ADS)

    Mishra, Sandeep Kumar; Suryaprakash, N.

    2015-10-01

    Rates of hydrogen/deuterium (H/D) exchange determined by 1H NMR spectroscopy are utilized to derive the strength of hydrogen bonds and to monitor the electronic effects in the site-specific halogen substituted benzamides and anilines. The theoretical fitting of the time dependent variation of the integral areas of 1H NMR resonances to the first order decay function permitted the determination of H/D exchange rate constants (k) and their precise half-lives (t1/2) with high degree of reproducibility. The comparative study also permitted the unambiguous determination of relative strength of hydrogen bonds and the contribution from electronic effects on the H/D exchange rate.

  15. Human recombinant [C22A] FK506-binding protein amide hydrogen exchange rates from mass spectrometry match and extend those from NMR.

    PubMed Central

    Zhang, Z.; Li, W.; Logan, T. M.; Li, M.; Marshall, A. G.

    1997-01-01

    Hydrogen/deuterium exchange behavior of human recombinant [C22A] FK506 binding protein (C22A FKBP) has been determined by protein fragmentation, combined with electrospray Fourier transform ion cyclotron resonance mass spectrometry (MS). After a specified period of H/D exchange in solution, C22A FKBP was digested by pepsin under slow exchange conditions (pH 2.4, 0 degree C), and then subjected to on-line HPLC/MS for deuterium analysis of each proteolytic peptide. The hydrogen exchange rate of each individual amide hydrogen was then determined independently by heteronuclear two-dimensional NMR on 15N-enriched C22A FKBP. A maximum entropy method (MEM) algorithm makes it possible to derive the distributions of hydrogen exchange rate constants from the MS-determined deuterium exchange-in curves in either the holoprotein or its proteolytic segments. The MEM-derived rate constant distributions of C22A FKBP and different segments of C22A FKBP are compared to the rate constants determined by NMR for individual amide protons. The rate constant distributions determined by both methods are consistent and complementary, thereby validating protein fragmentation/mass spectrometry as a reliable measure of hydrogen exchange in proteins. PMID:9336843

  16. Conformational Properties of α- or β-(1→6)-Linked Oligosaccharides: Hamiltonian Replica Exchange MD Simulations and NMR Experiments

    PubMed Central

    2015-01-01

    Conformational sampling for a set of 10 α- or β-(1→6)-linked oligosaccharides has been studied using explicit solvent Hamiltonian replica exchange (HREX) simulations and NMR spectroscopy techniques. Validation of the force field and simulation methodology is done by comparing calculated transglycosidic J coupling constants and proton–proton distances with the corresponding NMR data. Initial calculations showed poor agreement, for example, with >3 Hz deviation of the calculated 3J(H5,H6R) values from the experimental data, prompting optimization of the ω torsion angle parameters associated with (1→6)-linkages. The resulting force field is in overall good agreement (i.e., within ∼0.5 Hz deviation) from experimental 3J(H5,H6R) values, although some small limitations are evident. Detailed hydrogen bonding analysis indicates that most of the compounds lack direct intramolecular H-bonds between the two monosaccharides; however, minor sampling of the O6···HO2′ hydrogen bond is present in three compounds. The results verify the role of the gauche effect between O5 and O6 atoms in gluco- and manno-configured pyranosides causing the ω torsion angle to sample an equilibrium between the gt and gg rotamers. Conversely, galacto-configured pyranosides sample a population distribution in equilibrium between gt and tg rotamers, while the gg rotamer populations are minor. Water radial distribution functions suggest decreased accessibility to the O6 atom in the (1→6)-linkage as compared to the O6′ atom in the nonreducing sugar. The role of bridging water molecules between two sugar moieties on the distributions of ω torsion angles in oligosaccharides is also explored. PMID:24552401

  17. Ion-Exchange-Induced 2D-3D Conversion of HMA1-x FAx PbI3 Cl Perovskite into a High-Quality MA1-x FAx PbI3 Perovskite.

    PubMed

    Li, Ge; Zhang, Taiyang; Guo, Nanjie; Xu, Feng; Qian, Xufang; Zhao, Yixin

    2016-10-17

    High-quality phase-pure MA1-x FAx PbI3 planar films (MA=methylammonium, FA=formamidinium) with extended absorption and enhanced thermal stability are difficult to deposit by regular simple solution chemistry approaches owing to crystallization competition between the easy-to-crystallize but unwanted δ-FAPbI3 /MAPbI3 and FAx MA1-x PbI3 requiring rigid crystallization conditions. Here A 2D-3D conversion to transform compact 2D mixed composition HMA1-x FAx PbI3 Cl perovskite precursor films into 3D MA1-x FAx PbI3 (x=0.1-0.9) perovskites is presented. The designed Cl/I and H/FA(MA) ion exchange reaction induced fast transformation of compact 2D perovskite film, helping to form the phase-pure and high quality MA1-x FAx PbI3 without δ-FAPbI3 and MAPbI3 impurity. In all, we successfully developed a facile one-step method to fabricate high quality phase-pure MA1-x FAx PbI3 (x=0.1-0.9) perovskite films by 2D-3D conversion of HMA1-x FAx PbI3 Cl perovskite. This 2D-3D conversion is a promising strategy for lead halide perovskite fabrication.

  18. (127)I NMR calculations in binary metal iodides by PBE-GGA, YS-PBE0 and mBJ exchange correlation potentials.

    PubMed

    Bashi, M; Aliabad, H A Rahnamaye; Mowlavi, A A; Ahmad, Iftikhar

    We have calculated Nuclear Magnetic Resonance (NMR) spectroscopy for (127)I (quadrupolar nuclei I=5/2) in binary metal iodides XI (X=Li, Na, K, Rb and Cs) by using PBE- GGA, YS- PBE0 and mBJ exchange correlation potentials. The results show that the nature of bonds between Iodine and metal atoms are ionic. The main contribution in NMR spectroscopy is related to the induced current inside the atomic sphere and the remainder of the unit cell volume contributes only a few ppm. Obtained NMR shifts are compared with the NMR shielding data and the NMR shielding for metal-p band varies across the series about 221ppm. Density of states results indicate that the largest contribution in the shielding comes from the I-core electrons (1s and 4d). The NMR shielding graphs show that there are negative linear correlation with slope -1.18, -1.16 and -1.01 by PBE- GGA, YS- PBE0 and mBJ, respectively. The computed results by mBJ are in good agreement with the experimental values.

  19. Flexible and rigid structures in HIV-1 p17 matrix protein monitored by relaxation and amide proton exchange with NMR.

    PubMed

    Ohori, Yuka; Okazaki, Honoka; Watanabe, Satoru; Tochio, Naoya; Arai, Munehito; Kigawa, Takanori; Nishimura, Chiaki

    2014-03-01

    The HIV-1 p17 matrix protein is a multifunctional protein that interacts with other molecules including proteins and membranes. The dynamic structure between its folded and partially unfolded states can be critical for the recognition of interacting molecules. One of the most important roles of the p17 matrix protein is its localization to the plasma membrane with the Gag polyprotein. The myristyl group attached to the N-terminus on the p17 matrix protein functions as an anchor for binding to the plasma membrane. Biochemical studies revealed that two regions are important for its function: D14-L31 and V84-V88. Here, the dynamic structures of the p17 matrix protein were studied using NMR for relaxation and amide proton exchange experiments at the physiological pH of 7.0. The results revealed that the α12-loop, which includes the 14-31 region, was relatively flexible, and that helix 4, including the 84-88 region, was the most protected helix in this protein. However, the residues in the α34-loop near helix 4 had a low order parameter and high exchange rate of amide protons, indicating high flexibility. This region is probably flexible because this loop functions as a hinge for optimizing the interactions between helices 3 and 4. The C-terminal long region of K113-Y132 adopted a disordered structure. Furthermore, the C-terminal helix 5 appeared to be slightly destabilized due to the flexible C-terminal tail based on the order parameters. Thus, the dynamic structure of the p17 matrix protein may be related to its multiple functions.

  20. Characterisation of erythrocyte transmembrane exchange of trifluoroacetate using 19F-NMR: evidence for transport via the monocarboxylate transporter.

    PubMed

    Xu, A S; Kuchel, P W

    1993-07-25

    The transport of trifluoroacetate (TFA) and difluorophosphate (DFP) into and out of human and sheep erythrocytes was measured using 19F-NMR. The pathways for the transport in human erythrocytes were characterised by differentiating between the transport inhibition caused by different reagents. (1) Pre-treatment of human erythrocytes with N-ethylmaleimide (10 mM) caused a decrease of the membrane-permeability coefficients for TFA influx and efflux to 0.74 +/- 0.05 and 0.83 +/- 0.09-times, respectively, of those determined in the absence of inhibition. Concomitantly there was no apparent effect on the band-3-mediated transport of DFP. Thus, the decrease of the permeability of TFA is consistent with the inhibition being that of the monocarboxylate transporter. (2) Inhibition of TFA and DFP exchange was also seen in human erythrocytes treated with p-chloromercuriphenylsulfonate (pCMBS). The extent of inhibition reached a maximum value for the pCMBS concentrations beyond which further inhibition was not achieved and there was substantial residual exchange of the two solutes. (3) Residual flux of TFA was found in the presence of high concentrations of the inhibitors, alpha-cyano-4-hydroxycinnamate (> or = 4 mM) or 4,4'-dinitrostilbene-2,2'-disulfonate (> or = 1 mM) when each compound was used alone. (4) Complete inhibition of TFA uptake was obtained when human erythrocytes were treated with both alpha-cyano-4-hydroxycinnamate (4 mM) and a stilbene disulfonate. It was, therefore, concluded that simple diffusion of TFA via the lipid bilayer was negligible in human erythrocytes and that incomplete inhibition of the monocarboxylate transporter occurred when the compounds were used alone.

  1. Interactions and exchange of CO2 and H2O in coals: an investigation by low-field NMR relaxation

    PubMed Central

    Sun, Xiaoxiao; Yao, Yanbin; Liu, Dameng; Elsworth, Derek; Pan, Zhejun

    2016-01-01

    The mechanisms by which CO2 and water interact in coal remain unclear and these are key questions for understanding ECBM processes and defining the long-term behaviour of injected CO2. In our experiments, we injected helium/CO2 to displace water in eight water-saturated samples. We used low-field NMR relaxation to investigate CO2 and water interactions in these coals across a variety of time-scales. The injection of helium did not change the T2 spectra of the coals. In contrast, the T2 spectra peaks of micro-capillary water gradually decreased and those of macro-capillary and bulk water increased with time after the injection of CO2. We assume that the CO2 diffuses through and/or dissolves into the capillary water to access the coal matrix interior, which promotes desorption of water molecules from the surfaces of coal micropores and mesopores. The replaced water mass is mainly related to the Langmuir adsorption volume of CO2 and increases as the CO2 adsorption capacity increases. Other factors, such as mineral composition, temperature and pressure, also influence the effective exchange between water and CO2. Finally, we built a quantified model to evaluate the efficiency of water replacement by CO2 injection with respect to temperature and pressure. PMID:26817784

  2. Human- and computer-accessible 2D correlation data for a more reliable structure determination of organic compounds. Future roles of researchers, software developers, spectrometer managers, journal editors, reviewers, publisher and database managers toward artificial-intelligence analysis of NMR spectra.

    PubMed

    Jeannerat, Damien

    2017-01-01

    The introduction of a universal data format to report the correlation data of 2D NMR spectra such as COSY, HSQC and HMBC spectra will have a large impact on the reliability of structure determination of small organic molecules. These lists of assigned cross peaks will bridge signals found in NMR 1D and 2D spectra and the assigned chemical structure. The record could be very compact, human and computer readable so that it can be included in the supplementary material of publications and easily transferred into databases of scientific literature and chemical compounds. The records will allow authors, reviewers and future users to test the consistency and, in favorable situations, the uniqueness of the assignment of the correlation data to the associated chemical structures. Ideally, the data format of the correlation data should include direct links to the NMR spectra to make it possible to validate their reliability and allow direct comparison of spectra. In order to take the full benefits of their potential, the correlation data and the NMR spectra should therefore follow any manuscript in the review process and be stored in open-access database after publication. Keeping all NMR spectra, correlation data and assigned structures together at all time will allow the future development of validation tools increasing the reliability of past and future NMR data. This will facilitate the development of artificial intelligence analysis of NMR spectra by providing a source of data than can be used efficiently because they have been validated or can be validated by future users. Copyright © 2016 John Wiley & Sons, Ltd.

  3. Simple (17) O NMR method for studying electron self-exchange reaction between UO2 (2+) and U(4+) aqua ions in acidic solution.

    PubMed

    Bányai, István; Farkas, Ildikó; Tóth, Imre

    2016-06-01

    (17) O NMR spectroscopy is proven to be suitable and convenient method for studying the electron exchange by following the decrease of (17) O-enrichment in U(17) OO(2+) ion in the presence of U(4+) ion in aqueous solution. The reactions have been performed at room temperature using I = 5 M ClO4 (-) ionic medium in acidic solutions in order to determine the kinetics of electron exchange between the U(4+) and UO2 (2+) aqua ions. The rate equation is given as R = a[H(+) ](-2)  + R', where R' is an acid independent parallel path. R' depends on the concentration of the uranium species according to the following empirical rate equation: R' = k1 [UO(2 +) ](1/2) [U(4 +) ](1/2)  + k2 [UO(2 +) ](3/2) [U(4 +) ](1/2) . The mechanism of the inverse H(+) concentration-dependent path is interpreted as equilibrium formation of reactive UO2 (+) species from UO2 (2+) and U(4+) aqua ions and its electron exchange with UO2 (2+) . The determined rate constant of this reaction path is in agreement with the rate constant of UO2 (2+) -UO2 (+) , one electron exchange step calculated by Marcus theory, match the range given experimentally of it in an early study. Our value lies in the same order of magnitude as the recently calculated ones by quantum chemical methods. The acid independent part is attributed to the formation of less hydrolyzed U(V) species, i.e. UO(3+) , which loses enrichment mainly by electron exchange with UO2 (2+) ions. One can also conclude that (17) O NMR spectroscopy, or in general NMR spectroscopy with careful kinetic analysis, is a powerful tool for studying isotope exchange reactions without the use of sophisticated separation processes. Copyright © 2015 John Wiley & Sons, Ltd.

  4. Enhancing NMR of insensitive nuclei by transfer of SABRE spin hyperpolarization

    NASA Astrophysics Data System (ADS)

    Pravdivtsev, Andrey N.; Yurkovskaya, Alexandra V.; Zimmermann, Herbert; Vieth, Hans-Martin; Ivanov, Konstantin L.

    2016-09-01

    We describe the performance of methods for enhancing NMR (Nuclear Magnetic Resonance) signals of "insensitive", but important NMR nuclei, which are based on the SABRE (Signal Amplification By Reversible Exchange) technique, i.e., on spin order transfer from parahydrogen (H2 molecule in its nuclear singlet spin state) to a substrate in a transient organometallic complex. Here such transfer is performed at high magnetic fields by INEPT-type NMR pulse sequences, modified for SABRE. Signal enhancements up to three orders of magnitude are obtained for 15N nuclei; the possibility of sensitive detection of 2D-NMR 1H-15N spectra of SABRE complexes and substrates is demonstrated.

  5. Unexpected formation of 1-diethylaminobutadiene in photosensitized oxidation of triethylamine induced by 2,3-dihydro-oxoisoaporphine dyes. A 1H NMR and isotopic exchange study.

    PubMed

    De la Fuente, Julio R; Jullian, Carolina; Saitz, Claudio; Neira, Verónica; Poblete, Oscar; Sobarzo-Sánchez, Eduardo

    2005-10-28

    [reaction: see text] Photoreduction of oxoisoaporphine dyes occurs via a stepwise mechanism of electron-proton-electron transfer that leads to the N-hydrogen oxoisoaporphine anion. When triethylamine, TEA, was used as the electron donor in anaerobic conditions, 1-diethylaminobutadiene, DEAB, was one of the oxidation products of TEA, among diethylamine and acetaldehyde. DEAB was identified by (1)H NMR and GC-MS experiments by comparison with the authentic 1-diethylaminobutadiene. This is the first report of a butadienyl derivative formed in the dye-sensitized photooxidation of TEA. In addition, isotopic exchange experiments with TEA-d(15) and D(2)O show that the hydrogens at carbon-2 and carbon-4 of the butadienyl moiety are exchangeable. The observed isotopic exchange pattern could be explained by the head-to-tail coupling of an N,N-diethylvinylamine intermediate that exchanges hydrogens at the C-beta via the enammonium ion.

  6. Rapid exchange of fluoroethylamine via the Rhesus complex in human erythrocytes: 19F NMR magnetization transfer analysis showing competition by ammonia and ammonia analogues.

    PubMed

    Szekely, David; Chapman, Bogdan E; Bubb, William A; Kuchel, Philip W

    2006-08-01

    A remarkable recent discovery in red blood cell function is that the Rhesus antigen complex that for so long was considered to be simply a means of cell recognition is also the ammonia transporter. It catalyzes transmembrane exchange of ammonia on the subsecond time scale, and yet because of a lack of rapid-exchange methodology its kinetics had not been characterized. The flux of ammonia varies appreciably in diverse clinical states, and a convenient method for its characterization would be of basic and of clinical diagnostic value. Fluoroethylamine is water-soluble and when added to a suspension of human red blood cells (RBCs) displays the experimentally useful property of giving separate 19F NMR spectral peaks for the populations inside and outside the cells. By using two-site, one-dimensional magnetization exchange spectroscopy (1D-EXSY), the transmembrane exchange of fluoroethylamine was measured; it was found to occur on the subsecond time scale with an apparent first-order rate constant for efflux, under the equilibrium exchange conditions, of 3.4 s(-1). The method was used to characterize the concentration, temperature, and pH dependence of the exchange rate constant. We determined the extent of competitive inhibition exhibited by ammonia and two molecules that contain an amine group (ethylamine and methylamine). Inhibition of the exchange by incubating the suspension with anti-RhAG antibody, and no inhibition by anti-RhD antibody, suggested specificity of exchange via the RhAG protein of the Rh complex.

  7. Cationic Mn2+/H+ exchange leading a slow solid-state transformation of a 2D porphyrinic network at ambient conditions

    NASA Astrophysics Data System (ADS)

    Amayuelas, Eder; Fidalgo-Marijuan, Arkaitz; Bazán, Begoña; Urtiaga, Miren Karmele; Barandika, Gotzone; Lezama, Luis; Arriortua, María Isabel

    2017-03-01

    Metalloporphyrins exhibit outstanding chemical, physical and biological properties in dissolution, however, it is a challenge to synthesize them as stable solid frameworks. Long-time stability is crucial for future applications of these materials, and we have detected a slow, solid-state transformation of a 2D MnII-porphyrin at RT. The remarkable point is that this transformation showed up as a result of Electronic Paramagnetic Resonance measurements. Otherwise, the evolution of the system could have remained undetected. Thus, 2D [Mn3(TCPP)(H2O)4]·nD (1) (where TCPP is meso-tetra(4-carboxyphenyl)porphyrin and D is the solvent) has been synthesized hydrothermally, and characterised by means of X-ray diffraction (XRD), Thermogravimetry and X-ray thermodiffractometry (XRTD). This compound slowly transforms into [Mn(H4TCPP)(H2O)2]·nD (2) according to the equilibrium [Mn3(TCPP)]+4H+ ↔ [Mn(H4TCPP)]+2Mn2+. The evolution of the system has been studied through analysis of the distortion (both of the coordination sphere and the tetrapyrrolic macrocycle) and Density Functional Theory (DFT) quantum mechanical calculations.

  8. Assessing 2D electrophoretic mobility spectroscopy (2D MOSY) for analytical applications.

    PubMed

    Fang, Yuan; Yushmanov, Pavel V; Furó, István

    2016-12-08

    Electrophoretic displacement of charged entity phase modulates the spectrum acquired in electrophoretic NMR experiments, and this modulation can be presented via 2D FT as 2D mobility spectroscopy (MOSY) spectra. We compare in various mixed solutions the chemical selectivity provided by 2D MOSY spectra with that provided by 2D diffusion-ordered spectroscopy (DOSY) spectra and demonstrate, under the conditions explored, a superior performance of the former method. 2D MOSY compares also favourably with closely related LC-NMR methods. The shape of 2D MOSY spectra in complex mixtures is strongly modulated by the pH of the sample, a feature that has potential for areas such as in drug discovery and metabolomics. Copyright © 2016 The Authors. Magnetic Resonance in Chemistry published by John Wiley & Sons Ltd. StartCopTextCopyright © 2016 The Authors. Magnetic Resonance in Chemistry published by John Wiley & Sons Ltd.

  9. Optimum levels of exchangeable protons in perdeuterated proteins for proton detection in MAS solid-state NMR spectroscopy.

    PubMed

    Akbey, Umit; Lange, Sascha; Trent Franks, W; Linser, Rasmus; Rehbein, Kristina; Diehl, Anne; van Rossum, Barth-Jan; Reif, Bernd; Oschkinat, Hartmut

    2010-01-01

    We present a systematic study of the effect of the level of exchangeable protons on the observed amide proton linewidth obtained in perdeuterated proteins. Decreasing the amount of D(2)O employed in the crystallization buffer from 90 to 0%, we observe a fourfold increase in linewidth for both (1)H and (15)N resonances. At the same time, we find a gradual increase in the signal-to-noise ratio (SNR) for (1)H-(15)N correlations in dipolar coupling based experiments for H(2)O concentrations of up to 40%. Beyond 40%, a significant reduction in SNR is observed. Scalar-coupling based (1)H-(15)N correlation experiments yield a nearly constant SNR for samples prepared with < or =30% H(2)O. Samples in which more H(2)O is employed for crystallization show a significantly reduced NMR intensity. Calculation of the SNR by taking into account the reduction in (1)H T (1) in samples containing more protons (SNR per unit time), yields a maximum SNR for samples crystallized using 30 and 40% H(2)O for scalar and dipolar coupling based experiments, respectively. A sensitivity gain of 3.8 is obtained by increasing the H(2)O concentration from 10 to 40% in the CP based experiment, whereas the linewidth only becomes 1.5 times broader. In general, we find that CP is more favorable compared to INEPT based transfer when the number of possible (1)H,(1)H interactions increases. At low levels of deuteration (> or =60% H(2)O in the crystallization buffer), resonances from rigid residues are broadened beyond detection. All experiments are carried out at MAS frequency of 24 kHz employing perdeuterated samples of the chicken alpha-spectrin SH3 domain.

  10. Ratiometric analysis in hyperpolarized NMR (I): test of the two-site exchange model and the quantification of reaction rate constants.

    PubMed

    Li, Lin Z; Kadlececk, Stephen; Xu, He N; Daye, Dania; Pullinger, Benjamin; Profka, Harrilla; Chodosh, Lewis; Rizi, Rahim

    2013-10-01

    Conventional methods for the analysis of in vivo hyperpolarized (13) C NMR data from the lactate dehydrogenase (LDH) reaction usually make assumptions on the stability of rate constants and/or the validity of the two-site exchange model. In this study, we developed a framework to test the validity of the assumption of stable reaction rate constants and the two-site exchange model in vivo via ratiometric fitting of the time courses of the signal ratio L(t)/P(t). Our analysis provided evidence that the LDH enzymatic kinetics observed by hyperpolarized NMR are in near-equilibrium and satisfy the two-site exchange model for only a specific time window. In addition, we quantified both the forward and reverse exchange rate constants of the LDH reaction for the transgenic and mouse xenograft models of breast cancer using the ratio fitting method developed, which includes only two modeling parameters and is less sensitive to the influence of instrument settings/protocols, such as flip angles, degree of polarization and tracer dosage. We further compared the ratio fitting method with a conventional two-site exchange modeling method, i.e. the differential equation fitting method, using both the experimental and simulated hyperpolarized NMR data. The ratio fitting method appeared to fit better than the differential equation fitting method for the reverse rate constant on the mouse tumor data, with less relative errors on average, whereas the differential equation fitting method also resulted in a negative reverse rate constant for one tumor. The simulation results indicated that the accuracy of both methods depends on the width of the transport function, noise level and rate constant ratio; one method may be more accurate than the other based on the experimental/biological conditions aforementioned. We were able to categorize our tumor models into specific conditions of the computer simulation and to estimate the errors of rate quantification. We also discussed possible

  11. (129)Xe NMR of Mesoporous Silicas

    SciTech Connect

    Anderson, M.T.; Asink, R.A.; Kneller, J.M.; Pietrass, T.

    1999-04-23

    The porosities of three mesoporous silica materials were characterized with {sup 129}Xe NMR spectroscopy. The materials were synthesized by a sol-gel process with r = 0, 25, and 70% methanol by weight in an aqueous cetyltrimethylammonium bromide solution. Temperature dependent chemical shifts and spin lattice relaxation times reveal that xenon does not penetrate the pores of the largely disordered (r= 70%) silica. For both r = 0 and 25%, temperature dependent resonances corresponding to physisorbed xenon were observed. An additional resonance for the r = 25% sample was attributed to xenon between the disordered cylindrical pores. 2D NMR exchange experiments corroborate the spin lattice relaxation data which show that xenon is in rapid exchange between the adsorbed and the gas phase.

  12. NMR Method for Characterizing Microsecond-to-Millisecond Chemical Exchanges Utilizing Differential Multiple-Quantum Relaxation in High Molecular Weight Proteins.

    PubMed

    Toyama, Yuki; Osawa, Masanori; Yokogawa, Mariko; Shimada, Ichio

    2016-02-24

    Chemical exchange processes of proteins on the order of microseconds (μs) to milliseconds (ms) play critical roles in biological functions. Developments in methyl-transverse relaxation optimized spectroscopy (methyl-TROSY), which observes the slowly relaxing multiple quantum (MQ) coherences, have enabled the studies of biologically important large proteins. However, the analyses of μs to ms chemical exchange processes based on the methyl-TROSY principle are still challenging, because the interpretation of the chemical exchange contributions to the MQ relaxation profiles is complicated, as significant chemical shift differences occur in both (1)H and (13)C nuclei. Here, we report a new methyl-based NMR method for characterizing chemical exchanges, utilizing differential MQ relaxation rates and a heteronuclear double resonance pulse technique. The method enables quantitative evaluations of the chemical exchange processes, in which significant chemical shift differences exist in both the (1)H and (13)C nuclei. The versatility of the method is demonstrated with the application to KirBac1.1, with an apparent molecular mass of 200 kDa.

  13. Channel orientation anisotropy in perfluorosulfonic acid/SiO 2 composite proton exchange membranes: Water self-diffusion study using NMR

    NASA Astrophysics Data System (ADS)

    Filipoi, Carmen; Demco, Dan E.; Zhu, Xiaomin; Vinokur, Rostislav; Conradi, Oliver; Fechete, Radu; Möller, Martin

    2011-09-01

    A diffusion-exchange model with the assumption of two water pools was applied to describe the water transport in perfluorinated sulfonic acid (PFSA)/SiO 2 nanocomposites. The water diffusivity in-plane and through-plane in solution cast films was measured by NMR revealing higher in-plane mobility. Both diffusion coefficients reached maxima at ˜3%-wt. concentration in SiO 2. The anisotropy of the PFSA channels orientation reflected in the diffusivity anisotropy decreased with the increase in the nanofiller content. Water exchange rates reached a maximum at low concentration of silica. Gaussian displacement distribution for water diffusion was detected in PFSA membrane at 40 °C independent of the direction of gradient for small concentration in silica.

  14. Fully converged integral cross sections of collision induced dissociation, four-center, and single exchange reactions, and accuracy of the centrifugal sudden approximation in H2 + D2 reaction.

    PubMed

    Song, Hongwei; Lu, Yunpeng; Lee, Soo-Y

    2012-03-21

    The initial state selected time-dependent wave packet method was employed to calculate the integral cross sections for the H(2) + D(2) reaction with and without the centrifugal sudden (CS) approximation by including all important K (the projection of the total angular momentum on the body-fixed axis) blocks. With a full-dimensional model, the first fully converged coupled-channel (CC) cross sections for different competitive processes from the ground rotational state were obtained: collision induced dissociation (CID), four-center (4C) reaction and single exchange (SE) reaction. The effect of the total angular momentum J on the reaction dynamics of H(2) + D(2) and the accuracy of the CS approximation have also been studied. It was found that the CID and SE processes occur in a wide range of J values while the 4C process can only take place in a narrow window of J values. For this reason, the CC cross section for the 4C channel is merely comparable to the SE channel. A comparison of the integral cross sections from CC and CS calculations showed that the CS approximation works well for the CID process but not for the 4C and SE processes, and the discrepancy between the CC and CS cross sections grows larger as the translational energy and/or the vibrational energy increase(s).

  15. Investigation of cation environment and framework changes in silicotitanate exchange materials using solid-state 23Na, 29Si, and 133Cs MAS NMR

    NASA Astrophysics Data System (ADS)

    Cherry, Brian R.; Nyman, May; Alam, Todd M.

    2004-06-01

    Crystalline silicotitanate (CST), HNa 3Ti 4Si 2O 14·4H 2O and the Nb-substituted CST (Nb-CST), HNa 2Ti 3NbSi 2O 14·4H 2O, are highly selective Cs + sorbents, which makes them attractive materials for the selective removal of radioactive species from nuclear waste solutions. The structural basis for the improved Cs + selectivity in the niobium analogs was investigated through a series of solid-state magic angle spinning (MAS) NMR experiments. Changes in the local environment of the Na + and Cs + cations in both CST and Nb-CST materials as a function of weight percent cesium exchange were investigated using 23Na and 133Cs MAS NMR. Framework changes induced by Cs + loading and hydration state were investigated with 29Si MAS NMR. Multiple Cs + environments were observed in the CST and Nb-CST material. The relative population of these different Cs + environments varies with the extent of Cs + loading. Marked changes in the framework Si environment were noted with the initial incorporation of Cs +, however with increased Cs + loading the impact to the Si environment becomes less pronounced. The Cs + environment and Si framework structure were influenced by the Nb-substitution and were greatly affected by the amount of water present in the materials. The increased Cs + selectivity of the Nb-CST materials arises from both the chemistry and geometry of the tunnels and pores.

  16. {sup 1}H and {sup 23}Na MAS NMR spectroscopy of cationic species in CO{sub 2} selective alkaline earth metal porous silicoaluminophosphates prepared via liquid and solid state ion exchange

    SciTech Connect

    Arevalo-Hidalgo, Ana G.; Dugar, Sneha; Fu, Riqiang; Hernandez-Maldonado, Arturo J.

    2012-07-15

    The location of extraframework cations in Sr{sup 2+} and Ba{sup 2+} ion-exchanged SAPO-34 was estimated by means of {sup 1}H and {sup 23}Na MAS NMR spectroscopy and spectral deconvolution. Incorporation of the alkaline earth metal cations onto the SAPO framework was achieved via liquid state ion exchange, coupled partial detemplation/solid-state ion exchange, and combination of both techniques. MAS NMR revealed that the level of ion exchange was limited by the presence of protons and sodium cations near hexagonal prisms (site SI), which are relatively difficult to exchange with the alkaline earth metal due to steric and charge repulsion criteria. In addition, the presence of ammonium cations in the supercages facilitated the exchange of otherwise tenacious hydrogen as corroborated by unit cell compositional data as well as enhanced CO{sub 2} adsorption at low partial pressures. The extraframework ammonium species were produced from partial detemplation of the structure-directing agent employed for the SAPO-34 synthesis, tetraethylammonium. - Graphical abstract: MAS NMR was used to elucidate the position the cationic species in alkaline earth metal exchanged silicoaluminophosphates. These species played a significant role during the ion exchange process and, therefore, the materials ultimate CO{sub 2} adsorption performance. Highlights: Black-Right-Pointing-Pointer Location of extraframework Sr{sup 2+} or Ba{sup 2+} cations was estimated by means of {sup 1}H and {sup 23}Na MAS NMR. Black-Right-Pointing-Pointer Level of Sr{sup 2+} or Ba{sup 2+} ion exchange was limited by the presence of protons and sodium cations. Black-Right-Pointing-Pointer Presence of ammonium cations in the supercages facilitated the exchange. Black-Right-Pointing-Pointer Sr{sup 2+} and Ba{sup 2+} ion exchanged SAPOs are outstanding CO{sub 2} adsorbents.

  17. 1H NMR studies of substrate hydrogen exchange reactions catalyzed by L-methionine gamma-lyase.

    PubMed

    Esaki, N; Nakayama, T; Sawada, S; Tanaka, H; Soda, K

    1985-07-16

    Hydrogen exchange reactions of various L-amino acids catalyzed by L-methionine gamma-lyase (EC 4.4.1.11) have been studied. The enzyme catalyzes the rapid exchange of the alpha- and beta-hydrogens of L-methionine and S-methyl-L-cysteine with deuterium from the solvent. The rate of alpha-hydrogen exchange was about 40 times faster than that of the enzymatic elimination reaction of the sulfur-containing amino acids. The enzyme also catalyzes the exchange reaction of alpha- and beta-hydrogens of the following straight-chain L-amino acids which are not susceptible to elimination: norleucine, norvaline, alpha-aminobutyrate, and alanine. The exchange rates of the alpha-hydrogen and the total beta-hydrogens of L-alanine and L-alpha-aminobutyrate with deuterium followed first-order kinetics. For L-norvaline, L-norleucine, S-methyl-L-cysteine, and L-methionine, the rate of alpha-hydrogen exchange followed first-order kinetics, but the rate of total beta-hydrogen exchange decreased due to a primary isotope effect at the alpha-position. One beta-hydrogen of S-methyl-L-cysteine was exchanged faster than the other, although both the beta-hydrogens were exchanged completely with deuterium ultimately. L-Phenylalanine and L-tryptophan slowly underwent alpha-hydrogen exchange. The pro-R hydrogen of glycine was deuterated stereospecifically. None of the following amino acids were susceptible to the enzymatic hydrogen exchange: D isomers of the above amino acids, branched chain L-amino acids, acidic L-amino acids, and basic L-amino acids.(ABSTRACT TRUNCATED AT 250 WORDS)

  18. Protein folding and unfolding studied at atomic resolution by fast two-dimensional NMR spectroscopy.

    PubMed

    Schanda, Paul; Forge, Vincent; Brutscher, Bernhard

    2007-07-03

    Atom-resolved real-time studies of kinetic processes in proteins have been hampered in the past by the lack of experimental techniques that yield sufficient temporal and atomic resolution. Here we present band-selective optimized flip-angle short transient (SOFAST) real-time 2D NMR spectroscopy, a method that allows simultaneous observation of reaction kinetics for a large number of nuclear sites along the polypeptide chain of a protein with an unprecedented time resolution of a few seconds. SOFAST real-time 2D NMR spectroscopy combines fast NMR data acquisition techniques with rapid sample mixing inside the NMR magnet to initiate the kinetic event. We demonstrate the use of SOFAST real-time 2D NMR to monitor the conformational transition of alpha-lactalbumin from a molten globular to the native state for a large number of amide sites along the polypeptide chain. The kinetic behavior observed for the disappearance of the molten globule and the appearance of the native state is monoexponential and uniform along the polypeptide chain. This observation confirms previous findings that a single transition state ensemble controls folding of alpha-lactalbumin from the molten globule to the native state. In a second application, the spontaneous unfolding of native ubiquitin under nondenaturing conditions is characterized by amide hydrogen exchange rate constants measured at high pH by using SOFAST real-time 2D NMR. Our data reveal that ubiquitin unfolds in a gradual manner with distinct unfolding regimes.

  19. Quantitative chemical exchange saturation transfer with hyperpolarized nuclei (qHyper-CEST): Sensing xenon-host exchange dynamics and binding affinities by NMR

    SciTech Connect

    Kunth, M. Witte, C.; Schröder, L.

    2014-11-21

    The reversible binding of xenon to host molecules has found numerous applications in nuclear magnetic resonance studies. Quantitative characterization of the Xe exchange dynamics is important to understand and optimize the physico-chemical behavior of such Xe hosts, but is often challenging to achieve at low host concentrations. We have investigated a sensitive quantification technique based on chemical exchange saturation transfer with hyperpolarized nuclei, qHyper-CEST. Using simulated signals we demonstrated that qHyper-CEST yielded accurate and precise results and was robust in the presence of large amounts of noise (10%). This is of particular importance for samples with completely unknown exchange rates. Using these findings we experimentally determined the following exchange parameters for the Xe host cryptophane-A monoacid in dimethyl sulfoxide in one type of experiment: the ratio of bound and free Xe, the Xe exchange rate, the resonance frequencies of free and bound Xe, the Xe host occupancy, and the Xe binding constant. Taken together, qHyper-CEST facilitates sensitive quantification of the Xe exchange dynamics and binding to hydrophobic cavities and has the potential to analyze many different host systems or binding sites. This makes qHyper-CEST an indispensable tool for the efficient design of highly specific biosensors.

  20. Isolation and structural characterization of unusual pyranoanthocyanins and related anthocyanins from Staghorn sumac (Rhus typhina L.) via UPLC-ESI-MS, (1)H, (13)C, and 2D NMR spectroscopy.

    PubMed

    Kirby, Christopher W; Wu, Tao; Tsao, Rong; McCallum, Jason L

    2013-10-01

    The six major anthocyanins found in the burgundy coloured fruits of Staghorn sumac (Rhus typhina L.) were isolated and the structures of four compounds were determined by NMR spectroscopic methods as being: 7-O-methyl-delphinidin-3-O-(2″galloyl)-β-d-galactopyranoside; 7-O-methyl-cyanidin-3-O-(2″galloyl)-β-d-galactopyranoside; 7-O-methyl-delphinidin-3-O-(2″'galloyl)-β-d-galactopyranoside-4-vinyl-catechol-3″-O-β-d-glucopyranoside; and 7-O-methyl-cyanidin-3-O-(2″'galloyl)-β-d-galactopyranoside-4-vinyl-catechol-3″-O-β-d-glucopyranoside, respectively. Additionally, two related anthocyanin compounds, cyanidin-3-O-(2″galloyl)-β-d-galactopyranoside and 7-O-methyl-cyanidin-3-O-β-d-galactopyranoside were also recovered, with NMR spectroscopic values closely matching previous reports from other plant species. The prevalence of 7-O-methyl anthocyanins and their galloylated derivatives in sumac is highly unusual, and warrants special attention. Additionally, the in planta occurrence of two 7-O-methyl-pyranoanothocyanin-vinyl-catechol aglycones, Sumadin A and Sumadin B, and their derivatives is noted. To our knowledge, E-ring glycosylated vinyl-catechol pyranoanthocyanins were previously unknown.

  1. Proton and deuterium NMR experiments in zero field. [Perdeuterated p-demethoxybenzene, perdeuterated malonic acid, diethyl terephthalate-d4, nonadecane-2,2'-D2, sodium propionate-D2

    SciTech Connect

    Millar, J.M.

    1986-02-01

    High field solid-state NMR lineshapes suffer from inhomogeneous broadening since resonance frequencies are a function of molecular orientation. Time domain zero field NMR is a two-dimensional field-cycling technique which removes this broadening by probing the evolution of the spin system under zero applied field. The simplest version, the sudden transition experiment, induces zero field evolution by the sudden removal of the applied magnetic field. Theory and experimental results of this experiment and several variations using pulsed dc magnetic fuelds to initiate zero field evolution are presented. In particular, the pulsed indirect detection method allows detection of the zero field spectrum of one nuclear spin species via another (usually protons) by utilizing the level crossings which occur upon adiabatic demagnetization to zero field. Experimental examples of proton/deuteron systems are presented which demonstrate the method results in enhanced sensitivity relative to that obtained in sudden transition experiments performed directly on deuterium. High resolution /sup 2/H NQR spectra of a series of benzoic acid derivatives are obtained using the sudden transition and indirect detection methods. Librational oscillations in the water molecules of barium chlorate monohydrate are studied using proton and deuterium ZF experiments. 177 refs., 88 figs., 2 tabs.

  2. In-pore exchange and diffusion of carbonate solvent mixtures in nanoporous carbon

    DOE PAGES

    Alam, Todd M.; Osborn Popp, Thomas M.

    2016-06-04

    High resolution magic angle spinning (HRMAS) 1H NMR spectroscopy has been used to resolve different surface and in-pore solvent environments of ethylene carbonate (EC) and dimethyl carbonate (DMC) mixtures absorbed within nanoporous carbon (NPC). Two dimensional (2D) 1H HRMAS NMR exchange measurements revealed that the inhomogeneous broadened in-pore resonances have pore-to-pore exchange rates on the millisecond timescale. Pulsed-field gradient (PFG) NMR diffusometry revealed the in-pore self-diffusion constants for both EC and DMC were reduced by up to a factor of five with respect to the diffusion in the non-absorbed solvent mixtures.

  3. In-pore exchange and diffusion of carbonate solvent mixtures in nanoporous carbon

    NASA Astrophysics Data System (ADS)

    Alam, Todd M.; Osborn Popp, Thomas M.

    2016-08-01

    High resolution magic angle spinning (HRMAS) 1H NMR spectroscopy has been used to resolve different surface and in-pore solvent environments of ethylene carbonate (EC) and dimethyl carbonate (DMC) mixtures absorbed within nanoporous carbon (NPC). Two dimensional (2D) 1H HRMAS NMR exchange measurements revealed that the inhomogeneous broadened in-pore resonances have pore-to-pore exchange rates on the millisecond timescale. Pulsed-field gradient (PFG) NMR diffusometry revealed the in-pore self-diffusion constants for both EC and DMC were reduced by up to a factor of five with respect to the diffusion in the non-absorbed solvent mixtures.

  4. Probing the rate-limiting step for intramolecular transfer of a transcription factor between specific sites on the same DNA molecule by (15)Nz-exchange NMR spectroscopy.

    PubMed

    Ryu, Kyoung-Seok; Tugarinov, Vitali; Clore, G Marius

    2014-10-15

    The kinetics of translocation of the homeodomain transcription factor HoxD9 between specific sites of the same or opposite polarities on the same DNA molecule have been studied by (15)Nz-exchange NMR spectroscopy. We show that exchange occurs by two facilitated diffusion mechanisms: a second-order intermolecular exchange reaction between specific sites located on different DNA molecules without the protein dissociating into free solution that predominates at high concentrations of free DNA, and a first-order intramolecular process involving direct transfer between specific sites located on the same DNA molecule. Control experiments using a mixture of two DNA molecules, each possessing only a single specific site, indicate that transfer between specific sites by full dissociation of HoxD9 into solution followed by reassociation is too slow to measure by z-exchange spectroscopy. Intramolecular transfer with comparable rate constants occurs between sites of the same and opposing polarity, indicating that both rotation-coupled sliding and hopping/flipping (analogous to geminate recombination) occur. The half-life for intramolecular transfer (0.5-1 s) is many orders of magnitude larger than the calculated transfer time (1-100 μs) by sliding, leading us to conclude that the intramolecular transfer rates measured by z-exchange spectroscopy represent the rate-limiting step for a one-base-pair shift from the specific site to the immediately adjacent nonspecific site. At zero concentration of added salt, the intramolecular transfer rate constants between sites of opposing polarity are smaller than those between sites of the same polarity, suggesting that hopping/flipping may become rate-limiting at very low salt concentrations.

  5. 2D NMR analysis of highly restricted internal rotation in 2-methylthio-3H-4- p-bromophenyl)-7-[( ortho- and para-substituted)-phenylthio]-1,5-benzodiazepines

    NASA Astrophysics Data System (ADS)

    Cortes C., E.; Becerra L., M. I.; Osornio P., Y. M.; Díaz T., E.; Jankowski, K.

    2000-08-01

    The complete assignments of twelve 4-ary1-7-thioary1-1,5-benzodiazepines 1H and 13C spectra, performed with the use of high resolution variable solvent and temperature 1D and 2D techniques (e.g. HOMOCOSY, NOESY, HMQC and HMBC), lead to the determination of conformational equilibria between two rotamers having the aromatic ring of the thioaryl oriented in a perpendicular or helical orientation toward the benzodiazepine ring. The restricted rotation was evaluated from the population of these conformers.

  6. Characterization and 2D NMR study of the stable [9-21, 15-27] 2 disulfide intermediate in the folding of the 3 disulfide trypsin inhibitor EETI II.

    PubMed Central

    Le-Nguyen, D.; Heitz, A.; Chiche, L.; el Hajji, M.; Castro, B.

    1993-01-01

    The three disulfide Ecballium elaterium trypsin inhibitor II (EETI II) reduction with dithiothreitol (DTT) and reoxidation of the fully reduced derivative have been examined. A common stable intermediate has been observed for both processes. Isolation and sequencing of carboxymethylated material showed that the intermediate lacks the [2-19] bridge. The NMR study showed a very strong structural conservation as compared to the native EETI II, suggesting that the bridges are the [9-21] and [15-27] native ones. The differences occurred in sections 2-7 (containing the free cysteine 2 and the Arg 4-Ile 5 active site) and 19-21 (containing the second free cysteine). Distance geometry calculations and restrained molecular dynamics refinements were also in favor of a [9-21, 15-27] arrangement and resulted in a well-conserved (7-28) segment. PMID:8443596

  7. EXCHANGE

    SciTech Connect

    Boltz, J.C.

    1992-09-01

    EXCHANGE is published monthly by the Idaho National Engineering Laboratory (INEL), a multidisciplinary facility operated for the US Department of Energy (DOE). The purpose of EXCHANGE is to inform computer users about about recent changes and innovations in both the mainframe and personal computer environments and how these changes can affect work being performed at DOE facilities.

  8. Levothyroxine sodium revisited: A wholistic structural elucidation approach of new impurities via HPLC-HRMS/MS, on-line H/D exchange, NMR spectroscopy and chemical synthesis.

    PubMed

    Ruggenthaler, M; Grass, J; Schuh, W; Huber, C G; Reischl, R J

    2017-02-20

    The structural elucidation of unknown pharmaceutical impurities plays an important role in the quality control of newly developed and well-established active pharmaceutical ingredients (APIs). The United States Pharmacopeia (USP) monograph for the API Levothyroxine Sodium, a synthetic thyroid hormone, features two high pressure liquid chromatography (HPLC) methods using UV-VIS absorption detection to determine organic impurities in the drug substance. The impurity profile of the first USP method ("Procedure 1") has already been extensively studied, however for the second method ("Procedure 2"), which exhibits a significantly different impurity profile, no wholistic structural elucidation of impurities has been performed yet. Applying minor modifications to the chromatographic parameters of USP "Procedure 2" and using various comprehensive structural elucidation methods such as high resolution tandem mass spectrometry with on-line hydrogen-deuterium (H/D) exchange or two-dimensional nuclear magnetic resonance spectroscopy (NMR) we gained new insights about the complex impurity profile of the synthetic thyroid hormone. This resulted in the characterization of 24 compounds previously unknown to literature and the introduction of two new classes of Levothyroxine Sodium impurities. Five novel compounds were unambiguously identified via isolation or synthesis of reference substances and subsequent NMR spectroscopic investigation. Additionally, Collision-Induced Dissociation (CID)-type fragmentation of identified major impurities as well as neutral loss fragmentation patterns of many characterized impurities were discussed.

  9. Analysis of crude heparin by (1)H NMR, capillary electrophoresis, and strong-anion-exchange-HPLC for contamination by over sulfated chondroitin sulfate.

    PubMed

    Keire, David A; Trehy, Michael L; Reepmeyer, John C; Kolinski, Richard E; Ye, Wei; Dunn, Jamie; Westenberger, Benjamin J; Buhse, Lucinda F

    2010-03-11

    We previously published a strong-anion-exchange-high performance liquid chromatography (SAX-HPLC) method for the detection of the contaminant over sulfated chondroitin sulfate (OSCS) in heparin sodium active pharmaceutical ingredient (API). While APIs have been processed to remove impurities, crude heparins contain insoluble material, chondroitin sulfates, heparan sulfate, and proteins that may interfere with the recovery and measurement of OSCS. We examined 500MHz (1)H NMR, capillary electrophoresis (CE), and SAX-HPLC to quantify OSCS in crude heparin. Using our standard API protocol on OSCS spiked crude heparin samples; we observed a weight percent LOD and LOQ for the NMR approach of 0.1% and 0.3%, respectively, while the SAX-HPLC method gave values of 0.03% and 0.09%, respectively. CE data was not amenable to quantitative measurement of OSCS in crude heparin. We developed a modified HPLC sample preparation protocol using crude dissolved at the 100mg/mL level with a 2.5M NaCl solution. This SAX-HPLC approach gave a weight percent LOD of 0.02% and a LOQ of 0.07% and had better performance characteristics than that of the protocol used for APIs.

  10. Discrete and infinite 1D, 2D/3D cage frameworks with inclusion of anionic species and anion-exchange reactions of Ag3L2 type receptor with tetrahedral and octahedral anions.

    PubMed

    Liu, Hong-Ke; Huang, Xiaohua; Lu, Tianhong; Wang, Xiujian; Sun, Wei-Yin; Kang, Bei-Sheng

    2008-06-28

    Complexes [PF6 subset(Ag3(titmb)2](PF6)2 (8) and {SbF6 subset[Ag3(titmb)2](SbF6)2}.H2O.1.5 CH3OH (9) are obtained by reaction of titmb and Ag+ salts with different anions (PF6(-) and SbF6(-)), and crystal structures reveal that they are both M3L2 cage complexes with short Ag...F interactions between the silver atoms and the fluorine atoms of the anions. In complex 8, a novel cage dimer is formed by weak Ag...F contacts; an unique cage tetramer formed via Ag...pi interactions (Ag...eta5-imidazole) between dimers and an infinite 1D cage chain is presented. However, each of the external non-disordered SbF6(-) anions connect with six cage 9s via Ag...F contacts, and each cage 9 in turn connects with three SbF6(-) anions to form a 2D network cage layer; and the layers are connected by pi-pi interactions to form a 3D network. The anion-exchange reactions of four Ag3L2 type complexes ([BF4 subset(Ag3(titmb)2](BF4)2 (6), [ClO4 subset(Ag3(titmb)2](ClO4)2 (7b), [PF6 subset(Ag3(titmb)2](PF6)2 (8) and [SbF6 subset(Ag3(titmb)2](SbF6)2.1.5CH3OH (9)) with tetrahedral and octahedral anions (ClO4(-), BF4(-), PF6(-) and SbF6(-)) are also reported. The anion-exchange experiments demonstrate that the anion selective order is SbF6(-) > PF6(-) > BF4(-), ClO4(-), and this anion receptor is preferred to trap octahedral and tetrahedral anions rather than linear or triangle anions; SbF6(-) is the biggest and most preferable one, so far. The dimensions of cage complexes with or without internal anions, anion-exchange reactions, cage assembly and anion inclusions, silver(I) coordination environments, Ag-F and Ag-pi interactions of Ag3L2 complexes 1-9 are discussed.

  11. Synthesis and structural analysis using 2-D NMR of Sialyl Lewis X (SLe{sup x}) and Lewis X (Le{sup x}) oligosaccharides: Ligands related to E-selectin [ELAM-1] binding

    SciTech Connect

    Ball, G.E.; Nagy, J.O.; Brown, E.G.

    1992-06-17

    The sialyl Lewis X (SLe{sup x}) determinant (NeuAc-{alpha}-2,3-Gal-{beta}-1,4-[Fuc-{alpha}-1,3]-GlcNAc), compound 1, is a ligand for E-selectin (endothelial leucocyte adhesion molecule 1, or ELAM-1), a member of the selectin family of cell adhesion molecules. Interactions between E-selectin and leucocyte-bound SLe{sup x} or closely related oligosaccharides are thought to be important early events in the inflammation process. Binding analysis has shown that the sialic acid (NeuAc) and the fucose (Fuc) moieties are essential for high affinity. The related desialylated trisaccharide Le{sup x} (Gas-{beta}-1,4-[Fuc-{alpha}-1,3]-GlcNAc), for example, is not a high-affinity ligand for E-selectin. In this communication, the authors describe the syntheses of SLe{sup x} 1 and the {beta}-O-allyl glycoside of Le{sup x} 2 using a cloned fucosyltransferase and their complete NMR spectral assignments including ROESY and NOESY experiments in order to investigate the conformation of these compounds in solution. 25 refs., 2 figs.

  12. Characterization of enzyme-bound ligand dynamics by solid-state NMR in the presence of ligand exchange: L-phenylalanine on carboxypeptidase A.

    PubMed Central

    Zhang, H; Bryant, R G

    1995-01-01

    Deuterium NMR spectra were obtained for L-phenylalanine-d5, deuterated on the phenyl ring, in cross-linked polycrystalline samples of carboxypeptidase A containing different amounts of water. The deuterium powder pattern line shapes are simulated by extension of the theory to include both a local reorientational motion of the bound L-phenylalanine phenyl ring and exchange of the L-phenylalanine with an intracrystalline isotropic environment. The spectral simulations are consistent with the phenyl ring of the phenylalanine executing pi-flips in the bound environment at rates that vary from 3 x 10(4) Hz at 6% water content to 1 x 10(5) Hz at 21% water content. At all water contents studied, the ligand exchanges with an essentially isotropic environment in the crystal with a rate constant of approximately 2.5 x 10(-3) Hz. Although the dissociation constant for the L-phenylalanine is only 18 mM, the spectral simulations that reproduce the experimental line shape well do not require significant wobble of the phenyl ring rotation axis, which is consistent with the binding interactions identified by x-ray crystallography. Images FIGURE 3 PMID:7711255

  13. Folding of apomyoglobin: Analysis of transient intermediate structure during refolding using quick hydrogen deuterium exchange and NMR.

    PubMed

    Nishimura, Chiaki

    2017-01-01

    The structures of apomyoglobin folding intermediates have been widely analyzed using physical chemistry methods including fluorescence, circular dichroism, small angle X-ray scattering, NMR, mass spectrometry, and rapid mixing. So far, at least two intermediates (on sub-millisecond- and millisecond-scales) have been demonstrated for apomyoglobin folding. The combination of pH-pulse labeling and NMR is a useful tool for analyzing the kinetic intermediates at the atomic level. Its use has revealed that the latter-phase kinetic intermediate of apomyoglobin (6 ms) was composed of helices A, B, G and H, whereas the equilibrium intermediate, called the pH 4 molten-globule intermediate, was composed mainly of helices A, G and H. The improved strategy for the analysis of the kinetic intermediate was developed to include (1) the dimethyl sulfoxide method, (2) data processing with the various labeling times, and (3) a new in-house mixer. Particularly, the rapid mixing revealed that helices A and G were significantly more protected at the earlier stage (400 µs) of the intermediate (former-phase intermediate) than the other helices. Mutation studies, where each hydrophobic residue was replaced with an alanine in helices A, B, E, F, G and H, indicated that both non-native and native-like structures exist in the latter-phase folding intermediate. The N-terminal part of helix B is a weak point in the intermediate, and the docking of helix E residues to the core of the A, B, G and H helices was interrupted by a premature helix B, resulting in the accumulation of the intermediate composed of helices A, B, G and H. The prediction-based protein engineering produced important mutants: Helix F in a P88K/A90L/S92K/A94L mutant folded in the latter-phase intermediate, although helix F in the wild type does not fold even at the native state. Furthermore, in the L11G/W14G/A70L/G73W mutant, helix A did not fold but helix E did, which is similar to what was observed in the kinetic

  14. Vertical 2D Heterostructures

    NASA Astrophysics Data System (ADS)

    Lotsch, Bettina V.

    2015-07-01

    Graphene's legacy has become an integral part of today's condensed matter science and has equipped a whole generation of scientists with an armory of concepts and techniques that open up new perspectives for the postgraphene area. In particular, the judicious combination of 2D building blocks into vertical heterostructures has recently been identified as a promising route to rationally engineer complex multilayer systems and artificial solids with intriguing properties. The present review highlights recent developments in the rapidly emerging field of 2D nanoarchitectonics from a materials chemistry perspective, with a focus on the types of heterostructures available, their assembly strategies, and their emerging properties. This overview is intended to bridge the gap between two major—yet largely disjunct—developments in 2D heterostructures, which are firmly rooted in solid-state chemistry or physics. Although the underlying types of heterostructures differ with respect to their dimensions, layer alignment, and interfacial quality, there is common ground, and future synergies between the various assembly strategies are to be expected.

  15. 2D semiconductor optoelectronics

    NASA Astrophysics Data System (ADS)

    Novoselov, Kostya

    The advent of graphene and related 2D materials has recently led to a new technology: heterostructures based on these atomically thin crystals. The paradigm proved itself extremely versatile and led to rapid demonstration of tunnelling diodes with negative differential resistance, tunnelling transistors, photovoltaic devices, etc. By taking the complexity and functionality of such van der Waals heterostructures to the next level we introduce quantum wells engineered with one atomic plane precision. Light emission from such quantum wells, quantum dots and polaritonic effects will be discussed.

  16. NMR and Raman spectroscopy monitoring of proton/deuteron exchange in aqueous solutions of ionic liquids forming hydrogen bond: a role of anions, self-aggregation, and mesophase formation.

    PubMed

    Klimavicius, Vytautas; Gdaniec, Zofia; Kausteklis, Jonas; Aleksa, Valdemaras; Aidas, Kestutis; Balevicius, Vytautas

    2013-09-05

    The H/D exchange process in the imidazolium-based room temperature ionic liquids (RTILs) 1-decyl-3-methyl-imidazolium bromide- and chloride ([C10mim][Br] and [C10mim][Cl]) in D2O solutions of various concentrations was studied applying (1)H, (13)C NMR, and Raman spectroscopy. The time dependencies of integral intensities in NMR spectra indicate that the H/D exchange in [C10mim][Br] at very high dilution (10(-4) mole fraction of RTIL) runs only slightly faster than in [C10mim][Cl]. The kinetics of this process drastically changes above critical aggregation concentration (CAC). The time required to reach the apparent reaction saturation regime in the solutions of 0.01 mole fraction of RTIL was less 10 h for [C10mim][Br], whereas no such features were seen for [C10mim][Cl] even tens of days after the sample was prepared. The H/D exchange was not observed in the liquid crystalline gel mesophase. The role of anions, self-aggregation (micellization), and mesophase formation has been discussed. Crucial influence of Br(-) and Cl(-) anions on the H/D exchange rates above CAC could be related to the short-range ordering and molecular microdynamics, in particular that of water molecules. The concept of the conformational changes coupled with the H/D exchange in imidazolium-based ionic liquids with longer hydrocarbon chains can be rejected in the light of (13)C NMR experiment. The revealed changes in (13)C NMR spectra are caused by the secondary ((13)C) isotope effects not being the signal shifts due to the conformational trans-gauche transition.

  17. Relaxation-relaxation exchange experiments in porous media with portable Halbach-Magnets.

    NASA Astrophysics Data System (ADS)

    Haber, A.; Haber-Pohlmeier, S.; Casanova, F.; Blümich, B.

    2009-04-01

    Mobile NMR became a powerful tool following the development of portable NMR sensors for well logging. By now there are numerous applications of mobile NMR in materials analysis and chemical engineering where, for example, unique information about the structure, morphology and dynamics of polymers is obtained, and new opportunities are provided for geo-physical investigations [1]. In particular, dynamic information can be retrieved by two-dimensional Laplace exchange NMR, where the initial NMR relaxation environment is correlated with the final relaxation environment of molecules migrating from one environment to the other within a so-called NMR mixing time tm [2]. Relaxation-relaxation exchange experiments of water in inorganic porous media were performed at low and moderately inhomogeneous magnetic field with a simple, portable Halbach-Magnet. By conducting NMR transverse relaxation exchange experiments for several mixing times and converting the results to 2D T2 distributions (joint probability densities of transverse relaxation times T2) with the help of the inverse 2D Laplace Transformation (ILT), we obtained characteristic exchange times for different pore sizes. The results of first experiments on soil samples are reported, which reveal information about the complex pore structure of soil and the moisture content. References: 1. B. Blümich, J. Mauler, A. Haber, J. Perlo, E. Danieli, F. Casanova, Mobile NMR for Geo-Physical Analysis and Material Testing, Petroleum Science, xx (2009) xxx - xxx. 2. K. E. Washburn, P.T. Callaghan, Tracking pore to pore exchange using relaxation exchange spectroscopy, Phys. Rev. Lett. 97 (2006) 175502.

  18. Signal loss in 1D magic-angle spinning exchange NMR (CODEX): radio-frequency limitations and intermediate motions.

    PubMed

    Hackel, Christiane; Franz, Cornelius; Achilles, Anja; Saalwächter, Kay; Reichert, Detlef

    2009-08-28

    The popular 1D MAS exchange experiment CODEX suffers limitations due to signal loss during the finite recoupling periods, during which the magnetization evolves in the transverse plane. Here, we address the origins and possible improvements of this problem, aimed at (i) an optimization of the signal-to-noise ratio in the experiments, as well as harnessing intermediate-motion induced signal loss for obtaining approximate information on (ii) correlation times and (iii) potential distributions, where the latter are often found in polymeric systems. First, we show that the intensity of the signal is sensitive to the radiofrequency (rf) parameters of the carbon recoupling and proton decoupling, and care must be taken to gain optimal signal intensity. Optimum conditions are found for recoupling pulses being as short as possible for large chemical shift anisotropy (CSA) values, and approaching a ratio of 3 between the nutation frequencies for protonated carbons, calling for an individual adjustment in each case. Second, we demonstrate that the effect of intermediate motions can be studied semi-quantitatively by combining CODEX data with its constant-time modification CONTRA, which allows for a tuning of the signal loss due to intermediate motions. Third, for the case of samples featuring a distribution of correlation times, we propose a procedure to obtain an estimate of the proportion of molecular segments in the sample for which the CODEX data are representative, i.e., which share of segments moves truly in the slow-motion regime. The procedure involves the combination of CODEX data with a cross-polarisation (CP) reference experiment for an estimate of the full sample magnetization; it is demonstrated on the example of semi-crystalline poly(ethylene oxide).

  19. Inkjet printing of 2D layered materials.

    PubMed

    Li, Jiantong; Lemme, Max C; Östling, Mikael

    2014-11-10

    Inkjet printing of 2D layered materials, such as graphene and MoS2, has attracted great interests for emerging electronics. However, incompatible rheology, low concentration, severe aggregation and toxicity of solvents constitute critical challenges which hamper the manufacturing efficiency and product quality. Here, we introduce a simple and general technology concept (distillation-assisted solvent exchange) to efficiently overcome these challenges. By implementing the concept, we have demonstrated excellent jetting performance, ideal printing patterns and a variety of promising applications for inkjet printing of 2D layered materials.

  20. Complete 1H assignments of the non-exchangeable protons of the non self-complementary heptadeoxyribonucleotide d[(GTCGTCA).(TGACGAC)] and its component strands by high field NMR.

    PubMed

    Lown, J W; Hanstock, C C; Lobe, C G; Bleackley, C

    1985-06-01

    The non self complementary heptadeoxyribonucleotides d(GTCGTCA) and d(TGACGAC) were synthesized by the phosphotriester method. While complete 1H-NMR assignments of the former were obtained by a combination of one and two-dimensional techniques at room temperature, extensive stacking of the latter under these conditions dictated analysis at 50 degrees C when the lines were sharply resolved. The duplex form of the annealed strands under the conditions of the 1H-NMR experiment was established independently of the NMR evidence by 32P end labeling with T4 polynucleotide kinase followed by butt end joining using the absolute specificity of T4 ligase for double strand DNA. Analysis of the resulting ladder of polymers was performed using gel electrophoresis and autoradiography. Complete 1H-NMR assignments of the non-exchangeable protons in the self complementary heptamer was achieved. The assignments were confirmed using NOE differences, and two-dimensional COSY, and HH-INADEQUATE experiments at 400 and 500 MHz. The assignments are in accord with a conformation for the heptamer belonging to the B family of structures.

  1. Stacking structure of confined 1-butanol in SBA-15 investigated by solid-state NMR spectroscopy.

    PubMed

    Lin, Yun-Chih; Chou, Hung-Lung; Sarma, Loka Subramanyam; Hwang, Bing-Joe

    2009-10-12

    Understanding the complex thermodynamic behavior of confined amphiphilic molecules in biological or mesoporous hosts requires detailed knowledge of the stacking structures. Here, we present detailed solid-state NMR spectroscopic investigations on 1-butanol molecules confined in the hydrophilic mesoporous SBA-15 host. A range of NMR spectroscopic measurements comprising of (1)H spin-lattice (T(1)), spin-spin (T(2)) relaxation, (13)C cross-polarization (CP), and (1)H,(1)H two-dimensional nuclear Overhauser enhancement spectroscopy ((1)H,(1)H 2D NOESY) with the magic angle spinning (MAS) technique as well as static wide-line (2)H NMR spectra have been used to investigate the dynamics and to observe the stacking structure of confined 1-butanol in SBA-15. The results suggest that not only the molecular reorientation but also the exchange motions of confined molecules of 1-butanol are extremely restricted in the confined space of the SBA-15 pores. The dynamics of the confined molecules of 1-butanol imply that the (1)H,(1)H 2D NOESY should be an appropriate technique to observe the stacking structure of confined amphiphilc molecules. This study is the first to observe that a significant part of confined 1-butanol molecules are orientated as tilted bilayered structures on the surface of the host SBA-15 pores in a time-average state by solid-state NMR spectroscopy with the (1)H,(1)H 2D NOESY technique.

  2. E-2D Advanced Hawkeye Aircraft (E-2D AHE)

    DTIC Science & Technology

    2015-12-01

    Selected Acquisition Report (SAR) RCS: DD-A&T(Q&A)823-364 E-2D Advanced Hawkeye Aircraft (E-2D AHE) As of FY 2017 President’s Budget Defense...Office Estimate RDT&E - Research, Development, Test, and Evaluation SAR - Selected Acquisition Report SCP - Service Cost Position TBD - To Be Determined

  3. Giant spin-orbit effects on (1)H and (13)C NMR shifts for uranium(vi) complexes revisited: role of the exchange-correlation response kernel, bonding analyses, and new predictions.

    PubMed

    Greif, Anja H; Hrobárik, Peter; Autschbach, Jochen; Kaupp, Martin

    2016-11-09

    Previous relativistic quantum-chemical predictions of unusually large (1)H and (13)C NMR chemical shifts for ligand atoms directly bonded to a diamagnetic uranium(vi) center (P. Hrobárik, V. Hrobáriková, A. H. Greif and M. Kaupp, Angew. Chem., Int. Ed., 2012, 51, 10884) have been revisited by two- and four-component relativistic density functional methods. In particular, the effect of the exchange-correlation response kernel, which had been missing in the previously used two-component version of the Amsterdam Density Functional program, has been examined. Kernel contributions are large for cases with large spin-orbit (SO) contributions to the NMR shifts and may amount to up to ∼30% of the total shifts, which means more than a 50 ppm difference for the metal-bonded carbon shifts in some extreme cases. Previous calculations with a PBE-40HF functional had provided overall reasonable predictions, due to cancellation of errors between the missing kernel contributions and the enhanced exact-exchange (EXX) admixture of 40%. In the presence of an exchange-correlation kernel, functionals with lower EXX admixtures give already good agreement with experiments, and the PBE0 functional provides reasonable predictive quality. Most importantly, the revised approach still predicts unprecedented giant (1)H NMR shifts between +30 ppm and more than +200 ppm for uranium(vi) hydride species. We also predict uranium-bonded (13)C NMR shifts for some synthetically known organometallic U(vi) complexes, for which no corresponding signals have been detected to date. In several cases, the experimental lack of these signals may be attributed to unexpected spectral regions in which some of the (13)C NMR shifts can appear, sometimes beyond the usual measurement area. An extremely large uranium-bonded (13)C shift above 550 ppm, near the upper end of the diamagnetic (13)C shift range, is predicted for a known pincer carbene complex. Bonding analyses allow in particular the magnitude of the SO

  4. Extrinsic Cation Selectivity of 2D Membranes

    PubMed Central

    2017-01-01

    From a systematic study of the concentration driven diffusion of positive and negative ions across porous 2D membranes of graphene and hexagonal boron nitride (h-BN), we prove their cation selectivity. Using the current–voltage characteristics of graphene and h-BN monolayers separating reservoirs of different salt concentrations, we calculate the reversal potential as a measure of selectivity. We tune the Debye screening length by exchanging the salt concentrations and demonstrate that negative surface charge gives rise to cation selectivity. Surprisingly, h-BN and graphene membranes show similar characteristics, strongly suggesting a common origin of selectivity in aqueous solvents. For the first time, we demonstrate that the cation flux can be increased by using ozone to create additional pores in graphene while maintaining excellent selectivity. We discuss opportunities to exploit our scalable method to use 2D membranes for applications including osmotic power conversion. PMID:28157333

  5. Probing Hydronium Ion Histidine NH Exchange Rate Constants in the M2 Channel via Indirect Observation of Dipolar-Dephased (15)N Signals in Magic-Angle-Spinning NMR.

    PubMed

    Fu, Riqiang; Miao, Yimin; Qin, Huajun; Cross, Timothy A

    2016-12-14

    Water-protein chemical exchange in membrane-bound proteins is an important parameter for understanding how proteins interact with their aqueous environment, but has been difficult to observe in membrane-bound biological systems. Here, we demonstrate the feasibility of probing specific water-protein chemical exchange in membrane-bound proteins in solid-state MAS NMR. By spin-locking the (1)H magnetization along the magic angle, the (1)H spin diffusion is suppressed such that a water-protein chemical exchange process can be monitored indirectly by dipolar-dephased (15)N signals through polarization transfer from (1)H. In the example of the Influenza A full length M2 protein, the buildup of dipolar-dephased (15)N signals from the tetrad of His37 side chains have been observed as a function of spin-lock time. This confirms that hydronium ions are in exchange with protons in the His37 NH bonds at the heart of the M2 proton conduction mechanism, with an exchange rate constant of ∼1750 s(-1) for pH 6.2 at -10 °C.

  6. Exact e-e (exchange) correlations of 2-D quantum dots in magnetic field: Size extensive N = 3 , 4 , … , ‧ n ‧ -electron systems via multi-pole expansion

    NASA Astrophysics Data System (ADS)

    Aggarwal, Priyanka; Sharma, Shivalika; Singh, Sunny; Kaur, Harsimran; Hazra, Ram Kuntal

    2017-04-01

    Inclusion of coulomb interaction emerges with the complexity of either convergence of integrals or separation of variables of Schrödinger equations. For an N-electron system, interaction terms grow by N(N-1)/2 factors. Therefore, 2-e system stands as fundamental basic unit for generalized N-e systems. For the first time, we have evaluated e-e correlations in very simple and absolutely terminating finite summed hypergeometric series for 2-D double carrier parabolic quantum dot in both zero and arbitrary non-zero magnetic field (symmetric gauge) and have appraised these integrals in variational methods. The competitive role among confinement strength, magnetic field, mass of the carrier and dielectric constant of the medium on energy level diagram, level-spacing statistics, heat capacities (Cv at 1 K) and magnetization (T ∼ (0-1)K) is studied on systems spanning over wide range of materials (GaAs,Ge,CdS,SiO2 and He, etc). We have also constructed an exact theory for generalized correlated N-e 2-D quantum dots via multi-pole expansion but for the sake of compactness of the article we refrain from data.

  7. NMR at the Picomole Level of a DNA Adduct

    PubMed Central

    Kautz, Roger; Wang, Poguang; Giese, Roger W.

    2014-01-01

    We investigate the limit of detection for obtaining NMR data of a DNA adduct using modern microscale NMR instrumentation, once the adduct has been isolated at the pmol level. Eighty nanograms (130 pmol) of a DNA adduct standard, N-(2′-deoxyguanosin-8-yl)-2-acetylaminofluorene 5′-monophosphate (AAF-dGMP), in 1.5 μL of D2O with 10% methanol-d4, in a vial, was completely picked up as a droplet suspended in a fluorocarbon liquid, and loaded efficiently into a microcoil probe. This work demonstrates a practical manual method of droplet microfluidic sample loading, previously demonstrated using automated equipment, which provides a several-fold advantage over conventional flow injection. Eliminating dilution during injection and confining the sample into the observed volume realizes the full theoretical mass sensitivity of a microcoil, comparable to a micro-cryo probe. With 80 ng, an NMR spectrum acquired over 40 hr showed all of the resonances seen in a standard spectrum of AAF-dGMP, with a S/N of at least 10, despite broadening due to previously-noted effects of conformational exchange. Also a 2D TOCSY spectrum (total correlation spectroscopy) was acquired on 1.6 μg in 18 hr. This work helps to define the utility of NMR in combination with other analytical methods for the structural characterization of a small amount of a DNA adduct. PMID:24028148

  8. 1H NMR studies of ligand and H/D exchange reactions of cis- and trans-([14]aneN4)(H2O)RhH2+ in aqueous solutions.

    PubMed

    Lemma, Kelemu; Ellern, Arkady; Bakac, Andreja

    2003-06-02

    Substitution and exchange reactions of cis- and trans-L(1)(H(2)O)RhH(2+) (L(1) = 1,4,8,11-tetraazacyclotetradecane = [14]aneN(4)) were studied in aqueous solutions by UV-vis and (1)H NMR spectroscopies. At pH 1 and 25 degrees C, the substitution of SCN(-) for the coordinated molecule of water is rapid and thermodynamically favorable. Spectrophotometric determinations yielded the equilibrium constants K = 1.49 x 10(3) M(-1) (cis) and 1.44 x 10(3) (trans). (1)H NMR studies in D(2)O revealed a rapid dynamic process, interpreted as the exchange between coordinated water and X(-) (X = Cl, Br, or I). On the other hand, no line broadening was observed for the strongly bound ligands CN(-) and SCN(-). The complex trans-L(1)(D(2)O)RhH(2+) undergoes a base-catalyzed H/D exchange of the hydride in D(2)O with a rate constant of (1.45 +/- 0.02) x 10(3) M(-1) s(-1). The exchange in the cis isomer is very slow under similar conditions. The complex cis-[L(1)ClRhH](ClO(4)) crystallizes in the centrosymmetric Ponemacr; space group, unit cell dimensions a = 8.9805(11) A, b = 9.1598(11) A, c = 10.4081(13) A, alpha = 81.091(2) degrees, beta = 81.978(2) degrees, gamma = 88.850(2) degrees. The rhodium atom resides in a slightly distorted octahedral environment consisting of the four N atoms of the cyclam, a stereochemically active hydrogen, and a chlorine atom.

  9. Commensurate Superstructure of the {Cu(NO3)(H2O)}(HTae)(Bpy) Coordination Polymer: An Example of 2D Hydrogen-Bonding Networks as Magnetic Exchange Pathway.

    PubMed

    Fernández de Luis, Roberto; Larrea, Edurne S; Orive, Joseba; Lezama, Luis; Arriortua, María I

    2016-11-21

    The average and commensurate superstructures of the one-dimensional coordination polymer {Cu(NO3)(H2O)}(HTae)(Bpy) (H2Tae = 1,1,2,2-tetraacetylethane, Bpy = 4,4'-bipyridine) were determined by single-crystal X-ray diffraction, and the possible symmetry relations between the space group of the average structure and the superstructure were checked. The crystal structure consists in parallel and oblique {Cu(HTae)(Bpy)} zigzag metal-organic chains stacked along the [100] crystallographic direction. The origin of the fivefold c axis in the commensurate superstructure is ascribed to a commensurate modulation of the coordination environment of the copper atoms. The commensurately ordered nitrate groups and coordinated water molecules establish a two-dimensional hydrogen-bonding network. Moreover, the crystal structure shows a commensurate to incommensurate transition at room temperature. The release of the coordination water molecules destabilizes the crystal framework, and the compound shows an irreversible structure transformation above 100 °C. Despite the loss of crystallinity, the spectroscopic studies indicate that the main building blocks of the crystal framework are retained after the transformation. The hydrogen-bonding network not only plays a crucial role stabilizing the crystal structure but also is an important pathway for magnetic exchange transmission. In fact, the magnetic susceptibility curves indicate that after the loss of coordinated water molecules, and hence the collapse of the hydrogen-bonding network, the weak anti-ferromagnetic coupling observed in the initial compound is broken. The electron paramagnetic resonance spectra are the consequence of the average signals from Cu(II) with different orientations, indicating that the magnetic coupling is effective between them. In fact, X- and Q-band data are reflecting different situations; the X-band spectra show the characteristics of an exchange g-tensor, while the Q-band signals are coming from both

  10. NMR spectroscopic evidence for the intermediacy of XeF(3)(-) in XeF(2)/F(-) exchange, attempted syntheses and thermochemistry of XeF(3)(-) salts, and theoretical studies of the XeF(3)(-) anion.

    PubMed

    Vasdev, Neil; Moran, Matthew D; Tuononen, Heikki M; Chirakal, Raman; Suontamo, Reijo J; Bain, Alex D; Schrobilgen, Gary J

    2010-10-04

    The existence of the trifluoroxenate(II) anion, XeF(3)(-), had been postulated in a prior NMR study of the exchange between fluoride ion and XeF(2) in CH(3)CN solution. The enthalpy of activation for this exchange, ΔH(⧧), has now been determined by use of single selective inversion (19)F NMR spectroscopy to be 74.1 ± 5.0 kJ mol(-1) (0.18 M) and 56.9 ± 6.7 kJ mol(-1) (0.36 M) for equimolar amounts of [N(CH(3))(4)][F] and XeF(2) in CH(3)CN solvent. Although the XeF(3)(-) anion has been observed in the gas phase, attempts to prepare the Cs(+) and N(CH(3))(4)(+) salts of XeF(3)(-) have been unsuccessful, and are attributed to the low fluoride ion affinity of XeF(2) and fluoride ion solvation in CH(3)CN solution. The XeF(3)(-) anion would represent the first example of an AX(3)E(3) valence shell electron pair repulsion (VSEPR) arrangement of electron lone pair and bond pair domains. Fluorine-19 exchange between XeF(2) and the F(-) anion has also been probed computationally using coupled-cluster singles and doubles (CCSD) and density functional theory (DFT; PBE1PBE) methods. The energy-minimized geometry of the ground state shows that the F(-) anion is only weakly coordinated to XeF(2) (F(2)Xe---F(-); a distorted Y-shape possessing C(s) symmetry), while the XeF(3)(-) anion exists as a first-order transition state in the fluoride ion exchange mechanism, and is planar and Y-shaped (C(2v) symmetry). The molecular geometry and bonding of the XeF(3)(-) anion has been described and rationalized in terms of electron localization function (ELF) calculations, as well as the VSEPR model of molecular geometry. Quantum-chemical calculations, using the CCSD method and a continuum solvent model for CH(3)CN, accurately reproduced the transition-state enthalpy observed by (19)F NMR spectroscopy, and showed a negative but negligible enthalpy for the formation of the F(2)Xe---F(-) adduct in this medium.

  11. Optoelectronics with 2D semiconductors

    NASA Astrophysics Data System (ADS)

    Mueller, Thomas

    2015-03-01

    Two-dimensional (2D) atomic crystals, such as graphene and layered transition-metal dichalcogenides, are currently receiving a lot of attention for applications in electronics and optoelectronics. In this talk, I will review our research activities on electrically driven light emission, photovoltaic energy conversion and photodetection in 2D semiconductors. In particular, WSe2 monolayer p-n junctions formed by electrostatic doping using a pair of split gate electrodes, type-II heterojunctions based on MoS2/WSe2 and MoS2/phosphorene van der Waals stacks, 2D multi-junction solar cells, and 3D/2D semiconductor interfaces will be presented. Upon optical illumination, conversion of light into electrical energy occurs in these devices. If an electrical current is driven, efficient electroluminescence is obtained. I will present measurements of the electrical characteristics, the optical properties, and the gate voltage dependence of the device response. In the second part of my talk, I will discuss photoconductivity studies of MoS2 field-effect transistors. We identify photovoltaic and photoconductive effects, which both show strong photoconductive gain. A model will be presented that reproduces our experimental findings, such as the dependence on optical power and gate voltage. We envision that the efficient photon conversion and light emission, combined with the advantages of 2D semiconductors, such as flexibility, high mechanical stability and low costs of production, could lead to new optoelectronic technologies.

  12. 51V NMR and EPR Study of Reaction Kinetics and Mechanisms in V2O5 Gelation by Ion Exchange of Sodium Metavanadate Solutions

    DTIC Science & Technology

    1993-07-12

    initial reactions involve the consumption of the dioxovanadium cation (VVO 2+). The only other vanadium (V) species in solution, decavanadic acid...vanadium(V) species in solution, decavanadic acid, acts only as a source of dioxovanadium cations for the polymerization. The oxovanadium cation (VIO...further decavanadic acid decomposition to the dioxovanadium cation by furnishing protons. 51V MAS NMR of the resulting colloidal suspensions indicates that

  13. In-pore exchange and diffusion of carbonate solvent mixtures in nanoporous carbon

    SciTech Connect

    Alam, Todd M.; Osborn Popp, Thomas M.

    2016-06-04

    High resolution magic angle spinning (HRMAS) 1H NMR spectroscopy has been used to resolve different surface and in-pore solvent environments of ethylene carbonate (EC) and dimethyl carbonate (DMC) mixtures absorbed within nanoporous carbon (NPC). Two dimensional (2D) 1H HRMAS NMR exchange measurements revealed that the inhomogeneous broadened in-pore resonances have pore-to-pore exchange rates on the millisecond timescale. Pulsed-field gradient (PFG) NMR diffusometry revealed the in-pore self-diffusion constants for both EC and DMC were reduced by up to a factor of five with respect to the diffusion in the non-absorbed solvent mixtures.

  14. Highly crystalline 2D superconductors

    NASA Astrophysics Data System (ADS)

    Saito, Yu; Nojima, Tsutomu; Iwasa, Yoshihiro

    2016-12-01

    Recent advances in materials fabrication have enabled the manufacturing of ordered 2D electron systems, such as heterogeneous interfaces, atomic layers grown by molecular beam epitaxy, exfoliated thin flakes and field-effect devices. These 2D electron systems are highly crystalline, and some of them, despite their single-layer thickness, exhibit a sheet resistance more than an order of magnitude lower than that of conventional amorphous or granular thin films. In this Review, we explore recent developments in the field of highly crystalline 2D superconductors and highlight the unprecedented physical properties of these systems. In particular, we explore the quantum metallic state (or possible metallic ground state), the quantum Griffiths phase observed in out-of-plane magnetic fields and the superconducting state maintained in anomalously large in-plane magnetic fields. These phenomena are examined in the context of weakened disorder and/or broken spatial inversion symmetry. We conclude with a discussion of how these unconventional properties make highly crystalline 2D systems promising platforms for the exploration of new quantum physics and high-temperature superconductors.

  15. Extensions of 2D gravity

    SciTech Connect

    Sevrin, A.

    1993-06-01

    After reviewing some aspects of gravity in two dimensions, I show that non-trivial embeddings of sl(2) in a semi-simple (super) Lie algebra give rise to a very large class of extensions of 2D gravity. The induced action is constructed as a gauged WZW model and an exact expression for the effective action is given.

  16. Simultaneously cycled NMR spectroscopy.

    PubMed

    Parish, David M; Szyperski, Thomas

    2008-04-09

    Simultaneously cycled (SC) NMR was introduced and exemplified by implementing a set of 2-D [1H,1H] SC exclusive COSY (E.COSY) NMR experiments, that is, rf pulse flip-angle cycled (SFC), rf pulse phase cycled (SPC), and pulsed field gradient (PFG) strength cycled (SGC) E.COSY. Spatially selective 1H rf pulses were applied as composite pulses such that all steps of the respective cycles were affected simultaneously in different slices of the sample. This increased the data acquisition speed for an n-step cycle n-fold. A high intrinsic sensitivity was achieved by defining the cycles in a manner that the receiver phase remains constant for all steps of the cycle. Then, the signal resulting from applying the cycle corresponded to the sum of the signals from all steps of the cycle. Hence, the detected free induction decay did not have to be separated into the contributions arising from different slices, and read-out PFGs, which not only greatly reduce sensitivity but also negatively impact lineshapes in the direct dimension, were avoided. The current implementation of SFC E.COSY reached approximately 65% of the intrinsic sensitivity of the conventional phase cycled congener, making this experiment highly attractive whenever conventional data acquisition is sampling limited. Highly resolved SC E.COSY yielding accurate 3J-coupling values was recorded for the 416 Da plant alkaloid tomatidine within 80 min, that is, 12 times faster than with conventional phase cycled E.COSY. SC NMR is applicable for a large variety of NMR experiments and thus promises to be a valuable addition to the arsenal of approaches for tackling the NMR sampling problem to avoid sampling limited data acquisition.

  17. Dynamic nuclear polarization-enhanced 13C NMR spectroscopy of static biological solids

    PubMed Central

    Potapov, Alexey; Yau, Wai-Ming; Tycko, Robert

    2013-01-01

    We explore the possibility of using dynamic nuclear polarization (DNP) to enhance signals in structural studies of biological solids by solid state NMR without sample spinning. Specifically, we use 2D 13C-13C exchange spectroscopy to probe the peptide backbone torsion angles (ϕ,ψ) in a series of selectively 13C-labeled 40-residue β-amyloid (Aβ1–40) samples, in both fibrillar and non-fibrillar states. Experiments are carried out at 9.39 T and 8 K, using a static double-resonance NMR probe and low-power microwave irradiation at 264 GHz. In frozen solutions of Aβ1–40 fibrils doped with DOTOPA-TEMPO, we observe DNP signal enhancement factors of 16–21. We show that the orientation- and frequency-dependent spin polarization exchange between sequential backbone carbonyl 13C labels can be simulated accurately using a simple expression for the exchange rate, after experimentally determined homogeneous 13C lineshapes are incorporated in the simulations. The experimental 2D 13C-13C exchange spectra place constraints on the ϕ and ψ angles between the two carbonyl labels. Although the data are not sufficient to determine ϕ and ψ uniquely, the data do provide non-trivial constraints that could be included in structure calculations. With DNP at low temperatures, 2D 13C-13C exchange spectra can be obtained from a 3.5 mg sample of Aβ1–40 fibrils in 4 hr or less, despite the broad 13C chemical shift anisotropy line shapes that are observed in static samples. PMID:23562665

  18. Protein Motions and Folding Investigated by NMR Spectroscopy

    NASA Astrophysics Data System (ADS)

    Palmer, Arthur

    2002-03-01

    NMR spin relaxation spectroscopy is a powerful experimental approach for globally characterizing conformational dynamics of proteins in solution. Laboratory frame relaxation measurements are sensitive to overall rotational diffusion and internal motions on picosecond-nanosecond time scales, while rotating frame relaxation measurements are sensitive to chemical exchange processes on microsecond-millisecond time scales. The former approach is illustrated by ^15N laboratory-frame relaxation experiments as a function of temperature for the helical subdomain HP36 of the F-actin-binding headpiece domain of chicken villin. The data are analyzed using the model-free formalism to characterize order parameters and effective correlation times for intramolecular motions of individual ^15N sites. The latter approach is illustrated by ^13C Carr-Purcell-Meiboom-Gill relaxation measurements for the de novo designed α_2D protein and by ^15N rotating-frame relaxation measurements for the peripheral subunit-binding domain (PSBD) from the dihydrolopoamide acetyltransferase component of the pyruvate dehydrogenase multienzyme complex from Bacillus stearothermophilus. These experiments are used to determine the folding and unfolding kinetic rate constants for the two proteins. The results for HP36, α_2D, and PSBD illustrate the capability of current NMR methods for characterizing dynamic processes on multiple time scales in proteins.

  19. In vivo sup 23 Na and sup 31 P NMR measurement of a tonoplast Na sup + /H sup + exchange process and its characteristics in two barley cultivars

    SciTech Connect

    Fan, T.W.M.; Norlyn, J.; Epstein, E. ); Higashi, R.M. )

    1989-12-01

    A Na{sup +} uptake-associated vacuolar alkalinization was observed in roots of two barley cultivars (Arivat and the more salt-tolerant California Mariout) by using {sup 23}Na and {sup 31}P in vivo NMR spectroscopy. A NaCl uptake-associated broadening was also noted for both vacuolar P{sub i} and intracellular Na NMR peaks, consistent with Na{sup +} uptake into the same compartment as the vacuolar P{sub i}. A close coupling of Na{sup +} with H{sup +} transport (presumably the Na{sup +}/H{sup +} antiport) in vivo was evidence by qualitative and quantitative correlations between Na{sup +} accumulation and vacuolar alkalinization for both cultivars. Prolongation of the low NaCl pretreatment (30 mM) increased the activity of the putative antiport in Arivat but reduced it in California Mariout. This putative antiport also showed a dependence on NaCl concentration for California Mariout but not for Arivat. No cytoplasmic acidification accompanied the antiporter activity for either cultivar. The response of adenosine phosphates indicated that ATP utilization exceeded the capacity for ATP synthesis in Arivat, but the two processes seemed balanced in California Mariout. These comparisons provide clues to the role of the tonoplast Na{sup +}/H{sup +} antiport and compensatory cytoplasmic adjustments including pH, osymolytes, and energy phosphates in governing the different salt tolerance of the two cultivars.

  20. NMR Studies of Molecular Orientation and Dynamics in Spider silk

    NASA Astrophysics Data System (ADS)

    Michal, Carl; Eles, Philip

    2004-05-01

    Spider dragline silk has a unique combination of strength and extensibility that has been difficult to achieve in synthetic polymer fibres and has inspired industrial efforts to produce genetically engineered analogues. In light of these efforts elsewhere, we describe solid-state NMR experiments that elucidate the molecular structure and dynamics of this remarkable material. These experiments include the use of a 2-D exchange NMR experiment known as DECODER in which the sample is reoriented through a discrete angle during the mixing time. This experiment allows a reconstruction of the orientation distribution of the protein backbone. Our data is well described by a two-component distribution where the protein backbones of both components are preferentially aligned along the silk fibre. This experiment is also sensitive to molecular motion on a wide range of time-scales, and is employed to study changes in the silk as a function of fibre extension and hydration. Hydrated silk undergoes a remarkable phenomena known as supercontraction where fibres shrink by up to 50% in length while swelling in diameter. DECODER NMR of fully and partially supercontracted silk reveals that supercontraction occurs through a process of local phase transitions where water disrupts inter- and intra-chain hydrogen bonds.

  1. Dynamic NMR studies of ligand-receptor interactions: design and analysis of a rapidly exchanging complex of FKBP-12/FK506 with a 24 kDa calcineurin fragment.

    PubMed Central

    Fejzo, J.; Lepre, C. A.; Peng, J. W.; Su, M. S.; Thomson, J. A.; Moore, J. M.

    1996-01-01

    Dynamic NMR methods, such as differential line broadening and transferred NOE spectroscopy, are normally reserved for the study of small molecule ligand interactions with large protein receptors. Using a combination of isotope labeling and isotope edited NMR, we have extended these techniques to characterize interactions of a much larger protein/drug complex, FKBP-12/ FK506 with its receptor protein, calcineurin. In order to examine this multicomponent system by dynamic NMR methods, the 93 kDa, tightly bound FKBP-12/FK506/Cn complex was replaced with a lower affinity, rapidly exchanging system consisting of FKBP-12/FK506 (13 kDa), recombinant calcineurin subunit B (CnB) (20 kDa), and a synthetic peptide (4 kDa) corresponding to the B binding domain (BBD) of calcineurin catalytic subunit A (CnA). Analysis of 1H-13C HSQC data acquired for the FKBP-12/ 13C-FK506 and FKBP-12/13C-FK506/CnB/BBD complexes indicates that FKBP-12/FK506 and CnB/BBD are in fast exchange in the quaternary complex. Comparison of proton line widths shows significant broadening of resonances along the macrocycle backbone at 13-CH, 13-OMe, 15-OMe, 18-CH2, 20-CH, 21-CH, and 25-Me, as well as moderate broadening on the macrocycle backbone at 17-Me, 24-CH, and the pyranose 12-CH2 protons. The tri-substituted olefin and cyclohexyl groups also show moderate broadening at the 27-Me, 28-CH, and 30-CH2 positions, respectively. Unexpectedly, little line broadening was observed for the allyl resonances of FK506 in the quaternary complex, although 13C longitudinal relaxation measurements suggest this group also makes contacts with calcineurin. In addition, intermolecular transfer NOE peaks were observed for the allyl 37-CH2, 21-CH, 30-CH2, 13-OMe, 15-OMe, 17-Me, 25-Me, and 27-Me groups, indicating that these are potential sites on the FK506 molecule that interact with calcineurin. PMID:8880916

  2. Competing coexisting phases in 2D water

    NASA Astrophysics Data System (ADS)

    Zanotti, Jean-Marc; Judeinstein, Patrick; Dalla-Bernardina, Simona; Creff, Gaëlle; Brubach, Jean-Blaise; Roy, Pascale; Bonetti, Marco; Ollivier, Jacques; Sakellariou, Dimitrios; Bellissent-Funel, Marie-Claire

    2016-05-01

    The properties of bulk water come from a delicate balance of interactions on length scales encompassing several orders of magnitudes: i) the Hydrogen Bond (HBond) at the molecular scale and ii) the extension of this HBond network up to the macroscopic level. Here, we address the physics of water when the three dimensional extension of the HBond network is frustrated, so that the water molecules are forced to organize in only two dimensions. We account for the large scale fluctuating HBond network by an analytical mean-field percolation model. This approach provides a coherent interpretation of the different events experimentally (calorimetry, neutron, NMR, near and far infra-red spectroscopies) detected in interfacial water at 160, 220 and 250 K. Starting from an amorphous state of water at low temperature, these transitions are respectively interpreted as the onset of creation of transient low density patches of 4-HBonded molecules at 160 K, the percolation of these domains at 220 K and finally the total invasion of the surface by them at 250 K. The source of this surprising behaviour in 2D is the frustration of the natural bulk tetrahedral local geometry and the underlying very significant increase in entropy of the interfacial water molecules.

  3. Competing coexisting phases in 2D water

    PubMed Central

    Zanotti, Jean-Marc; Judeinstein, Patrick; Dalla-Bernardina, Simona; Creff, Gaëlle; Brubach, Jean-Blaise; Roy, Pascale; Bonetti, Marco; Ollivier, Jacques; Sakellariou, Dimitrios; Bellissent-Funel, Marie-Claire

    2016-01-01

    The properties of bulk water come from a delicate balance of interactions on length scales encompassing several orders of magnitudes: i) the Hydrogen Bond (HBond) at the molecular scale and ii) the extension of this HBond network up to the macroscopic level. Here, we address the physics of water when the three dimensional extension of the HBond network is frustrated, so that the water molecules are forced to organize in only two dimensions. We account for the large scale fluctuating HBond network by an analytical mean-field percolation model. This approach provides a coherent interpretation of the different events experimentally (calorimetry, neutron, NMR, near and far infra-red spectroscopies) detected in interfacial water at 160, 220 and 250 K. Starting from an amorphous state of water at low temperature, these transitions are respectively interpreted as the onset of creation of transient low density patches of 4-HBonded molecules at 160 K, the percolation of these domains at 220 K and finally the total invasion of the surface by them at 250 K. The source of this surprising behaviour in 2D is the frustration of the natural bulk tetrahedral local geometry and the underlying very significant increase in entropy of the interfacial water molecules. PMID:27185018

  4. Measurement and Quantification of Heterogeneity, Flow, and Mass Transfer in Porous Media Using NMR Low-Field Techiques

    NASA Astrophysics Data System (ADS)

    Paciok, E.; Olaru, A. M.; Haber, A.; van Landeghem, M.; Haber-Pohlmeier, S.; Sucre, O. E.; Perlo, J.; Casanova, F.; Blümich, B.; RWTH Aachen Mobile Low-Field NMR

    2011-12-01

    Nuclear magnetic resonance (NMR) is renowned for its unique potential to both reveal and correlate spectroscopic, relaxometric, spatial and dynamic properties in a large variety of organic and inorganic systems. NMR has no restrictions regarding sample opacity and is an entirely non-invasive method, which makes it the ideal tool for the investigation of porous media. However, for years NMR research of soils was limited by the use of high-field NMR devices, which necessitated elaborate NMR experiments and were not applicable to bulky samples or on-site field measurements. The evolution of low-field NMR devices during the past 20 years has brought forth portable, small-scale NMR systems with open and closed magnet arrangements specialized to specific NMR applications. In combination with recent advances in 2D-NMR Laplace methodology [1], low-field NMR has opened up the possibility to study real-life microporous systems ranging from granular media to natural soils and oil well boreholes. Thus, information becomes available, which before has not been accessible with high-field NMR. In this work, we present our recent progress in mobile low-field NMR probe design for field measurements of natural soils: a slim-line logging tool, which can be rammed into the soil of interest on-site. The performance of the device is demonstrated in measurements of moisture profiles of model soils [2] and field measurements of relaxometric properties and moisture profiles of natural soils [3]. Moreover, an improved concept of the slim-line logging tool is shown, with a higher excitation volume and a better signal-to-noise due to an improved coil design. Furthermore, we present our recent results in 2D exchange relaxometry and simulation. These include relaxation-relaxation experiments on natural soils with varying degree of moisture saturation, where we could draw a connection between the relaxometric properties of the soil to its pore size-related diffusivity and to its clay content

  5. Microscopic rearrangement of bound minor groove binders detected by NMR.

    PubMed

    Rettig, Michael; Germann, Markus W; Ismail, Mohamed A; Batista-Parra, Adalgisa; Munde, Manoj; Boykin, David W; Wilson, W David

    2012-05-17

    Thermodynamic and structural studies are commonly utilized to optimize small molecules for specific DNA interactions, and, thus, a significant amount of binding data is available. However, the dynamic processes that are involved in minor groove complex formation and maintenance are not fully understood. To help define the processes involved, we have conducted 1D and 2D NMR in conjunction with biosensor-SPR experiments with a variety of compounds and symmetric, as well as asymmetric, AT tract DNA sequences. Surprisingly, the NMR data clearly show exchange between equivalent binding sites for strongly binding compounds like netropsin and DB921 (Ka > 10(8) M(-1)) that does not involve dissociation off the DNA. A quantitative analysis of the data revealed that these bound exchange rates are indeed much faster than the macroscopic dissociation rates which were independently determined by biosensor-SPR. Additionally, we could show the existence of at least two 1:1 compound DNA complexes at the same site for the interaction of these compounds with an asymmetric DNA sequence. To explain this behavior we introduced a model in which the ligand is rapidly flipping between two orientations while in close association with the DNA. The ligand reorientation will contribute favorably to the binding entropy. As the potential of minor groove binders to form more than a single complex with asymmetric, as well as symmetric, duplexes is widely unknown, the consequences for binding thermodynamics and compound design are discussed.

  6. A novel improved method for analysis of 2D diffusion relaxation data—2D PARAFAC-Laplace decomposition

    NASA Astrophysics Data System (ADS)

    Tønning, Erik; Polders, Daniel; Callaghan, Paul T.; Engelsen, Søren B.

    2007-09-01

    This paper demonstrates how the multi-linear PARAFAC model can with advantage be used to decompose 2D diffusion-relaxation correlation NMR spectra prior to 2D-Laplace inversion to the T2- D domain. The decomposition is advantageous for better interpretation of the complex correlation maps as well as for the quantification of extracted T2- D components. To demonstrate the new method seventeen mixtures of wheat flour, starch, gluten, oil and water were prepared and measured with a 300 MHz nuclear magnetic resonance (NMR) spectrometer using a pulsed gradient stimulated echo (PGSTE) pulse sequence followed by a Carr-Purcell-Meiboom-Gill (CPMG) pulse echo train. By varying the gradient strength, 2D diffusion-relaxation data were recorded for each sample. From these double exponentially decaying relaxation data the PARAFAC algorithm extracted two unique diffusion-relaxation components, explaining 99.8% of the variation in the data set. These two components were subsequently transformed to the T2- D domain using 2D-inverse Laplace transformation and quantitatively assigned to the oil and water components of the samples. The oil component was one distinct distribution with peak intensity at D = 3 × 10 -12 m 2 s -1 and T2 = 180 ms. The water component consisted of two broad populations of water molecules with diffusion coefficients and relaxation times centered around correlation pairs: D = 10 -9 m 2 s -1, T2 = 10 ms and D = 3 × 10 -13 m 2 s -1, T2 = 13 ms. Small spurious peaks observed in the inverse Laplace transformation of original complex data were effectively filtered by the PARAFAC decomposition and thus considered artefacts from the complex Laplace transformation. The oil-to-water ratio determined by PARAFAC followed by 2D-Laplace inversion was perfectly correlated with known oil-to-water ratio of the samples. The new method of using PARAFAC prior to the 2D-Laplace inversion proved to have superior potential in analysis of diffusion-relaxation spectra, as it

  7. Dinuclear complexes formed with the triazacyclononane derivative ENOTA4-: high-pressure 17O NMR evidence of an associative water exchange on [MnII2(ENOTA)(H2O)2].

    PubMed

    Balogh, Edina; He, Zhenjie; Hsieh, Wenyuan; Liu, Shuang; Tóth, Eva

    2007-01-08

    Mn2+ has five unpaired d-electrons, a long electronic relaxation time, and labile water exchange, all of which make it an attractive candidate for contrast agent application in medical magnetic resonance imaging. In the quest for stable and nonlabile Mn2+ complexes, we explored a novel dimeric triazacyclononane-based ligand bearing carboxylate functional groups, H4ENOTA. The protonation constants of the ligand and the stability constants of the complexes formed with some endogenously important metals (Ca2+, Cu2+, Zn2+), as well as with Mn2+ and Ce3+, have been assessed by NMR methods, potentiometry, and UV-vis spectrophotometry. Overall, the thermodynamic stability of the complexes is lower as compared to that of the corresponding NOTA analogues (H3NOTA, 1,4,7-triaazacyclononane-1,4,7-triacetic acid). The crystal structure of Mn2(ENOTA)(H2O) x 5H2O contains two six-coordinated Mn2+, in addition to the three amine nitrogens and the two oxygens from the pendent monodentate carboxylate groups, and one water (Mn2) or one bridging carboxylate oxygen (Mn1) completes the coordination sphere of the metal ion. In an aqueous solution, this bridging carboxylate is replaced by a water molecule, as evidenced by the 17O chemical shifts and proton relaxivity data that point to monohydration for both metal ions in the dinuclear complex. A variable-temperature and -pressure 17O NMR study has been performed on [Mn2(ENOTA)(H2O)2] to assess the rate and, for the first time on a Mn2+ chelate, also the mechanism of the water exchange. The inner sphere water is slightly more labile in [Mn2(ENOTA)(H2O)2] (k298ex = 5.5 x 107 s-1) than in the aqua ion (2.1 x 107 s-1, Merbach, A. E.; et al. Inorg. Chem. 1980, 19, 3696). The water exchange proceeds via an almost limiting associative mechanism, as evidenced by the large negative activation volume (deltaV = -10.7 cm3 mol-1). The proton relaxivities measured on [Mn2(ENOTA)(H2O)2] show a low-field dispersion at approximately 0.1 MHz arising from

  8. Detailed Investigation of Ion Exchange in Ball Milled LiH+MgB2 System using Ultra-High Field NMR Spectroscopy

    SciTech Connect

    Hu, Jian Z.; Kwak, Ja Hun; Yang, Zhenguo; Wan, Xiufeng; Shaw, Leonard D.

    2010-06-01

    The present study with the detailed 1H-6Li cross polarization NMR analysis confirms the formation of a ternary compound, (Mg1-xLi2x)B2, during ball milling of LiH + ½ MgB2 at room temperature. The 6Li sites in (Mg1-xLi2x)B2 exhibit spinning sidebands (SSBs), whereas the 6Li sites in LiH do not. The SSBs and the very short spin-lattice relaxation time manifested by the 6Li sites in (Mg1-xLi2x)B2 indicate that the Li ions in (Mg1-xLi2x)B2 are located between the layered boron structures and close to Mg ions. The formation of (Mg1-xLi2x)B2 explains the previous observation that the LiH + ½ MgB2 mixture ball milled effectively has a greatly enhanced hydriding kinetics at temperatures below the melting point of LiBH4.

  9. 2D quasiperiodic plasmonic crystals

    PubMed Central

    Bauer, Christina; Kobiela, Georg; Giessen, Harald

    2012-01-01

    Nanophotonic structures with irregular symmetry, such as quasiperiodic plasmonic crystals, have gained an increasing amount of attention, in particular as potential candidates to enhance the absorption of solar cells in an angular insensitive fashion. To examine the photonic bandstructure of such systems that determines their optical properties, it is necessary to measure and model normal and oblique light interaction with plasmonic crystals. We determine the different propagation vectors and consider the interaction of all possible waveguide modes and particle plasmons in a 2D metallic photonic quasicrystal, in conjunction with the dispersion relations of a slab waveguide. Using a Fano model, we calculate the optical properties for normal and inclined light incidence. Comparing measurements of a quasiperiodic lattice to the modelled spectra for angle of incidence variation in both azimuthal and polar direction of the sample gives excellent agreement and confirms the predictive power of our model. PMID:23209871

  10. Valleytronics in 2D materials

    NASA Astrophysics Data System (ADS)

    Schaibley, John R.; Yu, Hongyi; Clark, Genevieve; Rivera, Pasqual; Ross, Jason S.; Seyler, Kyle L.; Yao, Wang; Xu, Xiaodong

    2016-11-01

    Semiconductor technology is currently based on the manipulation of electronic charge; however, electrons have additional degrees of freedom, such as spin and valley, that can be used to encode and process information. Over the past several decades, there has been significant progress in manipulating electron spin for semiconductor spintronic devices, motivated by potential spin-based information processing and storage applications. However, experimental progress towards manipulating the valley degree of freedom for potential valleytronic devices has been limited until very recently. We review the latest advances in valleytronics, which have largely been enabled by the isolation of 2D materials (such as graphene and semiconducting transition metal dichalcogenides) that host an easily accessible electronic valley degree of freedom, allowing for dynamic control.

  11. Unparticle example in 2D.

    PubMed

    Georgi, Howard; Kats, Yevgeny

    2008-09-26

    We discuss what can be learned about unparticle physics by studying simple quantum field theories in one space and one time dimension. We argue that the exactly soluble 2D theory of a massless fermion coupled to a massive vector boson, the Sommerfield model, is an interesting analog of a Banks-Zaks model, approaching a free theory at high energies and a scale-invariant theory with nontrivial anomalous dimensions at low energies. We construct a toy standard model coupling to the fermions in the Sommerfield model and study how the transition from unparticle behavior at low energies to free particle behavior at high energies manifests itself in interactions with the toy standard model particles.

  12. Studies of Transition Metal Complexes Using Dynamic NMR Techniques.

    NASA Astrophysics Data System (ADS)

    Coston, Timothy Peter John

    Available from UMI in association with The British Library. This Thesis is primarily concerned with the quantitative study of fluxional processes in, predominantly platinum(IV) complexes, with the ligands 1,1,2,2-tetrakis(methylthio)ethane (MeS)_2CHCH(SMe)_2 , and 1,1,2,2-tetrakis(methylthio)ethene (MeS) _2C=C(SMe)_2. Quantitative information relating to the energetics of these processes has been obtained by a combination of one- and two-dimensional NMR techniques. Chapter One provides an introduction to the background of fluxional processes in transition metal complexes together with data concerning the energetics of the processes that have already been studied by NMR techniques. Chapter Two provides a thorough grounding in NMR techniques, in particular those concerned with the quantitative measurement of rates involved in chemical exchange processes. A description of the use of 2D EXSY NMR spectroscopy in obtaining rate data is given. The properties of the magnetic isotope of platinum are given in Chapter Three. A general survey is also given of some additional compounds that have already been studied by platinum-195 spectroscopy. Chapter Four is concerned with the quantitative study of low temperature (<293 K) fluxionality (sulphur inversion) in the complexes (PtXMe_3 (MeS)_2CHCH(SMe) _2) (X = Cl, Br, I). These complexes were studied by dynamic nuclear magnetic resonance and the information regarding the rates of sulphur inversion was obtained by complete band-shape analysis. Chapter Five is concerned with high temperature (>333 K) fluxionality, of the previous complexes, as studied by a combination of one- and two -dimensional NMR techniques. Aside from obtaining thermodynamic parameters for all the processes, a new novel mechanism is proposed. Chapter Six is primarily concerned with the NMR investigation of the new dinuclear complexes ((PtXMe _3)_2(MeS) _2CHCH(SMe)_2) (X = Cl, Br, I). The solution properties have been established and thermo-dynamic parameters

  13. Quantum coherence selective 2D Raman–2D electronic spectroscopy

    PubMed Central

    Spencer, Austin P.; Hutson, William O.; Harel, Elad

    2017-01-01

    Electronic and vibrational correlations report on the dynamics and structure of molecular species, yet revealing these correlations experimentally has proved extremely challenging. Here, we demonstrate a method that probes correlations between states within the vibrational and electronic manifold with quantum coherence selectivity. Specifically, we measure a fully coherent four-dimensional spectrum which simultaneously encodes vibrational–vibrational, electronic–vibrational and electronic–electronic interactions. By combining near-impulsive resonant and non-resonant excitation, the desired fifth-order signal of a complex organic molecule in solution is measured free of unwanted lower-order contamination. A critical feature of this method is electronic and vibrational frequency resolution, enabling isolation and assignment of individual quantum coherence pathways. The vibronic structure of the system is then revealed within an otherwise broad and featureless 2D electronic spectrum. This method is suited for studying elusive quantum effects in which electronic transitions strongly couple to phonons and vibrations, such as energy transfer in photosynthetic pigment–protein complexes. PMID:28281541

  14. Quantum coherence selective 2D Raman-2D electronic spectroscopy

    NASA Astrophysics Data System (ADS)

    Spencer, Austin P.; Hutson, William O.; Harel, Elad

    2017-03-01

    Electronic and vibrational correlations report on the dynamics and structure of molecular species, yet revealing these correlations experimentally has proved extremely challenging. Here, we demonstrate a method that probes correlations between states within the vibrational and electronic manifold with quantum coherence selectivity. Specifically, we measure a fully coherent four-dimensional spectrum which simultaneously encodes vibrational-vibrational, electronic-vibrational and electronic-electronic interactions. By combining near-impulsive resonant and non-resonant excitation, the desired fifth-order signal of a complex organic molecule in solution is measured free of unwanted lower-order contamination. A critical feature of this method is electronic and vibrational frequency resolution, enabling isolation and assignment of individual quantum coherence pathways. The vibronic structure of the system is then revealed within an otherwise broad and featureless 2D electronic spectrum. This method is suited for studying elusive quantum effects in which electronic transitions strongly couple to phonons and vibrations, such as energy transfer in photosynthetic pigment-protein complexes.

  15. Quantum coherence selective 2D Raman-2D electronic spectroscopy.

    PubMed

    Spencer, Austin P; Hutson, William O; Harel, Elad

    2017-03-10

    Electronic and vibrational correlations report on the dynamics and structure of molecular species, yet revealing these correlations experimentally has proved extremely challenging. Here, we demonstrate a method that probes correlations between states within the vibrational and electronic manifold with quantum coherence selectivity. Specifically, we measure a fully coherent four-dimensional spectrum which simultaneously encodes vibrational-vibrational, electronic-vibrational and electronic-electronic interactions. By combining near-impulsive resonant and non-resonant excitation, the desired fifth-order signal of a complex organic molecule in solution is measured free of unwanted lower-order contamination. A critical feature of this method is electronic and vibrational frequency resolution, enabling isolation and assignment of individual quantum coherence pathways. The vibronic structure of the system is then revealed within an otherwise broad and featureless 2D electronic spectrum. This method is suited for studying elusive quantum effects in which electronic transitions strongly couple to phonons and vibrations, such as energy transfer in photosynthetic pigment-protein complexes.

  16. Entire-Dataset Analysis of NMR Fast-Exchange Titration Spectra: A Mg(2+) Titration Analysis for HIV-1 Ribonuclease H Domain.

    PubMed

    Karki, Ichhuk; Christen, Martin T; Spiriti, Justin; Slack, Ryan L; Oda, Masayuki; Kanaori, Kenji; Zuckerman, Daniel M; Ishima, Rieko

    2016-12-15

    This article communicates our study to elucidate the molecular determinants of weak Mg(2+) interaction with the ribonuclease H (RNH) domain of HIV-1 reverse transcriptase in solution. As the interaction is weak (a ligand-dissociation constant >1 mM), nonspecific Mg(2+) interaction with the protein or interaction of the protein with other solutes that are present in the buffer solution can confound the observed Mg(2+)-titration data. To investigate these indirect effects, we monitored changes in the chemical shifts of backbone amides of RNH by recording NMR (1)H-(15)N heteronuclear single-quantum coherence spectra upon titration of Mg(2+) into an RNH solution. We performed the titration under three different conditions: (1) in the absence of NaCl, (2) in the presence of 50 mM NaCl, and (3) at a constant 160 mM Cl(-) concentration. Careful analysis of these three sets of titration data, along with molecular dynamics simulation data of RNH with Na(+) and Cl(-) ions, demonstrates two characteristic phenomena distinct from the specific Mg(2+) interaction with the active site: (1) weak interaction of Mg(2+), as a salt, with the substrate-handle region of the protein and (2) overall apparent lower Mg(2+) affinity in the absence of NaCl compared to that in the presence of 50 mM NaCl. A possible explanation may be that the titrated MgCl2 is consumed as a salt and interacts with RNH in the absence of NaCl. In addition, our data suggest that Na(+) increases the kinetic rate of the specific Mg(2+) interaction at the active site of RNH. Taken together, our study provides biophysical insight into the mechanism of weak metal interaction on a protein.

  17. Direct observation of millisecond to second motions in proteins by dipolar CODEX NMR spectroscopy.

    PubMed

    Krushelnitsky, Alexey; deAzevedo, Eduardo; Linser, Rasmus; Reif, Bernd; Saalwächter, Kay; Reichert, Detlef

    2009-09-02

    We present a site-resolved study of slow (ms to s) motions in a protein in the solid (microcrystalline) state performed with the use of a modified version of the centerband-only detection of exchange (CODEX) NMR experiment. CODEX was originally based on measuring changes in molecular orientation by means of the chemical shift anisotropy (CSA) tensor, and in our modification, angular reorientations of internuclear vectors are observed. The experiment was applied to the study of slow (15)N-(1)H motions of the SH3 domain of chicken alpha-spectrin. The protein was perdeuterated with partial back-exchange of protons at labile sites. This allowed indirect (proton) detection of (15)N nuclei and thus a significant enhancement of sensitivity. The diluted proton system also made negligible proton-driven spin diffusion between (15)N nuclei, which interferes with the molecular exchange (motion) and hampers the acquisition of dynamic parameters. The experiment has shown that approximately half of the peaks in the 2D (15)N-(1)H correlation spectrum exhibit exchange in a different extent. The correlation time of the slow motion for most peaks is 1 to 3 s. This is the first NMR study of the internal dynamics of proteins in the solid state on the millisecond to second time scale with site-specific spectral resolution that provides both time-scale and geometry information about molecular motions.

  18. 2D aquifer characterization and improved prediction of hydraulic conductivity using surface Nuclear Magnetic Resonance

    NASA Astrophysics Data System (ADS)

    Dlugosch, Raphael; Günther, Thomas; Müller-Petke, Mike; Yaramanci, Ugur

    2014-05-01

    We present recent studies on the characterization of shallow aquifers using Nuclear Magnetic Resonance (NMR). NMR can help to gather detailed information about the water content and pore size related NMR relaxation time, of porous and water saturated material. The field application of surface NMR uses large wire loops placed at the surface of the Earth allows imaging the subsurface down to around hundred meters. First, a sophisticated inversion scheme is presented to simultaneously determine the two-dimensional (2D) distribution of the water content and the NMR relaxation time (T2*) in the subsurface from a surface NMR survey. The outstanding features of the new inversion scheme are its robustness to noisy data and the potential to distinguish aquifers of different lithology due to their specific NMR relaxation time. The successful application of the inversion scheme is demonstrated on two field cases both characterized by channel structures in the glacial sediments of Northern Germany. Second, we revise the prediction of hydraulic conductivity from NMR measurements for coarse-grained and unconsolidated sediments, commonly found in shallow aquifers. The presented Kozeny-Godefroy model replaces the empirical factors in known relations with physical, structural, and intrinsic NMR parameters. It additionally accounts for bulk water relaxation and is not limited to fast diffusion conditions. This improves the prediction of the hydraulic conductivity for clay-free sediments with grain sizes larger than medium sand. The model is validated by laboratory measurements on glass beads and sand samples. Combining the new inversion scheme and petrophysical model allows 2D imaging of the hydraulic conductivity in the subsurface from a surface NMR survey.

  19. Complete NMR analysis of oxytocin in phosphate buffer.

    PubMed

    Ohno, Akiko; Kawasaki, Nana; Fukuhara, Kiyoshi; Okuda, Haruhiro; Yamaguchi, Teruhide

    2010-02-01

    Complete NMR analysis of oxytocin (OXT) in phosphate buffer was elucidated by one-dimensional (1D)- and two-dimensional (2D)-NMR techniques, which involve the assignment of peptide amide NH protons and carbamoyl NH(2) protons. The (1)H-(15)N correlation of seven amide NH protons and three carbamoyl NH(2) protons were also shown by HSQC NMR of OXT without (15)N enrichment.

  20. Dipeptide Structural Analysis Using Two-Dimensional NMR for the Undergraduate Advanced Laboratory

    ERIC Educational Resources Information Center

    Gonzalez, Elizabeth; Dolino, Drew; Schwartzenburg, Danielle; Steiger, Michelle A.

    2015-01-01

    A laboratory experiment was developed to introduce students in either an organic chemistry or biochemistry lab course to two-dimensional nuclear magnetic resonance (2D NMR) spectroscopy using simple biomolecules. The goal of this experiment is for students to understand and interpret the information provided by a 2D NMR spectrum. Students are…

  1. Soils, Pores, and NMR

    NASA Astrophysics Data System (ADS)

    Pohlmeier, Andreas; Haber-Pohlmeier, Sabina; Haber, Agnes; Sucre, Oscar; Stingaciu, Laura; Stapf, Siegfried; Blümich, Bernhard

    2010-05-01

    Within Cluster A, Partial Project A1, the pore space exploration by means of Nuclear Magnetic Resonance (NMR) plays a central role. NMR is especially convenient since it probes directly the state and dynamics of the substance of interest: water. First, NMR is applied as relaxometry, where the degree of saturation but also the pore geometry controls the NMR signature of natural porous systems. Examples are presented where soil samples from the Selhausen, Merzenhausen (silt loams), and Kaldenkirchen (sandy loam) test sites are investigated by means of Fast Field Cycling Relaxometry at different degrees of saturation. From the change of the relaxation time distributions with decreasing water content and by comparison with conventional water retention curves we conclude that the fraction of immobile water is characterized by T1 < 5 ms. Moreover, the dependence of the relaxation rate on magnetic field strength allows the identification of 2D diffusion at the interfaces as the mechanism which governs the relaxation process (Pohlmeier et al. 2009). T2 relaxation curves are frequently measured for the rapid characterization of soils by means of the CPMG echo train. Basically, they contain the same information about the pore systems like T1 curves, since mostly the overall relaxation is dominated by surface relaxivity and the surface/volume ratio of the pores. However, one must be aware that T2 relaxation is additionally affected by diffusion in internal gradients, and this can be overcome by using sufficiently short echo times and low magnetic fields (Stingaciu et al. 2009). Second, the logic continuation of conventional relaxation measurements is the 2-dimensional experiment, where prior to the final detection of the CPMG echo train an encoding period is applied. This can be T1-encoding by an inversion pulse, or T2 encoding by a sequence of 90 and 180° pulses. During the following evolution time the separately encoded signals can mix and this reveals information about

  2. Assessment of the effects of pH, formulation and deformulation on the conformation of interferon alpha-2 by NMR.

    PubMed

    Panjwani, Naim; Hodgson, Derek J; Sauvé, Simon; Aubin, Yves

    2010-08-01

    This article reports the results of our investigation of the effects of pH and various formulations on the conformation of interferon (IFN) alpha-2a and IFN alpha-2b using the NMR fingerprinting assay. Samples of (15)N-IFN alpha-2 were produced and their activity was inferred by comparing their NMR spectra with those recorded for the corresponding European Directorate for the Quality of Medicines (EDQM) reference standards. The proteins were then mixed with appropriate excipients to reproduce formulations used in innovator products of Roferon-A and Intron-A and deformulated via cation-exchange chromatography. The conformation of IFN alpha-2 was monitored by two-dimensional (2D)-NMR spectroscopy at various pHs, after formulation and deformulation procedures. Our results show that the process does not alter the conformation of IFN alpha-2 and that the optimal pH for deformulation is 4.0 +/- 0.5. Variation in pH below 3.0 causes the protein to unfold, whereas above pH 4.5, the three-dimensional (3D) fold is maintained, but the NMR spectra indicate a propensity to oligomerize. This behaviour is reversible upon readjusting the pH to 3.5-4.5. Here, we demonstrate the applicability of NMR to assess the structure of protein therapeutics. The proposed method can assist in validating analytical methods that require deformulation of IFN-based products.

  3. NKG2D ligands as therapeutic targets

    PubMed Central

    Spear, Paul; Wu, Ming-Ru; Sentman, Marie-Louise; Sentman, Charles L.

    2013-01-01

    The Natural Killer Group 2D (NKG2D) receptor plays an important role in protecting the host from infections and cancer. By recognizing ligands induced on infected or tumor cells, NKG2D modulates lymphocyte activation and promotes immunity to eliminate ligand-expressing cells. Because these ligands are not widely expressed on healthy adult tissue, NKG2D ligands may present a useful target for immunotherapeutic approaches in cancer. Novel therapies targeting NKG2D ligands for the treatment of cancer have shown preclinical success and are poised to enter into clinical trials. In this review, the NKG2D receptor and its ligands are discussed in the context of cancer, infection, and autoimmunity. In addition, therapies targeting NKG2D ligands in cancer are also reviewed. PMID:23833565

  4. Hydrogen exchange in thermally denatured ribonuclease A

    SciTech Connect

    Robertson, A.D.; Baldwin, R.L. )

    1991-10-15

    Hydrogen exchange has been used to test for the presence of nonrandom structure in thermally denatured ribonuclease A (RNase A). Quenched-flow methods and 2d {sup 1}H NMR spectroscopy were used to measure exchange rates for 36 backbone amide protons (NHs) at 65C and at pH* (uncorrected pH measured in D{sub 2}O) values ranging from 1.5 to 3.8. The results show that exchange is approximately that predicted for a disordered polypeptide, the authors thus are unable to detect any stable hydrogen-bonded structure in thermally denatured RNase A. Two observations suggest, however, that the predicted rates should be viewed with some caution. First, they discovered that one of the approximations made by Molday et al, that exchange for valine NHs is similar to that for alanine NHs, had to modified; the exchange rates for valine NHs are about 4-fold slower. Second, the pH minima for exchange tend to fall at lower pH values than predicted, by as much as 0.45 pH units. The origin of the disagreement between predicted and observed pH minima is unknown but may be the high net positive charge on these proteins at low pH. This spectrum is reduced to a low level by adding guanidine hydrochloride. The nature of the residual structure responsible for this spectrum is not known. The results show that it is not stable helix formation by the three {alpha}-helices of native ribonuclease A, which would give measurable protection against amide proton exchange.

  5. NMR-Profiles of Protein Solutions

    PubMed Central

    Pedrini, Bill; Serrano, Pedro; Mohanty, Biswaranjan; Geralt, Michael; Wüthrich, Kurt

    2014-01-01

    NMR-Profiles are quantitative one-dimensional presentations of two-dimensional [15N,1H]-correlation spectra used to monitor the quality of protein solutions prior to and during NMR structure determinations and functional studies. In our current use in structural genomics projects, a NMR-Profile is recorded at the outset of a structure determination, using a uniformly 15N-labeled micro-scale sample of the protein. We thus assess the extent to which polypeptide backbone resonance assignments can be achieved with given NMR techniques, for example, conventional triple resonance experiments or APSY-NMR. With the availability of sequence-specific polypeptide backbone resonance assignments in the course of the structure determination, an “Assigned NMR-Profile” is generated, which visualizes the variation of the 15N–1H correlation cross peak intensities along the sequence and thus maps the sequence locations of polypeptide segments for which the NMR line shapes are affected by conformational exchange or other processes. The Assigned NMR-Profile provides a guiding reference during later stages of the structure determination, and is of special interest for monitoring the protein during functional studies, where dynamic features may be modulated during physiological functions. PMID:23839514

  6. Annotated Bibliography of EDGE2D Use

    SciTech Connect

    J.D. Strachan and G. Corrigan

    2005-06-24

    This annotated bibliography is intended to help EDGE2D users, and particularly new users, find existing published literature that has used EDGE2D. Our idea is that a person can find existing studies which may relate to his intended use, as well as gain ideas about other possible applications by scanning the attached tables.

  7. Staring 2-D hadamard transform spectral imager

    DOEpatents

    Gentry, Stephen M.; Wehlburg, Christine M.; Wehlburg, Joseph C.; Smith, Mark W.; Smith, Jody L.

    2006-02-07

    A staring imaging system inputs a 2D spatial image containing multi-frequency spectral information. This image is encoded in one dimension of the image with a cyclic Hadamarid S-matrix. The resulting image is detecting with a spatial 2D detector; and a computer applies a Hadamard transform to recover the encoded image.

  8. Ultrafast dynamics of metal plasmons induced by 2D semiconductor excitons in hybrid nanostructure arrays

    DOE PAGES

    Boulesbaa, Abdelaziz; Babicheva, Viktoriia E.; Wang, Kai; ...

    2016-11-17

    With the advanced progress achieved in the field of nanotechnology, localized surface plasmons resonances (LSPRs) are actively considered to improve the efficiency of metal-based photocatalysis, photodetection, and photovoltaics. Here, we report on the exchange of energy and electric charges in a hybrid composed of a two-dimensional tungsten disulfide (2D-WS2) monolayer and an array of aluminum (Al) nanodisks. Femtosecond pump-probe spectroscopy results indicate that within ~830 fs after photoexcitation of the 2D-WS2 semiconductor, energy transfer from the 2D-WS2 excitons excites the plasmons of the Al array. Then, upon the radiative and/or nonradiative damping of these excited plasmons, energy and/or electron transfermore » back to the 2D-WS2 semiconductor takes place as indicated by an increase in the reflected probe at the 2D exciton transition energies at later time-delays. This simultaneous exchange of energy and charges between the metal and the 2D-WS2 semiconductor resulted in an extension of the average lifetime of the 2D-excitons from ~15 to ~58 ps in absence and presence of the Al array, respectively. Furthermore, the indirectly excited plasmons were found to live as long as the 2D-WS2 excitons exist. Furthermore, the demonstrated ability to generate exciton-plasmons coupling in a hybrid nanostructure may open new opportunities for optoelectronic applications such as plasmonic-based photodetection and photocatalysis.« less

  9. Deciphering the Conformational Choreography of Zinc Coordination Complexes with Standard and Novel Proton NMR Techniques Combined with DFT Methods.

    PubMed

    Pucheta, Jose Enrique Herbert; Prim, Damien; Gillet, Jean Michel; Farjon, Jonathan

    2016-04-04

    The presence of water has been shown to deeply impact the stability and geometry of Zn complexes in solution. Evidence for tetra- and penta-coordinated species in a pyridylmethylamine-Zn(II) model complex is presented. Novel (1) H NMR tools such as T1 -filtered selective exchange spectroscopy and pure shifted gradient-encoded selective refocusing as well as classical 2D ((1) H-(1) H) exchange spectroscopy, diffusion-ordered spectroscopy and T1 ((1) H) measurements, in combination with density functional theory methods allow the full conformational dynamics of a pyridylmethylamine-Zn(II) complex to be revealed. Four conformers and two families of complexes depending on the hydration states are elucidated.

  10. Matrix models of 2d gravity

    SciTech Connect

    Ginsparg, P.

    1991-01-01

    These are introductory lectures for a general audience that give an overview of the subject of matrix models and their application to random surfaces, 2d gravity, and string theory. They are intentionally 1.5 years out of date.

  11. Matrix models of 2d gravity

    SciTech Connect

    Ginsparg, P.

    1991-12-31

    These are introductory lectures for a general audience that give an overview of the subject of matrix models and their application to random surfaces, 2d gravity, and string theory. They are intentionally 1.5 years out of date.

  12. Brittle damage models in DYNA2D

    SciTech Connect

    Faux, D.R.

    1997-09-01

    DYNA2D is an explicit Lagrangian finite element code used to model dynamic events where stress wave interactions influence the overall response of the system. DYNA2D is often used to model penetration problems involving ductile-to-ductile impacts; however, with the advent of the use of ceramics in the armor-anti-armor community and the need to model damage to laser optics components, good brittle damage models are now needed in DYNA2D. This report will detail the implementation of four brittle damage models in DYNA2D, three scalar damage models and one tensor damage model. These new brittle damage models are then used to predict experimental results from three distinctly different glass damage problems.

  13. 2D/3D switchable displays

    NASA Astrophysics Data System (ADS)

    Dekker, T.; de Zwart, S. T.; Willemsen, O. H.; Hiddink, M. G. H.; IJzerman, W. L.

    2006-02-01

    A prerequisite for a wide market acceptance of 3D displays is the ability to switch between 3D and full resolution 2D. In this paper we present a robust and cost effective concept for an auto-stereoscopic switchable 2D/3D display. The display is based on an LCD panel, equipped with switchable LC-filled lenticular lenses. We will discuss 3D image quality, with the focus on display uniformity. We show that slanting the lenticulars in combination with a good lens design can minimize non-uniformities in our 20" 2D/3D monitors. Furthermore, we introduce fractional viewing systems as a very robust concept to further improve uniformity in the case slanting the lenticulars and optimizing the lens design are not sufficient. We will discuss measurements and numerical simulations of the key optical characteristics of this display. Finally, we discuss 2D image quality, the switching characteristics and the residual lens effect.

  14. 2-d Finite Element Code Postprocessor

    SciTech Connect

    Sanford, L. A.; Hallquist, J. O.

    1996-07-15

    ORION is an interactive program that serves as a postprocessor for the analysis programs NIKE2D, DYNA2D, TOPAZ2D, and CHEMICAL TOPAZ2D. ORION reads binary plot files generated by the two-dimensional finite element codes currently used by the Methods Development Group at LLNL. Contour and color fringe plots of a large number of quantities may be displayed on meshes consisting of triangular and quadrilateral elements. ORION can compute strain measures, interface pressures along slide lines, reaction forces along constrained boundaries, and momentum. ORION has been applied to study the response of two-dimensional solids and structures undergoing finite deformations under a wide variety of large deformation transient dynamic and static problems and heat transfer analyses.

  15. Chemical Approaches to 2D Materials.

    PubMed

    Samorì, Paolo; Palermo, Vincenzo; Feng, Xinliang

    2016-08-01

    Chemistry plays an ever-increasing role in the production, functionalization, processing and applications of graphene and other 2D materials. This special issue highlights a selection of enlightening chemical approaches to 2D materials, which nicely reflect the breadth of the field and convey the excitement of the individuals involved in it, who are trying to translate graphene and related materials from the laboratory into a real, high-impact technology.

  16. Synthesis, spectroscopy, and hydrogen/deuterium exchange in high-spin iron(II) hydride complexes.

    PubMed

    Dugan, Thomas R; Bill, Eckhard; MacLeod, K Cory; Brennessel, William W; Holland, Patrick L

    2014-03-03

    Very few hydride complexes are known in which the metals have a high-spin electronic configuration. We describe the characterization of several high-spin iron(II) hydride/deuteride isotopologues and their exchange reactions with one another and with H2/D2. Though the hydride/deuteride signal is not observable in NMR spectra, the choice of isotope has an influence on the chemical shifts of distant protons in the dimers through the paramagnetic isotope effect on chemical shift. This provides the first way to monitor the exchange of H and D in the bridging positions of these hydride complexes. The rate of exchange depends on the size of the supporting ligand, and this is consistent with the idea that H2/D2 exchange into the hydrides occurs through the dimeric complexes rather than through a transient monomer. The understanding of H/D exchange mechanisms in these high-spin iron hydride complexes may be relevant to postulated nitrogenase mechanisms.

  17. NMR analysis of biodiesel

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Biodiesel is usually analyzed by the various methods called for in standards such as ASTM D6751 and EN 14214. Nuclear magnetic resonance (NMR) is not one of these methods. However, NMR, with 1H-NMR commonly applied, can be useful in a variety of applications related to biodiesel. These include monit...

  18. The IDOL–UBE2D complex mediates sterol-dependent degradation of the LDL receptor

    PubMed Central

    Zhang, Li; Fairall, Louise; Goult, Benjamin T.; Calkin, Anna C.; Hong, Cynthia; Millard, Christopher J.; Tontonoz, Peter; Schwabe, John W.R.

    2011-01-01

    We previously identified the E3 ubiquitin ligase IDOL as a sterol-dependent regulator of the LDL receptor (LDLR). The molecular pathway underlying IDOL action, however, remains to be determined. Here we report the identification and biochemical and structural characterization of an E2–E3 ubiquitin ligase complex for LDLR degradation. We identified the UBE2D family (UBE2D1–4) as E2 partners for IDOL that support both autoubiquitination and IDOL-dependent ubiquitination of the LDLR in a cell-free system. NMR chemical shift mapping and a 2.1 Å crystal structure of the IDOL RING domain–UBE2D1 complex revealed key interactions between the dimeric IDOL protein and the E2 enzyme. Analysis of the IDOL–UBE2D1 interface also defined the stereochemical basis for the selectivity of IDOL for UBE2Ds over other E2 ligases. Structure-based mutations that inhibit IDOL dimerization or IDOL–UBE2D interaction block IDOL-dependent LDLR ubiquitination and degradation. Furthermore, expression of a dominant-negative UBE2D enzyme inhibits the ability of IDOL to degrade the LDLR in cells. These results identify the IDOL–UBE2D complex as an important determinant of LDLR activity, and provide insight into molecular mechanisms underlying the regulation of cholesterol uptake. PMID:21685362

  19. Review of NMR characterization of pyrolysis oils

    SciTech Connect

    Hao, Naijia; Ben, Haoxi; Yoo, Chang Geun; Adhikari, Sushil; Ragauskas, Arthur J.

    2016-08-24

    Here, pyrolysis of renewable biomass has been developed as a method to produce green fuels and chemicals in response to energy security concerns as well as to alleviate environmental issues incurred with fossil fuel usage. However, pyrolysis oils still have limited commercial application, mainly because unprocessed oils cannot be readily blended with current petroleum-based transportation fuels. To better understand these challenges, researchers have applied diverse characterization techniques in the development of bio-oil studies. In particular, nuclear magnetic resonance (NMR) is a key spectroscopic characterization method through analysis of bio-oil components. This review highlights the NMR strategies for pyrolysis oil characterization and critically discusses the applications of 1H, 13C, 31P, 19F, and two-dimensional (2-D NMR) analyses such as heteronuclear single quantum correlation (HSQC) in representative pyrolysis oil studies.

  20. Review of NMR characterization of pyrolysis oils

    DOE PAGES

    Hao, Naijia; Ben, Haoxi; Yoo, Chang Geun; ...

    2016-08-24

    Here, pyrolysis of renewable biomass has been developed as a method to produce green fuels and chemicals in response to energy security concerns as well as to alleviate environmental issues incurred with fossil fuel usage. However, pyrolysis oils still have limited commercial application, mainly because unprocessed oils cannot be readily blended with current petroleum-based transportation fuels. To better understand these challenges, researchers have applied diverse characterization techniques in the development of bio-oil studies. In particular, nuclear magnetic resonance (NMR) is a key spectroscopic characterization method through analysis of bio-oil components. This review highlights the NMR strategies for pyrolysis oil characterizationmore » and critically discusses the applications of 1H, 13C, 31P, 19F, and two-dimensional (2-D NMR) analyses such as heteronuclear single quantum correlation (HSQC) in representative pyrolysis oil studies.« less

  1. Combining insights from solid-state NMR and first principles calculation: applications to the 19F NMR of octafluoronaphthalene.

    PubMed

    Robbins, Andrew J; Ng, William T K; Jochym, Dominik; Keal, Thomas W; Clark, Stewart J; Tozer, David J; Hodgkinson, Paul

    2007-05-21

    Advances in solid-state NMR methodology and computational chemistry are applied to the (19)F NMR of solid octafluoronaphthalene. It is demonstrated experimentally, and confirmed by density functional theory (DFT) calculations, that the spectral resolution in the magic-angle spinning spectrum is limited by the anisotropy of the bulk magnetic susceptibility (ABMS). This leads to the unusual observation that the resolution improves as the sample is diluted. DFT calculations provide assignments of each of the peaks in the (19)F spectrum, but the predictions are close to the limits of accuracy and correlation information from 2-D NMR is invaluable in confirming the assignments. The effects of non-Gaussian lineshapes on the use of 2-D NMR for mapping correlations of spectral frequencies (e.g. due to the ABMS) are also discussed.

  2. On-line NMR detection of microgram quantities of heparin-derived oligosaccharides and their structure elucidation by microcoil NMR.

    PubMed

    Korir, Albert K; Larive, Cynthia K

    2007-08-01

    The isolation and purification of sufficient quantities of heparin-derived oligosaccharides for characterization by NMR is a tedious and time-consuming process. In addition, the structural complexity and microheterogeneity of heparin makes its characterization a challenging task. The improved mass-sensitivity of microcoil NMR probe technology makes this technique well suited for characterization of mass-limited heparin-derived oligosaccharides. Although microcoil probes have poorer concentration sensitivity than conventional NMR probes, this limitation can be overcome by coupling capillary isotachophoresis (cITP) with on-line microcoil NMR detection (cITP-NMR). Strategies to improve the sensitivity of on-line NMR detection through changes in probe design and in the cITP-NMR experimental protocol are discussed. These improvements in sensitivity allow acquisition of cITP-NMR survey spectra facilitating tentative identification of unknown oligosaccharides. Complete structure elucidation for microgram quantities of the purified material can be carried out through acquisition of 2D NMR spectra using a CapNMR microcoil probe.

  3. Monoterpene Unknowns Identified Using IR, [to the first power]H-NMR, [to the thirteenth power]C-NMR, DEPT, COSY, and HETCOR

    ERIC Educational Resources Information Center

    Alty, Lisa T.

    2005-01-01

    A study identifies a compound from a set of monoterpenes using infrared (IR) and one-dimensional (1D) nuclear magnetic resonance (NMR) techniques. After identifying the unknown, each carbon and proton signal can be interpreted and assigned to the structure using the information in the two-dimensional (2D) NMR spectra, correlation spectroscopy…

  4. Orthotropic Piezoelectricity in 2D Nanocellulose

    NASA Astrophysics Data System (ADS)

    García, Y.; Ruiz-Blanco, Yasser B.; Marrero-Ponce, Yovani; Sotomayor-Torres, C. M.

    2016-10-01

    The control of electromechanical responses within bonding regions is essential to face frontier challenges in nanotechnologies, such as molecular electronics and biotechnology. Here, we present Iβ-nanocellulose as a potentially new orthotropic 2D piezoelectric crystal. The predicted in-layer piezoelectricity is originated on a sui-generis hydrogen bonds pattern. Upon this fact and by using a combination of ab-initio and ad-hoc models, we introduce a description of electrical profiles along chemical bonds. Such developments lead to obtain a rationale for modelling the extended piezoelectric effect originated within bond scales. The order of magnitude estimated for the 2D Iβ-nanocellulose piezoelectric response, ~pm V‑1, ranks this material at the level of currently used piezoelectric energy generators and new artificial 2D designs. Such finding would be crucial for developing alternative materials to drive emerging nanotechnologies.

  5. Orthotropic Piezoelectricity in 2D Nanocellulose

    PubMed Central

    García, Y.; Ruiz-Blanco, Yasser B.; Marrero-Ponce, Yovani; Sotomayor-Torres, C. M.

    2016-01-01

    The control of electromechanical responses within bonding regions is essential to face frontier challenges in nanotechnologies, such as molecular electronics and biotechnology. Here, we present Iβ-nanocellulose as a potentially new orthotropic 2D piezoelectric crystal. The predicted in-layer piezoelectricity is originated on a sui-generis hydrogen bonds pattern. Upon this fact and by using a combination of ab-initio and ad-hoc models, we introduce a description of electrical profiles along chemical bonds. Such developments lead to obtain a rationale for modelling the extended piezoelectric effect originated within bond scales. The order of magnitude estimated for the 2D Iβ-nanocellulose piezoelectric response, ~pm V−1, ranks this material at the level of currently used piezoelectric energy generators and new artificial 2D designs. Such finding would be crucial for developing alternative materials to drive emerging nanotechnologies. PMID:27708364

  6. Orthotropic Piezoelectricity in 2D Nanocellulose.

    PubMed

    García, Y; Ruiz-Blanco, Yasser B; Marrero-Ponce, Yovani; Sotomayor-Torres, C M

    2016-10-06

    The control of electromechanical responses within bonding regions is essential to face frontier challenges in nanotechnologies, such as molecular electronics and biotechnology. Here, we present Iβ-nanocellulose as a potentially new orthotropic 2D piezoelectric crystal. The predicted in-layer piezoelectricity is originated on a sui-generis hydrogen bonds pattern. Upon this fact and by using a combination of ab-initio and ad-hoc models, we introduce a description of electrical profiles along chemical bonds. Such developments lead to obtain a rationale for modelling the extended piezoelectric effect originated within bond scales. The order of magnitude estimated for the 2D Iβ-nanocellulose piezoelectric response, ~pm V(-1), ranks this material at the level of currently used piezoelectric energy generators and new artificial 2D designs. Such finding would be crucial for developing alternative materials to drive emerging nanotechnologies.

  7. 2D microwave imaging reflectometer electronics

    SciTech Connect

    Spear, A. G.; Domier, C. W. Hu, X.; Muscatello, C. M.; Ren, X.; Luhmann, N. C.; Tobias, B. J.

    2014-11-15

    A 2D microwave imaging reflectometer system has been developed to visualize electron density fluctuations on the DIII-D tokamak. Simultaneously illuminated at four probe frequencies, large aperture optics image reflections from four density-dependent cutoff surfaces in the plasma over an extended region of the DIII-D plasma. Localized density fluctuations in the vicinity of the plasma cutoff surfaces modulate the plasma reflections, yielding a 2D image of electron density fluctuations. Details are presented of the receiver down conversion electronics that generate the in-phase (I) and quadrature (Q) reflectometer signals from which 2D density fluctuation data are obtained. Also presented are details on the control system and backplane used to manage the electronics as well as an introduction to the computer based control program.

  8. Large Area Synthesis of 2D Materials

    NASA Astrophysics Data System (ADS)

    Vogel, Eric

    Transition metal dichalcogenides (TMDs) have generated significant interest for numerous applications including sensors, flexible electronics, heterostructures and optoelectronics due to their interesting, thickness-dependent properties. Despite recent progress, the synthesis of high-quality and highly uniform TMDs on a large scale is still a challenge. In this talk, synthesis routes for WSe2 and MoS2 that achieve monolayer thickness uniformity across large area substrates with electrical properties equivalent to geological crystals will be described. Controlled doping of 2D semiconductors is also critically required. However, methods established for conventional semiconductors, such as ion implantation, are not easily applicable to 2D materials because of their atomically thin structure. Redox-active molecular dopants will be demonstrated which provide large changes in carrier density and workfunction through the choice of dopant, treatment time, and the solution concentration. Finally, several applications of these large-area, uniform 2D materials will be described including heterostructures, biosensors and strain sensors.

  9. 2D microwave imaging reflectometer electronics.

    PubMed

    Spear, A G; Domier, C W; Hu, X; Muscatello, C M; Ren, X; Tobias, B J; Luhmann, N C

    2014-11-01

    A 2D microwave imaging reflectometer system has been developed to visualize electron density fluctuations on the DIII-D tokamak. Simultaneously illuminated at four probe frequencies, large aperture optics image reflections from four density-dependent cutoff surfaces in the plasma over an extended region of the DIII-D plasma. Localized density fluctuations in the vicinity of the plasma cutoff surfaces modulate the plasma reflections, yielding a 2D image of electron density fluctuations. Details are presented of the receiver down conversion electronics that generate the in-phase (I) and quadrature (Q) reflectometer signals from which 2D density fluctuation data are obtained. Also presented are details on the control system and backplane used to manage the electronics as well as an introduction to the computer based control program.

  10. 2D Distributed Sensing Via TDR

    DTIC Science & Technology

    2007-11-02

    plate VEGF CompositeSensor Experimental Setup Air 279 mm 61 78 VARTM profile: slope RTM profile: rectangle 22 1 Jul 2003© 2003 University of Delaware...2003 University of Delaware All rights reserved Vision: Non-contact 2D sensing ü VARTM setup constructed within TL can be sensed by its EM field: 2D...300.0 mm/ns. 1 2 1 Jul 2003© 2003 University of Delaware All rights reserved Model Validation “ RTM Flow” TDR Response to 139 mm VEGC

  11. Hyperpolarized 131Xe NMR spectroscopy

    NASA Astrophysics Data System (ADS)

    Stupic, Karl F.; Cleveland, Zackary I.; Pavlovskaya, Galina E.; Meersmann, Thomas

    2011-01-01

    Hyperpolarized (hp) 131Xe with up to 2.2% spin polarization (i.e., 5000-fold signal enhancement at 9.4 T) was obtained after separation from the rubidium vapor of the spin-exchange optical pumping (SEOP) process. The SEOP was applied for several minutes in a stopped-flow mode, and the fast, quadrupolar-driven T1 relaxation of this spin I = 3/2 noble gas isotope required a rapid subsequent rubidium removal and swift transfer into the high magnetic field region for NMR detection. Because of the xenon density dependent 131Xe quadrupolar relaxation in the gas phase, the SEOP polarization build-up exhibits an even more pronounced dependence on xenon partial pressure than that observed in 129Xe SEOP. 131Xe is the only stable noble gas isotope with a positive gyromagnetic ratio and shows therefore a different relative phase between hp signal and thermal signal compared to all other noble gases. The gas phase 131Xe NMR spectrum displays a surface and magnetic field dependent quadrupolar splitting that was found to have additional gas pressure and gas composition dependence. The splitting was reduced by the presence of water vapor that presumably influences xenon-surface interactions. The hp 131Xe spectrum shows differential line broadening, suggesting the presence of strong adsorption sites. Beyond hp 131Xe NMR spectroscopy studies, a general equation for the high temperature, thermal spin polarization, P, for spin I⩾1/2 nuclei is presented.

  12. Hyperpolarized 131Xe NMR spectroscopy

    PubMed Central

    Stupic, Karl F.; Cleveland, Zackary I.; Pavlovskaya, Galina E.; Meersmann, Thomas

    2011-01-01

    Hyperpolarized (hp) 131Xe with up to 2.2% spin polarization (i.e., 5000-fold signal enhancement at 9.4 T) was obtained after separation from the rubidium vapor of the spin-exchange optical pumping (SEOP) process. The SEOP was applied for several minutes in a stopped-flow mode, and the fast, quadrupolar-driven T1 relaxation of this spin I = 3/2 noble gas isotope required a rapid subsequent rubidium removal and swift transfer into the high magnetic field region for NMR detection. Because of the xenon density dependent 131Xe quadrupolar relaxation in the gas phase, the SEOP polarization build-up exhibits an even more pronounced dependence on xenon partial pressure than that observed in 129Xe SEOP. 131Xe is the only stable noble gas isotope with a positive gyromagnetic ratio and shows therefore a different relative phase between hp signal and thermal signal compared to all other noble gases. The gas phase 131Xe NMR spectrum displays a surface and magnetic field dependent quadrupolar splitting that was found to have additional gas pressure and gas composition dependence. The splitting was reduced by the presence of water vapor that presumably influences xenon-surface interactions. The hp 131Xe spectrum shows differential line broadening, suggesting the presence of strong adsorption sites. Beyond hp 131Xe NMR spectroscopy studies, a general equation for the high temperature, thermal spin polarization, P, for spin I⩾1/2 nuclei is presented. PMID:21051249

  13. Parallel Stitching of 2D Materials.

    PubMed

    Ling, Xi; Lin, Yuxuan; Ma, Qiong; Wang, Ziqiang; Song, Yi; Yu, Lili; Huang, Shengxi; Fang, Wenjing; Zhang, Xu; Hsu, Allen L; Bie, Yaqing; Lee, Yi-Hsien; Zhu, Yimei; Wu, Lijun; Li, Ju; Jarillo-Herrero, Pablo; Dresselhaus, Mildred; Palacios, Tomás; Kong, Jing

    2016-03-23

    Diverse parallel stitched 2D heterostructures, including metal-semiconductor, semiconductor-semiconductor, and insulator-semiconductor, are synthesized directly through selective "sowing" of aromatic molecules as the seeds in the chemical vapor deposition (CVD) method. The methodology enables the large-scale fabrication of lateral heterostructures, which offers tremendous potential for its application in integrated circuits.

  14. The basics of 2D DIGE.

    PubMed

    Beckett, Phil

    2012-01-01

    The technique of two-dimensional (2D) gel electrophoresis is a powerful tool for separating complex mixtures of proteins, but since its inception in the mid 1970s, it acquired the stigma of being a very difficult application to master and was generally used to its best effect by experts. The introduction of commercially available immobilized pH gradients in the early 1990s provided enhanced reproducibility and easier protocols, leading to a pronounced increase in popularity of the technique. However gel-to-gel variation was still difficult to control without the use of technical replicates. In the mid 1990s (at the same time as the birth of "proteomics"), the concept of multiplexing fluorescently labeled proteins for 2D gel separation was realized by Jon Minden's group and has led to the ability to design experiments to virtually eliminate gel-to-gel variation, resulting in biological replicates being used for statistical analysis with the ability to detect very small changes in relative protein abundance. This technology is referred to as 2D difference gel electrophoresis (2D DIGE).

  15. Parallel stitching of 2D materials

    DOE PAGES

    Ling, Xi; Wu, Lijun; Lin, Yuxuan; ...

    2016-01-27

    Diverse parallel stitched 2D heterostructures, including metal–semiconductor, semiconductor–semiconductor, and insulator–semiconductor, are synthesized directly through selective “sowing” of aromatic molecules as the seeds in the chemical vapor deposition (CVD) method. Lastly, the methodology enables the large-scale fabrication of lateral heterostructures, which offers tremendous potential for its application in integrated circuits.

  16. High-resolution, high-pressure NMR studies of proteins.

    PubMed Central

    Jonas, J; Ballard, L; Nash, D

    1998-01-01

    Advanced high-resolution NMR spectroscopy, including two-dimensional NMR techniques, combined with high pressure capability, represents a powerful new tool in the study of proteins. This contribution is organized in the following way. First, the specialized instrumentation needed for high-pressure NMR experiments is discussed, with specific emphasis on the design features and performance characteristics of a high-sensitivity, high-resolution, variable-temperature NMR probe operating at 500 MHz and at pressures of up to 500 MPa. An overview of several recent studies using 1D and 2D high-resolution, high-pressure NMR spectroscopy to investigate the pressure-induced reversible unfolding and pressure-assisted cold denaturation of lysozyme, ribonuclease A, and ubiquitin is presented. Specifically, the relationship between the residual secondary structure of pressure-assisted, cold-denatured states and the structure of early folding intermediates is discussed. PMID:9649405

  17. Application of 2D Non-Graphene Materials and 2D Oxide Nanostructures for Biosensing Technology

    PubMed Central

    Shavanova, Kateryna; Bakakina, Yulia; Burkova, Inna; Shtepliuk, Ivan; Viter, Roman; Ubelis, Arnolds; Beni, Valerio; Starodub, Nickolaj; Yakimova, Rositsa; Khranovskyy, Volodymyr

    2016-01-01

    The discovery of graphene and its unique properties has inspired researchers to try to invent other two-dimensional (2D) materials. After considerable research effort, a distinct “beyond graphene” domain has been established, comprising the library of non-graphene 2D materials. It is significant that some 2D non-graphene materials possess solid advantages over their predecessor, such as having a direct band gap, and therefore are highly promising for a number of applications. These applications are not limited to nano- and opto-electronics, but have a strong potential in biosensing technologies, as one example. However, since most of the 2D non-graphene materials have been newly discovered, most of the research efforts are concentrated on material synthesis and the investigation of the properties of the material. Applications of 2D non-graphene materials are still at the embryonic stage, and the integration of 2D non-graphene materials into devices is scarcely reported. However, in recent years, numerous reports have blossomed about 2D material-based biosensors, evidencing the growing potential of 2D non-graphene materials for biosensing applications. This review highlights the recent progress in research on the potential of using 2D non-graphene materials and similar oxide nanostructures for different types of biosensors (optical and electrochemical). A wide range of biological targets, such as glucose, dopamine, cortisol, DNA, IgG, bisphenol, ascorbic acid, cytochrome and estradiol, has been reported to be successfully detected by biosensors with transducers made of 2D non-graphene materials. PMID:26861346

  18. Application of 2D Non-Graphene Materials and 2D Oxide Nanostructures for Biosensing Technology.

    PubMed

    Shavanova, Kateryna; Bakakina, Yulia; Burkova, Inna; Shtepliuk, Ivan; Viter, Roman; Ubelis, Arnolds; Beni, Valerio; Starodub, Nickolaj; Yakimova, Rositsa; Khranovskyy, Volodymyr

    2016-02-06

    The discovery of graphene and its unique properties has inspired researchers to try to invent other two-dimensional (2D) materials. After considerable research effort, a distinct "beyond graphene" domain has been established, comprising the library of non-graphene 2D materials. It is significant that some 2D non-graphene materials possess solid advantages over their predecessor, such as having a direct band gap, and therefore are highly promising for a number of applications. These applications are not limited to nano- and opto-electronics, but have a strong potential in biosensing technologies, as one example. However, since most of the 2D non-graphene materials have been newly discovered, most of the research efforts are concentrated on material synthesis and the investigation of the properties of the material. Applications of 2D non-graphene materials are still at the embryonic stage, and the integration of 2D non-graphene materials into devices is scarcely reported. However, in recent years, numerous reports have blossomed about 2D material-based biosensors, evidencing the growing potential of 2D non-graphene materials for biosensing applications. This review highlights the recent progress in research on the potential of using 2D non-graphene materials and similar oxide nanostructures for different types of biosensors (optical and electrochemical). A wide range of biological targets, such as glucose, dopamine, cortisol, DNA, IgG, bisphenol, ascorbic acid, cytochrome and estradiol, has been reported to be successfully detected by biosensors with transducers made of 2D non-graphene materials.

  19. Increasing the sensitivity of 2D high-resolution NMR methods applied to quadrupolar nuclei

    NASA Astrophysics Data System (ADS)

    Amoureux, J. P.; Delevoye, L.; Steuernagel, S.; Gan, Z.; Ganapathy, S.; Montagne, L.

    2005-02-01

    Gan and Kwak recently proposed a soft-pulse added mixing (SPAM) idea in the classical two-pulse multiple-quantum magic-angle spinning scheme. In the SPAM method, a soft π/2 pulse is added after the second hard-pulse (conversion pulse) and all coherence orders in between them are constructively used to obtain the signal. We, here, further extend this idea to distributed samples where the signal mainly results from echo pathways and that from anti-echo pathways dies out after a few t1 increments. We show that, with a combination of SPAM and collection of fewer anti-echoes, an enhancement of the signal to noise ratio by a factor of ca. 3 may be obtained over the z-filtered version. This may prove to be useful even for samples with long T2' relaxation times.

  20. Increasing the sensitivity of 2D high-resolution NMR methods applied to quadrupolar nuclei.

    PubMed

    Amoureux, J P; Delevoye, L; Steuernagel, S; Gan, Z; Ganapathy, S; Montagne, L

    2005-02-01

    Gan and Kwak recently proposed a soft-pulse added mixing (SPAM) idea in the classical two-pulse multiple-quantum magic-angle spinning scheme. In the SPAM method, a soft pi/2 pulse is added after the second hard-pulse (conversion pulse) and all coherence orders in between them are constructively used to obtain the signal. We, here, further extend this idea to distributed samples where the signal mainly results from echo pathways and that from anti-echo pathways dies out after a few t1 increments. We show that, with a combination of SPAM and collection of fewer anti-echoes, an enhancement of the signal to noise ratio by a factor of ca. 3 may be obtained over the z-filtered version. This may prove to be useful even for samples with long T2' relaxation times.

  1. Synthesis and Characterization of 9-Hydroxyphenalenone Using 2D NMR Techniques

    ERIC Educational Resources Information Center

    Caes, Benjamin; Jensen, Dell, Jr.

    2008-01-01

    9-Hydroxyphenalenone is a planar multicyclic [beta]-keto-enol, which is synthesized via a Friedel-Crafts acylation followed by acid-catalyzed intramolecular Michael addition with the loss of a phenyl group in a one-pot reaction during a four-hour lab period. Tautomerization of the [beta]-keto-enol results in C[subscript 2v] symmetry on the NMR…

  2. Compatible embedding for 2D shape animation.

    PubMed

    Baxter, William V; Barla, Pascal; Anjyo, Ken-Ichi

    2009-01-01

    We present new algorithms for the compatible embedding of 2D shapes. Such embeddings offer a convenient way to interpolate shapes having complex, detailed features. Compared to existing techniques, our approach requires less user input, and is faster, more robust, and simpler to implement, making it ideal for interactive use in practical applications. Our new approach consists of three parts. First, our boundary matching algorithm locates salient features using the perceptually motivated principles of scale-space and uses these as automatic correspondences to guide an elastic curve matching algorithm. Second, we simplify boundaries while maintaining their parametric correspondence and the embedding of the original shapes. Finally, we extend the mapping to shapes' interiors via a new compatible triangulation algorithm. The combination of our algorithms allows us to demonstrate 2D shape interpolation with instant feedback. The proposed algorithms exhibit a combination of simplicity, speed, and accuracy that has not been achieved in previous work.

  3. Schottky diodes from 2D germanane

    NASA Astrophysics Data System (ADS)

    Sahoo, Nanda Gopal; Esteves, Richard J.; Punetha, Vinay Deep; Pestov, Dmitry; Arachchige, Indika U.; McLeskey, James T.

    2016-07-01

    We report on the fabrication and characterization of a Schottky diode made using 2D germanane (hydrogenated germanene). When compared to germanium, the 2D structure has higher electron mobility, an optimal band-gap, and exceptional stability making germanane an outstanding candidate for a variety of opto-electronic devices. One-atom-thick sheets of hydrogenated puckered germanium atoms have been synthesized from a CaGe2 framework via intercalation and characterized by XRD, Raman, and FTIR techniques. The material was then used to fabricate Schottky diodes by suspending the germanane in benzonitrile and drop-casting it onto interdigitated metal electrodes. The devices demonstrate significant rectifying behavior and the outstanding potential of this material.

  4. Static & Dynamic Response of 2D Solids

    SciTech Connect

    Lin, Jerry

    1996-07-15

    NIKE2D is an implicit finite-element code for analyzing the finite deformation, static and dynamic response of two-dimensional, axisymmetric, plane strain, and plane stress solids. The code is fully vectorized and available on several computing platforms. A number of material models are incorporated to simulate a wide range of material behavior including elasto-placicity, anisotropy, creep, thermal effects, and rate dependence. Slideline algorithms model gaps and sliding along material interfaces, including interface friction, penetration and single surface contact. Interactive-graphics and rezoning is included for analyses with large mesh distortions. In addition to quasi-Newton and arc-length procedures, adaptive algorithms can be defined to solve the implicit equations using the solution language ISLAND. Each of these capabilities and more make NIKE2D a robust analysis tool.

  5. Explicit 2-D Hydrodynamic FEM Program

    SciTech Connect

    Lin, Jerry

    1996-08-07

    DYNA2D* is a vectorized, explicit, two-dimensional, axisymmetric and plane strain finite element program for analyzing the large deformation dynamic and hydrodynamic response of inelastic solids. DYNA2D* contains 13 material models and 9 equations of state (EOS) to cover a wide range of material behavior. The material models implemented in all machine versions are: elastic, orthotropic elastic, kinematic/isotropic elastic plasticity, thermoelastoplastic, soil and crushable foam, linear viscoelastic, rubber, high explosive burn, isotropic elastic-plastic, temperature-dependent elastic-plastic. The isotropic and temperature-dependent elastic-plastic models determine only the deviatoric stresses. Pressure is determined by one of 9 equations of state including linear polynomial, JWL high explosive, Sack Tuesday high explosive, Gruneisen, ratio of polynomials, linear polynomial with energy deposition, ignition and growth of reaction in HE, tabulated compaction, and tabulated.

  6. Complete Assignment of (1)H-NMR Resonances of the King Cobra Neurotoxin CM-11.

    PubMed

    Pang, Yu-Xi; Liu, Wei-Dong; Liu, Ai-Zhuo; Pei, Feng-Kui

    1997-01-01

    The king cobra (Ophiophagus Hannah) neurotoxin CM-Il is long-chain peptide with 72 amino acid residues. Its complete assignment of (1)H-NMR resonances was obtained using various 2D-NMR technologies, including DQF-COSY, clean-TOCSY and NOESY.

  7. Quasiparticle interference in unconventional 2D systems

    NASA Astrophysics Data System (ADS)

    Chen, Lan; Cheng, Peng; Wu, Kehui

    2017-03-01

    At present, research of 2D systems mainly focuses on two kinds of materials: graphene-like materials and transition-metal dichalcogenides (TMDs). Both of them host unconventional 2D electronic properties: pseudospin and the associated chirality of electrons in graphene-like materials, and spin-valley-coupled electronic structures in the TMDs. These exotic electronic properties have attracted tremendous interest for possible applications in nanodevices in the future. Investigation on the quasiparticle interference (QPI) in 2D systems is an effective way to uncover these properties. In this review, we will begin with a brief introduction to 2D systems, including their atomic structures and electronic bands. Then, we will discuss the formation of Friedel oscillation due to QPI in constant energy contours of electron bands, and show the basic concept of Fourier-transform scanning tunneling microscopy/spectroscopy (FT-STM/STS), which can resolve Friedel oscillation patterns in real space and consequently obtain the QPI patterns in reciprocal space. In the next two parts, we will summarize some pivotal results in the investigation of QPI in graphene and silicene, in which systems the low-energy quasiparticles are described by the massless Dirac equation. The FT-STM experiments show there are two different interference channels (intervalley and intravalley scattering) and backscattering suppression, which associate with the Dirac cones and the chirality of quasiparticles. The monolayer and bilayer graphene on different substrates (SiC and metal surfaces), and the monolayer and multilayer silicene on a Ag(1 1 1) surface will be addressed. The fifth part will introduce the FT-STM research on QPI in TMDs (monolayer and bilayer of WSe2), which allow us to infer the spin texture of both conduction and valence bands, and present spin-valley coupling by tracking allowed and forbidden scattering channels.

  8. Compact 2-D graphical representation of DNA

    NASA Astrophysics Data System (ADS)

    Randić, Milan; Vračko, Marjan; Zupan, Jure; Novič, Marjana

    2003-05-01

    We present a novel 2-D graphical representation for DNA sequences which has an important advantage over the existing graphical representations of DNA in being very compact. It is based on: (1) use of binary labels for the four nucleic acid bases, and (2) use of the 'worm' curve as template on which binary codes are placed. The approach is illustrated on DNA sequences of the first exon of human β-globin and gorilla β-globin.

  9. 2D Metals by Repeated Size Reduction.

    PubMed

    Liu, Hanwen; Tang, Hao; Fang, Minghao; Si, Wenjie; Zhang, Qinghua; Huang, Zhaohui; Gu, Lin; Pan, Wei; Yao, Jie; Nan, Cewen; Wu, Hui

    2016-10-01

    A general and convenient strategy for manufacturing freestanding metal nanolayers is developed on large scale. By the simple process of repeatedly folding and calendering stacked metal sheets followed by chemical etching, free-standing 2D metal (e.g., Ag, Au, Fe, Cu, and Ni) nanosheets are obtained with thicknesses as small as 1 nm and with sizes of the order of several micrometers.

  10. Realistic and efficient 2D crack simulation

    NASA Astrophysics Data System (ADS)

    Yadegar, Jacob; Liu, Xiaoqing; Singh, Abhishek

    2010-04-01

    Although numerical algorithms for 2D crack simulation have been studied in Modeling and Simulation (M&S) and computer graphics for decades, realism and computational efficiency are still major challenges. In this paper, we introduce a high-fidelity, scalable, adaptive and efficient/runtime 2D crack/fracture simulation system by applying the mathematically elegant Peano-Cesaro triangular meshing/remeshing technique to model the generation of shards/fragments. The recursive fractal sweep associated with the Peano-Cesaro triangulation provides efficient local multi-resolution refinement to any level-of-detail. The generated binary decomposition tree also provides efficient neighbor retrieval mechanism used for mesh element splitting and merging with minimal memory requirements essential for realistic 2D fragment formation. Upon load impact/contact/penetration, a number of factors including impact angle, impact energy, and material properties are all taken into account to produce the criteria of crack initialization, propagation, and termination leading to realistic fractal-like rubble/fragments formation. The aforementioned parameters are used as variables of probabilistic models of cracks/shards formation, making the proposed solution highly adaptive by allowing machine learning mechanisms learn the optimal values for the variables/parameters based on prior benchmark data generated by off-line physics based simulation solutions that produce accurate fractures/shards though at highly non-real time paste. Crack/fracture simulation has been conducted on various load impacts with different initial locations at various impulse scales. The simulation results demonstrate that the proposed system has the capability to realistically and efficiently simulate 2D crack phenomena (such as window shattering and shards generation) with diverse potentials in military and civil M&S applications such as training and mission planning.

  11. Magnetic gating of a 2D topological insulator

    NASA Astrophysics Data System (ADS)

    Dang, Xiaoqian; Burton, J. D.; Tsymbal, Evgeny Y.

    2016-09-01

    Deterministic control of transport properties through manipulation of spin states is one of the paradigms of spintronics. Topological insulators offer a new playground for exploring interesting spin-dependent phenomena. Here, we consider a ferromagnetic ‘gate’ representing a magnetic adatom coupled to the topologically protected edge state of a two-dimensional (2D) topological insulator to modulate the electron transmission of the edge state. Due to the locked spin and wave vector of the transport electrons the transmission across the magnetic gate depends on the mutual orientation of the adatom magnetic moment and the current. If the Fermi energy matches an exchange-split bound state of the adatom, the electron transmission can be blocked due to the full back scattering of the incident wave. This antiresonance behavior is controlled by the adatom magnetic moment orientation so that the transmission of the edge state can be changed from 1 to 0. Expanding this consideration to a ferromagnetic gate representing a 1D chain of atoms shows a possibility to control the spin-dependent current of a strip of a 2D topological insulator by magnetization orientation of the ferromagnetic gate.

  12. Engineering light outcoupling in 2D materials.

    PubMed

    Lien, Der-Hsien; Kang, Jeong Seuk; Amani, Matin; Chen, Kevin; Tosun, Mahmut; Wang, Hsin-Ping; Roy, Tania; Eggleston, Michael S; Wu, Ming C; Dubey, Madan; Lee, Si-Chen; He, Jr-Hau; Javey, Ali

    2015-02-11

    When light is incident on 2D transition metal dichalcogenides (TMDCs), it engages in multiple reflections within underlying substrates, producing interferences that lead to enhancement or attenuation of the incoming and outgoing strength of light. Here, we report a simple method to engineer the light outcoupling in semiconducting TMDCs by modulating their dielectric surroundings. We show that by modulating the thicknesses of underlying substrates and capping layers, the interference caused by substrate can significantly enhance the light absorption and emission of WSe2, resulting in a ∼11 times increase in Raman signal and a ∼30 times increase in the photoluminescence (PL) intensity of WSe2. On the basis of the interference model, we also propose a strategy to control the photonic and optoelectronic properties of thin-layer WSe2. This work demonstrates the utilization of outcoupling engineering in 2D materials and offers a new route toward the realization of novel optoelectronic devices, such as 2D LEDs and solar cells.

  13. Irreversibility-inversions in 2D turbulence

    NASA Astrophysics Data System (ADS)

    Bragg, Andrew; de Lillo, Filippo; Boffetta, Guido

    2016-11-01

    We consider a recent theoretical prediction that for inertial particles in 2D turbulence, the nature of the irreversibility of their pair dispersion inverts when the particle inertia exceeds a certain value. In particular, when the particle Stokes number, St , is below a certain value, the forward-in-time (FIT) dispersion should be faster than the backward-in-time (BIT) dispersion, but for St above this value, this should invert so that BIT becomes faster than FIT dispersion. This non-trivial behavior arises because of the competition between two physically distinct irreversibility mechanisms that operate in different regimes of St . In 3D turbulence, both mechanisms act to produce faster BIT than FIT dispersion, but in 2D, the two mechanisms have opposite effects because of the inverse energy cascade in the turbulent velocity field. We supplement the qualitative argument given by Bragg et al. by deriving quantitative predictions of this effect in the short-time dispersion limit. These predictions are then confirmed by results of inertial particle dispersion in a direct numerical simulation of 2D turbulence.

  14. In vivo NMR for ¹³C Metabolic Flux Analysis.

    PubMed

    Roscher, Albrecht; Troufflard, Stéphanie; Taghki, Abdelghani Idrissi

    2014-01-01

    The use of in vivo NMR within the framework of Metabolic Flux Analysis in plants is presented. In vivo NMR allows to visualize the active metabolic network, to determine metabolic and isotopic steady state and to measure metabolic fluxes which are not necessarily accessible by isotopic steady state (stationary) Metabolic Flux Analysis. The kinetic data can be used as input for dynamic (nonstationary) Metabolic Flux Analysis. Both 1D and 2D NMR methods are employed.

  15. 1H and 13C NMR assignments for two new angular furanocoumarin glycosides from Peucedanum praeruptorum.

    PubMed

    Chang, Haitao; Okada, Yoshihito; Okuyama, Toru; Tu, Pengfei

    2007-07-01

    Two novel angular-type furanocoumarin glycosides, peucedanoside A (1) and peucedanoside B (2), along with a known compound apterin (3), were isolated from the roots of Peucedanum praeruptorum Dunn. Their chemical structures were determined by MS, NMR spectroscopy and chemical analysis. Complete assignments of the 1H and 13C NMR spectroscopic data were achieved by 1D and 2D NMR experiments including DEPT, HSQC, HMBC and ROESY.

  16. Three-Dimensional Maximum-Quantum Correlation HMQC NMR Spectroscopy (3D MAXY-HMQC)

    NASA Astrophysics Data System (ADS)

    Liu, Maili; Mao, Xi-An; Ye, Chaohui; Nicholson, Jeremy K.; Lindon, John C.

    1997-11-01

    The extension of two-dimensional maximum-quantum correlation spectroscopy (2D MAXY NMR), which can be used to simplify complex NMR spectra, to three dimensions (3D) is described. A new pulse sequence for 3D MAXY-HMQC is presented and exemplified using the steroid drug dexamethasone. The sensitivity and coherence transfer efficiency of the MAXY NMR approach has also been assessed in relation to other HMQC- and HSQC-based 3D methods.

  17. Helical jump motions of poly(L-lactic acid) chains in the α phase as revealed by solid-state NMR.

    PubMed

    Chen, Wei; Reichert, Detlef; Miyoshi, Toshikazu

    2015-03-26

    The molecular dynamics of Poly(L-lactic Acid) (PLLA) chains in the α phase was investigated by Solid-State NMR spectroscopy. (13)C high-resolution NMR clearly indicates that the crystalline signals split into 2, 3, and 4 signals for the CH3, CH and CO groups, respectively at 25 °C, while the amorphous signals give a broad component at the bottom of the crystalline signals. (13)C NMR spectra show that the crystalline line shape changes with increasing temperatures well above the glass transition temperature (Tg) and imply the presence of the molecular dynamics in the crystalline region. Comparisons of the evolution-time dependence of CODEX data and simulation results based on reorientation of chemical shift anisotropy (CSA) indicate that the chains in the α phase perform helical jump motions in the slow dynamic range at temperatures above 115 °C. The mixing-time dependence of the CODEX data yields an activation energy of Ea of (95 ± 8) kJ/mol for the helical jump motions. Moreover, two-dimensional exchange NMR with highly resolved signals for the CO group provides cross peaks among four well resolved signals due to the helical jumps. Comparison of 2D buildup curves of the cross peaks and calculated data determines that helical jump motions prefer largely uncorrelated random back-and-forth motions between the neighboring sites, possibly enabling large-scale chain diffusion in the crystalline regions.

  18. Use of marginal distributions constrained optimization (MADCO) for accelerated 2D MRI relaxometry and diffusometry

    NASA Astrophysics Data System (ADS)

    Benjamini, Dan; Basser, Peter J.

    2016-10-01

    Measuring multidimensional (e.g., 2D) relaxation spectra in NMR and MRI clinical applications is a holy grail of the porous media and biomedical MR communities. The main bottleneck is the inversion of Fredholm integrals of the first kind, an ill-conditioned problem requiring large amounts of data to stabilize a solution. We suggest a novel experimental design and processing framework to accelerate and improve the reconstruction of such 2D spectra that uses a priori information from the 1D projections of spectra, or marginal distributions. These 1D marginal distributions provide powerful constraints when 2D spectra are reconstructed, and their estimation requires an order of magnitude less data than a conventional 2D approach. This marginal distributions constrained optimization (MADCO) methodology is demonstrated here with a polyvinylpyrrolidone-water phantom that has 3 distinct peaks in the 2D D-T1 space. The stability, sensitivity to experimental parameters, and accuracy of this new approach are compared with conventional methods by serially subsampling the full data set. While the conventional, unconstrained approach performed poorly, the new method had proven to be highly accurate and robust, only requiring a fraction of the data. Additionally, synthetic T1 -T2 data are presented to explore the effects of noise on the estimations, and the performance of the proposed method with a smooth and realistic 2D spectrum. The proposed framework is quite general and can also be used with a variety of 2D MRI experiments (D-T2,T1 -T2, D -D, etc.), making these potentially feasible for preclinical and even clinical applications for the first time.

  19. 2D superconductivity by ionic gating

    NASA Astrophysics Data System (ADS)

    Iwasa, Yoshi

    2D superconductivity is attracting a renewed interest due to the discoveries of new highly crystalline 2D superconductors in the past decade. Superconductivity at the oxide interfaces triggered by LaAlO3/SrTiO3 has become one of the promising routes for creation of new 2D superconductors. Also, the MBE grown metallic monolayers including FeSe are also offering a new platform of 2D superconductors. In the last two years, there appear a variety of monolayer/bilayer superconductors fabricated by CVD or mechanical exfoliation. Among these, electric field induced superconductivity by electric double layer transistor (EDLT) is a unique platform of 2D superconductivity, because of its ability of high density charge accumulation, and also because of the versatility in terms of materials, stemming from oxides to organics and layered chalcogenides. In this presentation, the following issues of electric filed induced superconductivity will be addressed; (1) Tunable carrier density, (2) Weak pinning, (3) Absence of inversion symmetry. (1) Since the sheet carrier density is quasi-continuously tunable from 0 to the order of 1014 cm-2, one is able to establish an electronic phase diagram of superconductivity, which will be compared with that of bulk superconductors. (2) The thickness of superconductivity can be estimated as 2 - 10 nm, dependent on materials, and is much smaller than the in-plane coherence length. Such a thin but low resistance at normal state results in extremely weak pinning beyond the dirty Boson model in the amorphous metallic films. (3) Due to the electric filed, the inversion symmetry is inherently broken in EDLT. This feature appears in the enhancement of Pauli limit of the upper critical field for the in-plane magnetic fields. In transition metal dichalcogenide with a substantial spin-orbit interactions, we were able to confirm the stabilization of Cooper pair due to its spin-valley locking. This work has been supported by Grant-in-Aid for Specially

  20. Quantitative analysis of protein-ligand interactions by NMR.

    PubMed

    Furukawa, Ayako; Konuma, Tsuyoshi; Yanaka, Saeko; Sugase, Kenji

    2016-08-01

    Protein-ligand interactions have been commonly studied through static structures of the protein-ligand complex. Recently, however, there has been increasing interest in investigating the dynamics of protein-ligand interactions both for fundamental understanding of the underlying mechanisms and for drug development. NMR is a versatile and powerful tool, especially because it provides site-specific quantitative information. NMR has widely been used to determine the dissociation constant (KD), in particular, for relatively weak interactions. The simplest NMR method is a chemical-shift titration experiment, in which the chemical-shift changes of a protein in response to ligand titration are measured. There are other quantitative NMR methods, but they mostly apply only to interactions in the fast-exchange regime. These methods derive the dissociation constant from population-averaged NMR quantities of the free and bound states of a protein or ligand. In contrast, the recent advent of new relaxation-based experiments, including R2 relaxation dispersion and ZZ-exchange, has enabled us to obtain kinetic information on protein-ligand interactions in the intermediate- and slow-exchange regimes. Based on R2 dispersion or ZZ-exchange, methods that can determine the association rate, kon, dissociation rate, koff, and KD have been developed. In these approaches, R2 dispersion or ZZ-exchange curves are measured for multiple samples with different protein and/or ligand concentration ratios, and the relaxation data are fitted to theoretical kinetic models. It is critical to choose an appropriate kinetic model, such as the two- or three-state exchange model, to derive the correct kinetic information. The R2 dispersion and ZZ-exchange methods are suitable for the analysis of protein-ligand interactions with a micromolar or sub-micromolar dissociation constant but not for very weak interactions, which are typical in very fast exchange. This contrasts with the NMR methods that are used

  1. Pitfalls in the Measurement of Metabolite Concentrations Using the One-Pulse Experiment in in Vivo NMR: Commentary on ``On Neglecting Chemical Exchange Effects When Correcting in Vivo 31P MRS Data for Partial Saturation''

    NASA Astrophysics Data System (ADS)

    Spencer, Richard G. S.; Fishbein, Kenneth W.; Galban, Craig J.

    2001-04-01

    In an article in a previous issue of the Journal of Magnetic Resonance, Ouwerkerk and Bottomley (J. Magn. Reson.148, pp. 425-435, 2001) show that even in the presence of chemical exchange, the dependence of saturation factors on repetition time in the one-pulse experiment is approximately monoexponential. They conclude from this fact that the effect of chemical exchange on the use of saturation factors when correcting for partial saturation is negligible. We take issue with this conclusion and demonstrate that because saturation factors in the presence of chemical exchange are strongly dependent upon all of the chemical parameters of the system, that is, upon all T1's and M0's of resonances in the exchange network and upon the reaction rates themselves, it is problematic to apply saturation factor corrections in situations in which any of these parameters may change. The error criterion we establish reflects actual errors in quantitation, rather than departures from monoexponentiality.

  2. Rotary echo nutation NMR

    NASA Astrophysics Data System (ADS)

    Janssen, R.; Tijink, G. A. H.; Veeman, W. S.

    1988-01-01

    A two-dimensional solid state NMR experiment which combines rotary echoes and nutation NMR is investigated and used to study different sodium sites in zeolite NaA. It is shown that with this technique sodium ions with different relaxation rates in the rotating frame can be distinguished.

  3. Lectures on pulsed NMR

    SciTech Connect

    Pines, A.

    1988-08-01

    These lectures discuss some recent developments in pulsed NMR, emphasizing fundamental principles with selected illustrative applications. Major topics covered include multiple-quantum spectroscopy, spin decoupling, the interaction of spins with a quantized field, adiabatic rapid passage, spin temperature and statistics of cross-polarization, coherent averaging, and zero field NMR. 32 refs., 56 figs.

  4. Lectures on pulsed NMR

    SciTech Connect

    Pines, A.

    1986-09-01

    These lectures discuss some recent developments in pulsed NMR, emphasizing fundamental principles with selected illustrative applications. Major topics covered include multiple-quantum spectroscopy, spin decoupling, the interaction of spins with a quantized field, adiabatic rapid passage, spin temperature and statistics of cross-polarization, coherent averaging, and zero field NMR. 55 figs.

  5. Ultrafast dynamics of metal plasmons induced by 2D semiconductor excitons in hybrid nanostructure arrays

    SciTech Connect

    Boulesbaa, Abdelaziz; Babicheva, Viktoriia E.; Wang, Kai; Kravchenko, Ivan I.; Lin, Ming -Wei; Mahjouri-Samani, Masoud; Jacobs, Christopher B.; Puretzky, Alexander A.; Xiao, Kai; Ivanov, Ilia N.; Rouleau, Christopher M.; Geohegan, David B.

    2016-11-17

    With the advanced progress achieved in the field of nanotechnology, localized surface plasmons resonances (LSPRs) are actively considered to improve the efficiency of metal-based photocatalysis, photodetection, and photovoltaics. Here, we report on the exchange of energy and electric charges in a hybrid composed of a two-dimensional tungsten disulfide (2D-WS2) monolayer and an array of aluminum (Al) nanodisks. Femtosecond pump-probe spectroscopy results indicate that within ~830 fs after photoexcitation of the 2D-WS2 semiconductor, energy transfer from the 2D-WS2 excitons excites the plasmons of the Al array. Then, upon the radiative and/or nonradiative damping of these excited plasmons, energy and/or electron transfer back to the 2D-WS2 semiconductor takes place as indicated by an increase in the reflected probe at the 2D exciton transition energies at later time-delays. This simultaneous exchange of energy and charges between the metal and the 2D-WS2 semiconductor resulted in an extension of the average lifetime of the 2D-excitons from ~15 to ~58 ps in absence and presence of the Al array, respectively. Furthermore, the indirectly excited plasmons were found to live as long as the 2D-WS2 excitons exist. Furthermore, the demonstrated ability to generate exciton-plasmons coupling in a hybrid nanostructure may open new opportunities for optoelectronic applications such as plasmonic-based photodetection and photocatalysis.

  6. NMR logging apparatus

    DOEpatents

    Walsh, David O; Turner, Peter

    2014-05-27

    Technologies including NMR logging apparatus and methods are disclosed. Example NMR logging apparatus may include surface instrumentation and one or more downhole probes configured to fit within an earth borehole. The surface instrumentation may comprise a power amplifier, which may be coupled to the downhole probes via one or more transmission lines, and a controller configured to cause the power amplifier to generate a NMR activating pulse or sequence of pulses. Impedance matching means may be configured to match an output impedance of the power amplifier through a transmission line to a load impedance of a downhole probe. Methods may include deploying the various elements of disclosed NMR logging apparatus and using the apparatus to perform NMR measurements.

  7. D2d(23)-C84 versus Sc2C2@D2d(23)-C84: Impact of Endohedral Sc2C2 Doping on Chemical Reactivity in the Photolysis of Diazirine.

    PubMed

    Yamada, Michio; Tanabe, Yukiko; Dang, Jing-Shuang; Sato, Satoru; Mizorogi, Naomi; Hachiya, Makoto; Suzuki, Mitsuaki; Abe, Tsuneyuki; Kurihara, Hiroki; Maeda, Yutaka; Zhao, Xiang; Lian, Yongfu; Nagase, Shigeru; Akasaka, Takeshi

    2016-12-21

    We compared the chemical reactivity of D2d(23)-C84 and that of Sc2C2@D2d(23)-C84, both having the same carbon cage geometry, in the photolysis of 2-adamantane-2,3'-[3H]-diazirine, to clarify metal-atom doping effects on the chemical reactivity of the carbon cage. Experimental and computational studies have revealed that the chemical reactivity of the D2d(23)-C84 carbon cage is altered drastically by endohedral Sc2C2 doping. The reaction of empty D2d(23)-C84 with the diazirine under photoirradiation yields two adamantylidene (Ad) adducts. NMR spectroscopic studies revealed that the major Ad monoadduct (C84(Ad)-A) has a fulleroid structure and that the minor Ad monoadduct (C84(Ad)-B) has a methanofullerene structure. The latter was also characterized using X-ray crystallography. C84(Ad)-A is stable under photoirradiation, but it interconverted to C84(Ad)-B by heating at 80 °C. In contrast, the reaction of endohedral Sc2C2@D2d(23)-C84 with diazirine under photoirradiation affords four Ad monoadducts (Sc2C2@C84(Ad)-A, Sc2C2@C84(Ad)-B, Sc2C2@C84(Ad)-C, and Sc2C2@C84(Ad)-D). The structure of Sc2C2@C84(Ad)-C was characterized using X-ray crystallography. Thermal interconversion of Sc2C2@C84(Ad)-A and Sc2C2@C84(Ad)-B to Sc2C2@C84(Ad)-C was also observed. The reaction mechanisms of the Ad addition and thermal interconversion were elucidated from theoretical calculations. Calculation results suggest that C84(Ad)-B and Sc2C2@C84(Ad)-C are thermodynamically favorable products. Their different chemical reactivities derive from Sc2C2 doping, which raises the HOMO and LUMO levels of the D2d(23)-C84 carbon cage.

  8. Microcrystalline hexagonal tungsten bronze. 1. Basis of ion exchange selectivity for cesium and strontium.

    PubMed

    Griffith, Christopher S; Luca, Vittorio; Hanna, John V; Pike, Kevin J; Smith, Mark E; Thorogood, Gordon S

    2009-07-06

    The structural basis of selectivity for cesium and strontium of microcrystalline hexagonal tungsten bronze (HTB) phase Na(x)WO(3+x/2).zH(2)O has been studied using X-ray and neutron diffraction techniques, 1D and 2D (23)Na magic angle spinning (MAS) nuclear magnetic resonance (NMR) spectroscopy, and radiochemical ion exchange investigations. For the HTB system, this study has shown that scattering techniques alone provide an incomplete description of the disorder and rapid exchange of water (with tunnel cations) occurring in this system. However, 1D and 2D (23)Na MAS NMR has identified three sodium species within the HTB tunnels-species A, which is located at the center of the hexagonal window and is devoid of coordinated water, and species B and C, which are the di- and monohydrated variants, respectively, of species A. Although species B accords with the traditional crystallographic model of the HTB phase, this work is the first to propose and identify the anhydrous species A and monohydrate species C. The population (total) of species B and C decreases in comparison to that of species A with increasing exchange of either cesium or strontium; that is, species B and C appear more exchangeable than species A. Moreover, a significant proportion of tunnel water is redistributed by these cations. Multiple ion exchange investigations with radiotracers (137)Cs and (85)Sr have shown that for strontium there is a definite advantage in ensuring that any easily exchanged sodium is removed from the HTB tunnels prior to exchange. The decrease in selectivity (wrt cesium) is most probably due to the slightly smaller effective size of Sr(2+); namely, it is less of a good fit for the hexagonal window, ion exchange site. The selectivity of the HTB framework for cesium has been shown unequivocally to be defined by the structure of the hexagonal window, ion exchange site. Compromising the geometry of this window even in the slightest way by either (1) varying the cell volume through

  9. Periodically sheared 2D Yukawa systems

    SciTech Connect

    Kovács, Anikó Zsuzsa; Hartmann, Peter; Donkó, Zoltán

    2015-10-15

    We present non-equilibrium molecular dynamics simulation studies on the dynamic (complex) shear viscosity of a 2D Yukawa system. We have identified a non-monotonic frequency dependence of the viscosity at high frequencies and shear rates, an energy absorption maximum (local resonance) at the Einstein frequency of the system at medium shear rates, an enhanced collective wave activity, when the excitation is near the plateau frequency of the longitudinal wave dispersion, and the emergence of significant configurational anisotropy at small frequencies and high shear rates.

  10. ENERGY LANDSCAPE OF 2D FLUID FORMS

    SciTech Connect

    Y. JIANG; ET AL

    2000-04-01

    The equilibrium states of 2D non-coarsening fluid foams, which consist of bubbles with fixed areas, correspond to local minima of the total perimeter. (1) The authors find an approximate value of the global minimum, and determine directly from an image how far a foam is from its ground state. (2) For (small) area disorder, small bubbles tend to sort inwards and large bubbles outwards. (3) Topological charges of the same sign repel while charges of opposite sign attract. (4) They discuss boundary conditions and the uniqueness of the pattern for fixed topology.

  11. Codon Constraints on Closed 2D Shapes,

    DTIC Science & Technology

    2014-09-26

    19843$ CODON CONSTRAINTS ON CLOSED 2D SHAPES Go Whitman Richards "I Donald D. Hoffman’ D T 18 Abstract: Codons are simple primitives for describing plane...RSONAL AUT"ORtIS) Richards, Whitman & Hoffman, Donald D. 13&. TYPE OF REPORT 13b. TIME COVERED N/A P8 AT F RRrT t~r. Ago..D,) is, PlE COUNT Reprint...outlines, if figure and ground are ignored. Later, we will address the problem of indexing identical codon descriptors that have different figure

  12. Automation of peak-tracking analysis of stepwise perturbed NMR spectra.

    PubMed

    Banelli, Tommaso; Vuano, Marco; Fogolari, Federico; Fusiello, Andrea; Esposito, Gennaro; Corazza, Alessandra

    2017-02-01

    We describe a new algorithmic approach able to automatically pick and track the NMR resonances of a large number of 2D NMR spectra acquired during a stepwise variation of a physical parameter. The method has been named Trace in Track (TINT), referring to the idea that a gaussian decomposition traces peaks within the tracks recognised through 3D mathematical morphology. It is capable of determining the evolution of the chemical shifts, intensity and linewidths of each tracked peak.The performances obtained in term of track reconstruction and correct assignment on realistic synthetic spectra were high above 90% when a noise level similar to that of experimental data were considered. TINT was applied successfully to several protein systems during a temperature ramp in isotope exchange experiments. A comparison with a state-of-the-art algorithm showed promising results for great numbers of spectra and low signal to noise ratios, when the graduality of the perturbation is appropriate. TINT can be applied to different kinds of high throughput chemical shift mapping experiments, with quasi-continuous variations, in which a quantitative automated recognition is crucial.

  13. Exploring new Routes for Identifying Phosphorus Species in Terrestrial and Aquatic Ecosystems with 31P NMR

    NASA Astrophysics Data System (ADS)

    Vestergren, Johan; Persson, Per; Sundman, Annelie; Ilstedt, Ulrik; Giesler, Reiner; Schleucher, Jürgen; Gröbner, Gerhard

    2014-05-01

    Phosphorus (P) is the primary growth-limiting nutrient in some of the world's biomes. Rock phosphate is a non-renewable resource and the major source of agricultural fertilizers. Predictions of P consumption indicate that rock phosphate mining may peak within 35 years, with severe impacts on worldwide food production1. Organic P compounds constitute a major fraction of soil P, but little is known about the dynamics and bioavailability of organic P species. Our aim is to develop new liquid and solid state 31P-NMR (nuclear magnetic resonance) techniques to identify P-species in water and soils; information required for correlating P speciation with plant and soil processes2, and eventually to improve P use. Soil organic P is frequently extracted using NaOH/EDTA, followed by characterization of the extract by solution 31P-NMR. However, the obtained NMR spectra usually have poor resolution due to line broadening caused by the presence of paramagnetic ions. Therefore, we successfully developed an approach to avoid paramagnetic line broadening by precipitation of metal sulfides. Sulfide precipitation dramatically reduces NMR line widths for soil extracts, without affecting P-composition. The resulting highly improved resolution allowed us to apply for the first time 2D 1H,31P-NMR methods to identify different P monoesters in spectral regions which are extremely crowded in 1D NMR spectra.3 By exploiting 2D 1H-31P NMR spectra of soil extracts we were able to unambiguously identify individual organic P species by combining 31P and 1H chemical shifts and coupling constants. This approach is even suitable for a structural characterization of unknown P-components and for tracing degradation pathways between diesters and monoesters3,4.Currently we apply our approach on boreal4 and tropical soils with focus on Burkina Faso. In addition we also monitor P-species in aqueos ecosystems. For this purpose stream water from the Krycklan catchment in northern Sweden5 has been used to

  14. Remarks on thermalization in 2D CFT

    NASA Astrophysics Data System (ADS)

    de Boer, Jan; Engelhardt, Dalit

    2016-12-01

    We revisit certain aspects of thermalization in 2D conformal field theory (CFT). In particular, we consider similarities and differences between the time dependence of correlation functions in various states in rational and non-rational CFTs. We also consider the distinction between global and local thermalization and explain how states obtained by acting with a diffeomorphism on the ground state can appear locally thermal, and we review why the time-dependent expectation value of the energy-momentum tensor is generally a poor diagnostic of global thermalization. Since all 2D CFTs have an infinite set of commuting conserved charges, generic initial states might be expected to give rise to a generalized Gibbs ensemble rather than a pure thermal ensemble at late times. We construct the holographic dual of the generalized Gibbs ensemble and show that, to leading order, it is still described by a Banados-Teitelboim-Zanelli black hole. The extra conserved charges, while rendering c <1 theories essentially integrable, therefore seem to have little effect on large-c conformal field theories.

  15. Microwave Assisted 2D Materials Exfoliation

    NASA Astrophysics Data System (ADS)

    Wang, Yanbin

    Two-dimensional materials have emerged as extremely important materials with applications ranging from energy and environmental science to electronics and biology. Here we report our discovery of a universal, ultrafast, green, solvo-thermal technology for producing excellent-quality, few-layered nanosheets in liquid phase from well-known 2D materials such as such hexagonal boron nitride (h-BN), graphite, and MoS2. We start by mixing the uniform bulk-layered material with a common organic solvent that matches its surface energy to reduce the van der Waals attractive interactions between the layers; next, the solutions are heated in a commercial microwave oven to overcome the energy barrier between bulk and few-layers states. We discovered the minutes-long rapid exfoliation process is highly temperature dependent, which requires precise thermal management to obtain high-quality inks. We hypothesize a possible mechanism of this proposed solvo-thermal process; our theory confirms the basis of this novel technique for exfoliation of high-quality, layered 2D materials by using an as yet unknown role of the solvent.

  16. Analyzing protein-ligand interactions by dynamic NMR spectroscopy.

    PubMed

    Mittermaier, Anthony; Meneses, Erick

    2013-01-01

    Nuclear magnetic resonance (NMR) spectroscopy can provide detailed information on protein-ligand interactions that is inaccessible using other biophysical techniques. This chapter focuses on NMR-based approaches for extracting affinity and rate constants for weakly binding transient protein complexes with lifetimes of less than about a second. Several pulse sequences and analytical techniques are discussed, including line-shape simulations, spin-echo relaxation dispersion methods (CPMG), and magnetization exchange (EXSY) experiments.

  17. 17O NMR Study of Solvent Exchange in Some Aqueous [Co(tren)(X)(OH(2)/OH)](n)()(+), [Co(cyclen)(X)(OH(2)/OH)](n)()(+), and [Co(N-Mecyclen)(X)(OH(2)/OH)](n)()(+) Systems (X = NH(3), OH(2)/OH; n = 3, 2, 1)(1).

    PubMed

    Brasch, Nicola E.; Buckingham, David A.; Clark, Charles R.; Rogers, Andrew J.

    1998-09-21

    A (17)O NMR study (I = 1.0 M, NaClO(4) or NaOSO(2)CF(3), 25.0 degrees C) of solvent exchange in labeled p- and t-[Co(tren)(NH(3))OH(2)](3+), [Co(tren)(OH(2))(2)](3+), [Co(cyclen)(OH(2))(2)](3+), and [Co(N-Mecyclen)(OH(2))(2)](3+) ions (ca. 30% (17)O) in aqueous solution has shown that loss of coordinated OH(2) is slow for all of the complexes (k(ex)/s(-)(1) = 1.1 x 10(-)(5), 1.2 x 10(-)(5), 3.7 x 10(-)(5) (p-site)/8.7 x 10(-)(6) (t-site), 2 x 10(-)(4), and 2 x 10(-)(4), respectively). Values of k(ex) for solvent exchange in [Co(tren)(OH)(2)](+) have been determined as 9.7 x 10(-)(5) s(-)(1) (p-site) and 2.2 x 10(-)(7) s(-)(1) (t-site) Coordinated OH(-) in both p- and t-[Co(tren)(NH(3))OH](2+) also exchanges only slowly with solvent (k(ex)/s(-)(1)= 1.7 x 10(-)(4), and <1 x 10(-)(6), respectively), whereas exchange of coordinated solvent in the aqua-hydroxo complexes [Co(tren)(t-OH(2))(p-OH)](2+), [Co(cyclen)(OH(2))OH](2+), and [Co(N-Mecyclen)(OH(2))OH](2+) is much more rapid (k(ex)/s(-)(1) = 0.03 (p-site)/0.01 (t-site), 12 and 15, respectively). Ligand-OH(-) exchange in these latter systems is interpreted as occurring via (indirect) S(N)1(CB)-type processes on the corresponding aqua complexes: [Co(amine)OH](2+) right harpoon over left harpoon [Co(amine-H)OH(2)](2+) --> exchange. This type of pathway is seen to be more efficient when leaving-group departure is synchronous with proton transfer, and this appears to be more important for exchange in the cyclen and N-Mecyclen complexes where a reasonably acidic, adjacent syn NH proton is involved.

  18. 76 FR 13681 - Self-Regulatory Organizations; BATS Y-Exchange, Inc.; Notice of Filing and Immediate...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-03-14

    ... strategies. The Exchange currently offers the Parallel D, Parallel 2D, CYCLE and RECYCLE routing strategies... 2D, CYCLE and RECYCLE in securities priced under $1.00 per share. \\12\\ The Exchange's...

  19. 2-D or not 2-D, that is the question: A Northern California test

    SciTech Connect

    Mayeda, K; Malagnini, L; Phillips, W S; Walter, W R; Dreger, D

    2005-06-06

    Reliable estimates of the seismic source spectrum are necessary for accurate magnitude, yield, and energy estimation. In particular, how seismic radiated energy scales with increasing earthquake size has been the focus of recent debate within the community and has direct implications on earthquake source physics studies as well as hazard mitigation. The 1-D coda methodology of Mayeda et al. has provided the lowest variance estimate of the source spectrum when compared against traditional approaches that use direct S-waves, thus making it ideal for networks that have sparse station distribution. The 1-D coda methodology has been mostly confined to regions of approximately uniform complexity. For larger, more geophysically complicated regions, 2-D path corrections may be required. The complicated tectonics of the northern California region coupled with high quality broadband seismic data provides for an ideal ''apples-to-apples'' test of 1-D and 2-D path assumptions on direct waves and their coda. Using the same station and event distribution, we compared 1-D and 2-D path corrections and observed the following results: (1) 1-D coda results reduced the amplitude variance relative to direct S-waves by roughly a factor of 8 (800%); (2) Applying a 2-D correction to the coda resulted in up to 40% variance reduction from the 1-D coda results; (3) 2-D direct S-wave results, though better than 1-D direct waves, were significantly worse than the 1-D coda. We found that coda-based moment-rate source spectra derived from the 2-D approach were essentially identical to those from the 1-D approach for frequencies less than {approx}0.7-Hz, however for the high frequencies (0.7{le} f {le} 8.0-Hz), the 2-D approach resulted in inter-station scatter that was generally 10-30% smaller. For complex regions where data are plentiful, a 2-D approach can significantly improve upon the simple 1-D assumption. In regions where only 1-D coda correction is available it is still preferable over 2

  20. Guiding automated NMR structure determination using a global optimization metric, the NMR DP score

    PubMed Central

    Huang, Yuanpeng Janet; Mao, Binchen; Xu, Fei; Montelione, Gaetano

    2016-01-01

    ASDP is an automated NMR NOE assignment program. It uses a distinct bottom-up topology-constrained network anchoring approach for NOE interpretation, with 2D, 3D and/or 4D NOESY peak lists and resonance assignments as input, and generates unambiguous NOE constraints for iterative structure calculations. ASDP is designed to function interactively with various structure determination programs that use distance restraints to generate molecular models. In the CASD-NMR project, ASDP was tested and further developed using blinded NMR data, including resonance assignments, either raw or manually-curated (refined) NOESY peak list data, and in some cases 15N-1H residual dipolar coupling data. In these blinded tests, in which the reference structure was not available until after structures were generated, the fully-automated ASDP program performed very well on all targets using both the raw and refined NOESY peak list data. Improvements of ASDP relative to its predecessor program for automated NOESY peak assignments, AutoStructure, were driven by challenges provided by these CASD-NMR data. These algorithmic improvements include 1) using a global metric of structural accuracy, the Discriminating Power (DP) score, for guiding model selection during the iterative NOE interpretation process, and 2) identifying incorrect NOESY cross peak assignments caused by errors in the NMR resonance assignment list. These improvements provide a more robust automated NOESY analysis program, ASDP, with the unique capability of being utilized with alternative structure generation and refinement programs including CYANA, CNS, and/or Rosetta. PMID:26081575

  1. Two-dimensional 1H-NMR study of the spatial structure of neurotoxin II from Naja naja oxiana.

    PubMed

    Golovanov, A P; Lomize, A L; Arseniev, A S; Utkin, Y N; Tsetlin, V I

    1993-05-01

    The spatial structure of neurotoxin II from the venom of the central Asian cobra Naja naja oxiana was determined by two-dimensional 1H-NMR techniques and computational analysis. Nearly complete proton resonance assignments for 61 amino acid residues have been made using two-dimensional (2D) homonuclear total correlated spectroscopy, 2D homonuclear double-quantum-filtered correlated spectroscopy and 2D homonuclear NOE spectroscopy (NOESY) experiments. The cross-peak volumes in NOESY spectra spin-spin coupling constants of vicinal protons NH-C alpha H and C alpha H-C beta H and the observation of slow deuterium exchange of amide protons were used to define local structure and a set of constraints for distance geometry program DIANA. The average root-mean-square deviations are 53 pm for backbone heavy atoms and 118 pm for all heavy atoms of 19 final neurotoxin II conformations. The spatial structure is characterized by a short double-stranded (residues 1-5 and 13-17) and a triple-stranded (residues 22-30, 33-41 and 50-54) antiparallel beta-sheets.

  2. Transition to turbulence: 2D directed percolation

    NASA Astrophysics Data System (ADS)

    Chantry, Matthew; Tuckerman, Laurette; Barkley, Dwight

    2016-11-01

    The transition to turbulence in simple shear flows has been studied for well over a century, yet in the last few years has seen major leaps forward. In pipe flow, this transition shows the hallmarks of (1 + 1) D directed percolation, a universality class of continuous phase transitions. In spanwisely confined Taylor-Couette flow the same class is found, suggesting the phenomenon is generic to shear flows. However in plane Couette flow the largest simulations and experiments to-date find evidence for a discrete transition. Here we study a planar shear flow, called Waleffe flow, devoid of walls yet showing the fundamentals of planar transition to turbulence. Working with a quasi-2D yet Navier-Stokes derived model of this flow we are able to attack the (2 + 1) D transition problem. Going beyond the system sizes previously possible we find all of the required scalings of directed percolation and thus establish planar shears flow in this class.

  3. 2D quantum gravity from quantum entanglement.

    PubMed

    Gliozzi, F

    2011-01-21

    In quantum systems with many degrees of freedom the replica method is a useful tool to study the entanglement of arbitrary spatial regions. We apply it in a way that allows them to backreact. As a consequence, they become dynamical subsystems whose position, form, and extension are determined by their interaction with the whole system. We analyze, in particular, quantum spin chains described at criticality by a conformal field theory. Its coupling to the Gibbs' ensemble of all possible subsystems is relevant and drives the system into a new fixed point which is argued to be that of the 2D quantum gravity coupled to this system. Numerical experiments on the critical Ising model show that the new critical exponents agree with those predicted by the formula of Knizhnik, Polyakov, and Zamolodchikov.

  4. Simulation of Yeast Cooperation in 2D.

    PubMed

    Wang, M; Huang, Y; Wu, Z

    2016-03-01

    Evolution of cooperation has been an active research area in evolutionary biology in decades. An important type of cooperation is developed from group selection, when individuals form spatial groups to prevent them from foreign invasions. In this paper, we study the evolution of cooperation in a mixed population of cooperating and cheating yeast strains in 2D with the interactions among the yeast cells restricted to their small neighborhoods. We conduct a computer simulation based on a game theoretic model and show that cooperation is increased when the interactions are spatially restricted, whether the game is of a prisoner's dilemma, snow drifting, or mutual benefit type. We study the evolution of homogeneous groups of cooperators or cheaters and describe the conditions for them to sustain or expand in an opponent population. We show that under certain spatial restrictions, cooperator groups are able to sustain and expand as group sizes become large, while cheater groups fail to expand and keep them from collapse.

  5. 2D Electrostatic Actuation of Microshutter Arrays

    NASA Technical Reports Server (NTRS)

    Burns, Devin E.; Oh, Lance H.; Li, Mary J.; Jones, Justin S.; Kelly, Daniel P.; Zheng, Yun; Kutyrev, Alexander S.; Moseley, Samuel H.

    2015-01-01

    An electrostatically actuated microshutter array consisting of rotational microshutters (shutters that rotate about a torsion bar) were designed and fabricated through the use of models and experiments. Design iterations focused on minimizing the torsional stiffness of the microshutters, while maintaining their structural integrity. Mechanical and electromechanical test systems were constructed to measure the static and dynamic behavior of the microshutters. The torsional stiffness was reduced by a factor of four over initial designs without sacrificing durability. Analysis of the resonant behavior of the microshutter arrays demonstrates that the first resonant mode is a torsional mode occurring around 3000 Hz. At low vacuum pressures, this resonant mode can be used to significantly reduce the drive voltage necessary for actuation requiring as little as 25V. 2D electrostatic latching and addressing was demonstrated using both a resonant and pulsed addressing scheme.

  6. Graphene suspensions for 2D printing

    NASA Astrophysics Data System (ADS)

    Soots, R. A.; Yakimchuk, E. A.; Nebogatikova, N. A.; Kotin, I. A.; Antonova, I. V.

    2016-04-01

    It is shown that, by processing a graphite suspension in ethanol or water by ultrasound and centrifuging, it is possible to obtain particles with thicknesses within 1-6 nm and, in the most interesting cases, 1-1.5 nm. Analogous treatment of a graphite suspension in organic solvent yields eventually thicker particles (up to 6-10 nm thick) even upon long-term treatment. Using the proposed ink based on graphene and aqueous ethanol with ethylcellulose and terpineol additives for 2D printing, thin (~5 nm thick) films with sheet resistance upon annealing ~30 MΩ/□ were obtained. With the ink based on aqueous graphene suspension, the sheet resistance was ~5-12 kΩ/□ for 6- to 15-nm-thick layers with a carrier mobility of ~30-50 cm2/(V s).

  7. Canard configured aircraft with 2-D nozzle

    NASA Technical Reports Server (NTRS)

    Child, R. D.; Henderson, W. P.

    1978-01-01

    A closely-coupled canard fighter with vectorable two-dimensional nozzle was designed for enhanced transonic maneuvering. The HiMAT maneuver goal of a sustained 8g turn at a free-stream Mach number of 0.9 and 30,000 feet was the primary design consideration. The aerodynamic design process was initiated with a linear theory optimization minimizing the zero percent suction drag including jet effects and refined with three-dimensional nonlinear potential flow techniques. Allowances were made for mutual interference and viscous effects. The design process to arrive at the resultant configuration is described, and the design of a powered 2-D nozzle model to be tested in the LRC 16-foot Propulsion Wind Tunnel is shown.

  8. Numerical Evaluation of 2D Ground States

    NASA Astrophysics Data System (ADS)

    Kolkovska, Natalia

    2016-02-01

    A ground state is defined as the positive radial solution of the multidimensional nonlinear problem \\varepsilon propto k_ bot 1 - ξ with the function f being either f(u) =a|u|p-1u or f(u) =a|u|pu+b|u|2pu. The numerical evaluation of ground states is based on the shooting method applied to an equivalent dynamical system. A combination of fourth order Runge-Kutta method and Hermite extrapolation formula is applied to solving the resulting initial value problem. The efficiency of this procedure is demonstrated in the 1D case, where the maximal difference between the exact and numerical solution is ≈ 10-11 for a discretization step 0:00025. As a major application, we evaluate numerically the critical energy constant. This constant is defined as a functional of the ground state and is used in the study of the 2D Boussinesq equations.

  9. Metrology for graphene and 2D materials

    NASA Astrophysics Data System (ADS)

    Pollard, Andrew J.

    2016-09-01

    The application of graphene, a one atom-thick honeycomb lattice of carbon atoms with superlative properties, such as electrical conductivity, thermal conductivity and strength, has already shown that it can be used to benefit metrology itself as a new quantum standard for resistance. However, there are many application areas where graphene and other 2D materials, such as molybdenum disulphide (MoS2) and hexagonal boron nitride (h-BN), may be disruptive, areas such as flexible electronics, nanocomposites, sensing and energy storage. Applying metrology to the area of graphene is now critical to enable the new, emerging global graphene commercial world and bridge the gap between academia and industry. Measurement capabilities and expertise in a wide range of scientific areas are required to address this challenge. The combined and complementary approach of varied characterisation methods for structural, chemical, electrical and other properties, will allow the real-world issues of commercialising graphene and other 2D materials to be addressed. Here, examples of metrology challenges that have been overcome through a multi-technique or new approach are discussed. Firstly, the structural characterisation of defects in both graphene and MoS2 via Raman spectroscopy is described, and how nanoscale mapping of vacancy defects in graphene is also possible using tip-enhanced Raman spectroscopy (TERS). Furthermore, the chemical characterisation and removal of polymer residue on chemical vapour deposition (CVD) grown graphene via secondary ion mass spectrometry (SIMS) is detailed, as well as the chemical characterisation of iron films used to grow large domain single-layer h-BN through CVD growth, revealing how contamination of the substrate itself plays a role in the resulting h-BN layer. In addition, the role of international standardisation in this area is described, outlining the current work ongoing in both the International Organization of Standardization (ISO) and the

  10. Direct Self-Assembly of a 2D and 3D Star of David.

    PubMed

    Song, Bo; Zhang, Zhe; Wang, Kun; Hsu, Chih-Hao; Bolarinwa, Olapeju; Wang, Jing; Li, Yiming; Yin, Guang-Qiang; Rivera, Edwin; Yang, Hai-Bo; Liu, Changlin; Xu, Bingqian; Li, Xiaopeng

    2017-04-06

    Two- and three-dimensional metallosupramolecules shaped like a Star of David were synthesized by the self-assembly of a tetratopic pyridyl ligand with a 180° diplatinum(II) motif and Pd(II) ions, respectively. In contrast to other strategies, such as template-directed synthesis and stepwise self-assembly, this design enables the formation of 2D and 3D structures in one step and high yield. The structures were characterized by both one-dimensional ((1) H, (13) C, (31) P) and two-dimensional (COSY, NOESY, DOSY) NMR spectroscopy, ESI-MS, ion-mobility mass spectrometry (IM-MS), AFM, and TEM. The stabilities of the 2D and 3D structures were measured and compared by gradient tandem mass spectrometry (gMS(2) ). The high stability of the 3D Star of David was correlated to its high density of coordination sites (DOCS).

  11. NMR data visualization, processing, and analysis on mobile devices.

    PubMed

    Cobas, Carlos; Iglesias, Isaac; Seoane, Felipe

    2015-08-01

    Touch-screen computers are emerging as a popular platform for many applications, including those in chemistry and analytical sciences. In this work, we present our implementation of a new NMR 'app' designed for hand-held and portable touch-controlled devices, such as smartphones and tablets. It features a flexible architecture formed by a powerful NMR processing and analysis kernel and an intuitive user interface that makes full use of the smart devices haptic capabilities. Routine 1D and 2D NMR spectra acquired in most NMR instruments can be processed in a fully unattended way. More advanced experiments such as non-uniform sampled NMR spectra are also supported through a very efficient parallelized Modified Iterative Soft Thresholding algorithm. Specific technical development features as well as the overall feasibility of using NMR software apps will also be discussed. All aspects considered the functionalities of the app allowing it to work as a stand-alone tool or as a 'companion' to more advanced desktop applications such as Mnova NMR.

  12. Confirming the 3D Solution Structure of a Short Double-Stranded DNA Sequence Using NMR Spectroscopy

    ERIC Educational Resources Information Center

    Ruhayel, Rasha A.; Berners-Price, Susan J.

    2010-01-01

    2D [superscript 1]H NOESY NMR spectroscopy is routinely used to give information on the closeness of hydrogen atoms through space. This work is based on a 2D [superscript 1]H NOESY NMR spectrum of a 12 base-pair DNA duplex. This 6-h laboratory workshop aims to provide advanced-level chemistry students with a basic, yet solid, understanding of how…

  13. Persistence Measures for 2d Soap Froth

    NASA Astrophysics Data System (ADS)

    Feng, Y.; Ruskin, H. J.; Zhu, B.

    Soap froths as typical disordered cellular structures, exhibiting spatial and temporal evolution, have been studied through their distributions and topological properties. Recently, persistence measures, which permit representation of the froth as a two-phase system, have been introduced to study froth dynamics at different length scales. Several aspects of the dynamics may be considered and cluster persistence has been observed through froth experiment. Using a direct simulation method, we have investigated persistent properties in 2D froth both by monitoring the persistence of survivor cells, a topologically independent measure, and in terms of cluster persistence. It appears that the area fraction behavior for both survivor and cluster persistence is similar for Voronoi froth and uniform froth (with defects). Survivor and cluster persistent fractions are also similar for a uniform froth, particularly when geometries are constrained, but differences observed for the Voronoi case appear to be attributable to the strong topological dependency inherent in cluster persistence. Survivor persistence, on the other hand, depends on the number rather than size and position of remaining bubbles and does not exhibit the characteristic decay to zero.

  14. SEM signal emulation for 2D patterns

    NASA Astrophysics Data System (ADS)

    Sukhov, Evgenii; Muelders, Thomas; Klostermann, Ulrich; Gao, Weimin; Braylovska, Mariya

    2016-03-01

    The application of accurate and predictive physical resist simulation is seen as one important use model for fast and efficient exploration of new patterning technology options, especially if fully qualified OPC models are not yet available at an early pre-production stage. The methodology of using a top-down CD-SEM metrology to extract the 3D resist profile information, such as the critical dimension (CD) at various resist heights, has to be associated with a series of presumptions which may introduce such small, but systematic CD errors. Ideally, the metrology effects should be carefully minimized during measurement process, or if possible be taken into account through proper metrology modeling. In this paper we discuss the application of a fast SEM signal emulation describing the SEM image formation. The algorithm is applied to simulated resist 3D profiles and produces emulated SEM image results for 1D and 2D patterns. It allows estimating resist simulation quality by comparing CDs which were extracted from the emulated and from the measured SEM images. Moreover, SEM emulation is applied for resist model calibration to capture subtle error signatures through dose and defocus. Finally, it should be noted that our SEM emulation methodology is based on the approximation of physical phenomena which are taking place in real SEM image formation. This approximation allows achieving better speed performance compared to a fully physical model.

  15. Radiofrequency Spectroscopy and Thermodynamics of Fermi Gases in the 2D to Quasi-2D Dimensional Crossover

    NASA Astrophysics Data System (ADS)

    Cheng, Chingyun; Kangara, Jayampathi; Arakelyan, Ilya; Thomas, John

    2016-05-01

    We tune the dimensionality of a strongly interacting degenerate 6 Li Fermi gas from 2D to quasi-2D, by adjusting the radial confinement of pancake-shaped clouds to control the radial chemical potential. In the 2D regime with weak radial confinement, the measured pair binding energies are in agreement with 2D-BCS mean field theory, which predicts dimer pairing energies in the many-body regime. In the qausi-2D regime obtained with increased radial confinement, the measured pairing energy deviates significantly from 2D-BCS theory. In contrast to the pairing energy, the measured radii of the cloud profiles are not fit by 2D-BCS theory in either the 2D or quasi-2D regimes, but are fit in both regimes by a beyond mean field polaron-model of the free energy. Supported by DOE, ARO, NSF, and AFOSR.

  16. Extracting protein dynamics information from overlapped NMR signals using relaxation dispersion difference NMR spectroscopy.

    PubMed

    Konuma, Tsuyoshi; Harada, Erisa; Sugase, Kenji

    2015-12-01

    Protein dynamics plays important roles in many biological events, such as ligand binding and enzyme reactions. NMR is mostly used for investigating such protein dynamics in a site-specific manner. Recently, NMR has been actively applied to large proteins and intrinsically disordered proteins, which are attractive research targets. However, signal overlap, which is often observed for such proteins, hampers accurate analysis of NMR data. In this study, we have developed a new methodology called relaxation dispersion difference that can extract conformational exchange parameters from overlapped NMR signals measured using relaxation dispersion spectroscopy. In relaxation dispersion measurements, the signal intensities of fluctuating residues vary according to the Carr-Purcell-Meiboon-Gill pulsing interval, whereas those of non-fluctuating residues are constant. Therefore, subtraction of each relaxation dispersion spectrum from that with the highest signal intensities, measured at the shortest pulsing interval, leaves only the signals of the fluctuating residues. This is the principle of the relaxation dispersion difference method. This new method enabled us to extract exchange parameters from overlapped signals of heme oxygenase-1, which is a relatively large protein. The results indicate that the structural flexibility of a kink in the heme-binding site is important for efficient heme binding. Relaxation dispersion difference requires neither selectively labeled samples nor modification of pulse programs; thus it will have wide applications in protein dynamics analysis.

  17. NMR imaging microscopy

    SciTech Connect

    Not Available

    1986-10-01

    In the past several years, proton nuclear magnetic resonance (NMR) imaging has become an established technique in diagnostic medicine and biomedical research. Although much of the work in this field has been directed toward development of whole-body imagers, James Aguayo, Stephen Blackband, and Joseph Schoeninger of the Johns Hopkins University School of Medicine working with Markus Hintermann and Mark Mattingly of Bruker Medical Instruments, recently developed a small-bore NMR microscope with sufficient resolution to image a single African clawed toad cell (Nature 1986, 322, 190-91). This improved resolution should lead to increased use of NMR imaging for chemical, as well as biological or physiological, applications. The future of NMR microscopy, like that of many other newly emerging techniques, is ripe with possibilities. Because of its high cost, however, it is likely to remain primarily a research tool for some time. ''It's like having a camera,'' says Smith. ''You've got a way to look at things at very fine levels, and people are going to find lots of uses for it. But it is a very expensive technique - it costs $100,000 to add imaging capability once you have a high-resolution NMR, which itself is at least a $300,000 instrument. If it can answer even a few questions that can't be answered any other way, though, it may be well worth the cost.''

  18. Stoichiometric compounds of magnesium dichloride with ethanol for the supported Ziegler-Natta catalysis: first recognition and multidimensional MAS NMR study.

    PubMed

    Sozzani, Piero; Bracco, Silvia; Comotti, Angiolina; Simonutti, Roberto; Camurati, Isabella

    2003-10-22

    Ethanol associates easily with MgCl(2) to form adducts of complex architecture, but until now available characterization methods have failed to identify the pure stoichiometric compounds and their structures. To remedy this, we set about applying homonuclear and heteronuclear 2D correlated solid-state NMR spectroscopy to identify the pure compounds and the ethanol-to-magnesium coordination pattern. High spinning speed and Lee-Goldburg sequences were able to reduce the hydrogen spin-diffusion and homonuclear coupling in the crystalline solid, thus achieving high resolution also in the hydrogen domain. On this basis, the pure adducts, of interest as catalyst supports for Ziegler-Natta polymerization, were isolated for the first time. Magnesium coordination sites with given numbers of ligands and their multiplicity in the crystal cells were determined in the new-found stoichiometric complexes. Variable temperature and 2D carbon-carbon exchange NMR, as well as relaxation times in the fast motion regime, revealed the disordering phenomena generated by ethanol dynamics in the crystal. Decoding the intriguing polymorphism of the precursors permits to trace the genealogy of tailored MgCl(2) titanate granules, active as highly productive catalysts for the stereospecific polymerization of olefins.

  19. Accessing structure and dynamics of mobile phase in organic solids by real-time T1C filter PISEMA NMR spectroscopy.

    PubMed

    Zhang, Rongchun; Chen, Yuzhu; Chen, Tiehong; Sun, Pingchuan; Li, Baohui; Ding, Datong

    2012-01-26

    The structure and dynamic behavior of mobile components play a significant role in determining properties of solid materials. Herein, we propose a novel real-time spectrum-editing method to extract signals of mobile components in organic solids on the basis of the polarization inversion spin exchange at magic angle (PISEMA) pulse sequence and the difference in (13)C T(1) values of rigid and mobile components. From the dipolar splitting spectrum sliced along the heteronuclear dipolar coupling dimension of the 2D spectrum, the structural and dynamic information can be obtained, such as the distances between atoms, the dipolar coupling strength, the order parameter of the polymer backbone chain, and so on. Furthermore, our proposed method can be used to achieve the separation of overlapped NMR signals of mobile and rigid phases in the PISEMA experiment. The high efficacy of this 2D NMR method is demonstrated on organic solids, including crystalline L-alanine, semicrystalline polyamide-6, and the natural abundant silk fibroin.

  20. Flavonoids from Curcuma longa leaves and their NMR assignments.

    PubMed

    Jiang, Chia-Ling; Tsai, Sheng-Fa; Lee, Shoei-Sheng

    2015-01-01

    Chemical investigation of the n-BuOH-soluble fraction of the EtOH extract of the aerial part of Curcuma longa led to the isolation of 11 flavonol glycosides and one dihydroflavonol glucoside (1) via chromatography over Sephadex LH-20 and Lobar RP-18 columns. Although they are known, the 1H and 13C NMR data recorded in CD3OD rather than the common DMSO-d6 are doubly checked via extensive 2D NMR spectroscopic analyses, leading to some revisions of the reported data, especially for the glycon part.

  1. 2D discrete Fourier transform on sliding windows.

    PubMed

    Park, Chun-Su

    2015-03-01

    Discrete Fourier transform (DFT) is the most widely used method for determining the frequency spectra of digital signals. In this paper, a 2D sliding DFT (2D SDFT) algorithm is proposed for fast implementation of the DFT on 2D sliding windows. The proposed 2D SDFT algorithm directly computes the DFT bins of the current window using the precalculated bins of the previous window. Since the proposed algorithm is designed to accelerate the sliding transform process of a 2D input signal, it can be directly applied to computer vision and image processing applications. The theoretical analysis shows that the computational requirement of the proposed 2D SDFT algorithm is the lowest among existing 2D DFT algorithms. Moreover, the output of the 2D SDFT is mathematically equivalent to that of the traditional DFT at all pixel positions.

  2. Advanced NMR characterization of zeolite catalysts. Third quarterly report, March 1-May 31, 1984

    SciTech Connect

    Welsh, L.B.

    1984-06-01

    The program discussed in this report is a two-year two-phase joint UOP-University of Illinois study of the application of improved high resolution solid state nuclear magnetic resonance (NMR) techniques to the characterization of zeolite catalysts. During the first phase of this program very pure, and in some cases isotopically enriched faujasites will be prepared and studied by majic angle sample spinning NMR (MASS NMR) and variable angle sample spinning NMR (VASS NMR) on 500 and 360 MHz (Proton frequency) NMR spectrometers. During the second phase of this program these NMR techniques will be used to study the effects of impurity concentration, dealumination treatments and cation exchange on the NMR properties of faujasites. The initial emphasis of this program during Phase I is on the preparation and measurement of the NMR properties of /sup 17/O enriched Na-Y faujasites. The effort in each phase is broken into four tasks: (1) zeolite preparation. (2) standard zeolite characterization; (3) measurement of zeolite NMR properties; and (4) analysis of NMR data. The main efforts during the third three month period of the program have been the characterization of the /sup 17/O enriched zeolites, particularly X and Y zeolites, by high resolution sample spinning /sup 17/O NMR, and the preparation of additional /sup 17/O enriched zeolites. X and Y zeolites with Si/Al framework ratios from 1.22 to 7.6 have been prepared in either the Na, NH/sub 4/ or Ba form. MASS NMR and VASS NMR as well as static NMR measurements have been made on these materials for /sup 17/O NMR frequencies from 20.4 to 67.8 MHz. Computer simulations of the experimental NMR lineshapes are in progress. Results to date indicate that the observed spectra arise from two different types of oxygen sites, possibly O in Al-O-Si links and chemically bound OH groups. 2 references, 1 figure, 1 table.

  3. MAGNUM2D. Radionuclide Transport Porous Media

    SciTech Connect

    Langford, D.W.; Baca, R.G.

    1989-03-01

    MAGNUM2D was developed to analyze thermally driven fluid motion in the deep basalts below the Paco Basin at the Westinghouse Hanford Site. Has been used in the Basalt Waste Isolation Project to simulate nonisothermal groundwater flow in a heterogeneous anisotropic medium and heat transport in a water/rock system near a high level nuclear waste repository. Allows three representations of the hydrogeologic system: an equivalent porous continuum, a system of discrete, unfilled, and interconnecting fractures separated by impervious rock mass, and a low permeability porous continuum with several discrete, unfilled fractures traversing the medium. The calculations assume local thermodynamic equilibrium between the rock and groundwater, nonisothermal Darcian flow in the continuum portions of the rock, and nonisothermal Poiseuille flow in discrete unfilled fractures. In addition, the code accounts for thermal loading within the elements, zero normal gradient and fixed boundary conditions for both temperature and hydraulic head, and simulation of the temperature and flow independently. The Q2DGEOM preprocessor was developed to generate, modify, plot and verify quadratic two dimensional finite element geometries. The BCGEN preprocessor generates the boundary conditions for head and temperature and ICGEN generates the initial conditions. The GRIDDER postprocessor interpolates nonregularly spaced nodal flow and temperature data onto a regular rectangular grid. CONTOUR plots and labels contour lines for a function of two variables and PARAM plots cross sections and time histories for a function of time and one or two spatial variables. NPRINT generates data tables that display the data along horizontal or vertical cross sections. VELPLT differentiates the hydraulic head and buoyancy data and plots the velocity vectors. The PATH postprocessor plots flow paths and computes the corresponding travel times.

  4. MAGNUM2D. Radionuclide Transport Porous Media

    SciTech Connect

    Langford, D.W.; Baca, R.G.

    1988-08-01

    MAGNUM2D was developed to analyze thermally driven fluid motion in the deep basalts below the Paco Basin at the Westinghouse Hanford Site. Has been used in the Basalt Waste Isolation Project to simulate nonisothermal groundwater flow in a heterogeneous anisotropic medium and heat transport in a water/rock system near a high level nuclear waste repository. Allows three representations of the hydrogeologic system: an equivalent porous continuum, a system of discrete, unfilled, and interconnecting fractures separated by impervious rock mass, and a low permeability porous continuum with several discrete, unfilled fractures traversing the medium. The calculation assumes local thermodynamic equilibrium between the rock and groundwater, nonisothermal Darcian flow in the continuum portions of the rock, and nonisothermal Poiseuille flow in discrete unfilled fractures. In addition, the code accounts for thermal loading within the elements, zero normal gradient and fixed boundary conditions for both temperature and hydraulic head, and simulation of the temperature and flow independently. The Q2DGEOM preprocessor was developed to generate, modify, plot and verify quadratic two dimensional finite element geometries. The BCGEN preprocessor generates the boundary conditions for head and temperature and ICGEN generates the initial conditions. The GRIDDER postprocessor interpolates nonregularly spaced nodal flow and temperature data onto a regular rectangular grid. CONTOUR plots and labels contour lines for a function of two variables and PARAM plots cross sections and time histories for a function of time and one or two spatial variables. NPRINT generates data tables that display the data along horizontal or vertical cross sections. VELPLT differentiates the hydraulic head and buoyancy data and plots the velocity vectors. The PATH postprocessor plots flow paths and computes the corresponding travel times.

  5. NMR ANALYSIS OF MALE FATHEAD MINNOW URINARY METABOLITES: A POTENTIAL APPROACH FOR STUDYING IMPACTS OF CHEMICAL EXPOSURES

    EPA Science Inventory

    The potential for profiling endogenous metabolites in urine from male fathead minnows (Pimephales promelas) to assess chemical exposures was explored using nuclear magnetic resonance (NMR) spectroscopy. Both one dimensional (1D) and two dimensional (2D) NMR spectroscopy w...

  6. Generates 2D Input for DYNA NIKE & TOPAZ

    SciTech Connect

    Hallquist, J. O.; Sanford, Larry

    1996-07-15

    MAZE is an interactive program that serves as an input and two-dimensional mesh generator for DYNA2D, NIKE2D, TOPAZ2D, and CHEMICAL TOPAZ2D. MAZE also generates a basic template for ISLAND input. MAZE has been applied to the generation of input data to study the response of two-dimensional solids and structures undergoing finite deformations under a wide variety of large deformation transient dynamic and static problems and heat transfer analyses.

  7. MAZE96. Generates 2D Input for DYNA NIKE & TOPAZ

    SciTech Connect

    Sanford, L.; Hallquist, J.O.

    1992-02-24

    MAZE is an interactive program that serves as an input and two-dimensional mesh generator for DYNA2D, NIKE2D, TOPAZ2D, and CHEMICAL TOPAZ2D. MAZE also generates a basic template for ISLAND input. MAZE has been applied to the generation of input data to study the response of two-dimensional solids and structures undergoing finite deformations under a wide variety of large deformation transient dynamic and static problems and heat transfer analyses.

  8. NIKE2D96. Static & Dynamic Response of 2D Solids

    SciTech Connect

    Raboin, P.; Engelmann, B.; Halquist, J.O.

    1992-01-24

    NIKE2D is an implicit finite-element code for analyzing the finite deformation, static and dynamic response of two-dimensional, axisymmetric, plane strain, and plane stress solids. The code is fully vectorized and available on several computing platforms. A number of material models are incorporated to simulate a wide range of material behavior including elasto-placicity, anisotropy, creep, thermal effects, and rate dependence. Slideline algorithms model gaps and sliding along material interfaces, including interface friction, penetration and single surface contact. Interactive-graphics and rezoning is included for analyses with large mesh distortions. In addition to quasi-Newton and arc-length procedures, adaptive algorithms can be defined to solve the implicit equations using the solution language ISLAND. Each of these capabilities and more make NIKE2D a robust analysis tool.

  9. New Designs for NMR Core Scanning

    NASA Astrophysics Data System (ADS)

    Bluemich, B.; Anferova, S.; Talnishnikh, E.; Arnold, J.; Clauser, C.

    2006-12-01

    Within the last ten years, mobile magnetic resonance has moved from the oil field to many new areas of application. While the focus of mobile NMR in the past was on single-sided or inside-out NMR, the advent of tube-shaped Halbach magnets has introduced the conventional outside-in NMR concept to mobile NMR where the object is inside a magnet. Our Halbach magnet is constructed from small magnet blocks at light weight and low cost with a magnetic field sufficiently homogeneous. To automatize NMR measurements, the Halbach magnet is mounted on a sliding table to scan long core sections without human interaction. In homogeneous magnetic fields, the longitudinal relaxation time T1 and even the transverse relaxation time T2 are proportional to the pore diameters of rocks. Hence, the T1 and T2 signals map the pore-size distribution of the studied rock cores. For fully saturated samples the integral of the distribution curve is proportional to porosity. The porosity values from NMR measurements with the Halbach magnet are used to estimate permability. The Halbach magnet can be used for certain sample geometries in combination with exchangeable radio frequency (rf) coils with different diameters from 24 mm up to 80 mm. To measure standard Ocean Drilling Program (ODP)/Integrated Ocean Drilling Program (IODP) cores, which have a standard diameter of 60 mm and are split lengthwise after recovery, we use a surface figure-8 rf coil with an inner diameter of 60 mm. Besides 1D T2 measurements, we perform relaxation-relaxation correlation experiments, where T1 and T2 are measured in parallel. In this way, the influence of diffusion on the shape of the T2 distribution function is probed. A gradient coil system was designed to perform Pulsed Field Gradients (PFG) experiments. As the gradient coils restrict the axial access to the magnet, only cylindrical core plugs with 20 mm in diameter can be analysed by PFG NMR methods. The homogeneity of the magnetic field in the sensitive volume

  10. NMR study of the dynamics of cationic gemini surfactant 14-2-14 in mixed solutions with conventional surfactants.

    PubMed

    Jiang, Yan; Lu, Xing-Yu; Chen, Hong; Mao, Shi-Zhen; Liu, Mai-Li; Luo, Ping-Ya; Du, You-Ru

    2009-06-18

    Three kinds of conventional surfactants, namely, two nonionic surfactants [polyethylene glycol (23) lauryl ether (Brij-35) and Triton X-100 (TX-100)], one cationic surfactant [n-tetradecyltrimethyl ammonium bromide (TTAB)], and an anionic surfactant [sodium n-dodecyl sulfate (SDS)}, were mixed into the quaternary ammonium gemini surfactant [C(14)H(29)N(+)(CH(3))(2)](2)(CH(2))(2).2Br(-) (14-2-14) in aqueous solution. The exchange rate constants between 14-2-14 molecules in the mixed micelles and those in the bulk solution were detected using two nuclear magnetic resonance (NMR) methods: one-dimensional (1D) line shape analysis and two-dimensional (2D) exchange spectroscopy (EXSY). The results obtained from these two methods were consistent. Both showed that mixing a nonionic conventional surfactant, either Brij-35 or TX-100, enhanced the exchange process between the 14-2-14 molecules in the mixed micelles and those in the bulk solution. In contrast, the anionic surfactant SDS and the cationic surfactant TTAB slowed the process slightly.

  11. 2D Larkin-Imry-Ma state of deformed ABM phase of superfluid 3He in ``ordered'' aerogel

    NASA Astrophysics Data System (ADS)

    Dmitriev, Vladimir; Senin, Andrey; Yudin, Alexey

    2014-03-01

    We report NMR studies of high temperature superfluid phase of 3He in so called ``ordered'' aerogel1 which strands are almost parallel to each other. Previously, it was found that the NMR properties of this phase depend on whether it is obtained on cooling from the normal phase or on warming from the low temperature phase2. These two types of high temperature phase (called as ESP1 and ESP2) correspond to Anderson-Brinkman-Morel (ABM) phase with large polar distortion and with orbital vector being in 2D Larkin-Imry-Ma (LIM) state. Here we present results which show that the observed difference in NMR signatures of the ESP1 and the ESP2 states is due to that the corresponding 2D LIM states can be anisotropic. In the ESP1 phase the anisotropy is absent or small, while in the ESP2 phase the anisotropy is large. NMR data have allowed us to estimate values of these anisotropies.

  12. Optimizing Adiabaticity in NMR

    NASA Astrophysics Data System (ADS)

    Vandermause, Jonathan; Ramanathan, Chandrasekhar

    We demonstrate the utility of Berry's superadiabatic formalism for numerically finding control sequences that implement quasi-adiabatic unitary transformations. Using an iterative interaction picture, we design a shortcut to adiabaticity that reduces the time required to perform an adiabatic inversion pulse in liquid state NMR. We also show that it is possible to extend our scheme to two or more qubits to find adiabatic quantum transformations that are allowed by the control algebra, and demonstrate a two-qubit entangling operation in liquid state NMR. We examine the pulse lengths at which the fidelity of these adiabatic transitions break down and compare with the quantum speed limit.

  13. Ultrafast multidimensional Laplace NMR for a rapid and sensitive chemical analysis

    NASA Astrophysics Data System (ADS)

    Ahola, Susanna; Zhivonitko, Vladimir V.; Mankinen, Otto; Zhang, Guannan; Kantola, Anu M.; Chen, Hsueh-Ying; Hilty, Christian; Koptyug, Igor V.; Telkki, Ville-Veikko

    2015-09-01

    Traditional nuclear magnetic resonance (NMR) spectroscopy relies on the versatile chemical information conveyed by spectra. To complement conventional NMR, Laplace NMR explores diffusion and relaxation phenomena to reveal details on molecular motions. Under a broad concept of ultrafast multidimensional Laplace NMR, here we introduce an ultrafast diffusion-relaxation correlation experiment enhancing the resolution and information content of corresponding 1D experiments as well as reducing the experiment time by one to two orders of magnitude or more as compared with its conventional 2D counterpart. We demonstrate that the method allows one to distinguish identical molecules in different physical environments and provides chemical resolution missing in NMR spectra. Although the sensitivity of the new method is reduced due to spatial encoding, the single-scan approach enables one to use hyperpolarized substances to boost the sensitivity by several orders of magnitude, significantly enhancing the overall sensitivity of multidimensional Laplace NMR.

  14. Cosolvent Effects on Solute-Solvent Hydrogen-Bond Dynamics: Ultrafast 2D IR Investigations.

    PubMed

    Kashid, Somnath M; Jin, Geun Young; Bagchi, Sayan; Kim, Yung Sam

    2015-12-10

    Cosolvents strongly influence the solute-solvent interactions of biomolecules in aqueous environments and have profound effects on the stability and activity of several proteins and enzymes. Experimental studies have previously reported on the hydrogen-bond dynamics of water molecules in the presence of a cosolvent, but understanding the effects from a solute's perspective could provide greater insight into protein stability. Because carbonyl groups are abundant in biomolecules, the current study used 2D IR spectroscopy and molecular dynamics simulations to compare the hydrogen-bond dynamics of the solute's carbonyl group in aqueous solution, with and without the presence of DMSO as a cosolvent. 2D IR spectroscopy was used to quantitatively estimate the time scales of the hydrogen-bond dynamics of the carbonyl group in neat water and 1:1 DMSO/water solution. The 2D IR results show spectral signatures of a chemical exchange process: The presence of the cosolvent was found to lower the hydrogen-bond exchange rate by a factor of 5. The measured exchange rates were 7.50 × 10(11) and 1.48 × 10(11) s(-1) in neat water and 1:1 DMSO/water, respectively. Molecular dynamics simulations predict a significantly shorter carbonyl hydrogen-bond lifetime in neat water than in 1:1 DMSO/water and provide molecular insights into the exchange mechanism. The binding of the cosolvent to the solute was found to be accompanied by the release of hydrogen-bonded water molecules to the bulk. The widely different hydrogen-bond lifetimes and exchange rates with and without DMSO indicate a significant change in the ultrafast hydrogen-bond dynamics in the presence of a cosolvent, which, in turn, might play an important role in the stability and activity of biomolecules.

  15. NMR spectroscopy of RNA duplexes containing pseudouridine in supercooled water.

    PubMed

    Schroeder, Kersten T; Skalicky, Jack J; Greenbaum, Nancy L

    2005-07-01

    We have performed NMR experiments in supercooled water in order to decrease the temperature-dependent exchange of protons in RNA duplexes. NMR spectra of aqueous samples of RNA in bundles of narrow capillaries that were acquired at temperatures as low as -18 degrees C reveal resonances of exchangeable protons not seen at higher temperatures. In particular, we detected the imino protons of terminal base pairs and the imino proton of a non-base-paired pseudouridine in a duplex representing the eukaryotic pre-mRNA branch site helix. Analysis of the temperature dependence of chemical shift changes (thermal coefficients) for imino protons corroborated hydrogen bonding patterns observed in the NMR-derived structural model of the branch site helix. The ability to observe non-base-paired imino protons of RNA is of significant value in structure determination of RNA motifs containing loop and bulge regions.

  16. A high-pressure NMR probe for aqueous geochemistry.

    PubMed

    Pautler, Brent G; Colla, Christopher A; Johnson, Rene L; Klavins, Peter; Harley, Stephen J; Ohlin, C André; Sverjensky, Dimitri A; Walton, Jeffrey H; Casey, William H

    2014-09-08

    A non-magnetic piston-cylinder pressure cell is presented for solution-state NMR spectroscopy at geochemical pressures. The probe has been calibrated up to 20 kbar using in situ ruby fluorescence and allows for the measurement of pressure dependencies of a wide variety of NMR-active nuclei with as little as 10 μL of sample in a microcoil. Initial (11)B NMR spectroscopy of the H3BO3-catechol equilibria reveals a large pressure-driven exchange rate and a negative pressure-dependent activation volume, reflecting increased solvation and electrostriction upon boron-catecholate formation. The inexpensive probe design doubles the current pressure range available for solution NMR spectroscopy and is particularly important to advance the field of aqueous geochemistry.

  17. Mixing and Matching Detergents for Membrane Protein NMR Structure Determination

    SciTech Connect

    Columbus, Linda; Lipfert, Jan; Jambunathan, Kalyani; Fox, Daniel A.; Sim, Adelene Y.L.; Doniach, Sebastian; Lesley, Scott A.

    2009-10-21

    One major obstacle to membrane protein structure determination is the selection of a detergent micelle that mimics the native lipid bilayer. Currently, detergents are selected by exhaustive screening because the effects of protein-detergent interactions on protein structure are poorly understood. In this study, the structure and dynamics of an integral membrane protein in different detergents is investigated by nuclear magnetic resonance (NMR) and electron paramagnetic resonance (EPR) spectroscopy and small-angle X-ray scattering (SAXS). The results suggest that matching of the micelle dimensions to the protein's hydrophobic surface avoids exchange processes that reduce the completeness of the NMR observations. Based on these dimensions, several mixed micelles were designed that improved the completeness of NMR observations. These findings provide a basis for the rational design of mixed micelles that may advance membrane protein structure determination by NMR.

  18. CYP2D7 Sequence Variation Interferes with TaqMan CYP2D6*15 and *35 Genotyping

    PubMed Central

    Riffel, Amanda K.; Dehghani, Mehdi; Hartshorne, Toinette; Floyd, Kristen C.; Leeder, J. Steven; Rosenblatt, Kevin P.; Gaedigk, Andrea

    2016-01-01

    TaqMan™ genotyping assays are widely used to genotype CYP2D6, which encodes a major drug metabolizing enzyme. Assay design for CYP2D6 can be challenging owing to the presence of two pseudogenes, CYP2D7 and CYP2D8, structural and copy number variation and numerous single nucleotide polymorphisms (SNPs) some of which reflect the wild-type sequence of the CYP2D7 pseudogene. The aim of this study was to identify the mechanism causing false-positive CYP2D6*15 calls and remediate those by redesigning and validating alternative TaqMan genotype assays. Among 13,866 DNA samples genotyped by the CompanionDx® lab on the OpenArray platform, 70 samples were identified as heterozygotes for 137Tins, the key SNP of CYP2D6*15. However, only 15 samples were confirmed when tested with the Luminex xTAG CYP2D6 Kit and sequencing of CYP2D6-specific long range (XL)-PCR products. Genotype and gene resequencing of CYP2D6 and CYP2D7-specific XL-PCR products revealed a CC>GT dinucleotide SNP in exon 1 of CYP2D7 that reverts the sequence to CYP2D6 and allows a TaqMan assay PCR primer to bind. Because CYP2D7 also carries a Tins, a false-positive mutation signal is generated. This CYP2D7 SNP was also responsible for generating false-positive signals for rs769258 (CYP2D6*35) which is also located in exon 1. Although alternative CYP2D6*15 and *35 assays resolved the issue, we discovered a novel CYP2D6*15 subvariant in one sample that carries additional SNPs preventing detection with the alternate assay. The frequency of CYP2D6*15 was 0.1% in this ethnically diverse U.S. population sample. In addition, we also discovered linkage between the CYP2D7 CC>GT dinucleotide SNP and the 77G>A (rs28371696) SNP of CYP2D6*43. The frequency of this tentatively functional allele was 0.2%. Taken together, these findings emphasize that regardless of how careful genotyping assays are designed and evaluated before being commercially marketed, rare or unknown SNPs underneath primer and/or probe regions can impact

  19. CYP2D7 Sequence Variation Interferes with TaqMan CYP2D6 (*) 15 and (*) 35 Genotyping.

    PubMed

    Riffel, Amanda K; Dehghani, Mehdi; Hartshorne, Toinette; Floyd, Kristen C; Leeder, J Steven; Rosenblatt, Kevin P; Gaedigk, Andrea

    2015-01-01

    TaqMan™ genotyping assays are widely used to genotype CYP2D6, which encodes a major drug metabolizing enzyme. Assay design for CYP2D6 can be challenging owing to the presence of two pseudogenes, CYP2D7 and CYP2D8, structural and copy number variation and numerous single nucleotide polymorphisms (SNPs) some of which reflect the wild-type sequence of the CYP2D7 pseudogene. The aim of this study was to identify the mechanism causing false-positive CYP2D6 (*) 15 calls and remediate those by redesigning and validating alternative TaqMan genotype assays. Among 13,866 DNA samples genotyped by the CompanionDx® lab on the OpenArray platform, 70 samples were identified as heterozygotes for 137Tins, the key SNP of CYP2D6 (*) 15. However, only 15 samples were confirmed when tested with the Luminex xTAG CYP2D6 Kit and sequencing of CYP2D6-specific long range (XL)-PCR products. Genotype and gene resequencing of CYP2D6 and CYP2D7-specific XL-PCR products revealed a CC>GT dinucleotide SNP in exon 1 of CYP2D7 that reverts the sequence to CYP2D6 and allows a TaqMan assay PCR primer to bind. Because CYP2D7 also carries a Tins, a false-positive mutation signal is generated. This CYP2D7 SNP was also responsible for generating false-positive signals for rs769258 (CYP2D6 (*) 35) which is also located in exon 1. Although alternative CYP2D6 (*) 15 and (*) 35 assays resolved the issue, we discovered a novel CYP2D6 (*) 15 subvariant in one sample that carries additional SNPs preventing detection with the alternate assay. The frequency of CYP2D6 (*) 15 was 0.1% in this ethnically diverse U.S. population sample. In addition, we also discovered linkage between the CYP2D7 CC>GT dinucleotide SNP and the 77G>A (rs28371696) SNP of CYP2D6 (*) 43. The frequency of this tentatively functional allele was 0.2%. Taken together, these findings emphasize that regardless of how careful genotyping assays are designed and evaluated before being commercially marketed, rare or unknown SNPs underneath primer

  20. Modern NMR Spectroscopy.

    ERIC Educational Resources Information Center

    Jelinski, Lynn W.

    1984-01-01

    Discusses direct chemical information that can be obtained from modern nuclear magnetic resonance (NMR) methods, concentrating on the types of problems that can be solved. Shows how selected methods provide information about polymers, bipolymers, biochemistry, small organic molecules, inorganic compounds, and compounds oriented in a magnetic…

  1. Autonomous driving in NMR.

    PubMed

    Perez, Manuel

    2017-01-01

    The automatic analysis of NMR data has been a much-desired endeavour for the last six decades, as it is the case with any other analytical technique. This need for automation has only grown as advances in hardware; pulse sequences and automation have opened new research areas to NMR and increased the throughput of data. Full automatic analysis is a worthy, albeit hard, challenge, but in a world of artificial intelligence, instant communication and big data, it seems that this particular fight is happening with only one technique at a time (let this be NMR, MS, IR, UV or any other), when the reality of most laboratories is that there are several types of analytical instrumentation present. Data aggregation, verification and elucidation by using complementary techniques (e.g. MS and NMR) is a desirable outcome to pursue, although a time-consuming one if performed manually; hence, the use of automation to perform the heavy lifting for users is required to make the approach attractive for scientists. Many of the decisions and workflows that could be implemented under automation will depend on the two-way communication with databases that understand analytical data, because it is desirable not only to query these databases but also to grow them in as much of an automatic manner as possible. How these databases are designed, set up and the data inside classified will determine what workflows can be implemented. Copyright © 2016 John Wiley & Sons, Ltd.

  2. Observing and preventing rubidium runaway in a direct-infusion xenon-spin hyperpolarizer optimized for high-resolution hyper-CEST (chemical exchange saturation transfer using hyperpolarized nuclei) NMR

    SciTech Connect

    Witte, C.; Kunth, M.; Rossella, F.; Schröder, L.

    2014-02-28

    Xenon is well known to undergo host-guest interactions with proteins and synthetic molecules. As xenon can also be hyperpolarized by spin exchange optical pumping, allowing the investigation of highly dilute systems, it makes an ideal nuclear magnetic resonance probe for such host molecules. The utility of xenon as a probe can be further improved using Chemical Exchange Saturation Transfer using hyperpolarized nuclei (Hyper-CEST), but for highly accurate experiments requires a polarizer and xenon infusion system optimized for such measurements. We present the design of a hyperpolarizer and xenon infusion system specifically designed to meet the requirements of Hyper-CEST measurements. One key element of this design is preventing rubidium runaway, a chain reaction induced by laser heating that prevents efficient utilization of high photon densities. Using thermocouples positioned along the pumping cell we identify the sources of heating and conditions for rubidium runaway to occur. We then demonstrate the effectiveness of actively cooling the optical cell to prevent rubidium runaway in a compact setup. This results in a 2–3-fold higher polarization than without cooling, allowing us to achieve a polarization of 25% at continuous flow rates of 9 ml/min of {sup 129}Xe. The simplicity of this design also allows it to be retrofitted to many existing polarizers. Combined with a direction infusion system that reduces shot-to-shot noise down to 0.56% we have captured Hyper-CEST spectra in unprecedented detail, allowing us to completely resolve peaks separated by just 1.62 ppm. Due to its high polarization and excellent stability, our design allows the comparison of underlying theories of host-guest systems with experiment at low concentrations, something extremely difficult with previous polarizers.

  3. Observing and preventing rubidium runaway in a direct-infusion xenon-spin hyperpolarizer optimized for high-resolution hyper-CEST (chemical exchange saturation transfer using hyperpolarized nuclei) NMR.

    PubMed

    Witte, C; Kunth, M; Rossella, F; Schröder, L

    2014-02-28

    Xenon is well known to undergo host-guest interactions with proteins and synthetic molecules. As xenon can also be hyperpolarized by spin exchange optical pumping, allowing the investigation of highly dilute systems, it makes an ideal nuclear magnetic resonance probe for such host molecules. The utility of xenon as a probe can be further improved using Chemical Exchange Saturation Transfer using hyperpolarized nuclei (Hyper-CEST), but for highly accurate experiments requires a polarizer and xenon infusion system optimized for such measurements. We present the design of a hyperpolarizer and xenon infusion system specifically designed to meet the requirements of Hyper-CEST measurements. One key element of this design is preventing rubidium runaway, a chain reaction induced by laser heating that prevents efficient utilization of high photon densities. Using thermocouples positioned along the pumping cell we identify the sources of heating and conditions for rubidium runaway to occur. We then demonstrate the effectiveness of actively cooling the optical cell to prevent rubidium runaway in a compact setup. This results in a 2-3-fold higher polarization than without cooling, allowing us to achieve a polarization of 25% at continuous flow rates of 9 ml/min of (129)Xe. The simplicity of this design also allows it to be retrofitted to many existing polarizers. Combined with a direction infusion system that reduces shot-to-shot noise down to 0.56% we have captured Hyper-CEST spectra in unprecedented detail, allowing us to completely resolve peaks separated by just 1.62 ppm. Due to its high polarization and excellent stability, our design allows the comparison of underlying theories of host-guest systems with experiment at low concentrations, something extremely difficult with previous polarizers.

  4. Fabrication of 2D nanosheet through self assembly behavior of sulfamethoxypyridazine inclusion complexes with α- and β-cyclodextrins.

    PubMed

    Rajendiran, N; Venkatesh, G; Mohandass, T

    2014-04-05

    A 2D nanosheet was fabricated through the supramolecular self assembly of sulfamethoxypyridazine (SMP) and β-cyclodextrin (β-CD) inclusion complexes. HRTEM image exhibited 2D nanosheet morphology with a length of 1200mm and the sheet thickness of 60mm. It is noted that the nanosheet did not form a single layer aggregation but a bulk aggregation of SMP/β-CD inclusion complex. The formation of this multilayer 2D nanosheet based on the self assembly of SMP/β-CD inclusion complexes is proposed by the topological transformation as well as molecular modeling calculations. But, nanorods are formed in SMP/α-CD inclusion complex indicated that the nature of the CD determined the shape of the self assembled supramolecular architecture. The formation of nanomaterial was characterized by using FT-IR, DSC, PXRD, (1)H NMR, absorption, fluorescence and lifetime measurements.

  5. Two dimensional NMR spectroscopic approaches for exploring plant metabolome: A review

    PubMed Central

    Mahrous, Engy A.; Farag, Mohamed A.

    2014-01-01

    Today, most investigations of the plant metabolome tend to be based on either nuclear magnetic resonance (NMR) spectroscopy or mass spectrometry (MS), with or without hyphenation with chromatography. Although less sensitive than MS, NMR provides a powerful complementary technique for the identification and quantification of metabolites in plant extracts. NMR spectroscopy, well appreciated by phytochemists as a particularly information-rich method, showed recent paradigm shift for the improving of metabolome(s) structural and functional characterization and for advancing the understanding of many biological processes. Furthermore, two dimensional NMR (2D NMR) experiments and the use of chemometric data analysis of NMR spectra have proven highly effective at identifying novel and known metabolites that correlate with changes in genotype or phenotype. In this review, we provide an overview of the development of NMR in the field of metabolomics with special focus on 2D NMR spectroscopic techniques and their applications in phytomedicines quality control analysis and drug discovery from natural sources, raising more attention at its potential to reduce the gap between the pace of natural products research and modern drug discovery demand. PMID:25685540

  6. Fast automated protein NMR data collection and assignment by ADAPT-NMR on Bruker spectrometers

    NASA Astrophysics Data System (ADS)

    Lee, Woonghee; Hu, Kaifeng; Tonelli, Marco; Bahrami, Arash; Neuhardt, Elizabeth; Glass, Karen C.; Markley, John L.

    2013-11-01

    ADAPT-NMR (Assignment-directed Data collection Algorithm utilizing a Probabilistic Toolkit in NMR) supports automated NMR data collection and backbone and side chain assignment for [U-13C, U-15N]-labeled proteins. Given the sequence of the protein and data for the orthogonal 2D 1H-15N and 1H-13C planes, the algorithm automatically directs the collection of tilted plane data from a variety of triple-resonance experiments so as to follow an efficient pathway toward the probabilistic assignment of 1H, 13C, and 15N signals to specific atoms in the covalent structure of the protein. Data collection and assignment calculations continue until the addition of new data no longer improves the assignment score. ADAPT-NMR was first implemented on Varian (Agilent) spectrometers [A. Bahrami, M. Tonelli, S.C. Sahu, K.K. Singarapu, H.R. Eghbalnia, J.L. Markley, PLoS One 7 (2012) e33173]. Because of broader interest in the approach, we present here a version of ADAPT-NMR for Bruker spectrometers. We have developed two AU console programs (ADAPT_ORTHO_run and ADAPT_NMR_run) that run under TOPSPIN Versions 3.0 and higher. To illustrate the performance of the algorithm on a Bruker spectrometer, we tested one protein, chlorella ubiquitin (76 amino acid residues), that had been used with the Varian version: the Bruker and Varian versions achieved the same level of assignment completeness (98% in 20 h). As a more rigorous evaluation of the Bruker version, we tested a larger protein, BRPF1 bromodomain (114 amino acid residues), which yielded an automated assignment completeness of 86% in 55 h. Both experiments were carried out on a 500 MHz Bruker AVANCE III spectrometer equipped with a z-gradient 5 mm TCI probe. ADAPT-NMR is available at http://pine.nmrfam.wisc.edu/ADAPT-NMR in the form of pulse programs, the two AU programs, and instructions for installation and use.

  7. Fast automated protein NMR data collection and assignment by ADAPT-NMR on Bruker spectrometers.

    PubMed

    Lee, Woonghee; Hu, Kaifeng; Tonelli, Marco; Bahrami, Arash; Neuhardt, Elizabeth; Glass, Karen C; Markley, John L

    2013-11-01

    ADAPT-NMR (Assignment-directed Data collection Algorithm utilizing a Probabilistic Toolkit in NMR) supports automated NMR data collection and backbone and side chain assignment for [U-(13)C, U-(15)N]-labeled proteins. Given the sequence of the protein and data for the orthogonal 2D (1)H-(15)N and (1)H-(13)C planes, the algorithm automatically directs the collection of tilted plane data from a variety of triple-resonance experiments so as to follow an efficient pathway toward the probabilistic assignment of (1)H, (13)C, and (15)N signals to specific atoms in the covalent structure of the protein. Data collection and assignment calculations continue until the addition of new data no longer improves the assignment score. ADAPT-NMR was first implemented on Varian (Agilent) spectrometers [A. Bahrami, M. Tonelli, S.C. Sahu, K.K. Singarapu, H.R. Eghbalnia, J.L. Markley, PLoS One 7 (2012) e33173]. Because of broader interest in the approach, we present here a version of ADAPT-NMR for Bruker spectrometers. We have developed two AU console programs (ADAPT_ORTHO_run and ADAPT_NMR_run) that run under TOPSPIN Versions 3.0 and higher. To illustrate the performance of the algorithm on a Bruker spectrometer, we tested one protein, chlorella ubiquitin (76 amino acid residues), that had been used with the Varian version: the Bruker and Varian versions achieved the same level of assignment completeness (98% in 20 h). As a more rigorous evaluation of the Bruker version, we tested a larger protein, BRPF1 bromodomain (114 amino acid residues), which yielded an automated assignment completeness of 86% in 55 h. Both experiments were carried out on a 500 MHz Bruker AVANCE III spectrometer equipped with a z-gradient 5 mm TCI probe. ADAPT-NMR is available at http://pine.nmrfam.wisc.edu/ADAPT-NMR in the form of pulse programs, the two AU programs, and instructions for installation and use.

  8. Residual lens effects in 2D mode of auto-stereoscopic lenticular-based switchable 2D/3D displays

    NASA Astrophysics Data System (ADS)

    Sluijter, M.; IJzerman, W. L.; de Boer, D. K. G.; de Zwart, S. T.

    2006-04-01

    We discuss residual lens effects in multi-view switchable auto-stereoscopic lenticular-based 2D/3D displays. With the introduction of a switchable lenticular, it is possible to switch between a 2D mode and a 3D mode. The 2D mode displays conventional content, whereas the 3D mode provides the sensation of depth to the viewer. The uniformity of a display in the 2D mode is quantified by the quality parameter modulation depth. In order to reduce the modulation depth in the 2D mode, birefringent lens plates are investigated analytically and numerically, by ray tracing. We can conclude that the modulation depth in the 2D mode can be substantially decreased by using birefringent lens plates with a perfect index match between lens material and lens plate. Birefringent lens plates do not disturb the 3D performance of a switchable 2D/3D display.

  9. Differential CYP 2D6 metabolism alters primaquine pharmacokinetics.

    PubMed

    Potter, Brittney M J; Xie, Lisa H; Vuong, Chau; Zhang, Jing; Zhang, Ping; Duan, Dehui; Luong, Thu-Lan T; Bandara Herath, H M T; Dhammika Nanayakkara, N P; Tekwani, Babu L; Walker, Larry A; Nolan, Christina K; Sciotti, Richard J; Zottig, Victor E; Smith, Philip L; Paris, Robert M; Read, Lisa T; Li, Qigui; Pybus, Brandon S; Sousa, Jason C; Reichard, Gregory A; Marcsisin, Sean R

    2015-04-01

    Primaquine (PQ) metabolism by the cytochrome P450 (CYP) 2D family of enzymes is required for antimalarial activity in both humans (2D6) and mice (2D). Human CYP 2D6 is highly polymorphic, and decreased CYP 2D6 enzyme activity has been linked to decreased PQ antimalarial activity. Despite the importance of CYP 2D metabolism in PQ efficacy, the exact role that these enzymes play in PQ metabolism and pharmacokinetics has not been extensively studied in vivo. In this study, a series of PQ pharmacokinetic experiments were conducted in mice with differential CYP 2D metabolism characteristics, including wild-type (WT), CYP 2D knockout (KO), and humanized CYP 2D6 (KO/knock-in [KO/KI]) mice. Plasma and liver pharmacokinetic profiles from a single PQ dose (20 mg/kg of body weight) differed significantly among the strains for PQ and carboxy-PQ. Additionally, due to the suspected role of phenolic metabolites in PQ efficacy, these were probed using reference standards. Levels of phenolic metabolites were highest in mice capable of metabolizing CYP 2D6 substrates (WT and KO/KI 2D6 mice). PQ phenolic metabolites were present in different quantities in the two strains, illustrating species-specific differences in PQ metabolism between the human and mouse enzymes. Taking the data together, this report furthers understanding of PQ pharmacokinetics in the context of differential CYP 2D metabolism and has important implications for PQ administration in humans with different levels of CYP 2D6 enzyme activity.

  10. Mechanical characterization of 2D, 2D stitched, and 3D braided/RTM materials

    NASA Technical Reports Server (NTRS)

    Deaton, Jerry W.; Kullerd, Susan M.; Portanova, Marc A.

    1993-01-01

    Braided composite materials have potential for application in aircraft structures. Fuselage frames, floor beams, wing spars, and stiffeners are examples where braided composites could find application if cost effective processing and damage tolerance requirements are met. Another important consideration for braided composites relates to their mechanical properties and how they compare to the properties of composites produced by other textile composite processes being proposed for these applications. Unfortunately, mechanical property data for braided composites do not appear extensively in the literature. Data are presented in this paper on the mechanical characterization of 2D triaxial braid, 2D triaxial braid plus stitching, and 3D (through-the-thickness) braid composite materials. The braided preforms all had the same graphite tow size and the same nominal braid architectures, (+/- 30 deg/0 deg), and were resin transfer molded (RTM) using the same mold for each of two different resin systems. Static data are presented for notched and unnotched tension, notched and unnotched compression, and compression after impact strengths at room temperature. In addition, some static results, after environmental conditioning, are included. Baseline tension and compression fatigue results are also presented, but only for the 3D braided composite material with one of the resin systems.

  11. The 2DX robot: a membrane protein 2D crystallization Swiss Army knife.

    PubMed

    Iacovache, Ioan; Biasini, Marco; Kowal, Julia; Kukulski, Wanda; Chami, Mohamed; van der Goot, F Gisou; Engel, Andreas; Rémigy, Hervé-W

    2010-03-01

    Among the state-of-the-art techniques that provide experimental information at atomic scale for membrane proteins, electron crystallography, atomic force microscopy and solid state NMR make use of two-dimensional crystals. We present a cyclodextrin-driven method for detergent removal implemented in a fully automated robot. The kinetics of the reconstitution processes is precisely controlled, because the detergent complexation by cyclodextrin is of stoichiometric nature. The method requires smaller volumes and lower protein concentrations than established 2D crystallization methods, making it possible to explore more conditions with the same amount of protein. The method yielded highly ordered 2D crystals diffracting to high resolution from the pore-forming toxin Aeromonas hydrophila aerolysin (2.9A), the plant aquaporin SoPIP2;1 (3.1A) and the human aquaporin-8 (hAQP8; 3.3A). This new method outperforms traditional 2D crystallization approaches in terms of accuracy, flexibility, throughput, and allows the usage of detergents having low critical micelle concentration (CMC), which stabilize the structure of membrane proteins in solution.

  12. Computational Screening of 2D Materials for Photocatalysis.

    PubMed

    Singh, Arunima K; Mathew, Kiran; Zhuang, Houlong L; Hennig, Richard G

    2015-03-19

    Two-dimensional (2D) materials exhibit a range of extraordinary electronic, optical, and mechanical properties different from their bulk counterparts with potential applications for 2D materials emerging in energy storage and conversion technologies. In this Perspective, we summarize the recent developments in the field of solar water splitting using 2D materials and review a computational screening approach to rapidly and efficiently discover more 2D materials that possess properties suitable for solar water splitting. Computational tools based on density-functional theory can predict the intrinsic properties of potential photocatalyst such as their electronic properties, optical absorbance, and solubility in aqueous solutions. Computational tools enable the exploration of possible routes to enhance the photocatalytic activity of 2D materials by use of mechanical strain, bias potential, doping, and pH. We discuss future research directions and needed method developments for the computational design and optimization of 2D materials for photocatalysis.

  13. Lipid Bilayer-Bound Conformation of an Integral Membrane Beta Barrel Protein by Multidimensional MAS NMR

    PubMed Central

    Eddy, Matthew T.; Su, Yongchao; Silvers, Robert; Andreas, Loren; Clark, Lindsay; Wagner, Gerhard; Pintacuda, Guido; Emsley, Lyndon; Griffin, Robert G.

    2015-01-01

    The human voltage dependent anion channel 1 (VDAC) is a 32 kDa β-barrel integral membrane protein that controls the transport of ions across the outer mitochondrial membrane. Despite the determination of VDAC solution and diffraction structures, a structural basis for the mechanism of its function is not yet fully understood. Biophysical studies suggest VDAC requires a lipid bilayer to achieve full function, motivating the need for atomic resolution structural information of VDAC in a membrane environment. Here we report an essential step toward that goal: extensive assignments of backbone and side chain resonances for VDAC in DMPC lipid bilayers via magic angle spinning nuclear magnetic resonance (MAS NMR). VDAC reconstituted into DMPC lipid bilayers spontaneously forms 2-dimensional lipid crystals, showing remarkable spectral resolution (0.5–0.3 ppm for 13C line width and less than 0.5 ppm 15N line widths at 750 MHz). In addition to the benefits of working in a lipid bilayer, several distinct advantages are observed with the lipid crystalline preparation. First, the strong signals and sharp line widths facilitated extensive NMR resonance assignments for an integral membrane β-barrel protein in lipid bilayers by MAS NMR. Second, a large number of residues in loop regions were readily observed and assigned, which can be challenging in detergent-solubilized membrane proteins where loop regions are often not detected due to line broadening from conformational exchange. Third, complete backbone and side chain chemical shift assignments could be obtained for the first 25 residues, which comprise the functionally important N-terminus. The reported assignments allow us to compare predicted torsion angles for VDAC prepared in DMPC 2D lipid crystals, DMPC liposomes, and LDAO-solubilized samples to address the possible effects of the membrane mimetic environment on the conformation of the protein. Concluding, we discuss the strengths and weaknesses of the reported

  14. Lipid bilayer-bound conformation of an integral membrane beta barrel protein by multidimensional MAS NMR.

    PubMed

    Eddy, Matthew T; Su, Yongchao; Silvers, Robert; Andreas, Loren; Clark, Lindsay; Wagner, Gerhard; Pintacuda, Guido; Emsley, Lyndon; Griffin, Robert G

    2015-04-01

    The human voltage dependent anion channel 1 (VDAC) is a 32 kDa β-barrel integral membrane protein that controls the transport of ions across the outer mitochondrial membrane. Despite the determination of VDAC solution and diffraction structures, a structural basis for the mechanism of its function is not yet fully understood. Biophysical studies suggest VDAC requires a lipid bilayer to achieve full function, motivating the need for atomic resolution structural information of VDAC in a membrane environment. Here we report an essential step toward that goal: extensive assignments of backbone and side chain resonances for VDAC in DMPC lipid bilayers via magic angle spinning nuclear magnetic resonance (MAS NMR). VDAC reconstituted into DMPC lipid bilayers spontaneously forms two-dimensional lipid crystals, showing remarkable spectral resolution (0.5-0.3 ppm for (13)C line widths and <0.5 ppm (15)N line widths at 750 MHz). In addition to the benefits of working in a lipid bilayer, several distinct advantages are observed with the lipid crystalline preparation. First, the strong signals and sharp line widths facilitated extensive NMR resonance assignments for an integral membrane β-barrel protein in lipid bilayers by MAS NMR. Second, a large number of residues in loop regions were readily observed and assigned, which can be challenging in detergent-solubilized membrane proteins where loop regions are often not detected due to line broadening from conformational exchange. Third, complete backbone and side chain chemical shift assignments could be obtained for the first 25 residues, which comprise the functionally important N-terminus. The reported assignments allow us to compare predicted torsion angles for VDAC prepared in DMPC 2D lipid crystals, DMPC liposomes, and LDAO-solubilized samples to address the possible effects of the membrane mimetic environment on the conformation of the protein. Concluding, we discuss the strengths and weaknesses of the reported

  15. Charge exchange in zinc-neon

    NASA Technical Reports Server (NTRS)

    Chubb, D. L.

    1975-01-01

    Excitation of the 4d and 5p levels of Zn+ by charge exchange bewteen Ne+ and Zn was investigated. From measured electron temperature and line intensity ratios it was concluded that charge exchange is the dominate mechanism for populating the 4d2D5/2 level of Zn+. Comparison of Zn-Ne and Zn-Ar results imply the same conclusion. No evidence for charge exchange as the dominant pumping mechanism for the 5p2Pl/2, 5p2P3/2, or 4d2D3/2 levels was obtained.

  16. TLC and 31P-NMR analysis of low polarity phospholipids.

    PubMed

    Vyssotski, Mikhail; MacKenzie, Andrew; Scott, Dawn

    2009-04-01

    High-performance TLC and (31)P-NMR were assessed as methods of observing the presence of numerous low polarity phospholipids: bis-phosphatidic acid (BPA), semi-lyso bis-phosphatidic acid (SLBPA), N-acyl phosphatidylethanolamine (NAPE), N-(1,1-dimethyl-3-oxo-butyl)-phosphatidylethanolamine (diacetone adduct of PE, DOBPE), N-acetyl PE, phosphatidylmethanol (PM), phosphatidylethanol (PEt), phosphatidyl-n-propanol (PP), phosphatidyl-n-butanol (PB). Both techniques are non-discriminative and do not require the prior isolation of individual lipids. It appears that 2D TLC is superior to (31)P NMR in the analysis of low polarity phospholipids. All phosphatidylalcohols were well separated by 2D TLC. However, some compounds which can present difficulty in separation by 2D-TLC (e.g., SLBPA and NAPE; or DOBPE and N-acetyl PE) were easily distinguished using (31)P NMR so the methods are complimentary. A disadvantage of 2D TLC is that Rf values can vary with different brands and batches of TLC plates. The chemical shifts of (31)P NMR were less variable, and so a library of standards may not be necessary for peak identification. Another advantage of (31)P NMR is the ease of quantification of phospholipids. The applicability of the methods was tested on natural extracts of fish brain and cabbage stem.

  17. Synthetic Covalent and Non-Covalent 2D Materials.

    PubMed

    Boott, Charlotte E; Nazemi, Ali; Manners, Ian

    2015-11-16

    The creation of synthetic 2D materials represents an attractive challenge that is ultimately driven by their prospective uses in, for example, electronics, biomedicine, catalysis, sensing, and as membranes for separation and filtration. This Review illustrates some recent advances in this diverse field with a focus on covalent and non-covalent 2D polymers and frameworks, and self-assembled 2D materials derived from nanoparticles, homopolymers, and block copolymers.

  18. Derivatives of pyrazinecarboxylic acid: 1H, 13C and 15N NMR spectroscopic investigations.

    PubMed

    Holzer, Wolfgang; Eller, Gernot A; Datterl, Barbara; Habicht, Daniela

    2009-07-01

    NMR spectroscopic studies are undertaken with derivatives of 2-pyrazinecarboxylic acid. Complete and unambiguous assignment of chemical shifts ((1)H, (13)C, (15)N) and coupling constants ((1)H,(1)H; (13)C,(1)H; (15)N,(1)H) is achieved by combined application of various 1D and 2D NMR spectroscopic techniques. Unequivocal mapping of (13)C,(1)H spin coupling constants is accomplished by 2D (delta,J) long-range INEPT spectra with selective excitation. Phenomena such as the tautomerism of 3-hydroxy-2-pyrazinecarboxylic acid are discussed.

  19. NMR Studies of Peroxidases.

    NASA Astrophysics Data System (ADS)

    Veitch, Nigel Charles

    Available from UMI in association with The British Library. Requires signed TDF. Peroxidases are a haem-containing group of enzymes with a wide diversity of function within biological systems. While a common characteristic is the ability to catalyse the conversion of hydrogen peroxide to water, it is the accompanying processes of hormone synthesis and degradation which have generated such a high level of interest. However, information at the molecular level is limited to a single well-resolved crystal structure, that of yeast cytochrome c peroxidase. This thesis presents a strategy for the investigation of peroxidase structure and function based on proton nuclear magnetic resonance spectroscopy, a technique which has the ability to address aspects of both protein structure and protein dynamics in solution. The application of one- and two-dimensional NMR techniques has been developed in the context of plant peroxidases, notably the isoenzyme HRP-C derived from the horseradish root. Characterisation of the proton NMR spectra of HRP -C in resting and ligated states provided new information enabling the structure of the binding site for aromatic donor molecules, such as indole-3-propionic, ferulic and benzhydroxamic acids, to be resolved. In order to overcome difficulties encountered with a protein of the complexity of peroxidase, additional information was obtained from chemical shift parameters and the use of peroxidase variants produced by site-directed mutagenesis. A comparative study using NMR spectroscopy was undertaken for wild-type recombinant HRP-C expressed in Escherichia coli, and two protein variants with substitutions made to residues located on the distal side of the haem pocket, Phe41 to Val and Arg38 to Lys. NMR analyses of a plant peroxidase from barley grains and the fungal peroxidase from Coprinus cinereus were also successful using methods conceived with HRP-C. Examination of three specifically constructed recombinant protein variants of C. cinereus

  20. NMR imaging of materials

    SciTech Connect

    Vinegar, H.J.; Rothwell, W.P.

    1988-03-01

    A method for obtaining at least one petrophysical property of a porous material containing therein at least one preselected fluid, is described, comprising: NMR imaging the material to generate signals dependent upon both M(0) and T/sub 1/ and M(0) and T/sub 2/, generating separate M(0), T/sub 1/ and T/sub 2/ images from the signals, and determining at least one petrophysical property from at least one of the images.

  1. β-NMR

    NASA Astrophysics Data System (ADS)

    Morris, Gerald D.

    2014-01-01

    The β-NMR facility at ISAC is constructed specifically for experiments in condensed matter physics with radioactive ion beams. Using co-linear optical pumping, a 8Li + ion beam having a large nuclear spin polarisation and low energy (nominally 30 keV) can be generated. When implanted into materials these ions penetrate to shallow depths comparable to length scales of interest in the physics of surfaces and interfaces between materials. Such low-energy ions can be decelerated with simple electrostatic optics to enable depth-resolved studies of near-surface phenomena over the range of about 2-200 nm. Since the β-NMR signal is extracted from the asymmetry intrinsic to beta-decay and therefore monitors the polarisation of the radioactive probe nuclear magnetic moments, this technique is fundamentally a probe of local magnetism. More generally though, any phenomena which affects the polarisation of the implanted spins by, for example, a change in resonance frequency, line width or relaxation rate can be studied. The β-NMR program at ISAC currently supports a number of experiments in magnetism and superconductivity as well as novel ultra-thin heterostructures exhibiting properties that cannot occur in bulk materials. The general purpose zero/low field and high field spectrometers are configured to perform CW and pulsed RF nuclear magnetic resonance and spin relaxation experiments over a range of temperatures (3-300 K) and magnetic fields (0-9 T).

  2. Epitaxial 2D SnSe2/ 2D WSe2 van der Waals Heterostructures.

    PubMed

    Aretouli, Kleopatra Emmanouil; Tsoutsou, Dimitra; Tsipas, Polychronis; Marquez-Velasco, Jose; Aminalragia Giamini, Sigiava; Kelaidis, Nicolaos; Psycharis, Vassilis; Dimoulas, Athanasios

    2016-09-07

    van der Waals heterostructures of 2D semiconductor materials can be used to realize a number of (opto)electronic devices including tunneling field effect devices (TFETs). It is shown in this work that high quality SnSe2/WSe2 vdW heterostructure can be grown by molecular beam epitaxy on AlN(0001)/Si(111) substrates using a Bi2Se3 buffer layer. A valence band offset of 0.8 eV matches the energy gap of SnSe2 in such a way that the VB edge of WSe2 and the CB edge of SnSe2 are lined up, making this materials combination suitable for (nearly) broken gap TFETs.

  3. A study of a sector spectrophotometer and auroral O+(2P-2D) emissions

    NASA Technical Reports Server (NTRS)

    Swenson, G. R.

    1976-01-01

    The metastable O+(2P-2D) auroral emission was investigated. The neighboring OH contaminants and low intensity levels of the emission itself necessitated the evolution of an instrument capable of separating the emission from the contaminants and having a high sensitivity in the wavelength region of interest. A new type of scanning photometer was developed and its properties are discussed. The theoretical aspects of auroral electron interaction with atomic oxygen and the resultant O+(2P-2D) emissions were examined in conjunction with N2(+)1NEG emissions. Ground based measurements of O+(2P-2D) auroral emission intensities were made using the spatial scanning photometer (sector spectrophotometer). Simultaneous measurements of N2(+)1NEG sub 1,0 emission intensity were made in the same field of view using a tilting photometer. Time histories of the ratio of these two emissions made in the magnetic zenith during auroral breakup periods are given. Theories of I sub 7319/I sub 4278 of previous investigators were presented. A rocket measurement of N2(+)1NEG sub 0,0 and O+(2P-2D) emission in aurora was examined in detail and was found to agree with the ground based measurements. Theoretical examination resulted in the deduction of the electron impact efficiency generating O+(2P) and also suggests a large source of O+(2P) at low altitude. A possible source is charge exchange of N+(1S) with OI(3P).

  4. Circular photogalvanic effect caused by the transitions between edge and 2D states in a 2D topological insulator

    NASA Astrophysics Data System (ADS)

    Magarill, L. I.; Entin, M. V.

    2016-12-01

    The electron absorption and the edge photocurrent of a 2D topological insulator are studied for transitions between edge states to 2D states. The circular polarized light is found to produce the edge photocurrent, the direction of which is determined by light polarization and edge orientation. It is shown that the edge-state current is found to exceed the 2D current owing to the topological protection of the edge states.

  5. Access to experimentally infeasible spectra by pure-shift NMR covariance

    NASA Astrophysics Data System (ADS)

    Fredi, André; Nolis, Pau; Cobas, Carlos; Parella, Teodor

    2016-09-01

    Covariance processing is a versatile processing tool to generate synthetic NMR spectral representations without the need to acquire time-consuming experimental datasets. Here we show that even experimentally prohibited NMR spectra can be reconstructed by introducing key features of a reference 1D CHn-edited spectrum into standard 2D spectra. This general procedure is illustrated with the calculation of experimentally infeasible multiplicity-edited pure-shift NMR spectra of some very popular homonuclear (ME-psCOSY and ME-psTOCSY) and heteronuclear (ME-psHSQC-TOCSY and ME-psHMBC) experiments.

  6. NMR Methods, Applications and Trends for Groundwater Evaluation and Management

    NASA Astrophysics Data System (ADS)

    Walsh, D. O.; Grunewald, E. D.

    2011-12-01

    Nuclear magnetic resonance (NMR) measurements have a tremendous potential for improving groundwater characterization, as they provide direct detection and measurement of groundwater and unique information about pore-scale properties. NMR measurements, commonly used in chemistry and medicine, are utilized in geophysical investigations through non-invasive surface NMR (SNMR) or downhole NMR logging measurements. Our recent and ongoing research has focused on improving the performance and interpretation of NMR field measurements for groundwater characterization. Engineering advancements have addressed several key technical challenges associated with SNMR measurements. Susceptibility of SNMR measurements to environmental noise has been dramatically reduced through the development of multi-channel acquisition hardware and noise-cancellation software. Multi-channel instrumentation (up to 12 channels) has also enabled more efficient 2D and 3D imaging. Previous limitations in measuring NMR signals from water in silt, clay and magnetic geology have been addressed by shortening the instrument dead-time from 40 ms to 4 ms, and increasing the power output. Improved pulse sequences have been developed to more accurately estimate NMR relaxation times and their distributions, which are sensitive to pore size distributions. Cumulatively, these advancements have vastly expanded the range of environments in which SNMR measurements can be obtained, enabling detection of groundwater in smaller pores, in magnetic geology, in the unsaturated zone, and nearby to infrastructure (presented here in case studies). NMR logging can provide high-resolution estimates of bound and mobile water content and pore size distributions. While NMR logging has been utilized in oil and gas applications for decades, its use in groundwater investigations has been limited by the large size and high cost of oilfield NMR logging tools and services. Recently, engineering efforts funded by the US Department of

  7. Energy Efficiency of D2D Multi-User Cooperation.

    PubMed

    Zhang, Zufan; Wang, Lu; Zhang, Jie

    2017-03-28

    The Device-to-Device (D2D) communication system is an important part of heterogeneous networks. It has great potential to improve spectrum efficiency, throughput and energy efficiency cooperation of multiple D2D users with the advantage of direct communication. When cooperating, D2D users expend extraordinary energy to relay data to other D2D users. Hence, the remaining energy of D2D users determines the life of the system. This paper proposes a cooperation scheme for multiple D2D users who reuse the orthogonal spectrum and are interested in the same data by aiming to solve the energy problem of D2D users. Considering both energy availability and the Signal to Noise Ratio (SNR) of each D2D user, the Kuhn-Munkres algorithm is introduced in the cooperation scheme to solve relay selection problems. Thus, the cooperation issue is transformed into a maximum weighted matching (MWM) problem. In order to enhance energy efficiency without the deterioration of Quality of Service (QoS), the link outage probability is derived according to the Shannon Equation by considering the data rate and delay. The simulation studies the relationships among the number of cooperative users, the length of shared data, the number of data packets and energy efficiency.

  8. Integrating Mobile Multimedia into Textbooks: 2D Barcodes

    ERIC Educational Resources Information Center

    Uluyol, Celebi; Agca, R. Kagan

    2012-01-01

    The major goal of this study was to empirically compare text-plus-mobile phone learning using an integrated 2D barcode tag in a printed text with three other conditions described in multimedia learning theory. The method examined in the study involved modifications of the instructional material such that: a 2D barcode was used near the text, the…

  9. Efficient Visible Quasi-2D Perovskite Light-Emitting Diodes.

    PubMed

    Byun, Jinwoo; Cho, Himchan; Wolf, Christoph; Jang, Mi; Sadhanala, Aditya; Friend, Richard H; Yang, Hoichang; Lee, Tae-Woo

    2016-09-01

    Efficient quasi-2D-structure perovskite light-emitting diodes (4.90 cd A(-1) ) are demonstrated by mixing a 3D-structured perovskite material (methyl ammonium lead bromide) and a 2D-structured perovskite material (phenylethyl ammonium lead bromide), which can be ascribed to better film uniformity, enhanced exciton confinement, and reduced trap density.

  10. Adaptation algorithms for 2-D feedforward neural networks.

    PubMed

    Kaczorek, T

    1995-01-01

    The generalized weight adaptation algorithms presented by J.G. Kuschewski et al. (1993) and by S.H. Zak and H.J. Sira-Ramirez (1990) are extended for 2-D madaline and 2-D two-layer feedforward neural nets (FNNs).

  11. 2D Superexchange-mediated magnetization dynamics in an optical lattice

    NASA Astrophysics Data System (ADS)

    Goldschmidt, Elizabeth; Brown, Roger; Wyllie, Robert; Koller, Silvio; Foss-Feig, Michael; Porto, Trey

    2015-05-01

    The interplay of magnetic exchange interactions and tunneling underlies many complex quantum phenomena observed in real materials. We study nonequilibrium magnetization dynamics in an extended 2D system by loading effective spin-1/2 bosons into a spin-dependent optical lattice, and we use the lattice to separately control the resonance conditions for tunneling and superexchange. After preparing a nonequilibrium antiferromagnetically ordered state, we observe relaxation dynamics governed by two well-separated rates, which scale with the underlying Hamiltonian parameters associated with superexchange and tunneling. Remarkably, with tunneling off-resonantly suppressed, we are able to observe superexchange-dominated dynamics over two orders of magnitude in magnetic coupling strength, despite the presence of vacancies. In this regime, the measured timescales are in agreement with simple theoretical estimates, but the detailed dynamics of this 2D, strongly-correlated, and far-from-equilibrium quantum system remain out of reach of current computational techniques. Now at Georgia Tech Research Institute.

  12. Diffusion measurements by microscopic NMR imaging

    NASA Astrophysics Data System (ADS)

    Meyer, Ronald A.; Brown, Truman R.

    Proton NMR images of the brains of living mice with voxel sizes as small as 80 × 80 × 500 μm were acquired at 9.3 T by the 2D FT spin-echo method. Using gradients of 3.75 G/cm, images with pixel dimensions below 50 μm were of low sensitivity because of degradation of the echo due to diffusion and flow. In the absence of bulk flow, this decrease in image intensity as image pixel size is decreased can be used to measure the local self-diffusion coefficient of water ( DH 2O ) in small samples. By this method, DH 2O at 22°C was estimated to be 2.59, 2.13, 1.59, and 0.84 × 10 -5 cm 2/s in pure water, 10% gelatin, mouse skeletal muscle, and rat liver, respectively.

  13. NMR-based analysis of the chemical composition of Japanese persimmon aqueous extracts.

    PubMed

    Ryu, Shoraku; Furihata, Kazuo; Koda, Masanori; Wei, Feifei; Miyakawa, Takuya; Tanokura, Masaru

    2016-03-01

    Japanese persimmon (Diospyros kaki L.) is recognized as an outstanding source of biologically active compounds relating to many health benefits. In the present study, NMR spectroscopy provided a comprehensive metabolic overview of Japanese persimmon juice. Detailed signal assignments of Japanese persimmon juice were carried out using various 2D NMR techniques incorporated with broadband water suppression enhanced through T1 effects (BB-WET) or WET sequences, and 26 components, including minor components, were identified. In addition, most components were quantitatively evaluated by the integration of signals using conventional (1) H NMR and BB-WET NMR. This is the first detailed analysis combined with quantitative characterization of chemical components using NMR for Japanese persimmon. Copyright © 2015 John Wiley & Sons, Ltd.

  14. Digital NMR profiles as building blocks: assembling ¹H fingerprints of steviol glycosides.

    PubMed

    Napolitano, José G; Simmler, Charlotte; McAlpine, James B; Lankin, David C; Chen, Shao-Nong; Pauli, Guido F

    2015-04-24

    This report describes a fragment-based approach to the examination of congeneric organic compounds by NMR spectroscopy. The method combines the classic interpretation of 1D- and 2D-NMR data sets with contemporary computer-assisted NMR analysis. Characteristic NMR profiles of key structural motifs were generated by (1)H iterative full spin analysis and then joined together as building blocks to recreate the (1)H NMR spectra of increasingly complex molecules. To illustrate the methodology described, a comprehensive analysis of steviol (1), seven steviol glycosides (2-8) and two structurally related isosteviol compounds (9, 10) was carried out. The study also assessed the potential impact of this method on relevant aspects of natural product research including structural verification, chemical dereplication, and mixture analysis.

  15. Digital NMR Profiles as Building Blocks: Assembling 1H Fingerprints of Steviol Glycosides

    PubMed Central

    Napolitano, José G.; Simmler, Charlotte; McAlpine, James B.; Lankin, David C.; Chen, Shao-Nong; Pauli, Guido F.

    2015-01-01

    This report describes a fragment-based approach to the examination of congeneric organic compounds by NMR spectroscopy. The method combines the classic interpretation of 1D- and 2D-NMR data sets with contemporary computer-assisted NMR analysis. Characteristic NMR profiles of key structural motifs were generated by 1H iterative full spin analysis and then joined together as building blocks to recreate the 1H NMR spectra of increasingly complex molecules. To illustrate the methodology described, a comprehensive analysis of steviol (1), seven steviol glycosides (2–8) and two structurally related isosteviol compounds (9, 10) was carried out. The study also assessed the potential impact of this method on relevant aspects of natural product research including structural verification, chemical dereplication, and mixture analysis. PMID:25714117

  16. Regulation of ligands for the NKG2D activating receptor

    PubMed Central

    Raulet, David H.; Gasser, Stephan; Gowen, Benjamin G.; Deng, Weiwen; Jung, Heiyoun

    2014-01-01

    NKG2D is an activating receptor expressed by all NK cells and subsets of T cells. It serves as a major recognition receptor for detection and elimination of transformed and infected cells and participates in the genesis of several inflammatory diseases. The ligands for NKG2D are self-proteins that are induced by pathways that are active in certain pathophysiological states. NKG2D ligands are regulated transcriptionally, at the level of mRNA and protein stability, and by cleavage from the cell surface. In some cases, ligand induction can be attributed to pathways that are activated specifically in cancer cells or infected cells. We review the numerous pathways that have been implicated in the regulation of NKG2D ligands, discuss the pathologic states in which those pathways are likely to act, and attempt to synthesize the findings into general schemes of NKG2D ligand regulation in NK cell responses to cancer and infection. PMID:23298206

  17. 2D materials and van der Waals heterostructures.

    PubMed

    Novoselov, K S; Mishchenko, A; Carvalho, A; Castro Neto, A H

    2016-07-29

    The physics of two-dimensional (2D) materials and heterostructures based on such crystals has been developing extremely fast. With these new materials, truly 2D physics has begun to appear (for instance, the absence of long-range order, 2D excitons, commensurate-incommensurate transition, etc.). Novel heterostructure devices--such as tunneling transistors, resonant tunneling diodes, and light-emitting diodes--are also starting to emerge. Composed from individual 2D crystals, such devices use the properties of those materials to create functionalities that are not accessible in other heterostructures. Here we review the properties of novel 2D crystals and examine how their properties are used in new heterostructure devices.

  18. New generation transistor technologies enabled by 2D crystals

    NASA Astrophysics Data System (ADS)

    Jena, D.

    2013-05-01

    The discovery of graphene opened the door to 2D crystal materials. The lack of a bandgap in 2D graphene makes it unsuitable for electronic switching transistors in the conventional field-effect sense, though possible techniques exploiting the unique bandstructure and nanostructures are being explored. The transition metal dichalcogenides have 2D crystal semiconductors, which are well-suited for electronic switching. We experimentally demonstrate field effect transistors with current saturation and carrier inversion made from layered 2D crystal semiconductors such as MoS2, WS2, and the related family. We also evaluate the feasibility of such semiconducting 2D crystals for tunneling field effect transistors for low-power digital logic. The article summarizes the current state of new generation transistor technologies either proposed, or demonstrated, with a commentary on the challenges and prospects moving forward.

  19. ¹H NMR and hyperpolarized ¹³C NMR assays of pyruvate-lactate: a comparative study.

    PubMed

    Hill, Deborah K; Jamin, Yann; Orton, Matthew R; Tardif, Nicolas; Parkes, Harold G; Robinson, Simon P; Leach, Martin O; Chung, Yuen-Li; Eykyn, Thomas R

    2013-10-01

    Pyruvate-lactate exchange is mediated by the enzyme lactate dehydrogenase (LDH) and is central to the altered energy metabolism in cancer cells. The measurement of exchange kinetics using hyperpolarized (13) C NMR has provided a biomarker of response to novel therapeutics. However, the observable signal is restricted to the exchanging hyperpolarized (13) C pools and the endogenous pools of (12) C-labelled metabolites are invisible in these measurements. In this study, we investigated an alternative in vitro (1) H NMR assay, using [3-(13) C]pyruvate, and compared the measured kinetics with a hyperpolarized (13) C NMR assay, using [1-(13) C]pyruvate, under the same conditions in human colorectal carcinoma SW1222 cells. The apparent forward reaction rate constants (kPL ) derived from the two assays showed no significant difference, and both assays had similar reproducibility (kPL  = 0.506 ± 0.054 and kPL  = 0.441 ± 0.090 nmol/s/10(6) cells; mean ± standard deviation; n = 3); (1) H, (13) C assays, respectively). The apparent backward reaction rate constant (kLP ) could only be measured with good reproducibility using the (1) H NMR assay (kLP  = 0.376 ± 0.091 nmol/s/10(6) cells; mean ± standard deviation; n = 3). The (1) H NMR assay has adequate sensitivity to measure real-time pyruvate-lactate exchange kinetics in vitro, offering a complementary and accessible assay of apparent LDH activity.

  20. Estrogen-Induced Cholestasis Leads to Repressed CYP2D6 Expression in CYP2D6-Humanized Mice.

    PubMed

    Pan, Xian; Jeong, Hyunyoung

    2015-07-01

    Cholestasis activates bile acid receptor farnesoid X receptor (FXR) and subsequently enhances hepatic expression of small heterodimer partner (SHP). We previously demonstrated that SHP represses the transactivation of cytochrome P450 2D6 (CYP2D6) promoter by hepatocyte nuclear factor (HNF) 4α. In this study, we investigated the effects of estrogen-induced cholestasis on CYP2D6 expression. Estrogen-induced cholestasis occurs in subjects receiving estrogen for contraception or hormone replacement, or in susceptible women during pregnancy. In CYP2D6-humanized transgenic (Tg-CYP2D6) mice, cholestasis triggered by administration of 17α-ethinylestradiol (EE2) at a high dose led to 2- to 3-fold decreases in CYP2D6 expression. This was accompanied by increased hepatic SHP expression and subsequent decreases in the recruitment of HNF4α to CYP2D6 promoter. Interestingly, estrogen-induced cholestasis also led to increased recruitment of estrogen receptor (ER) α, but not that of FXR, to Shp promoter, suggesting a predominant role of ERα in transcriptional regulation of SHP in estrogen-induced cholestasis. EE2 at a low dose (that does not cause cholestasis) also increased SHP (by ∼ 50%) and decreased CYP2D6 expression (by 1.5-fold) in Tg-CYP2D6 mice, the magnitude of differences being much smaller than that shown in EE2-induced cholestasis. Taken together, our data indicate that EE2-induced cholestasis increases SHP and represses CYP2D6 expression in Tg-CYP2D6 mice in part through ERα transactivation of Shp promoter.

  1. Targeted fluorescence imaging enhanced by 2D materials: a comparison between 2D MoS2 and graphene oxide.

    PubMed

    Xie, Donghao; Ji, Ding-Kun; Zhang, Yue; Cao, Jun; Zheng, Hu; Liu, Lin; Zang, Yi; Li, Jia; Chen, Guo-Rong; James, Tony D; He, Xiao-Peng

    2016-08-04

    Here we demonstrate that 2D MoS2 can enhance the receptor-targeting and imaging ability of a fluorophore-labelled ligand. The 2D MoS2 has an enhanced working concentration range when compared with graphene oxide, resulting in the improved imaging of both cell and tissue samples.

  2. International Technical Exchange on 2D Atomic Sheets: Optoelectronics, Strain, and Energy Applications

    DTIC Science & Technology

    2015-01-15

    Austin, 10100 Burnet Rd, Austin, TX 78758, U.S.A. etutuc@mer.utexas.edu Abstract Vertical heterostructures consisting of atomic layers separated...accessible in single layer devices. In this presentation we discuss two examples of vertical heterostructures of atomic layer materials, where...Engineering Columbia University, New York, NY 10027 In this paper, we will discuss recent advances in the study of atomically thin layers of

  3. Magic Angle Spinning NMR Metabolomics

    SciTech Connect

    Zhi Hu, Jian

    2016-01-01

    Nuclear Magnetic Resonance (NMR) spectroscopy is a non-destructive, quantitative, reproducible, untargeted and unbiased method that requires no or minimal sample preparation, and is one of the leading analytical tools for metabonomics research [1-3]. The easy quantification and the no need of prior knowledge about compounds present in a sample associated with NMR are advantageous over other techniques [1,4]. 1H NMR is especially attractive because protons are present in virtually all metabolites and its NMR sensitivity is high, enabling the simultaneous identification and monitoring of a wide range of low molecular weight metabolites.

  4. Interactions of gemini surfactants with two model proteins: NMR, CD, and fluorescence spectroscopies.

    PubMed

    Amiri, Razieh; Bordbar, Abdol-Khalegh; García-Mayoral, Ma Flor; Khosropour, Ahmad Reza; Mohammadpoor-Baltork, Iraj; Menéndez, Margarita; Laurents, Douglas V

    2012-03-01

    Gemini surfactants have two polar head groups and two hydrocarbon tails. Compared with conventional surfactants, geminis have much lower (μM vs. mM) critical micelle concentrations and possess slower (ms vs. μs) monomer <-- / --> micelle kinetics. The structure of the gemini surfactants studied is [HOCH(2)CH(2)-, CH(3)-, CH(3)(CH(2))(15)-N(+)-(CH(2))(s)-N(+)-(CH(2))(15)CH(3),-CH(3),-CH(2)CH(2)OH]·2Br(-) where s=4, 5, or 6. Our objective is to reveal the effect of these cationic gemini surfactants on the structure and stability of two model proteins: Ribonuclease A (RNase A) and Hen Egg White Lysozyme (HEWL). 2D (1)H NMR and Circular Dichroism (CD) spectroscopies show that the conformation of RNase A and HEWL is unaffected at low to neutral pH where these proteins are positively charged, although hydrogen exchange shows that RNase A's conformational stability is slightly lowered. At alkaline pH, where these proteins lose their net positive charge, fluorescence and CD spectroscopies and ITC experiments show that they do interact with gemini surfactants, and multiple protein•gemini complexes are observed. Based on the results, we conclude that these cationic gemini surfactants neither interact strongly with nor severely destabilize these well folded proteins in physiological conditions, and we advance that they can serve as useful membrane mimetics for studying the interactions between membrane components and positively charged proteins.

  5. 2D vs. 3D mammography observer study

    NASA Astrophysics Data System (ADS)

    Fernandez, James Reza F.; Hovanessian-Larsen, Linda; Liu, Brent

    2011-03-01

    Breast cancer is the most common type of non-skin cancer in women. 2D mammography is a screening tool to aid in the early detection of breast cancer, but has diagnostic limitations of overlapping tissues, especially in dense breasts. 3D mammography has the potential to improve detection outcomes by increasing specificity, and a new 3D screening tool with a 3D display for mammography aims to improve performance and efficiency as compared to 2D mammography. An observer study using a mammography phantom was performed to compare traditional 2D mammography with this ne 3D mammography technique. In comparing 3D and 2D mammography there was no difference in calcification detection, and mass detection was better in 2D as compared to 3D. There was a significant decrease in reading time for masses, calcifications, and normals in 3D compared to 2D, however, as well as more favorable confidence levels in reading normal cases. Given the limitations of the mammography phantom used, however, a clearer picture in comparing 3D and 2D mammography may be better acquired with the incorporation of human studies in the future.

  6. Joint 2D and 3D phase processing for quantitative susceptibility mapping: application to 2D echo-planar imaging.

    PubMed

    Wei, Hongjiang; Zhang, Yuyao; Gibbs, Eric; Chen, Nan-Kuei; Wang, Nian; Liu, Chunlei

    2017-04-01

    Quantitative susceptibility mapping (QSM) measures tissue magnetic susceptibility and typically relies on time-consuming three-dimensional (3D) gradient-echo (GRE) MRI. Recent studies have shown that two-dimensional (2D) multi-slice gradient-echo echo-planar imaging (GRE-EPI), which is commonly used in functional MRI (fMRI) and other dynamic imaging techniques, can also be used to produce data suitable for QSM with much shorter scan times. However, the production of high-quality QSM maps is difficult because data obtained by 2D multi-slice scans often have phase inconsistencies across adjacent slices and strong susceptibility field gradients near air-tissue interfaces. To address these challenges in 2D EPI-based QSM studies, we present a new data processing procedure that integrates 2D and 3D phase processing. First, 2D Laplacian-based phase unwrapping and 2D background phase removal are performed to reduce phase inconsistencies between slices and remove in-plane harmonic components of the background phase. This is followed by 3D background phase removal for the through-plane harmonic components. The proposed phase processing was evaluated with 2D EPI data obtained from healthy volunteers, and compared against conventional 3D phase processing using the same 2D EPI datasets. Our QSM results were also compared with QSM values from time-consuming 3D GRE data, which were taken as ground truth. The experimental results show that this new 2D EPI-based QSM technique can produce quantitative susceptibility measures that are comparable with those of 3D GRE-based QSM across different brain regions (e.g. subcortical iron-rich gray matter, cortical gray and white matter). This new 2D EPI QSM reconstruction method is implemented within STI Suite, which is a comprehensive shareware for susceptibility imaging and quantification. Copyright © 2016 John Wiley & Sons, Ltd.

  7. NKG2D receptor and its ligands in host defense

    PubMed Central

    Lanier, Lewis L.

    2015-01-01

    NKG2D is an activating receptor expressed on the surface of natural killer (NK) cells, CD8+ T cells, and subsets of CD4+ T cells, iNKT cells, and γδ T cells. In humans NKG2D transmits signals by its association with the DAP10 adapter subunit and in mice alternatively spliced isoforms transmit signals either using DAP10 or DAP12 adapter subunits. Although NKG2D is encoded by a highly conserved gene (KLRK1) with limited polymorphism, the receptor recognizes an extensive repertoire of ligands, encoded by at least 8 genes in humans (MICA, MICB, RAET1E, RAET1G, RAET1H, RAET1I, RAET1L, and RAET1N), some with extensive allelic polymorphism. Expression of the NKG2D ligands is tightly regulated at the level of transcription, translation, and post-translation. In general healthy adult tissues do not express NKG2D glycoproteins on the cell surface, but these ligands can be induced by hyper-proliferation and transformation, as well as when cells are infected by pathogens. Thus, the NKG2D pathway serves a mechanism for the immune system to detect and eliminate cells that have undergone “stress”. Viruses and tumor cells have devised numerous strategies to evade detection by the NKG2D surveillance system and diversification of the NKG2D ligand genes likely has been driven by selective pressures imposed by pathogens. NKG2D provides an attractive target for therapeutics in the treatment of infectious diseases, cancer, and autoimmune diseases. PMID:26041808

  8. NKG2D Receptor and Its Ligands in Host Defense.

    PubMed

    Lanier, Lewis L

    2015-06-01

    NKG2D is an activating receptor expressed on the surface of natural killer (NK) cells, CD8(+) T cells, and subsets of CD4(+) T cells, invariant NKT cells (iNKT), and γδ T cells. In humans, NKG2D transmits signals by its association with the DAP10 adapter subunit, and in mice alternatively spliced isoforms transmit signals either using DAP10 or DAP12 adapter subunits. Although NKG2D is encoded by a highly conserved gene (KLRK1) with limited polymorphism, the receptor recognizes an extensive repertoire of ligands, encoded by at least eight genes in humans (MICA, MICB, RAET1E, RAET1G, RAET1H, RAET1I, RAET1L, and RAET1N), some with extensive allelic polymorphism. Expression of the NKG2D ligands is tightly regulated at the level of transcription, translation, and posttranslation. In general, healthy adult tissues do not express NKG2D glycoproteins on the cell surface, but these ligands can be induced by hyperproliferation and transformation, as well as when cells are infected by pathogens. Thus, the NKG2D pathway serves as a mechanism for the immune system to detect and eliminate cells that have undergone "stress." Viruses and tumor cells have devised numerous strategies to evade detection by the NKG2D surveillance system, and diversification of the NKG2D ligand genes likely has been driven by selective pressures imposed by pathogens. NKG2D provides an attractive target for therapeutics in the treatment of infectious diseases, cancer, and autoimmune diseases.

  9. 2-D Versus 3-D Magnetotelluric Data Interpretation

    NASA Astrophysics Data System (ADS)

    Ledo, Juanjo

    2005-09-01

    In recent years, the number of publications dealing with the mathematical and physical 3-D aspects of the magnetotelluric method has increased drastically. However, field experiments on a grid are often impractical and surveys are frequently restricted to single or widely separated profiles. So, in many cases we find ourselves with the following question: is the applicability of the 2-D hypothesis valid to extract geoelectric and geological information from real 3-D environments? The aim of this paper is to explore a few instructive but general situations to understand the basics of a 2-D interpretation of 3-D magnetotelluric data and to determine which data subset (TE-mode or TM-mode) is best for obtaining the electrical conductivity distribution of the subsurface using 2-D techniques. A review of the mathematical and physical fundamentals of the electromagnetic fields generated by a simple 3-D structure allows us to prioritise the choice of modes in a 2-D interpretation of responses influenced by 3-D structures. This analysis is corroborated by numerical results from synthetic models and by real data acquired by other authors. One important result of this analysis is that the mode most unaffected by 3-D effects depends on the position of the 3-D structure with respect to the regional 2-D strike direction. When the 3-D body is normal to the regional strike, the TE-mode is affected mainly by galvanic effects, while the TM-mode is affected by galvanic and inductive effects. In this case, a 2-D interpretation of the TM-mode is prone to error. When the 3-D body is parallel to the regional 2-D strike the TE-mode is affected by galvanic and inductive effects and the TM-mode is affected mainly by galvanic effects, making it more suitable for 2-D interpretation. In general, a wise 2-D interpretation of 3-D magnetotelluric data can be a guide to a reasonable geological interpretation.

  10. 1H and 13C NMR signal assignment of cucurbitacin derivatives from Citrullus colocynthis (L.) Schrader and Ecballium elaterium L. (Cucurbitaceae).

    PubMed

    Seger, Christoph; Sturm, Sonja; Mair, Maria-Elisabeth; Ellmerer, Ernst P; Stuppner, Hermann

    2005-06-01

    2D NMR-derived 1H and 13C NMR signal assignments of six structurally closely related cucurbitacin derivatives are presented. The investigated 2-O-beta-D-glucopyranosylcucurbitacins I, J, K, and L were obtained from Citrullus colocynthis (L.) Schrader whereas the aglyca cucurbitacin E and I were isolated from Ecballium elaterium L.

  11. Recent advances in 2D materials for photocatalysis.

    PubMed

    Luo, Bin; Liu, Gang; Wang, Lianzhou

    2016-04-07

    Two-dimensional (2D) materials have attracted increasing attention for photocatalytic applications because of their unique thickness dependent physical and chemical properties. This review gives a brief overview of the recent developments concerning the chemical synthesis and structural design of 2D materials at the nanoscale and their applications in photocatalytic areas. In particular, recent progress on the emerging strategies for tailoring 2D material-based photocatalysts to improve their photo-activity including elemental doping, heterostructure design and functional architecture assembly is discussed.

  12. Comparison of 2D and 3D gamma analyses

    SciTech Connect

    Pulliam, Kiley B.; Huang, Jessie Y.; Howell, Rebecca M.; Followill, David; Kry, Stephen F.; Bosca, Ryan; O’Daniel, Jennifer

    2014-02-15

    Purpose: As clinics begin to use 3D metrics for intensity-modulated radiation therapy (IMRT) quality assurance, it must be noted that these metrics will often produce results different from those produced by their 2D counterparts. 3D and 2D gamma analyses would be expected to produce different values, in part because of the different search space available. In the present investigation, the authors compared the results of 2D and 3D gamma analysis (where both datasets were generated in the same manner) for clinical treatment plans. Methods: Fifty IMRT plans were selected from the authors’ clinical database, and recalculated using Monte Carlo. Treatment planning system-calculated (“evaluated dose distributions”) and Monte Carlo-recalculated (“reference dose distributions”) dose distributions were compared using 2D and 3D gamma analysis. This analysis was performed using a variety of dose-difference (5%, 3%, 2%, and 1%) and distance-to-agreement (5, 3, 2, and 1 mm) acceptance criteria, low-dose thresholds (5%, 10%, and 15% of the prescription dose), and data grid sizes (1.0, 1.5, and 3.0 mm). Each comparison was evaluated to determine the average 2D and 3D gamma, lower 95th percentile gamma value, and percentage of pixels passing gamma. Results: The average gamma, lower 95th percentile gamma value, and percentage of passing pixels for each acceptance criterion demonstrated better agreement for 3D than for 2D analysis for every plan comparison. The average difference in the percentage of passing pixels between the 2D and 3D analyses with no low-dose threshold ranged from 0.9% to 2.1%. Similarly, using a low-dose threshold resulted in a difference between the mean 2D and 3D results, ranging from 0.8% to 1.5%. The authors observed no appreciable differences in gamma with changes in the data density (constant difference: 0.8% for 2D vs 3D). Conclusions: The authors found that 3D gamma analysis resulted in up to 2.9% more pixels passing than 2D analysis. It must

  13. Determining Transition State Geometries in Liquids Using 2D-IR

    SciTech Connect

    Harris, Charles; Cahoon, James F.; Sawyer, Karma R.; Schlegel, Jacob P.; Harris, Charles B.

    2007-12-11

    Many properties of chemical reactions are determined by the transition state connecting reactant and product, yet it is difficult to directly obtain any information about these short-lived structures in liquids. We show that two-dimensional infrared (2D-IR) spectroscopy can provide direct information about transition states by tracking the transformation of vibrational modes as a molecule crossed a transition state. We successfully monitored a simple chemical reaction, the fluxional rearrangement of Fe(CO)5, in which the exchange of axial and equatorial CO ligands causes an exchange of vibrational energy between the normal modes of the molecule. This energy transfer provides direct evidence regarding the time scale, transition state, and mechanism of the reaction.

  14. Remote NMR/MRI detection of laser polarized gases

    SciTech Connect

    Pines, Alexander; Saxena, Sunil; Moule, Adam; Spence, Megan; Seeley, Juliette A.; Pierce, Kimberly L.; Han, Song-I; Granwehr, Josef

    2006-06-13

    An apparatus and method for remote NMR/MRI spectroscopy having an encoding coil with a sample chamber, a supply of signal carriers, preferably hyperpolarized xenon and a detector allowing the spatial and temporal separation of signal preparation and signal detection steps. This separation allows the physical conditions and methods of the encoding and detection steps to be optimized independently. The encoding of the carrier molecules may take place in a high or a low magnetic field and conventional NMR pulse sequences can be split between encoding and detection steps. In one embodiment, the detector is a high magnetic field NMR apparatus. In another embodiment, the detector is a superconducting quantum interference device. A further embodiment uses optical detection of Rb--Xe spin exchange. Another embodiment uses an optical magnetometer using non-linear Faraday rotation. Concentration of the signal carriers in the detector can greatly improve the signal to noise ratio.

  15. Heteronuclear NMR assignments and secondary structure of the coiled coil trimerization domain from cartilage matrix protein in oxidized and reduced forms.

    PubMed Central

    Wiltscheck, R.; Kammerer, R. A.; Dames, S. A.; Schulthess, T.; Blommers, M. J.; Engel, J.; Alexandrescu, A. T.

    1997-01-01

    The C-terminal oligomerization domain of chicken cartilage matrix protein is a trimeric coiled coil comprised of three identical 43-residue chains. NMR spectra of the protein show equivalent magnetic environments for each monomer, indicating a parallel coiled coil structure with complete threefold symmetry. Sequence-specific assignments for 1H-, 15N-, and 13C-NMR resonances have been obtained from 2D 1H NOESY and TOCSY spectra, and from 3D HNCA, 15N NOESY-HSQC, and HCCH-TOCSY spectra. A stretch of alpha-helix encompassing five heptad repeats (35 residues) has been identified from intra-chain HN-HN and HN-H alpha NOE connectivities. 3JHNH alpha coupling constants, and chemical shift indices. The alpha-helix begins immediately downstream of inter-chain disulfide bonds between residues Cys 5 and Cys 7, and extends to near the C-terminus of the molecule. The threefold symmetry of the molecule is maintained when the inter-chain disulfide bonds that flank the N-terminus of the coiled coil are reduced. Residues Ile 21 through Glu 36 show conserved chemical shifts and NOE connectivities, as well as strong protection from solvent exchange in the oxidized and reduced forms of the protein. By contrast, residues Ile 10 through Val 17 show pronounced chemical shift differences between the oxidized and reduced protein. Strong chemical exchange NOEs between HN resonances and water indicate solvent exchange on time scales faster than 10 s, and suggests a dynamic fraying of the N-terminus of the coiled coil upon reduction of the disulfide bonds. Possible roles for the disulfide crosslinks of the oligomerization domain in the function of cartilage matrix protein are proposed. PMID:9260286

  16. Probing dynamics and mechanism of exchange process of quaternary ammonium dimeric surfactants, 14-s-14, in the presence of conventional surfactants.

    PubMed

    Liu, Jun; Jiang, Yan; Chen, Hong; Mao, Shi Zhen; Du, You Ru; Liu, Mai Li

    2012-12-27

    In this Article, we investigated effects of different types of conventional surfactants on exchange dynamics of quaternary ammonium dimeric surfactants, with chemical formula C(14)H(29)N(+)(CH(3))(2)- (CH(2))(s)-N(+)(CH(3))(2)C(14)H(29)·2Br(-), or 14-s-14 for short. Two nonionic surfactants, TritonX-100 (TX-100) and polyethylene glycol (23) laurylether (Brij-35), and one cationic surfactant, n-tetradecyltrimethyl ammonium bromide (TTAB), and one ionic surfactant, sodium dodecyl sulfate (SDS) were chosen as typical conventional surfactants. Exchange rates of 14-s-14 (s = 2, 3, and 4) between the micelle form and monomer in solution were detected by two NMR methods: one-dimensional (1D) line shape analysis and two-dimensional (2D) exchange spectroscopy (EXSY). Results show that the nonionic surfactants (TX-100 and Brij-35), the cationic surfactant (TTAB), and the ionic surfactant (SDS) respectively accelerated, barely influenced, and slowed the exchange rate of 14-s-14. The effect mechanism was investigated by the self-diffusion experiment, relaxation time measurements (T(2)/T(1)), the fluorescence experiment (I(1)/I(3)) and observed chemical shift variations. Results reveal that, nonionic conventional surfactants (TX-100 and Brij-35) loosened the molecule arrangement and decreased hydrophobic interactions in the micelle, and thus accelerated the exchange rate of 14-s-14. The cationic conventional surfactant (TTAB) barely changed the molecule arrangement and thus barely influenced the exchange rate of 14-s-14. The ionic conventional surfactant (SDS) introduced the electrostatic attraction effect, tightened the molecule arrangement, and increased hydrophobic interactions in the micelle, and thus slowed down the exchange rate of 14-s-14. Additionally, the two-step exchange mechanism of 14-s-14 in the mixed solution was revealed through interesting variation tendencies of exchange rates of 14-s-14.

  17. Double resonance rotational spectroscopy of CH2D+

    NASA Astrophysics Data System (ADS)

    Töpfer, Matthias; Jusko, Pavol; Schlemmer, Stephan; Asvany, Oskar

    2016-09-01

    Context. Deuterated forms of CH are thought to be responsible for deuterium enrichment in lukewarm astronomical environments. There is no unambiguous detection of CH2D+ in space to date. Aims: Four submillimetre rotational lines of CH2D+ are documented in the literature. Our aim is to present a complete dataset of highly resolved rotational lines, including millimetre (mm) lines needed for a potential detection. Methods: We used a low-temperature ion trap and applied a novel IR-mm-wave double resonance method to measure the rotational lines of CH2D+. Results: We measured 21 low-lying (J ≤ 4) rotational transitions of CH2D+ between 23 GHz and 1.1 THz with accuracies close to 2 ppb.

  18. Recovering 3D particle size distributions from 2D sections

    NASA Astrophysics Data System (ADS)

    Cuzzi, Jeffrey N.; Olson, Daniel M.

    2017-03-01

    We discuss different ways to convert observed, apparent particle size distributions from 2D sections (thin sections, SEM maps on planar surfaces, etc.) into true 3D particle size distributions. We give a simple, flexible, and practical method to do this; show which of these techniques gives the most faithful conversions; and provide (online) short computer codes to calculate both 2D-3D recoveries and simulations of 2D observations by random sectioning. The most important systematic bias of 2D sectioning, from the standpoint of most chondrite studies, is an overestimate of the abundance of the larger particles. We show that fairly good recoveries can be achieved from observed size distributions containing 100-300 individual measurements of apparent particle diameter.

  19. Phonon thermal conduction in novel 2D materials

    NASA Astrophysics Data System (ADS)

    Xu, Xiangfan; Chen, Jie; Li, Baowen

    2016-12-01

    Recently, there has been increasing interest in phonon thermal transport in low-dimensional materials, due to the crucial importance of dissipating and managing heat in micro- and nano-electronic devices. Significant progress has been achieved for one-dimensional (1D) systems, both theoretically and experimentally. However, the study of heat conduction in two-dimensional (2D) systems is still in its infancy due to the limited availability of 2D materials and the technical challenges of fabricating suspended samples that are suitable for thermal measurements. In this review, we outline different experimental techniques and theoretical approaches for phonon thermal transport in 2D materials, discuss the problems and challenges of phonon thermal transport measurements and provide a comparison between existing experimental data. Special attention will be given to the effects of size, dimensionality, anisotropy and mode contributions in novel 2D systems, including graphene, boron nitride, MoS2, black phosphorous and silicene.

  20. Recent developments in 2D layered inorganic nanomaterials for sensing

    NASA Astrophysics Data System (ADS)

    Kannan, Padmanathan Karthick; Late, Dattatray J.; Morgan, Hywel; Rout, Chandra Sekhar

    2015-08-01

    Two dimensional layered inorganic nanomaterials (2D-LINs) have recently attracted huge interest because of their unique thickness dependent physical and chemical properties and potential technological applications. The properties of these layered materials can be tuned via both physical and chemical processes. Some 2D layered inorganic nanomaterials like MoS2, WS2 and SnS2 have been recently developed and employed in various applications, including new sensors because of their layer-dependent electrical properties. This article presents a comprehensive overview of recent developments in the application of 2D layered inorganic nanomaterials as sensors. Some of the salient features of 2D materials for different sensing applications are discussed, including gas sensing, electrochemical sensing, SERS and biosensing, SERS sensing and photodetection. The working principles of the sensors are also discussed together with examples.

  1. Phonon thermal conduction in novel 2D materials.

    PubMed

    Xu, Xiangfan; Chen, Jie; Li, Baowen

    2016-12-07

    Recently, there has been increasing interest in phonon thermal transport in low-dimensional materials, due to the crucial importance of dissipating and managing heat in micro- and nano-electronic devices. Significant progress has been achieved for one-dimensional (1D) systems, both theoretically and experimentally. However, the study of heat conduction in two-dimensional (2D) systems is still in its infancy due to the limited availability of 2D materials and the technical challenges of fabricating suspended samples that are suitable for thermal measurements. In this review, we outline different experimental techniques and theoretical approaches for phonon thermal transport in 2D materials, discuss the problems and challenges of phonon thermal transport measurements and provide a comparison between existing experimental data. Special attention will be given to the effects of size, dimensionality, anisotropy and mode contributions in novel 2D systems, including graphene, boron nitride, MoS2, black phosphorous and silicene.

  2. Exact Solution of Ising Model in 2d Shortcut Network

    NASA Astrophysics Data System (ADS)

    Shanker, O.

    We give the exact solution to the Ising model in the shortcut network in the 2D limit. The solution is found by mapping the model to the square lattice model with Brascamp and Kunz boundary conditions.

  3. Technical Review of the UNET2D Hydraulic Model

    SciTech Connect

    Perkins, William A.; Richmond, Marshall C.

    2009-05-18

    The Kansas City District of the US Army Corps of Engineers is engaged in a broad range of river management projects that require knowledge of spatially-varied hydraulic conditions such as velocities and water surface elevations. This information is needed to design new structures, improve existing operations, and assess aquatic habitat. Two-dimensional (2D) depth-averaged numerical hydraulic models are a common tool that can be used to provide velocity and depth information. Kansas City District is currently using a specific 2D model, UNET2D, that has been developed to meet the needs of their river engineering applications. This report documents a tech- nical review of UNET2D.

  4. Reconstruction-based 3D/2D image registration.

    PubMed

    Tomazevic, Dejan; Likar, Bostjan; Pernus, Franjo

    2005-01-01

    In this paper we present a novel 3D/2D registration method, where first, a 3D image is reconstructed from a few 2D X-ray images and next, the preoperative 3D image is brought into the best possible spatial correspondence with the reconstructed image by optimizing a similarity measure. Because the quality of the reconstructed image is generally low, we introduce a novel asymmetric mutual information similarity measure, which is able to cope with low image quality as well as with different imaging modalities. The novel 3D/2D registration method has been evaluated using standardized evaluation methodology and publicly available 3D CT, 3DRX, and MR and 2D X-ray images of two spine phantoms, for which gold standard registrations were known. In terms of robustness, reliability and capture range the proposed method outperformed the gradient-based method and the method based on digitally reconstructed radiographs (DRRs).

  5. Alloyed 2D Metal-Semiconductor Atomic Layer Junctions.

    PubMed

    Kim, Ah Ra; Kim, Yonghun; Nam, Jaewook; Chung, Hee-Suk; Kim, Dong Jae; Kwon, Jung-Dae; Park, Sang Won; Park, Jucheol; Choi, Sun Young; Lee, Byoung Hun; Park, Ji Hyeon; Lee, Kyu Hwan; Kim, Dong-Ho; Choi, Sung Mook; Ajayan, Pulickel M; Hahm, Myung Gwan; Cho, Byungjin

    2016-03-09

    Heterostructures of compositionally and electronically variant two-dimensional (2D) atomic layers are viable building blocks for ultrathin optoelectronic devices. We show that the composition of interfacial transition region between semiconducting WSe2 atomic layer channels and metallic NbSe2 contact layers can be engineered through interfacial doping with Nb atoms. WxNb1-xSe2 interfacial regions considerably lower the potential barrier height of the junction, significantly improving the performance of the corresponding WSe2-based field-effect transistor devices. The creation of such alloyed 2D junctions between dissimilar atomic layer domains could be the most important factor in controlling the electronic properties of 2D junctions and the design and fabrication of 2D atomic layer devices.

  6. Dominant 2D magnetic turbulence in the solar wind

    NASA Technical Reports Server (NTRS)

    Bieber, John W.; Wanner, Wolfgang; Matthaeus, William H.

    1995-01-01

    There have been recent suggestions that solar wind magnetic turbulence may be a composite of slab geometry (wavevector aligned with the mean magnetic field) and 2D geometry (wavevectors perpendicular to the mean field). We report results of two new tests of this hypothesis using Helios measurements of inertial ranged magnetic spectra in the solar wind. The first test is based upon a characteristic difference between perpendicular and parallel reduced power spectra which is expected for the 2D component but not for the slab component. The second test examines the dependence of power spectrum density upon the magnetic field angle (i.e., the angle between the mean magnetic field and the radial direction), a relationship which is expected to be in opposite directions for the slab and 2D components. Both tests support the presence of a dominant (approximately 85 percent by energy) 2D component in solar wind magnetic turbulence.

  7. Studying Zeolite Catalysts with a 2D Model System

    SciTech Connect

    Boscoboinik, Anibal

    2016-12-07

    Anibal Boscoboinik, a materials scientist at Brookhaven’s Center for Functional Nanomaterials, discusses the surface-science tools and 2D model system he uses to study catalysis in nanoporous zeolites, which catalyze reactions in many industrial processes.

  8. ORION96. 2-d Finite Element Code Postprocessor

    SciTech Connect

    Sanford, L.A.; Hallquist, J.O.

    1992-02-02

    ORION is an interactive program that serves as a postprocessor for the analysis programs NIKE2D, DYNA2D, TOPAZ2D, and CHEMICAL TOPAZ2D. ORION reads binary plot files generated by the two-dimensional finite element codes currently used by the Methods Development Group at LLNL. Contour and color fringe plots of a large number of quantities may be displayed on meshes consisting of triangular and quadrilateral elements. ORION can compute strain measures, interface pressures along slide lines, reaction forces along constrained boundaries, and momentum. ORION has been applied to study the response of two-dimensional solids and structures undergoing finite deformations under a wide variety of large deformation transient dynamic and static problems and heat transfer analyses.

  9. Emerging and potential opportunities for 2D flexible nanoelectronics

    NASA Astrophysics Data System (ADS)

    Zhu, Weinan; Park, Saungeun; Akinwande, Deji

    2016-05-01

    The last 10 years have seen the emergence of two-dimensional (2D) nanomaterials such as graphene, transition metal dichalcogenides (TMDs), and black phosphorus (BP) among the growing portfolio of layered van der Waals thin films. Graphene, the prototypical 2D material has advanced rapidly in device, circuit and system studies that has resulted in commercial large-area applications. In this work, we provide a perspective of the emerging and potential translational applications of 2D materials including semiconductors, semimetals, and insulators that comprise the basic material set for diverse nanosystems. Applications include RF transceivers, smart systems, the so-called internet of things, and neurotechnology. We will review the DC and RF electronic performance of graphene and BP thin film transistors. 2D materials at sub-um channel length have so far enabled cut-off frequencies from baseband to 100GHz suitable for low-power RF and sub-THz concepts.

  10. NMR metabolic fingerprints of murine melanocyte and melanoma cell lines: application to biomarker discovery.

    PubMed

    Santana-Filho, Arquimedes Paixão de; Jacomasso, Thiago; Riter, Daniel Suss; Barison, Andersson; Iacomini, Marcello; Winnischofer, Sheila Maria Brochado; Sassaki, Guilherme Lanzi

    2017-02-15

    Melanoma is the most aggressive type of skin cancer and efforts to improve the diagnosis of this neoplasia are largely based on the use of cell lines. Metabolomics is currently undergoing great advancements towards its use to screening for disease biomarkers. Although NMR metabolomics includes both 1D and 2D methodologies, there is a lack of data in the literature regarding heteronuclear 2D NMR assignments of the metabolome from eukaryotic cell lines. The present study applied NMR-based metabolomics strategies to characterize aqueous and lipid extracts from murine melanocytes and melanoma cell lines with distinct tumorigenic potential, successfully obtaining fingerprints of the metabolites from the extracts of the cell lines by means of 2D NMR HSQC correlation maps. Relative amounts of the identified metabolites were compared between the 4 cell lines. Multivariate analysis of (1)H NMR data was able not only to differentiate the melanocyte cell line from the tumorigenic ones but also distinguish among the 3 tumorigenic cell lines. We also investigated the effects of mitogenic agents, and found that they can markedly influence the metabolome of the melanocyte cell line, resembling the pattern of most proliferative cell lines.

  11. NMR metabolic fingerprints of murine melanocyte and melanoma cell lines: application to biomarker discovery

    PubMed Central

    Santana-Filho, Arquimedes Paixão de; Jacomasso, Thiago; Riter, Daniel Suss; Barison, Andersson; Iacomini, Marcello; Winnischofer, Sheila Maria Brochado; Sassaki, Guilherme Lanzi

    2017-01-01

    Melanoma is the most aggressive type of skin cancer and efforts to improve the diagnosis of this neoplasia are largely based on the use of cell lines. Metabolomics is currently undergoing great advancements towards its use to screening for disease biomarkers. Although NMR metabolomics includes both 1D and 2D methodologies, there is a lack of data in the literature regarding heteronuclear 2D NMR assignments of the metabolome from eukaryotic cell lines. The present study applied NMR-based metabolomics strategies to characterize aqueous and lipid extracts from murine melanocytes and melanoma cell lines with distinct tumorigenic potential, successfully obtaining fingerprints of the metabolites from the extracts of the cell lines by means of 2D NMR HSQC correlation maps. Relative amounts of the identified metabolites were compared between the 4 cell lines. Multivariate analysis of 1H NMR data was able not only to differentiate the melanocyte cell line from the tumorigenic ones but also distinguish among the 3 tumorigenic cell lines. We also investigated the effects of mitogenic agents, and found that they can markedly influence the metabolome of the melanocyte cell line, resembling the pattern of most proliferative cell lines. PMID:28198377

  12. Structure elucidation and NMR assignments of two unusual monoterpene indole alkaloids from Psychotria stachyoides.

    PubMed

    Pimenta, Antonia Torres Avila; Braz-Filho, Raimundo; Delprete, Piero Giuseppe; de Souza, Elnatan Bezerra; Silveira, Edilberto Rocha; Lima, Mary Anne Sousa

    2010-09-01

    Two unusual monoterpene indole alkaloids, stachyoside (1) and nor-methyl-23-oxo-correantoside (2), have been isolated from the aerial parts of Psychotria stachyoides. The structural elucidation of both compounds was performed by the aid of HRESIMS, FT-IR, and 1D- and 2D-NMR techniques including COSY, HSQC, HMBC, and NOESY.

  13. Anisotropic 2D Materials for Tunable Hyperbolic Plasmonics.

    PubMed

    Nemilentsau, Andrei; Low, Tony; Hanson, George

    2016-02-12

    Motivated by the recent emergence of a new class of anisotropic 2D materials, we examine their electromagnetic modes and demonstrate that a broad class of the materials can host highly directional hyperbolic plasmons. Their propagation direction can be manipulated on the spot by gate doping, enabling hyperbolic beam reflection, refraction, and bending. The realization of these natural 2D hyperbolic media opens up a new avenue in dynamic control of hyperbolic plasmons not possible in the 3D version.

  14. RNA folding pathways and kinetics using 2D energy landscapes.

    PubMed

    Senter, Evan; Dotu, Ivan; Clote, Peter

    2015-01-01

    RNA folding pathways play an important role in various biological processes, such as (i) the hok/sok (host-killing/suppression of killing) system in E. coli to check for sufficient plasmid copy number, (ii) the conformational switch in spliced leader (SL) RNA from Leptomonas collosoma, which controls trans splicing of a portion of the '5 exon, and (iii) riboswitches--portions of the 5' untranslated region of messenger RNA that regulate genes by allostery. Since RNA folding pathways are determined by the energy landscape, we describe a novel algorithm, FFTbor2D, which computes the 2D projection of the energy landscape for a given RNA sequence. Given two metastable secondary structures A, B for a given RNA sequence, FFTbor2D computes the Boltzmann probability p(x, y) = Z(x,y)/Z that a secondary structure has base pair distance x from A and distance y from B. Using polynomial interpolationwith the fast Fourier transform,we compute p(x, y) in O(n(5)) time and O(n(2)) space, which is an improvement over an earlier method, which runs in O(n(7)) time and O(n(4)) space. FFTbor2D has potential applications in synthetic biology, where one might wish to design bistable switches having target metastable structures A, B with favorable pathway kinetics. By inverting the transition probability matrix determined from FFTbor2D output, we show that L. collosoma spliced leader RNA has larger mean first passage time from A to B on the 2D energy landscape, than 97.145% of 20,000 sequences, each having metastable structures A, B. Source code and binaries are freely available for download at http://bioinformatics.bc.edu/clotelab/FFTbor2D. The program FFTbor2D is implemented in C++, with optional OpenMP parallelization primitives.

  15. Supported and Free-Standing 2D Semimetals

    DTIC Science & Technology

    2015-01-15

    of this effort on focusing on rare- earth arsenides (RE-A), although not a van der Waals 2D solid, nonetheless, exhibits substantial 2D quantum size...this effort on focusing on rare- earth arsenides (RE- A), although not a van der Waals 20 solid, nonetheless, exhibits substantial 20 quantum size...Brongersma and S.R. Bank, "Rare- earth monopnictide alloys for tunable, epitaxial metals" in preparation. iii. S. Rahimi, E. M. Krivoy, J. Lee, M. E

  16. Application of 2-D graphical representation of DNA sequence

    NASA Astrophysics Data System (ADS)

    Liao, Bo; Tan, Mingshu; Ding, Kequan

    2005-10-01

    Recently, we proposed a 2-D graphical representation of DNA sequence [Bo Liao, A 2-D graphical representation of DNA sequence, Chem. Phys. Lett. 401 (2005) 196-199]. Based on this representation, we consider properties of mutations and compute the similarities among 11 mitochondrial sequences belonging to different species. The elements of the similarity matrix are used to construct phylogenic tree. Unlike most existing phylogeny construction methods, the proposed method does not require multiple alignment.

  17. phase_space_cosmo_fisher: Fisher matrix 2D contours

    NASA Astrophysics Data System (ADS)

    Stark, Alejo

    2016-11-01

    phase_space_cosmo_fisher produces Fisher matrix 2D contours from which the constraints on cosmological parameters can be derived. Given a specified redshift array and cosmological case, 2D marginalized contours of cosmological parameters are generated; the code can also plot the derivatives used in the Fisher matrix. In addition, this package can generate 3D plots of qH^2 and other cosmological quantities as a function of redshift and cosmology.

  18. A simultaneous 2D/3D autostereo workstation

    NASA Astrophysics Data System (ADS)

    Chau, Dennis; McGinnis, Bradley; Talandis, Jonas; Leigh, Jason; Peterka, Tom; Knoll, Aaron; Sumer, Aslihan; Papka, Michael; Jellinek, Julius

    2012-03-01

    We present a novel immersive workstation environment that scientists can use for 3D data exploration and as their everyday 2D computer monitor. Our implementation is based on an autostereoscopic dynamic parallax barrier 2D/3D display, interactive input devices, and a software infrastructure that allows client/server software modules to couple the workstation to scientists' visualization applications. This paper describes the hardware construction and calibration, software components, and a demonstration of our system in nanoscale materials science exploration.

  19. Phylogenetic tree construction based on 2D graphical representation

    NASA Astrophysics Data System (ADS)

    Liao, Bo; Shan, Xinzhou; Zhu, Wen; Li, Renfa

    2006-04-01

    A new approach based on the two-dimensional (2D) graphical representation of the whole genome sequence [Bo Liao, Chem. Phys. Lett., 401(2005) 196.] is proposed to analyze the phylogenetic relationships of genomes. The evolutionary distances are obtained through measuring the differences among the 2D curves. The fuzzy theory is used to construct phylogenetic tree. The phylogenetic relationships of H5N1 avian influenza virus illustrate the utility of our approach.

  20. THz Dynamic Nuclear Polarization NMR

    PubMed Central

    Nanni, Emilio A.; Barnes, Alexander B.; Griffin, Robert G.; Temkin, Richard J.

    2013-01-01

    Dynamic nuclear polarization (DNP) increases the sensitivity of nuclear magnetic resonance (NMR) spectroscopy by using high frequency microwaves to transfer the polarization of the electrons to the nuclear spins. The enhancement in NMR sensitivity can amount to a factor of well above 100, enabling faster data acquisition and greatly improved NMR measurements. With the increasing magnetic fields (up to 23 T) used in NMR research, the required frequency for DNP falls into the THz band (140–600 GHz). Gyrotrons have been developed to meet the demanding specifications for DNP NMR, including power levels of tens of watts; frequency stability of a few megahertz; and power stability of 1% over runs that last for several days to weeks. Continuous gyrotron frequency tuning of over 1 GHz has also been demonstrated. The complete DNP NMR system must include a low loss transmission line; an optimized antenna; and a holder for efficient coupling of the THz radiation to the sample. This paper describes the DNP NMR process and illustrates the THz systems needed for this demanding spectroscopic application. THz DNP NMR is a rapidly developing, exciting area of THz science and technology. PMID:24639915

  1. Mg NMR in DNA solutions: Dominance of site binding effects.

    PubMed

    Rose, D M; Bleam, M L; Record, M T; Bryant, R G

    1980-11-01

    (25)Mg NMR spectroscopy is applied to a study of magnesium ion interactions with DNA, which is considered as a model for a linear polyelectrolyte. It is demonstrated that the magnesium ion spectrum is complicated by a non-Lorent-zian line shape and is dominated by the effects of chemical exchange with macromolecule binding sites. A distinction is made between specific-site interactions in which the magnesium ion loses a water molecule from the first coordination sphere on binding and those interactions, referred to as territorial binding, in which the ion maintains its first coordination sphere complement of solvent. The first type of site-binding interactions are shown to dominate the magnesium ion NMR spectrum, based on a consideration of the magnitudes of the observed (25)Mg relaxation rates compared with (23)Na relaxation rates, the clear contributions of chemical exchange-limited relaxation, and an ion displacement experiment employing sodium.

  2. Regulation of NKG2D ligand gene expression.

    PubMed

    Eagle, Robert A; Traherne, James A; Ashiru, Omodele; Wills, Mark R; Trowsdale, John

    2006-03-01

    The activating immunoreceptor NKG2D has seven known host ligands encoded by the MHC class I chain-related MIC and ULBP/RAET genes. Why there is such diversity of NKG2D ligands is not known but one hypothesis is that they are differentially expressed in different tissues in response to different stresses. To explore this, we compared expression patterns and promoters of NKG2D ligand genes. ULBP/RAET genes were transcribed independent of each other in a panel of cell lines. ULBP/RAET gene expression was upregulated on infection with human cytomegalovirus; however, a clinical strain, Toledo, induced expression more slowly than did a laboratory strain, AD169. ULBP4/RAET1E was not induced by infection with either strain. To investigate the mechanisms behind the similarities and differences in NKG2D ligand gene expression a comparative sequence analysis of NKG2D ligand gene putative promoter regions was conducted. Sequence alignments demonstrated that there was significant sequence diversity; however, one region of high similarity between most of the genes is evident. This region contains a number of potential transcription factor binding sites, including those involved in shock responses and sites for retinoic acid-induced factors. Promoters of some NKG2D ligand genes are polymorphic and several sequence alterations in these alleles abolished putative transcription factor binding.

  3. CYP2D6 variability in populations from Venezuela.

    PubMed

    Moreno, Nancy; Flores-Angulo, Carlos; Villegas, Cecilia; Mora, Yuselin

    2016-12-01

    CYP2D6 is an important cytochrome P450 enzyme that plays an important role in the metabolism of about 25% of currently prescribed drugs. The presence of polymorphisms in the CYP2D6 gene may modulate enzyme level and activity, thereby affecting individual responses to pharmacological treatments. The most prevalent diseases in the admixed population from Venezuela are cardiovascular and cancer, whereas viral, bacterial and parasitic diseases, particularly malaria, are prevalent in Amerindian populations; in the treatment of these diseases, several drugs that are metabolized by CYP2D6 are used. In this work, we reviewed the data on CYP2D6 variability and predicted metabolizer phenotypes, in healthy volunteers of two admixed and five Amerindian populations from Venezuela. The Venezuelan population is very heterogeneous as a result of the genetic admixture of three major ethnical components: Europeans, Africans and Amerindians. There are noticeable inter-regional and inter-population differences in the process of mixing of this population. Hitherto, there are few published studies in Venezuela on CYP2D6; therefore, it is necessary to increase research in this regard, in particular to develop studies with a larger sample size. There is a considerable amount of work remaining before CYP2D6 is integrated into clinical practice in Venezuela.

  4. 2D microscopic model of graphene fracture properties

    NASA Astrophysics Data System (ADS)

    Hess, Peter

    2015-05-01

    An analytical two-dimensional (2D) microscopic fracture model based on Morse-type interaction is derived containing no adjustable parameter. From the 2D Young’s moduli and 2D intrinsic strengths of graphene measured by nanoindentation based on biaxial tension and calculated by density functional theory for uniaxial tension the widely unknown breaking force, line or edge energy, surface energy, fracture toughness, and strain energy release rate were determined. The simulated line energy agrees well with ab initio calculations and the fracture toughness of perfect graphene sheets is in good agreement with molecular dynamics simulations and the fracture toughness evaluated for defective graphene using the Griffith relation. Similarly, the estimated critical strain energy release rate agrees well with result of various theoretical approaches based on the J-integral and surface energy. The 2D microscopic model, connecting 2D and three-dimensional mechanical properties in a consistent way, provides a versatile relationship to easily access all relevant fracture properties of pristine 2D solids.

  5. Simultaneous measurement of J(HH) and two different (n)J(CH) coupling constants from a single multiply edited 2D cross-peak.

    PubMed

    Saurí, Josep; Parella, Teodor

    2013-07-01

    Three different J-editing methods (IPAP, E.COSY and J-resolved) are implemented in a single NMR experiment to provide spin-state-edited 2D cross-peaks from which a simultaneous measurement of different homonuclear and heteronuclear coupling constants can be performed. A new J-selHSQMBC-IPAP experiment is proposed for the independent measurement of two different (n)J(CH) coupling constants along the F2 and F1 dimensions of the same 2D cross-peak. In addition, the E.COSY pattern provides additional information about the magnitude and relative sign between J(HH) and (n)J(CH) coupling constants.

  6. Establishing resolution-improved NMR spectroscopy in high magnetic fields with unknown spatiotemporal variations

    SciTech Connect

    Zhang, Zhiyong; Cai, Shuhui; Zheng, Zhenyao; Lin, Yulan E-mail: lylfj2005@xmu.edu.cn; Chen, Zhong E-mail: lylfj2005@xmu.edu.cn; Smith, Pieter E. S.

    2015-12-28

    A half-century quest for higher magnetic fields has been an integral part of the progress undergone in the Nuclear Magnetic Resonance (NMR) study of materials’ structure and dynamics. Because 2D NMR relies on systematic changes in coherences’ phases as a function of an encoding time varied over a series of independent experiments, it generally cannot be applied in temporally unstable fields. This precludes most NMR methods from being used to characterize samples situated in hybrid or resistive magnets that are capable of achieving extremely high magnetic field strength. Recently, “ultrafast” NMR has been developed into an effective and widely applicable methodology enabling the acquisition of a multidimensional NMR spectrum in a single scan; it can therefore be used to partially mitigate the effects of temporally varying magnetic fields. Nevertheless, the strong interference of fluctuating fields with the spatial encoding of ultrafast NMR still severely restricts measurement sensitivity and resolution. Here, we introduce a strategy for obtaining high resolution NMR spectra that exploits the immunity of intermolecular zero-quantum coherences (iZQCs) to field instabilities and inhomogeneities. The spatial encoding of iZQCs is combined with a J-modulated detection scheme that removes the influence of arbitrary field inhomogeneities during acquisition. This new method can acquire high-resolution one-dimensional NMR spectra in large inhomogeneous and fluctuating fields, and it is tested with fields experimentally modeled to mimic those of resistive and resistive-superconducting hybrid magnets.

  7. CHEM2D: a two-dimensional, three-phase, nine-component chemical flood simulator. Volume I. CHEM2D technical description and FORTRAN code

    SciTech Connect

    Fanchi, J.R.

    1985-04-01

    Under the sponsorship of the US Department of Energy, a publicly available chemical simulator has been evaluated and substantially enhanced to serve as a useful tool for projecting polymer or chemical flood performance. The program, CHEM2D, is a two-dimensional, three-phase, nine-component finite-difference numerical simulator. It can model primary depletion, waterfloods, polymer floods, and micellar/polymer floods using heterogeneous linear, areal, or cross-sectional reservoir descriptions. The user may specify well performance as either pressure or rate constrained. Both a constant time step size and a variable time step size based on extrapolation of concentration changes are available as options. A solution technique which is implicit in pressure and explicit in saturations and concentrations is used. The major physical mechanisms that are modeled include adsorption, capillary trapping, cation exchange, dilution, dispersion, interfacial tension, binary or ternary phase behavior, non-Newtonian polymer rheology, and two-phase or three-phase relative permeability. Typical components include water, oil, surfactant, polymer, and three ions (chloride, calcium, and sodium). Components may partition amongst the aqueous, oleic, and microemulsion phases. Volume I of this report provides a discussion of the formulation and algorithms used within CHEM2D. Included in Volume I are a number of validation and illustrative examples, as well as the FORTRAN code. The CHEM2D user's manual, Volume II, contains both the input data sets for the examples presented in Volume I and an example output. All appendices and a phase behavior calculation program are collected in Volume III. 20 references.

  8. Folding of a heterogeneous β-hairpin peptide from temperature-jump 2D IR spectroscopy

    PubMed Central

    Jones, Kevin C.; Peng, Chunte Sam; Tokmakoff, Andrei

    2013-01-01

    We provide a time- and structure-resolved characterization of the folding of the heterogeneous β-hairpin peptide Tryptophan Zipper 2 (Trpzip2) using 2D IR spectroscopy. The amide I′ vibrations of three Trpzip2 isotopologues are used as a local probe of the midstrand contacts, β-turn, and overall β-sheet content. Our experiments distinguish between a folded state with a type I′ β-turn and a misfolded state with a bulged turn, providing evidence for distinct conformations of the peptide backbone. Transient 2D IR spectroscopy at 45 °C following a laser temperature jump tracks the nanosecond and microsecond kinetics of unfolding and the exchange between conformers. Hydrogen bonds to the peptide backbone are loosened rapidly compared with the 5-ns temperature jump. Subsequently, all relaxation kinetics are characterized by an observed 1.2 ± 0.2-μs exponential. Our time-dependent 2D IR spectra are explained in terms of folding of either native or nonnative contacts from a common compact disordered state. Conversion from the disordered state to the folded state is consistent with a zip-out folding mechanism. PMID:23382249

  9. Frequency Comb Assisted IR Measurements of H_3^+, H_2D^+ and D_2H^+ Transitions

    NASA Astrophysics Data System (ADS)

    Jusko, Pavol; Asvany, Oskar; Schlemmer, Stephan

    2016-06-01

    We present recent measurements of the fundamental transitions of H_3^+, H_2D^+ and D_2H^+ in a 4 K 22-pole trap by action spectroscopic techniques. Either Laser Induced Inhibition of Cluster Growth (He attachment at T≈4 K), endothermic reaction of H_3^+ with O_2, or deuterium exchange has been used as measurement scheme. We used a 3 μm optical parametric oscillator coupled to a frequency comb in order to achieve accuracy generally below 1 MHz. Five transitions of H_3^+, eleven of H_2D^+ and ten of D_2H^+ were recorder in our spectral range. We compare our H_3^+ results with two previous frequency comb assisted works. Moreover, accurate determination of the frequency allows us to predict pure rotational transitions for H_2D^+ and D_2H^+ in the THz range. P. Jusko, C. Konietzko, S. Schlemmer, O. Asvany, J. Mol. Spec. 319 (2016) 55 O. Asvany, S. Brünken, L. Kluge, S. Schlemmer, Appl. Phys. B 114 (2014) 203 O. Asvany, J. Krieg, S. Schlemmer, Rev. Sci. Instr. 83 (2012) 093110 J.N. Hodges, A.J. Perry, P.A. Jenkins, B.M. Siller, B.J. McCall, J. Chem. Phys. 139 (2013) 164201 H.-C. Chen, C.-Y. Hsiao, J.-L. Peng, T. Amano, J.-T. Shy, Phys. Rev. Lett. 109 (2012) 263002

  10. 2D Hexagonal Boron Nitride (2D-hBN) Explored for the Electrochemical Sensing of Dopamine.

    PubMed

    Khan, Aamar F; Brownson, Dale A C; Randviir, Edward P; Smith, Graham C; Banks, Craig E

    2016-10-04

    Crystalline 2D hexagonal boron nitride (2D-hBN) nanosheets are explored as a potential electrocatalyst toward the electroanalytical sensing of dopamine (DA). The 2D-hBN nanosheets are electrically wired via a drop-casting modification process onto a range of commercially available carbon supporting electrodes, including glassy carbon (GC), boron-doped diamond (BDD), and screen-printed graphitic electrodes (SPEs). 2D-hBN has not previously been explored toward the electrochemical detection/electrochemical sensing of DA. We critically evaluate the potential electrocatalytic performance of 2D-hBN modified electrodes, the effect of supporting carbon electrode platforms, and the effect of "mass coverage" (which is commonly neglected in the 2D material literature) toward the detection of DA. The response of 2D-hBN modified electrodes is found to be largely dependent upon the interaction between 2D-hBN and the underlying supporting electrode material. For example, in the case of SPEs, modification with 2D-hBN (324 ng) improves the electrochemical response, decreasing the electrochemical oxidation potential of DA by ∼90 mV compared to an unmodified SPE. Conversely, modification of a GC electrode with 2D-hBN (324 ng) resulted in an increased oxidation potential of DA by ∼80 mV when compared to the unmodified electrode. We explore the underlying mechanisms of the aforementioned examples and infer that electrode surface interactions and roughness factors are critical considerations. 2D-hBN is utilized toward the sensing of DA in the presence of the common interferents ascorbic acid (AA) and uric acid (UA). 2D-hBN is found to be an effective electrocatalyst in the simultaneous detection of DA and UA at both pH 5.0 and 7.4. The peak separations/resolution between DA and UA increases by ∼70 and 50 mV (at pH 5.0 and 7.4, respectively, when utilizing 108 ng of 2D-hBN) compared to unmodified SPEs, with a particularly favorable response evident in pH 5.0, giving rise to a

  11. Reducing acquisition times in multidimensional NMR with a time-optimized Fourier encoding algorithm.

    PubMed

    Zhang, Zhiyong; Smith, Pieter E S; Frydman, Lucio

    2014-11-21

    Speeding up the acquisition of multidimensional nuclear magnetic resonance (NMR) spectra is an important topic in contemporary NMR, with central roles in high-throughput investigations and analyses of marginally stable samples. A variety of fast NMR techniques have been developed, including methods based on non-uniform sampling and Hadamard encoding, that overcome the long sampling times inherent to schemes based on fast-Fourier-transform (FFT) methods. Here, we explore the potential of an alternative fast acquisition method that leverages a priori knowledge, to tailor polychromatic pulses and customized time delays for an efficient Fourier encoding of the indirect domain of an NMR experiment. By porting the encoding of the indirect-domain to the excitation process, this strategy avoids potential artifacts associated with non-uniform sampling schemes and uses a minimum number of scans equal to the number of resonances present in the indirect dimension. An added convenience is afforded by the fact that a usual 2D FFT can be used to process the generated data. Acquisitions of 2D heteronuclear correlation NMR spectra on quinine and on the anti-inflammatory drug isobutyl propionic phenolic acid illustrate the new method's performance. This method can be readily automated to deal with complex samples such as those occurring in metabolomics, in in-cell as well as in in vivo NMR applications, where speed and temporal stability are often primary concerns.

  12. Reducing acquisition times in multidimensional NMR with a time-optimized Fourier encoding algorithm

    SciTech Connect

    Zhang, Zhiyong; Smith, Pieter E. S.; Frydman, Lucio

    2014-11-21

    Speeding up the acquisition of multidimensional nuclear magnetic resonance (NMR) spectra is an important topic in contemporary NMR, with central roles in high-throughput investigations and analyses of marginally stable samples. A variety of fast NMR techniques have been developed, including methods based on non-uniform sampling and Hadamard encoding, that overcome the long sampling times inherent to schemes based on fast-Fourier-transform (FFT) methods. Here, we explore the potential of an alternative fast acquisition method that leverages a priori knowledge, to tailor polychromatic pulses and customized time delays for an efficient Fourier encoding of the indirect domain of an NMR experiment. By porting the encoding of the indirect-domain to the excitation process, this strategy avoids potential artifacts associated with non-uniform sampling schemes and uses a minimum number of scans equal to the number of resonances present in the indirect dimension. An added convenience is afforded by the fact that a usual 2D FFT can be used to process the generated data. Acquisitions of 2D heteronuclear correlation NMR spectra on quinine and on the anti-inflammatory drug isobutyl propionic phenolic acid illustrate the new method's performance. This method can be readily automated to deal with complex samples such as those occurring in metabolomics, in in-cell as well as in in vivo NMR applications, where speed and temporal stability are often primary concerns.

  13. Towards miniaturization of a structural genomics pipeline using micro-expression and microcoil NMR.

    PubMed

    Peti, Wolfgang; Page, Rebecca; Moy, Kin; O'Neil-Johnson, Mark; Wilson, Ian A; Stevens, Raymond C; Wüthrich, Kurt

    2005-12-01

    In structural genomics centers, nuclear magnetic resonance (NMR) screening is in increasing use as a tool to identify folded proteins that are promising targets for three-dimensional structure determination by X-ray crystallography or NMR spectroscopy. The use of 1D 1H NMR spectra or 2D [1H,15N]-correlation spectroscopy (COSY) typically requires milligram quantities of unlabeled or isotope-labeled protein, respectively. Here, we outline ways towards miniaturization of a structural genomics pipeline with NMR screening for folded globular proteins, using a high-density micro-fermentation device and a microcoil NMR probe. The proteins are micro-expressed in unlabeled or isotope-labeled media, purified, and then subjected to 1D 1H NMR and/or 2D [1H,15N]-COSY screening. To demonstrate that the miniaturization is functioning effectively, we processed nine mouse homologue protein targets and compared the results with those from the "macro-scale" Joint Center of Structural Genomics (JCSG) high-throughput pipeline. The results from the two pipelines were comparable, illustrating that the data were not compromised in the miniaturized approach.

  14. 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.

  15. Mechanisms of amyloid formation revealed by solution NMR

    PubMed Central

    Karamanos, Theodoros K.; Kalverda, Arnout P.; Thompson, Gary S.; Radford, Sheena E.

    2015-01-01

    Amyloid fibrils are proteinaceous elongated aggregates involved in more than fifty human diseases. Recent advances in electron microscopy and solid state NMR have allowed the characterization of fibril structures to different extents of refinement. However, structural details about the mechanism of fibril formation remain relatively poorly defined. This is mainly due to the complex, heterogeneous and transient nature of the species responsible for assembly; properties that make them difficult to detect and characterize in structural detail using biophysical techniques. The ability of solution NMR spectroscopy to investigate exchange between multiple protein states, to characterize transient and low-population species, and to study high molecular weight assemblies, render NMR an invaluable technique for studies of amyloid assembly. In this article we review state-of-the-art solution NMR methods for investigations of: (a) protein dynamics that lead to the formation of aggregation-prone species; (b) amyloidogenic intrinsically disordered proteins; and (c) protein–protein interactions on pathway to fibril formation. Together, these topics highlight the power and potential of NMR to provide atomic level information about the molecular mechanisms of one of the most fascinating problems in structural biology. PMID:26282197

  16. NMR study of strontium binding by a micaceous mineral.

    PubMed

    Bowers, Geoffrey M; Ravella, Ramesh; Komarneni, Sridhar; Mueller, Karl T

    2006-04-13

    The nature of strontium binding by soil minerals directly affects the transport and sequestration/remediation of radioactive strontium species released from leaking high-level nuclear waste storage tanks. However, the molecular-level structure of strontium binding sites has seldom been explored in phyllosilicate minerals by direct spectroscopic means and is not well-understood. In this work, we use solid-state NMR to analyze strontium directly and indirectly in a fully strontium-exchanged synthetic mica of nominal composition Na(4)Mg(6)Al(4)Si(4)O(20)F(4). Thermogravimetric analysis, X-ray diffraction analysis, and NMR evidence supports that heat treatment at 500 degrees C for 4 h fully dehydrates the mica, creating a hydrogen-free interlayer. Analysis of the strontium NMR spectrum of the heat-treated mica shows a single strontium environment with a quadrupolar coupling constant of 9.02 MHz and a quadrupolar asymmetry parameter of 1.0. These quadrupolar parameters are consistent with a highly distorted and asymmetric coordination environment that would be produced by strontium cations without water in the coordination sphere bound deep within the ditrigonal holes. Evidence for at least one additional strontium environment, where proton-strontium couplings may occur, was found via a (1)H-(87)Sr transfer of populations by double resonance NMR experiment. We conclude that the strontium cations in the proton-free interlayer are observable by (87)Sr NMR and bound through electrostatic interactions as nine coordinate inner-sphere complexes sitting in the ditrigonal holes. Partially hydrated strontium cations invisible to direct (87)Sr NMR are also present and located on the external mica surfaces, which are known to hydrate upon exposure to atmospheric moisture. These results demonstrate that modern pulsed NMR techniques and high fields can be used effectively to provide structural details of strontium binding by phyllosilicate minerals.

  17. NMR Study of Strontium Binding by a Micaceous Mineral

    SciTech Connect

    Bowers, Geoffrey M.; Ravella, Ramesh; Komarneni, S.; Mueller, Karl T.

    2006-04-13

    The nature of strontium binding by soil minerals directly affects the transport and sequestration/remediation of radioactive strontium species released from leaking high-level nuclear waste storage tanks. However, the molecular-level structure of strontium binding sites has seldom been explored in phyllosilicate minerals by direct spectroscopic means and is not well-understood. In this work, we use solid-state NMR to analyze strontium directly and indirectly in a fully strontium-exchanged synthetic mica of nominal composition Na4Mg6Al4Si4O20F4. Thermogravimetric analysis, X-ray diffraction analysis, and NMR evidence supports that heat treatment at 500 °C for 4 h fully dehydrates the mica, creating a hydrogen-free interlayer. Analysis of the strontium NMR spectrum of the heat-treated mica shows a single strontium environment with a quadrupolar coupling constant of 9.02 MHz and a quadrupolar asymmetry parameter of 1.0. These quadrupolar parameters are consistent with a highly distorted and asymmetric coordination environment that would be produced by strontium cations without water in the coordination sphere bound deep within the ditrigonal holes. Evidence for at least one additional strontium environment, where proton-strontium couplings may occur, was found via a 1H-87Sr transfer of populations by double resonance NMR experiment. We conclude that the strontium cations in the proton-free interlayer are observable by 87Sr NMR and bound through electrostatic interactions as nine coordinate inner-sphere complexes sitting in the ditrigonal holes. Partially hydrated strontium cations invisible to direct 87Sr NMR are also present and located on the external mica surfaces, which are known to hydrate upon exposure to atmospheric moisture. These results demonstrate that modern pulsed NMR techniques and high fields can be used effectively to provide structural details of strontium binding by phyllosilicate minerals.

  18. Monte Carlo simulations of intragrain spin effects in a quasi-2D Heisenberg model with uniaxial anisotropy.

    PubMed

    Leblanc, M D; Whitehead, J P; Plumer, M L

    2013-05-15

    A combination of Metropolis and modified Wolff cluster algorithms is used to examine the impact of uniaxial single-ion anisotropy on the phase transition to ferromagnetic order of Heisenberg macrospins on a 2D square lattice. This forms the basis of a model for granular perpendicular recording media where macrospins represent the magnetic moment of grains. The focus of this work is on the interplay between anisotropy D, intragrain exchange J' and intergrain exchange J on the ordering temperature T(C) and extends our previous reported analysis of the granular Ising model. The role of intragrain degrees of freedom in heat assisted magnetic recording is discussed.

  19. Monte Carlo simulations of intragrain spin effects in a quasi-2D Heisenberg model with uniaxial anisotropy

    NASA Astrophysics Data System (ADS)

    Leblanc, M. D.; Whitehead, J. P.; Plumer, M. L.

    2013-05-01

    A combination of Metropolis and modified Wolff cluster algorithms is used to examine the impact of uniaxial single-ion anisotropy on the phase transition to ferromagnetic order of Heisenberg macrospins on a 2D square lattice. This forms the basis of a model for granular perpendicular recording media where macrospins represent the magnetic moment of grains. The focus of this work is on the interplay between anisotropy D, intragrain exchange J‧ and intergrain exchange J on the ordering temperature TC and extends our previous reported analysis of the granular Ising model. The role of intragrain degrees of freedom in heat assisted magnetic recording is discussed.

  20. Versatile 1H-31P-31P COSY 2D NMR Techniques for the Characterization of Polyphosphorylated Small Molecules

    PubMed Central

    Majumdar, Ananya; Sun, Yan; Shah, Meha; Freel Meyers, Caren L.

    2010-01-01

    Di- and triphosphorylated small molecules represent key intermediates in a wide range of biological and chemical processes. The importance of polyphosphorylated species in biology and medicine underscores the need to develop methods for the detection and characterization of this compound class. We have reported two-dimensional HPP-COSY spectroscopy techniques to identify diphosphate-containing metabolic intermediates at sub-millimolar concentrations in the methylerythritol phosphate (MEP) isoprenoid biosynthetic pathway.1 In this work, we explore the scope of HPP-COSY based techniques to characterize a diverse group of small organic molecules bearing di- and tri-phosphorylated moieties. These include molecules containing P–O–P and P–C–P connectivities, multivalent P(III)–O–P(V) phosphorus nuclei with widely separated chemical shifts, as well as virtually overlapping 31P resonances exhibiting strong coupling effects. We also demonstrate the utility of these experiments to rapidly distinguish between mono- and diphosphates. A detailed protocol for optimizing these experiments to achieve best performance is presented. PMID:20408590

  1. RAPID 2D NMR METHOD FOR DETERMINING P-COUMARATE AND FERULATE LEVELS IN CORN (AND OTHER GRASS) CELL WALLS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Grass cell wall components are acylated by the hydroxycinnamates p-coumarate and ferulate. p-Coumarates largely acylate lignin sidechains, exclusively at the gamma-position, whereas ferulates primarily acylate the arabinosyl C5-position of arabinoxylans. Such components can be quantified as the corr...

  2. Solid state 1D and 2D NMR spectroscopic investigations of conformational changes of metal phytate compounds

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Phytate (myo-inositol-1,2,3,4,5,6-hexakisphosphate) (IP6) is the major organic phosphorus component in ceral grains, legumes and seeds high in oil. The high chelating ability of phytate decreases the nutritional availabilty of dietary metal ions (e.g., Ca2+, Fe3+ and Zn2+). Phytate could also decrea...

  3. Analysis of Radiation Induced Degradation in FPC-461 Fluoropolymers by Variable Temperature Multinuclear NMR

    SciTech Connect

    Chinn, S C; Wilson, T S; Maxwell, R S

    2004-10-27

    Solid state nuclear magnetic resonance techniques have been used to investigate aging mechanisms in a vinyl chloride:chlorotrifluoroethylene copolymer, FPC-461, due to exposure to {gamma}-radiation. Solid state {sup 1}H MAS NMR spectra revealed structural changes of the polymer upon irradiation under both air and nitrogen atmospheres. Considerable degradation is seen with {sup 1}H NMR in the vinyl chloride region of the polymer, particularly in the samples irradiated in air. {sup 19}F MAS NMR was used to investigate speciation in the chlorotrifluoroethylene blocks, though negligible changes were seen. {sup 1}H and {sup 19}F NMR at elevated temperature revealed increased segmental mobility and decreased structural heterogeneity within the polymer, yielding significant resolution enhancement over room temperature solid state detection. The effects of multi-site exchange are manifest in both the {sup 1}H and {sup 19}F NMR spectra as a line broadening and change in peak position as a function of temperature.

  4. Rapid Proton-Detected NMR Assignment for Proteins with Fast Magic Angle Spinning

    PubMed Central

    2015-01-01

    Using a set of six 1H-detected triple-resonance NMR experiments, we establish a method for sequence-specific backbone resonance assignment of magic angle spinning (MAS) nuclear magnetic resonance (NMR) spectra of 5–30 kDa proteins. The approach relies on perdeuteration, amide 2H/1H exchange, high magnetic fields, and high-spinning frequencies (ωr/2π ≥ 60 kHz) and yields high-quality NMR data, enabling the use of automated analysis. The method is validated with five examples of proteins in different condensed states, including two microcrystalline proteins, a sedimented virus capsid, and two membrane-embedded systems. In comparison to contemporary 13C/15N-based methods, this approach facilitates and accelerates the MAS NMR assignment process, shortening the spectral acquisition times and enabling the use of unsupervised state-of-the-art computational data analysis protocols originally developed for solution NMR. PMID:25102442

  5. Rapid proton-detected NMR assignment for proteins with fast magic angle spinning.

    PubMed

    Barbet-Massin, Emeline; Pell, Andrew J; Retel, Joren S; Andreas, Loren B; Jaudzems, Kristaps; Franks, W Trent; Nieuwkoop, Andrew J; Hiller, Matthias; Higman, Victoria; Guerry, Paul; Bertarello, Andrea; Knight, Michael J; Felletti, Michele; Le Marchand, Tanguy; Kotelovica, Svetlana; Akopjana, Inara; Tars, Kaspars; Stoppini, Monica; Bellotti, Vittorio; Bolognesi, Martino; Ricagno, Stefano; Chou, James J; Griffin, Robert G; Oschkinat, Hartmut; Lesage, Anne; Emsley, Lyndon; Herrmann, Torsten; Pintacuda, Guido

    2014-09-03

    Using a set of six (1)H-detected triple-resonance NMR experiments, we establish a method for sequence-specific backbone resonance assignment of magic angle spinning (MAS) nuclear magnetic resonance (NMR) spectra of 5-30 kDa proteins. The approach relies on perdeuteration, amide (2)H/(1)H exchange, high magnetic fields, and high-spinning frequencies (ωr/2π ≥ 60 kHz) and yields high-quality NMR data, enabling the use of automated analysis. The method is validated with five examples of proteins in different condensed states, including two microcrystalline proteins, a sedimented virus capsid, and two membrane-embedded systems. In comparison to contemporary (13)C/(15)N-based methods, this approach facilitates and accelerates the MAS NMR assignment process, shortening the spectral acquisition times and enabling the use of unsupervised state-of-the-art computational data analysis protocols originally developed for solution NMR.

  6. Regulation of ligands for the activating receptor NKG2D

    PubMed Central

    Mistry, Anita R; O'Callaghan, Chris A

    2007-01-01

    The outcome of an encounter between a cytotoxic cell and a potential target cell depends on the balance of signals from inhibitory and activating receptors. Natural Killer group 2D (NKG2D) has recently emerged as a major activating receptor on T lymphocytes and natural killer cells. In both humans and mice, multiple different genes encode ligands for NKG2D, and these ligands are non-classical major histocompatibility complex class I molecules. The NKG2D–ligand interaction triggers an activating signal in the cell expressing NKG2D and this promotes cytotoxic lysis of the cell expressing the ligand. Most normal tissues do not express ligands for NKG2D, but ligand expression has been documented in tumour and virus-infected cells, leading to lysis of these cells. Tight regulation of ligand expression is important. If there is inappropriate expression in normal tissues, this will favour autoimmune processes, whilst failure to up-regulate the ligands in pathological conditions would favour cancer development or dissemination of intracellular infection. PMID:17614877

  7. Rotation invariance principles in 2D/3D registration

    NASA Astrophysics Data System (ADS)

    Birkfellner, Wolfgang; Wirth, Joachim; Burgstaller, Wolfgang; Baumann, Bernard; Staedele, Harald; Hammer, Beat; Gellrich, Niels C.; Jacob, Augustinus L.; Regazzoni, Pietro; Messmer, Peter

    2003-05-01

    2D/3D patient-to-computed tomography (CT) registration is a method to determine a transformation that maps two coordinate systems by comparing a projection image rendered from CT to a real projection image. Applications include exact patient positioning in radiation therapy, calibration of surgical robots, and pose estimation in computer-aided surgery. One of the problems associated with 2D/3D registration is the fast that finding a registration includes sovling a minimization problem in six degrees-of-freedom in motion. This results in considerable time expenses since for each iteration step at least one volume rendering has to be computed. We show that by choosing an appropriate world coordinate system and by applying a 2D/2D registration method in each iteration step, the number of iterations can be grossly reduced from n6 to n5. Here, n is the number of discrete variations aroudn a given coordinate. Depending on the configuration of the optimization algorithm, this reduces the total number of iterations necessary to at least 1/3 of its original value. The method was implemented and extensively tested on simulated x-ray images of a pelvis. We conclude that this hardware-indepenent optimization of 2D/3D registration is a step towards increasing the acceptance of this promising method for a wide number of clinical applications.

  8. 2D nanostructures for water purification: graphene and beyond.

    PubMed

    Dervin, Saoirse; Dionysiou, Dionysios D; Pillai, Suresh C

    2016-08-18

    Owing to their atomically thin structure, large surface area and mechanical strength, 2D nanoporous materials are considered to be suitable alternatives for existing desalination and water purification membrane materials. Recent progress in the development of nanoporous graphene based materials has generated enormous potential for water purification technologies. Progress in the development of nanoporous graphene and graphene oxide (GO) membranes, the mechanism of graphene molecular sieve action, structural design, hydrophilic nature, mechanical strength and antifouling properties and the principal challenges associated with nanopore generation are discussed in detail. Subsequently, the recent applications and performance of newly developed 2D materials such as 2D boron nitride (BN) nanosheets, graphyne, molybdenum disulfide (MoS2), tungsten chalcogenides (WS2) and titanium carbide (Ti3C2Tx) are highlighted. In addition, the challenges affecting 2D nanostructures for water purification are highlighted and their applications in the water purification industry are discussed. Though only a few 2D materials have been explored so far for water treatment applications, this emerging field of research is set to attract a great deal of attention in the near future.

  9. 2D Materials for Optical Modulation: Challenges and Opportunities.

    PubMed

    Yu, Shaoliang; Wu, Xiaoqin; Wang, Yipei; Guo, Xin; Tong, Limin

    2017-02-21

    Owing to their atomic layer thickness, strong light-material interaction, high nonlinearity, broadband optical response, fast relaxation, controllable optoelectronic properties, and high compatibility with other photonic structures, 2D materials, including graphene, transition metal dichalcogenides and black phosphorus, have been attracting increasing attention for photonic applications. By tuning the carrier density via electrical or optical means that modifies their physical properties (e.g., Fermi level or nonlinear absorption), optical response of the 2D materials can be instantly changed, making them versatile nanostructures for optical modulation. Here, up-to-date 2D material-based optical modulation in three categories is reviewed: free-space, fiber-based, and on-chip configurations. By analysing cons and pros of different modulation approaches from material and mechanism aspects, the challenges faced by using these materials for device applications are presented. In addition, thermal effects (e.g., laser induced damage) in 2D materials, which are critical to practical applications, are also discussed. Finally, the outlook for future opportunities of these 2D materials for optical modulation is given.

  10. 2D DIGE saturation labeling for minute sample amounts.

    PubMed

    Arnold, Georg J; Fröhlich, Thomas

    2012-01-01

    The 2D DIGE technique, based on fluorophores covalently linked to amino acid side chain residues and the concept of an internal standard, has significantly improved reproducibility, sensitivity, and the dynamic range of protein quantification. In saturation DIGE, sulfhydryl groups of cysteines are labeled with cyanine dyes to completion, providing a so far unraveled sensitivity for protein detection and quantification in 2D gel-based proteomic experiments. Only a few micrograms of protein per 2D gel facilitate the analysis of about 2,000 analytes from complex mammalian cell or tissue samples. As a consequence, 2D saturation DIGE is the method of choice when only minute sample amounts are available for quantitative proteome analysis at the level of proteins rather than peptides. Since very low amounts of samples have to be handled in a reproducible manner, saturation DIGE-based proteomic experiments are technically demanding. Moreover, successful saturation DIGE approaches require a strict adherence to adequate reaction conditions at each step. This chapter is dedicated to colleagues already experienced in 2D PAGE protein separation and intends to support the establishment of this ultrasensitive technique in proteomic workgroups. We provide basic guidelines for the experimental design and discuss crucial aspects concerning labeling chemistry, sample preparation, and pitfalls caused by labeling artifacts. A detailed step-by-step protocol comprises all aspects from initial sample preparation to image analysis and statistical evaluation. Furthermore, we describe the generation of preparative saturation DIGE gels necessary for mass spectrometry-based spot identification.

  11. Mermin–Wagner fluctuations in 2D amorphous solids

    PubMed Central

    Illing, Bernd; Fritschi, Sebastian; Kaiser, Herbert; Klix, Christian L.; Maret, Georg; Keim, Peter

    2017-01-01

    In a recent commentary, J. M. Kosterlitz described how D. Thouless and he got motivated to investigate melting and suprafluidity in two dimensions [Kosterlitz JM (2016) J Phys Condens Matter 28:481001]. It was due to the lack of broken translational symmetry in two dimensions—doubting the existence of 2D crystals—and the first computer simulations foretelling 2D crystals (at least in tiny systems). The lack of broken symmetries proposed by D. Mermin and H. Wagner is caused by long wavelength density fluctuations. Those fluctuations do not only have structural impact, but additionally a dynamical one: They cause the Lindemann criterion to fail in 2D in the sense that the mean squared displacement of atoms is not limited. Comparing experimental data from 3D and 2D amorphous solids with 2D crystals, we disentangle Mermin–Wagner fluctuations from glassy structural relaxations. Furthermore, we demonstrate with computer simulations the logarithmic increase of displacements with system size: Periodicity is not a requirement for Mermin–Wagner fluctuations, which conserve the homogeneity of space on long scales. PMID:28137872

  12. Sparse radar imaging using 2D compressed sensing

    NASA Astrophysics Data System (ADS)

    Hou, Qingkai; Liu, Yang; Chen, Zengping; Su, Shaoying

    2014-10-01

    Radar imaging is an ill-posed linear inverse problem and compressed sensing (CS) has been proved to have tremendous potential in this field. This paper surveys the theory of radar imaging and a conclusion is drawn that the processing of ISAR imaging can be denoted mathematically as a problem of 2D sparse decomposition. Based on CS, we propose a novel measuring strategy for ISAR imaging radar and utilize random sub-sampling in both range and azimuth dimensions, which will reduce the amount of sampling data tremendously. In order to handle 2D reconstructing problem, the ordinary solution is converting the 2D problem into 1D by Kronecker product, which will increase the size of dictionary and computational cost sharply. In this paper, we introduce the 2D-SL0 algorithm into the reconstruction of imaging. It is proved that 2D-SL0 can achieve equivalent result as other 1D reconstructing methods, but the computational complexity and memory usage is reduced significantly. Moreover, we will state the results of simulating experiments and prove the effectiveness and feasibility of our method.

  13. Mean flow and anisotropic cascades in decaying 2D turbulence

    NASA Astrophysics Data System (ADS)

    Liu, Chien-Chia; Cerbus, Rory; Gioia, Gustavo; Chakraborty, Pinaki

    2015-11-01

    Many large-scale atmospheric and oceanic flows are decaying 2D turbulent flows embedded in a non-uniform mean flow. Despite its importance for large-scale weather systems, the affect of non-uniform mean flows on decaying 2D turbulence remains unknown. In the absence of mean flow it is well known that decaying 2D turbulent flows exhibit the enstrophy cascade. More generally, for any 2D turbulent flow, all computational, experimental and field data amassed to date indicate that the spectrum of longitudinal and transverse velocity fluctuations correspond to the same cascade, signifying isotropy of cascades. Here we report experiments on decaying 2D turbulence in soap films with a non-uniform mean flow. We find that the flow transitions from the usual isotropic enstrophy cascade to a series of unusual and, to our knowledge, never before observed or predicted, anisotropic cascades where the longitudinal and transverse spectra are mutually independent. We discuss implications of our results for decaying geophysical turbulence.

  14. 2-D Clinostat for Simulated Microgravity Experiments with Arabidopsis Seedlings

    NASA Astrophysics Data System (ADS)

    Wang, Hui; Li, Xugang; Krause, Lars; Görög, Mark; Schüler, Oliver; Hauslage, Jens; Hemmersbach, Ruth; Kircher, Stefan; Lasok, Hanna; Haser, Thomas; Rapp, Katja; Schmidt, Jürgen; Yu, Xin; Pasternak, Taras; Aubry-Hivet, Dorothée; Tietz, Olaf; Dovzhenko, Alexander; Palme, Klaus; Ditengou, Franck Anicet

    2016-04-01

    Ground-based simulators of microgravity such as fast rotating 2-D clinostats are valuable tools to study gravity related processes. We describe here a versatile g-value-adjustable 2-D clinostat that is suitable for plant analysis. To avoid seedling adaptation to 1 g after clinorotation, we designed chambers that allow rapid fixation. A detailed protocol for fixation, RNA isolation and the analysis of selected genes is described. Using this clinostat we show that mRNA levels of LONG HYPOCOTYL 5 (HY5), MIZU-KUSSEI 1 (MIZ1) and microRNA MIR163 are down-regulated in 5-day-old Arabidopsis thaliana roots after 3 min and 6 min of clinorotation using a maximal reduced g-force of 0.02 g, hence demonstrating that this 2-D clinostat enables the characterization of early transcriptomic events during root response to microgravity. We further show that this 2-D clinostat is able to compensate the action of gravitational force as both gravitropic-dependent statolith sedimentation and subsequent auxin redistribution (monitoring D R5 r e v :: G F P reporter) are abolished when plants are clinorotated. Our results demonstrate that 2-D clinostats equipped with interchangeable growth chambers and tunable rotation velocity are suitable for studying how plants perceive and respond to simulated microgravity.

  15. Faster and cleaner real-time pure shift NMR experiments.

    PubMed

    Mauhart, Johannes; Glanzer, Simon; Sakhaii, Peyman; Bermel, Wolfgang; Zangger, Klaus

    2015-10-01

    Real-time pure shift experiments provide highly resolved proton NMR spectra which do not require any special processing. Although being more sensitive than their pseudo 2D counterparts, their signal intensities per unit time are still far below regular NMR spectra. In addition, scalar coupling evolution during the individual data chunks produces decoupling sidebands. Here we show that faster and cleaner real-time pure shift spectra can be obtained through the implementation of two parameter alterations. Variation of the FID chunk lengths between individual transients significantly suppresses decoupling sidebands for any kind of real-time pure shift spectra and thus allows for example the analysis of minor components in compound mixtures. Shifting the excitation frequency between individual scans of real-time slice-selective pure shift spectra increases their sensitivity obtainable in unit time by allowing faster repetitions of acquisitions.

  16. 76 FR 77670 - Retail Commodity Transactions Under Commodity Exchange Act

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-12-14

    ... ``actual delivery'' as set forth in section 2(c)(2)(D)(ii)(III)(aa) of the Commodity Exchange Act (``CEA... application. In particular, new CEA section 2(c)(2)(D)(ii)(III)(aa) \\18\\ excepts a contract of sale that... involved.'' \\19\\ \\18\\ 7 U.S.C. 2(c)(2)(D)(ii)(III)(aa). \\19\\ The Commission has not adopted any...

  17. The MICA-129 dimorphism affects NKG2D signaling and outcome of hematopoietic stem cell transplantation

    PubMed Central

    Isernhagen, Antje; Malzahn, Dörthe; Viktorova, Elena; Elsner, Leslie; Monecke, Sebastian; von Bonin, Frederike; Kilisch, Markus; Wermuth, Janne Marieke; Walther, Neele; Balavarca, Yesilda; Stahl-Hennig, Christiane; Engelke, Michael; Walter, Lutz; Bickeböller, Heike; Kube, Dieter; Wulf, Gerald; Dressel, Ralf

    2015-01-01

    The MHC class I chain-related molecule A (MICA) is a highly polymorphic ligand for the activating natural killer (NK)-cell receptor NKG2D. A single nucleotide polymorphism causes a valine to methionine exchange at position 129. Presence of a MICA-129Met allele in patients (n = 452) undergoing hematopoietic stem cell transplantation (HSCT) increased the chance of overall survival (hazard ratio [HR] = 0.77, P = 0.0445) and reduced the risk to die due to acute graft-versus-host disease (aGVHD) (odds ratio [OR] = 0.57, P = 0.0400) although homozygous carriers had an increased risk to experience this complication (OR = 1.92, P = 0.0371). Overall survival of MICA-129Val/Val genotype carriers was improved when treated with anti-thymocyte globulin (HR = 0.54, P = 0.0166). Functionally, the MICA-129Met isoform was characterized by stronger NKG2D signaling, triggering more NK-cell cytotoxicity and interferon-γ release, and faster co-stimulation of CD8+ T cells. The MICA-129Met variant also induced a faster and stronger down-regulation of NKG2D on NK and CD8+ T cells than the MICA-129Val isoform. The reduced cell surface expression of NKG2D in response to engagement by MICA-129Met variants appeared to reduce the severity of aGVHD. PMID:26483398

  18. Complete assignments of 1H and 13C NMR data for three new arylnaphthalene lignan from Justicia procumbens.

    PubMed

    Liu, Guorui; Wu, Jun; Si, Jianyong; Wang, Junmei; Yang, Meihua

    2008-03-01

    Three new arylnaphthalene lignans, named neojusticin C (1), procumbenoside C (2) and procumbenoside D (3), have been isolated from the whole plant of Justicia procumbens, together with three known ones, justicidinoside B (4), justicidinoside C (5), and diphyllin-1-O-beta-D-apiofuranoside (6). The complete assignments of 1H and 13C NMR data for three new lignans were first obtained by means of 2D NMR techniques, including HSQC and HMBC.

  19. Exploring the use of Generalized Indirect Covariance to reconstruct pure shift NMR spectra: Current Pros and Cons

    NASA Astrophysics Data System (ADS)

    Fredi, André; Nolis, Pau; Cobas, Carlos; Martin, Gary E.; Parella, Teodor

    2016-05-01

    The current Pros and Cons of a processing protocol to generate pure chemical shift NMR spectra using Generalized Indirect Covariance are presented and discussed. The transformation of any standard 2D homonuclear and heteronuclear spectrum to its pure shift counterpart by using a reference DIAG spectrum is described. Reconstructed pure shift NMR spectra of NOESY, HSQC, HSQC-TOCSY and HSQMBC experiments are reported for the target molecule strychnine.

  20. Exploring the use of Generalized Indirect Covariance to reconstruct pure shift NMR spectra: Current Pros and Cons.

    PubMed

    Fredi, André; Nolis, Pau; Cobas, Carlos; Martin, Gary E; Parella, Teodor

    2016-05-01

    The current Pros and Cons of a processing protocol to generate pure chemical shift NMR spectra using Generalized Indirect Covariance are presented and discussed. The transformation of any standard 2D homonuclear and heteronuclear spectrum to its pure shift counterpart by using a reference DIAG spectrum is described. Reconstructed pure shift NMR spectra of NOESY, HSQC, HSQC-TOCSY and HSQMBC experiments are reported for the target molecule strychnine.

  1. Two dimensional NMR and NMR relaxation studies of coal structure

    SciTech Connect

    Zilm, K.W.

    1989-01-01

    This report covers the progress made on the title project during the past reporting period. Four major areas of inquiry are being pursued. Advanced solid state NMR methods are being developed to assay the distribution of the various important functional groups in coals that determine the reactivity of coals. Other methods are being developed which will also determine how these functional groups are linked together. A third area of investigation concerns how molecular mobility in coals impacts NMR relaxation times, which is important for interpretation of such data in terms of the mobile phase in coals model. Along the same lines the authors are also using these studies to establish protocols for obtaining the best quantitative response from coals in solid state C-13 NMR spectra. The effects of very high MAS rates (>10 kHz) on cross polarization dynamics are also being investigated for similar reasons. The authors have been reinvestigating the prospects of using zero field NMR types of techniques for two dimensional NMR structural analysis of complex organic solids such as coals. Currently MAS spin rates are not sufficiently high to permit zero field in high field NMR for protons in typical organic solids, however they are compatible with {sup 13}C-{sup 13}C dipolar couplings. In collaboration with Dr. Robert Tycko of AT T Bell Laboratories, inventor of the zero field in high field NMR method, the authors have performed the first zero field in high field {sup 13}C NMR experiments. These results are described. 9 refs., 2 figs.

  2. NMR Structural Studies of Antimicrobial Peptides: LPcin Analogs

    PubMed Central

    Jeong, Ji-Ho; Kim, Ji-Sun; Choi, Sung-Sub; Kim, Yongae

    2016-01-01

    Lactophoricin (LPcin), a component of proteose peptone (113–135) isolated from bovine milk, is a cationic amphipathic antimicrobial peptide consisting of 23 amino acids. We designed a series of N- or C-terminal truncated variants, mutated analogs, and truncated mutated analogs using peptide-engineering techniques. Then, we selected three LPcin analogs of LPcin-C8 (LPcin-YK1), LPcin-T2WT6W (LPcin-YK2), and LPcin-T2WT6W-C8 (LPcin-YK3), which may have better antimicrobial activities than LPcin, and successfully expressed them in E. coli with high yield. We elucidated the 3D structures and topologies of the three LPcin analogs in membrane environments by conducting NMR structural studies. We investigated the purity of the LPcin analogs and the α-helical secondary structures by performing 1H-15N 2D HSQC and HMQC-NOESY liquid-state NMR spectroscopy using protein-containing micelle samples. We measured the 3D structures and tilt angles in membranes by conducting 15N 1D and 2D 1H-15N SAMMY type solid-state NMR spectroscopy with an 800 MHz in-house-built 1H-15N double-resonance solid-state NMR probe with a strip-shield coil, using protein-containing large bicelle samples aligned and confirmed by molecular-dynamics simulations. The three LPcin analogs were found to be curved α-helical structures, with tilt angles of 55–75° for normal membrane bilayers, and their enhanced activities may be correlated with these topologies. PMID:26789765

  3. Secretory pathways generating immunosuppressive NKG2D ligands

    PubMed Central

    Baragaño Raneros, Aroa; Suarez-Álvarez, Beatriz; López-Larrea, Carlos

    2014-01-01

    Natural Killer Group 2 member D (NKG2D) activating receptor, present on the surface of various immune cells, plays an important role in activating the anticancer immune response by their interaction with stress-inducible NKG2D ligands (NKG2DL) on transformed cells. However, cancer cells have developed numerous mechanisms to evade the immune system via the downregulation of NKG2DL from the cell surface, including the release of NKG2DL from the cell surface in a soluble form. Here, we review the mechanisms involved in the production of soluble NKG2DL (sNKG2DL) and the potential therapeutic strategies aiming to block the release of these immunosuppressive ligands. Therapeutically enabling the NKG2D-NKG2DL interaction would promote immunorecognition of malignant cells, thus abrogating disease progression. PMID:25050215

  4. Splashing transients of 2D plasmons launched by swift electrons

    PubMed Central

    Lin, Xiao; Kaminer, Ido; Shi, Xihang; Gao, Fei; Yang, Zhaoju; Gao, Zhen; Buljan, Hrvoje; Joannopoulos, John D.; Soljačić, Marin; Chen, Hongsheng; Zhang, Baile

    2017-01-01

    Launching of plasmons by swift electrons has long been used in electron energy–loss spectroscopy (EELS) to investigate the plasmonic properties of ultrathin, or two-dimensional (2D), electron systems. However, the question of how a swift electron generates plasmons in space and time has never been answered. We address this issue by calculating and demonstrating the spatial-temporal dynamics of 2D plasmon generation in graphene. We predict a jet-like rise of excessive charge concentration that delays the generation of 2D plasmons in EELS, exhibiting an analog to the hydrodynamic Rayleigh jet in a splashing phenomenon before the launching of ripples. The photon radiation, analogous to the splashing sound, accompanies the plasmon emission and can be understood as being shaken off by the Rayleigh jet–like charge concentration. Considering this newly revealed process, we argue that previous estimates on the yields of graphene plasmons in EELS need to be reevaluated. PMID:28138546

  5. Available information in 2D motional Stark effect imaging.

    PubMed

    Creese, Mathew; Howard, John

    2010-10-01

    Recent advances in imaging techniques have allowed the extension of the standard polarimetric 1D motional Stark effect (MSE) diagnostic to 2D imaging of the internal magnetic field of fusion devices [J. Howard, Plasma Phys. Controlled Fusion 50, 125003 (2008)]. This development is met with the challenge of identifying and extracting the new information, which can then be used to increase the accuracy of plasma equilibrium and current density profile determinations. This paper develops a 2D analysis of the projected MSE polarization orientation and Doppler phase shift. It is found that, for a standard viewing position, the 2D MSE imaging system captures sufficient information to allow imaging of the internal vertical magnetic field component B(Z)(r,z) in a tokamak.

  6. Perception-based reversible watermarking for 2D vector maps

    NASA Astrophysics Data System (ADS)

    Men, Chaoguang; Cao, Liujuan; Li, Xiang

    2010-07-01

    This paper presents an effective and reversible watermarking approach for digital copyright protection of 2D-vector maps. To ensure that the embedded watermark is insensitive for human perception, we only select the noise non-sensitive regions for watermark embedding by estimating vertex density within each polyline. To ensure the exact recovery of original 2D-vector map after watermark extraction, we introduce a new reversible watermarking scheme based on reversible high-frequency wavelet coefficients modification. Within the former-selected non-sensitive regions, our watermarking operates on the lower-order vertex coordinate decimals with integer wavelet transform. Such operation further reduces the visual distortion caused by watermark embedding. We have validated the effectiveness of our scheme on our real-world city river/building 2D-vector maps. We give extensive experimental comparisons with state-of-the-art methods, including embedding capability, invisibility, and robustness over watermark attacking.

  7. Microscale 2D separation systems for proteomic analysis

    PubMed Central

    Xu, Xin; Liu, Ke; Fan, Z. Hugh

    2012-01-01

    Microscale 2D separation systems have been implemented in capillaries and microfabricated channels. They offer advantages of faster analysis, higher separation efficiency and less sample consumption than the conventional methods, such as liquid chromatography (LC) in a column and slab gel electrophoresis. In this article, we review their recent advancement, focusing on three types of platforms, including 2D capillary electrophoresis (CE), CE coupling with capillary LC, and microfluidic devices. A variety of CE and LC modes have been employed to construct 2D separation systems via sophistically designed interfaces. Coupling of different separation modes has also been realized in a number of microfluidic devices. These separation systems have been applied for the proteomic analysis of various biological samples, ranging from a single cell to tumor tissues. PMID:22462786

  8. 2D materials for photon conversion and nanophotonics

    NASA Astrophysics Data System (ADS)

    Tahersima, Mohammad H.; Sorger, Volker J.

    2015-09-01

    The field of two-dimensional (2D) materials has the potential to enable unique applications across a wide range of the electromagnetic spectrum. While 2D-layered materials hold promise for next-generation photon-conversion intrinsic limitations and challenges exist that shall be overcome. Here we discuss the intrinsic limitations as well as application opportunities of this new class of materials, and is sponsored by the NSF program Designing Materials to Revolutionize and Engineer our Future (DMREF) program, which links to the President's Materials Genome Initiative. We present general material-related details for photon conversion, and show that taking advantage of the mechanical flexibility of 2D materials by rolling MoS2/graphene/hexagonal boron nitride stack to a spiral solar cell allows for solar absorption up to 90%.

  9. Rapid-scan coherent 2D fluorescence spectroscopy.

    PubMed

    Draeger, Simon; Roeding, Sebastian; Brixner, Tobias

    2017-02-20

    We developed pulse-shaper-assisted coherent two-dimensional (2D) electronic spectroscopy in liquids using fluorescence detection. A customized pulse shaper facilitates shot-to-shot modulation at 1 kHz and is employed for rapid scanning over all time delays. A full 2D spectrum with 15 × 15 pixels is obtained in approximately 6 s of measurement time (plus further averaging if needed). Coherent information is extracted from the incoherent fluorescence signal via 27-step phase cycling. We exemplify the technique on cresyl violet in ethanol and recover literature-known oscillations as a function of population time. Signal-to-noise behavior is analyzed as a function of the amount of averaging. Rapid scanning provides a 2D spectrum with a root-mean-square error of < 0.05 after 1 min of measurement time.

  10. 2D-3D transition of gold cluster anions resolved

    NASA Astrophysics Data System (ADS)

    Johansson, Mikael P.; Lechtken, Anne; Schooss, Detlef; Kappes, Manfred M.; Furche, Filipp

    2008-05-01

    Small gold cluster anions Aun- are known for their unusual two-dimensional (2D) structures, giving rise to properties very different from those of bulk gold. Previous experiments and calculations disagree about the number of gold atoms nc where the transition to 3D structures occurs. We combine trapped ion electron diffraction and state of the art electronic structure calculations to resolve this puzzle and establish nc=12 . It is shown that theoretical studies using traditional generalized gradient functionals are heavily biased towards 2D structures. For a correct prediction of the 2D-3D crossover point it is crucial to use density functionals yielding accurate jellium surface energies, such as the Tao-Perdew-Staroverov-Scuseria (TPSS) functional or the Perdew-Burke-Ernzerhof functional modified for solids (PBEsol). Further, spin-orbit effects have to be included, and large, flexible basis sets employed. This combined theoretical-experimental approach is promising for larger gold and other metal clusters.

  11. IUPAP Award: Ion transport in 2D materials

    NASA Astrophysics Data System (ADS)

    Bao, Wenzhong

    Intercalation in 2D materials drastically influences both physical and chemical properties, which leads to a new degree of freedom for fundamental studies and expands the potential applications of 2D materials. In this talk, I will discuss our work in the past two years related to ion intercalation of 2D materials, including insertion of Li and Na ions in graphene and MoS2. We focused on both fundamental mechanism and potential application, e.g. we measured in-situ optical transmittance spectra and electrical transport properties of few-layer graphene (FLG) nanostructures upon electrochemical lithiation/delithiation. By observing a simultaneous increase of both optical transmittance and DC conductivity, strikingly different from other materials, we proposed its application as a next generation transparent electrode.

  12. 2d-retrieval For Mipas-envisat

    NASA Astrophysics Data System (ADS)

    Steck, T.; von Clarmann, T.; Grabowski, U.; Höpfner, M.

    Limb sounding of the Earth's atmosphere provides vertically high resolved profiles of geophysical parameters. The long ray path through the atmosphere makes limb sounders sensitive to even little abundant species. On the other hand, horizontal in- homogeneities, if not taken into account properly, can cause systematic errors within the retrieval process. Especially for limb emission measurements in the mid IR, at- mopheric temperature gradients result in considerable vmr retrieval errors if they are neglected. We present a dedicated method of taking full 2D fields of state parameters (indepen- dent of tangent points) into account in the forward model and in the retrieval. The basic idea is that the 2D state vector is updated sequentially for each limb scan. This method is applied to the 2D retrieval of temperature and vmr for simulated radiances as expected from MIPAS-ENVISAT.

  13. Genetics, genomics, and evolutionary biology of NKG2D ligands.

    PubMed

    Carapito, Raphael; Bahram, Seiamak

    2015-09-01

    Human and mouse NKG2D ligands (NKG2DLs) are absent or only poorly expressed by most normal cells but are upregulated by cell stress, hence, alerting the immune system in case of malignancy or infection. Although these ligands are numerous and highly variable (at genetic, genomic, structural, and biochemical levels), they all belong to the major histocompatibility complex class I gene superfamily and bind to a single, invariant, receptor: NKG2D. NKG2D (CD314) is an activating receptor expressed on NK cells and subsets of T cells that have a key role in the recognition and lysis of infected and tumor cells. Here, we review the molecular diversity of NKG2DLs, discuss the increasing appreciation of their roles in a variety of medical conditions, and propose several explanations for the evolutionary force(s) that seem to drive the multiplicity and diversity of NKG2DLs while maintaining their interaction with a single invariant receptor.

  14. Graphene based 2D-materials for supercapacitors

    NASA Astrophysics Data System (ADS)

    Palaniselvam, Thangavelu; Baek, Jong-Beom

    2015-09-01

    Ever-increasing energy demands and the depletion of fossil fuels are compelling humanity toward the development of suitable electrochemical energy conversion and storage devices to attain a more sustainable society with adequate renewable energy and zero environmental pollution. In this regard, supercapacitors are being contemplated as potential energy storage devices to afford cleaner, environmentally friendly energy. Recently, a great deal of attention has been paid to two-dimensional (2D) nanomaterials, including 2D graphene and its inorganic analogues (transition metal double layer hydroxides, chalcogenides, etc), as potential electrodes for the development of supercapacitors with high electrochemical performance. This review provides an overview of the recent progress in using these graphene-based 2D materials as potential electrodes for supercapacitors. In addition, future research trends including notable challenges and opportunities are also discussed.

  15. Chemical vapour deposition: Transition metal carbides go 2D

    DOE PAGES

    Gogotsi, Yury

    2015-08-17

    Here, the research community has been steadily expanding the family of few-atom-thick crystals beyond graphene, discovering new materials or producing known materials in a 2D state and demonstrating their unique properties1, 2. Recently, nanometre-thin 2D transition metal carbides have also joined this family3. Writing in Nature Materials, Chuan Xu and colleagues now report a significant advance in the field, showing the synthesis of large-area, high-quality, nanometre-thin crystals of molybdenum carbide that demonstrate low-temperature 2D superconductivity4. Moreover, they also show that other ultrathin carbide crystals, such as tungsten and tantalum carbides, can be grown by chemical vapour deposition with a highmore » crystallinity and very low defect concentration.« less

  16. Optoelectronics based on 2D TMDs and heterostructures

    NASA Astrophysics Data System (ADS)

    Huo, Nengjie; Yang, Yujue; Li, Jingbo

    2017-03-01

    2D materials including graphene and TMDs have proven interesting physical properties and promising optoelectronic applications. We reviewed the growth, characterization and optoelectronics based on 2D TMDs and their heterostructures, and demonstrated their unique and high quality of performances. For example, we observed the large mobility, fast response and high photo-responsivity in MoS2, WS2 and WSe2 phototransistors, as well as the novel performances in vdW heterostructures such as the strong interlayer coupling, am-bipolar and rectifying behaviour, and the obvious photovoltaic effect. It is being possible that 2D family materials could play an increasingly important role in the future nano- and opto-electronics, more even than traditional semiconductors such as silicon.