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Sample records for c-13 cpmg nmr

  1. Histidine side-chain dynamics and protonation monitored by C-13 CPMG NMR relaxation dispersion

    DEFF Research Database (Denmark)

    Hass, M. A. S.; Yilmaz, A.; Christensen, Hans Erik Mølager

    2009-01-01

    the chemical shift titration experiments, and the CPMG derived exchange rates agree with those obtained previously from N-15 backbone relaxation measurements. Compared to measurements of backbone nuclei, C-13(epsilon 1) dispersion provides a more direct method to monitor interchanging protonation states...... or other kinds of conformational changes of histidine side chains or their environment. Advantages and shortcomings of using the C-13(epsilon 1) dispersion experiments in combination with chemical shift titration experiments to obtain information on exchange dynamics of the histidine side chains......The use of C-13 NMR relaxation dispersion experiments to monitor micro-millisecond fluctuations in the protonation states of histidine residues in proteins is investigated. To illustrate the approach, measurements on three specifically C-13 labeled histidine residues in plastocyanin (PCu) from...

  2. Chirped CPMG for well-logging NMR applications.

    Science.gov (United States)

    Casabianca, Leah B; Mohr, Daniel; Mandal, Soumyajit; Song, Yi-Qiao; Frydman, Lucio

    2014-05-01

    In NMR well-logging, the measurement apparatus typically consists of a permanent magnet which is inserted into a bore, and the sample is the rock surrounding the borehole. When compared to the conditions of standard NMR experiments, this application is thus challenged by relatively weak and invariably inhomogeneous B0 and B1 fields. Chemical shift information is not generally obtained in these measurements. Instead, diffusivity, porosity and permeability information is collected from multi-echo decay measurements - most often using a Carr-Purcell Meiboom-Gill (CPMG) pulse sequence to enhance the experiment's limited sensitivity. In this work, we explore the consequences of replacing the hard square pulses used in a typical CPMG sequence with chirped pulses sweeping a range of frequencies. The greater bandwidths that for a maximum B1 level can be excited by chirped pulses translates into marked expansion of the detection volume, and thus significant signal-to-noise improvements when compared to standard CPMG acquisitions using hard pulses. This improvement, usually amounting to signal enhancements ⩾3, can be used to reduce the experimental time of NMR well-logging measurements, for measuring T2 even when B0 and B1 inhomogenieties complicate the measurements, and opening new opportunities in the determination of diffusional properties. Copyright © 2014 Elsevier Inc. All rights reserved.

  3. Application of 119Sn CPMG MAS NMR for Fast Characterization of Sn Sites in Zeolites with Natural 119Sn Isotope Abundance

    DEFF Research Database (Denmark)

    G. Kolyagin, Yury; V. Yakimo, Alexander; Tolborg, Søren

    2016-01-01

    119Sn CPMG MAS NMR is demonstrated to be a fast and efficient method for characterization of Sn-sites in Sn-containing zeolites. Tuning of the CPMG echo-train sequence decreases the experimental time by a factor of 5–40 in the case of as-synthesized and hydrated Sn-BEA samples and by 3 orders......-BEA zeolites with natural 119Sn isotope abundance using conventional MAS NMR equipment....

  4. No genetic footprints of the fat mass and obesity associated (FTO) gene in human plasma 1H CPMG NMR metabolic profiles

    DEFF Research Database (Denmark)

    Kjeldahl, K; Rasmussen, M.A.; Hasselbalch, Ann Louise

    2014-01-01

    In this paper it was investigated if any genotypic footprints from the fat mass and obesity associated (FTO) SNP could be found in 600 MHz 1H CPMG NMR profiles of around 1,000 human plasma samples from healthy Danish twins. The problem was addressed with a combination of univariate and multivariate...

  5. Dynamic NMR Q-space studies of microstructure with the multigrade CPMG sequence.

    Science.gov (United States)

    Hills, B P; Wright, K M; Snaar, J E

    1996-01-01

    A new approach to q-space studies of microstructure is proposed, which exploits the combined information contained in the water proton transverse relaxation time distribution and the frequency dependence of the apparent water diffusivity in heterogeneous systems. Using an automated two-dimensional multigrade CPMG sequence, both the pulse spacing and the amplitude of the applied field gradient are varied systematically and used to measure the frequency and wave vector dependence of the multiple exponential echo decay constants and amplitudes. Undesirable crossterms in the applied and background field gradients are eliminated by a simple procedure involving a sign reversal in the applied gradient. Nonlinear, local susceptibility-induced field gradients are shown to lead to enhanced, frequency-dependent apparent water diffusivities that are sensitive to the local microstructure.

  6. Solid-state C-13 and Co-59 NMR spectroscopy of C-13-methylcobalt(III) complexes with amine ligands

    DEFF Research Database (Denmark)

    Ooms, Kristopher J.; Bernard, Guy M.; Kadziola, Anders

    2009-01-01

    spectroscopy, which also established the negative sign of C-Q(Co-59). Cobalt-59 NMR spectroscopy was used to characterize the cobalt magnetic shielding tensor, to verify the magnitudes of C-Q(Co-59) and to establish the value of eta(Q), which is difficult to determine indirectly. The measurements show...... that the EFG tensors are either axially symmetric or close to being so but there is a wide range of C-Q values, from -40 MHz for the complex with X = H2O to -105 MHz with X = CN-. The Co chemical shift tensors are approximately axially symmetric with the spans. delta(11) - delta(33), ranging from 3700 to 5600...... ppm for X = H2O and CN-, respectively. The latter measurements also established the relative orientations of the Co EFG and chemical shift tensors. Density functional theory calculations of the Co-59 EFG and magnetic shielding tensors as well as of (1)J(Co-59, C-13) for the NO2- and N-3(-) complexes...

  7. Multinuclear solid-state high-resolution and C-13 -{Al-27} double-resonance magic-angle spinning NMR studies on aluminum alkoxides

    NARCIS (Netherlands)

    Abraham, A.; Prins, R.; Bokhoven, J.A. van; Eck, E.R.H. van; Kentgens, A.P.M.

    2006-01-01

    A combination of Al-27 magic-angle spinning (MAS)/multiple quantum (MQ)-MAS, C-13-H-1 CPMAS, and C-13-{Al-27} transfer of population in double-resonance (TRAPDOR) nuclear magnetic resonance (NMR) were used for the structural elucidation of the aluminum alkoxides aluminum ethoxide, aluminum

  8. Solid State C-13 and H-2 NMR Investigations of Paramagnetic Ni(II)(acac)(2)L-2 Complexes

    DEFF Research Database (Denmark)

    Lennartson, A.; Christensen, Lene Ulrikke; McKenzie, C. J.

    2014-01-01

    Nine structurally related paramagnetic acetylacetonato nickel(II) complexes: [Ni(acac)(2)] and trans-[Ni(acac)(2)(X)(2)]nH/D2O, X = H2O, D2O, NH3, MeOH, PMePh2, PMe2Ph, or [dppe](1/2), n = 0 or 1, dppe = 1,2-his(diphenylphosphino)ethane, as well as cis-[Ni(F-6-acac)(2)(D2O)(2)], F-6-acac = hexafl......Nine structurally related paramagnetic acetylacetonato nickel(II) complexes: [Ni(acac)(2)] and trans-[Ni(acac)(2)(X)(2)]nH/D2O, X = H2O, D2O, NH3, MeOH, PMePh2, PMe2Ph, or [dppe](1/2), n = 0 or 1, dppe = 1,2-his(diphenylphosphino)ethane, as well as cis-[Ni(F-6-acac)(2)(D2O)(2)], F-6-acac...... = hexafluoroacetylonato, have been characterized by solid state C-13 MAS NMR spectroscopy. H-2 MAS NMR was used to probe the local hydrogen bonding network in [Ni(acac)(2)(D2O)(2)]D2O and cis-[Ni(F-6-acac)(2)(D2O)(2)]. The complexes serve to benchmark the paramagnetic shift, which can be associated with the resonances...... of atoms of the coordinated ligands. The methine (CH) and methyl (CH3) have characteristic combinations of the isotropic shift (delta) and anisotropy parameters (d, eta). The size of the anisotropy (d), which is the sum of the chemical shift anisotropy (CSA) and the paramagnetic electron-nuclei dipolar...

  9. Finite pulse effects in CPMG pulse trains on paramagnetic materials.

    Science.gov (United States)

    Leskes, Michal; Grey, Clare P

    2015-09-14

    The Carr-Purcell-Meiboom-Gill (CPMG) sequence is commonly used in high resolution NMR spectroscopy and in magnetic resonance imaging for the measurement of transverse relaxation in systems that are subject to diffusion in internal or external gradients and is superior to the Hahn echo measurement, which is more sensitive to diffusion effects. Similarly, it can potentially be used to study dynamic processes in electrode materials for lithium ion batteries. Here we compare the (7)Li signal decay curves obtained with the CPMG and Hahn echo sequences under static conditions (i.e., in the absence of magic angle spinning) in paramagnetic materials with varying transition metal ion concentrations. Our results indicate that under CPMG pulse trains the lifetime of the (7)Li signal is substantially extended and is correlated with the strength of the electron-nuclear interaction. Numerical simulations and analytical calculations using Floquet theory suggest that the combination of large interactions and a train of finite pulses, results in a spin locking effect which significantly slows the signal's decay. While these effects complicate the interpretation of CPMG-based investigations of diffusion and chemical exchange in paramagnetic materials, they may provide a useful approach to extend the signal's lifetime in these often fast relaxing systems, enabling the use of correlation experiments. Furthermore, these results highlight the importance of developing a deeper understanding of the effects of the large paramagnetic interactions during multiple pulse experiments in order to extend the experimental arsenal available for static and in situ NMR investigations of paramagnetic materials.

  10. Observation of immobile regions in natural rubber at ambient temperature by solid-state C-13 CP/MAS NMR spectroscopy

    DEFF Research Database (Denmark)

    Larsen, F.H.; Rasmussen, T.; Pedersen, Walther Batsberg

    1999-01-01

    Employing C-13 CP/MAS NMR spectroscopy, the existence of immobile regions in natural rubber (cis-1,4-polyisoprene) corresponding to a few percent of the monomer units has been detected at ambient temperature. For synthetic rubbers no immobile regions have been detected at all. Applying different ...... physical and chemical treatments to natural rubber it is shown that mastication, gamma-irradiation, and increasing the temperature, slightly above the ambient, reduce the amount of immobile regions. (C) 1999 Elsevier Science Ltd. All rights reserved.......Employing C-13 CP/MAS NMR spectroscopy, the existence of immobile regions in natural rubber (cis-1,4-polyisoprene) corresponding to a few percent of the monomer units has been detected at ambient temperature. For synthetic rubbers no immobile regions have been detected at all. Applying different...

  11. Application of geometric approximation to the CPMG experiment: Two- and three-site exchange.

    Science.gov (United States)

    Chao, Fa-An; Byrd, R Andrew

    2017-04-01

    The Carr-Purcell-Meiboom-Gill (CPMG) experiment is one of the most classical and well-known relaxation dispersion experiments in NMR spectroscopy, and it has been successfully applied to characterize biologically relevant conformational dynamics in many cases. Although the data analysis of the CPMG experiment for the 2-site exchange model can be facilitated by analytical solutions, the data analysis in a more complex exchange model generally requires computationally-intensive numerical analysis. Recently, a powerful computational strategy, geometric approximation, has been proposed to provide approximate numerical solutions for the adiabatic relaxation dispersion experiments where analytical solutions are neither available nor feasible. Here, we demonstrate the general potential of geometric approximation by providing a data analysis solution of the CPMG experiment for both the traditional 2-site model and a linear 3-site exchange model. The approximate numerical solution deviates less than 0.5% from the numerical solution on average, and the new approach is computationally 60,000-fold more efficient than the numerical approach. Moreover, we find that accurate dynamic parameters can be determined in most cases, and, for a range of experimental conditions, the relaxation can be assumed to follow mono-exponential decay. The method is general and applicable to any CPMG RD experiment (e.g. N, C', Cα, Hα, etc.) The approach forms a foundation of building solution surfaces to analyze the CPMG experiment for different models of 3-site exchange. Thus, the geometric approximation is a general strategy to analyze relaxation dispersion data in any system (biological or chemical) if the appropriate library can be built in a physically meaningful domain. Published by Elsevier Inc.

  12. Application of geometric approximation to the CPMG experiment: Two- and three-site exchange

    Science.gov (United States)

    Chao, Fa-An; Byrd, R. Andrew

    2017-04-01

    The Carr-Purcell-Meiboom-Gill (CPMG) experiment is one of the most classical and well-known relaxation dispersion experiments in NMR spectroscopy, and it has been successfully applied to characterize biologically relevant conformational dynamics in many cases. Although the data analysis of the CPMG experiment for the 2-site exchange model can be facilitated by analytical solutions, the data analysis in a more complex exchange model generally requires computationally-intensive numerical analysis. Recently, a powerful computational strategy, geometric approximation, has been proposed to provide approximate numerical solutions for the adiabatic relaxation dispersion experiments where analytical solutions are neither available nor feasible. Here, we demonstrate the general potential of geometric approximation by providing a data analysis solution of the CPMG experiment for both the traditional 2-site model and a linear 3-site exchange model. The approximate numerical solution deviates less than 0.5% from the numerical solution on average, and the new approach is computationally 60,000-fold more efficient than the numerical approach. Moreover, we find that accurate dynamic parameters can be determined in most cases, and, for a range of experimental conditions, the relaxation can be assumed to follow mono-exponential decay. The method is general and applicable to any CPMG RD experiment (e.g. N, C‧, Cα, Hα, etc.) The approach forms a foundation of building solution surfaces to analyze the CPMG experiment for different models of 3-site exchange. Thus, the geometric approximation is a general strategy to analyze relaxation dispersion data in any system (biological or chemical) if the appropriate library can be built in a physically meaningful domain.

  13. Residue-specific pK(a) determination of lysine and arginine side chains by indirect N-15 and C-13 NMR spectroscopy : Application to apo calmodulin

    NARCIS (Netherlands)

    Andre, Ingemar; Linse, Sara; Mulder, Frans A. A.

    2007-01-01

    Electrostatic interactions in proteins can be probed experimentally through determination of residue-specific acidity constants, We describe here triple-resonance NMR techniques for direct determination of lysine and arginine side-chain protonation states in proteins. The experiments are based on

  14. Comparison of Three NMR Methods for Measuring Crosslink Density of Rubbers

    Directory of Open Access Journals (Sweden)

    GAO Peng-fei

    2017-12-01

    Full Text Available NMR is a frequently used technique for measuring crosslink density of rubbers. In this work, three commonly used proton NMR methods for measuring crosslink density of rubbers[i.e., 1H double-quantum (DQ NMR, 1H Hahn echo and 1H CPMG echo] were compared. Different approaches showed different results, and the origin of such discrepancy was discussed. The echo time dependence of the crosslink density measured with the CPMG echo method was studied. The ways to improve theCPMG echo-based measurements are discussed.

  15. Relaxation dispersion NMR spectroscopy for the study of protein allostery.

    Science.gov (United States)

    Farber, Patrick J; Mittermaier, Anthony

    2015-06-01

    Allosteric transmission of information between distant sites in biological macromolecules often involves collective transitions between active and inactive conformations. Nuclear magnetic resonance (NMR) spectroscopy can yield detailed information on these dynamics. In particular, relaxation dispersion techniques provide structural, dynamic, and mechanistic information on conformational transitions occurring on the millisecond to microsecond timescales. In this review, we provide an overview of the theory and analysis of Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion NMR experiments and briefly describe their application to the study of allosteric dynamics in the homeodomain from the PBX transcription factor (PBX-HD). CPMG NMR data show that local folding (helix/coil) transitions in one part of PBX-HD help to communicate information between two distant binding sites. Furthermore, the combination of CPMG and other spin relaxation data show that this region can also undergo local misfolding, reminiscent of conformational ensemble models of allostery.

  16. Multiecho scheme advances surface NMR for aquifer characterization

    Science.gov (United States)

    Grunewald, Elliot; Walsh, David

    2013-12-01

    nuclear magnetic resonance (NMR) is increasingly used as a method to noninvasively characterize aquifers. This technology follows a successful history of NMR logging, applied over decades to estimate hydrocarbon reservoir properties. In contrast to logging, however, surface methods have utilized relatively simple acquisition sequences, from which pore-scale properties may not be reliably and efficiently estimated. We demonstrate for the first time the capability of sophisticated multiecho measurements to rapidly record a surface NMR response that more directly reflects aquifer characteristics. Specifically, we develop an adaptation of the multipulse Carr-Purcell-Meiboom-Gill (CPMG) sequence, widely used in logging, to measure the T2 relaxation response in a single scan. We validate this approach in a field surface NMR data set and by direct comparison with an NMR log. Adoption of the CPMG marked a landmark advancement in the history of logging NMR; we have now realized this same advancement in the surface NMR method.

  17. Proton-decoupled CPMG: a better experiment for measuring (15)N R2 relaxation in disordered proteins.

    Science.gov (United States)

    Yuwen, Tairan; Skrynnikov, Nikolai R

    2014-04-01

    (15)N R2 relaxation is one of the most informative experiments for characterization of intrinsically disordered proteins (IDPs). Small changes in nitrogen R2 rates are often used to determine how IDPs respond to various biologically relevant perturbations such as point mutations, posttranslational modifications and weak ligand interactions. However collecting high-quality (15)N relaxation data can be difficult. Of necessity, the samples of IDPs are often prepared with low protein concentration and the measurement time can be limited because of rapid sample degradation. Furthermore, due to hardware limitations standard experiments such as (15)N spin-lock and CPMG can sample the relaxation decay only to ca. 150ms. This is much shorter than (15)N T2 times in disordered proteins at or near physiological temperature. As a result, the sampling of relaxation decay profiles in these experiments is suboptimal, which further lowers the precision of the measurements. Here we report a new implementation of the proton-decoupled (PD) CPMG experiment which allows one to sample (15)N R2 relaxation decay up to ca. 0.5-1s. The new experiment has been validated through comparison with the well-established spin-lock measurement. Using dilute samples of denatured ubiquitin, we have demonstrated that PD-CPMG produces up to 3-fold improvement in the precision of the data. It is expected that for intrinsically disordered proteins the gains may be even more substantial. We have also shown that this sequence has a number of favorable properties: (i) the spectra are recorded with narrow linewidth in nitrogen dimension; (ii) (15)N offset correction is small and easy to calculate; (iii) the experiment is immune to various spurious effects arising from solvent exchange; (iv) the results are stable with respect to pulse miscalibration and rf field inhomogeneity; (v) with minimal change, the pulse sequence can also be used to measure R2 relaxation of (15)N(ε) spins in arginine side chains. We

  18. An estimation method for improved extraction of the decay curve signal from CPMG-like measurements with a unilateral scanner.

    Science.gov (United States)

    Bergman, Elad; Yeredor, Arie; Nevo, Uri

    2014-08-01

    Unilateral NMR devices are valuable tools used to study non-invasively arbitrarily-sized objects. They have been utilized in various applications, including non-destructive testing and well logging. However, measurements with such scanners are characterized by a low sensitivity, which is mainly the result of the low and inhomogeneous magnetic field B0. The resulting poor signal to noise ratio (SNR) is a prominent limitation, as it deteriorates the accuracy of data analysis. Improving the SNR is typically done by the use of averaging repetitions that result in too long scan times. This work presents a statistical signal-processing method that can improve the sensitivity of a Carr-Purcell-Meiboom-Gill (CPMG)-like sequence for measurements of transverse-relaxation with unilateral scanners. The method improves the extraction of the decay curve from the noisy data. This is done by exploiting the redundancy in the acquired signal and by the use of the noise characteristics, which are both incorporated into a weighted least-squares estimation approach. This technique is especially effective in applications where RF shielding is not in use, and the measurements are corrupted by dominant non-white noise. The method performance was evaluated with a series of CPMG-like measurements applied on two samples. Decay curves were extracted from each measurement with the proposed method and were compared to a conventional extraction of the decay curve. All measurements showed a significant improvement in the accuracy of estimation of the decaying signal. Thus, the improvement in the sensitivity can be translated into a reduction in the acquisition times (by reducing the need in averaging repetitions) or to a more accurate fitting process of the traverse relaxation distribution. Copyright © 2014 Elsevier Inc. All rights reserved.

  19. An adaptive method for determining an acquisition parameter t0 in a modified CPMG sequence

    Science.gov (United States)

    Xing, Donghui; Fan, Yiren; Hao, Jianfei; Ge, Xinmin; Li, Chaoliu; Xiao, Yufeng; Wu, Fei

    2017-03-01

    The modified CPMG (Carr-Purcell-Meiboom-Gill) pulse sequence is a common sequence used for measuring the internal magnetic field gradient distribution of formation rocks, for which t0 (the duration of the first window) is a key acquisition parameter. In order to obtain the optimal t0, an adaptive method is proposed in this paper. By studying the factors influencing discriminant factor σ and its variation trend using T2-G forward numerical simulation, it is found that the optimal t0 corresponds to the maximum value of σ. Then combining the constraint condition of SNR (Signal Noise Ratio) of spin echo, an optimal t0 in modified CPMG pulse sequence is determined. This method can reduce the difficulties of operating T2-G experiments. Finally, the adaptive method is verified by the results of the T2-G experiments for four water-saturated sandstone samples.

  20. An adaptive method for determining an acquisition parameter t0 in a modified CPMG sequence.

    Science.gov (United States)

    Xing, Donghui; Fan, Yiren; Hao, Jianfei; Ge, Xinmin; Li, Chaoliu; Xiao, Yufeng; Wu, Fei

    2017-03-01

    The modified CPMG (Carr-Purcell-Meiboom-Gill) pulse sequence is a common sequence used for measuring the internal magnetic field gradient distribution of formation rocks, for which t0 (the duration of the first window) is a key acquisition parameter. In order to obtain the optimal t0, an adaptive method is proposed in this paper. By studying the factors influencing discriminant factor σ and its variation trend using T2-G forward numerical simulation, it is found that the optimal t0 corresponds to the maximum value of σ. Then combining the constraint condition of SNR (Signal Noise Ratio) of spin echo, an optimal t0 in modified CPMG pulse sequence is determined. This method can reduce the difficulties of operating T2-G experiments. Finally, the adaptive method is verified by the results of the T2-G experiments for four water-saturated sandstone samples. Copyright © 2017 Elsevier Inc. All rights reserved.

  1. Analysis of ethanol-soluble extractives in southern pine wood by low-field proton NMR

    Science.gov (United States)

    Thomas L. Eberhardt; Thomas Elder; Nicole Labbe

    2007-01-01

    Low-field portion NMR was evaluated as a nondestructive and rapid technique for measuring ethanol-soluble extractives in southern pine wood. Matchstick-sized wood specimens were steeped in extractive-containing solutions to generate extractive-enriched samples for analysis. decay curves obtained by the Carr-Purcell-Meiboom-gill (CPMG) pulse sequence were analyzed with...

  2. Quantifying disease activity in fatty-infiltrated skeletal muscle by IDEAL-CPMG in Duchenne muscular dystrophy.

    Science.gov (United States)

    Mankodi, Ami; Bishop, Courtney A; Auh, Sungyoung; Newbould, Rexford D; Fischbeck, Kenneth H; Janiczek, Robert L

    2016-10-01

    The purpose of this study was to explore the use of iterative decomposition of water and fat with echo asymmetry and least-squares estimation Carr-Purcell-Meiboom-Gill (IDEAL-CPMG) to simultaneously measure skeletal muscle apparent fat fraction and water T 2 (T 2,w ) in patients with Duchenne muscular dystrophy (DMD). In twenty healthy volunteer boys and thirteen subjects with DMD, thigh muscle apparent fat fraction was measured by Dixon and IDEAL-CPMG, with the IDEAL-CPMG also providing T 2,w as a measure of muscle inflammatory activity. A subset of subjects with DMD was followed up during a 48-week clinical study. The study was in compliance with the Patient Privacy Act and approved by the Institutional Review Board. Apparent fat fraction in the thigh muscles of subjects with DMD was significantly increased compared to healthy volunteer boys (p <0.001). There was a strong correlation between Dixon and IDEAL-CPMG apparent fat fraction. Muscle T 2,w measured by IDEAL-CPMG was independent of changes in apparent fat fraction. Muscle T 2,w was higher in the biceps femoris and vastus lateralis muscles of subjects with DMD (p <0.05). There was a strong correlation (p <0.004) between apparent fat fraction in all thigh muscles and six-minute walk distance (6MWD) in subjects with DMD. IDEAL-CPMG allowed independent and simultaneous quantification of skeletal muscle fatty degeneration and disease activity in DMD. IDEAL-CPMG apparent fat fraction and T 2,w may be useful as biomarkers in clinical trials of DMD as the technique disentangles two competing biological processes. Published by Elsevier B.V.

  3. Alternatives to Nuclear Overhauser Enhancement Spectroscopy Presat and Carr-Purcell-Meiboom-Gill Presat for NMR-Based Metabolomics.

    Science.gov (United States)

    Le Guennec, Adrien; Tayyari, Fariba; Edison, Arthur S

    2017-09-05

    NMR metabolomics are primarily conducted with 1D nuclear Overhauser enhancement spectroscopy (NOESY) presat for water suppression and Carr-Purcell-Meiboom-Gill (CPMG) presat as a T2 filter to remove macromolecule signals. Others pulse sequences exist for these two objectives but are not often used in metabolomics studies, because they are less robust or unknown to the NMR metabolomics community. However, recent improvements on alternative pulse sequences provide attractive alternatives to 1D NOESY presat and CPMG presat. We focus this perspective on PURGE, a water suppression technique, and PROJECT presat, a T2 filter. These two pulse sequences, when optimized, performed at least on par with 1D NOESY presat and CPMG presat, if not better. These pulse sequences were tested on common samples for metabolomics, human plasma, and urine.

  4. CPMG relaxation by diffusion with constant magnetic field gradient in a restricted geometry: numerical simulation and application.

    Science.gov (United States)

    Zhang, Gigi Q; Hirasaki, George J

    2003-07-01

    Carr-Purcell-Meiboom-Gill (CPMG) measurements are the primary nuclear magnetic resonance (NMR) technique used for evaluating formation properties and reservoir fluid properties in the well logging industry and laboratory sample analysis. The estimation of bulk volume irreducible (BVI), permeability, and fluid type relies on the accurate interpretation of the spin-spin relaxation time (T(2)) distribution. The interpretation is complicated when spin's self-diffusion in an inhomogeneous field and restricted geometry becomes dominant. The combined effects of field gradient, diffusion, and a restricted geometry are not easily evaluated analytically. We used a numerical method to evaluate the dependence of the free and restricted diffusion on the system parameters in the absence of surface relaxation, which usually can be neglected for the non-wetting fluids (e.g., oil or gas). The parameter space that defines the relaxation process is reduced to two dimensionless groups: D* and tau*. Three relaxation regimes: free diffusion, localization, and motionally averaging regimes are identified in the (log(10)D*, log(10)tau*) domain. The hypothesis that the normalized magnetization, M*, relaxes as a single exponential with a constant dimensionless relaxation time T*(2) is justified for most regions of the parameter space. The numerical simulation results are compared with the analytical solutions from the contour plots of T*(2). The locations of the boundaries between different relaxation regimes, derived from equalizing length scales, are challenged by observed discrepancies between numerical and analytical solutions. After adjustment of boundaries by equalizing T*(2), numerical simulation result and analytical solution match each other for every relaxation regime. The parameters, fluid diffusivity and pore length, can be estimated from analytical solutions in the free diffusion and motionally averaging regimes, respectively. Estimation of the parameters near the boundaries of

  5. C(13)-Norisoprenoid glucoconjugates from lulo (Solanum quitoense L.) leaves.

    Science.gov (United States)

    Osorio, C; Duque, C; Fujimoto, Y

    1999-04-01

    With the aid of multilayer coil countercurrent chromatography, subsequent acetylation, and liquid chromatographic purification of a glycosidic mixture obtained from lulo (Solanum quitoense L.) leaves, three C(13)-norisoprenoid glucoconjugates were isolated in pure form. Their structures were elucidated by NMR, MS, and CD analyses to be the novel (6R,9R)-13-hydroxy-3-oxo-alpha-ionol 9-O-beta-D-glucopyranoside (4a), the uncommon (3S,5R,8R)-3, 5-dihydroxy-6,7-megastigmadien-9-one 5-O-beta-D-glucopyranoside (citroside A) (5a), and the known (6S,9R)-vomifoliol 9-O-beta-D-glucopyranoside (6a). Enzymatic treatment of compound 5a showed the formation of 3-hydroxy-7,8-didehydro-beta-ionone (7), an important lulo peeling volatile, which in its turn after chemical reduction and heated acid catalyzed rearrangement generates beta-damascenone (9) and 3-hydroxy-beta-damascone (10).

  6. Carr-Purcell-Meiboom-Gill (CPMG) Imaging of Prostate Cancer: Quantitative T2 Values for Cancer Discrimination

    Science.gov (United States)

    Roebuck, Joseph R.; Haker, Steven J.; Mitsouras, Dimitris; Rybicki, Frank J.; Tempany, Clare M.; Mulkern, Robert V.

    2009-01-01

    Quantitative, apparent T2 values of suspected prostate cancer and healthy peripheral zone tissue in men with prostate cancer were measured using a Carr-Purcell-Meiboom-Gill (CPMG) imaging sequence in order to assess the cancer discrimination potential of tissue T2 values. The CPMG imaging sequence was used to image the prostates of 18 men with biopsy proven prostate cancer. Whole gland coverage with nominal voxel volumes of 0.54 × 1.1 × 4 mm3 was obtained in 10.7 minutes, resulting in data sets suitable for generating high quality images with variable T2-weighting and for evaluating quantitative T2 values on a pixel-by-pixel basis. Region-of-interest analysis of suspected healthy peripheral zone tissue and suspected cancer, identified on the basis of both T1- and T2-weighted signal intensities and available histopathology reports, yielded significantly (p < 0.0001) longer apparent T2 values in suspected healthy tissue (193 ± 49 ms) vs. suspected cancer (100 ± 26 ms), suggesting potential utility of this method as a tissue specific discrimination index for prostate cancer. We conclude that CPMG imaging of the prostate can be performed in reasonable scan times and can provide advantages over T2-weighted fast spin echo imaging alone, including quantitative T2 values for cancer discrimination as well as proton density maps without the point spread function degradation associated with short effective echo time fast spin echo (FSE) sequences. PMID:18823731

  7. Probing Microsecond Time Scale Dynamics in Proteins by Methyl H-1 Carr-Purcell-Meiboom-Gill Relaxation Dispersion NMR Measurements. Application to Activation of the Signaling Protein NtrC(r)

    NARCIS (Netherlands)

    Otten, Renee; Villali, Janice; Kern, Dorothee; Mulder, Frans A. A.

    2010-01-01

    To study microsecond processes by relaxation dispersion NMR spectroscopy, low power deposition and short pulses are crucial and encourage the development of experiments that employ H-1 Carr-Purcell-Meiboom-Gill (CPMG) pulse trains. Herein, a method is described for the comprehensive study of

  8. Sensitization of a stray-field NMR to vibrations: a potential for MR elastometry with a portable NMR sensor.

    Science.gov (United States)

    Mastikhin, Igor; Barnhill, Marie

    2014-11-01

    An NMR signal from a sample in a constant stray field of a portable NMR sensor is sensitized to vibrations. The CPMG sequence is synchronized to vibrations so that the constant gradient becomes an "effective" square-wave gradient, leading to the vibration-induced phase accumulation. The integrating nature of the spot measurement, combined with the phase distribution due to a non-uniform gradient and/or a wave field, leads to a destructive interference, the drop in the signal intensity and changes in the echo train shape. Vibrations with amplitudes as small as 140 nm were reliably detected with the permanent gradient of 12.4 T/m. The signal intensity depends on the phase offset between the vibrations and the pulse sequence. This approach opens the way for performing elastometry and micro-rheology measurements with portable NMR devices beyond the walls of a laboratory. Even without synchronization, if a vibration frequency is comparable to 1/2TE of the CPMG sequence, the signal can be severely affected, making it important for potential industrial applications of stray-field NMR. Copyright © 2014 Elsevier Inc. All rights reserved.

  9. European interlaboratory comparison of breath (CO2)-C-13 analysis

    NARCIS (Netherlands)

    Stellaard, F; Geypens, B

    1998-01-01

    The BIOMED I programme Stable Isotopes in Gastroenterology and Nutrition (SIGN) has focused upon evaluation and standardisation of stable isotope breath tests using C-13 labelled substrates. The programme dealt with comparison of C-13 substrates, test meats, test conditions, analysis techniques, and

  10. Use of NMR metabolomic plasma profiling methodologies to identify illicit growth-promoting administrations.

    Science.gov (United States)

    Graham, Stewart F; Ruiz-Aracama, Ainhoa; Lommen, Arjen; Cannizzo, Francesca T; Biolatti, Bartolomeo; Elliott, Christopher T; Mooney, Mark H

    2012-04-01

    Detection of growth-promoter use in animal production systems still proves to be an analytical challenge despite years of activity in the field. This study reports on the capability of NMR metabolomic profiling techniques to discriminate between plasma samples obtained from cattle treated with different groups of growth-promoting hormones (dexamethasone, prednisolone, oestradiol) based on recorded metabolite profiles. Two methods of NMR analysis were investigated-a Carr-Purcell-Meiboom-Gill (CPMG)-pulse sequence technique and a conventional (1)H NMR method using pre-extracted plasma. Using the CPMG method, 17 distinct metabolites could be identified from the spectra. (1)H NMR analysis of extracted plasma facilitated identification of 23 metabolites-six more than the alternative method and all within the aromatic region. Multivariate statistical analysis of acquired data from both forms of NMR analysis separated the plasma metabolite profiles into distinct sample cluster sets representative of the different animal study groups. Samples from both sets of corticosteroid-treated animals-dexamethasone and prednisolone-were found to be clustered relatively closely and had similar alterations to identified metabolite panels. Distinctive metabolite profiles, different from those observed within plasma from corticosteroid-treated animal plasma, were observed in oestradiol-treated animals and samples from these animals formed a cluster spatially isolated from control animal plasma samples. These findings suggest the potential use of NMR methodologies of plasma metabolite analysis as a high-throughput screening technique to aid detection of growth promoter use.

  11. The C-12/C-13 Ratio as a Chemistry Indicator

    Science.gov (United States)

    Wirstroem, Eva; Geppert, Wolf; Persson, Carina; Charnley, Steven

    2011-01-01

    Isotopic ratios of elements are considered powerful tools, e.g. in tracing the origin of solar system body materials, or the degree of nucleosynthesis processing throughout the Galaxy. In interstellar molecules, some isotopic ratios like H/D and C-12/C-13 can also be used as indicators of their chemical origin. Isotope fractionation in gas-phase chemical reactions and gas-dust interaction makes observations of the ratio between C-12 and C-13 isotopologues suitable to distinguish between different formation scenarios. We will present observations of the C-12/C-13 ratio in methanol and formaldehyde towards a sample of embedded, massive young stellar objects. In relation to this we also present results from theoretical modeling showing the usefulness of the C-12/C-13 ratio as a chemistry indicator.

  12. Combined relaxation and diffusion studies of porous media using the multigrade CPMG sequence.

    Science.gov (United States)

    Hills, B P; Wright, K M; Snaar, J E

    1996-01-01

    A new approach to q-space NMR studies of microstructure is proposed that exploits the combined information contained in the water proton transverse relaxation time distribution and the frequency dependence of the apparent water diffusivity. A simple protocol is used to eliminate undesirable crossterms in background susceptibility gradients. Local, microscopic nonlinearity in the applied field gradients is shown to lead to enhancement of the apparent water diffusivity in small pores at high frequencies. The relationships between NMR relaxation studies of pore emptying with sorption isotherms, electrical conductivity, and microbiological survival are indicated.

  13. Increased HOX C13 expression in metastatic melanoma progression

    Directory of Open Access Journals (Sweden)

    Cantile Monica

    2012-05-01

    Full Text Available Abstract Background The process of malignant transformation, progression and metastasis of melanoma is not completely understood. Recently, the microarray technology has been used to survey transcriptional differences that might provide insight into the metastatic process, but the validation of changing gene expression during metastatic transition period is poorly investigated. A large body of literature has been produced on the role of the HOX genes network in tumour evolution, suggesting the involvement of HOX genes in several types of human cancers. Deregulated paralogous group 13 HOX genes expression has been detected in melanoma, cervical cancer and odonthogenic tumors. Among these, Hox C13 is also involved in the expression control of the human keratin genes hHa5 and hHa2, and recently it was identified as a member of human DNA replication complexes. Methods In this study, to investigate HOX C13 expression in melanoma progression, we have compared its expression pattern between naevi, primary melanoma and metastasis. In addition HOXC13 profile pattern of expression has been evaluated in melanoma cell lines. Results Our results show the strong and progressive HOX C13 overexpression in metastatic melanoma tissues and cytological samples compared to nevi and primary melanoma tissues and cells. Conclusions The data presentated in the paper suggest a possible role of HOX C13 in metastatic melanoma switch.

  14. 17alpha/H/ hopane identified in oil shale of the Green River formation /Eocene/ by carbon-13 NMR.

    Science.gov (United States)

    Balogh, B.; Wilson, D. M.; Christiansen, P.; Burlingame, A. L.

    1973-01-01

    During an investigation of C-13 NMR shifts and the structural correspondence of pentacyclic triterpenes a C-13 NMR study was conducted on one of the most abundant components of the hexane soluble fraction of oil shale bitumen of the Green River formation. A rigorous proof was derived exclusively from C-13 NMR data for the structure of the important triterpenoid fossil molecule. It was established that the structure of the isolated triterpane was 17alpha(H) hopane.

  15. Workflow for Integrated Processing of Multicohort Untargeted (1)H NMR Metabolomics Data in Large-Scale Metabolic Epidemiology.

    Science.gov (United States)

    Karaman, Ibrahim; Ferreira, Diana L S; Boulangé, Claire L; Kaluarachchi, Manuja R; Herrington, David; Dona, Anthony C; Castagné, Raphaële; Moayyeri, Alireza; Lehne, Benjamin; Loh, Marie; de Vries, Paul S; Dehghan, Abbas; Franco, Oscar H; Hofman, Albert; Evangelou, Evangelos; Tzoulaki, Ioanna; Elliott, Paul; Lindon, John C; Ebbels, Timothy M D

    2016-12-02

    Large-scale metabolomics studies involving thousands of samples present multiple challenges in data analysis, particularly when an untargeted platform is used. Studies with multiple cohorts and analysis platforms exacerbate existing problems such as peak alignment and normalization. Therefore, there is a need for robust processing pipelines that can ensure reliable data for statistical analysis. The COMBI-BIO project incorporates serum from ∼8000 individuals, in three cohorts, profiled by six assays in two phases using both (1)H NMR and UPLC-MS. Here we present the COMBI-BIO NMR analysis pipeline and demonstrate its fitness for purpose using representative quality control (QC) samples. NMR spectra were first aligned and normalized. After eliminating interfering signals, outliers identified using Hotelling's T(2) were removed and a cohort/phase adjustment was applied, resulting in two NMR data sets (CPMG and NOESY). Alignment of the NMR data was shown to increase the correlation-based alignment quality measure from 0.319 to 0.391 for CPMG and from 0.536 to 0.586 for NOESY, showing that the improvement was present across both large and small peaks. End-to-end quality assessment of the pipeline was achieved using Hotelling's T(2) distributions. For CPMG spectra, the interquartile range decreased from 1.425 in raw QC data to 0.679 in processed spectra, while the corresponding change for NOESY spectra was from 0.795 to 0.636, indicating an improvement in precision following processing. PCA indicated that gross phase and cohort differences were no longer present. These results illustrate that the pipeline produces robust and reproducible data, successfully addressing the methodological challenges of this large multifaceted study.

  16. Simultaneous measurements of T1 and T2 during fast polymerization reaction using continuous wave-free precession NMR method.

    Science.gov (United States)

    Venâncio, Tiago; Colnago, Luiz Alberto

    2012-08-01

    Continuous wave-free precession (CWFP) pulse sequence employing time domain nuclear magnetic resonance spectroscopy (TD-NMR) was used to measure longitudinal (T(1)) and transverse relaxation times (T(2)), during the cure of a commercial epoxy resin (Araldite(TM)) with a 10-min solidification time. The intensity of the NMR signal after the first pulse and in the CWFP regime were used to monitor the concentration of the monomers, and the relaxation times were used to monitor the chain mobility. The main advantage of CWFP over the standard methods to measure relaxation times, inversion recovery (inv-rec) for T(1) and Carr-Purcell-Meiboom-Gill (CPMG) for T(2), is that the measurement of both relaxation times can be performed in a fast and single NMR experiment and, therefore, using a single reaction batch. CWFP is also as fast as the CPMG measurement but at least fivefold faster than the method to obtain T(1) using null point approximation in the inv-rec method. Therefore, the CWFP sequence can be used as a fast and general method to measure relaxation times in polymerization reactions, even with fast solidification time. As a TD-NMR technique, CWFP can be employed in any low-cost bench top TD-NMR equipment commonly used in an academic or industrial laboratory. Copyright © 2012 John Wiley & Sons, Ltd.

  17. Multi-platform subsystem for controlling acquisition, visualization and data organization of an NMR Digital Spectrometer: ToRM Console; Subsistema multiplataforma para controle de aquisicao, visualizacao e organizacao de dados do Espectrometro Digital de RM: ToRM Console

    Energy Technology Data Exchange (ETDEWEB)

    Silva, Danilo M.D.D. da; Pizetta, Daniel C.; Freire, Guilherme M.; Coelho, Felipe B.; Lourenco, Gustavo V.; Correa, Rodrigo R.M.; Martins, Mateus J.; Vidoto, Edson L.G.; Tannus, Alberto, E-mail: danilomendes@usp.br, E-mail: danilomendesdias@gmail.com [Universidade de Sao Paulo (CIERMag/USP), Sao Carlos, SP (Brazil). Int. de Fisica. Centro de Imagens e Espectroscopia ' in vivo' por Ressonancia Magnetica

    2013-08-15

    In this work, we present the recent results from the development of the CIERMag NMR Digital Spectrometer - a subsystem for controlling acquisition, visualization and data organization. Some aspects of the architecture and features will be shown, including a demonstration with CPMG method for transversal relaxation time (T{sub 2}) measurement using the system. With these achievements, ToRM Console is now being prepared to be an MRI scanner in a near future (author)

  18. Sensitive and robust electrophoretic NMR: Instrumentation and experiments

    Science.gov (United States)

    Hallberg, Fredrik; Furó, István; Yushmanov, Pavel V.; Stilbs, Peter

    2008-05-01

    Although simple as a concept, electrophoretic NMR (eNMR) has so far failed to find wider application. Problems encountered are mainly due to disturbing and partly irreproducible convection-like bulk flow effects from both electro-osmosis and thermal convection. Additionally, bubble formation at the electrodes and rf noise pickup has constrained the typical sample geometry to U-tube-like arrangements with a small filling factor and a low resulting NMR sensitivity. Furthermore, the sign of the electrophoretic mobility cancels out in U-tube geometries. We present here a new electrophoretic sample cell based on a vertically placed conventional NMR sample tube with bubble-suppressing palladium metal as electrode material. A suitable radiofrequency filter design prevents noise pickup by the NMR sample coil from the high-voltage leads which extend into the sensitive sample volume. Hence, the obtained signal-to-noise ratio of this cell is one order of magnitude higher than that of our previous U-tube cells. Permitted by the retention of the sign of the displacement-related signal phase in the new cell design, an experimental approach is described where bulk flow effects by electro-osmosis and/or thermal convection are compensated through parallel monitoring of a reference signal from a non-charged species in the sample. This approach, together with a CPMG-like pulse train scheme provides a superior first-order cancellation of non-electrophoretic bulk flow effects.

  19. Impact of chemotherapy on metabolic reprogramming: Characterization of the metabolic profile of breast cancer MDA-MB-231 cells using 1H HR-MAS NMR spectroscopy.

    Science.gov (United States)

    Maria, Roberta M; Altei, Wanessa F; Selistre-de-Araujo, Heloisa S; Colnago, Luiz A

    2017-11-30

    Doxorubicin, cisplatin, and tamoxifen are part of many chemotherapeutic regimens. However, studies investigating the effect of chemotherapy on the metabolism of breast cancer cells are still limited. We used 1H high-resolution magic angle spinning (HR-MAS) NMR spectroscopy to study the metabolic profile of human breast cancer MDA-MB-231 cells either untreated (control) or treated with tamoxifen, cisplatin, and doxorubicin. 1H HR-MAS NMR single pulse spectra evidenced signals from all mobile cell compounds, including fatty acids (membranes), water-soluble proteins, and metabolites. NMR spectra showed that phosphocholine (i.e., a biomarker of breast cancer malignant transformation) signals were stronger in control than in treated cells, but significantly decreased upon treatment with tamoxifen/cisplatin. NMR spectra acquired with Carr-Purcell-Meiboom-Gill (CPMG) pulse sequence were interpreted only qualitatively because signal areas were attenuated according to their transverse relaxation times (T2). The CPMG method was used to identify soluble metabolites such as organic acids, amino acids, choline and derivatives, taurine, guanidine acetate, tyrosine, and phenylalanine. The fatty acid variations observed by single pulse as well as the lactate, acetate, glycine, and phosphocholine variations observed through CPMG 1H HR-MAS NMR have potential to characterize both responder and non-responder tumors in a molecular level. Additionally, we emphasized that comparable tumors (i.e., with the same origin, in this case breast cancer) may respond totally differently to chemotherapy. Our observations reinforce the theory that alterations in cellular metabolism may contribute to the development of a malignant phenotype and cell resistance. Copyright © 2017 Elsevier B.V. All rights reserved.

  20. Non-uniform sampling of NMR relaxation data

    DEFF Research Database (Denmark)

    Schwarz-Linnet, Troels; Teilum, Kaare

    2016-01-01

    The use of non-uniform sampling of NMR spectra may give significant reductions in the data acquisition time. For quantitative experiments such as the measurement of spin relaxation rates, non-uniform sampling is however not widely used as inaccuracies in peak intensities may lead to errors...... in the extracted dynamic parameters. By systematic reducing the coverage of the Nyquist grid of (15)N Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion datasets for four different proteins and performing a full data analysis of the resulting non-uniform sampled datasets, we have compared the performance...... reconstructs the non-uniform sampled spectra with high accuracy. For two of the four analyzed datasets, a coverage of only 20 % results in essentially the same results as the fully sampled data. As exemplified by other data, such a low coverage is in general not enough to produce reliable results. We find...

  1. Analysis of Inevitable Variation in C13 or HNMR Spectra Derived from One Substance for a aStructure Elucidation on the Basis of a Concept of Informational Homology

    OpenAIRE

    Kudo, Yoshihiro; Sato, Noriko; Sugai, Toshitaka

    1992-01-01

    Abstract In order to design a spectral comparison complementary with structure elucidation, actual aspects of differences among C13- or H-nmr spectra of a common compound were examined. Two handbooks, one for C13- and one for H-nmr spectra, were assumed to be data bases of the reference spectra. The handbooks were searched for common substances whose about 400 spectra were used as exercises in three books. It was confirmed that spectral variation was inevitable whenever spectral data are extr...

  2. C-13 Tracer experiments and metabolite balancing for metabolic flux analysis

    DEFF Research Database (Denmark)

    Schmidt, Karsten; Marx, A.; de Graaf, A. A.

    1998-01-01

    Conventional metabolic flux analysis uses the information gained from determination of measurable fluxes and a steady-state assumption for intracellular metabolites to calculate the metabolic fluxes in a given metabolic network. The determination of intracellular fluxes depends heavily on the cor......Conventional metabolic flux analysis uses the information gained from determination of measurable fluxes and a steady-state assumption for intracellular metabolites to calculate the metabolic fluxes in a given metabolic network. The determination of intracellular fluxes depends heavily...... through the pentose phosphate pathway. Hence, wrong assumptions on the presence or activity of transhydrogenation reactions will result in wrong estimations of the intracellular flux distribution. Using C-13 tracer experiments and NMR analysis, flux analysis can be performed on the basis of only well...... are two different approaches to the determination of intracellular fluxes, both methods can be used to verify each other or to discuss the origin and significance of deviations in the results. Flux analysis based entirely on metabolite balancing and flux analysis, including labeling information, have been...

  3. 26 CFR 1.381(c)(13)-1 - Involuntary conversions.

    Science.gov (United States)

    2010-04-01

    ... 26 Internal Revenue 4 2010-04-01 2010-04-01 false Involuntary conversions. 1.381(c)(13)-1 Section 1.381(c)(13)-1 Internal Revenue INTERNAL REVENUE SERVICE, DEPARTMENT OF THE TREASURY (CONTINUED) INCOME TAX (CONTINUED) INCOME TAXES Insolvency Reorganizations § 1.381(c)(13)-1 Involuntary conversions...

  4. 40 CFR 721.6505 - Polymers of C13C15 oxoalcohol ethoxolates.

    Science.gov (United States)

    2010-07-01

    ... 40 Protection of Environment 30 2010-07-01 2010-07-01 false Polymers of C13C15 oxoalcohol... Specific Chemical Substances § 721.6505 Polymers of C13C15 oxoalcohol ethoxolates. (a) Chemical substance... polymers of C13C15 oxoalcohol ethoxolates (PMNs P-96-950/951) are subject to reporting under this section...

  5. Measurement of the Dissociation-Equilibrium Constants for Low Affinity Antibiotic Binding Interaction with Bacterial Ribosomes by the T2 (CPMG) and Line-Broadening Methods

    Science.gov (United States)

    Verdier, L.; Gharbi-Benarous, J.; Bertho, G.; Mauvais, P.; Girault, J.-P.

    1999-10-01

    In this study the dissociation constants of the low antibiotic-ribosomes interaction were determined by the T2 (CPMG), the Carr-Purcell-Meiboom-Gill spin-echo decay rate and the line-broadening methods. Three MLSB antibiotics were studied, a macrolide roxithromycin, a ketolide HMR 3647 and a lincosamide clindamycin for their weak interaction with three bacterial ribosomes, E. coli, Staphylococcus aureus sensitive and resistant to erythromycin. Nous avons mesuré la constante de dissociation, Kd correspondant à l'interaction faible antibiotique-ribosome bactérien pour des antibiotiques de différentes classes, un macrolide (roxithromycine), un kétolide (HMR 3647) et une lincosamide (clindamycine) avec des ribosomes de différentes souches bactériennes (E. coli, Staphylococcus aureus sensible ou résistant à l'erythromycin) par deux méthodes : l'une basée sur la variation des largeurs de raies et l'autre sur les temps de relaxation transversaux T2 en utilisant une séquence CPMG.

  6. NMR of geophysical drill cores with a mobile Halbach scanner

    Energy Technology Data Exchange (ETDEWEB)

    Talnishnikh, E.

    2007-08-21

    This thesis is devoted to a mobile NMR with an improved Halbach scanner. This is a lightweight tube-shaped magnet with sensitive volume larger and a homogeneity of the magnetic field higher than the previous prototype version. The improved Halbach scanner is used for analysis of water-saturated drill cores and plugs with diameters up to 60 mm. To provide the analysis, the standard 1D technique with the CPMG sequence as well as 2D correlation experiments were successfully applied and adapted to study properties of fluid-saturated sediments. Afterwards the Halbach scanner was calibrated to fast non-destructive measurements of porosity, relaxation time distributions, and estimation of permeability. These properties can be calculated directly from the NMR data using the developed methodology. Any independent measurements of these properties with other methods are not needed. One of the main results of this work is the development of a new NMR on-line core scanner for measurements of porosity in long cylindrical and semi cylindrical drill cores. Also dedicated software was written to operate the NMR on-line core scanner. The physical background of this work is the study of the diffusion influence on transverse relaxation. The diffusion effect in the presence of internal gradients in porous media was probed by 1D and 2D experiments. The transverse relaxation time distributions obtained from 1D and from 2D experiments are comparable but different in fine details. Two new methodologies were developed based on the results of this study. First is the methodology quantifying the influence of diffusion in the internal gradients of water-saturated sediments on transverse relaxation from 2D correlation experiments. The second one is the correction of the permeability estimation from the NMR data taking in account the influence of the diffusion. Furthermore, PFG NMR technique was used to study restricted diffusion in the same kind of samples. Preliminary results are reported

  7. Transport of C-13-labelled linoleic and C-13-labelled caprylic acid in rat plasma after administration of specific structured triacylglycerols

    DEFF Research Database (Denmark)

    Vistisen, Bodil; Høy, Carl-Erik

    2004-01-01

    the transport of dietary C-13-labelled fatty acids in rat plasma to compare the chylomicron fatty acid metabolism after administration of specific structured, long chain and medium chain triacylglycerols. Rats were fed ML*M, M*LM*, L*L*L* or M*M*M* (L=linoleic acid, 18:2n-6, M=caprylic acid, 8:0, * = C-13......-labelled fatty acid) by gavage. A maximum transport of 0.5% of the administered C-13-labelled 18:2n-6 was observed in 1mL rat plasma both after administration of L*L*L* and ML*M, while approximately 0.04% of the administered C-13-labelled 8:0 was detected in 1mL plasma following administration of M......*M*M* or M*LM*. After L*L*L* administration C-13-labelled 20:4n-6 was observed in plasma, probably formed by elongation and desaturation of 18:2n-6 in the enterocyte or liver cells. Furthermore, C-13-labelled 16:0, 48:0, 18: 1n-9 and 20:4n-6 were observed in plasma of rats fed M*M*M* and M*LM* due...

  8. 119Sn MAS NMR Study of Probe Molecules Interaction with Sn-BEA: The Origin of Penta- and Hexacoordinated Tin Formation

    DEFF Research Database (Denmark)

    Yakimov, Alexander V.; G. Kolyagin, Yury; Tolborg, Søren

    2016-01-01

    119Sn CPMG MAS NMR was applied to study the adsorption of acetonitrile, methanol, isopropanol, isobutanol and water over Sn-BEA enriched with 119Sn isotope. Two signals observed at ca. -422 and -443 ppm over dehydrated samples were attributed to tetracoordinated framework tin sites with strong...... and weak Lewis acidity, respectively. The adsorption of acetonitrile and methanol resulted in observation of pentacoordinated tin species, due to the formation of 1:1 adsorption complexes over both Sn-sites. Water adsorption led first to formation of pentacoordinated tin species, which were further...

  9. Organic matter decomposition : bridging the gap between Rock-Eval pyrolysis and chemical characterization (CPMAS C-13 NMR)

    OpenAIRE

    Albrecht, R; Sebag, David; Verrecchia, E.

    2015-01-01

    Organic matter (OM) is a key component of soils but information on its chemistry and behavior in soils is still incomplete. Numerous methods are commonly used to characterize and monitor OM dynamics, but only a few include the qualities required to become routine techniques i.e. simple, rapid, accurate and at low cost. Rock-Eval pyrolysis (RE pyrolysis) is a good candidate, as it provides an overview of OM properties by monitoring four components related to the main major classes of organic c...

  10. C-13 NMR Spectroscopy of N-Heterocyclic Carbenes Can Selectively Probe sigma Donation in Gold(I) Complexes

    NARCIS (Netherlands)

    Marchione, Demian; Izquierdo, Maria A.; Bistoni, Giovanni; Havenith, Remco W. A.; Macchioni, Alceo; Zuccaccia, Daniele; Tarantelli, Francesco; Belpassi, Leonardo

    The Dewar-Chatt-Duncanson (DCD) model provides a successful theoretical framework to describe the nature of the chemical bond in transition-metal compounds and is especially useful in structural chemistry and catalysis. However, how to actually measure its constituents (substrate- to-metal donation

  11. Sensitivity-enhanced C-13 MR spectroscopy of the human brain at 3 Tesla

    NARCIS (Netherlands)

    Klomp, D.W.J.; Renema, W.K.J.; Graaf, M. van der; Galan, B.E. de; Kentgens, A.P.M.; Heerschap, A.

    2006-01-01

    A new coil design for sensitivity-enhanced C-13 MR spectroscopy (MRS) of the human brain is presented. The design includes a quadrature transmit/receive head coil optimized for C-13 MR sensitivity. Loss-less blocking circuits inside the coil conductors allow this coil to be used inside a homogeneous

  12. 26 CFR 1.501(c)(13)-1 - Cemetery companies and crematoria.

    Science.gov (United States)

    2010-04-01

    ... 26 Internal Revenue 7 2010-04-01 2010-04-01 true Cemetery companies and crematoria. 1.501(c)(13)-1...) INCOME TAX (CONTINUED) INCOME TAXES (CONTINUED) Exempt Organizations § 1.501(c)(13)-1 Cemetery companies and crematoria. (a) Nonprofit mutual cemetery companies. A nonprofit cemetery company may be entitled...

  13. Yield and enrichment studies of C-13 isotope by multi-photon ...

    Indian Academy of Sciences (India)

    e-mail: gmanoj@cat.ernet.in. MS received 11 March 2003; revised 17 May 2003. Abstract. Multi-photon dissociation of Freon-22 (CF2HCl) at low temperatures has been carried out to separate the C-13 isotope using a TEA CO2 laser. Yield and enrichment of C-13 isotope in the product C2F4 are studied at 9P(22) laser line ...

  14. Yield and enrichment studies of C-13 isotope by multi-photon ...

    Indian Academy of Sciences (India)

    Multi-photon dissociation of Freon-22 (CF2HCl) at low temperatures has been carried out to separate the C-13 isotope using a TEA CO2 laser. Yield and enrichment of C-13 isotope in the product C2F4 are studied at 9(22) laser line as a function of temperature (-50°C to 30°C). It is observed that at a given fluence when ...

  15. Comparative study of inversion methods of three-dimensional NMR and sensitivity to fluids

    Science.gov (United States)

    Tan, Maojin; Wang, Peng; Mao, Keyu

    2014-04-01

    Three-dimensional nuclear magnetic resonance (3D NMR) logging can simultaneously measure transverse relaxation time (T2), longitudinal relaxation time (T1), and diffusion coefficient (D). These parameters can be used to distinguish fluids in the porous reservoirs. For 3D NMR logging, the relaxation mechanism and mathematical model, Fredholm equation, are introduced, and the inversion methods including Singular Value Decomposition (SVD), Butler-Reeds-Dawson (BRD), and Global Inversion (GI) methods are studied in detail, respectively. During one simulation test, multi-echo CPMG sequence activation is designed firstly, echo trains of the ideal fluid models are synthesized, then an inversion algorithm is carried on these synthetic echo trains, and finally T2-T1-D map is built. Futhermore, SVD, BRD, and GI methods are respectively applied into a same fluid model, and the computing speed and inversion accuracy are compared and analyzed. When the optimal inversion method and matrix dimention are applied, the inversion results are in good aggreement with the supposed fluid model, which indicates that the inversion method of 3D NMR is applieable for fluid typing of oil and gas reservoirs. Additionally, the forward modeling and inversion tests are made in oil-water and gas-water models, respectively, the sensitivity to the fluids in different magnetic field gradients is also examined in detail. The effect of magnetic gradient on fluid typing in 3D NMR logging is stuied and the optimal manetic gradient is choosen.

  16. Seasonal C-13 variations of methane from an anoxic marine sediment

    Science.gov (United States)

    Blair, Neal; Desmarais, David S.; Martens, Christopher S.

    1985-01-01

    Recent analyses of glacial ice suggest that the atmospheric concentration of methane has doubled in the last several hundred years, presumably due to anthropogenic perturbations of the relevant biogeochemical cycles. In principal, carbon isotopic measurements of atmospheric methane would provide information concerning changes in the sources and sinks of methane. The isotopic composition of methane is dependent on the source of the methane carbon, the mechanism of methane synthesis, and the degree and mode of oxidation which the methane has experienced. Unfortunately, few carbon isotopic measurements of atmospheric variations have been reported, so conclusions about temporal isotopic variations cannot be made. Also, before isotopic measurements of atmospheric methane can be used to identify changes in methane isotopic composition from different sources must be obtained. Methane bubbles from the anoxic sediments of Cape Lookout Bight, NC exhibit seasonal C-13 variations. The C-13 values ranged from -58 in August to -64 in the winter months with the evolution of the C-13 enriched gas occurring during periods of peak methane production. Even though a few intramolecular C-13 measurements of the pore water acetate have been made (methyl group, -26 per mil; carbonyl, -6 per mil), it is not clear how the acetate fermentation pathway affects the methane C-13/C-12 composition.

  17. Measuring diffusion-relaxation correlation maps using non-uniform field gradients of single-sided NMR devices.

    Science.gov (United States)

    Nogueira d'Eurydice, Marcel; Galvosas, Petrik

    2014-11-01

    Single-sided NMR systems are becoming a relevant tool in industry and laboratory environments due to their low cost, low maintenance and capacity to evaluate quantity and quality of hydrogen based materials. The performance of such devices has improved significantly over the last decade, providing increased field homogeneity, field strength and even controlled static field gradients. For a class of these devices, the configuration of the permanent magnets provides a linear variation of the magnetic field and can be used in diffusion measurements. However, magnet design depends directly on its application and, according to the purpose, the field homogeneity may significantly be compromised. This may prevent the determination of diffusion properties of fluids based on the natural inhomogeneity of the field using known techniques. This work introduces a new approach that extends the applicability of diffusion-editing CPMG experiments to NMR devices with highly inhomogeneous magnetic fields, which do not vary linearly in space. Herein, we propose a method to determine a custom diffusion kernel based on the gradient distribution, which can be seen as a signature of each NMR device. This new diffusion kernel is then utilised in the 2D inverse Laplace transform (2D ILT) in order to determine diffusion-relaxation correlation maps of homogeneous multi-phasic fluids. The experiments were performed using NMR MObile Lateral Explore (MOLE), which is a single-sided NMR device designed to maximise the volume at the sweet spot with enhanced depth penetration. Copyright © 2014 Elsevier Inc. All rights reserved.

  18. Metabolic network analysis of Penicillium chrysogenum using C-13-labeled glucose

    DEFF Research Database (Denmark)

    Christensen, Bjarke; Nielsen, Jens

    2000-01-01

    Using C-13-labeled glucose fed to a penicillin-overproducing strain of Penicillium chrysogenum, the intracellular fluxes were quantified, and the presence of two new pathways, not previously described in this organism, is suggested. Thus, glycine was synthesized not only by serine hydroxymethyltr......Using C-13-labeled glucose fed to a penicillin-overproducing strain of Penicillium chrysogenum, the intracellular fluxes were quantified, and the presence of two new pathways, not previously described in this organism, is suggested. Thus, glycine was synthesized not only by serine...

  19. Particulate organic matter delta C-13 variations across the Drake Passage

    Science.gov (United States)

    Rau, G. H.; Takahashi, T.; Des Marais, D. J.; Sullivan, C. W.

    1991-01-01

    Particulate organic matter (POM) was sampled during two cruise transects across the Drake Passage during March 1986 to investigate the unusual C-13 depletion in high-latitude Southern Ocean plankton. This POM delta C-13 transition from -23.2 o/oo at 53.3 deg S to values as low as -30.3 o/oo at above 62 deg S does not track previously reported abrupt changes in water chemistry and plankton species composition associated with the Polar Front Zone. The north-south isotopic trend is not accompanied by significant changes in POM carbon or nitrogen concentrations, or in POM C/N. Differences in plankton standing crop or biochemistry (e.g. lipid content) do not appear responsible for the isotopic trends observed. The latitudinal change in POM delta C-13 is highly correlated with water temperature and with the calculated concentration of CO2 (aq) at equilibrium with atmospheric CO2. These observations are consistent with the hypothesis that CO2 (aq) significantly influences POM delta C-13 in ocean surface waters.

  20. Enhanced Production of Palmarumycins C12 and C13 in Mycelial ...

    African Journals Online (AJOL)

    Purpose: To evaluate in situ macroporous resin adsorption for enhancement of palmarumycins C12 and C13 production in mycelial liquid culture of the endophytic fungus Berkleasmium sp. Dzf12. Methods: Ten macroporous adsorption resins (D-101, D1300, HPD-100, X-5, AB-8, DM130, ADS-17, DA-201, NKA-9 and S-8) ...

  1. Adulteration of honey : relation between microscopic analysis and delta C-13 measurements

    NARCIS (Netherlands)

    Kerkvliet, JD; Meijer, HAJ

    2000-01-01

    Upon routine microscopic analysis of some honey samples, parenchyma cells, single rings of ring vessels and epidermal cells are found. These cells originate from the sugar cane stem. We investigated whether there was a relation between these plant fragments and the delta C-13 value of honey. 17

  2. An explanation for the high stability of polycarboxythiophenes in photovoltaic devices—A solid-state NMR dipolar recoupling study

    DEFF Research Database (Denmark)

    Bierring, M.; Nielsen, J.S.; Siu, Ana

    2008-01-01

    acid carbon atoms were measured by C-13 solid-state magic-angle-spinning (MAS) NMR using symmetry-based double-quantum (2Q) dipolar recoupling. This revealed the presence of C-13-C-13 distances of 3.85 angstrom, which correspond to the C-C distance in hydrogen-bonded carboxylic acid dimers. In spite...... of the presence of carboxylic groups in the polymer as demonstrated by C-13 CP/MAS NMR and IR spectroscopy, the absence of carboxylic protons in solid state H-1 NMR spectra indicate that they are mobile. We link the extraordinary stability of this system to the rigid nature, cross-linking through a hydrogen...

  3. Maximization of yield of C-13 isotope by multiphoton dissociation of ...

    Indian Academy of Sciences (India)

    Abstract. Selective multi-photon dissociation (MPD) of Freon-22 (CF2HCl) molecules has been carried out using a TEA CO2 laser at various CO2 laser lines. (9P(20)-9P(26)) in order to maximize the yield of C-13 isotope in the product (C2F4) at an enrichment factor of 100. The effects of laser pulse tail due to the presence of ...

  4. NMR of lignins

    Science.gov (United States)

    John Ralph; Larry L. Landucci

    2010-01-01

    This chapter will consider the basic aspects and findings of several forms of NMR spectroscopy, including separate discussions of proton, carbon, heteronuclear, and multidimensional NMR. Enhanced focus will be on 13C NMR, because of its qualitative and quantitative importance, followed by NMR’s contributions to our understanding of lignin...

  5. C12/C13-ratio determination in nanodiamonds by atom-probe tomography.

    Science.gov (United States)

    Lewis, Josiah B; Isheim, Dieter; Floss, Christine; Seidman, David N

    2015-12-01

    The astrophysical origins of ∼ 3 nm-diameter meteoritic nanodiamonds can be inferred from the ratio of C12/C13. It is essential to achieve high spatial and mass resolving power and minimize all sources of signal loss in order to obtain statistically significant measurements. We conducted atom-probe tomography on meteoritic nanodiamonds embedded between layers of Pt. We describe sample preparation, atom-probe tomography analysis, 3D reconstruction, and bias correction. We present new data from meteoritic nanodiamonds and terrestrial standards and discuss methods to correct isotopic measurements made with the atom-probe tomograph. Copyright © 2015 Elsevier B.V. All rights reserved.

  6. Analysis of oil content and oil quality in oilseeds by low-field NMR; Analise do teor e da qualidade dos lipideos presentes em sementes de oleaginosas por RMN de baixo campo

    Energy Technology Data Exchange (ETDEWEB)

    Constantino, Andre F.; Lacerda Junior, Valdemar; Santos, Reginaldo B. dos; Greco, Sandro J.; Silva, Renzo C.; Neto, Alvaro C.; Barbosa, Lucio L.; Castro, Eustaquio V.R. de [Universidade Federal do Espirito Santo (UFES), Vitoria, ES (Brazil). Departamento de Quimica; Freitas, Jair C.C. [Universidade Federal do Espirito Santo (UFES), Vitoria, ES (Brazil). Departamento de Fisica

    2014-07-01

    To choose among the variety of oleaginous plants for biodiesel production, the oil content of several matrices was determined through different low-field {sup 1}H nuclear magnetic resonance (NMR) experiments with varied pulse sequences, namely single-pulse, spin-echo, CPMG, and CWFP. The experiments that involved the first three sequences showed high correlation with each other and with the solvent extraction method. The quality of the vegetable oils was also evaluated on the basis of the existing correlation between the T{sub 2} values of the oils and their properties, such as viscosity, iodine index, and cetane index. These analyses were performed using HCA and PCA chemometric tools. The results were sufficiently significant to allow separation of the oleaginous matrices according to their quality. Thus, the low-field {sup 1}H NMR technique was confirmed as an important tool to aid in the selection of oleaginous matrices for biodiesel production. (author)

  7. Site-specific enzymatic hydrolysis of taxanes at C-10 and C-13.

    Science.gov (United States)

    Hanson, R L; Wasylyk, J M; Nanduri, V B; Cazzulino, D L; Patel, R N; Szarka, L J

    1994-09-02

    The production of large amounts of paclitaxel for use as an anticancer treatment has been a challenging problem because of the low concentration of the compound in yew trees and its occurrence as part of a mixture of other taxanes. Two novel enzymes were isolated to facilitate the production of 10-deacetylbaccatin III, a precursor used for semisynthesis of paclitaxel and analogs. A strain of Nocardioides albus (SC13911) was isolated from soil and found to produce an extracellular enzyme that specifically removed the C-13 side chain from paclitaxel, cephalomannine, 7-beta-xylosyltaxol, 7-beta-xylosyl-10-deacetyltaxol, and 10-deacetyltaxol. The enzyme was purified to near homogeneity to give a polypeptide with 47,000 M(r) on a sodium dodecyl sulfate gel. A strain of Nocardioides luteus (SC13912) isolated from soil was found to produce an intracellular 10-deacetylase that removed the 10-acetate from baccatin III and paclitaxel. The 10-deacetylase was purified to give a polypeptide with 40,000 M(r) on a sodium dodecyl sulfate gel. Treatment of extracts prepared from a variety of yew cultivars with the C-13-deacylase and C-10-deacetylase converted a complex mixture of taxanes primarily to 10-deacetylbaccatin III and increased the amount of this key precursor by 4-24 times.

  8. 119Sn MAS NMR Study of Probe Molecules Interaction with Sn-BEA: The Origin of Penta- and Hexacoordinated Tin Formation

    DEFF Research Database (Denmark)

    Yakimov, Alexander V.; G. Kolyagin, Yury; Tolborg, Søren

    2016-01-01

    119Sn CPMG MAS NMR was applied to study the adsorption of acetonitrile, methanol, isopropanol, isobutanol and water over Sn-BEA enriched with 119Sn isotope. Two signals observed at ca. -422 and -443 ppm over dehydrated samples were attributed to tetracoordinated framework tin sites with strong...... and weak Lewis acidity, respectively. The adsorption of acetonitrile and methanol resulted in observation of pentacoordinated tin species, due to the formation of 1:1 adsorption complexes over both Sn-sites. Water adsorption led first to formation of pentacoordinated tin species, which were further...... converted into hexacoordinated species at longer reaction times. The latter transformation was found to be kinetically limited and was attributed to chemical interaction of tin sites with water, such as hydrolysis of Si-O-Sn bonds. The adsorption of isopropanol and isobutanol was accompanied...

  9. Phenotypic characterization of glucose repression mutants of Saccharomyce cerevisiae usinge experiments with C-13-labelled glucose

    DEFF Research Database (Denmark)

    Vijayendran, Raghevendran; Gombert, A.K.; Christensen, B.

    2004-01-01

    glucose. Through GC-MS analysis of the C-13 incorporated into the amino acids of cellular proteins, it was possible to obtain quantitative information on the function of the central carbon metabolism in the different mutants. Traditionally, such labelling data have been used to quantify metabolic fluxes...... through the use of a suitable mathematical model, but here we show that the raw labelling data may also be used directly for phenotypic characterization of different mutant strains. Different glucose derepressed strains investigated employed are the disruption mutants reg1, hxk2, grr1, mig1 and mig1mig2...... and the reference strain CEN.PK113-7D. Principal components analysis of the summed fractional labelling data show that deleting the genes HXK2 and GRR1 results in similar phenotype at the fluxome level, with a partial alleviation of glucose repression on the respiratory metabolism. Furthermore, deletion...

  10. Tetrafibricin: synthesis of the C1-C13, C15-C25, and C27-C40 fragments.

    Science.gov (United States)

    BouzBouz, Samir; Cossy, Janine

    2004-09-30

    [structure: see text] A sequence of chemoselective cross-metathesis reactions and enantioselective allyltitanations of aldehydes has been used to prepare the C1-C13, C15-C26, and C27-C40 fragments of tetrafibricin.

  11. Orientation-dependent (19)F dipolar couplings within a trifluoromethyl group are revealed by static multipulse NMR in the solid state.

    Science.gov (United States)

    Grage, S L; Ulrich, A S

    2000-09-01

    The homonuclear dipolar coupling between the three equivalent (19)F-spins of a trifluoromethyl group, rotating about its threefold symmetry axis, was studied by multipulse solid-state NMR. A modified CPMG sequence was used first to resolve the dipolar splitting of a powder sample, and then to follow its orientation-dependence in uniaxially aligned samples. Our aim is to employ the CF(3)-group as a highly sensitive reporter to describe the mobility and spacial alignment of (19)F-labeled molecules in biomembranes. As an example, the fluorinated anti-inflammatory drug, flufenamic acid, was embedded as a guest compound in lipid bilayers. Undistorted (19)F dipolar spectra of its CF(3)-group were obtained without (1)H-decoupling, revealing a sharp triplet lineshape. When an oriented membrane sample was tilted in the magnetic field, the change in dipolar splittings confirmed that the guest molecule is motionally averaged about the membrane normal, as expected. A different behavior of flufenamic acid, however, was observed under conditions of low bilayer hydration. From this set of orientation-dependent lineshapes we conclude that the axis of motional averaging becomes aligned perpendicular to the sample normal. It thus appears that flufenamic acid induces a hexagonal phase in the membrane at low hydration. Finally, the dipolar (19)F NMR experiments were extended to frozen samples, where no molecular diffusion occurs besides the fast rotation about the CF(3)-axis. Also under these conditions, the CPMG experiment with composite pulses could successfully resolve the dipolar coupling between the three (19)F-nuclei. Copyright 2000 Academic Press.

  12. NMR logging apparatus

    Science.gov (United States)

    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.

  13. The ^{12}C/^{13}C Ratio in the Galactic Center: Implications for Galactic Chemical Evolution and Isotope Chemistry

    Science.gov (United States)

    Halfen, DeWayne T.; Ziurys, Lucy M.

    2017-06-01

    Observations from a spectral-line survey of Sgr B2(N) of the ^{12}C and ^{13}C isotopologues of H_2CS, CH_3CCH, NH_2CHO, CH_2CHCN, and CH_3CH_2CN have been analyzed to more accurately establish the ^{12}C/^{13}C ratio in this cloud. The wide spectral coverage has enabled an accurate evaluation of the ^{12}C/^{13}C ratios in these low abundance molecules, based on numerous transitions. The lines typically exhibited two distinct velocity components at 64 and 73 km s^{-1}. The ^{12}C/^{13}C ratio was found to be in the range 18-24 for all 5 molecules, for optically thin transitions, with an average value of 20.5, and did not significantly vary between the two velocity components. The Galactic gradient has been revised to be ^{12}C/^{13}C = 6.08(0.48) D_{GC} + 15.7(2.9). Furthermore, the ^{12}C/^{13}C ratio did not change with substitution site on the molecule. Therefore, there appears to be very little chemical fractionation or isotope-selective photodissociation occurring in Sgr B2(N), and the ^{12}C/^{13}C ratios are a true reflection of the isotopic abundances generated by stellar nucleosynthesis.

  14. Stereoselective Interaction of Phenylbutazone with [12C/13C]Warfarin Pseudoracemates in Man

    Science.gov (United States)

    O'Reilly, Robert A.; Trager, William F.; Motley, Catherine H.; Howald, William

    1980-01-01

    To evaluate the interaction of phenylbutazone with racemic warfarin or R,S-(±)-warfarin in man, S-(−)-warfarin or levowarfarin was synthesized with 13C label in the 2-position of the coumarin nucleus and added to [12C]R(+)-warfarin or dextrowarfarin to form a [12C/13C]pseudoracemate of warfarin. In six normal human subjects, a single oral dose of this “cold labeled” pseudoracemate, 1.5 mg/kg body weight, was administered with and without a daily dosage of phenylbutazone, 300 mg orally, beginning 3 d before the warfarin dose and continuing throughout the hypoprothrombinemia. Plasma samples were obtained daily and analyzed for warfarin content and for one-stage prothrombin activity. Unchanged warfarin in the plasma was fractionated by normal-phase, high-pressure liquid chromatography, and the enantiomorphic ratios were determined by chemical-ionization mass spectrometry with pentadeuteriowarfarin as the internal standard. A highly significant augmentation of the hypoprothrombinemia of the pseudoracemate occurred during the phenylbutazone regimen (P phenylbutazone regimen compared with administration of warfarin alone. It was concluded that phenylbutazone augmented the hypoprothrombinemia of pseudoracemic warfarin stereoselectively by inhibiting the metabolic disposition of the more hypoprothrombinemic levowarfarin, yet reduced the plasma levels of pseudoracemic warfarin by greatly augmenting the metabolic disposition of dextrowarfarin. PMID:7354137

  15. A portable single-sided magnet system for remote NMR measurements of pulmonary function.

    Science.gov (United States)

    Dabaghyan, Mikayel; Muradyan, Iga; Hrovat, Alan; Butler, James; Frederick, Eric; Zhou, Feng; Kyriazis, Angelos; Hardin, Charles; Patz, Samuel; Hrovat, Mirko

    2014-12-01

    In this work, we report initial results from a light-weight, low field magnetic resonance device designed to make relative pulmonary density measurements at the bedside. The development of this device necessarily involves special considerations for the magnet, RF and data acquisition schemes as well as a careful analysis of what is needed to provide useful information in the ICU. A homogeneous field region is created remotely from the surface of the magnet such that when the magnet is placed against the chest, an NMR signal is measured from a small volume in the lung. In order to achieve portability, one must trade off field strength and therefore spatial resolution. We report initial measurements from a ping-pong ball size region in the lung as a function of lung volume. As expected, we measured decreased signal at larger lung volumes since lung density decreases with increasing lung volume. Using a CPMG sequence with ΔTE=3.5 ms and a 20 echo train, a signal to noise ratio ~1100 was obtained from an 8.8mT planar magnet after signal averaging for 43 s. This is the first demonstration of NMR measurements made on a human lung with a light-weight planar NMR device. We argue that very low spatial resolution measurements of different lobar lung regions will provide useful diagnostic information for clinicians treating Acute Respiratory Distress Syndrome as clinicians want to avoid ventilator pressures that cause either lung over distension (too much pressure) or lung collapse (too little pressure). Copyright © 2014 John Wiley & Sons, Ltd.

  16. CO2 and 12C:13C Isotopic Ratios on Phoebe and Iapetus

    Science.gov (United States)

    Clark, R. N.; Brown, R. H.; Cruikshank, D. P.

    2016-12-01

    Cassini VIMS has obtained spatially resolved 0.35 to 5.1 micron reflectance spectra of Saturn's satellites beginning with the Phoebe fly-by in 2004 and a close fly-by of Iapetus in 2007. Both surfaces contain relatively abundant CO2. The new (2016 RC19) calibration of VIMS has provided a significant increase in the data quality, such that isotopic absorption bands in CO2 are now well defined. CO2 on Saturn's icy satellites is trapped (Cruikshank et al., 2010, Icarus v206 p561; Pinilla-Alonso et al. 2011, Icarus v211, p75i), predominantly in the dark material (Clark et al. 2012, Icarus v218 p831). Clark et al. modeled the CO2 abundance as 2.8% on Iapetus and 3.7% on Phoebe. The main 12CO2 band in VIMS spectra on Iapetus occurs at 4.253 microns and Phoebe at 4.266 microns. The 13CO2 absorption is strong on Phoebe at 4.367 microns and weak on Iapetus at 4.387 microns. Converting the Phoebe, Iapetus, and a lab reflectance spectrum (of trace H2O-CO2 mixture on a diffuse substrate), we derive preliminary values for the ratio of the equivalent widths of the 12C and 13C absorptions as 19±2 on Phoebe, 82±8 on Iapetus, and 98±10 for the laboratory spectrum. These ratios are related to the 12C/13C ratio, but there may be effects due to intra-molecular and inter-molecular coupling that will contribute to systematic errors in the isotopic abundances derived using equivalent-width measurements that we've yet to quantify. We Believe the effects are small, and will be attempting to quantify them in the future. For comparison, the terrestrial value of the 12C/13C ratio is 90.17, and vibrational coupling may explain the slightly high lab mixture result. The local interstellar medium is 69±15 (Boogert et al., 2000, A&A). Because the CO2 bands on Phoebe and Iapetus dark material have different positions, and because the observed 13C absorption strengths are so different, the surface evolutions must be different. The large enrichment in 13C on Phoebe argues for significant

  17. Noise reduction of nuclear magnetic resonance (NMR) transversal data using improved wavelet transform and exponentially weighted moving average (EWMA)

    Science.gov (United States)

    Ge, Xinmin; Fan, Yiren; Li, Jiangtao; Wang, Yang; Deng, Shaogui

    2015-02-01

    NMR logging and core NMR signals acts as an effective way of pore structure evaluation and fluid discrimination, but it is greatly contaminated by noise for samples with low magnetic resonance intensity. Transversal relaxation time (T2) spectrum obtained by inversion of decay signals intrigued by Carr-Purcell-Meiboom-Gill (CPMG) sequence may deviate from the truth if the signal-to-noise ratio (SNR) is imperfect. A method of combing the improved wavelet thresholding with the EWMA is proposed for noise reduction of decay data. The wavelet basis function and decomposition level are optimized in consideration of information entropy and white noise estimation firstly. Then a hybrid threshold function is developed to avoid drawbacks of hard and soft threshold functions. To achieve the best thresholding values of different levels, a nonlinear objective function based on SNR and mean square error (MSE) is constructed, transforming the problem to a task of finding optimal solutions. Particle swarm optimization (PSO) is used to ensure the stability and global convergence. EWMA is carried out to eliminate unwanted peaks and sawtooths of the wavelet denoised signal. With validations of numerical simulations and experiments, it is demonstrated that the proposed approach can reduce the noise of T2 decay data perfectly.

  18. Selective conversion of plasma glucose into CO2 by Saccharomyces cerevisiae for the measurement of C-13 abundance by isotope ratio mass spectrometry : proof of principle

    NARCIS (Netherlands)

    Rembacz, Krzysztof P.; Faber, Klaas Nico; Stellaard, Frans

    2007-01-01

    To study carbohydrate digestion and glucose absorption, time-dependent C-13 enrichment in plasma glucose is measured after oral administration of naturally occurring C-13-enriched carbohydrates. The isotope enrichment of the administered carbohydrate is low (APE <0.1%) and plasma C-13 glucose

  19. 1H NMR investigation of changes in the metabolic profile of synovial fluid in bilateral canine osteoarthritis with unilateral joint denervation.

    Science.gov (United States)

    Damyanovich, A Z; Staples, J R; Marshall, K W

    1999-03-01

    High resolution 1H-nuclear magnetic resonance (NMR) techniques have been used to compare the effects of unilateral knee-joint denervation on the biochemical profiles of synovial fluid in a bilateral canine model of osteoarthritis. Paired synovial fluid samples were obtained from seven dogs all of which had previously undergone bilateral anterior cruciate ligament transection, unilateral knee denervation and contralateral sham nerve exposure. All synovial fluid samples were then analyzed using 500 MHz 1H-CPMG spin-echo NMR Spectroscopy to assess differences in endogenous metabolite levels between the paired fluids. The results indicate statistically significant increases in glycerol, hydroxybutyrate, glutamine/glutamate, creatinine/creatine, acetate and N-acetyl-glycoprotein concentrations in synovial fluids from denervated with respect to control knees. Furthermore, significant trends towards elevated lactate, alanine and pyruvate levels in the denervated knee fluids are consistent with our previous findings comparing NMR spectroscopy metabolic profiles of normal and osteoarthritic canine synovial fluids. This study lends support to the principle of neurogenic acceleration of OA in that the observed differences in metabolite concentrations found in the denervated knee fluids seem to correlate with metabolic changes resulting from aggravation of the OA process caused by joint denervation. Copyright 1999 OsteoArthritis Research Society International.

  20. Metabolomic analysis with (1)H-NMR for non-invasive diagnosis of hepatic fibrosis degree in patients with chronic hepatitis C.

    Science.gov (United States)

    Gabbani, Tommaso; Marsico, Maria; Bernini, Patrizia; Lorefice, Elisabetta; Grappone, Cecilia; Biagini, Maria Rosa; Milani, Stefano; Annese, Vito

    2017-06-13

    The assessment of fibrosis degree in liver diseases is based on several non-invasive techniques, but none has been accurate. This study employed proton nuclear magnetic resonance spectroscopy to identify metabolic profiles in serum and urine, specific for different fibrosis degree in chronic hepatitis C patients. 71 plasma, 73 serum, and 578 urine samples were collected. All samples were analyzed using (1)H-NMR spectroscopy technique and three different NMR spectra were acquired for each serum/plasma sample. The data analyses were performed by partial least square regression, principal component analysis, and Monte Carlo cross-validation in a supervised methodology. The cross-validation test correctly assigned each sample to its specific donor with 98.44% accuracy for urine samples and 65% for serum/plasma samples. Advanced fibrosis and cirrhosis were recognized with 71% sensitivity for CPMG plasma spectra and 69% specificity for NOESY serum spectra. Accuracy for NOESY serum spectra was 68%. Noesy spectra recognized advanced fibrosis and cirrhosis with 71% sensitivity, 30% specificity, and 50% accuracy in urine samples. Metabolomic analysis of urine spectra using (1)H-NMR spectroscopy can recognize a specific individual profile in all patients with chronic hepatitis C. However, this method cannot yet differentiate with sufficient accuracy, patients with advanced fibrosis from patients with milder disease. Copyright © 2017 Editrice Gastroenterologica Italiana S.r.l. Published by Elsevier Ltd. All rights reserved.

  1. Variation in water-use efficiency and delta-C-13 levels in eucalyptus-grandis clones

    CSIR Research Space (South Africa)

    Olbrich, BW

    1993-10-01

    Full Text Available . It is suggested that differences between sample trees in carbon allocation and leaf-to-air vapour pressure deficits may account for the poor correlation between delta-C-13 and WUE in the four E. grandis clones studied....

  2. NMR, water and plants

    NARCIS (Netherlands)

    As, van H.

    1982-01-01

    This Thesis describes the application of a non-destructive pulsed proton NMR method mainly to measure water transport in the xylem vessels of plant stems and in some model systems. The results are equally well applicable to liquid flow in other biological objects than plants, e.g. flow of blood and

  3. Single-sided NMR

    CERN Document Server

    Casanova, Federico; Blümich, Bernhard

    2011-01-01

    Single-Sided NMR describes the design of the first functioning single-sided tomograph, the related measurement methods, and a number of applications. One of the key advantages to this method is the speed at which the images are obtained.

  4. NMR for chemists and biologists

    CERN Document Server

    Carbajo, Rodrigo J

    2013-01-01

    This book offers a concise introduction to the field of nuclear magnetic resonance or NMR. It presents the basic foundations of NMR in a non-mathematical way and provides an overview of both recent and important biological applications of NMR.

  5. CH4 production via CO2 reduction in a temperate bog - A source of (C-13)-depleted CH4

    Science.gov (United States)

    Lansdown, J. M.; Quay, P. D.; King, S. L.

    1992-01-01

    The paper reports measurements, taken over two annual cycles, of the flux and delta(C-13) of CH4 released from an acidic peat bog located in the foothills of the Cascade Range in Washington state, U.S. Measurements of the rate of aceticlastic methanogenesis and CO2 reduction in peat soil, using (C-14)-labeled acetate and sodium bicarbonate, show that acetate was not an important CH4 precursor and that CO2 reduction could account for all of the CH4 production. The in situ kinetic isotope effect for CO2 reduction, calculated using the delta-(C-13) of soil water CO2 and CH4 flux, was 0.932 +/- 0.007.

  6. Medical Isotope Program: O-18, C-13, and Xe-129 Final Report CRADA No. TC-2043-02

    Energy Technology Data Exchange (ETDEWEB)

    Scheibner, K. F. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Fought, J. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    2017-09-27

    This was a collaborative effort between the University of California, Lawrence Livermore National Laboratory (LLNL) and Spectra Gases, Inc., to develop new and cheaper sources of Oxgyen-18 (O-18), Carbon-13 (C-13), and Xenon-129 (Xe-129), and to develop new applications of these stable medical isotopes in medicine resulting in a substantial increase in stable isotopes that are important to human health sciences.

  7. NMR Studies of Peroxidases.

    Science.gov (United States)

    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

  8. Two new Ni(II) Schiff base complexes : X-ray absolute structure determination, synthesis of a N-15-labelled complex and full assignment of its H-1 NMR and C-13 NMR spectra

    NARCIS (Netherlands)

    Langer, Vratislav; Popkov, Alexander; Nadvornik, Milan; Lycka, Antonin

    2007-01-01

    The Ni(II) complex of the Schiff base of (S)-N-(2-benzoyl-4-chlorophenyl)-1-benzylpyrrolidine-2-carboxamide and glycine (1) [GKCI] and the hemihydrate of the Ni(II) complex of the Schiff base of (S)-N-(2-benzoylphenyl)-1-benzylpyrrolidine-2-carboxamide and 2-aminoisobutiric acid (2) Me(2)GK] were

  9. Analysis of cocondensation of melamine and urea through carbon 13 enriched formaldehyde with C-13 nuclear magnetic resonance spectroscopy

    Science.gov (United States)

    Bunichiro Tomita; Chung-Yun Hse

    1995-01-01

    The urea-formaldehyde (UF) resins, melamine-formaldehyde (MF) resins, and melamine-ureaformaldehyde (MUF) cocondensed resins were synthesized using the labeling method with 13C enriched formaldehyde under neutral conditions and their 13C-NMR (nuclear magnetic resonance) spectra were analyzed. The remarkable down-field...

  10. NMR spectroscopic study and DFT calculations of GIAO NMR ...

    African Journals Online (AJOL)

    1H, proton coupled and decoupled 13C, DEPT, HETCOR NMR spectra, the magnitude of one bond 1JCH coupling constants and 13C NMR spin-lattice relaxation time (T1) of 1,9-diaminononane (danon, C9H22N2) have been reported for the first time. 1H, 13C NMR chemical shifts and 1JCH coupling constants of danon ...

  11. DETERMINATION OF THE 3-DIMENSIONAL SOLUTION STRUCTURE OF THE HISTIDINE-CONTAINING PHOSPHOCARRIER PROTEIN HPR FROM ESCHERICHIA-COLI USING MULTIDIMENSIONAL NMR-SPECTROSCOPY

    NARCIS (Netherlands)

    VANNULAND, NAJ; GROTZINGER, J; DIJKSTRA, K; SCHEEK, RM; ROBILLARD, GT

    1992-01-01

    We recorded several types of heteronuclear three-dimensional (3D) NMR spectra on N-15-enriched and C-13/N-15-enriched histidine-containing phosphocarrier protein, HPr, to extend the backbone assignments [van Nuland, N. A. J., van Dijk, A. A., Dijkstra, K., van Hoesel, F. H. J., Scheek, R. M. &

  12. An NMR and ab initio quantum chemical study of acid-base equilibria for conformationally constrained acidic alpha-amino acids in aqueous solution

    DEFF Research Database (Denmark)

    Nielsen, Peter Aadal; Jaroszewski, Jerzy W.; Norrby, Per-Ola

    2001-01-01

    The protonation states of a series of piperidinedicarboxylic acids (PDAs), which are conformationally constrained acidic alpha -amino acids, have been studied by C-13 NMR titration in water. The resulting data have been correlated with theoretical results obtained by HF/6-31+G* calculations using...

  13. Solution NMR in structural genomics.

    Science.gov (United States)

    Yee, Adelinda; Gutmanas, Aleksandras; Arrowsmith, Cheryl H

    2006-10-01

    Structural genomics (also known as structural proteomics) aims to generate accurate three-dimensional models for all folded, globular proteins and domains in the protein universe to understand the relationship between protein sequence, structure and function. NMR spectroscopy of small (structural genomics projects for more than six years now. Recent advances coming from traditional NMR structural biology laboratories as well as large scale centers and consortia using NMR for structural genomics promise to facilitate NMR analysis making it even a more efficient and increasingly automated procedure.

  14. Magic Angle Spinning NMR Metabolomics

    Energy Technology Data Exchange (ETDEWEB)

    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.

  15. NMR-based plasma metabolomic discrimination for male fertility assessment of rats treated with Eurycoma longifolia extracts.

    Science.gov (United States)

    Ebrahimi, Forough; Ibrahim, Baharudin; Teh, Chin-Hoe; Murugaiyah, Vikneswaran; Chan, Kit-Lam

    2017-06-01

    the fertility assessment in humans through the quantitative metabolomic analysis of plasma without requiring semen. TA: Tongkat Ali; LOD: limit of detection; LOQ: limit of quantification; HPLC-UV: high performance liquid chromatography-ultrviolet; PDA: photodiode array; NMR: nuclear magnetic resonance; FID: free induction decay; LC-MS: liquid chromatography-mass spectrometry; GC-MS: gas chromatography-mass spectrometry; HSQC: heteronuclear single quantum coherence; CPMG: Carr-Purcell-Meibum-Gill; VLDL: very low density lipoprotein; HDL: high density lipoprotein; EDTA: ethylenediaminetetraacetic acid; ANOVA: analysis of variance; AMIX: analysis of mixtures; SIMCA: soft independent modeling of class analogy; PCA: principal components analysis; OPLS-DA: orthogonal partial least-squares discriminant analysis; VIP: variable importance plot; AUROC: area under the receiver operating characteristic; TSP: sodium 3-(trimethylsilyl) propionate- 2,2,3,3- d4; DSA: deuterated 4-dimethyl-4-silapentane-1-ammonium trifluoroacetate; ESI: electrospray ionization; TCA: trichloroacetic acid; ACN: acetonitrile; dd H 2 O: distilled deionized water; FSH: follicle-stimulating hormone; LH: luteinizing hormone; OECD: Organisation for Economic Co-operation and Development.

  16. NMR in pulsed magnetic field

    KAUST Repository

    Abou-Hamad, Edy

    2011-09-01

    Nuclear magnetic resonance (NMR) experiments in pulsed magnetic fields up to 30.4 T focused on 1H and 93Nb nuclei are reported. Here we discuss the advantage and limitation of pulsed field NMR and why this technique is able to become a promising research tool. © 2011 Elsevier Inc. All Rights Reserved.

  17. Embedded NMR Sensor to Monitor Compressive Strength Development and Pore Size Distribution in Hydrating Concrete

    Directory of Open Access Journals (Sweden)

    Floriberto Díaz-Díaz

    2013-11-01

    Full Text Available In cement-based materials porosity plays an important role in determining their mechanical and transport properties. This paper describes an improved low–cost embeddable miniature NMR sensor capable of non-destructively measuring evaporable water loss and porosity refinement in low and high water-to-cement ratio cement-based materials. The sensor consists of two NdFeB magnets having their North and South poles facing each other, separated by 7 mm to allow space for a Faraday cage containing a Teflon tube and an ellipsoidal RF coil. To account for magnetic field changes due to temperature variations, and/or the presence of steel rebars, or frequency variation due to sample impedance, an external tuning circuit was employed. The sensor performance was evaluated by analyzing the transverse magnetization decay obtained with a CPMG measurement from different materials, such as a polymer phantom, fresh white and grey cement pastes with different w/c ratios and concrete with low (0.30 and high (0.6 w/c ratios. The results indicated that the sensor is capable of detecting changes in water content in fresh cement pastes and porosity refinement caused by cement hydration in hardened materials, even if they are prepared with a low w/c ratio (w/c = 0.30. The short lifetime component of the transverse relaxation rate is directly proportional to the compressive strength of concrete determined by destructive testing. The r2 (0.97 from the linear relationship observed is similar to that obtained using T2 data from a commercial Oxford Instruments 12.9 MHz spectrometer.

  18. Fundamentals of Protein NMR Spectroscopy

    CERN Document Server

    Rule, Gordon S

    2006-01-01

    NMR spectroscopy has proven to be a powerful technique to study the structure and dynamics of biological macromolecules. Fundamentals of Protein NMR Spectroscopy is a comprehensive textbook that guides the reader from a basic understanding of the phenomenological properties of magnetic resonance to the application and interpretation of modern multi-dimensional NMR experiments on 15N/13C-labeled proteins. Beginning with elementary quantum mechanics, a set of practical rules is presented and used to describe many commonly employed multi-dimensional, multi-nuclear NMR pulse sequences. A modular analysis of NMR pulse sequence building blocks also provides a basis for understanding and developing novel pulse programs. This text not only covers topics from chemical shift assignment to protein structure refinement, as well as the analysis of protein dynamics and chemical kinetics, but also provides a practical guide to many aspects of modern spectrometer hardware, sample preparation, experimental set-up, and data pr...

  19. Highly efficient F-19 heteronuclear decoupling in solid-state NMR spectroscopy using supercycled refocused-CW irradiation

    DEFF Research Database (Denmark)

    Equbal, Asif; Basse, Kristoffer; Nielsen, Niels Christian

    2016-01-01

    We present heteronuclear F-19 refocused CW (rCW) decoupling pulse sequences for solid-state magic-angle- spinning NMR applications. The decoupling sequences have been designed specifically to ensure suppression of the pertinent C-13-F-19 dipolar coupling interactions while simultaneously suppress......We present heteronuclear F-19 refocused CW (rCW) decoupling pulse sequences for solid-state magic-angle- spinning NMR applications. The decoupling sequences have been designed specifically to ensure suppression of the pertinent C-13-F-19 dipolar coupling interactions while simultaneously...... of which clearly render the new rCW schemes the methods of choice for 19F decoupling in rigid, fluorinated compounds - which is further supported by a Floquet-based theoretical analysis....

  20. Applications of unilateral NMR in nondestructive testing

    OpenAIRE

    Sharma, Shatrughan

    2004-01-01

    In general, in NMR spectroscopy a sample is prepared for the NMR measurement, positioned in the magnet, measured, and discarded. But when non-destructiveness of the sample is more important, it becomes important to rely on relaxation analysis at low resolution NMR. If the samples are big in size the unilateral or single-sided NMR in inhomogeneous fields is an important choice. Unilateral NMR or inside-out NMR is one recognized technique in the field of low resolution NMR. The NMR-MOUSE (Mobil...

  1. H-1, C-13 and N-15 resonance assignments of human DCL-1 (CD302) extracellular domain

    Czech Academy of Sciences Publication Activity Database

    Pospíšilová, Eliška; Kavan, Daniel; Novák, Petr; Chmelík, Josef

    2016-01-01

    Roč. 10, č. 1 (2016), s. 189-192 ISSN 1874-2718 R&D Projects: GA MŠk(CZ) LO1509; GA MŠk(CZ) EE2.3.20.0055; GA MŠk(CZ) EE2.3.30.0003; GA MŠk(CZ) ED1.1.00/02.0109 Institutional support: RVO:61388971 Keywords : DCL-1 (CD302) * C-type lectin like receptor * Protein NMR Subject RIV: EE - Microbiology, Virology Impact factor: 0.459, year: 2016

  2. C13C4.5/Spinster, an evolutionarily conserved protein that regulates fertility in C. elegans through a lysosome-mediated lipid metabolism process.

    Science.gov (United States)

    Han, Mei; Chang, Hao; Zhang, Peng; Chen, Tao; Zhao, Yanhua; Zhang, Yongdeng; Liu, Pingsheng; Xu, Tao; Xu, Pingyong

    2013-05-01

    Lipid droplets, which are conserved across almost all species, are cytoplasmic organelles used to store neutral lipids. Identification of lipid droplet regulators will be conducive to resolving obesity and other fat-associated diseases. In this paper, we selected 11 candidates that might be associated with lipid metabolism in Caenorhabditis elegans. Using a BODIPY 493/503-based flow cytometry screen, 6 negative and 3 positive regulators of fat content were identified. We selected one negative regulator of lipid content, C13C4.5, for future study. C13C4.5 was mainly expressed in the worm intestine. We found that this gene was important for maintaining the metabolism of lipid droplets. Biochemical results revealed that 50% of triacylglycerol (TAG) was lost in C13C4.5 knockout worms. Stimulated Raman scattering (SRS) signals in C13C4.5 mutants showed only 49.6% of the fat content in the proximal intestinal region and 86.3% in the distal intestinal region compared with wild type animals. The mean values of lipid droplet size and intensity in C13C4.5 knockout animals were found to be significantly decreased compared with those in wild type worms. The LMP-1-labeled membrane structures in worm intestines were also enlarged in C13C4.5 mutant animals. Finally, fertility defects were found in C13C4.5(ok2087) mutants. Taken together, these results indicate that C13C4.5 may regulate the fertility of C. elegans by changing the size and fat content of lipid droplets by interfering with lysosomal morphology and function.

  3. Annual reports on NMR spectroscopy

    CERN Document Server

    Webb, Graham A; McCarthy, M J

    1995-01-01

    Over recent years, no other technique has grown to such importance as that of NMR spectroscopy. It is used in all branches of science where precise structural determination is required and where the nature of interactions and reactions in solution is being studied. Annual Reports on NMR Spectroscopy has established itself as a means for the specialist and non-specialist alike to become familiar with new applications of the technique in all branches of chemistry, including biochemistry, and pharmaceutics. This volume focuses on theoretical aspects of NMR nuclear shielding and on applications of

  4. NMR and EPR Studies of Free-Radical Intermediates from Experiments Mimicking the Winds on Mars

    DEFF Research Database (Denmark)

    Jakobsen, Hans J.; Song, Likai; Gan, Zhehong

    2016-01-01

    -enriched methane ((CH4)-C-13 and CD4), carbon dioxide ((CO2)-C-13), hydrogen (H-2(2)) and oxygen (O-17(2)). The solid-state Si free-radical intermediate and gas reaction and silicate products are formed in a specially designed rotating apparatus, which by mechanical tumbling mimics the winds and collision......A new kind of solid gas chemical reactions has been investigated using solid-state powder H-2, C-13, and Si-29 NMR and EPR spectroscopies. These studies involve reactions between a silicate-created Si free-radical intermediate and a few ordinary gases such as isotopically H-2-, C-13-, and O-17...... speed of the mineral particles on Mars. It is shown that the "hard" quartz (SiO2) or corundum (alpha-AL(2)O(3)) grain particles, used to simulate the collision particles in a rotating Pyrex (borosilicate) reaction flask, act as an abrasive on the "soft" Pyrex flask and thereby create a silicate Si free...

  5. NMR Studies of Polymer Nanocomposites

    National Research Council Canada - National Science Library

    Greenbaum, Steve

    2001-01-01

    .... The primary tool is pulsed field gradient NMR. A static field gradient method was developed which makes possible variable pressure diffusion measurement, and the application to the important fuel cell membrane NAFION constitute the first results...

  6. β-NMR sample optimization

    CERN Document Server

    Zakoucka, Eva

    2013-01-01

    During my summer student programme I was working on sample optimization for a new β-NMR project at the ISOLDE facility. The β-NMR technique is well-established in solid-state physics and just recently it is being introduced for applications in biochemistry and life sciences. The β-NMR collaboration will be applying for beam time to the INTC committee in September for three nuclei: Cu, Zn and Mg. Sample optimization for Mg was already performed last year during the summer student programme. Therefore sample optimization for Cu and Zn had to be completed as well for the project proposal. My part in the project was to perform thorough literature research on techniques studying Cu and Zn complexes in native conditions, search for relevant binding candidates for Cu and Zn applicable for ß-NMR and eventually evaluate selected binding candidates using UV-VIS spectrometry.

  7. Development of Two-Dimensional NMR

    Indian Academy of Sciences (India)

    IAS Admin

    Two-dimensional NMR, COSY,. NOESY, 2D MRI, biomolecular structure determination. The development of Fourier transform NMR in the mid. 1960's, did parallel processing of the collection of NMR data, increased the signal/noise ratio by two orders of magnitude and made it possible to record the proton NMR spectra of.

  8. Optical pumping and xenon NMR

    Energy Technology Data Exchange (ETDEWEB)

    Raftery, M. Daniel [Univ. of California, Berkeley, CA (United States)

    1991-11-01

    Nuclear Magnetic Resonance (NMR) spectroscopy of xenon has become an important tool for investigating a wide variety of materials, especially those with high surface area. The sensitivity of its chemical shift to environment, and its chemical inertness and adsorption properties make xenon a particularly useful NMR probe. This work discusses the application of optical pumping to enhance the sensitivity of xenon NMR experiments, thereby allowing them to be used in the study of systems with lower surface area. A novel method of optically-pumping 129Xe in low magnetic field below an NMR spectrometer and subsequent transfer of the gas to high magnetic field is described. NMR studies of the highly polarized gas adsorbed onto powdered samples with low to moderate surface areas are now possible. For instance, NMR studies of optically-pumped xenon adsorbed onto polyacrylic acid show that xenon has a large interaction with the surface. By modeling the low temperature data in terms of a sticking probability and the gas phase xenon-xenon interaction, the diffusion coefficient for xenon at the surface of the polymer is determined. The sensitivity enhancement afforded by optical pumping also allows the NMR observation of xenon thin films frozen onto the inner surfaces of different sample cells. The geometry of the thin films results in interesting line shapes that are due to the bulk magnetic susceptibility of xenon. Experiments are also described that combine optical pumping with optical detection for high sensitivity in low magnetic field to observe the quadrupoler evolution of 131 Xe spins at the surface of the pumping cells. In cells with macroscopic asymmetry, a residual quadrupolar interaction causes a splitting in the 131Xe NMR frequencies in bare Pyrex glass cells and cells with added hydrogen.

  9. Optical pumping and xenon NMR

    Energy Technology Data Exchange (ETDEWEB)

    Raftery, M.D.

    1991-11-01

    Nuclear Magnetic Resonance (NMR) spectroscopy of xenon has become an important tool for investigating a wide variety of materials, especially those with high surface area. The sensitivity of its chemical shift to environment, and its chemical inertness and adsorption properties make xenon a particularly useful NMR probe. This work discusses the application of optical pumping to enhance the sensitivity of xenon NMR experiments, thereby allowing them to be used in the study of systems with lower surface area. A novel method of optically-pumping [sup 129]Xe in low magnetic field below an NMR spectrometer and subsequent transfer of the gas to high magnetic field is described. NMR studies of the highly polarized gas adsorbed onto powdered samples with low to moderate surface areas are now possible. For instance, NMR studies of optically-pumped xenon adsorbed onto polyacrylic acid show that xenon has a large interaction with the surface. By modeling the low temperature data in terms of a sticking probability and the gas phase xenon-xenon interaction, the diffusion coefficient for xenon at the surface of the polymer is determined. The sensitivity enhancement afforded by optical pumping also allows the NMR observation of xenon thin films frozen onto the inner surfaces of different sample cells. The geometry of the thin films results in interesting line shapes that are due to the bulk magnetic susceptibility of xenon. Experiments are also described that combine optical pumping with optical detection for high sensitivity in low magnetic field to observe the quadrupoler evolution of 131 Xe spins at the surface of the pumping cells. In cells with macroscopic asymmetry, a residual quadrupolar interaction causes a splitting in the [sup 131]Xe NMR frequencies in bare Pyrex glass cells and cells with added hydrogen.

  10. Development of C13-norisoprenoids, carotenoids and other volatile compounds in Vitis vinifera L. Cv. Pinot noir grapes.

    Science.gov (United States)

    Yuan, Fang; Qian, Michael C

    2016-02-01

    Developmental changes in the carotenoids and volatile compounds of Pinot noir grape berries were investigated in this study from pea size to harvest during 2012. HPLC analysis showed continued decrease of lutein, β-carotene, neochrome a and neoxanthin continued to decrease during berry development, with rapid decrease of lutein and (9'z)-neoxanthin occurred two weeks before véraison. Neochrome b and violaxanthin accumulated at early development and started to decrease two weeks before véraison. Volatile analysis demonstrated that total β-damascenone, TDN and vitispirane all increased dramatically, especially at later stage of ripening, whereas the changes for α-ionone and β-ionone were not obvious. The correlation between carotenoids and C13-norisoprenoids in the grape berries was compound-dependent, suggesting dependency on enzyme activity and specificity. In addition, C6-alcohols accumulated before véraison and decreased towards maturation, and 3-isobutyl-2-methoxyprazine decreased with increasing maturity. Copyright © 2015 Elsevier Ltd. All rights reserved.

  11. Land Use Effects on Atmospheric C-13 Imply a Sizable Terrestrial CO2 Sink in Tropical Latitudes

    Science.gov (United States)

    Townsend, Alan R.; Asner, Gregory P.; Tans, Pieter P.; White, James W. C.

    2000-01-01

    Records of atmospheric CO2 and 13-CO2, can be used to distinguish terrestrial vs. oceanic exchanges of CO2 with the atmosphere. However, this approach has proven difficult in the tropics, partly due to extensive land conversion from C-3 to C-4 vegetation. We estimated the effects of such conversion on biosphere-atmosphere C-13 exchange for 1991 through 1999, and then explored how this 'land-use disequilibrium' altered the partitioning of net atmospheric CO2 exchanges between ocean and land using NOAA-CMDL data and a 2D, zonally averaged atmospheric transport model. Our results show sizable CO2 uptake in C-3-dominated tropical regions in seven of the nine years; 1997 and 1998, which included a strong ENSO event, are near neutral. Since these fluxes include any deforestation source, our findings imply either that such sources are smaller than previously estimated, and/or the existence of a large terrestrial CO2 sink in equatorial latitudes.

  12. Determination of the isotopic (C-13/C-12) discrimination by terrestrial biology from a global network of observations

    Energy Technology Data Exchange (ETDEWEB)

    Bakwin, P.S.; Tans, P.P.; White, J.W.C.; Andres, R.J. [NOAA, Boulder, CO (United States). Climate Monitoring and Diagnostics Laboratory

    1998-09-01

    Data from the National Oceanic and Atmospheric Administration/Climate Monitoring and Diagnostics Laboratory global air sampling network are analysed in order to extract the signatures of isotopic (C-13/C-12) discrimination by the terrestrial iota and of fossil fuel combustion for the regions surrounding the sampling sites. Measurements of carbon monoxide (CO) are used to give an estimate of the contribution of fossil fuel combustion to the short-term variability of carbon dioxide. In general, variations of CO{sub 2} are more strongly dominated by biological exchange, so the isotopic signature of fossil fuel combustion, while consistent with inventory estimates, is not well constrained by the observations. Conversely, results for isotope discrimination by the terrestrial biosphere are not strongly dependent on assumptions about fossil fuel combustion. The analysis appears valid primarily for stations fairly near continental source/sink regions, particularly for midlatitude regions of the northern hemisphere. For these stations a mean discrimination of -16.8 per mil (%) is derived, with site-to-site variability of 0.8% and with little or no consistent latitudinal gradient.

  13. Determinations of the 12C/13C Ratio for the Secondary Stars of AE Aquarii, SS Cygni, and RU Pegasi

    Science.gov (United States)

    Harrison, Thomas E.; Marra, Rachel E.

    2017-07-01

    We present new moderate-resolution near-infrared spectroscopy of three CVs obtained using GNIRS on Gemini-North. These spectra covered three 13CO bandheads found in the K-band, allowing us to derive the isotopic abundance ratios for carbon. We find small 12C/13C ratios for all three donor stars. In addition, these three objects show carbon deficits, with AE Aqr being the most extreme ([C/Fe] = -1.4). This result confirms the conjecture that the donor stars in some long-period CVs have undergone considerable nuclear evolution prior to becoming semi-contact binaries. In addition to the results for carbon, we find that the abundance of sodium is enhanced in these three objects, and the secondary stars in both RU Peg and SS Cyg suffer magnesium deficits. Explaining such anomalies appears to require higher mass progenitors than commonly assumed for the donor stars of CVs. Based on observations obtained at the Gemini Observatory, which is operated by the Association of Universities for Research in Astronomy, Inc., under a cooperative agreement with the NSF on behalf of the Gemini partnership: the National Science Foundation (United States), the National Research Council (Canada), CONICYT (Chile), Ministerio de Ciencia, Tecnología e Innovación Productiva (Argentina), and Ministério da Ciência, Tecnologia e Inovação (Brazil).

  14. Medical applications of NMR imaging and NMR spectroscopy with stable isotopes. Summary

    Energy Technology Data Exchange (ETDEWEB)

    Matwiyoff, N.A.

    1983-01-01

    The current status of NMR imaging and NMR spectroscopy are summarized. For the most part examples from the March 1983 Puerto Rico symposium are used to illustrate the utility of NMR in medicine. 18 refs., 5 figs.

  15. Letter to the Editor: H-1, C-13 and N-15 Assignments for the Archaeglobus fulgidis Protein AF2095.

    Energy Technology Data Exchange (ETDEWEB)

    Powers, Robert; Acton, Thomas; Chiang, Yiwen; Rajan, Paranji K.; Cort, John R.; Kennedy, Michael A.; Liu, Jinfeng; Ma, LiChung; Rost, Burkhard; Montelione, Gaetano

    2004-09-01

    The Human genome project promises to provide an unprecedented wealth of information on cell biology, development, evolution and physiology. Translating this immense increase in genomic information into advances in medicine and human health requires a concerted effort to explore and investigate the structure and molecular activity for the vast amount of proteins in the Human proteome that lack any such explicit experimental information. Structural genomics is providing a means to determine the molecular and cellular function of these proteins by characterizing the complete range of protein folds (Montelione, 2001). By annotating sequence information with a protein structure, it is sometimes possible to decipher the biochemical activity of hypothetical proteins from structural similarity and the conservation of spatial arrangement of active site residues. Homology can often be inferred by structural similarity even in the absence of recognizable sequence similarity, and can sometimes be used to identify functional relationships between distantly related proteins. Determining an experimental structure for each protein in a proteome is currently impractical because of the significant time commitment and resources required by X-ray and NMR. Therefore, the current paradigm of structural genomics is to determine a representative structure for each cluster of homologous protein domain sequences that lack similarity to a protein domain with a known structure. In this manner, comparative modeling using a single experimental structure can provide approximate but useful 3D structural information for an entire protein domain family. The Northeast Structural Genomics Consortium (NESG; www.nesg.org) is a pilot project funded by the National Institutes of Health Protein Structure Initiative, focusing on proteins from eukaryotic model organisms including humans. The thermophillic archaea Archaeglobus fulgidis AF2095 protein is an example of a protein of unknown biological function

  16. 12C/13C and 14N/15N isotopic ratios in HCN in the middle atmosphere of Titan from Cassini/CIRS data

    Science.gov (United States)

    Mathé, Christophe; Vinatier, Sandrine; Bézard, Bruno; Nixon, Conor A.

    2017-10-01

    Our study aims at constraining the 12C/13C and 14N/15N isotopic ratios in HCN, the most abundant nitrile in Titan’s atmosphere, which can provide information on physical and chemical process occurring during the formation and/or destruction of this molecule.Over the last decade, several estimations of the 12C/13C and 14N/15N isotopic ratios in HCN were performed from ground-based, Herschel and Cassini observations (Bézard et al,2014). The 14N/15N ratio lies in the range 56-76, which corresponds to half of the 14N/15N ratio in N2 (major N-bearing molecule in Titan’s atmosphere). This nitrogen isotopic fractionation mostly originates from the photodissociation of N2 (Liang et al, 2007). The 12C/13C ratio lies in the range 75-108, in agreement with the 12C/13C ratio in CH4 (major C-bearing molecule). Recent disk-averaged ALMA observations indicate 12C/13C and 14N/15N ratios equal to ˜90 and ˜72, respectively (Molter et al, 2016).Vinatier et al (2007) derived 14N/15N and 12C/13C ratios in two different regions (equator and north pole) from Cassini/CIRS (Composite InfraRed Spectrometer) observations at the beginning of the Cassini mission. 14N/15N was similar for both latitudes while the 12C/13C ratio displayed a possible enhancement at the equator.We present here a new study of the 12C/13C and 14N/15N isotopic ratios in HCN from CIRS. We analyzed limb observations (0.5 cm-1 resolution) from northern winter to early spring at poles, mid-latitudes and equator in order to investigate potential spatial and seasonal changes of these isotopic ratios in Titan’s middle atmosphere. These preliminary results will be presented and compared with previous observations.References:Bézard et al., Cambrigde University Press, 2014Liang et al., The Astrophysical Jounral Letters, 2007Molter et al., The Astronomical Journal, 2016Vinatier et al., Icarus, 2007

  17. Comparison of the Quantitative Values of C-14 and C-13 UBT to Reflect the Presence and Degree of Ongoing Helicobacter pylori Infection

    Energy Technology Data Exchange (ETDEWEB)

    Lim, Seok Tae; Kim, Dong Wook; Jeong, Hwan Jeong; Sohn, Myung Hee [Chonbuk National University Medical School, Jeonju (Korea, Republic of)

    2008-06-15

    A urea breath test (UBT) using C-14 or C-13 has been developed for identifying Helicobacter (H) pylori infection on the basis of urease production with release of labeled CO{sub 2}. We investigated if the C-14 and C-13 UBT have the difference to reflect the presence and degree of H. pylori infection detected by gastroduodenoscopic biopsies (GBx) in the same patients. Thirty eight patients (M:F=28:10, age 53.4{+-}13.0 yrs) with upper gastrointestinal symptoms such as indigestion, gastric fullness or pain consecutively underwent C-14 UBT, GBx and C-13 UBT within one week before medications. For the C-14 UBT, a single breath sample was collected at 10 minutes after ingestion of C-14 urea (37 KBq) capsule and counting was done in a liquid scintillation counter for 1 minute, and the results were classified as positive ({>=}200 dpm), intermediate (50{approx}199 dpm) or negative (<50 dpm). For the C-13 UBT, the results were classified as positive ({>=}2.5) or negative (<2.5). The results of GBx with Giemsa stain were graded 0 (normal) to 4 (diffuse) according to the distribution of H. pylori by the Wyatt method. We compared C-14 UBT and C-13 UBT results with GBx grade as a gold standard. The prevalence of H. pylori infection by GBx with Giemsa stain was 25/38 (65.8%). In the assessment of the presence of H. pylori infection, the C-14 UBT global performance yielded sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV) and accuracy of 92.0%, 92.3%, 95.8%, 91.7% and 92.1%, respectively. However, the C-13 UBT had sensitivity, specificity, PPV, NPV and accuracy of 96.0%, 84.6%, 92.3%, 91.7% and 92.1%, respectively. The more significant correlation in C-14 than C-13 UBT (r=0.948 vs r=0.819, p<0.001) was found between the value of UBT and the grade of distribution of H. pylori infection. We conclude that the diagnostic performance between C-14 and C-13 UBT to detect H. pylori infection is not significantly different, but the value of C-14 UBT

  18. Identification of critical amino acids in an immunodominant IgE epitope of Pen c 13, a major allergen from Penicillium citrinum.

    Directory of Open Access Journals (Sweden)

    Jui-Chieh Chen

    Full Text Available BACKGROUND: Pen c 13, identified as a 33-kDa alkaline serine protease, is a major allergen secreted by Penicillium citrinum. Detailed knowledge about the epitopes responsible for IgE binding would help inform the diagnosis/prognosis of fungal allergy and facilitate the rational design of hypoallergenic candidate vaccines. The goal of the present study was to characterize the IgE epitopes of Pen c 13. METHODOLOGY/PRINCIPAL FINDINGS: Serum samples were collected from 10 patients with mold allergy and positive Pen c 13 skin test results. IgE-binding epitopes on rPen c 13 were mapped using an enzymatic digestion and chemical cleavage method, followed by dot-blotting and mass spectrometry. A B-cell epitope-predicting server and molecular modeling were used to predict the residues most likely involved in IgE binding. Theoretically predicted IgE-binding regions were further confirmed by site-directed mutagenesis assays. At least twelve different IgE-binding epitopes located throughout Pen c 13 were identified. Of these, peptides S16 (A(148-E(166 and S22 (A(243-K(274 were recognized by sera from 90% and 100% of the patients tested, and were further confirmed by inhibition assays. Peptide S22 was selected for further analysis of IgE-binding ability. The results of serum screening showed that the majority of IgE-binding ability resided in the C-terminus. One Pen c 13 mutant, G270A (T(261-K(274, exhibited clearly enhanced IgE reactivity, whereas another, K274A, exhibited dramatically reduced IgE reactivity. CONCLUSIONS/SIGNIFICANCE: Experimental analyses confirmed in silico-predicted residues involved in an important antigenic region of Pen c 13. The G270A mutant of Pen c 13 has the potential to serve as an additional tool for the diagnosis/prognosis of mold allergy, and the K274A mutant, as a hypoallergenic form of the epitope, may provide a framework for the design and development of a safe and efficient therapeutic strategy for treating human allergic

  19. Flow NMR of complex systems

    Energy Technology Data Exchange (ETDEWEB)

    Scheler, U.; Bagusat, F. [Leibniz-Inst. fuer Polymerforschung Dresden e.V., Dresden (Germany)

    2007-07-01

    A combination of NMR imaging and pulsed field gradient (PFG) NMR is applied to investigate flow. NMR longitudinal relaxation is used to generate contrast in a binary system of oil and water. The spatial distribution of each component and its flow pattern are measured separately. As a model a Couette cell with an additional area of high shear is used as model geometry. While a flat smooth interface is found at rest, the interface become bent under rotation, finally emulgation starts because of the velocity differences between the components. Flow from a submillimeter tube into a wide box and out of the box is investigated as well to understand shear-induced mixing and demixing. (orig.)

  20. NMR and dynamics of biopolymers

    Energy Technology Data Exchange (ETDEWEB)

    Lian, L.Y.; Barsukov, I.L. [Leicester Univ. (United Kingdom)

    1994-12-31

    Several basic experimental analytical NMR techniques that are frequently used for the qualitative and quantitative analysis of dynamic and exchange processes, focusing on proteins systems, are described: chemical exchange (slow exchange, fast exchange, intermediate exchange), heteronuclear relaxation measurements (relaxation parameters, strategy of relaxation data analysis, experimental results and examples, motional model interpretation of relaxation data, homonuclear relaxation); slow large-scale exchange and hydrogen-deuterium exchange are also studied: mechanisms of hydrogen exchange in a native protein, methods for measuring amide exchange rates by NMR, interpretation of amide exchange rates. 9 fig., 3 tab., 56 ref.

  1. Lithotype characterizations by Nuclear Magnetic Resonance (NMR): A case study on limestone and associated rocks from the eastern Dahomey Basin, Nigeria

    Science.gov (United States)

    Olatinsu, O. B.; Olorode, D. O.; Clennell, B.; Esteban, L.; Josh, M.

    2017-05-01

    Three representative rock types (limestone, sandstone, and shale) and glauconite samples collected from Ewekoro Quarry, eastern Dahomey Basin in Nigeria were characterized using low field 2 MHz and 20 MHz Nuclear Magnetic Resonance (NMR) techniques. NMR T2 relaxation time decay measurement was conducted on disc samples under partial water-saturation and full water-saturation conditions using CPMG spin-echo routine. The T2 relaxation decay was converted into T2 distribution in the time domain to assess and evaluate the pore size distribution of the samples. Good agreement exists between water content from T2 NMR distributions and water imbibition porosity (WIP) technique. Results show that the most useful characteristics to discriminate the different facies come from full saturation NMR 2 MHz pore size distribution (PSD). Shale facies depict a quasi-unimodal distribution with greater than 90% contribution from clay bound water component (T2s) coupled to capillary bound water component (T2i) centred on 2 ms. The other facies with well connected pore structure show either bimodal or trimodal T2 distribution composed of the similar clay bound water component centred on 0.3 ms and quasi-capillary bound water component centred on 10 ms. But their difference depends on the movable water T2 component (T2l) that does not exist in the glauconite facies (bimodal distribution) while it exists in both the sandstone and limestone facies. The basic difference between the limestone and sandstone facies is related to the longer T2 coupling: T2i and T2l populations are coupled in sandstone generating a single population which convolves both populations (bimodal distribution). Limestone with a trimodal distribution attests to the fact that carbonate rocks have more complex pore system than siliclastic rocks. The degree of pore connectivity is highest in sandstone, followed by limestone and least in glauconite. Therefore a basic/quick NMR log run on samples along a geological

  2. Electrostatic Interactions in the Binding Pathway of a Transient Protein Complex Studied by NMR and Isothermal Titration Calorimetry*

    Science.gov (United States)

    Meneses, Erick; Mittermaier, Anthony

    2014-01-01

    Much of our knowledge of protein binding pathways is derived from extremely stable complexes that interact very tightly, with lifetimes of hours to days. Much less is known about weaker interactions and transient complexes because these are challenging to characterize experimentally. Nevertheless, these types of interactions are ubiquitous in living systems. The combination of NMR relaxation dispersion Carr–Purcell–Meiboom–Gill (CPMG) experiments and isothermal titration calorimetry allows the quantification of rapid binding kinetics for complexes with submillisecond lifetimes that are difficult to study using conventional techniques. We have used this approach to investigate the binding pathway of the Src homology 3 (SH3) domain from the Fyn tyrosine kinase, which forms complexes with peptide targets whose lifetimes are on the order of about a millisecond. Long range electrostatic interactions have been shown to play a critical role in the binding pathways of tightly binding complexes. The role of electrostatics in the binding pathways of transient complexes is less well understood. Similarly to previously studied tight complexes, we find that SH3 domain association rates are enhanced by long range electrostatics, whereas short range interactions are formed late in the docking process. However, the extent of electrostatic association rate enhancement is several orders of magnitudes less, whereas the electrostatic-free basal association rate is significantly greater. Thus, the SH3 domain is far less reliant on electrostatic enhancement to achieve rapid association kinetics than are previously studied systems. This suggests that there may be overall differences in the role played by electrostatics in the binding pathways of extremely stable versus transient complexes. PMID:25122758

  3. Diode laser absorption spectrometry for (CO2)-C-13/(CO2)-C-12 isotope ratio analysis : Investigation on precision and accuracy levels

    NARCIS (Netherlands)

    Castrillo, A; Casa, G; Kerstel, E; Gianfrani, L

    2005-01-01

    Near-infrared laser spectroscopy is used to measure the C-13/C-12 isotope abundance ratio in gas phase carbon dioxide. The spectrometer, developed expressly for field applications, is based on a 2 mu m distributed feedback diode laser in combination with sensitive wavelength modulation detection. It

  4. Land-use related organic matter dynamics in North Cameroon soils assessed by C-13 analysis of soil organic matter fractions

    NARCIS (Netherlands)

    Sevink, J; Obale-Ebanga, F; Meijer, HAJ

    Topsoil samples from cultivated and adjacent non-cultivated fields on three major agricultural soils in North Cameroon were fractionated into particle-size fractions that were analysed subsequently for their C and C-13 contents. The aim was to obtain further insight into the dynamics of soil organic

  5. Reassessment of the C-13/C-12 and C-14/C-12 isotopic fractionation ratio and its impact on high-precision radiocarbon dating

    NARCIS (Netherlands)

    Fahrni, Simon M.; Southon, John R.; Santos, Guaciara M.; Palstra, Sanne W. L.; Meijer, Harro A. J.; Xu, Xiaomei

    2017-01-01

    The vast majority of radiocarbon measurement results (C-14/C-12 isotopic ratios or sample activities) are corrected for isotopic fractionation processes (measured as C-13/C-12 isotopic ratios) that occur in nature, in sample preparation and measurement. In 1954 Harmon Craig suggested a value of 2.0

  6. Synthesis of C13-C25 fragment of 24-demethylbafilomycin C(1) via diastereoselective aldol reactions of a ketone boron enolate as the key step.

    Science.gov (United States)

    Guan, Yucui; Wu, Jinlong; Sun, Liang; Dai, Wei-Min

    2007-06-22

    An efficient synthesis of the C13-C25 fragment is described for 24-demethylbafilomycin C1, a new member of the plecomacrolide family isolated from fermentation broth of Streptomyces sp. CS which is a commensal microbe of Maytenus hookeri. The targeted C13-C25 fragment possesses five oxygenated and three methyl-substituted stereogenic centers. It is obtained through formation of the C17-C18 syn aldol by using an ethyl ketone boron enolate with diastereomeric ratios of 95:5 and 83:17, respectively, for the chiral aldehydes substituted with acetoxy and methoxyacetoxy groups at C15. The results confirm the observation that the stereochemistry at C22 of the ketone is determinant to the diastereoselectivity of the aldol reaction. The synthesized C13-C25 fragment having a methoxyacetoxy group at C15 is considered as a useful precursor for construction of the 16-membered ring lactone of 24-demethylbafilomycin C1 through an aldol condensation of the methoxyacetate followed by formation of the C12-C13 double bond via a diene-ene RCM reaction.

  7. Push-through Direction Injectin NMR Automation

    Science.gov (United States)

    Nuclear magnetic resonance (NMR) and mass spectrometry (MS) are the two major spectroscopic techniques successfully used in metabolomics studies. The non-invasive, quantitative and reproducible characteristics make NMR spectroscopy an excellent technique for detection of endogeno...

  8. Biomolecular NMR: Past and future.

    Science.gov (United States)

    Markley, John L; Westler, William Milo

    2017-08-15

    The editors of this special volume suggested this topic, presumably because of the perspective lent by our combined >90-year association with biomolecular NMR. What follows is our personal experience with the evolution of the field, which we hope will illustrate the trajectory of change over the years. As for the future, one can confidently predict that it will involve unexpected advances. Our narrative is colored by our experience in using the NMR Facility for Biomedical Studies at Carnegie-Mellon University (Pittsburgh) and in developing similar facilities at Purdue (1977-1984) and the University of Wisconsin-Madison (1984-). We have enjoyed developing NMR technology and making it available to collaborators and users of these facilities. Our group's association with the Biological Magnetic Resonance data Bank (BMRB) and with the Worldwide Protein Data Bank (wwPDB) has also been rewarding. Of course, many groups contributed to the early growth and development of biomolecular NMR, and our brief personal account certainly omits many important milestones. Copyright © 2017 Elsevier Inc. All rights reserved.

  9. Deuterium Exchange Kinetics by NMR.

    Science.gov (United States)

    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)

  10. High resolution NMR theory and chemical applications

    CERN Document Server

    Becker, Edwin D

    1969-01-01

    High Resolution NMR: Theory and Chemical Applications focuses on the applications of nuclear magnetic resonance (NMR), as well as chemical shifts, lattices, and couplings. The book first offers information on the theory of NMR, including nuclear spin and magnetic moment, spin lattice relaxation, line widths, saturation, quantum mechanical description of NMR, and ringing. The text then ponders on instrumentation and techniques and chemical shifts. Discussions focus on the origin of chemical shifts, reference compounds, empirical correlations of chemical shifts, modulation and phase detection,

  11. Time domain NMR applied to food products

    NARCIS (Netherlands)

    Duynhoven, van J.P.M.; Voda, A.; Witek, M.M.; As, van H.

    2010-01-01

    Time-domain NMR is being used throughout all areas of food science and technology. A wide range of one- and two-dimensional relaxometric and diffusometric applications have been implemented on cost-effective, robust and easy-to-use benchtop NMR equipment. Time-domain NMR applications do not only

  12. nmr spectroscopic study and dft calculations of giao nmr shieldings

    African Journals Online (AJOL)

    Preferred Customer

    bond 1JCH coupling constants and 13C NMR spin-lattice relaxation time (T1) of 1,9-diaminononane (danon,. C9H22N2) ... The 13C spin-lattice relaxation time is the important experimental quantity for examining the dynamical ..... Montgomery, J.A.; Vreven, T.; Kudin, K.N.; Burant, J.C.; Millam, J.M.; Iyengar, S.S.;. Tomasi, J.

  13. Polymers under mechanical stress- an NMR investigation

    Energy Technology Data Exchange (ETDEWEB)

    Boehme, Ute; Scheler, Ulrich [Leibniz Institute of Polymer Research Dresden (Germany); Xu, Bo; Leisen, Johannes; Beckham, Haskell W. [Georgia Institute of Technology, Atlanta, Georgia (United States)

    2010-07-01

    Low-field NMR using permanent magnets in Halbach arrangements permit NMR investigation without the limits present in high-field NMR. The lower field in conjunction with confined stray field permit the application of NMR, in particular relaxation NMR in a stretching apparatus and a rheometer. Crystalline and amorphous fraction of semi-crystalline polymers are distinguished by their transverse relaxation times. Upon mechanical load the relaxation times of the amorphous fraction changes as seen in in-situ measurements on polypropylene rods. During the formation of a neck the crystalline fraction becomes more prominent.

  14. PVT Degradation Studies: NMR Analysis

    Energy Technology Data Exchange (ETDEWEB)

    Cho, Herman M. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Kouzes, Richard T. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

    2017-06-06

    Under certain environmental conditions, polyvinyl toluene (PVT) plastic scintillator has been observed to undergo internal fogging. Nuclear magnetic resonance spectroscopy has been used to elucidate the state of water inside the PVT. The deuterium NMR results show that water absorbed by PVT under warm, humid conditions enters several distinct environments, and when the PVT is transferred from incubation to ambient temperature and humidity the water is lost on a time scale of a few hours from these samples. Most of the deuterium NMR peaks can be assigned to bulk liquid water, but almost 35% of the detected signal intensity is contained in a resonance that resembles spectra of water contained in nanometer-scale pores in mesoporous carbon.

  15. Sorption isotherm measurements by NMR.

    Science.gov (United States)

    Leisen, Johannes; Beckham, Haskell W; Benham, Michael

    2002-01-01

    An experimental setup is described for the automated recording of sorption isotherms by NMR experiments at precisely defined levels of relative humidity (RH). Implementation is demonstrated for a cotton fabric; Bloch decays. T1 and T2* relaxation times were measured at predefined steps of increasing and decreasing relative humidities (RHs) so that a complete isotherm of NMR properties was obtained. Bloch decays were analyzed by fitting to relaxation functions consisting or a slow- and a fast-relaxing component. The fraction of slow-relaxing component was greater than the fraction of sorbed moisture determined from gravimetric sorption data. The excess slow-relaxing component was attributed to plasticized segments of the formerly rigid cellulose matrix. T1 and T2* sorption isotherms exhibit hysteresis similar to gravimetric sorption isotherms. However, correlating RH to moisture content (MC) reveals that both relaxation constants depend only on MC, and not on the history of moisture exposure.

  16. NMR hyperpolarization techniques for biomedicine.

    Science.gov (United States)

    Nikolaou, Panayiotis; Goodson, Boyd M; Chekmenev, Eduard Y

    2015-02-16

    Recent developments in NMR hyperpolarization have enabled a wide array of new in vivo molecular imaging modalities, ranging from functional imaging of the lungs to metabolic imaging of cancer. This Concept article explores selected advances in methods for the preparation and use of hyperpolarized contrast agents, many of which are already at or near the phase of their clinical validation in patients. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  17. {sup 1} H and {sup 13} C NMR studies on the enoling of 5-benzyl barbituric acids; Estudos por H-1 e C-13 RMN da enolizacao de acidos 5-benzil barbituricos

    Energy Technology Data Exchange (ETDEWEB)

    Villar, Jose Daniel Figueroa; Santos, Nedina Lucia dos; Cruz, Elizabete Rangel [Instituto Militar de Engenharia (IME), Rio de Janeiro, RJ (Brazil). Secao de Quimica

    1991-12-31

    This work shows that the derivatives of the 5-benzyl barbituric acids hydroxylated at the ortho position of the aromatic ring only exist in the enol form. and that the alkylation of this hydroxyl gives products which exist mainly in the ketone form of the DMSO 5 refs., 2 figs., 2 tabs.

  18. Dynamic pulsed-field-gradient NMR

    CERN Document Server

    Sørland, Geir Humborstad

    2014-01-01

    Dealing with the basics, theory and applications of dynamic pulsed-field-gradient NMR NMR (PFG NMR), this book describes the essential theory behind diffusion in heterogeneous media that can be combined with NMR measurements to extract important information of the system being investigated. This information could be the surface to volume ratio, droplet size distribution in emulsions, brine profiles, fat content in food stuff, permeability/connectivity in porous materials and medical applications currently being developed. Besides theory and applications it will provide the readers with background knowledge on the experimental set-ups, and most important, deal with the pitfalls that are numerously present in work with PFG-NMR. How to analyze the NMR data and some important basic knowledge on the hardware will be explained, too.

  19. The future of NMR-based metabolomics.

    Science.gov (United States)

    Markley, John L; Brüschweiler, Rafael; Edison, Arthur S; Eghbalnia, Hamid R; Powers, Robert; Raftery, Daniel; Wishart, David S

    2017-02-01

    The two leading analytical approaches to metabolomics are mass spectrometry (MS) and nuclear magnetic resonance (NMR) spectroscopy. Although currently overshadowed by MS in terms of numbers of compounds resolved, NMR spectroscopy offers advantages both on its own and coupled with MS. NMR data are highly reproducible and quantitative over a wide dynamic range and are unmatched for determining structures of unknowns. NMR is adept at tracing metabolic pathways and fluxes using isotope labels. Moreover, NMR is non-destructive and can be utilized in vivo. NMR results have a proven track record of translating in vitro findings to in vivo clinical applications. Copyright © 2016 The Author(s). Published by Elsevier Ltd.. All rights reserved.

  20. An Inversion Recovery NMR Kinetics Experiment

    OpenAIRE

    Williams, Travis J.; Kershaw, Allan D.; Li, Vincent; Wu, Xinping

    2011-01-01

    A convenient laboratory experiment is described in which NMR magnetization transfer by inversion recovery is used to measure the kinetics and thermochemistry of amide bond rotation. The experiment utilizes Varian spectrometers with the VNMRJ 2.3 software, but can be easily adapted to any NMR platform. The procedures and sample data sets in this article will enable instructors to use inversion recovery as a laboratory activity in applied NMR classes and provide research students with a conveni...

  1. Applications of NMR in Dairy Research

    Directory of Open Access Journals (Sweden)

    Anthony D. Maher

    2014-03-01

    Full Text Available NMR is a robust analytical technique that has been employed to investigate the properties of many substances of agricultural relevance. NMR was first used to investigate the properties of milk in the 1950s and has since been employed in a wide range of studies; including properties analysis of specific milk proteins to metabolomics techniques used to monitor the health of dairy cows. In this brief review, we highlight the different uses of NMR in the dairy industry.

  2. observed by high pressure NMR and NQR

    Indian Academy of Sciences (India)

    Abstract. NMR and NQR studies on two interesting systems (URu2Si2, CeTIn5) were performed under high pressure. (1) URu2Si2: In the pressure range 3.0 to 8.3 kbar, we have observed new 29Si. NMR signals arising from the antiferromagnetic (AF) region besides the previously observed 29Si. NMR signals which come ...

  3. Structural variation in ethylenediamine and -diphosphine adducts of (2,6-Me2C6H3S)2Pb: a single crystal X-ray diffraction and 207Pb solid-state NMR spectroscopy study.

    Science.gov (United States)

    Rossini, Aaron J; Macgregor, Alan W; Smith, Anita S; Schatte, Gabriele; Schurko, Robert W; Briand, Glen G

    2013-07-14

    Coordination complexes of (2,6-Me2C6H3S)2Pb (1) with flexible bidentate ligands have been prepared to explore new bonding environments for Pb(II) thiolates. The reaction of 1 with a series of ethylenediamine and ethylenediphosphine ligands resulted in isolation of the adducts [(2,6-Me2C6H3S)2Pb]2(tmeda) (9), [(2,6-Me2C6H3S)2Pb]3(dmpe) (10) and [(2,6-Me2C6H3S)2Pb]2(dppe) (11) [tmeda = N,N,N',N'-tetramethylethylenediamine; dmpe = bis(dimethylphosphino)ethane; dppe = bis(diphenylphosphino)ethane]. The X-ray crystal structure of 9 shows a dinuclear species in which tmeda is chelating a ψ-trigonal bipyramidal S2N2 Pb centre via axial and equatorial sites. The structure of 10 displays a trinuclear structural unit in which dmpe is chelating a ψ-trigonal bipyramidal S2P2 Pb centre via equatorial sites. Compounds 9 and 10 also contain a second unique metal centre with ψ-tetrahedral S3Pb bonding motifs. The structure of 11 shows the dppe ligand bridging two Pb ψ-tetrahedral S2P metal bonding environments. Static (207)Pb solid-state NMR (SSNMR) spectra of 9-11 and [Ph4As][(PhS)3Pb] (12) were acquired with cross polarization (CP)-CPMG and frequency swept pulse (WURST)-CPMG pulse sequences, and the efficiencies of these pulse sequences are compared. The (207)Pb SSNMR spectra reveal that the lead chemical shift anisotropies (CSA) vary greatly between the different Pb sites, and are generally large in magnitude. DFT calculations are utilized to relate the orientations of the (207)Pb nuclear magnetic shielding tensors to the molecular structures, and to aid in spectral assignment where multiple Pb centres are present. The combination of X-ray diffraction, (207)Pb SSNMR and DFT is shown to be invaluable for the structural characterization of these important structural motifs, and should find wide-ranging application to numerous lead coordination compounds.

  4. Spin-Exchange Pumped NMR Gyros

    CERN Document Server

    Walker, Thad G

    2016-01-01

    We present the basic theory governing spin-exchange pumped NMR gyros. We review the basic physics of spin-exchange collisions and relaxation as they pertain to precision NMR. We present a simple model of operation as an NMR oscillator and use it to analyze the dynamic response and noise properties of the oscillator. We discuss the primary systematic errors (differential alkali fields, quadrupole shifts, and offset drifts) that limit the bias stability, and discuss methods to minimize them. We give with a brief overview of a practical implementation and performance of an NMR gyro built by Northrop-Grumman Corporation, and conclude with some comments about future prospects.

  5. NMR spectroscopy using liquid crystal solvents

    CERN Document Server

    Emsley, JW

    2013-01-01

    NMR Spectroscopy using Liquid Crystal Solvents covers the importance of using a liquid crystal solvent in NMR to derive nuclear dipolar spin-spin coupling constants. This book is composed of ten chapters, and begins with a brief description of the features and benefits of liquid crystal in NMR spectroscopic analysis. The succeeding chapters deal with the mode of operation of nuclear spin Hamiltonian for partially oriented molecules and the analysis of NMR spectra of partially oriented molecules, as well as the determination of rigid molecule structure. These topics are followed by discussions

  6. NMR-Based Metabolomics of Oral Biofluids.

    Science.gov (United States)

    Schirra, Horst Joachim; Ford, Pauline J

    2017-01-01

    NMR-based metabolomics is an established technique for characterizing the metabolite profile of biological fluids and investigating how metabolite profiles change in response to biological and/or clinical stimuli. Thus, NMR-based metabolomics has the potential to discover biomarkers for diagnosis, prognosis, and/or therapy of clinical conditions, as well as to unravel the physiology underlying clinical conditions. Here, we describe a detailed protocol for NMR-based metabolomics of oral biofluids, including sample collection, sample handling, NMR data acquisition, and processing. In addition, we give a general overview of the statistical analysis of the resulting metabolomic data.

  7. Access to NMR Spectroscopy for Two-Year College Students: The NMR Site at Trinity University

    Science.gov (United States)

    Mills, Nancy S.; Shanklin, Michael

    2011-01-01

    Students at two-year colleges and small four-year colleges have often obtained their exposure to NMR spectroscopy through "canned" spectra because the cost of an NMR spectrometer, particularly a high-field spectrometer, is prohibitive in these environments. This article describes the design of a NMR site at Trinity University in which…

  8. NMR studies of oriented molecules

    Energy Technology Data Exchange (ETDEWEB)

    Sinton, S.W.

    1981-11-01

    Deuterium and proton magnetic resonance are used in experiments on a number of compounds which either form liquid crystal mesophases themselves or are dissolved in a liquid crystal solvent. Proton multiple quantum NMR is used to simplify complicated spectra. The theory of nonselective multiple quantum NMR is briefly reviewed. Benzene dissolved in a liquid crystal are used to demonstrate several outcomes of the theory. Experimental studies include proton and deuterium single quantum (..delta..M = +-1) and proton multiple quantum spectra of several molecules which contain the biphenyl moiety. 4-Cyano-4'-n-pentyl-d/sub 11/-biphenyl (5CB-d/sub 11/) is studied as a pure compound in the nematic phase. The obtained chain order parameters and dipolar couplings agree closely with previous results. Models for the effective symmetry of the biphenyl group in 5CB-d/sub 11/ are tested against the experimental spectra. The dihedral angle, defined by the planes containing the rings of the biphenyl group, is found to be 30 +- 2/sup 0/ for 5DB-d/sub 11/. Experiments are also described for 4,4'-d/sub 2/-biphenyl, 4,4' - dibromo-biphenyl, and unsubstituted biphenyl.

  9. Inter-specific and ontogenic differences in delta C-13 and delta N-15 values and Hg and Cd concentrations in cephalopods

    OpenAIRE

    Chouvelon, Tiphaine; Spitz, Jerome; Cherel, Y; Caurant, Florence; Sirmel, R.; Mendez-Fernandez, P.; Bustamante, Paco

    2011-01-01

    Chemical tracers (e. g. stable isotopes or trace metals) are increasingly used to study trophic ecology and feeding habits of marine organisms and various factors can affect their values. The aim of the present study was to provide information on ontogenic effects on stable carbon and nitrogen values (delta C-13 and delta N-15) and on cadmium (Cd) and mercury (Hg) concentrations in 5 cephalopod species from the Bay of Biscay (North-East Atlantic Ocean). To this end, individuals belonging to 3...

  10. Identification of in vivo enzyme activities in the cometabolism of glucose and acetate by Saccharomyces cerevisiae by using C-13-labeled substrates

    DEFF Research Database (Denmark)

    Santos, Maria Margarida M. dos; Gombert, A.K.; Christensen, B.

    2003-01-01

    A detailed characterization of the central metabolic network of Saccharomyces cerevisiae CEN.PK 113-7D was carried out during cometabolism. of different mixtures of glucose and acetate, using aerobic C-limited chemostats in which one of these two substrates was labeled with C-13. To confirm...... metabolism and amino acid biosynthesis. Malic enzyme flux increased linearly with increasing acetate fraction. During growth on a very-high-acetate fraction, the activity of malic enzyme satisfied the biosynthetic needs of pyruvate in the mitochondria, while in the cytosol pyruvate was supplied via pyruvate...

  11. An Inversion Recovery NMR Kinetics Experiment

    Science.gov (United States)

    Williams, Travis J.; Kershaw, Allan D.; Li, Vincent; Wu, Xinping

    2011-01-01

    A convenient laboratory experiment is described in which NMR magnetization transfer by inversion recovery is used to measure the kinetics and thermochemistry of amide bond rotation. The experiment utilizes Varian spectrometers with the VNMRJ 2.3 software, but can be easily adapted to any NMR platform. The procedures and sample data sets in this…

  12. A Guided Inquiry Approach to NMR Spectroscopy

    Science.gov (United States)

    Parmentier, Laura E.; Lisensky, George C.; Spencer, Brock

    1998-04-01

    We present a novel way to introduce NMR spectroscopy into the general chemistry curriculum as part of a week-long aspirin project in our one-semester introductory course. Aspirin is synthesized by reacting salicylic acid and acetic anhydride. Purity is determined by titration and IR and NMR spectroscopy. Students compare IR and NMR spectra of their aspirin product to a series of reference spectra obtained by the class. Students are able to interpret the IR spectra of their aspirin using IR data from previous experiments. NMR is introduced by having students collect 1H NMR spectra of a series of reference compounds chosen to include some of the structural features of aspirin and compare spectra and structures of the reference compounds to develop a correlation chart for chemical shifts. This process is done in small groups using shared class data and is guided by a series of questions designed to relate the different kinds of hydrogen atoms to number and position of peaks in the NMR spectrum. Students then identify the peaks in the NMR spectrum of their aspirin product and relate percent purity by titration with spectral results and percent yield. This is an enjoyable project that combines the synthesis of a familiar material with a guided inquiry-based introduction to NMR spectroscopy.

  13. Synthesis and NMR Elucidation of Novel Pentacycloundecane ...

    African Journals Online (AJOL)

    Herein we report the synthesis and NMR elucidation of five novel pentacycloundecane (PCU)-derived short peptides as potential HIV protease inhibitors. 1H and 13C spectral analysis show major overlapping of methine resonance of the PCU 'cage' thereby making it extremely difficult to assign the NMR signals. Attachment ...

  14. An Integrated Laboratory Project in NMR Spectroscopy.

    Science.gov (United States)

    Hudson, Reggie L.; Pendley, Bradford D.

    1988-01-01

    Describes an advanced NMR project that can be done with a 60-MHz continuous-wave proton spectrometer. Points out the main purposes are to give students experience in second-order NMR analysis, the simplification of spectra by raising the frequency, and the effect of non-hydrogen nuclei on proton resonances. (MVL)

  15. Using Cloud Storage for NMR Data Distribution

    Science.gov (United States)

    Soulsby, David

    2012-01-01

    An approach using Google Groups as method for distributing student-acquired NMR data has been implemented. We describe how to configure NMR spectrometer software so that data is uploaded to a laboratory section specific Google Group, thereby removing bottlenecks associated with printing and processing at the spectrometer workstation. Outside of…

  16. 1H-NMR-based metabolic analysis of human serum reveals novel markers of myocardial energy expenditure in heart failure patients.

    Directory of Open Access Journals (Sweden)

    Zhiyong Du

    Full Text Available OBJECTIVE: Elevated myocardial energy expenditure (MEE is related with reduced left ventricular ejection fraction, and has also been documented as an independent predictor of cardiovascular mortality. However, the serum small-molecule metabolite profiles and pathophysiological mechanisms of elevated MEE in heart failure (HF are still lacking. Herein, we used 1H-NMR-based metabolomics analysis to screen for potential biomarkers of MEE in HF. METHODS: A total of 61 subjects were enrolled, including 46 patients with heart failure and 15 age-matched controls. Venous serum samples were collected from subjects after an 8-hour fast. An INOVA 600 MHz nuclear magnetic resonance spectrometer with Carr-Purcell-Melboom-Gill (CPMG pulse sequence was employed for the metabolomics analysis and MEE was calculated using colored Doppler echocardiography. Metabolomics data were processed using orthogonal signal correction and regression analysis was performed using the partial least squares method. RESULTS: The mean MEE levels of HF patients and controls were 139.61±58.18 cal/min and 61.09±23.54 cal/min, respectively. Serum metabolomics varied with MEE changed, and 3-hydroxybutyrate, acetone and succinate were significantly elevated with the increasing MEE. Importantly, these three metabolites were independent of administration of angiotensin converting enzyme inhibitor, β-receptor blockers, diuretics and statins (P>0.05. CONCLUSIONS: These results suggested that in patients with heart failure, MEE elevation was associated with significant changes in serum metabolomics profiles, especially the concentration of 3-hydroxybutyrate, acetone and succinate. These compounds could be used as potential serum biomarkers to study myocardial energy mechanism in HF patients.

  17. Carbon-13 NMR spectroscopy of biological systems

    CERN Document Server

    Beckmann, Nicolau

    1995-01-01

    This book is intended to provide an in-depth understanding of 13C NMR as a tool in biological research. 13C NMR has provided unique information concerning complex biological systems, from proteins and nucleic acids to animals and humans. The subjects addressed include multidimensional heteronuclear techniques for structural studies of molecules in the liquid and solid states, the investigation of interactions in model membranes, the elucidation of metabolic pathwaysin vitro and in vivo on animals, and noninvasive metabolic studies performed on humans. The book is a unique mix of NMR methods and biological applications which makes it a convenient reference for those interested in research in this interdisciplinary area of physics, chemistry, biology, and medicine.Key Features* An interdisciplinary text with emphasis on both 13C NMR methodology and the relevant biological and biomedical issues* State-of-the-art 13C NMR techniques are described; Whenever possible, their advantages over other approaches are empha...

  18. Challenges and perspectives in quantitative NMR.

    Science.gov (United States)

    Giraudeau, Patrick

    2017-01-01

    This perspective article summarizes, from the author's point of view at the beginning of 2016, the major challenges and perspectives in the field of quantitative NMR. The key concepts in quantitative NMR are first summarized; then, the most recent evolutions in terms of resolution and sensitivity are discussed, as well as some potential future research directions in this field. A particular focus is made on methodologies capable of boosting the resolution and sensitivity of quantitative NMR, which could open application perspectives in fields where the sample complexity and the analyte concentrations are particularly challenging. These include multi-dimensional quantitative NMR and hyperpolarization techniques such as para-hydrogen-induced polarization or dynamic nuclear polarization. Because quantitative NMR cannot be dissociated from the key concepts of analytical chemistry, i.e. trueness and precision, the methodological developments are systematically described together with their level of analytical performance. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

  19. NMR and MRI apparatus and method

    Energy Technology Data Exchange (ETDEWEB)

    Clarke, John; Kelso, Nathan; Lee, SeungKyun; Moessle, Michael; Myers, Whittier; McDermott, Robert; ten Haken, Bernard; Pines, Alexander; Trabesinger, Andreas

    2007-03-06

    Nuclear magnetic resonance (NMR) signals are detected in microtesla fields. Prepolarization in millitesla fields is followed by detection with an untuned dc superconducting quantum interference device (SQUID) magnetometer. Because the sensitivity of the SQUID is frequency independent, both signal-to-noise ratio (SNR) and spectral resolution are enhanced by detecting the NMR signal in extremely low magnetic fields, where the NMR lines become very narrow even for grossly inhomogeneous measurement fields. Additional signal to noise benefits are obtained by use of a low noise polarization coil, comprising litz wire or superconducting materials. MRI in ultralow magnetic field is based on the NMR at ultralow fields. Gradient magnetic fields are applied, and images are constructed from the detected NMR signals.

  20. NMR-based milk metabolomics

    DEFF Research Database (Denmark)

    Sundekilde, Ulrik; Larsen, Lotte Bach; Bertram, Hanne Christine S.

    2013-01-01

    Milk is a key component in infant nutrition worldwide and, in the Western parts of the world, also in adult nutrition. Milk of bovine origin is both consumed fresh and processed into a variety of dairy products including cheese, fermented milk products, and infant formula. The nutritional quality...... and processing capabilities of bovine milk is closely associated to milk composition. Metabolomics is ideal in the study of the low-molecular-weight compounds in milk, and this review focuses on the recent nuclear magnetic resonance (NMR)-based metabolomics trends in milk research, including applications linking...... the milk metabolite profiling with nutritional aspects, and applications which aim to link the milk metabolite profile to various technological qualities of milk. The metabolite profiling studies encompass the identification of novel metabolites, which potentially can be used as biomarkers or as bioactive...

  1. NMR studies of sedimentary tetrapyrroles

    Energy Technology Data Exchange (ETDEWEB)

    Keely, B.J.; Maxwell, J.R. (Univ. of Bristol (England))

    Structural assignments of sedimentary biological markers rely mostly on the use of GC and GC-MS techniques, involving both chromatographic and mass spectral comparisons with synthetic standards in addition to de facto mass spectral interpretation. Difficulties experienced in the analysis of sedimentary porphyrins by GC-MS (which until very recently required derivatization), and the desire to understand the origins and geochemical transformations of these components and their precursors, have led to more extensive structural investigations than usually accorded to other classes of biological marker. This paper briefly reviews recent developments in {sup 1}H NMR studies of chlorins and porphyrins of sedimentary origin, with particular reference to correlated spectroscopy (COSY), which allows elucidation of spin-coupled systems.

  2. NMR-based metabolomics applications

    DEFF Research Database (Denmark)

    Iaccarino, Nunzia

    ’s phenotype. This approach finds an increasing number of applications in many areas including medical, pharmaceutical, food and environmental sciences. The combined use of NMR spectroscopy and chemometrics techniques, is able to provide the metabolic “fingerprint” of the various samples. This PhD project...... focused on the analysis of various samples covering a wide range of fields, namely, food and nutraceutical sciences, cell metabolomics and medicine using a metabolomics approach. Indeed, the first part of the thesis describes two exploratory studies performed on Algerian extra virgin olive oil and apple...... juice from ancient Danish apple cultivars. Both studies revealed variety-related peculiarities that would have been difficult to detect by means of traditional analysis. The second part of the project includes four metabolomics studies performed on samples of biological origin. In particular, the first...

  3. Preprocessing of NMR metabolomics data.

    Science.gov (United States)

    Euceda, Leslie R; Giskeødegård, Guro F; Bathen, Tone F

    2015-05-01

    Metabolomics involves the large scale analysis of metabolites and thus, provides information regarding cellular processes in a biological sample. Independently of the analytical technique used, a vast amount of data is always acquired when carrying out metabolomics studies; this results in complex datasets with large amounts of variables. This type of data requires multivariate statistical analysis for its proper biological interpretation. Prior to multivariate analysis, preprocessing of the data must be carried out to remove unwanted variation such as instrumental or experimental artifacts. This review aims to outline the steps in the preprocessing of NMR metabolomics data and describe some of the methods to perform these. Since using different preprocessing methods may produce different results, it is important that an appropriate pipeline exists for the selection of the optimal combination of methods in the preprocessing workflow.

  4. Structural fidelity and NMR relaxation analysis in a prototype RNA hairpin.

    Science.gov (United States)

    Giambaşu, George M; York, Darrin M; Case, David A

    2015-05-01

    RNA hairpins are widespread and very stable motifs that contribute decisively to RNA folding and biological function. The GTP1G2C3A4C5U6U7C8G9G10U11G12C13C14 construct (with a central UUCG tetraloop) has been extensively studied by solution NMR, and offers and excellent opportunity to evaluate the structure and dynamical description afforded by molecular dynamics (MD) simulations. Here, we compare average structural parameters and NMR relaxation rates estimated from a series of multiple independent explicit solvent MD simulations using the two most recent RNA AMBER force fields (ff99 and ff10). Predicted overall tumbling times are ∼20% faster than those inferred from analysis of NMR data and follow the same trend when temperature and ionic strength is varied. The Watson-Crick stem and the "canonical" UUCG loop structure are maintained in most simulations including the characteristic syn conformation along the glycosidic bond of G9, although some key hydrogen bonds in the loop are partially disrupted. Our analysis pinpoints G9-G10 backbone conformations as a locus of discrepancies between experiment and simulation. In general the results for the more recent force-field parameters (ff10) are closer to experiment than those for the older ones (ff99). This work provides a comprehensive and detailed comparison of state of the art MD simulations against a wide variety of solution NMR measurements. © 2015 Giambaşu et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2011-01-01

    on decoupling efficiency as well as scaling factors. Indirect detection with assistance of PMLGm$\\bar{x}$ during INEPTR transfer proved to offer the highest sensitivity gains of 3-10. In addition, the CRAMPS sequence was applied under fast MAS to increase the 1H resolution during t1 evolution in the traditional, 13C detected HETCOR scheme. Two naturally abundant solids, tripeptide N-formyl-L-methionyl-L-leucyl-L-phenylalanine (f-MLF-OH) and brown coal, with well ordered and highly disordered structures, respectively, are studied to confirm the capabilities of these techniques. Concomitantly, a simple optimization of 1H homonuclear dipolar decoupling at MAS rates exceeding 10 kHz was developed (Chapter 4). The fine-tuned decoupling efficiency can be obtained by minimizing the signal loss due to transverse relaxation in a simple spin-echo experiment, using directly the sample of interest. The excellent agreement between observed decoupling pattern and earlier theoretical predictions confirmed the utility of this strategy. The properties of naturally abundant surface-bound fluorocarbon groups in mesoporous silica nanoparticles (MSNs) were investigated by the above-mentioned multidimensional solid-state NMR experiments and theoretical modeling (Chapter 5). Two conformations of (pentafluorophenyl)propyl groups (abbreviated as PFP) were determined as PFP-prone and PFP-upright, whose aromatic rings are located above the siloxane bridges and in roughly upright position, respectively. Several 1D and 2D NMR techniques were implemented in the characterizations, including indirectly detected 1H{l_brace}13C{r_brace} and 19F{l_brace}13C{r_brace} 2D HETCOR, Carr-Purcell-Meiboom-Gill (CPMG) assisted 29Si direct polarization and 29Si19F 2D experiments, 2D double-quantum (DQ) 19F MAS NMR spectra and spin-echo measurements

  6. Studies on the synthesis of bafilomycin A(1): stereochemical aspects of the fragment assembly aldol reaction for construction of the C(13)-C25) segment.

    Science.gov (United States)

    Roush, William R; Bannister, Thomas D; Wendt, Michael D; Jablonowski, Jill A; Scheidt, Karl A

    2002-06-14

    Highly stereoselective syntheses of aldols 8a-c corresponding to the C(13)-C(25) segment of bafilomycin A(1) were developed by routes involving fragment assembly aldol reactions of chiral aldehyde 6a and the chiral methyl ketones 7. A remote chelation effect plays a critical role in determining the stereoselectivity of the key aldol coupling of 6a and the lithium enolate of 7b. The protecting group for C(23)-OH of the chiral aldehyde fragment also influences the selectivity of the lithium enolate aldol reaction. In contrast, the aldol reaction of 6a and the chlorotitanium enolates of 7a,c were much less sensitive to the nature of the C(15)-hydroxyl protecting group. Studies of the reactions of chiral aldehydes with Takai's (gamma-methoxyallyl)chromium reagent 40 are also described. The stereoselectivity of these reactions is also highly dependent on the protecting groups and stereochemistry of the chiral aldehyde substrates.

  7. Fatty acid biomarkers: validation of food web and trophic markers using C-13-labelled fatty acids in juvenile sandeel ( Ammodytes tobianus )

    DEFF Research Database (Denmark)

    Dalsgaard, Anne Johanne Tang; St. John, Michael

    2004-01-01

    A key issue in marine science is parameterizing trophic interactions in marine food webs, thereby developing an understanding of the importance of top-down and bottom-up controls on populations of key trophic players. This study validates the utility of fatty acid food web and trophic markers using...... C-13-labelled fatty acids to verify the conservative incorporation of fatty acid tracers by juvenile sandeel (Ammodytes tobianus) and assess their uptake, clearance, and metabolic turnover rates. Juvenile sandeel were fed for 16 days in the laboratory on a formulated diet enriched in (13)C16......), respectively. Lack of temporal trends in nonlabelled fatty acids confirmed the conservative incorporation of labelled fatty acids by the fish....

  8. Scalar operators in solid-state NMR

    Energy Technology Data Exchange (ETDEWEB)

    Sun, Boqin [Univ. of California, Berkeley, CA (United States)

    1991-11-01

    Selectivity and resolution of solid-state NMR spectra are determined by dispersion of local magnetic fields originating from relaxation effects and orientation-dependent resonant frequencies of spin nuclei. Theoretically, the orientation-dependent resonant frequencies can be represented by a set of irreducible tensors. Among these tensors, only zero rank tensors (scalar operators) are capable of providing high resolution NMR spectra. This thesis presents a series of new developments in high resolution solid-state NMR concerning the reconstruction of various scalar operators motion in solid C60 is analyzed.

  9. Graphical programming for broadband pulse NMR spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Belmonte, S.B. [Universidade do Estado (UERJ), Rio de Janeiro, RJ (Brazil). Dept. de Engenharia Eletronica; Oliveira, I.S.; Guimaraes, A.P. [Centro Brasileiro de Pesquisas Fisicas (CBPF), Rio de Janeiro, RJ (Brazil)

    1997-12-31

    In a broadband pulsed nuclear magnetic resonance (NMR) spectrometer we often need to sweep the excitation frequency over a wide range, and acquire the spin echo components in quadrature for further spectral analysis. Computer languages such as C or Pascal have been traditionally applied to the development of software control of laboratory equipment, and consequently, the automatization of NMR experiments. However, the use of graphical languages have proved to be a flexible and convenient way for experiment and data acquisition control. In our application we use the graphical language Labview for the automatic control of a broadband pulse NMR spectrometer, dedicated to the study of magnetic metal systems. (author) 2 refs., 2 figs.

  10. Graphical programming for pulse automated NMR experiments

    Energy Technology Data Exchange (ETDEWEB)

    Belmonte, S.B. [Universidade do Estado, Rio de Janeiro, RJ (Brazil); Oliveira, I.S.; Guimaraes, A.P. [Centro Brasileiro de Pesquisas Fisicas (CBPF), Rio de Janeiro, RJ (Brazil)

    1999-01-01

    We describe a software program designed to control a broadband pulse Nuclear Magnetic Resonance (NMR) spectrometer used in zero-field NMR studies of magnetic metals. The software is written in the graphical language LabVIEW. This type of programming allows modifications and the inclusion of new routines to be easily made by the non-specialist, without changing the basic structure of the program. The program corrects for differences in the gain of the two acquisition channels [U (phase) and V (quadrature)], and automatic baseline subtraction. We present examples of measurements of NMR spectra, spin-echo decay (T{sub 2}), and quadrupolar oscillations, performed in magnetic intermetallic compounds. (author)

  11. NMR reaction monitoring in flow synthesis

    Directory of Open Access Journals (Sweden)

    M. Victoria Gomez

    2017-02-01

    Full Text Available Recent advances in the use of flow chemistry with in-line and on-line analysis by NMR are presented. The use of macro- and microreactors, coupled with standard and custom made NMR probes involving microcoils, incorporated into high resolution and benchtop NMR instruments is reviewed. Some recent selected applications have been collected, including synthetic applications, the determination of the kinetic and thermodynamic parameters and reaction optimization, even in single experiments and on the μL scale. Finally, software that allows automatic reaction monitoring and optimization is discussed.

  12. Oriented solid-state NMR spectrosocpy

    DEFF Research Database (Denmark)

    Bertelsen, Kresten

    This thesis is concerned with driving forward oriented solid-state NMR spectroscopy as a viable technique for studying peptides in membrane bilayers. I will show that structural heterogeneity is an intrinsic part of the peptide/lipid system and that NMR can be used to characterize static...... and dynamic structural features of the peptides and its local surroundings. In fact one need to take into account the dynamical features of the system in order to correctly predict the structure from oriented solid-state NMR spectra.      ...

  13. Rheology of Blood by NMR

    Science.gov (United States)

    Han, Song-I.; Marseille, Oliver; Gehlen, Christa; Blümich, Bernhard

    2001-09-01

    Pipe flow of blood in tubes of 1 and 7 mm inner diameter, respectively, was investigated employing two-dimensional NMR velocity imaging and PFG propagator measurements at different Reynolds numbers between 10 and 3500. The results are compared to flow of a water/glycerol mixture of matching viscosity under identical conditions. The transition from laminar to turbulent flow is observed by both a flattening of the velocity profile and a change of the propagator shape. For blood flow this transition is found to be shifted toward higher Reynolds numbers as compared to the transition of the water/glycerol mixture. This observation is in agreement with predictions from hydraulic measurements and is a consequence of the non-Newtonian flow characteristics of blood as a suspension of erythrocytes and plasma. Likewise, a deviation from the laminar flow condition is observed for blood at low Reynolds numbers between 10 and 100. This phenomenon is unknown for Newtonian liquids and is explained by the onset of a geometrical arrangement of the erythrocytes, the so-called rouleaux effect.

  14. Development of Two-Dimensional NMR

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 20; Issue 11. Development of Two-Dimensional NMR: Strucure Determination of Biomolecules in Solution. Anil Kumar. General Article Volume 20 Issue 11 November 2015 pp 995-1002 ...

  15. Bayesian Peak Picking for NMR Spectra

    Directory of Open Access Journals (Sweden)

    Yichen Cheng

    2014-02-01

    Full Text Available Protein structure determination is a very important topic in structural genomics, which helps people to understand varieties of biological functions such as protein-protein interactions, protein–DNA interactions and so on. Nowadays, nuclear magnetic resonance (NMR has often been used to determine the three-dimensional structures of protein in vivo. This study aims to automate the peak picking step, the most important and tricky step in NMR structure determination. We propose to model the NMR spectrum by a mixture of bivariate Gaussian densities and use the stochastic approximation Monte Carlo algorithm as the computational tool to solve the problem. Under the Bayesian framework, the peak picking problem is casted as a variable selection problem. The proposed method can automatically distinguish true peaks from false ones without preprocessing the data. To the best of our knowledge, this is the first effort in the literature that tackles the peak picking problem for NMR spectrum data using Bayesian method.

  16. NMR analysis of compositional heterogeneity in polysaccharides

    Science.gov (United States)

    Many copolysaccharides are compositionally heterogeneous, and the composition determined by the usual analytical or spectroscopic methods provides only an average value. For some polysaccharides, the NMR data contain copolymer sequence information, such as diad, triad, and tetrad sequence intensiti...

  17. Relaxation time estimation in surface NMR

    Energy Technology Data Exchange (ETDEWEB)

    Grunewald, Elliot D.; Walsh, David O.

    2017-03-21

    NMR relaxation time estimation methods and corresponding apparatus generate two or more alternating current transmit pulses with arbitrary amplitudes, time delays, and relative phases; apply a surface NMR acquisition scheme in which initial preparatory pulses, the properties of which may be fixed across a set of multiple acquisition sequence, are transmitted at the start of each acquisition sequence and are followed by one or more depth sensitive pulses, the pulse moments of which are varied across the set of multiple acquisition sequences; and apply processing techniques in which recorded NMR response data are used to estimate NMR properties and the relaxation times T.sub.1 and T.sub.2* as a function of position as well as one-dimensional and two-dimension distributions of T.sub.1 versus T.sub.2* as a function of subsurface position.

  18. Bayesian Peak Picking for NMR Spectra

    KAUST Repository

    Cheng, Yichen

    2014-02-01

    Protein structure determination is a very important topic in structural genomics, which helps people to understand varieties of biological functions such as protein-protein interactions, protein–DNA interactions and so on. Nowadays, nuclear magnetic resonance (NMR) has often been used to determine the three-dimensional structures of protein in vivo. This study aims to automate the peak picking step, the most important and tricky step in NMR structure determination. We propose to model the NMR spectrum by a mixture of bivariate Gaussian densities and use the stochastic approximation Monte Carlo algorithm as the computational tool to solve the problem. Under the Bayesian framework, the peak picking problem is casted as a variable selection problem. The proposed method can automatically distinguish true peaks from false ones without preprocessing the data. To the best of our knowledge, this is the first effort in the literature that tackles the peak picking problem for NMR spectrum data using Bayesian method.

  19. The eNMR platform for structural biology

    NARCIS (Netherlands)

    Bonvin, A.M.J.J.|info:eu-repo/dai/nl/113691238; Rosato, A.; Wassenaar, T.A.|info:eu-repo/dai/nl/297077775

    2010-01-01

    The e-NMR project is a European cooperation initiative that aims at providing the bio-NMR user community with a software platform integrating and streamlining the computational approaches necessary for the analysis of bio-NMR data. The e-NMR platform is based on a Grid computational infrastructure.

  20. Frontiers of NMR in Molecular Biology

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1999-08-25

    NMR spectroscopy is expanding the horizons of structural biology by determining the structures and describing the dynamics of blobular proteins in aqueous solution, as well as other classes of proteins including membrane proteins and the polypeptides that form the aggregates diagnostic of prion and amyloid diseases. Significant results are also emerging on DNA and RNA oligomers and their complexes with proteins. This meeting focused attention on key structural questions emanating from molecular biology and how NMR spectroscopy can be used to answer them.

  1. NMR studies of multiphase flows II

    Energy Technology Data Exchange (ETDEWEB)

    Altobelli, S.A.; Caprihan, A.; Fukushima, E. [Lovelace Institutes, Albuquerque, NM (United States)] [and others

    1995-12-31

    NMR techniques for measurements of spatial distribution of material phase, velocity and velocity fluctuation are being developed and refined. Versions of these techniques which provide time average liquid fraction and fluid phase velocity have been applied to several concentrated suspension systems which will not be discussed extensively here. Technical developments required to further extend the use of NMR to the multi-phase flow arena and to provide measurements of previously unobtainable parameters are the focus of this report.

  2. Physiological monitoring during nmr measurements of animals

    Science.gov (United States)

    Schmidt, Paul G.; Smith, E. Norbert

    With the introduction of whole animal NMR, simultaneous measurement of various physiological parameters becomes desirable. Described is a system for monitoring body temperature, electrocardiogram, and respiration during surface coil measurement of 31P NMR using unanesthetized animals. Passive filtering is used to remove rf pulses from the physiological signals. Provision is made for electrically stimulating the animal. The principles are adaptable to other physiological parameters, and the probe could be modified for other nuclei.

  3. NMRbox: A Resource for Biomolecular NMR Computation.

    Science.gov (United States)

    Maciejewski, Mark W; Schuyler, Adam D; Gryk, Michael R; Moraru, Ion I; Romero, Pedro R; Ulrich, Eldon L; Eghbalnia, Hamid R; Livny, Miron; Delaglio, Frank; Hoch, Jeffrey C

    2017-04-25

    Advances in computation have been enabling many recent advances in biomolecular applications of NMR. Due to the wide diversity of applications of NMR, the number and variety of software packages for processing and analyzing NMR data is quite large, with labs relying on dozens, if not hundreds of software packages. Discovery, acquisition, installation, and maintenance of all these packages is a burdensome task. Because the majority of software packages originate in academic labs, persistence of the software is compromised when developers graduate, funding ceases, or investigators turn to other projects. To simplify access to and use of biomolecular NMR software, foster persistence, and enhance reproducibility of computational workflows, we have developed NMRbox, a shared resource for NMR software and computation. NMRbox employs virtualization to provide a comprehensive software environment preconfigured with hundreds of software packages, available as a downloadable virtual machine or as a Platform-as-a-Service supported by a dedicated compute cloud. Ongoing development includes a metadata harvester to regularize, annotate, and preserve workflows and facilitate and enhance data depositions to BioMagResBank, and tools for Bayesian inference to enhance the robustness and extensibility of computational analyses. In addition to facilitating use and preservation of the rich and dynamic software environment for biomolecular NMR, NMRbox fosters the development and deployment of a new class of metasoftware packages. NMRbox is freely available to not-for-profit users. Copyright © 2017 Biophysical Society. All rights reserved.

  4. Direct Comparison of 19F qNMR and 1H qNMR by Characterizing Atorvastatin Calcium Content

    National Research Council Canada - National Science Library

    Yang Liu; Zhaoxia Liu; Huaxin Yang; Lan He

    2016-01-01

    .... Most of the reports were based on proton qNMR (1H qNMR) and only a few fluorine qNMR (19F qNMR) were reported. No research has been conducted to directly compare the advantage and disadvantage between these two methods...

  5. Solution-state NMR investigation of DNA binding interactions in Escherichia coli formamidopyrimidine-DNA glycosylase (Fpg): a dynamic description of the DNA/protein interface.

    Science.gov (United States)

    Buchko, Garry W; McAteer, Kathleen; Wallace, Susan S; Kennedy, Michael A

    2005-03-02

    Formamidopyrimidine-DNA glycosylase (Fpg) is a base excision repair (BER) protein that removes oxidative DNA lesions. Recent crystal structures of Fpg bound to DNA revealed residues involved in damage recognition and enzyme catalysis, but failed to shed light on the dynamic nature of the processes. To examine the structural and dynamic changes that occur in solution when Fpg binds DNA, NMR spectroscopy was used to study Escherichia coli Fpg free in solution and bound to a double-stranded DNA oligomer containing 1,3-propanediol (13-PD), a non-hydrolyzable abasic-site analogue. Only 209 out of a possible 251 (83%) free-precession 15N/1H HSQC cross peaks were observed and 180 of these were assignable, indicating that approximately 30% of the residues undergo intermediate motion on the NMR timescale, broadening the resonances beyond detection or making them intractable in backbone assignment experiments. The majority of these affected residues were in the polypeptide linker region and the interface between the N- and C-terminal domains. DNA titration experiments revealed line broadening and chemical shift perturbations for backbone amides nearby and distant from the DNA binding surface, but failed to quench the intermediate timescale motion observed for free Fpg, including those residues directly involved in DNA binding, notwithstanding a nanomolar dissociation constant for 13-PD binding. Indeed, after binding to 13-PD, at least approximately 40% of the Fpg residues undergo intermediate timescale motion even though all other residues exhibit tight DNA binding characteristic of slow exchange. CPMG-HSQC experiments revealed millisecond to microsecond motion for the backbone amides of D91 and H92 that were quenched upon binding 13-PD. In free Fpg, heteronuclear 1H-15N NOE experiments detected picosecond timescale backbone motion in the alphaF-beta9 loop, the region primarily responsible for chemically discriminating 8-oxoguanine (8-oxoG) over normal guanine, that was

  6. Structural Monitoring of Oligosaccharides through 13C Enrichment and NMR Observation of Acetyl Groups

    Science.gov (United States)

    Yu, Fei; Prestegard, J. H.

    2006-01-01

    Structural characterization of biomolecules by NMR methods frequently requires the enrichment of magnetically active isotopes at particular molecular sites. Introduction is usually achieved biosynthetically through the use of bacterial cultures grown on isotopically enriched media, but for certain types of molecules—cell-surface carbohydrates of mammalian origin, for example—this is not practical. Here we explore a means of introducing 13C-enriched sites, postisolation in natural carbohydrate products, and illustrate an ability to acquire sufficient information to select appropriate conformational models from among energetically allowed sets. The application presented involves replacement of native N-acetyl groups with 13C-labeled acetyl groups in a simple disaccharide derivative, (GlcNAc)2-OBu, or O-butyl-chitobiose. The assignment of the two acetyl groups introduced is based on a novel combination of NMR and mass spectrometry data. Structural information is obtained from chemical shift anisotropy offsets of 13C carbonyl resonances and 13C-13C dipolar couplings between the labeled methyl and carbonyl carbons of the acetyl groups. Although the application is to a relatively simple system, it lays the groundwork for application to biologically important complex carbohydrate systems. PMID:16782783

  7. Use of NMR and NMR Prediction Software to Identify Components in Red Bull Energy Drinks

    Science.gov (United States)

    Simpson, Andre J.; Shirzadi, Azadeh; Burrow, Timothy E.; Dicks, Andrew P.; Lefebvre, Brent; Corrin, Tricia

    2009-01-01

    A laboratory experiment designed as part of an upper-level undergraduate analytical chemistry course is described. Students investigate two popular soft drinks (Red Bull Energy Drink and sugar-free Red Bull Energy Drink) by NMR spectroscopy. With assistance of modern NMR prediction software they identify and quantify major components in each…

  8. NMR Spectra through the Eyes of a Student: Eye Tracking Applied to NMR Items

    Science.gov (United States)

    Topczewski, Joseph J.; Topczewski, Anna M.; Tang, Hui; Kendhammer, Lisa K.; Pienta, Norbert J.

    2017-01-01

    Nuclear magnetic resonance spectroscopy (NMR) plays a key role in introductory organic chemistry, spanning theory, concepts, and experimentation. Therefore, it is imperative that the instruction methods for NMR are both efficient and effective. By utilizing eye tracking equipment, the researchers were able to monitor how second-semester organic…

  9. Performance of the WeNMR CS-Rosetta3 web server in CASD-NMR.

    Science.gov (United States)

    van der Schot, Gijs; Bonvin, Alexandre M J J

    2015-08-01

    We present here the performance of the WeNMR CS-Rosetta3 web server in CASD-NMR, the critical assessment of automated structure determination by NMR. The CS-Rosetta server uses only chemical shifts for structure prediction, in combination, when available, with a post-scoring procedure based on unassigned NOE lists (Huang et al. in J Am Chem Soc 127:1665-1674, 2005b, doi: 10.1021/ja047109h). We compare the original submissions using a previous version of the server based on Rosetta version 2.6 with recalculated targets using the new R3FP fragment picker for fragment selection and implementing a new annotation of prediction reliability (van der Schot et al. in J Biomol NMR 57:27-35, 2013, doi: 10.1007/s10858-013-9762-6), both implemented in the CS-Rosetta3 WeNMR server. In this second round of CASD-NMR, the WeNMR CS-Rosetta server has demonstrated a much better performance than in the first round since only converged targets were submitted. Further, recalculation of all CASD-NMR targets using the new version of the server demonstrates that our new annotation of prediction quality is giving reliable results. Predictions annotated as weak are often found to provide useful models, but only for a fraction of the sequence, and should therefore only be used with caution.

  10. Continuous Flow 1H and 13C NMR Spectroscopy in Microfluidic Stripline NMR Chips

    NARCIS (Netherlands)

    Oosthoek-de Vries, Anna Jo; Bart, Jacob; Tiggelaar, Roald M.; Janssen, Johannes W.G.; van Bentum, Jan (P.J.M.); Gardeniers, Han J.G.E.; Kentgens, Arno P.M.

    2017-01-01

    Microfluidic stripline NMR technology not only allows for NMR experiments to be performed on small sample volumes in the submicroliter range, but also experiments can easily be performed in continuous flow because of the stripline's favorable geometry. In this study we demonstrate the possibility of

  11. Crystallographic and dynamic aspects of solid-state NMR calibration compounds: towards ab initio NMR crystallography

    DEFF Research Database (Denmark)

    Li, Xiaozhou; Tapmeyer, Lukas; Bolte, Michael

    2016-01-01

    The excellent results of dispersion-corrected density functional theory (DFT-D) calculations for static systems have been well established over the past decade. The introduction of dynamics into DFT-D calculations is a target, especially for the field of molecular NMR crystallography. Four 13C ss-NMR...

  12. Effect of retinoic acid on cell-cell adhesiveness in cloned BHK21/C13 cells which form piling-up colonies.

    Science.gov (United States)

    Kamei, H

    1983-10-01

    The effect was studied of retinoic acid (RA) on cell-cell adhesiveness in Ag8-1 cells, which are piling-up colony-forming cells cloned from a Syrian hamster kidney fibroblastic cell line BHK21/C13. From the piled-up part of the colonies grown with RA (10 microM), many cells were dissociated by mere shaking or pipetting. The dissociated cells soon adhered to and spread on plastic surfaces in the presence of RA. The number of cells per colony increased almost at the same rate in the presence or absence of RA. The effect of RA on the appearance of cells dissociable from colonies was noticeable above 0.1 microM, prominent from 1 to 10 microM, greater when added in the earlier stages of colony formation and negligible when added just before the dissociation assay. Single cells from the monolayer culture grown with RA (10 microM) had less tendency to aggregate than did those from the control culture. Cells from the colonies grown with RA adhered to and spread on a plastic dish for bacterial use, but control cells seldom adhered. These results indicate that RA decreases the cell-cell adhesiveness or suppresses the development of it but increases cell-substratum adhesiveness.

  13. An isotope approach based on C-13 pulse-chase labelling vs. the root trenching method to separate heterotrophic and autotrophic respiration in cultivated peatlands

    Energy Technology Data Exchange (ETDEWEB)

    Biasi, C.; Pitkamaki, A. S.; Tavi, N. M.; Koponen, H. T.; Martikainen, P. J. [Univ.of Eastern Finland, Kuopio (Finland). Dept. of Environmental Science], e-mail: christina.biasi@uef.fi

    2012-11-01

    We tested an isotope method based on C-13 pulse-chase labelling for determining the fractional contribution of soil microbial respiration to overall soil respiration in an organic soil (cutaway peatland, eastern Finland), cultivated with the bioenergy crop, reed canary grass. The plants were exposed to CO{sub 2}-13 for five hours and the label was thereafter determined in CO{sub 2} derived from the soil-root system. A two-pool isotope mixing model was used to separate sources of respiration. The isotopic approach showed that a minimum of 50% of the total CO{sub 2} originated from soil-microbial respiration. Even though the method uses undisturbed soil-plant systems, it has limitations concerning the experimental determination of the true isotopic signal of all components contributing to autotrophic respiration. A trenching experiment which was comparatively conducted resulted in a 71% fractional contribution of soil-microbial respiration. This value was likely overestimated. Further studies are needed to evaluate critically the output from these two partitioning approaches. (orig.)

  14. D-seco-Vitamin D analogs having reversed configurations at C-13 and C-14: Synthesis, docking studies and biological evaluation.

    Science.gov (United States)

    Szybinski, Marcin; Sokolowska, Katarzyna; Sicinski, Rafal R; Plum, Lori A; DeLuca, Hector F

    2017-10-01

    Prompted by results of molecular modeling performed on the seco-d-ring-vitamins D, we turned our attention to such analogs, having reversed configurations at C-13 and C-14, as the next goals of our studies on the structure-activity relationship for vitamin D compounds. First, we developed an efficient total synthesis of the "upper" C/seco-d-ring fragment with a 7-carbon side chain. Then, we coupled it with A-ring fragments using Sonogashira or Wittig-Horner protocol, providing the targeted D-seco analogs of 1α,25-dihydroxyvitamin D 3 and 1α,25-dihydroxy-19-norvitamin D 3 possessing a vinyl substituent at C-14 and a double bond between C-17 and C-20. The affinities of the synthesized vitamin D analogs to the full-length recombinant rat VDR were examined, as well as their differentiating and transcriptional activities. In these in vitro tests, they were significantly less active compared to 1α,25-(OH) 2 D 3 . Moreover, it was established that the analogs tested in vivo in rats showed no calcemic potency. Copyright © 2016 Elsevier Ltd. All rights reserved.

  15. Synthesis and in Vitro Antiproliferative Evaluation of C-13 Epimers of Triazolyl-d-Secoestrone Alcohols: The First Potent 13α-d-Secoestrone Derivative.

    Science.gov (United States)

    Szabó, Johanna; Jerkovics, Nóra; Schneider, Gyula; Wölfling, János; Bózsity, Noémi; Minorics, Renáta; Zupkó, István; Mernyák, Erzsébet

    2016-05-12

    The syntheses of C-13 epimeric 3-[(1-benzyl-1,2,3-triazol-4-yl)methoxy]-d-secoestrones are reported. Triazoles were prepared from 3-(prop-2-inyloxy)-d-secoalcohols and p-substituted benzyl azides via Cu(I)-catalyzed azide-alkyne cycloaddition (CuAAC). The antiproliferative activities of the products and their precursors were determined in vitro against a panel of human adherent cervical (HeLa, SiHa and C33A), breast (MCF-7, MDA-MB-231, MDA-MB-361 and T47D) and ovarian (A2780) cell lines by means of MTT assays. The orientation of the angular methyl group and the substitution pattern of the benzyl group of the azide greatly influenced the cell growth-inhibitory potential of the compounds. The 13β derivatives generally proved to be more potent than their 13α counterparts. Introduction of a benzyltriazolylmethyl group onto the 3-OH position seemed to be advantageous. One 13α compound containing an unsubstituted benzyltriazolyl function displayed outstanding antiproliferative activities against three cell lines.

  16. NMR methodologies in the analysis of blueberries.

    Science.gov (United States)

    Capitani, Donatella; Sobolev, Anatoly P; Delfini, Maurizio; Vista, Silvia; Antiochia, Riccarda; Proietti, Noemi; Bubici, Salvatore; Ferrante, Gianni; Carradori, Simone; De Salvador, Flavio Roberto; Mannina, Luisa

    2014-06-01

    An NMR analytical protocol based on complementary high and low field measurements is proposed for blueberry characterization. Untargeted NMR metabolite profiling of blueberries aqueous and organic extracts as well as targeted NMR analysis focused on anthocyanins and other phenols are reported. Bligh-Dyer and microwave-assisted extractions were carried out and compared showing a better recovery of lipidic fraction in the case of microwave procedure. Water-soluble metabolites belonging to different classes such as sugars, amino acids, organic acids, and phenolic compounds, as well as metabolites soluble in organic solvent such as triglycerides, sterols, and fatty acids, were identified. Five anthocyanins (malvidin-3-glucoside, malvidin-3-galactoside, delphinidin-3-glucoside, delphinidin-3-galactoside, and petunidin-3-glucoside) and 3-O-α-l-rhamnopyranosyl quercetin were identified in solid phase extract. The water status of fresh and withered blueberries was monitored by portable NMR and fast-field cycling NMR. (1) H depth profiles, T2 transverse relaxation times and dispersion profiles were found to be sensitive to the withering. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  17. Protein secondary structure of Green Lynx spider dragline silk investigated by solid-state NMR and X-ray diffraction.

    Science.gov (United States)

    Xu, Dian; Shi, Xiangyan; Thompson, Forrest; Weber, Warner S; Mou, Qiushi; Yarger, Jeffery L

    2015-11-01

    In this study, the secondary structure of the major ampullate silk from Peucetia viridans (Green Lynx) spiders is characterized by X-ray diffraction and solid-state NMR spectroscopy. From X-ray diffraction measurement, β-sheet nanocrystallites were observed and found to be highly oriented along the fiber axis, with an orientational order, fc≈0.98. The size of the nanocrystallites was determined to be on average 2.5nm×3.3nm×3.8nm. Besides a prominent nanocrystalline region, a partially oriented amorphous region was also observed with an fa≈0.89. Two-dimensional (13)C-(13)C through-space and through-bond solid-state NMR experiments were employed to elucidate structure details of P. viridans silk proteins. It reveals that β-sheet nanocrystallites constitutes 40.0±1.2% of the protein and are dominated by alanine-rich repetitive motifs. Furthermore, based upon the NMR data, 18±1% of alanine, 60±2% glycine and 54±2% serine are incorporated into helical conformations. Copyright © 2015 Elsevier B.V. All rights reserved.

  18. Flow NMR of polymers in external fields

    Energy Technology Data Exchange (ETDEWEB)

    Boehme, Ute; Bagusat, Frank; Scheler, Ulrich [Leibniz Institute of Polymer Research Dresden (Germany)

    2008-07-01

    Pulsed-field gradient NMR is applied to study the motion of polymers in an external electric field and under mechanical shear. The application of an electric field drives motion of charged species. In conjunction with the diffusion coefficient from the electrophoretic mobility the effective charge per molecule is derived. The electric field applicable in the aqueous system is too weak to deform the polymer or even abstract counterions. In a shear flow established in a Couette cell partial orientation of polymer chains is measured via residual dipolar couplings. The entire flow field in a non-symmetric flow cell is monitored by a combination of PFG NMR and NMR imaging exhibiting regions of high shear and locally low shear, where polymers relax.

  19. Characterization by NMR of ozonized methyl linoleate

    Energy Technology Data Exchange (ETDEWEB)

    Diaz, Maritza F. [National Center for Scientific Research, Havana (Cuba). Ozone Research Center. Dept. of Ozonized Substances]. E-mail: maritza.diaz@cnic.edu.cu; Gavin, Jose A. [University of the Laguna, Tenerife (Spain)

    2007-07-01

    In the present study ozonized methyl linoleate with peroxide index of 1,800 mmol-equiv kg{sup -1} was chemically characterized. Ozonation of methyl linoleate produced hydroperoxides, ozonides and aldehydes which were identified by {sup 1}H and {sup 13}C NMR two-dimensional. The standard methyl linoleate and ozonized methyl linoleate shown very similar {sup 1}H NMR spectra except for the signals at {delta} 9.7 and {delta} 9.6 that correspond to aldehydic hydrogen, {delta} 5.7 and {delta} 5.5 (olefinic signals from hydroperoxides) and {delta} 5.2 ppm (multiplet from ozonides methynic hydrogen). Other resonance assignments are based on the connectivities provided by the hydrogen scalar coupling constants. These results indicate that NMR spectroscopy can provide valuable information about the amount of formed oxygenated compounds in the ozonized methyl linoleate in order to use it to follow up ozone therapy and chemistry of ozonized vegetable oil. (author)

  20. NMR metabolomics of renal cancer: an overview.

    Science.gov (United States)

    Gil, Ana M; de Pinho, Paula Guedes; Monteiro, Márcia S; Duarte, Iola F

    2015-09-23

    This paper reviews the use of NMR metabolomics for the metabolic characterization of renal cancer. The existing challenges in the clinical management of this disease are first presented, followed by a brief introduction to the metabolomics approach, in the context of cancer research. A subsequent review of the literature on NMR metabolic studies of renal cancer reveals that the subject has been clearly underdeveloped, compared with other types of cancer, particularly regarding cultured cells and tissue analysis. NMR analysis of biofluids has focused on blood (plasma or serum) metabolomics, comprising no account of studies on human urine, in spite of its noninvasiveness and physiological proximity to the affected organs. Finally, some areas of potential future development are identified.

  1. The eNMR platform for structural biology

    OpenAIRE

    Bonvin, Alexandre M. J. J.; Rosato, Antonio; Wassenaar, Tsjerk A.

    2010-01-01

    The e-NMR project is a European cooperation initiative that aims at providing the bio-NMR user community with a software platform integrating and streamlining the computational approaches necessary for the analysis of bio-NMR data. The e-NMR platform is based on a Grid computational infrastructure. A main focus of the current implementation of the e-NMR platform is on streamlining structure determination protocols. Indeed, to facilitate the use of NMR spectroscopy in the life sciences, the eN...

  2. Concentrations of higher dicarboxylic acids C5–C13 in fresh snow samples collected at the High Alpine Research Station Jungfraujoch during CLACE 5 and 6

    Directory of Open Access Journals (Sweden)

    K. Sieg

    2009-03-01

    Full Text Available Samples of freshly fallen snow were collected at the high alpine research station Jungfraujoch (Switzerland in February and March 2006 and 2007, during the Cloud and Aerosol Characterization Experiments (CLACE 5 and 6. In this study a new technique has been developed and demonstrated for the measurement of organic acids in fresh snow. The melted snow samples were subjected to solid phase extraction and resulting solutions analysed for organic acids by HPLC-MS-TOF using negative electrospray ionization. A series of linear dicarboxylic acids from C5 to C13 and phthalic acid, were identified and quantified. In several samples the biogenic acid pinonic acid was also observed. In fresh snow the median concentration of the most abundant acid, adipic acid, was 0.69 μg L−1 in 2006 and 0.70 μg L−1 in 2007. Glutaric acid was the second most abundant dicarboxylic acid found with median values of 0.46 μg L−1 in 2006 and 0.61 μg L−1 in 2007, while the aromatic acid phthalic acid showed a median concentration of 0.34 μg L−1 in 2006 and 0.45 μg L−1 in 2007. The concentrations in the samples from various snowfall events varied significantly, and were found to be dependent on the back trajectory of the air mass arriving at Jungfraujoch. Air masses of marine origin showed the lowest concentrations of acids whereas the highest concentrations were measured when the air mass was strongly influenced by boundary layer air.

  3. Updating the Geomagnetic Polarity Time Scale with Marine Magnetic Anomalies (Chrons C13-C33, 33-83 Ma): A Progress Report

    Science.gov (United States)

    Quigley, K. W.; Malinverno, A.

    2016-12-01

    Marine magnetic anomalies are found in ocean basins worldwide, and are the result of the magnetization of basaltic rocks formed at seafloor spreading centers. Because the earth's geomagnetic field has reversed throughout history, these detected anomalies record the history of reversals on the flanks of mid-ocean ridges. Magnetic anomalies define the geometry of magnetized polarity blocks in the crust, and the width of these blocks combined with absolute ages and some assumptions on the variation of spreading rates can give us a Geomagnetic Polarity Time Scale (GPTS). Time scales are important in many fields of the earth sciences to determine past rates of change, correlate geological events, and constrain the history of seafloor spreading and plate motion. Our goal is to determine an improved GPTS for the Eocene-Late Cretaceous (Chrons C13-C33). The current GPTS is based on an assumption of smoothly varying spreading rates in the South Atlantic. To better constrain the duration of polarity chrons, we will minimize spreading rate fluctuations in several regions worldwide besides the South Atlantic. Our work thus far has focused on methods of analysis for the marine magnetic anomaly data. The Pacific-Antarctic ridge was chosen as a starting point for the project because of new data and clear anomalies in mid to high latitudes. In our analysis, we select magnetic anomaly data from cruises, project data onto a plate motion flow line, identify anomalies, and compare modeled and measured anomalies. We apply a Monte Carlo sampling method that allows us to estimate start and end distances along a flow line for polarity chrons in each ship track, and quantify the uncertainty of those distances. Using the estimated block model distances, we can determine how spreading rates change between chrons along each ship track for any given GPTS. With the method we developed, our goal is to use block model distances from several spreading centers to determine a GPTS that minimizes the

  4. New Designs for NMR Core Scanning

    Science.gov (United States)

    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

  5. Direct Comparison of 19F qNMR and 1H qNMR by Characterizing Atorvastatin Calcium Content

    OpenAIRE

    Yang Liu; Zhaoxia Liu; Huaxin Yang; Lan He

    2016-01-01

    Quantitative nuclear magnetic resonance (qNMR) is a powerful tool in measuring drug content because of its high speed, sensitivity, and precision. Most of the reports were based on proton qNMR (1H qNMR) and only a few fluorine qNMR (19F qNMR) were reported. No research has been conducted to directly compare the advantage and disadvantage between these two methods. In the present study, both 19F and 1H qNMR were performed to characterize the content of atorvastatin calcium with the same intern...

  6. EXPERIMENTAL AND THEORETICAL NMR STUDY OF 4-(1 ...

    African Journals Online (AJOL)

    Preferred Customer

    experimental and theoretical data have showed that the molecular geometry and the ... 1D and 2D hetero- and homonuclear NMR methods enable to ... The essence of this study is briefly to report experimental and theoretical NMR features of.

  7. nmrML: a community supported open data standard for the description, storage, and exchange of NMR data.

    Science.gov (United States)

    Schober, Daniel; Jacob, Daniel; Wilson, Michael; Cruz, Joseph A; Marcu, Ana; Grant, Jason R; Moing, Annick; Deborde, Catherine; de Figueiredo, Luis F; Haug, Kenneth; Rocca-Serra, Philippe; Easton, John M; Ebbels, Timothy M D; Hao, Jie; Ludwig, Christian; Günther, Ulrich L; Rosato, Antonio; Klein, Matthias S; Lewis, Ian; Luchinat, Claudio; Jones, Andrew R; Grauslys, Arturas; Larralde, Martin; Yokochi, Masashi; Kobayashi, Naohiro; Porzel, Andrea; Griffin, Julian; Viant, Mark R; Wishart, David S; Steinbeck, Christoph; Salek, Reza M; Neumann, Steffen

    2017-10-16

    NMR is a widely used analytical technique with a growing number of repositories available. As a result, demands for a vendor-agnostic, open data format for long-term archiving of NMR data have emerged with the aim to ease and encourage sharing, comparison and reuse of NMR data. Here we present nmrML, an open XML-based exchange and storage format for NMR spectral data. The nmrML format is intended to be fully compatible with existing NMR data for chemical, biochemical and metabolomics experiments. nmrML can capture raw NMR data, spectral data acquisition parameters and, where available, spectral metadata such as chemical structures associated with spectral assignments. The nmrML format is compatible with pure-compound NMR data for reference spectral libraries as well as NMR data from complex bio-mixtures i.e. metabolomics experiments. To facilitate format conversions, we provide nmrML converters for Bruker and Agilent/Varian vendor formats. In addition, easy-to-use web-based spectral viewing, processing and spectral assignment tools that read and write nmrML have been developed. Software libraries and web services for data validation are available for tool developers and end-users. The nmrML format has already been adopted for capturing and disseminating NMR data for small molecules by several open source data processing tools and metabolomics reference spectral libraries, e.g. serving as storage format for the MetaboLights data repository. The nmrML open access data standard has been endorsed by the Metabolomics Standards Initiative (MSI) and we here encourage user participation and feedback to increase usability and make it a successful standard.

  8. Hyperpolarized NMR Probes for Biological Assays

    Directory of Open Access Journals (Sweden)

    Sebastian Meier

    2014-01-01

    Full Text Available During the last decade, the development of nuclear spin polarization enhanced (hyperpolarized molecular probes has opened up new opportunities for studying the inner workings of living cells in real time. The hyperpolarized probes are produced ex situ, introduced into biological systems and detected with high sensitivity and contrast against background signals using high resolution NMR spectroscopy. A variety of natural, derivatized and designed hyperpolarized probes has emerged for diverse biological studies including assays of intracellular reaction progression, pathway kinetics, probe uptake and export, pH, redox state, reactive oxygen species, ion concentrations, drug efficacy or oncogenic signaling. These probes are readily used directly under natural conditions in biofluids and are often directly developed and optimized for cellular assays, thus leaving little doubt about their specificity and utility under biologically relevant conditions. Hyperpolarized molecular probes for biological NMR spectroscopy enable the unbiased detection of complex processes by virtue of the high spectral resolution, structural specificity and quantifiability of NMR signals. Here, we provide a survey of strategies used for the selection, design and use of hyperpolarized NMR probes in biological assays, and describe current limitations and developments.

  9. Synthesis and NMR Elucidation of Novel Pentacycloundecane ...

    African Journals Online (AJOL)

    NICO

    2012-01-24

    Jan 24, 2012 ... Herein we report the synthesis and NMR elucidation of five novel pentacycloundecane (PCU)-derived short peptides as potential. HIV protease inhibitors. 1H and 13C spectral analysis show major overlapping of methine resonance of the PCU 'cage' thereby making it extremely difficult to assign the NMR ...

  10. Developments in Solid-State NMR

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 20; Issue 11. Developments in Solid-State NMR. K V Ramanathan. General Article Volume 20 Issue 11 November 2015 pp 1040-1052. Fulltext. Click here to view fulltext PDF. Permanent link: http://www.ias.ac.in/article/fulltext/reso/020/11/1040-1052 ...

  11. Bench-top NMR-food

    NARCIS (Netherlands)

    Voda, M.A.; Duynhoven, Van J.

    2016-01-01

    In food research and development, relaxometric and diffusometric benchtop NMR methods have been used to obtain quantitative phase compositional and food microstructural parameters in a routine manner. The most commonly used applications are assessment of solid fat content, and water and oil

  12. NMR Analysis of Some Pentacycloundecanedione Derivatives

    African Journals Online (AJOL)

    NJD

    In the proton NMR spectrum the methylene protons are registered as an AB spin system at 2.03 and 1.89 ppm. A relatively complex pattern between 2.68 and 3.15 ppm, which integrates to eight protons represents the eight methine protons. The signals of the geminal PCU bridge methylene protons. (H-4) are registered as ...

  13. Quantification of complex mixtures by NMR

    NARCIS (Netherlands)

    Duynhoven, van J.P.M.; Velzen, van E.; Jacobs, D.M.

    2013-01-01

    NMR has firmly established itself as an analytical tool that can quantify analyte concentrations in complex mixtures in a rapid, cost-effective, accurate and precise manner. Here, the technological advances with respect to instrumentation, sample preparation, data acquisition and data processing

  14. Structures of Biomolecules by NMR Spectroscopy

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 20; Issue 11. Structures of Biomolecules by NMR Spectroscopy. Hanudatta S Atreya. General Article Volume 20 Issue 11 November 2015 pp 1033-1039. Fulltext. Click here to view fulltext PDF. Permanent link:

  15. Solid-state NMR for bacterial biofilms

    Science.gov (United States)

    Reichhardt, Courtney; Cegelski, Lynette

    2014-04-01

    Bacteria associate with surfaces and one another by elaborating an extracellular matrix to encapsulate cells, creating communities termed biofilms. Biofilms are beneficial in some ecological niches, but also contribute to the pathogenesis of serious and chronic infectious diseases. New approaches and quantitative measurements are needed to define the composition and architecture of bacterial biofilms to help drive the development of strategies to interfere with biofilm assembly. Solid-state nuclear magnetic resonance (NMR) is uniquely suited to the examination of insoluble and complex macromolecular and whole-cell systems. This article highlights three examples that implement solid-state NMR to deliver insights into bacterial biofilm composition and changes in cell-wall composition as cells transition to the biofilm lifestyle. Most recently, solid-state NMR measurements provided a total accounting of the protein and polysaccharide components in the extracellular matrix of an Escherichia coli biofilm and transformed our qualitative descriptions of matrix composition into chemical parameters that permit quantitative comparisons among samples. We present additional data for whole biofilm samples (cells plus the extracellular matrix) that complement matrix-only analyses. The study of bacterial biofilms by solid-state NMR is an exciting avenue ripe with many opportunities and we close the article by articulating some outstanding questions and future directions in this area.

  16. NMR and mushrooms : imaging post harvest senescence

    NARCIS (Netherlands)

    Donker, H.C.W.

    1999-01-01

    The objective of the study described in this thesis was to explore the potentials of NMR for the study of water relations in harvested mushrooms ( Agaricus bisporus ). Since harvested mushrooms tend to continue their growth after harvest, their morphogenesis is heavily

  17. NMR characterization of polymers: Review and update

    Science.gov (United States)

    NMR spectroscopy is a major technique for the characterization and analysis of polymers. A large number of methodologies have been developed in both the liquid and the solid state, and the literature has grown considerably (1-5). The field now covers a broad spectrum of activities, including polym...

  18. Theoretical molecular structure, vibrational frequencies and NMR ...

    African Journals Online (AJOL)

    Theoretical results have been successfully compared with available experimental data in the literature. Regarding the calculations, 2mpe-4bb prefers enol-imine form and DFT method is superior to HF approach except for predicting bond lengths. KEY WORDS: Schiff bases, Normal mode frequencies, HF, DFT, NMR. Bull.

  19. NMR Analysis of Some Pentacycloundecanedione Derivatives

    African Journals Online (AJOL)

    NJD

    The complete NMR elucidation of four pentacycloundecanedione (PCUdione) derivatives is described. Major proton shifts occur when additions are performed on the carbonyl carbons. Some of the carbon signals are also transposed. Despite the fact that the signals of the methine protons on the cage skeleton experience ...

  20. AB INITIO STUDY, INVESTIGATION OF NMR SHIELDING ...

    African Journals Online (AJOL)

    Preferred Customer

    Ab initio study, investigation of NMR shielding tensors, NBO and vibrational frequency. Bull. Chem. Soc. Ethiop. 2010, 24(2). 231. Gas phase results. In order to study mechanism of the reactions, structure corresponding to reactants, transition states and products were optimized in level of theory. Figure 1 shows the ...

  1. Al NMR: a novel NMR data processing program optimized for sparse sampling

    Energy Technology Data Exchange (ETDEWEB)

    Gledhill, John M.; Wand, A. Joshua, E-mail: wand@mail.med.upenn.edu [University of Pennsylvania, Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine (United States)

    2012-01-15

    Sparse sampling in biomolecular multidimensional NMR offers increased acquisition speed and resolution and, if appropriate conditions are met, an increase in sensitivity. Sparse sampling of indirectly detected time domains combined with the direct truly multidimensional Fourier transform has elicited particular attention because of the ability to generate a final spectrum amenable to traditional analysis techniques. A number of sparse sampling schemes have been described including radial sampling, random sampling, concentric sampling and variations thereof. A fundamental feature of these sampling schemes is that the resulting time domain data array is not amenable to traditional Fourier transform based processing and phasing correction techniques. In addition, radial sampling approaches offer a number of advantages and capabilities that are also not accessible using standard NMR processing techniques. These include sensitivity enhancement, sub-matrix processing and determination of minimal sets of sampling angles. Here we describe a new software package (Al NMR) that enables these capabilities in the context of a general NMR data processing environment.

  2. CASD-NMR: critical assessment of automated structure determination by NMR

    NARCIS (Netherlands)

    Rosato, A.; van der Schot, G.; Bonvin, A.M.J.J.|info:eu-repo/dai/nl/113691238

    2009-01-01

    NMR spectroscopy is currently the only technique for determining the solution structure of biological macromolecules. This typically requires both the assignment of resonances and a labor-intensive analysis of multidimensional nuclear Overhauser effect spectroscopy (NOESY) spectra, in which peaks

  3. Petrophysical properties of greensand as predicted from NMR measurements

    DEFF Research Database (Denmark)

    Hossain, Zakir; Grattoni, Carlos A.; Solymar, Mikael

    2011-01-01

    ABSTRACT: Nuclear magnetic resonance (NMR) is a useful tool in reservoir evaluation. The objective of this study is to predict petrophysical properties from NMR T2 distributions. A series of laboratory experiments including core analysis, capillary pressure measurements, NMR T2 measurements...

  4. Recent excitements in protein NMR: Large proteins and biologically ...

    Indian Academy of Sciences (India)

    2016-10-14

    Oct 14, 2016 ... Paramagnetic NMR. Paramagnetism arises from unpaired electrons. As the mag- netic moment of electrons is ~1000 times more than protons, the presence of an unpaired electron near the nucleus causes pronounced paramagnetic effects; leading to dramatic out- come of NMR spectra. As, NMR restraints ...

  5. OPENCORE NMR: open-source core modules for implementing an integrated FPGA-based NMR spectrometer.

    Science.gov (United States)

    Takeda, Kazuyuki

    2008-06-01

    A tool kit for implementing an integrated FPGA-based NMR spectrometer [K. Takeda, A highly integrated FPGA-based nuclear magnetic resonance spectrometer, Rev. Sci. Instrum. 78 (2007) 033103], referred to as the OPENCORE NMR spectrometer, is open to public. The system is composed of an FPGA chip and several peripheral boards for USB communication, direct-digital synthesis (DDS), RF transmission, signal acquisition, etc. Inside the FPGA chip have been implemented a number of digital modules including three pulse programmers, the digital part of DDS, a digital quadrature demodulator, dual digital low-pass filters, and a PC interface. These FPGA core modules are written in VHDL, and their source codes are available on our website. This work aims at providing sufficient information with which one can, given some facility in circuit board manufacturing, reproduce the OPENCORE NMR spectrometer presented here. Also, the users are encouraged to modify the design of spectrometer according to their own specific needs. A home-built NMR spectrometer can serve complementary roles to a sophisticated commercial spectrometer, should one comes across such new ideas that require heavy modification to hardware inside the spectrometer. This work can lower the barrier of building a handmade NMR spectrometer in the laboratory, and promote novel and exciting NMR experiments.

  6. In vivo carbon-edited detection with proton echo-planar spectroscopic imaging (ICED PEPSI) : [3,4-(CH2)-C-13] glutamate/glutamine tomography in rat brain

    NARCIS (Netherlands)

    Hyder, F; Renken, R; Rothman, DL

    1999-01-01

    A method for in vivo carbon-edited detection with proton echo-planar spectroscopic imaging (ICED PEPSI) is described. This method is composed of an echo-planar based acquisition implemented with C-13-H-1 J editing spectroscopy and is intended for high temporal and spatial resolution in vivo

  7. C13orf18 and C1orf166 (MULAN) DNA genes methylation are not associated with cervical cancer and precancerous lesions of human papillomavirus genotypes in Iranian women

    National Research Council Canada - National Science Library

    Sohrabi, Amir; Mirab-Samiee, Siamak; Rahnamaye-Farzami, Marjan; Rafizadeh, Mitra; Akhavan, Setareh; Hashemi-Bahremani, Mohammad; Modarresl, Mohammad Hossein

    2014-01-01

    .... C13orf18 and C1orf166 (MUL1 or Mulan) DNA methylation as potential biomarkers and risk factors was investigated in 112 liquid based cytology and Formalin-Fixed Paraffin- Embedded tissue specimens in Iranian females with cervical...

  8. NMR CHARACTERIZATIONS OF PROPERTIES OF HETEROGENEOUS MEDIA

    Energy Technology Data Exchange (ETDEWEB)

    C.T. Philip Chang; Changho Choi; Jeromy T. Hollenshead; Rudi Michalak; Jack Phan; Ramon Saavedra; John C. Slattery; Jinsoo Uh; Randi Valestrand; A. Ted Watson; Song Xue

    2005-01-01

    A critical and long-standing need within the petroleum industry is the specification of suitable petrophysical properties for mathematical simulation of fluid flow in petroleum reservoirs (i.e., reservoir characterization). The development of accurate reservoir characterizations is extremely challenging. Property variations may be described on many scales, and the information available from measurements reflect different scales. In fact, experiments on laboratory core samples, well-log data, well-test data, and reservoir-production data all represent information potentially valuable to reservoir characterization, yet they all reflect information about spatial variations of properties at different scales. Nuclear magnetic resonance (NMR) spectroscopy and imaging (MRI) provide enormous potential for developing new descriptions and understandings of heterogeneous media. NMR has the rare capability to probe permeable media non-invasively, with spatial resolution, and it provides unique information about molecular motions and interactions that are sensitive to morphology. NMR well-logging provides the best opportunity ever to resolve permeability distributions within petroleum reservoirs. We develop MRI methods to determine, for the first time, spatially resolved distributions of porosity and permeability within permeable media samples that approach the intrinsic scale: the finest resolution of these macroscopic properties possible. To our knowledge, this is the first time that the permeability is actually resolved at a scale smaller than the sample. In order to do this, we have developed a robust method to determine of relaxation distributions from NMR experiments and a novel implementation and analysis of MRI experiments to determine the amount of fluid corresponding to imaging regions, which are in turn used to determine porosity and saturation distributions. We have developed a novel MRI experiment to determine velocity distributions within flowing experiments, and

  9. Solid state NMR of biopolymers and synthetic polymers

    Energy Technology Data Exchange (ETDEWEB)

    Jelinski, Lynn W. [Cornell Univ., Geneva, NY (United States)

    1995-12-31

    Solid state NMR has been invaluable in evaluating the structure, phase separation, and dynamics of polymers. Because polymers are generally used in the solid state, solid state NMR is especially powerful because it provides information about the materials in their native state. This review gives a general overview of solid state NMR, concentrating on solid state {sup 13} C and {sup 2} H NMR. It then focuses on two examples: the biopolymer spider silka and the engineering material polyurethane. It illustrates how solid state NMR can provide new information about synthetic and bio-polymers. (author) 11 refs., 5 figs., 3 tabs.

  10. NMR shielding calculations across the periodic table: diamagnetic uranium compounds. 2. Ligand and metal NMR.

    Science.gov (United States)

    Schreckenbach, Georg

    2002-12-16

    In this and a previous article (J. Phys. Chem. A 2000, 104, 8244), the range of application for relativistic density functional theory (DFT) is extended to the calculation of nuclear magnetic resonance (NMR) shieldings and chemical shifts in diamagnetic actinide compounds. Two relativistic DFT methods are used, ZORA ("zeroth-order regular approximation") and the quasirelativistic (QR) method. In the given second paper, NMR shieldings and chemical shifts are calculated and discussed for a wide range of compounds. The molecules studied comprise uranyl complexes, [UO(2)L(n)](+/-)(q); UF(6); inorganic UF(6) derivatives, UF(6-n)Cl(n), n = 0-6; and organometallic UF(6) derivatives, UF(6-n)(OCH(3))(n), n = 0-5. Uranyl complexes include [UO(2)F(4)](2-), [UO(2)Cl(4)](2-), [UO(2)(OH)(4)](2-), [UO(2)(CO(3))(3)](4-), and [UO(2)(H(2)O)(5)](2+). For the ligand NMR, moderate (e.g., (19)F NMR chemical shifts in UF(6-n)Cl(n)) to excellent agreement [e.g., (19)F chemical shift tensor in UF(6) or (1)H NMR in UF(6-n)(OCH(3))(n)] has been found between theory and experiment. The methods have been used to calculate the experimentally unknown (235)U NMR chemical shifts. A large chemical shift range of at least 21,000 ppm has been predicted for the (235)U nucleus. ZORA spin-orbit appears to be the most accurate method for predicting actinide metal chemical shifts. Trends in the (235)U NMR chemical shifts of UF(6-n)L(n) molecules are analyzed and explained in terms of the calculated electronic structure. It is argued that the energy separation and interaction between occupied and virtual orbitals with f-character are the determining factors.

  11. Solid-state NMR basic principles and practice

    CERN Document Server

    Apperley, David C; Hodgkinson, Paul

    2014-01-01

    Nuclear Magnetic Resonance (NMR) has proved to be a uniquely powerful and versatile tool for analyzing and characterizing chemicals and materials of all kinds. This book focuses on the latest developments and applications for "solid-state" NMR, which has found new uses from archaeology to crystallography to biomaterials and pharmaceutical science research. The book will provide materials engineers, analytical chemists, and physicists, in and out of lab, a survey of the techniques and the essential tools of solid-state NMR, together with a practical guide on applications. In this concise introduction to the growing field of solid-state nuclear magnetic resonance spectroscopy The reader will find: * Basic NMR concepts for solids, including guidance on the spin-1/2 nuclei concept * Coverage of the quantum mechanics aspects of solid state NMR and an introduction to the concept of quadrupolar nuclei * An understanding relaxation, exchange and quantitation in NMR * An analysis and interpretation of NMR data, with e...

  12. NMR-based diffusion lattice imaging.

    Science.gov (United States)

    Laun, Frederik Bernd; Müller, Lars; Kuder, Tristan Anselm

    2016-03-01

    Nuclear magnetic resonance (NMR) diffusion experiments are widely employed as they yield information about structures hindering the diffusion process, e.g., about cell membranes. While it has been shown in recent articles that these experiments can be used to determine the shape of closed pores averaged over a volume of interest, it is still an open question how much information can be gained in open well-connected systems. In this theoretical work, it is shown that the full structure information of connected periodic systems is accessible. To this end, the so-called "SEquential Rephasing by Pulsed field-gradient Encoding N Time intervals" (SERPENT) sequence is used, which employs several diffusion encoding gradient pulses with different amplitudes. Two two-dimensional solid matrices that are surrounded by an NMR-visible medium are considered: a hexagonal lattice of cylinders and a rectangular lattice of isosceles triangles.

  13. NMR-based diffusion lattice imaging

    Science.gov (United States)

    Laun, Frederik Bernd; Müller, Lars; Kuder, Tristan Anselm

    2016-03-01

    Nuclear magnetic resonance (NMR) diffusion experiments are widely employed as they yield information about structures hindering the diffusion process, e.g., about cell membranes. While it has been shown in recent articles that these experiments can be used to determine the shape of closed pores averaged over a volume of interest, it is still an open question how much information can be gained in open well-connected systems. In this theoretical work, it is shown that the full structure information of connected periodic systems is accessible. To this end, the so-called "SEquential Rephasing by Pulsed field-gradient Encoding N Time intervals" (SERPENT) sequence is used, which employs several diffusion encoding gradient pulses with different amplitudes. Two two-dimensional solid matrices that are surrounded by an NMR-visible medium are considered: a hexagonal lattice of cylinders and a rectangular lattice of isosceles triangles.

  14. Strange kinetics, porous media, and NMR

    Energy Technology Data Exchange (ETDEWEB)

    Kimmich, Rainer

    2002-11-01

    Nuclear magnetic resonance (NMR) techniques cover a broad range of length and time scales on which dynamic properties of fluids confined in porous media can be investigated. This report refers to field-cycling NMR relaxometry, field gradient NMR diffusometry and NMR microscopy. The objective was to examine diffusion, hydrodynamic dispersion, flow, and thermal convection under the influence of geometrical confinements and surface interactions in porous media. The anomalous character of these phenomena will be demonstrated and discussed in comparison with computer simulations and theoretical concepts. The first part of this presentation is devoted to nanoporous samples. It is shown that molecular Levy walks along inner surfaces occur under certain conditions. Mutual 'obstruction' of molecules in molecular sieves and zeolites is another source of diffusion anomaly known as single-file diffusion which can be described by Gaussian propagators with a diffusion coefficient depending on time in a certain limit. In the case of polymers confined in narrow artificial tubes of a porous solid matrix, the characteristics of reptation were experimentally verified. The second part mainly refers to 'trapping' effects as a source of anomalous transport characterised by non-Gaussian propagators. Model objects fabricated on the basis of percolation cluster models were examined with respect to flow, diffusion, thermal convection and hydrodynamic dispersion. The elucidation of transport laws in model systems of well defined and mathematically describable geometries is considered to be a promising way for the exploration of the structure/dynamics relationship in porous media as a long-term objective.

  15. Structure of high-resolution NMR spectra

    CERN Document Server

    Corio, PL

    2012-01-01

    Structure of High-Resolution NMR Spectra provides the principles, theories, and mathematical and physical concepts of high-resolution nuclear magnetic resonance spectra.The book presents the elementary theory of magnetic resonance; the quantum mechanical theory of angular momentum; the general theory of steady state spectra; and multiple quantum transitions, double resonance and spin echo experiments.Physicists, chemists, and researchers will find the book a valuable reference text.

  16. NMR characteristics of rat mammary tumors

    Energy Technology Data Exchange (ETDEWEB)

    Osbakken, M.; Kreider, J.; Taczanowsky, P.

    1984-01-01

    12 rats were injected intradermally with 13762A rat mammary adenocarcinoma (1 x 10/sup 6/ cells). 3 rats died before completion of the study and 2 rat had tumor regression; the first 3 were excluded from data analysis. NMR imaging with a 1.5K gauss resistive magnet at 2, 3, 4, and 5 weeks after injection demonstrated increasing tumor mass. Saturation recovery (SR), inversion recovery (IR), and spin echo (SE) pulse sequence images and T/sub 1/ calculation were done for tumor characterization. (Tumor size was too small to identify at 2 weeks.) 3 rats were sacrificed after the last 3 imaging periods for histological studies, done to distinguish solid tumor mass from necrosis. Planimetry of tumor areas showed that as tumors grew in size, the ratio of necrotic area to area of solid tumor increased (week 3 = .3 +- .11; week 4 = .45 +- .07; week 5 = .51 +- 05); simultaneous calculated T/sub 1/ values also increased (week 3 = .35 +- .15; week 4 = .45 +- .06; week 5 = .42 +- 03). Qualitative NMR image T/sub 1/ values also increased as evidenced by progression of SR and IR tumor image intensity from very bright compared to the rest of the body at week 3 to less intense than other structures at week 5. These findings indicate that change in T/sub 1/ may be secondary to the pathophysiological change in the tumor (the increasing in necrosis, associated with increased free water). Thus, the range of T/sub 1/ values obtained in tumors in this study (and in previous studies) may be due to change in tumor physiology and anatomy. Careful correlation of histological with NMR data may allow ultimate use of NMR relaxation characteristics for determination of the physiological state of tumors.

  17. Quantitative calibration of radiofrequency NMR Stark effects.

    Science.gov (United States)

    Tarasek, Matthew R; Kempf, James G

    2011-10-01

    Nuclear magnetic resonance (NMR) Stark responses can occur in quadrupolar nuclei for an electric field oscillating at twice the usual NMR frequency (2ω(0)). Calibration of responses to an applied E field is needed to establish nuclear spins as probes of native E fields within material and molecular systems. We present an improved approach and apparatus for accurate measurement of quadrupolar Stark effects. Updated values of C(14) (the response parameter in cubic crystals) were obtained for both (69)Ga and (75)As in GaAs. Keys to improvement include a modified implementation of voltage dividers to assess the 2ω(0) amplitude, |E|, and the stabilization of divider response by reduction of stray couplings in 2ω(0) circuitry. Finally, accuracy was enhanced by filtering sets of |E| through a linear response function that we established for the radiofrequency amplifier. Our approach is verified by two types of spectral results. Steady-state 2ω(0) excitation to presaturate NMR spectra yielded C(14) = (2.59 ± 0.06) × 10(12) m(-1) for (69)Ga at room-temperature and 14.1 T. For (75)As, we obtained (3.1 ± 0.1) × 10(12) m(-1). Both values reconcile with earlier results from 77 K and below 1 T, whereas current experiments are at room temperature and 14.1 T. Finally, we present results where few-microsecond pulses of the 2ω(0) field induced small (tens of Hz) changes in high-resolution NMR line shapes. There too, spectra collected vs |E| agree with the model for response, further establishing the validity of our protocols to specify |E|.

  18. 3D Reconstruction of NMR Images

    Directory of Open Access Journals (Sweden)

    Peter Izak

    2007-01-01

    Full Text Available This paper introduces experiment of 3D reconstruction NMR images scanned from magnetic resonance device. There are described methods which can be used for 3D reconstruction magnetic resonance images in biomedical application. The main idea is based on marching cubes algorithm. For this task was chosen sophistication method by program Vision Assistant, which is a part of program LabVIEW.

  19. NMR studies of dynamic biomolecular conformational ensembles.

    Science.gov (United States)

    Torchia, Dennis A

    2015-02-01

    Multidimensional heteronuclear NMR approaches can provide nearly complete sequential signal assignments of isotopically enriched biomolecules. The availability of assignments together with measurements of spin relaxation rates, residual spin interactions, J-couplings and chemical shifts provides information at atomic resolution about internal dynamics on timescales ranging from ps to ms, both in solution and in the solid state. However, due to the complexity of biomolecules, it is not possible to extract a unique atomic-resolution description of biomolecular motions even from extensive NMR data when many conformations are sampled on multiple timescales. For this reason, powerful computational approaches are increasingly applied to large NMR data sets to elucidate conformational ensembles sampled by biomolecules. In the past decade, considerable attention has been directed at an important class of biomolecules that function by binding to a wide variety of target molecules. Questions of current interest are: "Does the free biomolecule sample a conformational ensemble that encompasses the conformations found when it binds to various targets; and if so, on what time scale is the ensemble sampled?" This article reviews recent efforts to answer these questions, with a focus on comparing ensembles obtained for the same biomolecules by different investigators. A detailed comparison of results obtained is provided for three biomolecules: ubiquitin, calmodulin and the HIV-1 trans-activation response RNA. Published by Elsevier B.V.

  20. Principles of high resolution NMR in solids

    CERN Document Server

    Mehring, Michael

    1983-01-01

    The field of Nuclear Magnetic Resonance (NMR) has developed at a fascinating pace during the last decade. It always has been an extremely valuable tool to the organic chemist by supplying molecular "finger print" spectra at the atomic level. Unfortunately the high resolution achievable in liquid solutions could not be obtained in solids and physicists and physical chemists had to live with unresolved lines open to a wealth of curve fitting procedures and a vast amount of speculations. High resolution NMR in solids seemed to be a paradoxon. Broad structure­ less lines are usually encountered when dealing with NMR in solids. Only with the recent advent of mUltiple pulse, magic angle, cross-polarization, two-dimen­ sional and multiple-quantum spectroscopy and other techniques during the last decade it became possible to resolve finer details of nuclear spin interactions in solids. I have felt that graduate students, researchers and others beginning to get involved with these techniques needed a book which trea...

  1. Structural characterization of Heusler compounds using NMR

    Energy Technology Data Exchange (ETDEWEB)

    Wurmehl, Sabine; Fecher, Gerhard; Balke, Benjamin; Ksenofontov, Vadim; Jung, Verena; Felser, Claudia [Johannes Gutenberg - Universitaet, 55099 Mainz (Germany); Wojcik, Marek [Institute of Physics, Polish Academy of Sciences, 02-668 Warszawa (Poland)

    2007-07-01

    The L2{sub 1} ordered Heusler alloys Co{sub 2}Mn{sub 1-x}Fe{sub x}Si with 0{<=}x{<=}1 attracted much scientific interest, as they are predicted to show high spin polarisation at the Fermi-energy. Therefore Co{sub 2}Mn{sub 1-x}Fe{sub x}Si samples were investigated using spin echo nuclear magnetic resonance (NMR) measurements. This method provides a tool to measure the hyperfine fields. The hyperfine fields represent a very sensitive local probe to order-disorder phenomena. The NMR measurements of polycrystalline Co{sub 2}FeSi samples exhibit a two-peak spectrum with an additional shoulder. This additional signals are attributed to second-order quadrupole splitting, a so called asymmetric line broadening and might be caused by tension within the structure (strain). This effect occurs even in highly ordered systems. Thus previous structural results are corroborated, demonstrating even locally a very high degree of order in Co{sub 2}FeSi. The NMR spectra of the series Co{sub 2}Mn{sub 1-x}Fe{sub x}Si (0.1{<=}x{<=}0.9) exhibit multiplet structures. These might be explained by quadrupole splitting and statistical distribution of Mn and Fe atoms on the Mn site. In summary, the high degree of order in Co{sub 2}Mn{sub 1-x}Fe{sub x}Si is shown.

  2. Multispectral dual isotope and NMR image analysis

    Energy Technology Data Exchange (ETDEWEB)

    Vannier, M.W.; Beihn, R.M.; Butterfield, R.L.; De Land, F.H.

    1985-05-01

    Dual isotope scintigraphy and nuclear magnetic resonance imaging produce image data that is intrinsically multispectral. That is multiple images of the same anatomic region are generated with different gray scale distribution and morphologic content that is largely redundant. Image processing technology, originally developed by NASA for satellite imaging, is available for multispectral analysis. These methods have been applied to provide tissue characterization. Tissue specific information encoded in the grapy scale data from dual isotope and NMR studies may be extracted using multispectral pattern recognition methods. The authors used table lookup minimum distance, maximum likelihood and cluster analysis techniques with data sets from Ga-67 / Tc-99m, 1-131 labeled antibodies / Tc-99m, Tc-99m perfusion / Xe-133 ventilation, and NMR studies. The results show; tissue characteristic signatures exist in dual isotope and NMR imaging, and these spectral signatures are identifiable using multispectral image analysis and provide tissue classification maps with scatter diagrams that facilitate interpretation and assist in elucidating subtle changes.

  3. Protein NMR structures refined without NOE data.

    Science.gov (United States)

    Ryu, Hyojung; Kim, Tae-Rae; Ahn, SeonJoo; Ji, Sunyoung; Lee, Jinhyuk

    2014-01-01

    The refinement of low-quality structures is an important challenge in protein structure prediction. Many studies have been conducted on protein structure refinement; the refinement of structures derived from NMR spectroscopy has been especially intensively studied. In this study, we generated flat-bottom distance potential instead of NOE data because NOE data have ambiguity and uncertainty. The potential was derived from distance information from given structures and prevented structural dislocation during the refinement process. A simulated annealing protocol was used to minimize the potential energy of the structure. The protocol was tested on 134 NMR structures in the Protein Data Bank (PDB) that also have X-ray structures. Among them, 50 structures were used as a training set to find the optimal "width" parameter in the flat-bottom distance potential functions. In the validation set (the other 84 structures), most of the 12 quality assessment scores of the refined structures were significantly improved (total score increased from 1.215 to 2.044). Moreover, the secondary structure similarity of the refined structure was improved over that of the original structure. Finally, we demonstrate that the combination of two energy potentials, statistical torsion angle potential (STAP) and the flat-bottom distance potential, can drive the refinement of NMR structures.

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

    Science.gov (United States)

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

    2015-08-01

    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 (15)N-(1)H 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 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.

  5. CcpNmr AnalysisAssign: a flexible platform for integrated NMR analysis

    Energy Technology Data Exchange (ETDEWEB)

    Skinner, Simon P.; Fogh, Rasmus H. [University of Leicester, Department of Molecular and Cell Biology, Leicester Institute for Structural- and Chemical Biology (United Kingdom); Boucher, Wayne [University of Cambridge, Department of Biochemistry (United Kingdom); Ragan, Timothy J.; Mureddu, Luca G.; Vuister, Geerten W., E-mail: gv29@le.ac.uk [University of Leicester, Department of Molecular and Cell Biology, Leicester Institute for Structural- and Chemical Biology (United Kingdom)

    2016-10-15

    NMR spectroscopy is an indispensably powerful technique for the analysis of biomolecules under ambient conditions, both for structural- and functional studies. However, in practice the complexity of the technique has often frustrated its application by non-specialists. In this paper, we present CcpNmr version-3, the latest software release from the Collaborative Computational Project for NMR, for all aspects of NMR data analysis, including liquid- and solid-state NMR data. This software has been designed to be simple, functional and flexible, and aims to ensure that routine tasks can be performed in a straightforward manner. We have designed the software according to modern software engineering principles and leveraged the capabilities of modern graphics libraries to simplify a variety of data analysis tasks. We describe the process of backbone assignment as an example of the flexibility and simplicity of implementing workflows, as well as the toolkit used to create the necessary graphics for this workflow. The package can be downloaded from www.ccpn.ac.uk/v3-software/downloads http://www.ccpn.ac.uk/v3-software/downloads and is freely available to all non-profit organisations.

  6. NMR spectroscopy of experimentally shocked single crystal quartz: A reexamination of the NMR shock barometer

    Science.gov (United States)

    Fiske, P. S.; Gratz, A. J.; Nellis, W. J.

    1993-01-01

    Cygan and others report a broadening of the Si-29 nuclear magnetic resonance (NMR) peak for synthetic quartz powders with increasing shock pressure which they propose as a shock wave barometer for natural systems. These results are expanded by studying single crystal quartz shocked to 12 and 33 GPa using the 6.5 m two-stage light-gas gun at Lawrence Livermore National Laboratories. Our NMR results differ substantially from those of Cygan and others and suggest that the proposed shock wave barometer may require refinement. The difference in results between this study and that of Cygan and others is most likely caused by different starting materials (single crystal vs. powder) and different shock loading histories. NMR results from single crystal studies may be more applicable to natural systems.

  7. Protein Structure Determination Using Protein Threading and Sparse NMR Data

    Energy Technology Data Exchange (ETDEWEB)

    Crawford, O.H.; Einstein, J.R.; Xu, D.; Xu, Y.

    1999-11-14

    It is well known that the NMR method for protein structure determination applies to small proteins and that its effectiveness decreases very rapidly as the molecular weight increases beyond about 30 kD. We have recently developed a method for protein structure determination that can fully utilize partial NMR data as calculation constraints. The core of the method is a threading algorithm that guarantees to find a globally optimal alignment between a query sequence and a template structure, under distance constraints specified by NMR/NOE data. Our preliminary tests have demonstrated that a small number of NMR/NOE distance restraints can significantly improve threading performance in both fold recognition and threading-alignment accuracy, and can possibly extend threading's scope of applicability from structural homologs to structural analogs. An accurate backbone structure generated by NMR-constrained threading can then provide a significant amount of structural information, equivalent to that provided by the NMR method with many NMR/NOE restraints; and hence can greatly reduce the amount of NMR data typically required for accurate structure determination. Our preliminary study suggests that a small number of NMR/NOE restraints may suffice to determine adequately the all-atom structure when those restraints are incorporated in a procedure combining threading, modeling of loops and sidechains, and molecular dynamics simulation. Potentially, this new technique can expand NMR's capability to larger proteins.

  8. Knowns and unknowns in metabolomics identified by multidimensional NMR and hybrid MS/NMR methods

    Energy Technology Data Exchange (ETDEWEB)

    Bingol, Kerem; Brüschweiler, Rafael

    2017-02-01

    Metabolomics continues to make rapid progress through the development of new and better methods and their applications to gain insight into the metabolism of a wide range of different biological systems from a systems biology perspective. Customization of NMR databases and search tools allows the faster and more accurate identification of known metabolites, whereas the identification of unknowns, without a need for extensive purification, requires new strategies to integrate NMR with mass spectrometry, cheminformatics, and computational methods. For some applications, the use of covalent and non-covalent attachments in the form of labeled tags or nanoparticles can significantly reduce the complexity of these tasks.

  9. Fast automated protein NMR data collection and assignment by ADAPT-NMR on Bruker spectrometers

    Science.gov (United States)

    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.

  10. Direct Comparison of 19F qNMR and 1H qNMR by Characterizing Atorvastatin Calcium Content

    Directory of Open Access Journals (Sweden)

    Yang Liu

    2016-01-01

    Full Text Available Quantitative nuclear magnetic resonance (qNMR is a powerful tool in measuring drug content because of its high speed, sensitivity, and precision. Most of the reports were based on proton qNMR (1H qNMR and only a few fluorine qNMR (19F qNMR were reported. No research has been conducted to directly compare the advantage and disadvantage between these two methods. In the present study, both 19F and 1H qNMR were performed to characterize the content of atorvastatin calcium with the same internal standard. Linearity, precision, and results from two methods were compared. Results showed that 19F qNMR has similar precision and sensitivity to 1H qNMR. Both methods generate similar results compared to mass balance method. Major advantage from 19F qNMR is that the analyte signal is with less or no interference from impurities. 19F qNMR is an excellent approach to quantify fluorine-containing analytes.

  11. Direct Comparison of 19F qNMR and 1H qNMR by Characterizing Atorvastatin Calcium Content

    Science.gov (United States)

    Liu, Yang; Liu, Zhaoxia; Yang, Huaxin

    2016-01-01

    Quantitative nuclear magnetic resonance (qNMR) is a powerful tool in measuring drug content because of its high speed, sensitivity, and precision. Most of the reports were based on proton qNMR (1H qNMR) and only a few fluorine qNMR (19F qNMR) were reported. No research has been conducted to directly compare the advantage and disadvantage between these two methods. In the present study, both 19F and 1H qNMR were performed to characterize the content of atorvastatin calcium with the same internal standard. Linearity, precision, and results from two methods were compared. Results showed that 19F qNMR has similar precision and sensitivity to 1H qNMR. Both methods generate similar results compared to mass balance method. Major advantage from 19F qNMR is that the analyte signal is with less or no interference from impurities. 19F qNMR is an excellent approach to quantify fluorine-containing analytes. PMID:27688925

  12. Nqrs Data for C29H43LiO8S [C16H32LiO8·C13H11S] (Subst. No. 1619)

    Science.gov (United States)

    Chihara, H.; Nakamura, N.

    This document is part of Subvolume B 'Substances Containing C10H16 … Zn' of Volume 48 'Nuclear Quadrupole Resonance Spectroscopy Data' of Landolt-Börnstein - Group III 'Condensed Matter'. It contains an extract of Section '3.2 Data tables' of the Chapter '3 Nuclear quadrupole resonance data' providing the NQRS data for C29H43LiO8S [C16H32LiO8·C13H11S] (Subst. No. 1619)

  13. Direct 13C NMR Detection in HPLC Hyphenation Mode

    DEFF Research Database (Denmark)

    Wubshet, Sileshi Gizachew; Johansen, Kenneth; Nyberg, Nils

    2012-01-01

    is indubitable in simplifying structural elucidations. In the current study, we demonstrated direct (13)C NMR detection of triterpenoids from a Ganoderma lucidum extract in hyphenation mode. The combined advantage of a cryogenically cooled probe, miniaturization, and multiple trapping enabled the first reported......Solid phase extraction (SPE) was introduced as a crucial step in the HPLC-SPE-NMR technique to enable online analyte enrichment from which proton-detected NMR experiments on submicrogram amounts from complex mixtures were possible. However, the significance of direct-detected (13)C NMR experiments...... application of HPLC-SPE-NMR analysis using direct-detected (13)C NMR spectra. HPLC column loading, accumulative SPE trappings, and the effect of different elution solvents were evaluated and optimized. A column loading of approximately 600 mug of a prefractionated triterpenoid mixture, six trappings...

  14. (S)Pinning down protein interactions by NMR

    DEFF Research Database (Denmark)

    Teilum, Kaare; Kunze, Micha Ben Achim; Erlendsson, Simon

    2017-01-01

    all types of protein reactions, which can span orders of magnitudes in affinities, reaction rates and lifetimes of states. As the more versatile technique, solution NMR spectroscopy offers a remarkable catalogue of methods that can be successfully applied to the quantitative as well as qualitative...... descriptions of protein interactions. In this review we provide an easy-access approach to NMR for the non-NMR specialist and describe how and when solution state NMR spectroscopy is the method of choice for addressing protein ligand interaction. We describe very briefly the theoretical background...... and illustrate simple protein-ligand interactions and as well as typical strategies for measuring binding constants using NMR spectroscopy. Finally, this review provides examples of caveats of the method as well as the options to improve the outcome of an NMR analysis of a protein interaction reaction...

  15. Studying assembly of the BAM complex in native membranes by cellular solid-state NMR spectroscopy.

    Science.gov (United States)

    Pinto, Cecilia; Mance, Deni; Julien, Manon; Daniels, Mark; Weingarth, Markus; Baldus, Marc

    2017-11-29

    Significant progress has been made in obtaining structural insight into the assembly of the β-barrel assembly machinery complex (BAM). These crystallography and electron microscopy studies used detergent as a membrane mimetic and revealed structural variations in the central domain, BamA, as well as in the lipoprotein BamC. We have used cellular solid-state NMR spectroscopy to examine the entire BamABCDE complex in native outer membranes and obtained data on the BamCDE subcomplex in outer membranes, in addition to synthetic bilayers. To reduce spectral crowding, we utilized proton-detected experiments and employed amino-acid specific isotope-labelling in (13C, 13C) correlation experiments. Taken together, the results provide insight into the overall fold and assembly of the BAM complex in native membranes, in particular regarding the structural flexibility of BamC in the absence of the core unit BamA. Copyright © 2017 Elsevier Inc. All rights reserved.

  16. Polymorphs of Theophylline Characterized by DNP Enhanced Solid-State NMR.

    Science.gov (United States)

    Pinon, Arthur C; Rossini, Aaron J; Widdifield, Cory M; Gajan, David; Emsley, Lyndon

    2015-11-02

    We show how dynamic nuclear polarization (DNP) enhanced solid-state NMR spectroscopy can be used to characterize polymorphs and solvates of organic solids. We applied DNP to three polymorphs and one hydrated form of the asthma drug molecule theophylline. For some forms of theophylline, sample grinding and impregnation with the radical-containing solution, which are necessary to prepare the samples for DNP, were found to induce polymorphic transitions or desolvation between some forms. We present protocols for sample preparation for solid-state magic-angle spinning (MAS) DNP experiments that avoid the polymorphic phase transitions in theophylline. These protocols include cryogrinding, grinding under inert atmosphere, and the appropriate choice of the impregnating liquid. By applying these procedures, we subsequently demonstrate that two-dimensional correlation experiments, such as (1)H-(13)C and (1)H-(15)N HETCOR or (13)C-(13)C INADEQUATE, can be obtained at natural isotopic abundance in reasonable times, thus enabling more advanced structural characterization of polymorphs.

  17. Rovibrational and temperature effects in theoretical studies of NMR parameters

    DEFF Research Database (Denmark)

    Faber, Rasmus; Kaminsky, Jakub; Sauer, Stephan P. A.

    2016-01-01

    The demand for high precision calculations of NMR shieldings (or their related values, chemical shifts δ) and spin-spin coupling constants facilitating and supporting detailed interpretations of NMR spectra increases hand in hand with the development of computational techniques and hardware...... resources. Highly sophisticated calculations including even relativistic effects are nowadays possible for these properties. However, NMR parameters depend not only on molecular structure and environment but also on molecular flexibility and temperature and the apparent success of theoretical predictions...

  18. Fluid-Rock Characterization and Interactions in NMR Well Logging

    Energy Technology Data Exchange (ETDEWEB)

    Hirasaki, George J.; Mohanty, Kishore K.

    2003-02-10

    The objective of this project was to characterize the fluid properties and fluid-rock interactions that are needed for formation evaluation by NMR well logging. The advances made in the understanding of NMR fluid properties are summarized in a chapter written for an AAPG book on NMR well logging. This includes live oils, viscous oils, natural gas mixtures, and the relation between relaxation time and diffusivity.

  19. Nuclear Magnetic Resonance Logging While Drilling (NMR-LWD)

    OpenAIRE

    Blanz, Martin; Kruspe, Thomas; Thern, Holger Frank; Kurz, Gerhard Alfons

    2015-01-01

    NMR T2 distribution measurement is our chosen everyday method for NMR logging while drilling oil and gas wells. This method yields straightforward preparation and execution of the job as well as a normally easy interpretation of the measured data. For instance, gas and light oil discrimination against water is feasible by direct observation of the T2 distribution. A condition for this measurement method is a NMR logging tool that hardly moves while drilling and in addition uses a small static...

  20. Metal glasses in microscopic scale: NMR studies

    Energy Technology Data Exchange (ETDEWEB)

    Tompa, K.; Bakonyi, I.; Varga, L. (Hungarian Academy of Sciences, Budapest. Central Research Inst. for Physics)

    1984-01-01

    A variety of amorphous metallic glasses was prepared by electrolysis, chemical reduction or fast cooling. Local orders, structural symmetry and topology were studied by means of NMR. Dipole-dipole and quadrupole interactions were analysed in Ni-P, Ni-Cu-P and Ni-B metallic glasses containing sup(31)P or sup(11)B nuclei. Experimentally determined signal widths were compared with the calculated values of model structures. The good agreement indicates structural identities of the nickel-containing glasses and the assumed models.

  1. Multiple-quantum NMR in solids

    Energy Technology Data Exchange (ETDEWEB)

    Yen, Yu-Sze [Univ. of California, Berkeley, CA (United States)

    1982-11-01

    Time domain multiple-quantum (MQ) nuclear magnetic resonance (NMR) spectroscopy is a powerful tool for spectral simplification and for providing new information on molecular dynamics. In this thesis, applications of MQ NMR are presented and show distinctly the advantages of this method over the conventional single-quantum NMR. Chapter 1 introduces the spin Hamiltonians, the density matrix formalism and some basic concepts of MQ NMR spectroscopy. In chapter 2, 14N double-quantum coherence is observed with high sensitivity in isotropic solution, using only the magnetization of bound protons. Spin echoes are used to obtain the homogeneous double-quantum spectrum and to suppress a large H2O solvent signal. Chapter 3 resolves the main difficulty in observing high MQ transitions in solids. Due to the profusion of spin transitions in a solid, individual lines are unresolved. Excitation and detection of high quantum transitions by normal schemes are thus difficult. To ensure that overlapping lines add constructively and thereby to enhance sensitivity, time-reversal pulse sequences are used to generate all lines in phase. Up to 22-quantum 1H absorption in solid adamantane is observed. A time dependence study shows an increase in spin correlations as the excitation time increased. In chapter 4, a statistical theory of MQ second moments is developed for coupled spins of spin I = 1/2. The model reveals that the ratio of the average dipolar coupling to the rms value largely determines the dependence of second moments on the number of quanta. The results of this model are checked against computer-calculated and experimental second moments, and show good agreement. A simple scheme is proposed in chapter 5 for sensitivity improvement in a MQ experiment. The scheme involves acquiring all of the signal energy available in the detection period by applying pulsed spinlocking and sampling between pulses. Using this technique on polycrystalline

  2. Touch NMR: An NMR Data Processing Application for the iPad

    Science.gov (United States)

    Li, Qiyue; Chen, Zhiwei; Yan, Zhiping; Wang, Cheng; Chen, Zhong

    2014-01-01

    Nuclear magnetic resonance (NMR) spectroscopy has become one of the most powerful technologies to aid research in numerous scientific disciplines. With the development of consumer electronics, mobile devices have played increasingly important roles in our daily life. However, there is currently no application available for mobile devices able to…

  3. Extracting protein dynamics information from overlapped NMR signals using relaxation dispersion difference NMR spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Konuma, Tsuyoshi [Icahn School of Medicine at Mount Sinai, Department of Structural and Chemical Biology (United States); Harada, Erisa [Suntory Foundation for Life Sciences, Bioorganic Research Institute (Japan); Sugase, Kenji, E-mail: sugase@sunbor.or.jp, E-mail: sugase@moleng.kyoto-u.ac.jp [Kyoto University, Department of Molecular Engineering, Graduate School of Engineering (Japan)

    2015-12-15

    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.

  4. 31 P-NMR, 77 Se-NMR and mass spectral studies on some ...

    African Journals Online (AJOL)

    A series of aminophosphines were prepared by controlled condensation reaction between PCl3 or PhPCl2 and amines, and they were converted into the corresponding chalcogenides. 31P-NMR and mass spectral data were collected for characterization of these asymmetrically substituted phosphines, and in addition, ...

  5. NMR structural studies of oligosaccharides and other natural products

    OpenAIRE

    Kjærulff, Louise; Gotfredsen, Charlotte Held

    2014-01-01

    NMR spektroskopi er et af de vigtigste værktøjer til analyse og strukturopklaring af kemiske stoffer og bruges inden for mange forskellige forskningsområder. Denne afhandling omhandler NMR-spektroskopisk strukturanalyse af små molekyler i vandig eller organisk opløsning, både i forhold til metodeudvikling og strukturopklaring vha. NMR spektroskopi. HMBC+ er et nyudviklet pseudo-3D NMR eksperiment til måling af n+1JHH homonukleare koblingskonstanter over 3-4 bindinger i små molekyler, observer...

  6. Optimization and practical implementation of ultrafast 2D NMR experiments

    Energy Technology Data Exchange (ETDEWEB)

    Queiroz Junior, Luiz H. K., E-mail: professorkeng@gmail.com [Universidade Federal de Sao Carlos (UFSC), SP (Brazil). Departamento de Quimica; Universidade Federal de Goias (UFGO), Goiania, GO (Brazil). Inst. de Quimica; Ferreira, Antonio G. [Universidade Federal de Sao Carlos (UFSC), SP (Brazil). Departamento de Quimica; Giraudeau, Patrick [Universite de Nantes (France). CNRS, Chimie et Interdisciplinarite: Synthese, Analyse, Modelisation

    2013-09-01

    Ultrafast 2D NMR is a powerful methodology that allows recording of a 2D NMR spectrum in a fraction of second. However, due to the numerous non-conventional parameters involved in this methodology its implementation is no trivial task. Here, an optimized experimental protocol is carefully described to ensure efficient implementation of ultrafast NMR. The ultrafast spectra resulting from this implementation are presented based on the example of two widely used 2D NMR experiments, COSY and HSQC, obtained in 0.2 s and 41 s, respectively. (author)

  7. Evaluation of fast 2D NMR for metabolomics.

    Science.gov (United States)

    Guennec, Adrien Le; Giraudeau, Patrick; Caldarelli, Stefano

    2014-06-17

    Two-dimensional nuclear magnetic resonance (2D NMR) is increasingly explored as a tool for metabolomics because of its superior resolution compared to one-dimensional NMR (1D NMR). However, 2D NMR is characterized by longer acquisition times, which makes it less suitable for high-throughput studies. In this Article, we evaluated two methods for the acceleration of nD NMR, ultrafast (UF) and nonuniform sampling (NUS), in the context of metabolomics. To this end, model samples mimicking the metabolic profile variations in serum from subjects affected by colorectal cancer and controls were analyzed by 1D (1)H NMR along with conventional and accelerated DQF-COSY and HSQC. A statistical analysis (OPLS-DA) yielded similar results for the group separation with all techniques, but biomarker identification from 2D spectra was substantially enhanced, both in terms of number of molecules and easiness of assignment. Most interestingly, fast 2D NMR techniques lead to similar results as conventional 2D NMR, opening the way for high-throughput metabolomics studies using 2D NMR.

  8. Method development in quantitative NMR towards metrologically traceable organic certified reference materials used as 31P qNMR standards

    OpenAIRE

    Weber, Michael; Hellriegel, Christine; Rueck, Alexander; Wuethrich, Juerg; Jenks, Peter; Obkircher, Markus

    2014-01-01

    Quantitative nuclear magnetic resonance (qNMR) spectroscopy is employed by an increasing number of analytical and industrial laboratories for the assignment of content and quantitative determination of impurities. Within the last few years, it was demonstrated that 1H qNMR can be performed with high accuracy leading to measurement uncertainties below 1?% relative. It was even demonstrated that the combination of 1H qNMR with metrological weighing can lead to measurement uncertainties below 0....

  9. Assessment of Bone Microstructural Changes by NMR

    Science.gov (United States)

    Ni, Qingwen; Wang, Xiaodu

    2008-03-01

    Previous studies have shown that age related increases in bone porosity without significant changes in bone mineral density (BMD) (without bone microstructural information) result in a decrease in bone strength. Bone fracture toughness is also significantly correlated to changes in porosity, microarchitecture, collagen integrity, microdamage, and water distribution, all of which are measures of bone quality. Unfortunately, current technology does not allow the non-destructive and non-invasive detection of bone water distribution or other measures of bone quality including microporosity. On the other hand, Nuclear Magnetic Resonance (NMR) proton spin-spin (T2) relaxation time measurements and computational analytical method have been used to determine microstructural characteristics of various types of fluid filled porous materials. The study in here is to demonstrate that non-destructive and non-invasive NMR proton spin-spin (T2) relaxation techniques has been developed and applied to quantify the porosity, pore size distribution and water distribution in human cortical bone. This new bone microstructural information can then be used as descriptions of bone quality and, along or in combination with existing method (BMD) to more accurately assess bone fracture risk, and the results could help doctors and researchers to detect osteoporosis and other conditions related to weak bones in persons.

  10. NMR-based diffusion pore imaging.

    Science.gov (United States)

    Laun, Frederik Bernd; Kuder, Tristan Anselm; Wetscherek, Andreas; Stieltjes, Bram; Semmler, Wolfhard

    2012-08-01

    Nuclear magnetic resonance (NMR) diffusion experiments offer a unique opportunity to study boundaries restricting the diffusion process. In a recent Letter [Phys. Rev. Lett. 107, 048102 (2011)], we introduced the idea and concept that such diffusion experiments can be interpreted as NMR imaging experiments. Consequently, images of closed pores, in which the spins diffuse, can be acquired. In the work presented here, an in-depth description of the diffusion pore imaging technique is provided. Image artifacts due to gradient profiles of finite duration, field inhomogeneities, and surface relaxation are considered. Gradients of finite duration lead to image blurring and edge enhancement artifacts. Field inhomogeneities have benign effects on diffusion pore images, and surface relaxation can lead to a shrinkage and shift of the pore image. The relation between boundary structure and the imaginary part of the diffusion weighted signal is analyzed, and it is shown that information on pore coherence can be obtained without the need to measure the phase of the diffusion weighted signal. Moreover, it is shown that quite arbitrary gradient profiles can be used for diffusion pore imaging. The matrices required for numerical calculations are stated and provided as supplemental material.

  11. NMR assessment on bone simulated under microgravity

    Science.gov (United States)

    Ni, Q.; Qin, Y.

    Introduction Microgravity-induced bone loss has been suggested to be similar to disuse-osteoporosis on Earth which constitutes a challenging public health problem No current non-destructive method can provide the microstructural changes in bone particularly on cortical bone Recently the authors have applied low field nuclear magnetic resonance NMR spin-spin relaxation technique and computational analysis method to determine the porosity pore size distribution and microdamage of cortical bone 1-3 The studies by the authors have shown that this technology can be used to characterize microstructural changes as well as bone water distribution bound and mobile water changes of weightless treated simulating a microgravity condition turkey and mouse cortical bone We further determinate that the NMR spin-spin relaxation time T 2 spectrum derived parameters can be used as descriptions of bone quality e g matrix water distribution and porosity size distributions and alone or in combination with current techniques bone mineral density measurements more accurately predict bone mechanical properties Methods underline Bone sample preparation Two kinds of animal samples were collected and prepared for designed experiments from SUNY Cortical bones of the mid-diaphyses of the ulnae of 1-year-old male turkeys were dissected from freshly slaughtered animals Eight samples were categorized from normal or control and four samples were 4-week disuse treated by functionally isolated osteotomies disuse A total of 12

  12. NMR-Metabolic Methodology in the Study of GM Foods

    Science.gov (United States)

    The 1H NMR methodology used in the study of genetically modified (GM) foodstuff is discussed. The study of transgenic lettuce (Lactuca sativa cv "Luxor") over-expressing the KNAT1 gene from Arabidopsis is presented as a novel study-case. The 1H NMR metabolic profiling was carried out. Twenty-two wat...

  13. nmr spectroscopic study and dft calculations of vibrational analyses ...

    African Journals Online (AJOL)

    Preferred Customer

    ANALYSES, GIAO NMR SHIELDINGS AND 1JCH, 1JCC SPIN-SPIN COUPLING. CONSTANTS ... proton coupled and uncoupled 13C, 15N, DEPT, COSY, HETCOR, INADEQUATE NMR spectra and the magnitude ... methodology an interesting variety of spin-spin coupling constants can be calculated with good accuracy in ...

  14. Facing and Overcoming Sensitivity Challenges in Biomolecular NMR Spectroscopy

    DEFF Research Database (Denmark)

    Ardenkjær-Larsen, Jan Henrik; Boebinger, Gregory S.; Comment, Arnaud

    2015-01-01

    In the Spring of 2013, NMR spectroscopists convened at the Weizmann Institute in Israel to brainstorm on approaches to improve the sensitivity of NMR experiments, particularly when applied in biomolecular settings. This multi‐author interdisciplinary Review presents a state‐of‐the‐art description...

  15. Advanced solid-state NMR spectroscopy of natural organic matter.

    Science.gov (United States)

    Mao, Jingdong; Cao, Xiaoyan; Olk, Dan C; Chu, Wenying; Schmidt-Rohr, Klaus

    2017-05-01

    Solid-state NMR is essential for the characterization of natural organic matter (NOM) and is gaining importance in geosciences and environmental sciences. This review is intended to highlight advanced solid-state NMR techniques, especially a systematic approach to NOM characterization, and their applications to the study of NOM. We discuss some basics of how to acquire high-quality and quantitative solid-state 13 C NMR spectra, and address some common technical mistakes that lead to unreliable spectra of NOM. The identification of specific functional groups in NOM, primarily based on 13 C spectral-editing techniques, is described and the theoretical background of some recently-developed spectral-editing techniques is provided. Applications of solid-state NMR to investigating nitrogen (N) in NOM are described, focusing on limitations of the widely used 15 N CP/MAS experiment and the potential of improved advanced NMR techniques for characterizing N forms in NOM. Then techniques used for identifying proximities, heterogeneities and domains are reviewed, and some examples provided. In addition, NMR techniques for studying segmental dynamics in NOM are reviewed. We also briefly discuss applications of solid-state NMR to NOM from various sources, including soil organic matter, aquatic organic matter, organic matter in atmospheric particulate matter, carbonaceous meteoritic organic matter, and fossil fuels. Finally, examples of NMR-based structural models and an outlook are provided. Copyright © 2016 Elsevier B.V. All rights reserved.

  16. Fluid-Rock Characterization and Interactions in NMR Well Logging

    Energy Technology Data Exchange (ETDEWEB)

    George J. Hirasaki; Kishore K. Mohanty

    2005-09-05

    The objective of this report is to characterize the fluid properties and fluid-rock interactions that are needed for formation evaluation by NMR well logging. The advances made in the understanding of NMR fluid properties are summarized in a chapter written for an AAPG book on NMR well logging. This includes live oils, viscous oils, natural gas mixtures, and the relation between relaxation time and diffusivity. Oil based drilling fluids can have an adverse effect on NMR well logging if it alters the wettability of the formation. The effect of various surfactants on wettability and surface relaxivity are evaluated for silica sand. The relation between the relaxation time and diffusivity distinguishes the response of brine, oil, and gas in a NMR well log. A new NMR pulse sequence in the presence of a field gradient and a new inversion technique enables the T{sub 2} and diffusivity distributions to be displayed as a two-dimensional map. The objectives of pore morphology and rock characterization are to identify vug connectivity by using X-ray CT scan, and to improve NMR permeability correlation. Improved estimation of permeability from NMR response is possible by using estimated tortuosity as a parameter to interpolate between two existing permeability models.

  17. Designing of high-resolution photoresists: use of modern NMR ...

    Indian Academy of Sciences (India)

    Applications of improved 1-D/ 2-D NMR spectroscopic techniques have been reviewed for quantitatively estimating the incorporation of different monomers and degree of linearity in resin microstructure. Comparison of the NMR data with those from lithography leads to a distinct correlation between resin microstructure and ...

  18. Probe for high resolution NMR with sample reorientation

    Science.gov (United States)

    Pines, A.; Samoson, A.

    1990-02-06

    An improved NMR probe and method are described which substantially improve the resolution of NMR measurements made on powdered or amorphous or otherwise orientationally disordered samples. The apparatus mechanically varies the orientation of the sample such that the time average of two or more sets of spherical harmonic functions are zero. 8 figs.

  19. Bringing NMR and IR Spectroscopy to High Schools

    Science.gov (United States)

    Bonjour, Jessica L.; Hass, Alisa L.; Pollock, David W.; Huebner, Aaron; Frost, John A.

    2017-01-01

    Development of benchtop, portable Fourier transform nuclear magnetic resonance (NMR) and infrared (IR) spectrometers has opened up opportunities for creating university-high school partnerships that provide high school students with hands-on experience with NMR and IR instruments. With recent changes to the international baccalaureate chemistry…

  20. Quantification of (1)H NMR Spectra from Human Plasma.

    Science.gov (United States)

    de Graaf, Robin A; Prinsen, Hetty; Giannini, Cosimo; Caprio, Sonia; Herzog, Raimund I

    2015-12-01

    Human plasma is a biofluid that is high in information content, making it an excellent candidate for metabolomic studies. (1)H NMR has been a popular technique to detect several dozen metabolites in blood plasma. In order for (1)H NMR to become an automated, high-throughput method, challenges related to (1) the large signal from lipoproteins and (2) spectral overlap between different metabolites have to be addressed. Here diffusion-weighted (1)H NMR is used to separate lipoprotein and metabolite signals based on their large difference in translational diffusion. The metabolite (1)H NMR spectrum is then quantified through spectral fitting utilizing full prior knowledge on the metabolite spectral signatures. Extension of the scan time by 3 minutes or 15% per sample allowed the acquisition of a (1)H NMR spectrum with high diffusion weighting. The metabolite (1)H NMR spectra could reliably be modeled with 28 metabolites. Excellent correlation was found between results obtained with diffusion NMR and ultrafiltration. The combination of minimal sample preparation together with minimal user interaction during processing and quantification provides a metabolomics technique for automated, quantitative (1)H NMR of human plasma.

  1. Rapid prediction of multi-dimensional NMR data sets

    NARCIS (Netherlands)

    Gradmann, S.H.E.; Ader, C.|info:eu-repo/dai/nl/326096639; Heinrich, I.; Nand, D.|info:eu-repo/dai/nl/337731403; Dittmann, M.; Cukkemane, A.A.|info:eu-repo/dai/nl/33285907X; van Dijk, M.|info:eu-repo/dai/nl/325811113; Bonvin, A.M.J.J.|info:eu-repo/dai/nl/113691238; Engelhard, M.; Baldus, M.|info:eu-repo/dai/nl/314410864

    2012-01-01

    We present a computational environment for Fast Analysis of multidimensional NMR DAta Sets (FANDAS) that allows assembling multidimensional data sets from a variety of input parameters and facilitates comparing and modifying such “in silico” data sets during the various stages of the NMR data

  2. $\\beta$-NMR of copper isotopes in ionic liquids

    CERN Multimedia

    We propose to test the feasibility of spin-polarization and $\\beta$-NMR studies on several short-lived copper isotopes, $^{58}$ Cu, $^{74}$Cu and $^{75}$Cu in crystals and liquids. The motivation is given by biological studies of Cu with $\\beta$-NMR in liquid samples, since Cu is present in a large number of enzymes involved in electron transfer and activation of oxygen. The technique is based on spin-polarization via optical pumping in the new VITO beamline. We will use the existing lasers, NMR magnet and NMR chambers and we will prepare a new optical pumping system. The studies will be devoted to tests of achieved $\\beta$-asymmetry in solid hosts, the behaviour of asymmetry when increasing vacuum, and finally NMR scans in ionic liquids. The achieved spin polarization will be also relevant for the plans to measure with high precision the magnetic moments of neutron-rich Cu isotopes.

  3. Orientational Glasses: NMR and Electric Susceptibility Studies

    Directory of Open Access Journals (Sweden)

    Neil Sullivan

    2017-11-01

    Full Text Available We review the results of a wide range of nuclear magnetic resonance (NMRmeasurements of the local order parameters and the molecular dynamics of solid ortho-para hydrogen mixtures and solid nitrogen-argon mixtures that form novel molecular orientational glass states at low temperatures. From the NMR measurements, the distribution of the order parameters can be deduced and, in terms of simple models, used to analyze the thermodynamic measurements of the heat capacities of these systems. In addition, studies of the dielectric susceptibilities of the nitrogen-argon mixtures are reviewed in terms of replica symmetry breaking analogous to that observed for spin glass states. It is shown that this wide set of experimental results is consistent with orientation or quadrupolar glass ordering of the orientational degrees of freedom.

  4. NMR studies of polysaccharides from brown seaweeds

    Energy Technology Data Exchange (ETDEWEB)

    Noseda, M.D.; Tisher, C.A.; Gorin, P.A.J.; Duarte, M.E.R. [Parana Univ., Curitiba, PR (Brazil). Dept. de Bioquimica; Cerezo, A.S. [Buenos Aires Univ. Nacional (Argentina). Dept. de Quimica Organica

    1997-12-31

    Alginic acid is the major intercellular polysaccharide serving as matrix in the brown algae and is comprised of an unbranched chain of (1->4)-linked {beta}-D-mannuronic acid (M) and {alpha}-L-guluronic acid (G), arranged in a blockwise fashion. The composition of the monomer residues and the block structure varies depending on the source of the polymer. The selective binding of cations to alginate accounts for its ability to form gels, which is dependent on the number and lenght of the G-blocks. They are widely used industrially for their ability to retain water, and for their gelling, viscosifying and stabilizing properties (Smidsrod and draget, 1996). In this study, alginate composition and block structure in Sargassum stenophyllum has been determined by chemical methods and NMR spectroscopic analysis. (author) 4 refs., 3 figs.

  5. Two-Dimensional NMR Lineshape Analysis

    Science.gov (United States)

    Waudby, Christopher A.; Ramos, Andres; Cabrita, Lisa D.; Christodoulou, John

    2016-04-01

    NMR titration experiments are a rich source of structural, mechanistic, thermodynamic and kinetic information on biomolecular interactions, which can be extracted through the quantitative analysis of resonance lineshapes. However, applications of such analyses are frequently limited by peak overlap inherent to complex biomolecular systems. Moreover, systematic errors may arise due to the analysis of two-dimensional data using theoretical frameworks developed for one-dimensional experiments. Here we introduce a more accurate and convenient method for the analysis of such data, based on the direct quantum mechanical simulation and fitting of entire two-dimensional experiments, which we implement in a new software tool, TITAN (TITration ANalysis). We expect the approach, which we demonstrate for a variety of protein-protein and protein-ligand interactions, to be particularly useful in providing information on multi-step or multi-component interactions.

  6. Long Lived NMR Signal in Bone

    CERN Document Server

    Zhang, Boyang; Khitrin, Anatoly; Jerschow, Alexej

    2012-01-01

    Solids and rigid tissues such as bone, ligaments, and tendons, typically appear dark in magnetic resonance imaging (MRI), which is due to the extremely short-lived proton nuclear magnetic resonance (NMR) signals. This short lifetime is due to strong dipolar interactions between immobilized proton spins, which render it challenging to detect these signals with sufficient resolution and sensitivity. Here we show the possibility of exciting long-lived signals in cortical bone tissue with a signature consistent with that of bound water signals. Contrary to long-standing belief, it is further shown that dipolar coupling networks are an integral requirement for the excitation of these long-lived signals. The use of these signals could enhance the ability to visualize rigid tissues and solid samples with high sensitivity, resolution, and specificity via MRI.

  7. NMR Metabolomics Analysis of Parkinson's Disease

    Science.gov (United States)

    Lei, Shulei; Powers, Robert

    2015-01-01

    Parkinson's disease (PD) is a neurodegenerative disease, which is characterized by progressive death of dopaminergic neurons in the substantia nigra pars compacta. Although mitochondrial dysfunction and oxidative stress are linked to PD pathogenesis, its etiology and pathology remain to be elucidated. Metabolomics investigates metabolite changes in biofluids, cell lysates, tissues and tumors in order to correlate these metabolomic changes to a disease state. Thus, the application of metabolomics to investigate PD provides a systematic approach to understand the pathology of PD, to identify disease biomarkers, and to complement genomics, transcriptomics and proteomics studies. This review will examine current research into PD mechanisms with a focus on mitochondrial dysfunction and oxidative stress. Neurotoxin-based PD animal models and the rationale for metabolomics studies in PD will also be discussed. The review will also explore the potential of NMR metabolomics to address important issues related to PD treatment and diagnosis. PMID:26078917

  8. NMR structures reveal how oxidation inactivates thrombomodulin.

    Science.gov (United States)

    Wood, Matthew J; Becvar, L Amaya; Prieto, Judith Helena; Melacini, Giuseppe; Komives, Elizabeth A

    2003-10-21

    Oxidation of Met 388, one of the three linker residues connecting the fourth and fifth EGF-like domains of thrombomodulin (TM), is deleterious for TM activity. An NMR structure of the smallest active fragment of TM (TMEGF45) and a crystal structure of a larger fragment (TMEGF456) bound to thrombin both show that Met 388 is packed into the fifth domain. Using multidimensional NMR, we have solved the structure of TMEGF45 in which Met 388 is oxidized (TMEGF45ox) and the structure of TMEGF45 in which Met 388 is mutated to Leu (TMEGF45ML). Comparison of the structures shows that the fifth domain has a somewhat different structure depending on the residue at position 388, and several of the thrombin-binding residues are packed into the fifth domain in the oxidized protein while they are exposed and free to interact with thrombin in the native structure and the Met-Leu mutant. This observation is consistent with kinetic measurements showing that the K(m) for TMEGF45ox binding to thrombin is 3.3-fold higher than for the native protein. Most importantly, the connection between the two domains, as indicated by interdomain NOEs, appears to be essential for activity. In the TMEGF45ox structure which has a reduced k(cat) for protein C activation by the thrombin-TMEGF45ox complex, interaction between the two domains is lost. Conversely, a tighter connection is observed between the two domains in TMEGF45ML, which has a higher k(cat) for protein C activation by the thrombin-TMEGF45ML complex.

  9. ImatraNMR: Novel software for batch integration and analysis of quantitative NMR spectra

    Science.gov (United States)

    Mäkelä, A. V.; Heikkilä, O.; Kilpeläinen, I.; Heikkinen, S.

    2011-08-01

    Quantitative NMR spectroscopy is a useful and important tool for analysis of various mixtures. Recently, in addition of traditional quantitative 1D 1H and 13C NMR methods, a variety of pulse sequences aimed for quantitative or semiquantitative analysis have been developed. To obtain actual usable results from quantitative spectra, they must be processed and analyzed with suitable software. Currently, there are many processing packages available from spectrometer manufacturers and third party developers, and most of them are capable of analyzing and integration of quantitative spectra. However, they are mainly aimed for processing single or few spectra, and are slow and difficult to use when large numbers of spectra and signals are being analyzed, even when using pre-saved integration areas or custom scripting features. In this article, we present a novel software, ImatraNMR, designed for batch analysis of quantitative spectra. In addition to capability of analyzing large number of spectra, it provides results in text and CSV formats, allowing further data-analysis using spreadsheet programs or general analysis programs, such as Matlab. The software is written with Java, and thus it should run in any platform capable of providing Java Runtime Environment version 1.6 or newer, however, currently it has only been tested with Windows and Linux (Ubuntu 10.04). The software is free for non-commercial use, and is provided with source code upon request.

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

    Science.gov (United States)

    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. Copyright © 2015 John Wiley & Sons, Ltd.

  11. Determination of surface relaxivity from NMR diffusion measurements.

    Science.gov (United States)

    Slijkerman, W F; Hofman, J P

    1998-01-01

    Nuclear magnetic resonance (NMR) T2-decay measurements are usually interpreted in terms of pore-size distributions. The T2 relaxation time of a water-wet pore is proportional to the size of the pore via surface relaxivity. Quantitative knowledge of the surface relaxivity is important when T2 spectra are to be used for further use such as NMR derived capillary curves. In this study, we demonstrate that surface relaxivity can be directly determined from NMR measurements. Diffusion of hydrogen spins is restricted by the pore size and this effect is independent of surface relaxivity. Hence, surface relaxivity can be determined by combining restricted diffusion and T2-relaxation. The latter two effects are measured simultaneously in a NMR T2 decay measurement performed in a static magnetic field gradient. This method generalises existing ones for uniform pore systems to full pore-size distributions of realistic rocks. We have performed laboratory NMR diffusion measurements on a number of sandstone core plugs. The surface relaxivities found from these data are compared to those obtained from other methods. This method of measuring surface relaxivity can in principle be applied to NMR data obtained in boreholes which leads to a new application of NMR logging in the characterisation of oil and gas reservoirs.

  12. Can NMR solve some significant challenges in metabolomics?

    Science.gov (United States)

    Nagana Gowda, G. A.; Raftery, Daniel

    2015-11-01

    The field of metabolomics continues to witness rapid growth driven by fundamental studies, methods development, and applications in a number of disciplines that include biomedical science, plant and nutrition sciences, drug development, energy and environmental sciences, toxicology, etc. NMR spectroscopy is one of the two most widely used analytical platforms in the metabolomics field, along with mass spectrometry (MS). NMR's excellent reproducibility and quantitative accuracy, its ability to identify structures of unknown metabolites, its capacity to generate metabolite profiles using intact bio-specimens with no need for separation, and its capabilities for tracing metabolic pathways using isotope labeled substrates offer unique strengths for metabolomics applications. However, NMR's limited sensitivity and resolution continue to pose a major challenge and have restricted both the number and the quantitative accuracy of metabolites analyzed by NMR. Further, the analysis of highly complex biological samples has increased the demand for new methods with improved detection, better unknown identification, and more accurate quantitation of larger numbers of metabolites. Recent efforts have contributed significant improvements in these areas, and have thereby enhanced the pool of routinely quantifiable metabolites. Additionally, efforts focused on combining NMR and MS promise opportunities to exploit the combined strength of the two analytical platforms for direct comparison of the metabolite data, unknown identification and reliable biomarker discovery that continue to challenge the metabolomics field. This article presents our perspectives on the emerging trends in NMR-based metabolomics and NMR's continuing role in the field with an emphasis on recent and ongoing research from our laboratory.

  13. Solid-state 73Ge NMR spectroscopy of simple organogermanes.

    Science.gov (United States)

    Hanson, Margaret A; Sutrisno, Andre; Terskikh, Victor V; Baines, Kim M; Huang, Yining

    2012-10-22

    Germanium-73 is an extremely challenging nucleus to examine by NMR spectroscopy due to its unfavorable NMR properties. Through the use of an ultrahigh (21.1 T) magnetic field, a systematic study of a series of simple organogermanes was carried out. In those cases for which X-ray structural data were available, correlations were drawn between the NMR parameters and structural metrics. These data were combined with DFT calculations to obtain insight into the structures of several compounds with unknown crystal structures. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  14. Nanoscale NMR and NQR with Nitrogen Vacancy Centers

    Science.gov (United States)

    Urbach, Elana; Lovchinsky, Igor; Sanchez-Yamagishi, Javier; Choi, Soonwon; Bylinskii, Alexei; Dwyer, Bo; Andersen, Trond; Sushkov, Alex; Park, Hongkun; Lukin, Mikhail

    2016-05-01

    Nuclear quadrupole resonance (NQR) is a powerful tool which is used to detect quadrupolar interaction in nuclear spins with I > 1/2. Conventional NQR and NMR technology, however, rely on measuring magnetic fields from a macroscopic number of spins. Extending NMR and NQR techniques to the nanoscale could allow us to learn structural information about interesting materials and biomolecules. We present recent progress on using Nitrogen-Vacancy (NV) centers in diamond to perform room temperature nanoscale NMR and NQR spectroscopy on small numbers of nuclear spins in hexagonal boron nitride.

  15. NMR study of the gelation of a designed gelator.

    Science.gov (United States)

    Brand, Torsten; Nolis, Pau; Richter, Sven; Berger, Stefan

    2008-06-01

    The gelation of a designed gelator was investigated by different NMR methods, which showed a clear thermal hysteresis. Two very simple approaches for the NMR determination of the gelation point are suggested. One involves the observation of the NMR integral, and the other records the ratio of the diffusion coefficients between the gelator and the solvent. Differential behavior of the gelator protons are interpreted as a hint that a part of the gelator molecule might still be flexible as in the dissolved state. Copyright (c) 2008 John Wiley & Sons, Ltd

  16. NMR contributions to structural dynamics studies of intrinsically disordered proteins☆

    Science.gov (United States)

    Konrat, Robert

    2014-01-01

    Intrinsically disordered proteins (IDPs) are characterized by substantial conformational plasticity. Given their inherent structural flexibility X-ray crystallography is not applicable to study these proteins. In contrast, NMR spectroscopy offers unique opportunities for structural and dynamic studies of IDPs. The past two decades have witnessed significant development of NMR spectroscopy that couples advances in spin physics and chemistry with a broad range of applications. This article will summarize key advances in basic physical-chemistry and NMR methodology, outline their limitations and envision future R&D directions. PMID:24656082

  17. Room temperature chiral discrimination in paramagnetic NMR spectroscopy

    CERN Document Server

    Soncini, Alessandro

    2016-01-01

    A recently proposed theory of chiral discrimination in NMR spectroscopy based on the detection of a molecular electric polarization $\\mathbf{P}$ rotating in a plane perpendicular to the NMR magnetic field [A. D. Buckingham, J. Chem. Phys. $\\mathbf{140}$, 011103 (2014)], is here generalized to paramagnetic systems. Our theory predicts new contributions to $\\mathbf{P}$, varying as the square of the inverse temperature. Ab initio calculations for ten Dy$^{3+}$ complexes, at 293K, show that in strongly anisotropic paramagnetic molecules $\\mathbf{P}$ can be more than 1000 times larger than in diamagnetic molecules, making paramagnetic NMR chiral discrimination amenable to room temperature detection.

  18. Characterisation of triacetone triperoxide (TATP) conformers using LC-NMR.

    Science.gov (United States)

    Haroune, Nicolas; Crowson, Andrew; Campbell, Bill

    2011-06-01

    Previous studies [1,2] have reported the existence of two conformers of TATP. This study demonstrates the ability of LC-NMR to separate and characterise the individual conformers. The NMR data is consistent with the proposed structures for the two conformers. Re-equilibration can be followed by NMR and the kinetics of the process studied. Over the past decade the use of the explosive TATP in terrorist devices has increased. Therefore, the ability to analyse and characterise this material has assumed greater importance. Copyright © 2010 Forensic Science Society. All rights reserved.

  19. NMR Studies of Protein Structure and Dynamics

    Science.gov (United States)

    Li, Xiang

    Available from UMI in association with The British Library. Requires signed TDF. This thesis describes applications of 2D homonuclear NMR techniques to the study of protein structure and dynamics in solution. The sequential assignments for the 3G-residue bovine Pancreatic Polypeptide (bPP) are reported. The secondary and tertiary structure of bPP in solution has been determined from experimental NMR data. bPP has a well defined C-terminal alpha-helix and a rather ordered conformation in the N-terminal region. The two segments are joined by a turn which is poorly defined. Both the N- and the C-terminus are highly disordered. The mean solution structure of bPP is remarkably similar to the crystal structure of avian Pancreatic Polypeptide (aPP). The average conformations of most side-chains from the alpha-helix of bPP in solution are closely similar to those of aPP in the crystalline state. A large number of side-chains of bPP, however, show significant conformational averaging in solution. The 89-residue kringle domain of urokinase from both human and recombinant sources has been investigated. Sequential assignments based primarily on the recombinant sample and the determination of secondary structure are presented. Two helices have been identified; one of these corresponds to that reported for t-PA kringle 2, but does not exist in other kringles with known structures. The second helix is thus far unique to the urokinase kringle. Three antiparallel beta-sheets and three tight turns have also been identified. The tertiary fold of the molecule conforms broadly to that found for other kringles. Three regions in the urokinase kringle exhibit high local mobility; one of these, the Pro56-Pro62 segment, forms part of the proposed binding site. The other two mobile regions are the N- and C-termini which are likely to form the interfaces between the kringle and the other two domains (EGF and protease) in urokinase. The differential dynamic behaviours of the kringle and

  20. Dilute Bicellar Solutions for Structural NMR Work

    Science.gov (United States)

    Struppe, Jochem; Vold, Regitze R.

    1998-12-01

    Deuterium NMR spectroscopy has been employed to characterize the concentration dependence of orientational order in DMPC/DHPC bicellar solutions with molar ratiosq= [DMPC]/[DHPC] = 3.3, 2.7, and 2.3. The stability of a discotic nematic phase can, in general, be predicted from a simple Onsager picture involving the size and concentration of the mesogenic unit, but for the bicellar solutions this model is not adequate. Specifically, macroscopic alignment is observed at total lipid concentrations well below that, 1-10% (w/w) predicted by Onsager's model. Thus the discotic nematic phase is stable to ≈3-5% (w/w) forq= 3.3-2.3, and the bicellar order is highest just before phase separation occurs at the minimum total phospholipid concentration. This implies the presence of a DHPCbic⇄ DHPCsolequilibrium in establishing bicellar size, thereby extending the range of concentrations for which alignment occurs. Bicellar morphology has been verified for a wide range of concentrations, temperatures, andq-values, but as viscosity measurements demonstrate, major morphological changes take place as the temperature is reduced below 30°C.

  1. A multinuclear static NMR study of geopolymerisation

    Energy Technology Data Exchange (ETDEWEB)

    Favier, Aurélie, E-mail: aurelie.favier@epfl.ch [Univ Paris-Est, IFSTTAR, Materials Department, 14-20 bd Newton, F-77447 Marne la Vallée Cedex 2 (France); Habert, Guillaume [Institute for Construction and Infrastructure Management, ETH Zurich, CH-8093 Zurich (Switzerland); Roussel, Nicolas [Univ Paris-Est, IFSTTAR, Materials Department, 14-20 bd Newton, F-77447 Marne la Vallée Cedex 2 (France); D' Espinose de Lacaillerie, Jean-Baptiste [Ecole Supérieure de Physique et de Chimie Indusrtrielles de la Ville de Paris (ESPCI), ParisTech, PSL Research University, Soft Matter Sciences and Engineering Laboratory SIMM, CNRS UMR 7615, 10 rue Vauquelin, F-75005 Paris (France)

    2015-09-15

    Geopolymers are inorganic binders obtained by alkali activation of aluminosilicates. While the structure of geopolymers is now well understood, the details of the geopolymerisation reaction and their impact on the rheology of the paste remain uncertain. In this work, we follow the elastic properties of a paste made with metakaolin and sodium silicate solution. After the first sharp increase of elastic modulus occurring a few hundred of seconds after mixing and related to the heterogeneous formation of an alumina–silicate gel with a molar ratio Si/Al < 4 located at the grains boundaries, we focus on the progressive increase in elastic modulus on a period of few hours during the setting of the geopolymer. In this study, we combine the study of rheological properties of the paste with {sup 23}Na, {sup 27}Al and {sup 29}Si static NMR measurement in order to better understand the origin of this second increase in elastic modulus. Our results show that, after a few hours, Al and Na evolution in the liquid phase are concomitant. This suggests the precipitation of an aluminosilicate phase where Al is in tetrahedral position and Na compensates the charge. Furthermore, Si speciation confirms this result and allows us to identify the precipitation of a product, which has a chemical composition close to the final composition of geopolymer. This study provides strong evidence for a heterogeneous formation of an aluminosilicate glass directly from the first gel and the silicate solution without the need for a reorganisation of Gel 1 into Gel 2.

  2. Cell signaling, post-translational protein modifications and NMR spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Theillet, Francois-Xavier [In-cell NMR Group, Department of NMR-Supported Structural Biology, Leibniz Institute of Molecular Pharmacology (FMP Berlin) (Germany); Smet-Nocca, Caroline [Universite Lille Nord de France, CNRS UMR 8576 (France); Liokatis, Stamatios; Thongwichian, Rossukon; Kosten, Jonas [In-cell NMR Group, Department of NMR-Supported Structural Biology, Leibniz Institute of Molecular Pharmacology (FMP Berlin) (Germany); Yoon, Mi-Kyung; Kriwacki, Richard W. [St. Jude Children' s Research Hospital, Department of Structural Biology (United States); Landrieu, Isabelle; Lippens, Guy [Universite Lille Nord de France, CNRS UMR 8576 (France); Selenko, Philipp, E-mail: selenko@fmp-berlin.de [In-cell NMR Group, Department of NMR-Supported Structural Biology, Leibniz Institute of Molecular Pharmacology (FMP Berlin) (Germany)

    2012-11-15

    Post-translationally modified proteins make up the majority of the proteome and establish, to a large part, the impressive level of functional diversity in higher, multi-cellular organisms. Most eukaryotic post-translational protein modifications (PTMs) denote reversible, covalent additions of small chemical entities such as phosphate-, acyl-, alkyl- and glycosyl-groups onto selected subsets of modifiable amino acids. In turn, these modifications induce highly specific changes in the chemical environments of individual protein residues, which are readily detected by high-resolution NMR spectroscopy. In the following, we provide a concise compendium of NMR characteristics of the main types of eukaryotic PTMs: serine, threonine, tyrosine and histidine phosphorylation, lysine acetylation, lysine and arginine methylation, and serine, threonine O-glycosylation. We further delineate the previously uncharacterized NMR properties of lysine propionylation, butyrylation, succinylation, malonylation and crotonylation, which, altogether, define an initial reference frame for comprehensive PTM studies by high-resolution NMR spectroscopy.

  3. Interfaces in polymer nanocomposites – An NMR study

    Energy Technology Data Exchange (ETDEWEB)

    Böhme, Ute; Scheler, Ulrich, E-mail: scheler@ipfdd.de [Leibniz-Institut für Polymerforschung Dresden e.V., Hohe Str. 6, 01069 Dresden (Germany)

    2016-03-09

    Nuclear Magnetic Resonance (NMR) is applied for the investigation of polymer nanocomposites. Solid-state NMR is applied to study the modification steps to compatibilize layered double hydroxides with non-polar polymers. {sup 1}H relaxation NMR gives insight on the polymer dynamics over a wide range of correlation times. For the polymer chain dynamics the transverse relaxation time T{sub 2} is most suited. In this presentation we report on two applications of T{sub 2} measurements under external mechanical stress. In a low-field system relaxation NMR studies are performed in-situ under uniaxial stress. High-temperature experiments in a Couette cell permit the investigation of the polymer dynamics in the melt under shear flow.

  4. A covariance NMR toolbox for MATLAB and OCTAVE.

    Science.gov (United States)

    Short, Timothy; Alzapiedi, Leigh; Brüschweiler, Rafael; Snyder, David

    2011-03-01

    The Covariance NMR Toolbox is a new software suite that provides a streamlined implementation of covariance-based analysis of multi-dimensional NMR data. The Covariance NMR Toolbox uses the MATLAB or, alternatively, the freely available GNU OCTAVE computer language, providing a user-friendly environment in which to apply and explore covariance techniques. Covariance methods implemented in the toolbox described here include direct and indirect covariance processing, 4D covariance, generalized indirect covariance (GIC), and Z-matrix transform. In order to provide compatibility with a wide variety of spectrometer and spectral analysis platforms, the Covariance NMR Toolbox uses the NMRPipe format for both input and output files. Additionally, datasets small enough to fit in memory are stored as arrays that can be displayed and further manipulated in a versatile manner within MATLAB or OCTAVE. Copyright © 2010 Elsevier Inc. All rights reserved.

  5. Structural, vibrational, NMR, quantum chemical, DNA binding and ...

    Indian Academy of Sciences (India)

    -one oxime (HL¹) and 3-(pyridin-2-ylmethylimino)-pentan-2-one oxime (HL²) have been synthesized and characterized by elemental analysis, IR and NMR techniques. The conformational behavior was investigated using the density functional ...

  6. NMR with Combined Antiangiogenic and Radiation Therapies - Breast Cancer

    National Research Council Canada - National Science Library

    Brown, Stephen

    2000-01-01

    The original goal of the present study was to determine optimal strategies for combining radiation and antiangiogenic therapies in spontaneous murine tumors and to evaluate the potential of Nuclear Magnetic Resonance (NMR...

  7. NMR study of hydrogen in cathodically charged Inconel 718

    Energy Technology Data Exchange (ETDEWEB)

    Raizman, A.; Barak, J.; Zamir, D. (Israel Atomic Energy Commission, Yavne. Soreq Nuclear Research Center); Eliezer, D. (Ben-Gurion Univ. of the Negev, Beersheba (Israel))

    1983-11-01

    An NMR signal of protons in cathodically charged Inconel 718 has been detected. T/sub 1/, T/sub 2/, line shift and line width have been measured. Conclusions about hydrogen behavior in Inconel have been drawn.

  8. Optical analogue of 2D heteronuclear double-quantum NMR

    CERN Document Server

    Tollerud, Jonathan

    2016-01-01

    Heteronuclear multi-quantum spectroscopy is a powerful part of the NMR toolbox, commonly used to identify specific sequences of atoms in complex pulse sequences designed to determine the structure of complex molecules, including proteins. Optical coherent multidimensional spectroscopy (CMDS) is analogous to multidimensional NMR and many of the techniques of NMR have been adapted for application in the optical regime. This has been highly successful, with CMDS being used to understand energy transfer in photosynthesis and many body effects in semiconductor nanostructures amongst many other scientific breakthroughs. Experimental challenges have, however, prevented the translation of heteronuclear multi-quantum NMR to the optical regime, where capabilities to isolate signals in otherwise congested spectra, reduce acquisition times and enable more incisive probes of multi-particle correlations and complex electronic systems would have great benefit. Here we utilise a diffraction based pulseshaper to impose the tw...

  9. International NMR-based Environmental Metabolomics Intercomparison Exercise

    Science.gov (United States)

    Several fundamental requirements must be met so that NMR-based metabolomics and the related technique of metabonomics can be formally adopted into environmental monitoring and chemical risk assessment. Here we report an intercomparison exercise which has evaluated the effectivene...

  10. NMR methods for the investigation of structure and transport

    Energy Technology Data Exchange (ETDEWEB)

    Hardy, Edme H. [Karlsruher Institut fuer Technologie (KIT), Karlsruhe (Germany). Inst. fuer Mechanische Verfahrenstechnik und Mechanik

    2012-07-01

    Extensive derivations of required fundamental relations for readers with engineering background New applications based on MRI, PGSE-NMR, and low-field NMR New concepts in quantitative data evaluation and image analysis Methods of nuclear magnetic resonance (NMR) are increasingly applied in engineering sciences. The book summarizes research in the field of chemical and process engineering performed at the Karlsruhe Institute of Technology (KIT). Fundamentals of the methods are exposed for readers with an engineering background. Applications cover the fields of mechanical process engineering (filtration, solid-liquid separation, powder mixing, rheometry), chemical process engineering (trickle-bed reactor, ceramic sponges), bioprocess engineering (biofilm growth), and food process engineering (microwave heating, emulsions). Magnetic Resonance Imaging (MRI) as well as low-field NMR are covered with notes on hardware. Emphasis is placed on quantitative data analysis and image processing. (orig.)

  11. Noninvasive detection of nanoparticle clustering by water proton NMR

    Energy Technology Data Exchange (ETDEWEB)

    Taraban, Marc B.; Truong, Huy C.; Ilavsky, Jan; DePaz, Roberto A.; Lobo, Brian; Yu, Y. Bruce

    2017-06-01

    It is shown that water proton NMR can detect uncontrolled clustering of inert nanoparticles (NPs) formulated as aqueous suspensions. The clustering of NPs causes the compartmentalization of water molecules, leading to accelerated proton spin de-coherence, and hence, much faster water transverse relaxation rates. The results suggest that water proton NMR can be used to noninvasively inspect NP products by commercial end users and researchers.

  12. Flow units from integrated WFT and NMR data

    Energy Technology Data Exchange (ETDEWEB)

    Kasap, E.; Altunbay, M.; Georgi, D.

    1997-08-01

    Reliable and continuous permeability profiles are vital as both hard and soft data required for delineating reservoir architecture. They can improve the vertical resolution of seismic data, well-to-well stratigraphic correlations, and kriging between the well locations. In conditional simulations, permeability profiles are imposed as the conditioning data. Variograms, covariance functions and other geostatistical indicators are more reliable when based on good quality permeability data. Nuclear Magnetic Resonance (NMR) logging and Wireline Formation Tests (WFT) separately generate a wealth of information, and their synthesis extends the value of this information further by providing continuous and accurate permeability profiles without increasing the cost. NMR and WFT data present a unique combination because WFTs provide discrete, in situ permeability based on fluid-flow, whilst NMR responds to the fluids in the pore space and yields effective porosity, pore-size distribution, bound and moveable fluid saturations, and permeability. The NMR permeability is derived from the T{sub 2}-distribution data. Several equations have been proposed to transform T{sub 2} data to permeability. Regardless of the transform model used, the NMR-derived permeabilities depend on interpretation parameters that may be rock specific. The objective of this study is to integrate WFT permeabilities with NMR-derived, T{sub 2} distribution-based permeabilities and thereby arrive at core quality, continuously measured permeability profiles. We outlined the procedures to integrate NMR and WFT data and applied the procedure to a field case. Finally, this study advocates the use of hydraulic unit concepts to extend the WFT-NMR derived, core quality permeabilities to uncored intervals or uncored wells.

  13. Fluid-Rock Characterization and Interactions in NMR Well Logging

    Energy Technology Data Exchange (ETDEWEB)

    Hirasaki, George J.; Mohanty, Kishore K.

    2003-02-10

    The objective of this project was to characterize the fluid properties and fluid-rock interactions which are needed for formation evaluation by NMR well logging. NMR well logging is finding wide use in formation evaluation. The formation parameters commonly estimated were porosity, permeability, and capillary bound water. Special cases include estimation of oil viscosity, residual oil saturation, location of oil/water contact, and interpretation on whether the hydrocarbon is oil or gas.

  14. Multidimensional NMR Inversion without Kronecker Products: Multilinear Inversion

    OpenAIRE

    Medellín, David; Ravi, Vivek R.; Torres-Verdín, Carlos

    2016-01-01

    Multidimensional NMR inversion using Kronecker products poses several challenges. First, kernel compression is only possible when the kernel matrices are separable, and in recent years, there has been an increasing interest in NMR sequences with non-separable kernels. Second, in three or more dimensions, the singular value decomposition is not unique; therefore kernel compression is not well-defined for higher dimensions. Without kernel compression, the Kronecker product yields matrices that ...

  15. Method development in quantitative NMR towards metrologically traceable organic certified reference materials used as (31)P qNMR standards.

    Science.gov (United States)

    Weber, Michael; Hellriegel, Christine; Rueck, Alexander; Wuethrich, Juerg; Jenks, Peter; Obkircher, Markus

    2015-04-01

    Quantitative nuclear magnetic resonance (qNMR) spectroscopy is employed by an increasing number of analytical and industrial laboratories for the assignment of content and quantitative determination of impurities. Within the last few years, it was demonstrated that (1)H qNMR can be performed with high accuracy leading to measurement uncertainties below 1 % relative. It was even demonstrated that the combination of (1)H qNMR with metrological weighing can lead to measurement uncertainties below 0.1 % when highly pure substances are used. Although qNMR reference standards are already available as certified reference materials (CRM) providing traceability on the basis of (1)H qNMR experiments, there is an increasing demand for purity assays on phosphorylated organic compounds and metabolites requiring CRM for quantification by (31)P qNMR. Unfortunately, the number of available primary phosphorus standards is limited to a few inorganic CRM which only can be used for the analysis of water-soluble analytes but fail when organic solvents must be employed. This paper presents the concept of value assignment by (31)P qNMR measurements for the development of CRM and describes different approaches to establish traceability to primary Standard Reference Material from the National Institute of Standards and Technology (NIST SRM). Phosphonoacetic acid is analyzed as a water-soluble CRM candidate, whereas triphenyl phosphate is a good candidate for the use as qNMR reference material in organic solvents. These substances contain both nuclei, (1)H and (31)P, and the concept is to show that it is possible to indirectly quantify a potential phosphorus standard via its protons using (1)H qNMR. The same standard with its assigned purity can then be used for the quantification of an analyte via its phosphorus using (31)P qNMR. For the validation of the concept, triphenyl phosphate and phosphonoacetic acid have been used as (31)P qNMR standards to determine the purity of the analyte

  16. Proton NMR relaxation in hydrous melts

    Energy Technology Data Exchange (ETDEWEB)

    Braunstein, J.; Bacarella, A.L.; Benjamin, B.M.; Brown, L.L.; Girard, C.

    1976-01-01

    Pulse and continuous wave NMR measurements are reported for protons in hydrous melts of calcium nitrate at temperatures between -4 and 120/sup 0/C. Although measured in different temperature ranges, spin-lattice (T/sub 1/) and spin-spin (T/sub 2/) relaxation times appear to be nearly equal to each other and proportional to the self-diffusion coefficients of solute metal cations such as Cd/sup 2 +/. At temperatures near 50/sup 0/C, mean Arrhenius coefficients ..delta.. H/sub T/sub 1// (kcal/mol) are 7.9, 7.3, and 4.8, respectively, for melts containing 2.8, 4.0, and 8.0 moles of water per mole of calcium nitrate, compared to 4.6 kcal/mol for pure water. Temperature dependence of T/sub 1/ and T/sub 2/ in Ca(NO/sub 3/)/sub 2/-2.8 H/sub 2/O between -4 and 120/sup 0/C are non-Arrhenius and can be represented by a Fulcher-type equation with a ''zero mobility temperature'' (T/sub 0/) of 225/sup 0/K, close to the value of T/sub 0/ for solute diffusion, electrical conductance and viscosity. Resolution of the relaxation rates into correlation times for intramolecular (rotational) and intermolecular (translational) diffusional motion is discussed in terms of the Bloembergen-Purcell-Pound and more recent models for dipolar relaxation. (auth)

  17. Noninvasive testing of art and cultural heritage by mobile NMR.

    Science.gov (United States)

    Blümich, Bernhard; Casanova, Federico; Perlo, Juan; Presciutti, Federica; Anselmi, Chiara; Doherty, Brenda

    2010-06-15

    Nuclear magnetic resonance (NMR) has many applications in science, medicine, and technology. Conventional instrumentation is large and expensive, however, because superconducting magnets offer maximum sensitivity. Yet NMR devices can also be small and inexpensive if permanent magnets are used, and samples need not be placed within the magnet but can be examined externally in the stray magnetic field. Mobile stray-field NMR is a method of growing interest for nondestructive testing of a diverse range of materials and processes. A well-known stray-field sensor is the commercially available NMR-MOUSE, which is small and can readily be carried to an object to be studied. In this Account, we describe mobile stray-field NMR, with particular attention to its use in analyzing objects of cultural heritage. The most common data recorded are relaxation measurements of (1)H because the proton is the most sensitive NMR nucleus, and relaxation can be measured despite the inhomogeneous magnetic field that typically accompanies a simple magnet design. Through NMR relaxation, the state of matter can be analyzed locally, and the signal amplitude gives the proton density. A variety of stray-field sensors have been designed. Small devices weighing less than a kilogram have a shallow penetration depth of just a few millimeters and a resolution of a few micrometers. Access to greater depths requires larger sensors that may weigh 30 kg or more. The use of these sensors is illustrated by selected examples, including examinations of (i) the stratigraphy of master paintings, (ii) binder aging, (iii) the deterioration of paper, (iv) wood density in master violins, (v) the moisture content and moisture profiles in walls covered with paintings and mosaics, and (vi) the evolution of stone conservation treatments. The NMR data provide unique information to the conservator on the state of the object--including past conservation measures. The use of mobile NMR remains relatively new, expanding

  18. Accurate, fully-automated NMR spectral profiling for metabolomics.

    Science.gov (United States)

    Ravanbakhsh, Siamak; Liu, Philip; Bjorndahl, Trent C; Bjordahl, Trent C; Mandal, Rupasri; Grant, Jason R; Wilson, Michael; Eisner, Roman; Sinelnikov, Igor; Hu, Xiaoyu; Luchinat, Claudio; Greiner, Russell; Wishart, David S

    2015-01-01

    Many diseases cause significant changes to the concentrations of small molecules (a.k.a. metabolites) that appear in a person's biofluids, which means such diseases can often be readily detected from a person's "metabolic profile"-i.e., the list of concentrations of those metabolites. This information can be extracted from a biofluids Nuclear Magnetic Resonance (NMR) spectrum. However, due to its complexity, NMR spectral profiling has remained manual, resulting in slow, expensive and error-prone procedures that have hindered clinical and industrial adoption of metabolomics via NMR. This paper presents a system, BAYESIL, which can quickly, accurately, and autonomously produce a person's metabolic profile. Given a 1D 1H NMR spectrum of a complex biofluid (specifically serum or cerebrospinal fluid), BAYESIL can automatically determine the metabolic profile. This requires first performing several spectral processing steps, then matching the resulting spectrum against a reference compound library, which contains the "signatures" of each relevant metabolite. BAYESIL views spectral matching as an inference problem within a probabilistic graphical model that rapidly approximates the most probable metabolic profile. Our extensive studies on a diverse set of complex mixtures including real biological samples (serum and CSF), defined mixtures and realistic computer generated spectra; involving > 50 compounds, show that BAYESIL can autonomously find the concentration of NMR-detectable metabolites accurately (~ 90% correct identification and ~ 10% quantification error), in less than 5 minutes on a single CPU. These results demonstrate that BAYESIL is the first fully-automatic publicly-accessible system that provides quantitative NMR spectral profiling effectively-with an accuracy on these biofluids that meets or exceeds the performance of trained experts. We anticipate this tool will usher in high-throughput metabolomics and enable a wealth of new applications of NMR in

  19. Accurate, fully-automated NMR spectral profiling for metabolomics.

    Directory of Open Access Journals (Sweden)

    Siamak Ravanbakhsh

    Full Text Available Many diseases cause significant changes to the concentrations of small molecules (a.k.a. metabolites that appear in a person's biofluids, which means such diseases can often be readily detected from a person's "metabolic profile"-i.e., the list of concentrations of those metabolites. This information can be extracted from a biofluids Nuclear Magnetic Resonance (NMR spectrum. However, due to its complexity, NMR spectral profiling has remained manual, resulting in slow, expensive and error-prone procedures that have hindered clinical and industrial adoption of metabolomics via NMR. This paper presents a system, BAYESIL, which can quickly, accurately, and autonomously produce a person's metabolic profile. Given a 1D 1H NMR spectrum of a complex biofluid (specifically serum or cerebrospinal fluid, BAYESIL can automatically determine the metabolic profile. This requires first performing several spectral processing steps, then matching the resulting spectrum against a reference compound library, which contains the "signatures" of each relevant metabolite. BAYESIL views spectral matching as an inference problem within a probabilistic graphical model that rapidly approximates the most probable metabolic profile. Our extensive studies on a diverse set of complex mixtures including real biological samples (serum and CSF, defined mixtures and realistic computer generated spectra; involving > 50 compounds, show that BAYESIL can autonomously find the concentration of NMR-detectable metabolites accurately (~ 90% correct identification and ~ 10% quantification error, in less than 5 minutes on a single CPU. These results demonstrate that BAYESIL is the first fully-automatic publicly-accessible system that provides quantitative NMR spectral profiling effectively-with an accuracy on these biofluids that meets or exceeds the performance of trained experts. We anticipate this tool will usher in high-throughput metabolomics and enable a wealth of new applications of

  20. 1H-NMR, 1H-NMR T2-edited, and 2D-NMR in bipolar disorder metabolic profiling.

    Science.gov (United States)

    Sethi, Sumit; Pedrini, Mariana; Rizzo, Lucas B; Zeni-Graiff, Maiara; Mas, Caroline Dal; Cassinelli, Ana Cláudia; Noto, Mariane N; Asevedo, Elson; Cordeiro, Quirino; Pontes, João G M; Brasil, Antonio J M; Lacerda, Acioly; Hayashi, Mirian A F; Poppi, Ronei; Tasic, Ljubica; Brietzke, Elisa

    2017-12-01

    The objective of this study was to identify molecular alterations in the human blood serum related to bipolar disorder, using nuclear magnetic resonance (NMR) spectroscopy and chemometrics. Metabolomic profiling, employing 1H-NMR, 1H-NMR T2-edited, and 2D-NMR spectroscopy and chemometrics of human blood serum samples from patients with bipolar disorder (n = 26) compared with healthy volunteers (n = 50) was performed. The investigated groups presented distinct metabolic profiles, in which the main differential metabolites found in the serum sample of bipolar disorder patients compared with those from controls were lipids, lipid metabolism-related molecules (choline, myo-inositol), and some amino acids (N-acetyl-L-phenyl alanine, N-acetyl-L-aspartyl-L-glutamic acid, L-glutamine). In addition, amygdalin, α-ketoglutaric acid, and lipoamide, among other compounds, were also present or were significantly altered in the serum of bipolar disorder patients. The data presented herein suggest that some of these metabolites differentially distributed between the groups studied may be directly related to the bipolar disorder pathophysiology. The strategy employed here showed significant potential for exploring pathophysiological features and molecular pathways involved in bipolar disorder. Thus, our findings may contribute to pave the way for future studies aiming at identifying important potential biomarkers for bipolar disorder diagnosis or progression follow-up.

  1. NMR imaging and cryoporometry of swelling clays

    Science.gov (United States)

    Dvinskikh, Sergey V.; Szutkowski, Kosma; Petrov, Oleg V.; Furó, István.

    2010-05-01

    strength as well as investigating the effect of the confining geometry and material surface properties seem to be worth to pursue. Acknowledgements: This work has been supported by the Swedish Nuclear Fuel and Waste Management Co (SKB) and the Swedish Research Council VR. References: [1] Dvinskikh S. V., Szutkowski K., Furó I. MRI profiles over a very wide concentration ranges: application to swelling of a bentonite clay. J. Magn. Reson. 198, 146 (2009). [2] Petrov O. V., Furó I. NMR cryoporometry: Principles, applications and potential. Prog. Nucl. Magn. Reson. Spec. 54, 97 (2009).

  2. GC-MS and NMR analysis of the bioactive compounds from the crude extracts of Waltheria indica and the histopathological changes induced in albino rats challenged with Naja nigricollis venom

    Directory of Open Access Journals (Sweden)

    Philip Ilani

    2016-05-01

    Full Text Available Objective: To develop a characteristic fingerprint of the different chemical compounds of plant by gas chromatography-mass spectrometer (GC-MS and nuclear magnetic resonance (NMR analysis and assess the effect of the crude extract on histological changes induced in Naja nigricollis (N. nigricollis envenomed albino rats. Methods: The coarsely powdered Waltheria indica (W. indica whole plant material was extracted using 70% methanol. GC-MS analysis was carried out using a Shimadzu GC-MS QP 2010 plus system of gas chromatography interfaced to a mass spectrometer. The identification of components was based on National Institute of Standard and Technology-08 and Willey-8 libraries. Hydrogen-NMR spectra of the extracts was performed using Bruker Biospin Avance 400-MHz NMR spectrophotometer with a 5 mm broad inverse probe head, equipped with shielded z-gradient accessories and C-13 NMR hetero-nuclear single quantum correction was carried out using the Brucker’s standard pulse library. The efficacy of the crude extract of W. indica whole plant was tested and the lesions induced in the liver, brain and kidney of albino rats challenged with N. nigricollis were analyzed by light microscopy. Results: The identification of the bioactive compounds from W. indica by GC-MS analysis revealed 41 peaks. A total of 38 compounds were identified with majority having important pharmacological activities that included anti-microbial, anti-cancer, anti-oxidant antiinflammatory, anti-allergenic, anti-ageing, anti-arthritic, larvicidal, anti-convulsant and herbicidal activities. C-13 and hydrogen-NMR analysis of W. indica elucidated key bioactive compounds in the whole plant that were consistent with the classes of bioactive compounds detected by GC-MS analysis. The efficacy of the crude extract of W. indica whole plant in ameliorating histopathological lesions induced in the liver, brain and kidney of albino rats challenged with N. nigricollis venom revealed the

  3. NMR of a Phospholipid: Modules for Advanced Laboratory Courses

    Science.gov (United States)

    Gaede, Holly C.; Stark, Ruth E.

    2001-09-01

    A laboratory project is described that builds upon the NMR experience undergraduates receive in organic chemistry with a battery of NMR experiments that investigate egg phosphatidylcholine (egg PC). This material, often labeled in health food stores as lecithin, is a major constituent of mammalian cell membranes. The NMR experiments may be used to make resonance assignments, to study molecular organization in model membranes, to test the effects of instrumental parameters, and to investigate the physics of nuclear spin systems. A suite of modular NMR exercises is described, so that the instructor may tailor the laboratory sessions to biochemistry, instrumental analysis, or physical chemistry. The experiments include solution-state one-dimensional (1D) 1H, 13C, and 31P experiments; two-dimensional (2D) TOtal Correlated SpectroscopY (TOCSY); and the spectral editing technique of Distortionless Enhancement by Polarization Transfer (DEPT). To demonstrate the differences between solution and solid-state NMR spectroscopy and instrumentation, a second set of experiments generates 1H, 13C, and 31P spectra of egg PC dispersed in aqueous solution, under both static and magic-angle spinning conditions.

  4. First Principles NMR Study of Fluorapatite under Pressure

    Science.gov (United States)

    Pavan, Barbara; Ceresoli, Davide; Tecklenburg, Mary M. J.; Fornari, Marco

    2012-01-01

    NMR is the technique of election to probe the local properties of materials. Herein we present the results of density functional theory (DFT) ab initio calculations of the NMR parameters for fluorapatite (FAp), a calcium orthophosphate mineral belonging to the apatite family, by using the GIPAW method [Pickard and Mauri, 2001]. Understanding the local effects of pressure on apatites is particularly relevant because of their important role in many solid state and biomedical applications. Apatites are open structures, which can undergo complex anisotropic deformations, and the response of NMR can elucidate the microscopic changes induced by an applied pressure. The computed NMR parameters proved to be in good agreement with the available experimental data. The structural evaluation of the material behavior under hydrostatic pressure (from −5 to +100 kbar) indicated a shrinkage of the diameter of the apatitic channel, and a strong correlation between NMR shielding and pressure, proving the sensitivity of this technique to even small changes in the chemical environment around the nuclei. This theoretical approach allows the exploration of all the different nuclei composing the material, thus providing a very useful guidance in the interpretation of experimental results, particularly valuable for the more challenging nuclei such as 43Ca and 17O. PMID:22770669

  5. Application of fluorine NMR for structure identification of steroids.

    Science.gov (United States)

    Ampt, Kirsten A M; Aspers, Ruud L E G; Jaeger, Martin; Geutjes, Pepijn E T J; Honing, Maarten; Wijmenga, Sybren S

    2011-05-01

    Fluorinated steroids were examined using 1D and 2D homo- and heteronuclear (19)F NMR, such as (19)F-(1) H and (19)F-(13)C. The utilization of fluorine NMR accounted for spectral simplification and resulted in a straightforward pathway for the determination of structures including the configuration of these compounds; these steroids present an illustrative example for other types of fluorinated compounds, which are increasingly encountered in drug discovery. The potential of (19)F NMR is elaborated on in detail for two compounds containing diastereotopic fluorines with different coupling patterns. The analysis of the coupling patterns and the through-space interactions resulted in the determination of the structure and configuration. Heteronuclear correlation experiments, i.e. (19)F-(1)H HETCOR, (19)F-(13)C HMQC and HMBC, and (19)F-(1)H HOESY, were applied to determine first the relative stereochemistry and then the molecular configuration at C4 and C5 of a steroidal compound bearing a fused three-membered ring with two fluorine substituents. These examples proved (19)F NMR to be a useful addition to the extensively used (1)H and (13)C NMR within structure elucidation and configuration determination of small molecules. Copyright © 2011 John Wiley & Sons, Ltd.

  6. Theoretical Modeling of 99 Tc NMR Chemical Shifts

    Energy Technology Data Exchange (ETDEWEB)

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

    2016-09-06

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

  7. The NMR Probe of High-T$_{c}$ Materials

    CERN Document Server

    Walstedt, Russell E

    2008-01-01

    The NMR probe has yielded a vast array of data for the high-Tc materials, corresponding to different compounds, ionic sites, and nuclear species, as well as to a wide variety of experimental conditions. Over the twenty years, since the discovery of superconducting cuprates, ongoing analysis and discussion of cuprate NMR data have resulted in a wealth of important insights into the physics of these exotic systems. The aims of this monograph are threefold. First, it reviews NMR methodology as it has been applied to the cuprate studies. This is addressed to NMR practitioners and to physics laypersons alike. Next, it presents a review of cuprate NMR measurements and the wide variety of phenomena which they represent. The third phase is to recount the theoretical model calculations and other proposals which have been put forward to account for these data. Parts two and three are presented in parallel, as there are many aspects to both topics, each with its own interesting history. There is, even twenty years on, a...

  8. NMR Characterization of Flavanone Naringenin 7-O-Glycoside Diastereomer

    Directory of Open Access Journals (Sweden)

    SUN Li-juan

    2017-12-01

    Full Text Available To discriminate R and S flavanone glycoside using NMR, the mixture of R and S naringenin 7-O-glycoside was first isolated from Gleditsia sinensis. 1H and 13C NMR data of the mixture were recorded with 1H NMR, 13C NMR, 1H-1H COSY, 1H-13C HSQC and 1H-13C HMBC in DMSO-d6 solution. The two diastereomers were then separated with chiral chromatographic isolation, with their absolute configurations determined by circular dichroism. To avoid the disturbance of protons from glucose residues to dihydroflavonoid, 1H NMR spectra were acquired for pure R and S naringenin 7-O-glycoside and their mixture in CD3CN. The two diastereomers showed the largest proton chemical shift differences at the end group of glucose residue (H-1" with a chemical shift difference of 9.4 Hz. The OH-5 proton showed a chemical shift difference of 5.8 Hz. The chemical shift of the three protons on ring C were all influenced by configuration.

  9. The GNAT: a new tool for processing NMR data.

    Science.gov (United States)

    Castañar, Laura; Poggetto, Guilherme Dal; Colbourne, Adam; Morris, Gareth A; Nilsson, Mathias

    2018-02-02

    The GNAT (General NMR Analysis Toolbox) is a free and open-source software package for processing, visualizing and analysing NMR data. It supersedes the popular DOSY Toolbox, which has a narrower focus on diffusion NMR. Data import of most common formats from the major NMR platforms is supported, as well as a GNAT generic format. Key basic processing of NMR data (e.g. Fourier transformation, baseline correction, phasing) is catered for within the programme, as well as more advanced techniques (e.g. reference deconvolution, pure shift FID reconstruction). Analysis tools include DOSY and SCORE for diffusion data, ROSY T1 /T2 estimation for relaxation data, and PARAFAC for multilinear analysis. The GNAT is written for the MATLAB® language and comes with a user-friendly graphical user interface. The standard version is intended to run with a MATLAB installation, but completely free-standing compiled versions for Windows, Mac, and Linux are also freely available. This article is protected by copyright. All rights reserved.

  10. Selected topics in solution-phase biomolecular NMR spectroscopy

    Science.gov (United States)

    Kay, Lewis E.; Frydman, Lucio

    2017-05-01

    Solution bio-NMR spectroscopy continues to enjoy a preeminent role as an important tool in elucidating the structure and dynamics of a range of important biomolecules and in relating these to function. Equally impressive is how NMR continues to 'reinvent' itself through the efforts of many brilliant practitioners who ask increasingly demanding and increasingly biologically relevant questions. The ability to manipulate spin Hamiltonians - almost at will - to dissect the information of interest contributes to the success of the endeavor and ensures that the NMR technology will be well poised to contribute to as yet unknown frontiers in the future. As a tribute to the versatility of solution NMR in biomolecular studies and to the continued rapid advances in the field we present a Virtual Special Issue (VSI) that includes over 40 articles on various aspects of solution-state biomolecular NMR that have been published in the Journal of Magnetic Resonance in the past 7 years. These, in total, help celebrate the achievements of this vibrant field.

  11. Effective rotational correlation times of proteins from NMR relaxation interference

    Science.gov (United States)

    Lee, Donghan; Hilty, Christian; Wider, Gerhard; Wüthrich, Kurt

    2006-01-01

    Knowledge of the effective rotational correlation times, τc, for the modulation of anisotropic spin-spin interactions in macromolecules subject to Brownian motion in solution is of key interest for the practice of NMR spectroscopy in structural biology. The value of τc enables an estimate of the NMR spin relaxation rates, and indicates possible aggregation of the macromolecular species. This paper reports a novel NMR pulse scheme, [ 15N, 1H]-TRACT, which is based on transverse relaxation-optimized spectroscopy and permits to determine τc for 15N- 1H bonds without interference from dipole-dipole coupling of the amide proton with remote protons. [ 15N, 1H]-TRACT is highly efficient since only a series of one-dimensional NMR spectra need to be recorded. Its use is suggested for a quick estimate of the rotational correlation time, to monitor sample quality and to determine optimal parameters for complex multidimensional NMR experiments. Practical applications are illustrated with the 110 kDa 7,8-dihydroneopterin aldolase from Staphylococcus aureus, the uniformly 15N-labeled Escherichia coli outer membrane protein X (OmpX) in 60 kDa mixed OmpX/DHPC micelles with approximately 90 molecules of unlabeled 1,2-dihexanoyl- sn-glycero-3-phosphocholine (DHPC), and the 16 kDa pheromone-binding protein from Bombyx mori, which cover a wide range of correlation times.

  12. Time domain NMR evaluation of poly(vinyl alcohol xerogels

    Directory of Open Access Journals (Sweden)

    Elton Jorge da Rocha Rodrigues

    Full Text Available Abstract Poly(vinyl alcohol (PVA-based chemically cross-linked xerogels, both neat and loaded with nanoparticulate hydrophilic silica (SiO2, were obtained and characterized mainly through time domain NMR experiments (TD-NMR. Fourier-transform infrared (FT-IR and wide angle X-ray diffraction (WAXD analyses were employed as secondary methods. TD-NMR, through the interpretation of the spin-lattice relaxation constant values and related information, showed both cross-linking and nanoparticle influences on PVA matrix. SiO2 does not interact chemically with the PVA chains, but has effect on its molecular mobility, as investigated via TD-NMR. Apparent energy of activation, spin-lattice time constant and size of spin domains in the sample have almost linear dependence with the degree of cross-linking of the PVA and are affected by the addition of SiO2. These three parameters were derived from a single set of TD-NMR experiments, which demonstrates the versatility of the technique for characterization of inorganic-organic hybrid xerogels, an important class of materials.

  13. Study of cultured fibroblasts in vivo using NMR

    Energy Technology Data Exchange (ETDEWEB)

    Karczmar, G.S.

    1984-08-01

    The goal was to study the compartmentation of phosphorylated glycolytic intermediates in intact Chicken Embryo Fibroblasts (CEFs) using /sup 31/P NMR at 109 MHz. A technique for maintaining functional cells at high densities in an NMR magnet is described. Signals were detected from cytoplasmic inorganic phosphate (P/sub i/), ATP, NAD, NADH, phosphorylcholine and phosphorylethanolamine. The effect of external glucose on cytoplasmic pools of phosphates was studied. When cells were perfused with glucose-free medium the rate of glycolysis decreased, the amplitudes of the ATP resonances decreased, and the P/sub i/ intensity increased. The quantity of NMR-detectable P/sub i/ produced was significantly greater than the quantity of NMR-detectable ATP which was lost. Experiments with /sup 32/P labeled P/sub i/ showed that as the concentration of glucose in the medium was increase, the amount of phosphate sequestered in the cells increased. We conclude that there is a pool of P/sub i/ which is not detected by high resolution NMR and that the size of this pool increases as the rate of glycolysis increase. Longtitudinal relaxation times of intracellular phosphates in normal, transformed, and primary CEFs were measured. The results demonstrate that relaxation times of phosphates are sensitive to structural and metabolic changes which occur when cells are grown in culture. 59 references. 31 figures.

  14. Time domain NMR evaluation of poly(vinyl alcohol) xerogels

    Energy Technology Data Exchange (ETDEWEB)

    Rodrigues, Elton Jorge da Rocha; Cavalcante, Maxwell de Paula; Tavares, Maria Ines Bruno, E-mail: mibt@ima.ufrj.br [Universidade Federal do Rio de Janeiro (IMA/UFRJ), Rio de Janeiro, RJ (Brazil). Centro de Tecnologia. Instituto de Macromoleculas Professora Eloisa Mano

    2016-05-15

    Poly(vinyl alcohol) (PVA)-based chemically cross-linked xerogels, both neat and loaded with nanoparticulate hydrophilic silica (SiO{sub 2}), were obtained and characterized mainly through time domain NMR experiments (TD-NMR). Fourier-transform infrared (FT-IR) and wide angle X-ray diffraction (WAXD) analyses were employed as secondary methods. TD-NMR, through the interpretation of the spin-lattice relaxation constant values and related information, showed both cross-linking and nanoparticle influences on PVA matrix. SiO{sub 2} does not interact chemically with the PVA chains, but has effect on its molecular mobility, as investigated via TD-NMR. Apparent energy of activation, spin-lattice time constant and size of spin domains in the sample have almost linear dependence with the degree of cross-linking of the PVA and are affected by the addition of SiO{sub 2}. These three parameters were derived from a single set of TD-NMR experiments, which demonstrates the versatility of the technique for characterization of inorganic-organic hybrid xerogels, an important class of materials. (author)

  15. NMRFx Processor: a cross-platform NMR data processing program

    Energy Technology Data Exchange (ETDEWEB)

    Norris, Michael; Fetler, Bayard [One Moon Scientific, Inc. (United States); Marchant, Jan [University of Maryland Baltimore County, Howard Hughes Medical Institute (United States); Johnson, Bruce A., E-mail: bruce.johnson@asrc.cuny.edu [One Moon Scientific, Inc. (United States)

    2016-08-15

    NMRFx Processor is a new program for the processing of NMR data. Written in the Java programming language, NMRFx Processor is a cross-platform application and runs on Linux, Mac OS X and Windows operating systems. The application can be run in both a graphical user interface (GUI) mode and from the command line. Processing scripts are written in the Python programming language and executed so that the low-level Java commands are automatically run in parallel on computers with multiple cores or CPUs. Processing scripts can be generated automatically from the parameters of NMR experiments or interactively constructed in the GUI. A wide variety of processing operations are provided, including methods for processing of non-uniformly sampled datasets using iterative soft thresholding. The interactive GUI also enables the use of the program as an educational tool for teaching basic and advanced techniques in NMR data analysis.

  16. NMR-Metabolic Methodology in the Study of GM Foods

    Directory of Open Access Journals (Sweden)

    Irene D’Amico

    2010-01-01

    Full Text Available The 1H-NMR methodology used in the study of genetically modified (GM foods is discussed. Transgenic lettuce (Lactuca sativa cv "Luxor" over-expressing the Arabidopsis KNAT1 gene is presented as a case study. Twenty-two water-soluble metabolites (amino acids, organic acids, sugars present in leaves of conventional and GM lettuce were monitored by NMR and quantified at two developmental stages. The NMR spectra did not reveal any difference in metabolite composition between the GM lettuce and the wild type counterpart. Statistical analyses of metabolite variables highlighted metabolism variation as a function of leaf development as well as the transgene. A main effect of the transgene was in altering sugar metabolism.

  17. NMRFx Processor: a cross-platform NMR data processing program.

    Science.gov (United States)

    Norris, Michael; Fetler, Bayard; Marchant, Jan; Johnson, Bruce A

    2016-08-01

    NMRFx Processor is a new program for the processing of NMR data. Written in the Java programming language, NMRFx Processor is a cross-platform application and runs on Linux, Mac OS X and Windows operating systems. The application can be run in both a graphical user interface (GUI) mode and from the command line. Processing scripts are written in the Python programming language and executed so that the low-level Java commands are automatically run in parallel on computers with multiple cores or CPUs. Processing scripts can be generated automatically from the parameters of NMR experiments or interactively constructed in the GUI. A wide variety of processing operations are provided, including methods for processing of non-uniformly sampled datasets using iterative soft thresholding. The interactive GUI also enables the use of the program as an educational tool for teaching basic and advanced techniques in NMR data analysis.

  18. Variable-temperature NMR and conformational analysis of Oenothein B

    Energy Technology Data Exchange (ETDEWEB)

    Santos, Suzana C.; Carvalho, Ariadne G.; Fortes, Gilmara A.C.; Ferri, Pedro H.; Oliveira, Anselmo E. de, E-mail: suzana.quimica.ufg@hotmail.com [Universidade Federal de Goias (UFGO), Goiania, GO (Brazil). Instituto de Quimica

    2014-02-15

    Oenothein B is a dimeric hydrolyzable tannin with a wide range of biological activities, such as antitumour, anti-inflammatory and antiviral. Its nuclear magnetic resonance (NMR) at room temperature show duplications and broadening of signals. Experiments of 1D and 2D NMR at lower temperatures were useful for the complete NMR assignments of all hydrogens and carbons. The 3D structure of the most stable conformer was determined for the first time by nuclear Overhauser effect spectroscopy (NOESY) experiment (-20 deg C) and density functional theory (DFT)(B3LYP/6-31G)/ polarizable continuum model (PCM) quantum chemical calculations. The favoured conformation showed a highly compacted geometry and a lack of symmetry, in which the two valoneoyl groups showed distinct conformational parameters and stabilities. (author)

  19. RNA structure determination by solid-state NMR spectroscopy.

    Science.gov (United States)

    Marchanka, Alexander; Simon, Bernd; Althoff-Ospelt, Gerhard; Carlomagno, Teresa

    2015-05-11

    Knowledge of the RNA three-dimensional structure, either in isolation or as part of RNP complexes, is fundamental to understand the mechanism of numerous cellular processes. Because of its flexibility, RNA represents a challenge for crystallization, while the large size of cellular complexes brings solution-state NMR to its limits. Here, we demonstrate an alternative approach on the basis of solid-state NMR spectroscopy. We develop a suite of experiments and RNA labeling schemes and demonstrate for the first time that ssNMR can yield a RNA structure at high-resolution. This methodology allows structural analysis of segmentally labelled RNA stretches in high-molecular weight cellular machines—independent of their ability to crystallize—and opens the way to mechanistic studies of currently difficult-to-access RNA-protein assemblies.

  20. Unequivocal determination of complex molecular structures using anisotropic NMR measurements.

    Science.gov (United States)

    Liu, Yizhou; Saurí, Josep; Mevers, Emily; Peczuh, Mark W; Hiemstra, Henk; Clardy, Jon; Martin, Gary E; Williamson, R Thomas

    2017-04-07

    Assignment of complex molecular structures from nuclear magnetic resonance (NMR) data can be prone to interpretational mistakes. Residual dipolar couplings and residual chemical shift anisotropy provide a spatial view of the relative orientations between bonds and chemical shielding tensors, respectively, regardless of separation. Consequently, these data constitute a reliable reporter of global structural validity. Anisotropic NMR parameters can be used to evaluate investigators' structure proposals or structures generated by computer-assisted structure elucidation. Application of the method to several complex structure assignment problems shows promising results that signal a potential paradigm shift from conventional NMR data interpretation, which may be of particular utility for compounds not amenable to x-ray crystallography. Copyright © 2017, American Association for the Advancement of Science.

  1. A decade in prostate cancer: from NMR to metabolomics.

    Science.gov (United States)

    DeFeo, Elita M; Wu, Chin-Lee; McDougal, W Scott; Cheng, Leo L

    2011-05-17

    Over the past 30 years, continuous progress in the application of nuclear magnetic resonance (NMR) spectroscopy and magnetic resonance spectroscopic imaging (MRSI) to the detection, diagnosis and characterization of human prostate cancer has turned what began as scientific curiosity into a useful clinical option. In vivo MRSI technology has been integrated into the daily care of prostate cancer patients, and innovations in ex vivo methods have helped to establish NMR-based prostate cancer metabolomics. Metabolomic and multimodality imaging could be the future of the prostate cancer clinic--particularly given the rationale that more accurate interrogation of a disease as complex as human prostate cancer is most likely to be achieved through paradigms involving multiple, instead of single and isolated, parameters. The research and clinical results achieved through in vivo MRSI and ex vivo NMR investigations during the first 11 years of the 21st century illustrate areas where these technologies can be best translated into clinical practice.

  2. Ligand screening by saturation-transfer difference (STD) NMR spectroscopy.

    Energy Technology Data Exchange (ETDEWEB)

    Krishnan, V V

    2005-04-26

    NMR based methods to screen for high-affinity ligands have become an indispensable tool for designing rationalized drugs, as these offer a combination of good experimental design of the screening process and data interpretation methods, which together provide unprecedented information on the complex nature of protein-ligand interactions. These methods rely on measuring direct changes in the spectral parameters, that are often simpler than the complex experimental procedures used to study structure and dynamics of proteins. The goal of this review article is to provide the basic details of NMR based ligand-screening methods, with particular focus on the saturation transfer difference (STD) experiment. In addition, we provide an overview of other NMR experimental methods and a practical guide on how to go about designing and implementing them.

  3. Monitoring protein folding through high pressure NMR spectroscopy.

    Science.gov (United States)

    Roche, Julien; Royer, Catherine A; Roumestand, Christian

    2017-11-01

    High-pressure is a well-known perturbation method used to destabilize globular proteins. It is perfectly reversible, which is essential for a proper thermodynamic characterization of a protein equilibrium. In contrast to other perturbation methods such as heat or chemical denaturant that destabilize protein structures uniformly, pressure exerts local effects on regions or domains of a protein containing internal cavities. When combined with NMR spectroscopy, hydrostatic pressure offers the possibility to monitor at a residue level the structural transitions occurring upon unfolding and to determine the kinetic properties of the process. High-pressure NMR experiments can now be routinely performed, owing to the recent development of commercially available high-pressure sample cells. This review summarizes recent advances and some future directions of high-pressure NMR techniques for the characterization at atomic resolution of the energy landscape of protein folding. Copyright © 2017 Elsevier B.V. All rights reserved.

  4. Structural properties of carbon nanotubes derived from 13C NMR

    KAUST Repository

    Abou-Hamad, E.

    2011-10-10

    We present a detailed experimental and theoretical study on how structural properties of carbon nanotubes can be derived from 13C NMR investigations. Magic angle spinning solid state NMR experiments have been performed on single- and multiwalled carbon nanotubes with diameters in the range from 0.7 to 100 nm and with number of walls from 1 to 90. We provide models on how diameter and the number of nanotube walls influence NMR linewidth and line position. Both models are supported by theoretical calculations. Increasing the diameter D, from the smallest investigated nanotube, which in our study corresponds to the inner nanotube of a double-walled tube to the largest studied diameter, corresponding to large multiwalled nanotubes, leads to a 23.5 ppm diamagnetic shift of the isotropic NMR line position δ. We show that the isotropic line follows the relation δ = 18.3/D + 102.5 ppm, where D is the diameter of the tube and NMR line position δ is relative to tetramethylsilane. The relation asymptotically tends to approach the line position expected in graphene. A characteristic broadening of the line shape is observed with the increasing number of walls. This feature can be rationalized by an isotropic shift distribution originating from different diamagnetic shielding of the encapsulated nanotubes together with a heterogeneity of the samples. Based on our results, NMR is shown to be a nondestructive spectroscopic method that can be used as a complementary method to, for example, transmission electron microscopy to obtain structural information for carbon nanotubes, especially bulk samples.

  5. MetAssimulo: simulation of realistic NMR metabolic profiles.

    Science.gov (United States)

    Muncey, Harriet J; Jones, Rebecca; De Iorio, Maria; Ebbels, Timothy M D

    2010-10-06

    Probing the complex fusion of genetic and environmental interactions, metabolic profiling (or metabolomics/metabonomics), the study of small molecules involved in metabolic reactions, is a rapidly expanding 'omics' field. A major technique for capturing metabolite data is 1H-NMR spectroscopy and this yields highly complex profiles that require sophisticated statistical analysis methods. However, experimental data is difficult to control and expensive to obtain. Thus data simulation is a productive route to aid algorithm development. MetAssimulo is a MATLAB-based package that has been developed to simulate 1H-NMR spectra of complex mixtures such as metabolic profiles. Drawing data from a metabolite standard spectral database in conjunction with concentration information input by the user or constructed automatically from the Human Metabolome Database, MetAssimulo is able to create realistic metabolic profiles containing large numbers of metabolites with a range of user-defined properties. Current features include the simulation of two groups ('case' and 'control') specified by means and standard deviations of concentrations for each metabolite. The software enables addition of spectral noise with a realistic autocorrelation structure at user controllable levels. A crucial feature of the algorithm is its ability to simulate both intra- and inter-metabolite correlations, the analysis of which is fundamental to many techniques in the field. Further, MetAssimulo is able to simulate shifts in NMR peak positions that result from matrix effects such as pH differences which are often observed in metabolic NMR spectra and pose serious challenges for statistical algorithms. No other software is currently able to simulate NMR metabolic profiles with such complexity and flexibility. This paper describes the algorithm behind MetAssimulo and demonstrates how it can be used to simulate realistic NMR metabolic profiles with which to develop and test new data analysis techniques

  6. NMR Logging to Estimate Hydraulic Conductivity in Unconsolidated Aquifers.

    Science.gov (United States)

    Knight, Rosemary; Walsh, David O; Butler, James J; Grunewald, Elliot; Liu, Gaisheng; Parsekian, Andrew D; Reboulet, Edward C; Knobbe, Steve; Barrows, Mercer

    2016-01-01

    Nuclear magnetic resonance (NMR) logging provides a new means of estimating the hydraulic conductivity (K) of unconsolidated aquifers. The estimation of K from the measured NMR parameters can be performed using the Schlumberger-Doll Research (SDR) equation, which is based on the Kozeny-Carman equation and initially developed for obtaining permeability from NMR logging in petroleum reservoirs. The SDR equation includes empirically determined constants. Decades of research for petroleum applications have resulted in standard values for these constants that can provide accurate estimates of permeability in consolidated formations. The question we asked: Can standard values for the constants be defined for hydrogeologic applications that would yield accurate estimates of K in unconsolidated aquifers? Working at 10 locations at three field sites in Kansas and Washington, USA, we acquired NMR and K data using direct-push methods over a 10- to 20-m depth interval in the shallow subsurface. Analysis of pairs of NMR and K data revealed that we could dramatically improve K estimates by replacing the standard petroleum constants with new constants, optimal for estimating K in the unconsolidated materials at the field sites. Most significant was the finding that there was little change in the SDR constants between sites. This suggests that we can define a new set of constants that can be used to obtain high resolution, cost-effective estimates of K from NMR logging in unconsolidated aquifers. This significant result has the potential to change dramatically the approach to determining K for hydrogeologic applications. © 2015, National Ground Water Association.

  7. MetAssimulo:Simulation of Realistic NMR Metabolic Profiles

    Directory of Open Access Journals (Sweden)

    De Iorio Maria

    2010-10-01

    Full Text Available Abstract Background Probing the complex fusion of genetic and environmental interactions, metabolic profiling (or metabolomics/metabonomics, the study of small molecules involved in metabolic reactions, is a rapidly expanding 'omics' field. A major technique for capturing metabolite data is 1H-NMR spectroscopy and this yields highly complex profiles that require sophisticated statistical analysis methods. However, experimental data is difficult to control and expensive to obtain. Thus data simulation is a productive route to aid algorithm development. Results MetAssimulo is a MATLAB-based package that has been developed to simulate 1H-NMR spectra of complex mixtures such as metabolic profiles. Drawing data from a metabolite standard spectral database in conjunction with concentration information input by the user or constructed automatically from the Human Metabolome Database, MetAssimulo is able to create realistic metabolic profiles containing large numbers of metabolites with a range of user-defined properties. Current features include the simulation of two groups ('case' and 'control' specified by means and standard deviations of concentrations for each metabolite. The software enables addition of spectral noise with a realistic autocorrelation structure at user controllable levels. A crucial feature of the algorithm is its ability to simulate both intra- and inter-metabolite correlations, the analysis of which is fundamental to many techniques in the field. Further, MetAssimulo is able to simulate shifts in NMR peak positions that result from matrix effects such as pH differences which are often observed in metabolic NMR spectra and pose serious challenges for statistical algorithms. Conclusions No other software is currently able to simulate NMR metabolic profiles with such complexity and flexibility. This paper describes the algorithm behind MetAssimulo and demonstrates how it can be used to simulate realistic NMR metabolic profiles with

  8. Quantitating metabolites in protein precipitated serum using NMR spectroscopy.

    Science.gov (United States)

    Nagana Gowda, G A; Raftery, Daniel

    2014-06-03

    Quantitative NMR-based metabolite profiling is challenged by the deleterious effects of abundant proteins in the intact blood plasma/serum, which underscores the need for alternative approaches. Protein removal by ultrafiltration using low molecular weight cutoff filters thus represents an important step. However, protein precipitation, an alternative and simple approach for protein removal, lacks detailed quantitative assessment for use in NMR based metabolomics. In this study, we have comprehensively evaluated the performance of protein precipitation using methanol, acetonitrile, perchloric acid, and trichloroacetic acid and ultrafiltration approaches using 1D and 2D NMR, based on the identification and absolute quantitation of 44 human blood metabolites, including a few identified for the first time in the NMR spectra of human serum. We also investigated the use of a "smart isotope tag," (15)N-cholamine for further resolution enhancement, which resulted in the detection of a number of additional metabolites. (1)H NMR of both protein precipitated and ultrafiltered serum detected all 44 metabolites with comparable reproducibility (average CV, 3.7% for precipitation; 3.6% for filtration). However, nearly half of the quantified metabolites in ultrafiltered serum exhibited 10-74% lower concentrations; specifically, tryptophan, benzoate, and 2-oxoisocaproate showed much lower concentrations compared to protein precipitated serum. These results indicate that protein precipitation using methanol offers a reliable approach for routine NMR-based metabolomics of human blood serum/plasma and should be considered as an alternative to ultrafiltration. Importantly, protein precipitation, which is commonly used by mass spectrometry (MS), promises avenues for direct comparison and correlation of metabolite data obtained from the two analytical platforms to exploit their combined strength in the metabolomics of blood.

  9. Handbook of proton-NMR spectra and data index

    CERN Document Server

    Asahi Research Center Co, Ltd

    2013-01-01

    Handbook of Proton-NMR Spectra and Data: Index to Volumes 1-10 compiles four types of indexes used in charting the proton-NMR spectral database -Chemical Name Index, Molecular Formula Index, Substructure Index, and Chemical Shift Index. The Chemical Name Index compiles all chemical names in alphabetical order, followed by a spectrum number. When the desired organic compound cannot be found in the Chemical Name Index or its nomenclature is unclear, it becomes necessary to look for a compound by means of its molecular formula, hence the Molecular Formula Index. A unique notation system for repre

  10. Precision Measurements with a Dual Species NMR Oscillator

    Science.gov (United States)

    Sorensen, Susan; Thrasher, Daniel; Weber, Joshua; Korver, Anna; Walker, Thad

    2017-04-01

    We present progress towards a dual species nuclear magnetic oscillator using synchronous spin exchange optical pumping. By applying the bias field as a sequence of alkali 2 πn pulses, we generate alkali polarization transverse to the bias field. The alkali polarization is then modulated at the noble gas resonance so that through spin exchange collisions the noble gas becomes polarized. This novel method of NMR suppresses the alkali field frequency shift by at least a factor of 2500 as compared to longitudinal NMR. We will present a detailed noise analysis of the apparatus as well as plans for measuring earth's rotation. Research supported by the NSF and Northrop-Grumman Corp.

  11. MVAPACK: a complete data handling package for NMR metabolomics.

    Science.gov (United States)

    Worley, Bradley; Powers, Robert

    2014-05-16

    Data handling in the field of NMR metabolomics has historically been reliant on either in-house mathematical routines or long chains of expensive commercial software. Thus, while the relatively simple biochemical protocols of metabolomics maintain a low barrier to entry, new practitioners of metabolomics experiments are forced to either purchase expensive software packages or craft their own data handling solutions from scratch. This inevitably complicates the standardization and communication of data handling protocols in the field. We report a newly developed open-source platform for complete NMR metabolomics data handling, MVAPACK, and describe its application on an example metabolic fingerprinting data set.

  12. NMR STUDY OF MOLECULAR REFORIENTATION UNDER FIVEFOLD SYMMETRY SOLID PERMETHYLFERROCENE

    Energy Technology Data Exchange (ETDEWEB)

    Wemmer, D.E.; Ruben, D.J.; Pines, A.

    1980-08-01

    The ring reorientation in permethylferrocene has been studied using high resolution solid state {sup 13}C NMR. The constraints which symmetry places upon the number and types of motional parameters which may be determined from the NMR spectrum are discussed. From comparison of the experimental lineshapes in the slow reorientation temperatures range with theoretical models for random rotations and symmetry related jumps, it is concluded that the reorientation occurs as jumps between symmetry related orientations with jumps of 2{pi}/5 highly favored over 4{pi}/5. The activation energy derived for the jump process is 13.5 kjoules/mole.

  13. Combination of NMR relaxometry and mechanical testing during vulcanisation

    Energy Technology Data Exchange (ETDEWEB)

    Kahle, Stefan; Hehn, Manfred; Raich, Hans-Peter; Nussbaum, Walter; Bluemler, Peter; Wilhelm, Manfred

    2008-07-01

    A new design for an in-situ combination of NMR and rheological measurements is presented. The NMR is based on a BRUKER MINISPEC spectrometer. The magnet is self-made via a construction of 64 permanent magnets in a so called MANDHALA arrangement. The magnetic field strength reaches about 0.23 T, corresponding to a {sup 1}H resonance frequency of about 9.5 MHz. For the in-situ rheological measurements a Scarabaeus SISV50 instrument with modified sample cells is utilized. This unique combination and first measurements are presented.

  14. Use of NMR in profiling of cocaine seizures

    DEFF Research Database (Denmark)

    Pagano, Bruno; Lauri, Ilaria; De Tito, Stefano

    2013-01-01

    Cocaine is the most widely used illicit drug, and its origin is always the focus of intense investigation aimed at identifying the trafficking routes. Since NMR represents a unique methodology for performing chemical identification and quantification, here it is proposed a strategy based on (1)H...... NMR spectral analysis in conjunction with multivariate analysis to identify the chemical "fingerprint" of cocaine samples, and to link cocaine samples based on this information. The most relevant spectral regions containing the fingerprint have been identified: δH 0.86-0.96, 1.50-1.56, 5.90-5.93, 6...

  15. NMR spectroscopy applied to the eye: Drugs and metabolic studies

    Energy Technology Data Exchange (ETDEWEB)

    Saether, Oddbjoern

    2005-07-01

    NMR spectroscopy has been extensively applied in biomedical research during the last decades. It has proved to be an analytical tool of great value. From being mainly used in chemistry, technological developments have expanded the application of NMR spectroscopy to a great wealth of disciplines. With this method, biochemical information can be obtained by analysing tissue extracts. Moreover, NMR spectroscopy is increasingly employed for pharmacokinetic studies and analysis of biofluids. Technological progress has provided increased sensitivity and resolution in the spectra, which enable even more of the complexity of biological samples to be elucidated. With the implementation of high-resolution magic angle spinning (HR-MAS) NMR spectroscopy in biomedicine, intact tissue samples or biopsies can be investigated. Thus, NMR spectroscopy has an ever-increasing impact in metabolic screening of human samples and in animal models, and methods are also increasingly realised in vivo. The present work, NMR spectroscopy applied to eye research, consists of two main parts. Firstly, the feasibility to monitor fluorinated ophthalmic drugs directly in the eye was assessed. Secondly, HR-MAS H1 NMR spectroscopy was applied for metabolic profiling of the anterior eye segment, specifically to analyse metabolic changes in intact corneal and lenticular samples after cataractogenic insults. This work included metabonomics with the application of pattern recognition methods to analyse HR-MAS spectra of eye tissues. Optimisation strategies were explored for F19 NMR detection of fluorinated drugs in a phantom eye. S/N gains in F19 NMR spectroscopy were achieved by implementing time-share H1 decoupling at 2.35 T. The method is advantageous for compounds displaying broad spectral coupling patterns, though detection of drugs at concentrations encountered in the anterior eye segment after topical application was not feasible. Higher magnetic fields and technological improvements could enable

  16. De-noising methods for NMR logging echo signals based on wavelet transform

    Science.gov (United States)

    Xie, Ranhong; Wu, Youbin; Liu, Kang; Liu, Mi; Xiao, Lizhi

    2014-06-01

    The signal-to-noise ratio (SNR) of the echo signals in nuclear magnetic resonance (NMR) is one of the most important factors that affect the effective application of NMR logging. Wavelet transform can be used to remove the noise and improve the SNR of echo signals in NMR logging. This paper uses three de-noising methods to treat the NMR echo signals: modulus maxima, spatial correlation and wavelet threshold based on wavelet transform. The effects of the three methods in the noise reduction of NMR echo signals were compared by numerical simulation, core experiment and NMR logging data. The results show that while these three methods can all effectively improve the SNR of NMR echo signals and the NMR T2 inversion results, the most effective among them is the wavelet threshold method, which can obtain a higher SNR and provides more accurate formation porosity.

  17. 103Rh NMR spectroscopy and its application to rhodium chemistry.

    Science.gov (United States)

    Ernsting, Jan Meine; Gaemers, Sander; Elsevier, Cornelis J

    2004-09-01

    Rhodium is used for a number of large processes that rely on homogeneous rhodium-catalyzed reactions, for instance rhodium-catalyzed hydroformylation of alkenes, carbonylation of methanol to acetic acid and hydrodesulfurization of thiophene derivatives (in crude oil). Many laboratory applications in organometallic chemistry and catalysis involve organorhodium chemistry and a wealth of rhodium coordination compounds is known. For these and other areas, 103Rh NMR spectroscopy appears to be a very useful analytical tool. In this review, most of the literature concerning 103Rh NMR spectroscopy published from 1989 up to and including 2003 has been covered. After an introduction to several experimental methods for the detection of the insensitive 103Rh nucleus, a discussion of factors affecting the transition metal chemical shift is given. Computational aspects and calculations of chemical shifts are also briefly addressed. Next, the application of 103Rh NMR in coordination and organometallic chemistry is elaborated in more detail by highlighting recent developments in measurement and interpretation of 103Rh NMR data, in relation to rhodium-assisted reactions and homogeneous catalysis. The dependence of the 103Rh chemical shift on the ligands at rhodium in the first coordination sphere, on the complex geometry, oxidation state, temperature, solvent and concentration is treated. Several classes of compounds and special cases such as chiral rhodium compounds are reviewed. Finally, a section on scalar coupling to rhodium is provided. 2004 John Wiley & Sons, Ltd.

  18. Nondestructive NMR technique for moisture determination in radioactive materials.

    Energy Technology Data Exchange (ETDEWEB)

    Aumeier, S.; Gerald, R.E. II; Growney, E.; Nunez, L.; Kaminski, M.

    1998-12-04

    This progress report focuses on experimental and computational studies used to evaluate nuclear magnetic resonance (NMR) spectroscopy and magnetic resonance imaging (MRI) for detecting, quantifying, and monitoring hydrogen and other magnetically active nuclei ({sup 3}H, {sup 3}He, {sup 239}Pu, {sup 241}Pu) in Spent nuclear fuels and packaging materials. The detection of moisture by using a toroid cavity NMR imager has been demonstrated in SiO{sub 2} and UO{sub 2} systems. The total moisture was quantified by means of {sup 1}H NMR detection of H{sub 2}O with a sensitivity of 100 ppm. In addition, an MRI technique that was used to determine the moisture distribution also enabled investigators to discriminate between bulk and stationary water sorbed on the particles. This imaging feature is unavailable in any other nondestructive assay (NDA) technique. Following the initial success of this program, the NMR detector volume was scaled up from the original design by a factor of 2000. The capacity of this detector exceeds the size specified by DOE-STD-3013-96.

  19. FT-IR, NMR SPECTROSCOPIC and QUANTUM MECHANICAL ...

    African Journals Online (AJOL)

    predicting NMR properties and vibrational frequencies of the synthesized ferrocene based systems. KEY WORDS: .... solving self-consistent field equation iteratively and optimizations were performed without any molecular ..... symmetric stretching bands having various intensities at 2850 and 2926 cm. ) arise from CH2 ...

  20. Simultaneous acquisition of three NMR spectra in a single ...

    Indian Academy of Sciences (India)

    form (GFT) NMR spectroscopy, parallel data acquisition and non-uniform sampling. The following spectra are acquired ... experiments take minutes to hours to acquire, whereas. 3D experiments, which can take up to a few days, ... ing of 902 peaks reported to be present in the blood serum. The chemical shift values were ...

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

    Science.gov (United States)

    Berjanskii, Mark V; Wishart, David S

    2017-11-01

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

  2. NMR and NQR study of the thermodynamically stable quasicrystals

    Energy Technology Data Exchange (ETDEWEB)

    Shastri, Ananda [Iowa State Univ., Ames, IA (United States)

    1995-02-10

    27Al and 61,65Cu NMR measurements are reported for powder samples of stable AlCuFe and AlCuRu icosahedral quasicrystals and their crystalline approximants, and for a AlPdMn single grain quasicrystal. Furthermore, 27Al NQR spectra at 4.2 K have been observed in the AlCuFe and AlCuRu samples. From the quadrupole perturbed NMR spectra at different magnetic fields, and from the zero field NQR spectra, a wide distribution of local electric field gradient (EFG) tensor components and principal axis system orientations was found at the Al site. A model EFG calculation based on a 1/1 AlCuFe approximant was successful in explaining the observed NQR spectra. It is concluded that the average local gradient is largely determined by the p-electron wave function at the Al site, while the width of the distribution is due to the lattice contribution to the EFG. Comparison of 63Cu NMR with 27Al NMR shows that the EFG distribution at the two sites is similar, but that the electronic contribution to the EFG is considerably smaller at the Cu site, in agreement with a more s-type wave function of the conduction electrons.

  3. Ancient Roman wall paintings mapped nondestructively by portable NMR.

    Science.gov (United States)

    Haber, Agnes; Blümich, Bernhard; Souvorova, Daria; Del Federico, Eleonora

    2011-09-01

    The stratigraphies of decorated walls in ancient Herculaneum, Italy, were analyzed by single-sided (1)H NMR. A large version of the NMR-MOUSE® with a maximum penetration depth of 25 mm was used to map proton density profiles at different positions of the Mosaic of Neptune and Amphitrite showing considerable differences between different tesserae and the mortar bed at different times of the year. In the House of the Black Room, different mortar layers were observed on painted walls as well as different proton content in different areas due to different moisture levels and different conservation treatments. The proton density profiles of the differently treated areas indicated that one method leads to higher moisture content than the other. Untreated wall paintings from different times were profiled in a recently excavated room at the Villa of the Papyri showing two different types of mortar layer structures which identify two different techniques of preparing the walls for painting. Reflectance Fourier mid-infrared spectroscopy and in situ X-ray fluorescence measurements complemented the NMR measurements and provided additional insight into the identification of organic coatings as well as the nature of the pigments used, respectively. The information acquired nondestructively by NMR is valued for elaborating conservation strategies and for identifying different schools of craftsmen who prepared the mortar supports of the wall paintings.

  4. Numerical simulation of NQR/NMR: Applications in quantum computing.

    Science.gov (United States)

    Possa, Denimar; Gaudio, Anderson C; Freitas, Jair C C

    2011-04-01

    A numerical simulation program able to simulate nuclear quadrupole resonance (NQR) as well as nuclear magnetic resonance (NMR) experiments is presented, written using the Mathematica package, aiming especially applications in quantum computing. The program makes use of the interaction picture to compute the effect of the relevant nuclear spin interactions, without any assumption about the relative size of each interaction. This makes the program flexible and versatile, being useful in a wide range of experimental situations, going from NQR (at zero or under small applied magnetic field) to high-field NMR experiments. Some conditions specifically required for quantum computing applications are implemented in the program, such as the possibility of use of elliptically polarized radiofrequency and the inclusion of first- and second-order terms in the average Hamiltonian expansion. A number of examples dealing with simple NQR and quadrupole-perturbed NMR experiments are presented, along with the proposal of experiments to create quantum pseudopure states and logic gates using NQR. The program and the various application examples are freely available through the link http://www.profanderson.net/files/nmr_nqr.php. Copyright © 2011 Elsevier Inc. All rights reserved.

  5. Dynamics in photosynthetic transient complexes studied by paramagnetic NMR spectroscopy

    NARCIS (Netherlands)

    Scanu, Sandra

    2013-01-01

    This PhD thesis focuses on fundamental aspects of protein-protein interactions. A multidisciplinary methodology for the detection and visualization of transient, lowly-populated encounter protein complexes is described. The new methodology combined paramagnetic NMR spectroscopy with computational

  6. Solid-State NMR Spectroscopy for the Physical Chemistry Laboratory

    Science.gov (United States)

    Kinnun, Jacob J.; Leftin, Avigdor; Brown, Michael F.

    2013-01-01

    Solid-state nuclear magnetic resonance (NMR) spectroscopy finds growing application to inorganic and organic materials, biological samples, polymers, proteins, and cellular membranes. However, this technique is often neither included in laboratory curricula nor typically covered in undergraduate courses. On the other hand, spectroscopy and…

  7. Improved baseline in 29Si NMR spectra of water glasses.

    Science.gov (United States)

    Schraml, Jan; Sandor, Peter; Korec, Stefan; Krump, Martin; Foller, Bronislav

    2013-07-01

    It is shown by experiments that replacing one-pulse sequence by RIDE (ring down elimination) pulse sequence may dramatically improve the baseline of (29)Si NMR spectra and eliminate the signal from the probe. Copyright © 2013 John Wiley & Sons, Ltd.

  8. NMR-based screening of membrane protein ligands

    NARCIS (Netherlands)

    Yanamala, Naveena; Dutta, Arpana; Beck, Barbara; Van Fleet, Bart; Hay, Kelly; Yazbak, Ahmad; Ishima, Rieko; Doemling, Alexander; Klein-Seetharaman, Judith

    2010-01-01

    Membrane proteins pose problems for the application of NMR-based ligand-screening methods because of the need to maintain the proteins in a membrane mimetic environment such as detergent micelles: they add to the molecular weight of the protein, increase the viscosity of the solution, interact with

  9. Identification of Spinel Iron Oxide Nanoparticles by 57Fe NMR

    Directory of Open Access Journals (Sweden)

    SangGap Lee

    2011-12-01

    Full Text Available We have synthesized and studied monodisperse iron oxide nanoparticles of smaller than 10 nm to identify between the two spinel phases, magnetite and maghemite. It is shown that 57Fe NMR spectroscopy is a promising tool for distinguishing between the two phases.

  10. Supporting Information Synthesis and NMR Elucidation of Novel ...

    African Journals Online (AJOL)

    NICO

    1. Supporting Information. Synthesis and NMR Elucidation of Novel Octa-Amino Acid Resorcin[4]arenes derivatives. Iman Elidrisi,. [a]. Pralav V. Bhatt,. [b]. Thavendran Govender,. [b]. Hendrik G. Kruger,. [b] and. Glenn E. M. Maguire,. [a]. * a. School of Chemistry, University of KwaZulu--Natal, Westville Campus, Private Bag.

  11. Ab initio study, investigation of NMR shielding tensors, NBO and ...

    African Journals Online (AJOL)

    The bond lengths, bond angles, dipole moment, electron affinity, ionization potential, electronegativy, absolute hardness, highest occupied molecular orbital (HOMO) and the energy of the lowest unoccupied molecular orbital (LUMO) of the studied compounds were calculated in gas phase and water. NMR analysis of ...

  12. Novel Dodecaarylporphyrins: Synthesis and Variable Temperature NMR Studies

    Energy Technology Data Exchange (ETDEWEB)

    Cancilla, Mark; Lebrilla, Carlito; Ma, Jian-Guo; Medforth, Craig J.; Muzzi, Cinzia M.; Shelnutt, John A.; Smith, Kevin M.; Voss, Lisa

    1999-05-05

    An investigation of the synthesis of novel dodecaarylporphyrins using the Suzuki coupling reaction of arylboronic acids with octabromotetraarylporphyrins is reported. Studies of the dynamic properties of these new porphyrins using variable temperature (VT) 1H NMR spectroscopy and molecular mechanics provide interesting insights into their dynamic properties, including the first determination of {beta} aryl rotation in a porphyrin system.

  13. Detecting and Quantifying Organic Contaminants in Sediments with NMR

    Science.gov (United States)

    Fay, E. L.; Knight, R. J.

    2015-12-01

    Nuclear magnetic resonance (NMR) methods have the potential to detect and monitor free-phase organic contaminants in sediments, both in the laboratory and in the field. NMR directly detects signal from hydrogen-bearing fluids; the signal amplitude is proportional to the total amount of hydrogen present, while the signal decay rate provides information about fluid properties and interactions with the surrounding sediments. Contrasting relaxation times (T2) or diffusion coefficients (D) allow the separation of water signal from contaminant signal. In this work, we conduct a laboratory study to assess the use of NMR measurements to detect and quantify diesel, gasoline, crude oil, and tri-chloroethylene in sediments. We compare the T2 distributions for sediments containing only water, only contaminant, and both water and contaminant, confirming that the identification and quantification of contaminants using T2 data alone is limited by overlapping water and contaminant T2 distributions in some sediments. We leverage the contrast between the diffusion coefficient of water and that of diesel and crude oil to separate contaminant signal from water signal in D-T2 maps. D-T2 distributions are measured both using a pulsed gradient method and a static gradient method similar to methods used with logging tools, allowing us to compare the ability of each method to quantify diesel and crude oil when water is also present. There is the potential to apply these methods to characterize and monitor contaminated sites using commercially available NMR logging tools.

  14. NMR structural studies of protein-small molecule interactions

    NARCIS (Netherlands)

    Shah, Dipen M.

    2014-01-01

    The research presented in the thesis describes the development and implementation of solution based NMR methods that provide 3D structural information on the protein-small molecule complexes. These methods can be critical for structure based drug design and can be readily applied in the early stages

  15. NMR measurements on obliquely evaporated Co-Cr films

    NARCIS (Netherlands)

    Lodder, J.C.; van Kranenburg, H.; Takei, K.; Maeda, Y.

    1993-01-01

    The distribution of the hyperfine fields or the resonance frequencies in metals and alloys obtained by NMR measurements have been known for a long time. Recently, new experimental data have been published about thin films for studying their chemical inhomogeneities. An example is the study on

  16. [Sigma]-adducts of pyrimidines and pteridines : an NMR study

    NARCIS (Netherlands)

    Geerts, J.P.

    1978-01-01

    This thesis deals with the results obtained by an NMR investigation on anionic σ-adducts that are formed between a number of pyrimidines and potassium amide in liquid ammonia and the covalent addition complexes that are formed between a number of pteridines and liquid ammonia or

  17. Ligand-target interactions: what can we learn from NMR?

    Science.gov (United States)

    Carlomagno, Teresa

    2005-01-01

    The conformation of the ligand in complex with a macromolecular target can be studied by nuclear magnetic resonance (NMR) in solution for both tightly and weakly forming complexes. In the weak binding regime (k(off) > 10(4) Hz), the structure of the bound ligand is accessible also for very large complexes (>100 kDa), which are not amenable to NMR studies in the tight binding regime. Here I review the state-of-the-art NMR methodology used for screening ligands and for the structural investigation of bound ligand conformations, in both tight and weak binding regimes. The advantages and disadvantages of each approach are critically described. The NMR methodology used to investigate transiently forming complexes has expanded considerably in the past few years, opening new possibilities for a detailed description of ligand-target interactions. Novel methods for the determination of the bound ligand conformation, in particular transferred cross-correlated relaxation, are thoroughly reviewed, and their advantages with respect to established methodology are discussed, using the epothilone-tubulin complex as a primary example.

  18. NMR and the water-holding issue of pork.

    Science.gov (United States)

    Bertram, H C; Andersen, H J

    2007-11-01

    Consumers' awareness of food quality has never been more pronounced. Meat forms a substantial part of the food consumption, and accordingly techniques to control the quality of meat are needed. In addition, a better understanding of how basic biochemical and biophysical factors influence the final meat quality is also required for optimization of the quality. Water-holding capacity (WHC) is a major quality attribute of fresh meat. However, the exact mechanisms determining the WHC of meat are not fully understood. Especially, characteristics about proposed water populations in the meat and how they are interrelated with drip loss need to be studied further. Moreover, the distribution and mobility of water in muscle during its conversion to meat and how they are affected by intrinsic and extrinsic factors are poorly elucidated. Nuclear magnetic resonance (NMR) has during recent years gained increasing use within different areas of muscle physiology and meat science. NMR (1)H relaxation methodologies enable detection of the mobility of protons in heterogeneous materials and thereby provide possibilities for a characterization of the properties of water. The objective of this presentation is to give an overview of the use of NMR relaxation measurements to characterize the proposed water populations in meat and investigate how the distribution and mobility of the water changes postmortem. In addition, applications of NMR spectroscopy in metabolic studies will be considered.

  19. Study of cultured fibroblasts in vivo using NMR

    Energy Technology Data Exchange (ETDEWEB)

    Karczmar, G.S.

    1984-01-01

    The goal of this thesis was to study the compartmentation of phosphorylated glycolytic intermediates in intact Chicken Embryo Fibroblasts (CEFs) using /sup 31/P NMR at 109 MHz. Because glycolysis is regulated differently in normal and virally transformed CEFs, NMR experiments were performed on both types of cells. A technique for maintaining functional cells at high densities in an NMR magnet is described. Signals were detected from cytoplasmic inorganic phosphate (P/sub i/), ATP, NAD, NADH, phosphorylcholine and phosphorylethanolamine. The effect of external glucose on cytoplasmic pools of phosphates was studied. However, experiments with /sup 32/P labelled P/sub i/ showed that as the concentration of glucose in the medium was increased, the amount of phosphate sequestered in the cells increased. They conclude that there is a pool of P/sub i/ which is not detected by high resolution of NMR and that the size of this pool increases as the rate of glycolysis increases. These effects were found only in cultured cells; the data for transformed and normal cells were similar. Longitudinal relaxation times of intracellular phosphates in normal, transformed, and primary CEFs were measured.

  20. Recent excitements in protein NMR: Large proteins and biologically ...

    Indian Academy of Sciences (India)

    The advent of Transverse Relaxation Optimized SpectroscopY (TROSY) and perdeuteration allowed biomolecularNMR spectroscopists to overcome the size limitation barrier (~20 kDa) in de novo structure determination of proteins.The utility of these techniques was immediately demonstrated on large proteins and protein ...

  1. A primer to nutritional metabolomics by NMR spectroscopy and chemometrics

    DEFF Research Database (Denmark)

    Savorani, Francesco; Rasmussen, Morten Arendt; Mikkelsen, Mette Skau

    2013-01-01

    This paper outlines the advantages and disadvantages of using high throughput NMR metabolomics for nutritional studies with emphasis on the workflow and data analytical methods for generation of new knowledge. The paper describes one-by-one the major research activities in the interdisciplinary...

  2. Pulsed zero field NMR of solids and liquid crystals

    Energy Technology Data Exchange (ETDEWEB)

    Thayer, A.M.

    1987-02-01

    This work describes the development and applications to solids and liquid crystals of zero field nuclear magnetic resonance (NMR) experiments with pulsed dc magnetic fields. Zero field NMR experiments are one approach for obtaining high resolution spectra of amorphous and polycrystalline materials which normally (in high field) display broad featureless spectra. The behavior of the spin system can be coherently manipulated and probed in zero field with dc magnetic field pulses which are employed in a similar manner to radiofrequency pulses in high field NMR experiments. Nematic phases of liquid crystalline systems are studied in order to observe the effects of the removal of an applied magnetic field on sample alignment and molecular order parameters. In nematic phases with positive and negative magnetic susceptibility anisotropies, a comparison between the forms of the spin interactions in high and low fields is made. High resolution zero field NMR spectra of unaligned smectic samples are also obtained and reflect the symmetry of the liquid crystalline environment. These experiments are a sensitive measure of the motionally induced asymmetry in biaxial phases. Homonuclear and heteronuclear solute spin systems are compared in the nematic and smectic phases. Nonaxially symmetric dipolar couplings are reported for several systems. The effects of residual fields in the presence of a non-zero asymmetry parameter are discussed theoretically and presented experimentally. Computer programs for simulations of these and other experimental results are also reported. 179 refs., 75 figs.

  3. Contribution of proton NMR relaxation to the investigation of ...

    Indian Academy of Sciences (India)

    We present in this work a review concerning wide frequency range 1 proton NMR relaxation studies performed in compounds exhibiting columnar mesophases, namely the Colho mesophase in the case of a liquid crystal of discotic molecules and the h mesophase in the case of a liquid crystal of biforked molecules.

  4. NMR Probe for Electrons in Semiconductor Mesoscopic Structures

    Indian Academy of Sciences (India)

    2009-11-14

    Nov 14, 2009 ... Strongly correlated electron systems: Overview. Problem: How to detect the electronic state in nanoscale structures. Two examples where the usual methods don't work. Solution: We showed NMR techniques can be very useful in such circumstances. Outline ...

  5. Ordering in nematic liquid crystals from NMR cross-polarization ...

    Indian Academy of Sciences (India)

    2015-11-27

    Nov 27, 2015 ... The measurement of dipolar couplings between nuclei is a convenient way of obtatining directly liquid crystalline ordering through NMR since the coupling is dependent on the average orientation of the dipolar vector in the magnetic field which also aligns the liquid crystal. However, measurement of the ...

  6. Ordering in nematic liquid crystals from NMR cross-polarization ...

    Indian Academy of Sciences (India)

    Abstract. The measurement of dipolar couplings between nuclei is a convenient way of obtatining directly liquid crystalline ordering through NMR since the coupling is dependent on the average orientation of the dipolar vector in the magnetic field which also aligns the liquid crystal. However, measurement of the dipolar ...

  7. Structure of Coordination Complexes: The Synergy between NMR ...

    African Journals Online (AJOL)

    Illustrative examples of how NMR spectroscopy and computational chemistry data can be used in synergy to gain information on structure, coordination mode, bonding, symmetry and isomeric distribution of transition metal complexes, is presented. Isomer distribution and the most stable structures in a series of ...

  8. Graphical interpretation of Boolean operators for protein NMR assignments

    NARCIS (Netherlands)

    Verdegem, Dries; Dijkstra, Klaas; Hanoulle, Xavier; Lippens, Guy

    We have developed a graphics based algorithm for semi-automated protein NMR assignments. Using the basic sequential triple resonance assignment strategy, the method is inspired by the Boolean operators as it applies "AND"-, "OR"- and "NOT"-like operations on planes pulled out of the classical

  9. Evaluation of Thin Bed Using Resistivity Borehole and NMR Imaging ...

    African Journals Online (AJOL)

    To better characterize thin beds and maximize reservoir potential, the resistivity borehole imaging and NMR techniques were adopted in this research study. In addition, the Thomas Stieber equations using laminated sand-shale sequence were employed in calculating parameters such as sand porosity, hydrocarbon ...

  10. synthesis and nmr elucidation of novel pentacycloundecane derived ...

    African Journals Online (AJOL)

    NICO

    SYNTHESIS AND NMR ELUCIDATION OF NOVEL. PENTACYCLOUNDECANE DERIVED PEPTIDES. Rajshekhar Karpoormath, a. Oluseye K. Onajole, a. Thavendran Govender, b. Glenn E. M. Maguire, a and Hendrik G. Kruger a* a. School of Chemistry, University of KwaZulu-Natal, Durban 4001, South Africa b. School of ...

  11. Two-dimensional NMR studies of allyl palladium complexes of ...

    Indian Academy of Sciences (India)

    Administrator

    h3-Allyl complexes are intermediates in organic synthetic reactions such as allylic alkylation and amination. There is growing interest in understanding the structures of chiral h3-allyl intermediates as this would help to unravel the mechanism of enantioselective C–C bond forming reactions. Two-dimensional NMR study is a.

  12. Synthesis, IR and NMR spectral correlations in some symmetrical ...

    African Journals Online (AJOL)

    A series of diimines have been synthesized by coupling of diamine with substituted benzaldehydes. The purities of these diimines were checked by their analytical and spectroscopic data. The spectral frequencies νCN (cm-1), NMR chemical shifts (δ, ppm) of C-H and C=N of these diimines have been correlated with ...

  13. Adiabatic Low-Pass J Filters for Artifact Suppression in Heteronuclear NMR

    DEFF Research Database (Denmark)

    Meier, Sebastian; Benie, Andrew J; Duus, Jens Øllgaard

    2009-01-01

    NMR artifact purging: Modern NMR experiments depend on efficient coherence transfer pathways for their sensitivity and on suppression of undesired pathways leading to artifacts for their spectral clarity. A novel robust adiabatic element suppresses hard-to-get-at artifacts.......NMR artifact purging: Modern NMR experiments depend on efficient coherence transfer pathways for their sensitivity and on suppression of undesired pathways leading to artifacts for their spectral clarity. A novel robust adiabatic element suppresses hard-to-get-at artifacts....

  14. Unilateral NMR applied to the conservation of works of art.

    Science.gov (United States)

    Del Federico, Eleonora; Centeno, Silvia A; Kehlet, Cindie; Currier, Penelope; Stockman, Denise; Jerschow, Alexej

    2010-01-01

    In conventional NMR, samples from works of art in sizes above those considered acceptable in the field of art conservation would have to be removed to place them into the bore of large superconducting magnets. The portable permanent-magnet-based systems, by contrast, can be used in situ to study works of art, in a noninvasive manner. One of these portable NMR systems, NMR-MOUSE(R), measures the information contained in one pixel in an NMR image from a region of about 1 cm(2), which can be as thin as 2-3 microm. With such a high depth resolution, profiles through the structures of art objects can be measured to characterize the materials, the artists' techniques, and the deterioration processes. A novel application of the technique to study a deterioration process and to follow up a conservation treatment is presented in which micrometer-thick oil stains on paper are differentiated and characterized. In this example, the spin-spin relaxation T (2) of the stain is correlated to the iodine number and to the degree of cross-linking of the oil, parameters that are crucial in choosing an appropriate conservation treatment to remove them. It is also shown that the variation of T (2) over the course of treatments with organic solvents can be used to monitor the progress of the conservation interventions. It is expected that unilateral NMR in combination with multivariate data analysis will fill a gap within the set of high-spatial-resolution techniques currently available for the noninvasive analysis of materials in works of art, where procedures to study the inorganic components are currently far more developed than those suitable for the study of the organic components.

  15. Study of correlations in molecular motion by multiple quantum NMR

    Energy Technology Data Exchange (ETDEWEB)

    Tang, J.H.

    1981-11-01

    Nuclear magnetic resonance is a very useful tool for characterizing molecular configurations through the measurement of transition frequencies and dipolar couplings. The measurement of spectral lineshapes, spin-lattice relaxation times, and transverse relaxation times also provide us with valuable information about correlations in molecular motion. The new technique of multiple quantum nuclear magnetic resonance has numerous advantages over the conventional single quantum NMR techniques in obtaining information about static and dynamic interactions of coupled spin systems. In the first two chapters, the theoretical background of spin Hamiltonians and the density matrix formalism of multiple quantum NMR is discussed. The creation and detection of multiple quantum coherence by multiple pulse sequence are discussed. Prototype multiple quantum spectra of oriented benzene are presented. Redfield relaxation theory and the application of multiple quantum NMR to the study of correlations in fluctuations are presented. A specific example of an oriented methyl group relaxed by paramagnetic impurities is studied in detail. The study of possible correlated motion between two coupled methyl groups by multiple quantum NMR is presented. For a six spin system it is shown that the four-quantum spectrum is sensitive to two-body correlations, and serves a ready test of correlated motion. The study of the spin-lattice dynamics of orienting or tunneling methyl groups (CH/sub 3/ and CD/sub 3/) at low temperatures is presented. The anisotropic spin-lattice relaxation of deuterated hexamethylbenzene, caused by the sixfold reorientation of the molecules, is investigated, and the NMR spectrometers and other experimental details are discussed.

  16. NMR in natural products: understanding conformation, configuration and receptor interactions.

    Science.gov (United States)

    Carlomagno, Teresa

    2012-05-01

    Covering: up to 2011. Natural products are of tremendous importance in both traditional and modern medicine. For medicinal chemistry natural products represent a challenge, as their chemical synthesis and modification are complex processes, which require many, often stereo-selective, synthetic steps. A prerequisite for the design of analogs of natural products, with more accessible synthetic routes, is the availability of their bioactive conformation. Nuclear Magnetic Resonance (NMR) spectroscopy and X-ray crystallography are the two techniques of choice to investigate the structure of natural products. In this review, I describe the most recent advances in NMR to study the conformation of natural products either free in solution or bound to their cellular receptors. In chapter 2, I focus on the use of residual dipolar couplings (RDC). On the basis of a few examples, I discuss the benefit of complementing classical NMR parameters, such as NOEs and scalar couplings, with dipolar couplings to simultaneously determine both the conformation and the relative configuration of natural products in solution. Chapter 3 is dedicated to the study of the structure of natural products in complex with their cellular receptors and is further divided in two sections. In the first section, I describe two solution-state NMR methodologies to investigate the binding mode of low-affinity ligands to macromolecular receptors. The first approach, INPHARMA (Interligand Noes for PHArmacophore Mapping), is based on the observation of interligand NOEs between two small molecules binding competitively to a common receptor. INPHARMA reveals the relative binding mode of the two ligands, thus allowing ligand superimposition. The second approach is based on paramagnetic relaxation enhancement (PRE) of ligand resonances in the presence of a receptor containing a paramagnetic center. In the second section, I focus on solid-state NMR spectroscopy as a tool to access the bioactive conformation of

  17. NMR metabolomics for assessment of exercise effects with mouse biofluids

    Energy Technology Data Exchange (ETDEWEB)

    Le Moyec, Laurence; Mille-Hamard, Laurence; Breuneval, Carole; Petot, Helene; Billat, Veronique L. [Universite Evry Val d' Essonne, UBIAE INSERM U902, Evry Cedex (France); Triba, Mohamed N. [Universite Paris 13, CSPBAT UMR 7244, Bobigny (France)

    2012-08-15

    Exercise modulates the metabolome in urine or blood as demonstrated previously for humans and animal models. Using nuclear magnetic resonance (NMR) metabolomics, the present study compares the metabolic consequences of an exhaustive exercise at peak velocity (Vp) and at critical velocity (Vc) on mice. Since small-volume samples (blood and urine) were collected, dilution was necessary to acquire NMR spectra. Consequently, specific processing methods were applied before statistical analysis. According to the type of exercise (control group, Vp group and Vc group), 26 male mice were divided into three groups. Mice were sacrificed 2 h after the end of exercise, and urine and blood samples were drawn from each mouse. Proton NMR spectra were acquired with urine and deproteinized blood. The NMR data were aligned with the icoshift method and normalised using the probabilistic quotient method. Finally, data were analysed with the orthogonal projection of latent-structure analysis. The spectra obtained with deproteinized blood can neither discriminate the control mice from exercised mice nor discriminate according to the duration of the exercise. With urine samples, a significant statistical model can be estimated when comparing the control mice to both groups, Vc and Vp. The best model is obtained according to the exercise duration with all mice. Taking into account the spectral regions having the highest correlations, the discriminant metabolites are allantoin, inosine and branched-chain amino acids. In conclusion, metabolomic profiles assessed with NMR are highly dependent on the exercise. These results show that urine samples are more informative than blood samples and that the duration of the exercise is a more important parameter to influence the metabolomic status than the exercise velocity. (orig.)

  18. Structure elucidation and complete NMR spectral assignments of new furostanol glycosides from Solanum torvum.

    Science.gov (United States)

    Lu, Yuanyuan; Luo, Jianguang; Kong, Lingyi

    2009-09-01

    Two new furostanol glycosides, torvosides O (1) and P (2), were isolated from leaves of Solanum torvum. Their structures were completely and unambiguously assigned by one- and two-dimensional NMR techniques ((1)H NMR, (13)C NMR, TOCSY, HSQC, ROESY and HMBC), ESI-MS spectrometry and chemical methods. Copyright (c) 2009 John Wiley & Sons, Ltd.

  19. Fine-scale measurements of diffusivity in a microbial mat with NMR imaging

    NARCIS (Netherlands)

    Wieland, A.; Dusschoten, van D.; Damgaard, L.R.; Beer, de D.; Kuhl, M.; As, van H.

    2001-01-01

    Noninvasive 1H-nuclear magnetic resonance (NMR) imaging was used to investigate the diffusive properties of microbial mats in two dimensions. Pulsed field gradient NMR was used to acquire images of the H2O diffusion coefficient, Ds and multiecho imaging NMR was used to obtain images of the water

  20. LC-NMR coupling technology: recent advancements and applications in natural products analysis

    NARCIS (Netherlands)

    Exarchou, V.; Krucker, M.; Beek, van T.A.; Vervoort, J.J.M.; Gerothanassis, I.P.; Albert, K.

    2005-01-01

    An overview of recent advances in nuclear magnetic resonance (NMR) coupled with separation technologies and their application in natural product analysis is given and discussed. The different modes of LC-NMR operation are described, as well as how technical improvements assist in establishing LC-NMR

  1. A First Laboratory Utilizing NMR for Undergraduate Education: Characterization of Edible Fats and Oils by Quantitative [superscript 13]C NMR

    Science.gov (United States)

    Fry, Charles G.; Hofstetter, Heike; Bowman, Matthew D.

    2017-01-01

    Quantitative [superscript 13]C NMR provides a straightforward method of analyzing edible oils in undergraduate chemistry laboratories. [superscript 13]C spectra are relatively easy to understand, and are much simpler to analyze and workup than corresponding [superscript 1]H spectra. Average chain length, degree of saturation, and average…

  2. 1H NMR spectra dataset and solid-state NMR data of cowpea (Vigna unguiculata)

    DEFF Research Database (Denmark)

    Alves Filho, Elenilson G.; Silva, Lorena M. A.; Teofilo, Elizita M.

    2017-01-01

    In this article the NMR data from chemical shifts, coupling constants, and structures of all the characterized compounds were provided, beyond a complementary PCA evaluation for the corresponding manuscript (E.G. Alves Filho, L.M.A. Silva, E.M. Teofilo, F.H. Larsen, E.S. de Brito, 2017) [3]. In a...

  3. 71Ga-77Se connectivities and proximities in gallium selenide crystal and glass probed by solid-state NMR.

    Science.gov (United States)

    Nagashima, Hiroki; Trébosc, Julien; Calvez, Laurent; Pourpoint, Frédérique; Mear, François; Lafon, Olivier; Amoureux, Jean-Paul

    2017-09-01

    We introduce two-dimensional (2D) 71Ga-77Se through-bond and through-space correlation experiments. Such correlations are achieved using (i) the J-mediated Refocused Insensitive Nuclei Enhanced by Polarization Transfer (J-RINEPT) method with 71Ga excitation and 77Se Carr-Purcell-Meiboon-Gill (CPMG) detection, as well as (ii) the J- or dipolar-mediated Hetero-nuclear Multiple-Quantum Correlation (J- or D-HMQC) schemes with 71Ga excitation and quadrupolar CPMG (QCPMG) detection. These methods are applied to the crystalline β-Ga2Se3 and the 0.2Ga2Se3-0.8GeSe2 glass. Such glass leads to a homogeneous and reproducible glass-ceramic, which is a good alternative to single-crystalline Ge and polycrystalline ZnSe materials for making lenses transparent in the IR range for thermal imaging applications. We show that 2D 71Ga-77Se correlation experiments allow resolving the 77Se signals of molecular units, which are not resolved in the 1D 77Se CPMG spectrum. Additionally, the build-up curves of the J-RINEPT and the J-HMQC experiments allow the estimate of the 71Ga-77Se J-couplings via one and three-bonds in the three-dimensional network of β-Ga2Se3. Furthermore, these build-up curves show that the one-bond 1J71Ga-77Se couplings in the 0.2Ga2Se3-0.8GeSe2 glass are similar to those measured for β-Ga2Se3. We also report 2D 71Ga Satellite Transition Magic-Angle Spinning (STMAS) spectrum of β-Ga2Se3 using QCPMG detection at high magnetic field and high Magic-Angle Spinning frequency using large radio frequency field. Such spectrum allows separating the signal of β-Ga2Se3 and that of an impurity. Copyright © 2017 Elsevier Inc. All rights reserved.

  4. NightShift: NMR shift inference by general hybrid model training - a framework for NMR chemical shift prediction

    Science.gov (United States)

    2013-01-01

    Background NMR chemical shift prediction plays an important role in various applications in computational biology. Among others, structure determination, structure optimization, and the scoring of docking results can profit from efficient and accurate chemical shift estimation from a three-dimensional model. A variety of NMR chemical shift prediction approaches have been presented in the past, but nearly all of these rely on laborious manual data set preparation and the training itself is not automatized, making retraining the model, e.g., if new data is made available, or testing new models a time-consuming manual chore. Results In this work, we present the framework NightShift (NMR Shift Inference by General Hybrid Model Training), which enables automated data set generation as well as model training and evaluation of protein NMR chemical shift prediction. In addition to this main result – the NightShift framework itself – we describe the resulting, automatically generated, data set and, as a proof-of-concept, a random forest model called Spinster that was built using the pipeline. Conclusion By demonstrating that the performance of the automatically generated predictors is at least en par with the state of the art, we conclude that automated data set and predictor generation is well-suited for the design of NMR chemical shift estimators. The framework can be downloaded from https://bitbucket.org/akdehof/nightshift. It requires the open source Biochemical Algorithms Library (BALL), and is available under the conditions of the GNU Lesser General Public License (LGPL). We additionally offer a browser-based user interface to our NightShift instance employing the Galaxy framework via https://ballaxy.bioinf.uni-sb.de/. PMID:23496927

  5. NightShift: NMR shift inference by general hybrid model training--a framework for NMR chemical shift prediction.

    Science.gov (United States)

    Dehof, Anna Katharina; Loew, Simon; Lenhof, Hans-Peter; Hildebrandt, Andreas

    2013-03-16

    NMR chemical shift prediction plays an important role in various applications in computational biology. Among others, structure determination, structure optimization, and the scoring of docking results can profit from efficient and accurate chemical shift estimation from a three-dimensional model.A variety of NMR chemical shift prediction approaches have been presented in the past, but nearly all of these rely on laborious manual data set preparation and the training itself is not automatized, making retraining the model, e.g., if new data is made available, or testing new models a time-consuming manual chore. In this work, we present the framework NightShift (NMR Shift Inference by General Hybrid Model Training), which enables automated data set generation as well as model training and evaluation of protein NMR chemical shift prediction.In addition to this main result - the NightShift framework itself - we describe the resulting, automatically generated, data set and, as a proof-of-concept, a random forest model called Spinster that was built using the pipeline. By demonstrating that the performance of the automatically generated predictors is at least en par with the state of the art, we conclude that automated data set and predictor generation is well-suited for the design of NMR chemical shift estimators.The framework can be downloaded from https://bitbucket.org/akdehof/nightshift. It requires the open source Biochemical Algorithms Library (BALL), and is available under the conditions of the GNU Lesser General Public License (LGPL). We additionally offer a browser-based user interface to our NightShift instance employing the Galaxy framework via https://ballaxy.bioinf.uni-sb.de/.

  6. NMR Study of Rotational Tunneling in Solid Methanes.

    Science.gov (United States)

    Buchman, Saps

    This work describes a low temperature NMR study of methane and its deuterated modifications in a 7T magnetic field and at temperatures as low as 35mK. The deuteron NMR absorption line has been observed in the deuterated methanes in phase III, while the proton resonance was observed in CH(,4). Solid CD(,4) has been studied in the temperature range 35mK - 455mK. At the lower temperatures the area of the NMR absorption line shows an increase of up to 50% over that expected from the Curie law alone. This is interpreted as evidence for spin-species conversion associated with the thermal relaxation of an array of tunneling levels. The width of the NMR line increases at low temperatures, and this increase is consistent with the increase in the intermolecular second moment due to spin-species conversion. Our data are compared with tunneling level models developed on the basis of neutron scattering experiments. Measurements of the nuclear spin-lattice relaxation time and of the spin-species conversion time are also presented. For CHD(,3) the deuteron absorption line is strongly temperature dependent in the range 40mK - 700mK, and is completely narrowed at 4K. A tunneling level model is developed which reproduces the temperature dependence of the NMR lineshape. It is found that the lineshape is determined by the interaction of the quadrupolar moment of the deuterons with the gradient of the electric field of the molecular carbon-deuteron bond. The quadrupolar coupling constant is measured: e('2)qQ/h = 158 (+OR-) 8kHZ. It is found that spin-species conversion does not occur in CHD(,3) over a time scale of ten hours. The broadening of the absorption line is consistent with the size of the intramolecular dipolar interactions. The derivative NMR line in CH(,2)D(,2) in the temperature range 40mK - 70mK agrees with the predictions of a tunneling level model derived from neutron scattering and thermodynamic measurements. No CH(,3)D deuteron resonance line with satisfactory signal

  7. Miniature NMR spectrometer to analyse minerals at Mars

    Science.gov (United States)

    de Morais Mendonca Teles, Antonio

    There are some equipments and apparatuses for the study of interesting astrobiological places as planet Mars and moons Europa, Titan and Enceladus. As for Mars, some robotic missions have already analyzed its atmosphere and surface, using equipment with resolution down to milimetric scale. The NASA's Opportunity and Spirit rovers used microscope to study the sub-surface of the red planet at milimetric depth in drilled holes on rocks. In 1996, a NASA team announced the finding of organic molecules and morphological structures at nanometric scale, inside a meteorite which came from Mars. These possibly could be derived from an ancient Martian signature of biochemical activity, hypothetically, a fossilized `Archae-type' microorgan-ism. . In order to be acquired better resolutions for the mineralogical study of samples of its surface, it is necessary the use of nuclear magnetic resonance (NMR) spectrometers, with which one can obtain detailed astrobiological information below micrometer scale. NMR spectrome-ters are big equipment, but there are already miniature, lightweight, NMR spectrometers being developed which do not contain permanent magnets -they are designed to operate without applied magnetic fields; instead, they exploit the natural magnetic fields of the mineral phases (that contain iron) to be studied. These fields give rise to nuclear magnetic resonance of the isotope 57Fe at frequencies in the approximate range of 60 to 74 MHz. Such instrument has a mass of only 65 g (battery included) and consumes a power of only 0.2 W. It will be interesting the use of NMR spectroscopy at Mars. So, here in this paper, with the objective of the search for hypothetical extinct or extant life on Mars, I propose that in future robotic missions and a possible manned research at Mars, to be used miniature NMR spectrometers -rovers can have at the end of their robotic arms such those spectrometers and also astronauts can use those miniature NMR spectrometers to in-situ do very

  8. Determining petrophysical properties of low resistivity reservoirs using nuclear magnetic resonance (NMR) log

    Energy Technology Data Exchange (ETDEWEB)

    Hamada, G.M.; El-Blehed, M.S.; Al-Awad Musaed, N.J. [King Saud Univ., Riyadh (Saudi Arabia). Dept. of Petroleum Engineering

    1999-11-01

    The use of Nuclear Magnetic Resonance (NMR) to provide information on the productivity of low resistivity reservoirs and low resistivity contrast reservoirs was discussed. Resistivity logs have shown to be very effective in the evaluation of normal reservoirs. However, it has been shown that for low resistivity reservoirs it is very difficult to accurately determine the petrophysical parameters using conventional logs because it is difficult to determine water hydrocarbon contact. NMR has proven to be a very cost-effective tool to accurately determine the petrophysical properties of reservoir rock. When analysing NMR data, the following aspects of NMR techniques were used: (1) T1/T2 ratio for fluid identification, (2) the difference between NMR derived porosity and total porosity to determine the types of clay minerals, and (3) NMR relaxation properties to identify the fluids nature and rock properties. In this study, high contrast NMR identified the fluid nature of two formations and accurately identified the height of the oil column.

  9. Development of a micro flow-through cell for high field NMR spectroscopy.

    Energy Technology Data Exchange (ETDEWEB)

    Alam, Todd Michael; McIntyre, Sarah K.

    2011-05-01

    A highly transportable micro flow-through detection cell for nuclear magnetic resonance (NMR) spectroscopy has been designed, fabricated and tested. This flow-through cell allows for the direct coupling between liquid chromatography (LC) and gel permeation chromatography (GPC) resulting in the possibility of hyphenated LC-NMR and GPC-NMR. The advantage of the present flow cell design is that it is independent and unconnected to the detection probe electronics, is compatible with existing commercial high resolution NMR probes, and as such can be easily implemented at any NMR facility. Two different volumes were fabricated corresponding to between {approx}3.8 and 10 {micro}L detection volume. Examples of the performance of the cell on different NMR instruments, and using different NMR detection probes were demonstrated.

  10. Bioagent detection using miniaturized NMR and nanoparticle amplification : final LDRD report.

    Energy Technology Data Exchange (ETDEWEB)

    Clewett, C. F. M.; Adams, David Price; Fan, Hongyou; Williams, John D.; Sillerud, Laurel O.; Alam, Todd Michael; Aldophi, Natalie L. (New Mexico Resonance, Albuquerque, NM); McDowell, Andrew F. (New Mexico Resonance, Albuquerque, NM)

    2006-11-01

    This LDRD program was directed towards the development of a portable micro-nuclear magnetic resonance ({micro}-NMR) spectrometer for the detection of bioagents via induced amplification of solvent relaxation based on superparamagnetic nanoparticles. The first component of this research was the fabrication and testing of two different micro-coil ({micro}-coil) platforms: namely a planar spiral NMR {micro}-coil and a cylindrical solenoid NMR {micro}-coil. These fabrication techniques are described along with the testing of the NMR performance for the individual coils. The NMR relaxivity for a series of water soluble FeMn oxide nanoparticles was also determined to explore the influence of the nanoparticle size on the observed NMR relaxation properties. In addition, The use of commercially produced superparamagnetic iron oxide nanoparticles (SPIONs) for amplification via NMR based relaxation mechanisms was also demonstrated, with the lower detection limit in number of SPIONs per nanoliter (nL) being determined.

  11. The fluorescence properties and NMR analysis of protopine and allocryptopine

    Energy Technology Data Exchange (ETDEWEB)

    Kubala, Martin, E-mail: mkubala@prfnw.upol.c [Department of Biophysics, Faculty of Science, Palacky University, tr. 17. listopadu 12, CZ-77146 Olomouc (Czech Republic); Vacek, Jan [Department of Medical Chemistry and Biochemistry, Faculty of Medicine and Dentistry, Palacky University, Hnevotinska 3, CZ-77515 Olomouc (Czech Republic); Popa, Igor [Department of Inorganic Chemistry, Faculty of Science, Palacky University, tr. 17. listopadu 12, CZ-77146 Olomouc (Czech Republic); Janovska, Marika [Department of Biophysics, Faculty of Science, Palacky University, tr. 17. listopadu 12, CZ-77146 Olomouc (Czech Republic); Kosina, Pavel; Ulrichova, Jitka [Department of Medical Chemistry and Biochemistry, Faculty of Medicine and Dentistry, Palacky University, Hnevotinska 3, CZ-77515 Olomouc (Czech Republic); Travnicek, Zdenek [Department of Inorganic Chemistry, Faculty of Science, Palacky University, tr. 17. listopadu 12, CZ-77146 Olomouc (Czech Republic); Simanek, Vilim [Department of Medical Chemistry and Biochemistry, Faculty of Medicine and Dentistry, Palacky University, Hnevotinska 3, CZ-77515 Olomouc (Czech Republic)

    2011-07-15

    The fluorescence properties of protopine and allocryptopine in aqueous and organic environments are described for the first time. The fluorescence of alkaloids and their pH-dependent interconversion to cationic forms (transannular interaction) were studied using steady-state and time-resolved fluorescence techniques. For the analysis of tricyclic base and cis/trans tetracyclic cations of the alkaloids, NMR and X-ray crystallography were used. - Highlights: {yields} We describe fundamental fluorescence characteristics of alkaloids protopine and allocryptopine. {yields} We analyzed the pH-dependent transitions and cis/trans isomerization. {yields} These two alkaloids can be better distinguished by their fluorescence decay characteristics. {yields} The fluorescence parameters are related to the NMR and crystallographic structural data.

  12. Structure and Dynamic Properties of Membrane Proteins using NMR

    DEFF Research Database (Denmark)

    Rösner, Heike; Kragelund, Birthe

    2012-01-01

    conformational changes. Their structural and functional decoding is challenging and has imposed demanding experimental development. Solution nuclear magnetic resonance (NMR) spectroscopy is one of the techniques providing the capacity to make a significant difference in the deciphering of the membrane protein...... structure-function paradigm. The method has evolved dramatically during the last decade resulting in a plethora of new experiments leading to a significant increase in the scientific repertoire for studying membrane proteins. Besides solving the three-dimensional structures using state-of-the-art approaches......-populated states, this review seeks to introduce the vast possibilities solution NMR can offer to the study of membrane protein structure-function analyses with special focus on applicability. © 2012 American Physiological Society. Compr Physiol 2:1491-1539, 2012....

  13. Auto-tuning for NMR probe using LabVIEW

    Science.gov (United States)

    Quen, Carmen; Pham, Stephanie; Bernal, Oscar

    2014-03-01

    Typical manual NMR-tuning method is not suitable for broadband spectra spanning several megahertz linewidths. Among the main problems encountered during manual tuning are pulse-power reproducibility, baselines, and transmission line reflections, to name a few. We present a design of an auto-tuning system using graphic programming language, LabVIEW, to minimize these problems. The program uses a simplified model of the NMR probe conditions near perfect tuning to mimic the tuning process and predict the position of the capacitor shafts needed to achieve the desirable impedance. The tuning capacitors of the probe are controlled by stepper motors through a LabVIEW/computer interface. Our program calculates the effective capacitance needed to tune the probe and provides controlling parameters to advance the motors in the right direction. The impedance reading of a network analyzer can be used to correct the model parameters in real time for feedback control.

  14. Low-frequency NMR with a non-resonant circuit.

    Science.gov (United States)

    Hopper, Timothy; Mandal, Soumyajit; Cory, David; Hürlimann, Martin; Song, Yi-Qiao

    2011-05-01

    Nuclear magnetic resonance typically utilizes a tuned resonance circuit with impedance matching to transmit power and receive signal. The efficiency of such a tuned coil is often described in terms of the coil quality factor, Q. However, in field experiments such as in well-logging, the circuit Q can vary dramatically throughout the depth of the wellbore due to temperature or fluid salinity variations. Such variance can result in erroneous setting of NMR circuit parameters (tuning and matching) and subsequent errors in measurements. This paper investigates the use of a non-resonant transmitter to reduce the circuit sensitivity on Q and demonstrates that such circuits can be efficient in delivering power and current to the coil. We also describe a tuned receiver circuit whose resonant frequency can be controlled digitally. Experimental results show that a range of common NMR experiments can be performed with our circuits. Copyright © 2011 Elsevier Inc. All rights reserved.

  15. NMR Studies and Molecular Dynamic Simulation of Synthetic Dendritic Antigens

    Directory of Open Access Journals (Sweden)

    Ezequiel Perez-Inestrosa

    2011-09-01

    Full Text Available A series of synthetic benzylpenicillinoylated dendrimers has been prepared using up to 4th generation PAMAM dendrimers. These nanoconjugates, as nanosized Dendritic Antigens, are useful in the diagnostic evaluation of drug allergy due to specific molecular recognition with the Human Immunological System (IgE. The morphology and dimensions of the conjugates coupled to the orientation of the peripheral benzylpenicillin residues in the dendrimers may play key roles in such molecular recognition processes. Herein, the characterization and conformation of these structures are studied by a detailed analysis of 1D (1H and 13C NMR and 2D NMR (1H,1H-NOESY spectra. These dendrimers in explicit solvent were studied by the atomistic forcefield-based molecular dynamics. Structural properties such as shape, radius-of-gyration and distribution of the monomers will be discussed in relation to the experimental observations.

  16. Development and Investigation of NMR tools for chiral compound identification

    Energy Technology Data Exchange (ETDEWEB)

    Alam, Todd Michael [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States). Electronic, Optical and Nano Materials; Lansdon, Rick [Oak Ridge Inst. for Science and Education (ORISE), Oak Ridge, TN (United States)

    2014-09-01

    The goal behind the assigned summer project was to investigate the ability of nuclear magnetic resonance spectroscopy (NMR) to identify enantiomers of select chiral organo-fluorophosphates (OFPs) compounds which are analogs of chemical warfare agents (CWAs, e.g. Sarin). This involved investigations utilizing chiral solvating agents (CSAs) and characterizing the binding phenomena with cyclodextrins. The resolution of OFPs enantiomers using NMR would be useful for research into toxicodynamics and toxicokinetics in biological systems due to the widely differing properties of the CWA enantiomers [1]. The optimization of decontamination abilities in the case of a CWA events, with this method’s potential rapidity and robustness, as well as the development of models correlating chiral compounds with CSAs for optimal resolution are all rational benefits of this research.

  17. Study of β-NMR for Liquid Biological Samples

    CERN Document Server

    Beattie, Caitlin

    2017-01-01

    β-NMR is an exotic form of NMR spectroscopy that allows for the characterization of matter based on the anisotropic β-decay of radioactive probe nuclei. This has been shown to be an effective spectroscopic technique for many different compounds, but its use for liquid biological samples is relatively unexplored. The work at the VITO line of ISOLDE seeks to employ this technique to study such samples. Currently, preparations are being made for an experiment to characterize DNA G-quadruplexes and their interactions with stabilizing cations. More specifically, the work in which I engaged as a summer student focused on the experiment’s liquid handling system and the stability of the relevant biological samples under vacuum.

  18. Monitoring Cocrystal Formation via In Situ Solid-State NMR.

    Science.gov (United States)

    Mandala, Venkata S; Loewus, Sarel J; Mehta, Manish A

    2014-10-02

    A detailed understanding of the mechanism of organic cocrystal formation remains elusive. Techniques that interrogate a reacting system in situ are preferred, though experimentally challenging. We report here the results of a solid-state in situ NMR study of the spontaneous formation of a cocrystal between a pharmaceutical mimic (caffeine) and a coformer (malonic acid). Using (13)C magic angle spinning NMR, we show that the formation of the cocrystal may be tracked in real time. We find no direct evidence for a short-lived, chemical shift-resolved amorphous solid intermediate. However, changes in the line width and line center of the malonic acid methylene resonance, in the course of the reaction, provide subtle clues to the mode of mass transfer that underlies cocrystal formation.

  19. Structural analysis of teicoplanin A2 by 2d NMR

    Science.gov (United States)

    Heald, Sarah L.; Mueller, Luciano; Jeffs, Peter W.

    The analysis of the intact glycopeptide antibiotic, teicoplanin A 2, by two-dimensional proton NMR is described. Delayed-correlation spectroscopy (COSY), double-quantum coherence experiments (DACE), and nuclear Overhauser spectroscopy (NOESY) are utilized to confirm the primary structure. Distance constraints derived from NOESY data integrated with computer-assisted molecular modeling and force-field energy minimization yields a proposed three-dimensional solution-state conformation. Included are NMR methods developed for improved accuracy of distance measurements from 2D NOE experiments obtained on samples dissolved in DMSO- d6/water. The effects of different pulse sequences for water suppression on the 2D NOE spectral results are compared. Clear indication that teicoplanin exists in two unequally populated conformations which are in slow exchange is revealed by the presence of cross peaks attributable to conformational interchange in the NOESY spectra.

  20. Susceptibility-matched plugs for microcoil NMR probes

    Science.gov (United States)

    Kc, Ravi; Gowda, Yashas N.; Djukovic, Danijel; Henry, Ian D.; Park, Gregory H. J.; Raftery, Daniel

    2010-07-01

    For mass-limited samples, the residual sample volume outside the detection coil is an important concern, as is good base line resolution. Here, we present the construction and evaluation of magnetic susceptibility-matched plugs for microcoil NMR sample cells which address these issues. Mixed-epoxy glue and ultem tube plugs that have susceptibility values close to those of perfluorocarbon FC-43 (fluorinert) and copper were used in small volume (0.5-2 μL) and larger volume (15-20 μL) thin glass capillary sample cells. Using these plugs, the sample volume efficiency (i.e. ratio of active volume to total sample volume in the microcoil NMR cell) was improved by 6-12-fold without sensitivity and resolution trade-offs. Comparison with laser etched or heat etched microcoil sample cells is provided. The approaches described are potentially useful in metabolomics for biomarkers detection in mass limited biological samples.

  1. NMR metabolomics of human blood and urine in disease research.

    Science.gov (United States)

    Duarte, Iola F; Diaz, Sílvia O; Gil, Ana M

    2014-05-01

    This paper reviews the main applications of NMR metabolomics of blood and urine in disease research, over the last 5 years. The broad range of disease types addressed attests the increasing interest within the academic and medical communities to explore the recognised potential of metabolomics to (1) provide insight into underlying disease pathogenesis and (2) unveil new metabolic markers for disease diagnosis and follow up. Importantly, most recent studies reveal an increasing awareness of possible limitations and pitfalls of the metabolomics approach, together with efforts for improved study design and statistical validation, which are crucial requisites for the sound development of NMR metabolomics and its progress into the clinical setting. Copyright © 2013 Elsevier B.V. All rights reserved.

  2. $^{31}$Mg $\\beta$-NMR applied in chemistry and biochemistry

    CERN Multimedia

    Magnesium ions, Mg$^{2+}$, are essential in biological systems, taking part in practically all phosphate chemistry, in photosynthesis as an integral component of chlorophyll, and they are regulated via transport through selective membrane proteins. Nonetheless, the function of magnesium ions in biochemistry is difficult to characterize, as it is practically invisible to current experimental techniques. With this proposal we aim to advance the use of $^{31}$Mg $\\beta$-NMR to liquid samples, building on the experience from the successful Letter of Intent INTC-I-088 “$\\beta$-NMR as a novel technique for biological applications”. Initially a series of experiments will be conducted aiming to characterize the coordination chemistry of Mg$^{2+}$ in ionic liquids (ILs), demonstrating that it is possible within the lifetime of the radioisotope to achieve binding of Mg$^{2+}$ to a molecule dissolved in the IL. ILs are chosen as they display a very low vapor pressure, and are thus straightforwardly compatible with t...

  3. Theoretical and experimental study of 15N NMR protonation shifts.

    Science.gov (United States)

    Semenov, Valentin A; Samultsev, Dmitry O; Krivdin, Leonid B

    2015-06-01

    A combined theoretical and experimental study revealed that the nature of the upfield (shielding) protonation effect in 15N NMR originates in the change of the contribution of the sp(2)-hybridized nitrogen lone pair on protonation resulting in a marked shielding of nitrogen of about 100 ppm. On the contrary, for amine-type nitrogen, protonation of the nitrogen lone pair results in the deshielding protonation effect of about 25 ppm, so that the total deshielding protonation effect of about 10 ppm is due to the interplay of the contributions of adjacent natural bond orbitals. A versatile computational scheme for the calculation of 15N NMR chemical shifts of protonated nitrogen species and their neutral precursors is proposed at the density functional theory level taking into account solvent effects within the supermolecule solvation model. Copyright © 2015 John Wiley & Sons, Ltd.

  4. Computational Protocols for Prediction of Solute NMR Relative Chemical Shifts

    DEFF Research Database (Denmark)

    Eriksen, Janus Juul; Olsen, Jógvan Magnus Haugaard; Aidas, Kestutis

    2011-01-01

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

  5. NMR structure of the HIV-1 reverse transcriptase thumb subdomain

    Energy Technology Data Exchange (ETDEWEB)

    Sharaf, Naima G. [University of Pittsburgh, School of Medicine, Department of Structural Biology and Pittsburgh Center for HIV Protein Interactions (United States); Brereton, Andrew E. [Oregon State University, Department of Biochemistry and Biophysics, 2011 Ag & Life Sciences Bldg (United States); Byeon, In-Ja L. [University of Pittsburgh, School of Medicine, Department of Structural Biology and Pittsburgh Center for HIV Protein Interactions (United States); Andrew Karplus, P. [Oregon State University, Department of Biochemistry and Biophysics, 2011 Ag & Life Sciences Bldg (United States); Gronenborn, Angela M., E-mail: amg100@pitt.edu [University of Pittsburgh, School of Medicine, Department of Structural Biology and Pittsburgh Center for HIV Protein Interactions (United States)

    2016-12-15

    The solution NMR structure of the isolated thumb subdomain of HIV-1 reverse transcriptase (RT) has been determined. A detailed comparison of the current structure with dozens of the highest resolution crystal structures of this domain in the context of the full-length enzyme reveals that the overall structures are very similar, with only two regions exhibiting local conformational differences. The C-terminal capping pattern of the αH helix is subtly different, and the loop connecting the αI and αJ helices in the p51 chain of the full-length p51/p66 heterodimeric RT differs from our NMR structure due to unique packing interactions in mature RT. Overall, our data show that the thumb subdomain folds independently and essentially the same in isolation as in its natural structural context.

  6. Double rotation NMR studies of zeolites and aluminophosphate molecular sieves

    Energy Technology Data Exchange (ETDEWEB)

    Jelinek, Raz [Univ. of California, Berkeley, CA (United States)

    1993-07-01

    Goal is to study the organization and structures of guest atoms and molecules and their reactions on internal surfaces within pores of zeolites and aluminophosphate molecular sieves. 27Al and 23Na double rotation NMR (DOR) is used since it removes the anisotropic broadening in NMR spectra of quadrupolar nuclei, thus increasing resolution. This work concentrates on probing aluminum framework atoms in aluminophosphate molecular sieves and sodium extra framework cations in porous aluminosilicates. In aluminophosphates, ordering and electronic environments of the framework 27Al nuclei are modified upon adsorption of water molecules within the channels; a relation is sought between the sieve channel topology and the organization of adsorbed water, as well as the interaction between the Al nuclei and the water molecules. Extra framework Na+ cations are directly involved in adsorption processes and reactions in zeolite cavities.

  7. 19F-NMR study of fluorinated corticosteroids

    Science.gov (United States)

    Joseph-Nathan, P.; Espñeira, J.; Santillan, R. L.

    19F-NMR measurements of fluorinated corticosteroids by continuous wave time averaging at 94.1 MHz allowed specific spectral determination of the highly insoluble underivatized compounds. The wide range of chemical shifts as well as observation of 1H 19F coupling constants evidences the potential inherent in this technique for the conformational analysis of the B ring of this type of molecule.

  8. Quantitative 1D saturation profiles on chalk by NMR

    DEFF Research Database (Denmark)

    Olsen, Dan; Topp, Simon; Stensgaard, Anders

    1996-01-01

    Quantitative one-dimensional saturation profiles showing the distribution of water and oil in chalk core samples are calculated from NMR measurements utilizing a 1D CSI spectroscopy pulse sequence. Saturation profiles may be acquired under conditions of fluid flow through the sample. Results reveal...... that strong saturation gradients exist in chalk core samples after core floods, due to capillary effects. The method is useful in analysis of corefloods, e.g., for determination of capillary pressure functions...

  9. Study of an organogelator by diffusion-ordered NMR spectroscopy.

    Science.gov (United States)

    Dama, Murali; Berger, Stefan

    2013-05-09

    The low-molecular weight organogelator 2,3-di-n-decyloxyanthracene was synthezised and dissolved in dimethyl sulfoxide. With diffusion-ordered NMR spectroscopy, the temperature dependence of the diffusion coefficients was measured and a clear hysteresis of the gelation was observed between 320 and 330 K. This hysteresis was interpreted with respect to different entanglement behavior on heating and cooling. No alignment of the gelator with respect to the magnetic field was found despite its 14 π-electrons.

  10. NMR Studies of Lithium Iodide Based Solid Electrolytes

    DEFF Research Database (Denmark)

    Dupree, R.; Howells, R. J.; Hooper, A.

    1983-01-01

    In mixture of LiI with γAl2O3 the ionic conductivity is found to increase by up to three orders of magnitude over pure LiI. NMR measurements of7Li relaxation times were performed on both anhydrous LiI and a mixture of LiI with 30m/o γAl2O3. The relaxation is found to be purely dipolar in origin f...

  11. NMR clinical imaging and spectroscopy: Its impact on nuclear medicine

    Energy Technology Data Exchange (ETDEWEB)

    1990-02-02

    This is a collection of four papers describing aspects of past and future use of nuclear magnetic resonance as a clinical diagnostic tool. The four papers are entitled (1) What Does NMR Offer that Nuclear Medicine Does Not? by Jerry W. Froelich, (2) Oncological Imaging: Now, Future and Impact Jerry W. Froelich, (3) Magnetic Resonance Spectroscopy/Spectroscopic Imaging and Nuclear Medicine: Past, Present and Future by H. Cecil Charles, and (4) MR Cardiology: Now, Future and Impact by Robert J. Herfkens.

  12. NMR clinical imaging and spectroscopy: Its impact on nuclear medicine

    Energy Technology Data Exchange (ETDEWEB)

    1990-02-02

    This is a collection of four papers describing aspects of past and future use of nuclear magnetic resonance as a clinical diagnostic tool. The four papers are entitled (1) What Does NMR Offer that Nuclear Medicine Does Not by Jerry W. Froelich, (2) Oncological Imaging: Now, Future and Impact Jerry W. Froelich, (3) Magnetic Resonance Spectroscopy/Spectroscopic Imaging and Nuclear Medicine: Past, Present and Future by H. Cecil Charles, and (4) MR Cardiology: Now, Future and Impact by Robert J. Herfkens.

  13. Conformational analysis of protein structures derived from NMR data.

    Science.gov (United States)

    MacArthur, M W; Thornton, J M

    1993-11-01

    A study is presented of the conformational characteristics of NMR-derived protein structures in the Protein Data Bank compared to X-ray structures. Both ensemble and energy-minimized average structures are analyzed. We have addressed the problem using the methods developed for crystal structures by examining the distribution of phi, psi, and chi angles as indicators of global conformational irregularity. All these features in NMR structures occur to varying degrees in multiple conformational states. Some measures of local geometry are very tightly constrained by the methods used to generate the structure, e.g., proline phi angles, alpha-helix phi,psi angles, omega angles, and C alpha chirality. The more lightly restrained torsion angles do show increased clustering as the number of overall experimental observations increases. phi, psi, and chi 1 angle conformational heterogeneity is strongly correlated with accessibility but shows additional differences which reflect the differing number of observations possible in NMR for the various side chains (e.g., many for Trp, few for Ser). In general, we find that the core is defined to a notional resolution of 2.0 to 2.3 A. Of real interest is the behavior of surface residues and in particular the side chains where multiple rotameric states in different structures can vary from 10% to 88%. Later generation structures show a much tighter definition which correlates with increasing use of J-coupling information, stereospecific assignments, and heteronuclear techniques. A suite of programs is being developed to address the special needs of NMR-derived structures which will take into account the existence of increased mobility in solution.

  14. NMR methods for the investigation of structure and transport

    CERN Document Server

    Hardy, Edme H

    2011-01-01

    Methods of nuclear magnetic resonance (NMR) are increasingly applied in engineering sciences. The book summarizes research in the field of chemical and process engineering performed at the Karlsruhe Institute of Technology (KIT). Fundamentals of the methods are exposed for readers with an engineering background. Applications cover the fields of mechanical process engineering (filtration, solid-liquid separation, powder mixing, rheometry), chemical process engineering (trickle-bed reactor, ceramic sponges), bioprocess engineering (biofilm growth), and food process engineering (microwave heating

  15. Inverse problem for in vivo NMR spatial localization

    Energy Technology Data Exchange (ETDEWEB)

    Hasenfeld, A.C.

    1985-11-01

    The basic physical problem of NMR spatial localization is considered. To study diseased sites, one must solve the problem of adequately localizing the NMR signal. We formulate this as an inverse problem. As the NMR Bloch equations determine the motion of nuclear spins in applied magnetic fields, a theoretical study is undertaken to answer the question of how to design magnetic field configurations to achieve these localized excited spin populations. Because of physical constraints in the production of the relevant radiofrequency fields, the problem factors into a temporal one and a spatial one. We formulate the temporal problem as a nonlinear transformation, called the Bloch Transform, from the rf input to the magnetization response. In trying to invert this transformation, both linear (for the Fourier Transform) and nonlinear (for the Bloch Transform) modes of radiofrequency excitation are constructed. The spatial problem is essentially a statics problem for the Maxwell equations of electromagnetism, as the wavelengths of the radiation considered are on the order of ten meters, and so propagation effects are negligible. In the general case, analytic solutions are unavailable, and so the methods of computer simulation are used to map the rf field spatial profiles. Numerical experiments are also performed to verify the theoretical analysis, and experimental confirmation of the theory is carried out on the 0.5 Tesla IBM/Oxford Imaging Spectrometer at the LBL NMR Medical Imaging Facility. While no explicit inverse is constructed to ''solve'' this problem, the combined theoretical/numerical analysis is validated experimentally, justifying the approximations made. 56 refs., 31 figs.

  16. Optimized "detectors" for dynamics analysis in solid-state NMR

    Science.gov (United States)

    Smith, Albert A.; Ernst, Matthias; Meier, Beat H.

    2018-01-01

    Relaxation in nuclear magnetic resonance (NMR) results from stochastic motions that modulate anisotropic NMR interactions. Therefore, measurement of relaxation-rate constants can be used to characterize molecular-dynamic processes. The motion is often characterized by Markov processes using an auto-correlation function, which is assumed to be a sum of multiple decaying exponentials. We have recently shown that such a model can lead to severe misrepresentation of the real motion, when the real correlation function is more complex than the model. Furthermore, multiple distributions of motion may yield the same set of dynamics data. Therefore, we introduce optimized dynamics "detectors" to characterize motions which are linear combinations of relaxation-rate constants. A detector estimates the average or total amplitude of motion for a range of motional correlation times. The information obtained through the detectors is less specific than information obtained using an explicit model, but this is necessary because the information contained in the relaxation data is ambiguous, if one does not know the correct motional model. On the other hand, if one has a molecular dynamics trajectory, one may calculate the corresponding detector responses, allowing direct comparison to experimental NMR dynamics analysis. We describe how to construct a set of optimized detectors for a given set of relaxation measurements. We then investigate the properties of detectors for a number of different data sets, thus gaining an insight into the actual information content of the NMR data. Finally, we show an example analysis of ubiquitin dynamics data using detectors, using the DIFRATE software.

  17. New insight into the microtexture of chalks from NMR analysis

    DEFF Research Database (Denmark)

    Faÿ-Gomord, Ophélie; Soete, Jeroen; Katika, Konstantina

    2016-01-01

    An integrated petrographical and petrophysical study was carried out on a set of 35 outcrop chalk samples, covering a wide range of lithologies and textures. In this study various chalk rock-types have been characterized, in terms of microtextures and porous network, by integrating both geologica...... related to intraparticle pores within fossils. For all samples, permeability was inferred from NMR spectra using SDR (Schlumberger Doll Research) model....

  18. Conventions and nomenclature for double diffusion encoding NMR and MRI

    DEFF Research Database (Denmark)

    Shemesh, Noam; Jespersen, Sune N; Alexander, Daniel C

    2015-01-01

    Stejskal and Tanner's ingenious pulsed field gradient design from 1965 has made diffusion NMR and MRI the mainstay of most studies seeking to resolve microstructural information in porous systems in general and biological systems in particular. Methods extending beyond Stejskal and Tanner's desig...... to the standard, macroscopic, fractional anisotropy conventionally obtained by diffusion MR. Finally, we discuss future vistas and perspectives for DDE. Magn Reson Med, 2015. © 2015 Wiley Periodicals, Inc....

  19. NMR studies of selective population inversion and spin clustering

    Energy Technology Data Exchange (ETDEWEB)

    Baum, J.S.

    1986-02-01

    This work describes the development and application of selective excitation techniques in Nuclear Magnetic Resonance. Composite pulses and multiple-quantum methods are used to accomplish various goals, such as broadband and narrowband excitation in liquids, and collective excitation of groups of spins in solids. These methods are applied to a variety of problems, including non-invasive spatial localization, spin cluster size characterization in disordered solids and solid state NMR imaging.

  20. Integrated standardization concept for Angelica botanicals using quantitative NMR

    Science.gov (United States)

    Gödecke, Tanja; Yao, Ping; Napolitano, José G.; Nikolić, Dejan; Dietz, Birgit M.; Bolton, Judy L.; van Breemen, Richard B.; Farnsworth, Norman R.; Chen, Shao-Nong; Lankin, David C.; Pauli, Guido F.

    2011-01-01

    Despite numerous in vitro/vivo and phytochemical studies, the active constituents of Angelica sinensis (AS) have not been conclusively identified for the standardization to bioactive markers. Phytochemical analyses of AS extracts and fractions that demonstrate activity in a panel of in vitro bioassays, have repeatedly pointed to ligustilide as being (associated with) the active principle(s). Due to the chemical instability of ligustilide and related issues in GC/LC analyses, new methods capable of quantifying ligustilide in mixtures that do not rely on an identical reference standard are in high demand. This study demonstrates how NMR can satisfy the requirement for simultaneous, multi-target quantification and qualitative identification. First, the AS activity was concentrated into a single fraction by RP-solid-phase extraction, as confirmed by an (anti-)estrogenicity and cytotoxicity assay. Next, a quantitative 1H NMR (qHNMR) method was established and validated using standard compounds and comparing processing methods. Subsequent 1D/2D NMR and qHNMR analysis led to the identification and quantification of ligustilide and other minor components in the active fraction, and to the development of quality criteria for authentic AS preparations. The absolute and relative quantities of ligustilide, six minor alkyl phthalides, and groups of phenylpropanoids, polyynes, and poly-unsaturated fatty acids were measured by a combination of qHNMR and 2D COSY. The qNMR approach enables multi-target quality control of the bioactive fraction, and enables the integrated biological and chemical standardization of AS botanicals. This methodology can potentially be transferred to other botanicals with active principles that act synergistically, or that contain closely related and/or constituents, which have not been conclusively identified as the active principles. PMID:21907766

  1. HIGH FIELD 13C NMR SPECTROSCOPIC ANALYSIS OF THE ...

    African Journals Online (AJOL)

    a

    These shifts are assigned to the C-2 carbon atoms of Sat in the β and α glyceridic positions. The. 34.114 ppm and the 34.0846 ppm are assigned to C-2 of O and L in the α position. These assignments were based on established data [9-11]. Table 1. 13C NMR chemical shifts of Jatropha curcas oil. Chemical shift (ppm).

  2. Solid state NMR studies of materials for energy technology

    Science.gov (United States)

    Nambukara Kodiweera Arachchilage, Chandana K.

    Presented in this dissertation are NMR investigations of the dynamical and structural properties of materials for energy conversion and storage devices. 1H and 2H NMR was used to study water and methanol transportation in sulfonated poly(arylene ether ketone) based membranes for direct methanol fuel cells (DMFC). These results are presented in chapter 3. The amount of liquid in the membrane and ion exchange capacity (IEC) are two main factors that govern the dynamics in these membranes. Water and methanol diffusion coefficients also are comparable. Chapters 4 and 5 are concerned with 31P and 1H NMR in phosphoric acid doped PBI membranes (para-PBI and 2OH-PBI) as well as PBI membranes containing ionic liquids (H3PO4/PMIH2PO4/PBI). These membranes are designed for higher-temperature fuel cell operation. In general, stronger short and long range interactions were observed in the 2OH-PBI matrix, yielding reduced proton transport compared to that of para-PBI. In the case of H3PO4/PMIH2PO 4/PBI, both conductivity and diffusion are higher for the sample with molar ratio 2/4/1. Finally, chapter 6 is devoted to the 31P NMR MAS study of phosphorus-containing structural groups on the surfaces of micro/mesoporous activated carbons. Two spectral features were observed and the narrow feature identifies surface phosphates while the broad component identifies heterogeneous subsurface phosphorus environments including phosphate and more complex structure multiple P-C, P-N and P=N bonds.

  3. A Training Program in Breast Cancer Research Using NMR Techniques

    Science.gov (United States)

    2006-07-01

    mortality. Breast cancer can exist not only in the form of masses, but also in the forms of microcalcifications , asymmetric density, and architectural...treatment of breast cancer calls for early detection of cancerous lesions (e.g., clustered microcalcifications and masses associated with malignant...DAMD17-00-1-0291 TITLE: A Training Program in Breast Cancer Research Using NMR Techniques PRINCIPAL INVESTIGATOR: Paul C. Wang, Ph.D

  4. 3D Reconstruction of NMR Images by LabVIEW

    Directory of Open Access Journals (Sweden)

    Peter IZAK

    2007-01-01

    Full Text Available This paper introduces the experiment of 3D reconstruction NMR images via virtual instrumentation - LabVIEW. The main idea is based on marching cubes algorithm and image processing implemented by module of Vision assistant. The two dimensional images shot by the magnetic resonance device provide information about the surface properties of human body. There is implemented algorithm which can be used for 3D reconstruction of magnetic resonance images in biomedical application.

  5. Automated Pre-processing for NMR Assignments with Reduced Tedium

    Energy Technology Data Exchange (ETDEWEB)

    2004-05-11

    An important rate-limiting step in the reasonance asignment process is accurate identification of resonance peaks in MNR spectra. NMR spectra are noisy. Hence, automatic peak-picking programs must navigate between the Scylla of reliable but incomplete picking, and the Charybdis of noisy but complete picking. Each of these extremes complicates the assignment process: incomplete peak-picking results in the loss of essential connectivities, while noisy picking conceals the true connectivities under a combinatiorial explosion of false positives. Intermediate processing can simplify the assignment process by preferentially removing false peaks from noisy peak lists. This is accomplished by requiring consensus between multiple NMR experiments, exploiting a priori information about NMR spectra, and drawing on empirical statistical distributions of chemical shift extracted from the BioMagResBank. Experienced NMR practitioners currently apply many of these techniques "by hand", which is tedious, and may appear arbitrary to the novice. To increase efficiency, we have created a systematic and automated approach to this process, known as APART. Automated pre-processing has three main advantages: reduced tedium, standardization, and pedagogy. In the hands of experienced spectroscopists, the main advantage is reduced tedium (a rapid increase in the ratio of true peaks to false peaks with minimal effort). When a project is passed from hand to hand, the main advantage is standardization. APART automatically documents the peak filtering process by archiving its original recommendations, the accompanying justifications, and whether a user accepted or overrode a given filtering recommendation. In the hands of a novice, this tool can reduce the stumbling block of learning to differentiate between real peaks and noise, by providing real-time examples of how such decisions are made.

  6. Study of Magnetic Nanocomposites by NMR and Bulk Magnetization Techniques

    Directory of Open Access Journals (Sweden)

    Matveev V.

    2014-07-01

    Full Text Available Magnetic nanocomposites possess complex and nonuniform magnetic structure. As a result it is necessary to use different physical methods to describe their properties. In this work we have applied a combination of micro and macro approaches to understand more deeply magnetic properties of some cobaltcontaining nanocomposites. Testing of magnetic structure of the samples at molecular level was done with NMR and Mössbauer techniques whereas static (SQUID and dynamic magnetic (M2, see below measurements – at macro level.

  7. 14N NMR of amminecobalt(III) compounds

    DEFF Research Database (Denmark)

    Kofod, Pauli

    2003-01-01

    Directly detected ammine 14N NMR chemical shifts of 20 amminecobalt(III) compounds are reported. The coordination shifts, δCS = δcoord − δfree, are in all cases negative and range from −4.4 ppm for the trans ammine ligand in [Co(NH3)5(CH3)]2+ to −73.6 ppm for the trans ammine ligand in [Co(NH3)5(F...

  8. Mobile NMR: An essential tool for protecting our cultural heritage.

    Science.gov (United States)

    Baias, Maria

    2017-01-01

    What is 'cultural heritage'? Is it simply our legacy of physical artifacts - or is it our collective legacy as human societies - how we want to be remembered by future generations? With time, negligence, and even military conflict working to erase the past, we must ask: Can a better understanding of our shared heritage assists us in addressing cultural differences in the present day? And how can science both help us understand the historic record and work to preserve it? In this perspective article, we examine an emerging scientific method, mobile nuclear magnetic resonance (NMR), which can help us examine in a non-invasive way important objects and sites of our cultural heritage. Following these investigations, one can envisage ways for protecting our global heritage for future generations. For this purpose, we examine how this method can be used to non-destructively explore historical artifacts, which can lead to understanding the science behind the creation of these treasured items - paintings, frescoes, parchments, historical buildings, musical instruments, ancient mummies, and other artifacts. This perspective article follows few relevant examples from the scientific literature where mobile NMR has been applied in a non-invasive way to analyze objects of cultural heritage. One can envision possible future advancements of this technique and further applications where portable NMR can be used for conservation of cultural heritage. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

  9. A study of sup 3 He films using SQUID NMR

    CERN Document Server

    Dyball, H C J

    2001-01-01

    Confinement of superfluid sup 3 He to a geometry of order the coherence length is predicted to produce interesting size effects and modify the superfluid phase diagram. This thesis describes the development of an experiment to measure these effects using NMR as a probe of the spin dynamics. A pulsed NMR spectrometer was developed with a low T sub c SQUID as the first stage amplifier. The sample was located in a receiver coil that formed part of a tuned circuit with the SQUID input coil. The first spectrometer was operated in an open-loop configuration but was later converted to use feedback to stabilize the SQUID gain. This later version used a DC SQUID with APF operating in flux-locked loop using the Direct Offset Integration Technique. The noise was limited by the Johnson noise in the tuned circuit in tests down to 1.5 K and the estimated noise temperature was approx 100 mK. NMR signals were observed at approx 1 MHz from low-density sup 3 He samples adsorbed on a Mylar substrate which were in reasonable agr...

  10. Slice selection and T1 contrast in FLASH NMR imaging

    Science.gov (United States)

    Hänicke, Wolfgang; Merboldt, Klaus-Dietmar; Frahm, Jens

    This paper describes the signal intensity in rapid FLASH NMR imaging as a function of the repetition time, the NMR relaxation times, the flip angle, and the shape of the tailored RF pulses used for slice selection. In the absence or after elimination of signal contributions from transverse coherences the theoretical treatment may be confined to a steady state of the longitudinal magnetization. It turns out that deviations from a rectangular excitation profile due to imperfect pulse shapes strongly alter both the dynamic approach to steady-state conditions and the resulting saturation behavior as expected from theoretical expressions. As a consequence the signal-to-noise and image contrast become dependent on the actual slice profile. In T1 images calculated from series of FLASH images with different flip angles or repetition times qualitative relations between tissues with different T1 values are borne out correctly, whereas the accuracy of T1 relaxation times may not be satisfactory. No restrictions are expected for 3D imaging using a spatially homogeneous RF excitation. Experiments have been carried out on phantoms and human volunteers using a Bruker 2.35 T 40 cm NMR system.

  11. Multivariate analysis relating oil shale geochemical properties to NMR relaxometry

    Science.gov (United States)

    Birdwell, Justin E.; Washburn, Kathryn E.

    2015-01-01

    Low-field nuclear magnetic resonance (NMR) relaxometry has been used to provide insight into shale composition by separating relaxation responses from the various hydrogen-bearing phases present in shales in a noninvasive way. Previous low-field NMR work using solid-echo methods provided qualitative information on organic constituents associated with raw and pyrolyzed oil shale samples, but uncertainty in the interpretation of longitudinal-transverse (T1–T2) relaxometry correlation results indicated further study was required. Qualitative confirmation of peaks attributed to kerogen in oil shale was achieved by comparing T1–T2 correlation measurements made on oil shale samples to measurements made on kerogen isolated from those shales. Quantitative relationships between T1–T2 correlation data and organic geochemical properties of raw and pyrolyzed oil shales were determined using partial least-squares regression (PLSR). Relaxometry results were also compared to infrared spectra, and the results not only provided further confidence in the organic matter peak interpretations but also confirmed attribution of T1–T2 peaks to clay hydroxyls. In addition, PLSR analysis was applied to correlate relaxometry data to trace element concentrations with good success. The results of this work show that NMR relaxometry measurements using the solid-echo approach produce T1–T2 peak distributions that correlate well with geochemical properties of raw and pyrolyzed oil shales.

  12. NMRFAM-SPARKY: enhanced software for biomolecular NMR spectroscopy.

    Science.gov (United States)

    Lee, Woonghee; Tonelli, Marco; Markley, John L

    2015-04-15

    SPARKY (Goddard and Kneller, SPARKY 3) remains the most popular software program for NMR data analysis, despite the fact that development of the package by its originators ceased in 2001. We have taken over the development of this package and describe NMRFAM-SPARKY, which implements new functions reflecting advances in the biomolecular NMR field. NMRFAM-SPARKY has been repackaged with current versions of Python and Tcl/Tk, which support new tools for NMR peak simulation and graphical assignment determination. These tools, along with chemical shift predictions from the PACSY database, greatly accelerate protein side chain assignments. NMRFAM-SPARKY supports automated data format interconversion for interfacing with a variety of web servers including, PECAN , PINE, TALOS-N, CS-Rosetta, SHIFTX2 and PONDEROSA-C/S. The software package, along with binary and source codes, if desired, can be downloaded freely from http://pine.nmrfam.wisc.edu/download_packages.html. Instruction manuals and video tutorials can be found at http://www.nmrfam.wisc.edu/nmrfam-sparky-distribution.htm. whlee@nmrfam.wisc.edu or markley@nmrfam.wisc.edu Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press.

  13. NMR metabolite profiling of Greek grape marc spirits.

    Science.gov (United States)

    Fotakis, Charalambos; Christodouleas, Dionysis; Kokkotou, Katerina; Zervou, Maria; Zoumpoulakis, Panagiotis; Moulos, Panagiotis; Liouni, Maria; Calokerinos, Antony

    2013-06-01

    This (1)H NMR based study profiles metabolites in Greek grape marc distillates, tsipouro and tsikoudia. Eightysix samples of indigenous and international varieties, stemming from major vine growing regions of Greece were investigated. The monitoring protocol addressed the global metabolic profile of untreated samples and accomplished the unambiguous assignment of 35 metabolites. NMR spectra were acquired by applying the robust, sensitive and rapid WET1D NMR pulse sequence, which succeeded to unveil the presence of minor compounds in a high ethanol matrix. PCA classified the samples according to their provenance, incorporating also information related to the variety, vintage year and production process within each formed regional assembly. Metabolites such as fusel alcohols, polyols, ethyl esters, mono- and di-saccharides were associated with the classification of samples. OPLS-DA ascribed to samples of common regional entity characteristic genotypic metabolites and probed to the potential influence of the vintage effect. Finally, metabolite profiling underlined the influence of the fermentation and distillation procedures. Copyright © 2012 Elsevier Ltd. All rights reserved.

  14. A small-diameter NMR logging tool for groundwater investigations

    Science.gov (United States)

    Walsh, David; Turner, Peter; Grunewald, Elliot; Zhang, Hong; Butler, James J.; Reboulet, Ed; Knobbe, Steve; Christy, Tom; Lane, John W.; Johnson, Carole D.; Munday, Tim; Fitzpatrick, Andrew

    2013-01-01

    A small-diameter nuclear magnetic resonance (NMR) logging tool has been developed and field tested at various sites in the United States and Australia. A novel design approach has produced relatively inexpensive, small-diameter probes that can be run in open or PVC-cased boreholes as small as 2 inches in diameter. The complete system, including surface electronics and various downhole probes, has been successfully tested in small-diameter monitoring wells in a range of hydrogeological settings. A variant of the probe that can be deployed by a direct-push machine has also been developed and tested in the field. The new NMR logging tool provides reliable, direct, and high-resolution information that is of importance for groundwater studies. Specifically, the technology provides direct measurement of total water content (total porosity in the saturated zone or moisture content in the unsaturated zone), and estimates of relative pore-size distribution (bound vs. mobile water content) and hydraulic conductivity. The NMR measurements show good agreement with ancillary data from lithologic logs, geophysical logs, and hydrogeologic measurements, and provide valuable information for groundwater investigations.

  15. NMR Investigation of Equilibrium Micelle of Two Head Surfactants

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Meong Soo; Nam, Ki Dae [School of Chemical Engineering, Chungbuk National University, Cheongju (Korea); Jeong, Hwan Kyeong [AMLCD Division Semiconductor Samsung Electronics, Chunan (Korea); Lee, Hyang Woo [Department of Cosmetology, Keochang Provincial College, Keochang (Korea)

    2001-06-01

    The two-headed surfactant, disodium 4-n-alkyl-3-sulfonato succinate, has been synthesized by the monoesterification of maleic anhydride and n-alkanol(C{sub 8} {approx} C{sub 12}) and addition of sodium bisulfite to the corresponding monoester. The equilibrium micellar properties formed by these aqueous compounds, and the conformations of the alkyl long chain length that comprised of the interior of micellar, have been investigated using a combination of 1-D NMR and homonuclear/heteronuclear 2-D NMR techniques. The cmc' and the aggregation numbers determined from the NMR experiments were in an agreement with previous results found in the literatures for other types of two-headed surfactant systems. The amphiphiles had high cmc' and low aggregation numbers compared to single-headed surfactants of a comparable chain length. All these results were attributed to the addition a second headgroup to a single-headed, single-tailed surfactant. 27 refs., 6 figs., 4 tabs.

  16. 1H NMR spectroscopy-based interventional metabolic phenotyping

    DEFF Research Database (Denmark)

    Lauridsen, Michael B.; Bliddal, Henning; Christensen, Robin

    2010-01-01

    1H NMR spectroscopy-based metabolic phenotyping was used to identify biomarkers in the plasma of patients with rheumatoid arthritis (RA). Forty-seven patients with RA (23 with active disease at baseline and 24 in remission) and 51 healthy subjects were evaluated during a one-year follow-up with a......1H NMR spectroscopy-based metabolic phenotyping was used to identify biomarkers in the plasma of patients with rheumatoid arthritis (RA). Forty-seven patients with RA (23 with active disease at baseline and 24 in remission) and 51 healthy subjects were evaluated during a one-year follow......-up with assessments of disease activity (DAS-28) and 1H NMR spectroscopy of plasma samples. Discriminant analysis provided evidence that the metabolic profiles predicted disease severity. Cholesterol, lactate, acetylated glycoprotein, and lipid signatures were found to be candidate biomarkers for disease severity....... The results also supported the link between RA and coronary artery disease. Repeated assessment using mixed linear models showed that the predictors obtained from metabolic profiles of plasma at baseline from patients with active RA were significantly different from those of patients in remission (P=0...

  17. A small-diameter NMR logging tool for groundwater investigations.

    Science.gov (United States)

    Walsh, David; Turner, Peter; Grunewald, Elliot; Zhang, Hong; Butler, James J; Reboulet, Ed; Knobbe, Steve; Christy, Tom; Lane, John W; Johnson, Carole D; Munday, Tim; Fitzpatrick, Andrew

    2013-01-01

    A small-diameter nuclear magnetic resonance (NMR) logging tool has been developed and field tested at various sites in the United States and Australia. A novel design approach has produced relatively inexpensive, small-diameter probes that can be run in open or PVC-cased boreholes as small as 2 inches in diameter. The complete system, including surface electronics and various downhole probes, has been successfully tested in small-diameter monitoring wells in a range of hydrogeological settings. A variant of the probe that can be deployed by a direct-push machine has also been developed and tested in the field. The new NMR logging tool provides reliable, direct, and high-resolution information that is of importance for groundwater studies. Specifically, the technology provides direct measurement of total water content (total porosity in the saturated zone or moisture content in the unsaturated zone), and estimates of relative pore-size distribution (bound vs. mobile water content) and hydraulic conductivity. The NMR measurements show good agreement with ancillary data from lithologic logs, geophysical logs, and hydrogeologic measurements, and provide valuable information for groundwater investigations. © 2013, National Ground Water Association.

  18. NMR studies of molecules in liquid crystals and graphite

    Energy Technology Data Exchange (ETDEWEB)

    Rosen, M.E.

    1992-06-01

    NMR experiments to measure proton dipole couplings were performed on a series of n-alkanes (n-hexane through n-decane) dissolved in nematic liquid crystals. Computer modeling of the experimental NMR-spectra was done using several different models for intermolecular interactions in these systems. The model of Photinos et al. was found to be best in describing the intermolecular interactions in these systems and can provide a statistical picture of the conformation and orientation of the alkane molecules in their partially-oriented environment. Order parameters and conformational distributions for the alkanes can be calculated from the modeling. The alkanes are found to have conformational distributions very much like those found in liquid alkanes. Proton NMR spectra of tetrahydrofuran (THF) intercalated in two graphite intercalation compounds were also measured. Computer simulations of these spectra provide a picture of THF in the constrained environment between the graphene layers where the THF is oriented at a particular angle, can translate and rotate freely, but does not appear to pseudorotate.

  19. NMR-based Stable Isotope Resolved Metabolomics in systems biochemistry.

    Science.gov (United States)

    Lane, Andrew N; Fan, Teresa W-M

    2017-08-15

    Metabolism is the basic activity of live cells, and monitoring the metabolic state provides a dynamic picture of the cells or tissues, and how they respond to external changes, for in disease or treatment with drugs. NMR is an extremely versatile analytical tool that can be applied to a wide range of biochemical problems. Despite its modest sensitivity its versatility make it an ideal tool for analyzing biochemical dynamics both in vitro and in vivo, especially when coupled with its isotope editing capabilities, from which isotope distributions can be readily determined. These are critical for any analyses of flux in live organisms. This review focuses on the utility of NMR spectroscopy in metabolomics, with an emphasis on NMR applications in stable isotope-enriched tracer research for elucidating biochemical pathways and networks with examples from nucleotide biochemistry. The knowledge gained from this area of research provides a ready link to genomic, epigenomic, transcriptomic, and proteomic information to achieve systems biochemical understanding of living cells and organisms. Copyright © 2017 Elsevier Inc. All rights reserved.

  20. Rheo-NMR Measurements of Cocoa Butter Crystallized Under

    Energy Technology Data Exchange (ETDEWEB)

    Mudge, E.; Mazzanti, G

    2009-01-01

    Modifications of a benchtop NMR instrument were made to apply temperature control to a shearing NMR cell. This has enabled the determination in situ of the solid fat content (SFC) of cocoa butter under shearing conditions. The cocoa butter was cooled at 3 C/min to three final temperatures of 17.5, 20.0, and 22.5 C with applied shear rates between 45 and 720 s-1. Polymorphic transitions of the cocoa butter were determined using synchrotron X-ray diffraction with an identical shearing system constructed of Lexan. Sheared samples were shown to have accelerated phase transitions compared to static experiments. In experiments where form V was confirmed to be the dominant polymorph, the final SFC averaged around 50%. However, when other polymorphic forms were formed, a lower SFC was measured because the final temperature was within the melting range of that polymorph and only partial crystallization happened. A shear rate of 720 s-1 delayed phase transitions, likely due to viscous heating of the sample. Pulsed NMR is an invaluable tool for determining the crystalline fraction in hydrogen containing materials, yet its use for fundamental and industrial research on fat or alkanes crystallization under shear has only recently been developed.

  1. Faster imaging with a portable unilateral NMR device.

    Science.gov (United States)

    Liberman, Asaf; Bergman, Elad; Sarda, Yifat; Nevo, Uri

    2013-06-01

    Unilateral NMR devices are important tools in various applications such as non-destructive testing and well logging, but are not applied routinely for imaging, primarily because B0 inhomogeneity in these scanners leads to a relatively low signal and requires use of the slow single point imaging scan scheme. Enabling high quality, fast imaging could make this affordable and portable technology practical for various imaging applications as well as for new applications that are not yet feasible with MRI technology. The goal of this work was to improve imaging times in a portable unilateral NMR scanner. Both Compressed Sensing and Fast Spin Echo were modified and applied to fit the unique characteristics of a unilateral device. Two printed phantoms, allowing high resolution images, were scanned with both methods and compared to a standard scan and to a low pass scan to evaluate performance. Both methods were found to be feasible with a unilateral device, proving ways to accelerate single point imaging in such scanners. This outcome encourages us to explore how to further accelerate imaging times in unilateral NMR devices so that this technology might become clinically applicable in the future. Copyright © 2013 Elsevier Inc. All rights reserved.

  2. Prediction of Gestational Diabetes through NMR Metabolomics of Maternal Blood.

    Science.gov (United States)

    Pinto, Joana; Almeida, Lara M; Martins, Ana S; Duarte, Daniela; Barros, António S; Galhano, Eulália; Pita, Cristina; Almeida, Maria do Céu; Carreira, Isabel M; Gil, Ana M

    2015-06-05

    Metabolic biomarkers of pre- and postdiagnosis gestational diabetes mellitus (GDM) were sought, using nuclear magnetic resonance (NMR) metabolomics of maternal plasma and corresponding lipid extracts. Metabolite differences between controls and disease were identified through multivariate analysis of variable selected (1)H NMR spectra. For postdiagnosis GDM, partial least squares regression identified metabolites with higher dependence on normal gestational age evolution. Variable selection of NMR spectra produced good classification models for both pre- and postdiagnostic GDM. Prediagnosis GDM was accompanied by cholesterol increase and minor increases in lipoproteins (plasma), fatty acids, and triglycerides (extracts). Small metabolite changes comprised variations in glucose (up regulated), amino acids, betaine, urea, creatine, and metabolites related to gut microflora. Most changes were enhanced upon GDM diagnosis, in addition to newly observed changes in low-Mw compounds. GDM prediction seems possible exploiting multivariate profile changes rather than a set of univariate changes. Postdiagnosis GDM is successfully classified using a 26-resonance plasma biomarker. Plasma and extracts display comparable classification performance, the former enabling direct and more rapid analysis. Results and putative biochemical hypotheses require further confirmation in larger cohorts of distinct ethnicities.

  3. Structure modeling of RNA using sparse NMR constraints

    Science.gov (United States)

    Williams, Benfeard; Zhao, Bo; Tandon, Arpit; Ding, Feng; Weeks, Kevin M.

    2017-01-01

    Abstract RNAs fold into distinct molecular conformations that are often essential for their functions. Accurate structure modeling of complex RNA motifs, including ubiquitous non-canonical base pairs and pseudoknots, remains a challenge. Here, we present an NMR-guided all-atom discrete molecular dynamics (DMD) platform, iFoldNMR, for rapid and accurate structure modeling of complex RNAs. We show that sparse distance constraints from imino resonances, which can be readily obtained from routine NMR experiments and easier to compile than laborious assignments of non-solvent-exchangeable protons, are sufficient to direct a DMD search for low-energy RNA conformers. Benchmarking on a set of RNAs with complex folds spanning up to 56 nucleotides in length yields structural models that recapitulate experimentally determined structures with all-heavy-atom RMSDs ranging from 2.4 to 6.5 Å. This platform represents an efficient approach for high-throughput RNA structure modeling and will facilitate analysis of diverse, newly discovered functional RNAs. PMID:29165648

  4. NMR assignments of sparsely labeled proteins using a genetic algorithm.

    Science.gov (United States)

    Gao, Qi; Chalmers, Gordon R; Moremen, Kelley W; Prestegard, James H

    2017-04-01

    Sparse isotopic labeling of proteins for NMR studies using single types of amino acid ((15)N or (13)C enriched) has several advantages. Resolution is enhanced by reducing numbers of resonances for large proteins, and isotopic labeling becomes economically feasible for glycoproteins that must be expressed in mammalian cells. However, without access to the traditional triple resonance strategies that require uniform isotopic labeling, NMR assignment of crosspeaks in heteronuclear single quantum coherence (HSQC) spectra is challenging. We present an alternative strategy which combines readily accessible NMR data with known protein domain structures. Based on the structures, chemical shifts are predicted, NOE cross-peak lists are generated, and residual dipolar couplings (RDCs) are calculated for each labeled site. Simulated data are then compared to measured values for a trial set of assignments and scored. A genetic algorithm uses the scores to search for an optimal pairing of HSQC crosspeaks with labeled sites. While none of the individual data types can give a definitive assignment for a particular site, their combination can in most cases. Four test proteins previously assigned using triple resonance methods and a sparsely labeled glycosylated protein, Robo1, previously assigned by manual analysis, are used to validate the method and develop a criterion for identifying sites assigned with high confidence.

  5. Hyperpolarized xenon NMR and MRI signal amplification by gas extraction

    Science.gov (United States)

    Zhou, Xin; Graziani, Dominic; Pines, Alexander

    2009-01-01

    A method is reported for enhancing the sensitivity of NMR of dissolved xenon by detecting the signal after extraction to the gas phase. We demonstrate hyperpolarized xenon signal amplification by gas extraction (Hyper-SAGE) in both NMR spectra and magnetic resonance images with time-of-flight information. Hyper-SAGE takes advantage of a change in physical phase to increase the density of polarized gas in the detection coil. At equilibrium, the concentration of gas-phase xenon is ≈10 times higher than that of the dissolved-phase gas. After extraction the xenon density can be further increased by several orders of magnitude by compression and/or liquefaction. Additionally, being a remote detection technique, the Hyper-SAGE effect is further enhanced in situations where the sample of interest would occupy only a small proportion of the traditional NMR receiver. Coupled with targeted xenon biosensors, Hyper-SAGE offers another path to highly sensitive molecular imaging of specific cell markers by detection of exhaled xenon gas. PMID:19805177

  6. Constrained optimization for position calibration of an NMR field camera.

    Science.gov (United States)

    Chang, Paul; Nassirpour, Sahar; Eschelbach, Martin; Scheffler, Klaus; Henning, Anke

    2017-11-20

    Knowledge of the positions of field probes in an NMR field camera is necessary for monitoring the B0 field. The typical method of estimating these positions is by switching the gradients with known strengths and calculating the positions using the phases of the FIDs. We investigated improving the accuracy of estimating the probe positions and analyzed the effect of inaccurate estimations on field monitoring. The field probe positions were estimated by 1) assuming ideal gradient fields, 2) using measured gradient fields (including nonlinearities), and 3) using measured gradient fields with relative position constraints. The fields measured with the NMR field camera were compared to fields acquired using a dual-echo gradient recalled echo B0 mapping sequence. Comparisons were done for shim fields from second- to fourth-order shim terms. The position estimation was the most accurate when relative position constraints were used in conjunction with measured (nonlinear) gradient fields. The effect of more accurate position estimates was seen when compared to fields measured using a B0 mapping sequence (up to 10%-15% more accurate for some shim fields). The models acquired from the field camera are sensitive to noise due to the low number of spatial sample points. Position estimation of field probes in an NMR camera can be improved using relative position constraints and nonlinear gradient fields. Magn Reson Med, 2017. © 2017 International Society for Magnetic Resonance in Medicine. © 2017 International Society for Magnetic Resonance in Medicine.

  7. 13C-NMR chemical shift databases as a quick tool to evaluate structural models of humic substances

    DEFF Research Database (Denmark)

    Nyrop Albers, Christian; Hansen, Poul Erik

    2010-01-01

    Models for humic and fulvic acids are discussed based on 13C liquid state NMR spectra combined with results from elemental analysis and titration studies. The analysis of NMR spectra is based on a full reconstruction of the NMR spectrum done with help of 13C-NMR data bases by adding up chemical...

  8. GC-MS DETERMINATION OF RATIOS OF STABLE-ISOTOPE LABELED TO NATURAL UREA USING [(CN2)-C-13-N-15]UREA FOR STUDYING UREA KINETICS IN SERUM AND AS A MEANS TO VALIDATE ROUTINE METHODS FOR THE QUANTITATIVE ASSAY OF UREA IN DIALYSATE

    NARCIS (Netherlands)

    WOLTHERS, BG; TEPPER, T; WITHAG, A; NAGEL, GT; DEHAAN, THY; VANLEEUWEN, JJ; STEGEMAN, CA; HUISMAN, RM

    A GC-MS determination of urea in serum or spent dialysate is described, using (CN2)-C-13-N-15-labelled urea and assaying the area ratio of labelled to natural urea by mass fragmentographic monitoring of fragments m/e 153 and 156, after its eventual conversion into the trimethylsilylether-derivative

  9. Hydrothermal changes in wheat starch monitored by two-dimensional NMR.

    Science.gov (United States)

    Kovrlija, R; Rondeau-Mouro, C

    2017-01-01

    The temperature-dependent changes in wheat starch powder and wheat starch-water mixtures were monitored in real-time throughout the heating/cooling program using a classical one-dimensional T1 method and a novel bi-dimensional approach to correlate spin-lattice and spin-spin relaxation times (T1-T2) including acquisition of the FID signal. The influence of two controlling factors (i.e. water content (11%, 35-50%, wet basis) and temperature (20-90°C and back to 20°C)) on water distribution and starch transformation was investigated. Quantitative analysis of 2D T1-T2 maps greatly facilitated the interpretation of T1 relaxation times, which have been interpreted rather narrowly in the literature when classically measured in one-dimension. Application of the new IR-FID-CPMG sequence allowed distinction between different proton pools with different T1 relaxation times, particularly when the starch gelatinization occurred. The quantification of each T1 component permitted to assign the short T1 to slow cross relaxation phenomena, highlighting proton chemical and/or diffusional exchanges between water and starch. Copyright © 2016 Elsevier Ltd. All rights reserved.

  10. An EPR and 1H NMR active mixed-valence manganese (III/II/III) trinuclear compound.

    Science.gov (United States)

    Tangoulis, V; Malamatari, D A; Spyroulias, G A; Raptopoulou, C P; Terzis, A; Kessissoglou, D P

    2000-06-12

    A mixed-valence Mn(III)-Mn(II)-Mn(III) trinuclear complex of stoichiometry MnIIIMnIIMnIII(Hsaladhp)2(Sal)4.2CH3CN (1), where H3saladhp is a tridentate Schiff-base ligand, has been structurally characterized with X-ray crystallography. The Mn(III)Mn(II)Mn(III) angles are strictly 180 degrees as required by crystallographic inversion symmetry. The complex is valence-trapped with two terminal Mn(III) ions in a distorted square pyramidal geometry. The Mn(III)...Mn(II) separation is 3.495 A. The trinuclear complex shows small antiferromagnetic exchange J coupling. The magnetic parameters obtained from the fitting procedure in the temperature range 10-300 K are J1 = -5.7 cm-1, g = 2.02, zJ = -0.19 cm-1, and R = 0.004. The EPR spectrum was obtained at 4 K in CHCl3 and in tetrahydrofuran glasses. The low-field EPR signal is a superposition of two signals, one centered around g = 3.6 and the other, for which hyperfine structure is observed, centered around g = 4.1 indicating an S = 3/2 state. In addition, there is a 19-line signal at g = 2.0. The multiline signal compares well with that observed for the S2 or S0* states of the oxygen-evolving complex. 1H NMR data reveal that the trinuclear compound keeps its integrity into the CHCl3 solution. Crystal data for complex 1: [C54H52N4O18Mn3], M = 1209.82, triclinic, space group P1, a = 10.367(6) A, b = 11.369(6) A, c = 13.967(8) A; alpha = 112.56(1) degree, beta = 93.42(2) degrees, gamma = 115.43(1) degree, Z = 1.

  11. Two dimensional NMR and NMR relaxation studies of coal structure. Progress report, January 1, 1993--March 31, 1993

    Energy Technology Data Exchange (ETDEWEB)

    Zilm, K.W.

    1993-07-01

    This report covers the progress made on the title project for the project 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 that determine the reactivity of coals. Special attention is being paid to methods that are compatible with the very high magic angle sample spinning rates needed for operation at the high magnetic field strengths available today. Polarization inversion methods utilizing the difference in heat capacities of small groups of spins are particularly promising. Methods combining proton-proton spin diffusion with {sup 13}C CPMAS readout are being developed to determine the connectivity of functional groups in coals in a high sensitivity relay type of experiment. Additional work is aimed at delineating the role of methyl group rotation in the proton NMR relaxation behavior of coals.

  12. Two dimensional NMR and NMR relaxation studies of coal structure. Progress report, April 1, 1992--June 30, 1992

    Energy Technology Data Exchange (ETDEWEB)

    Zilm, K.W.

    1992-09-01

    This report covers the progress made on the title project for the project 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 that determine the reactivity of coals. Special attention is being paid to methods that are compatible with the very high magic angle sample spinning rates needed for operation at the high magnetic field strengths available today. Polarization inversion methods utilizing the difference in heat capacities of small groups of spins are particularly promising. Methods combining proton-proton spin diffusion with {sup 13}C CPMAS readout are being developed to determine the connectivity of functional groups in coals in a high sensitivity relay type of experiment. Additional work is aimed at delineating the role of methyl group rotation in the proton NMR relaxation behavior of coals.

  13. A new laboratory approach to shale analysis using NMR relaxometry

    Science.gov (United States)

    Washburn, Kathryn E.; Birdwell, Justin E.; Baez, Luis; Beeney, Ken; Sonnenberg, Steve

    2013-01-01

    Low-field nuclear magnetic resonance (LF-NMR) relaxometry is a non-invasive technique commonly used to assess hydrogen-bearing fluids in petroleum reservoir rocks. Measurements made using LF-NMR provide information on rock porosity, pore-size distributions, and in some cases, fluid types and saturations (Timur, 1967; Kenyon et al., 1986; Straley et al., 1994; Brown, 2001; Jackson, 2001; Kleinberg, 2001; Hurlimann et al., 2002). Recent improvements in LF-NMR instrument electronics have made it possible to apply methods used to measure pore fluids to assess highly viscous and even solid organic phases within reservoir rocks. T1 and T2 relaxation responses behave very differently in solids and liquids; therefore the relationship between these two modes of relaxation can be used to differentiate organic phases in rock samples or to characterize extracted organic materials. Using T1-T2 correlation data, organic components present in shales, such as kerogen and bitumen, can be examined in laboratory relaxometry measurements. In addition, implementation of a solid-echo pulse sequence to refocus T2 relaxation caused by homonuclear dipolar coupling during correlation measurements allows for improved resolution of solid-phase protons. LF-NMR measurements of T1 and T2 relaxation time distributions were carried out on raw oil shale samples from the Eocene Green River Formation and pyrolyzed samples of these shales processed by hydrous pyrolysis and techniques meant to mimic surface and in-situ retorting. Samples processed using the In Situ Simulator approach ranged from bitumen and early oil generation through to depletion of petroleum generating potential. The standard T1-T2 correlation plots revealed distinct peaks representative of solid- and liquid-like organic phases; results on the pyrolyzed shales reflect changes that occurred during thermal processing. The solid-echo T1 and T2 measurements were used to improve assessment of the solid organic phases, specifically

  14. NMR spectroscopic study of organic phosphate esters coprecipitated with calcite

    Science.gov (United States)

    Phillips, Brian L.; Zhang, Zelong; Kubista, Laura; Frisia, Silvia; Borsato, Andrea

    2016-06-01

    Organic phosphorus incorporated in calcite during laboratory precipitation experiments and in natural cave deposits was investigated by solid-state NMR spectroscopy. For calcite precipitated in the presence of organic phosphoesters of varying size and functionality, solid-state 31P{1H} CP/MAS NMR shows that the phosphoesters were incorporated intact into the solid. Systematic changes in the 31P NMR chemical shift of the phosphate group were observed between the solid phosphoester and that incorporated in the solid precipitate, yielding 31P NMR chemical shifts of the coprecipitates in the range of +1.8 to -2.2 ppm. These chemical shifts are distinct from that of similarly prepared calcite coprecipitated with inorganic phosphate, 3.5 ppm. Only minor changes were noted in the phosphoester 31P chemical shift anisotropy (CSA) which suggests no significant change in the local structure of the phosphate group, which is dominated by C-O-P bonding. Close spatial proximity of the organic phosphate group to calcite structural components was revealed by 31P/13C rotational echo double resonance (REDOR) experiments for coprecipitates prepared with 13C-labeled carbonate. All coprecipitates showed significant 31P dephasing effects upon 13C-irradiation, signaling atomic-scale proximity to carbonate carbon. The dephasing rate for smaller organophosphate molecules is similar to that observed for inorganic phosphate, whereas much slower dephasing was observed for larger molecules having long and/or bulky side-chains. This result suggests that small organic molecules can be tightly enclosed within the calcite structure, whereas significant structural disruption required to accommodate the larger organic molecules leads to longer phosphate-carbonate distances. Comparison of 31P NMR spectroscopic data from the synthetic coprecipitates with those from calcite moonmilk speleothems indicates that phosphorus occurs mainly as inorganic orthophosphate in the natural deposits, although small

  15. Revealing metabolic phenotypes in plants: inputs from NMR analysis.

    Science.gov (United States)

    Ratcliffe, R G; Shachar-Hill, Y

    2005-02-01

    Assessing the performance of the plant metabolic network, with its varied biosynthetic capacity and its characteristic subcellular compartmentation, remains a considerable challenge. The complexity of the network is such that it is not yet possible to build large-scale predictive models of the fluxes it supports, whether on the basis of genomic and gene expression analysis or on the basis of more traditional measurements of metabolites and their interconversions. This limits the agronomic and biotechnological exploitation of plant metabolism, and it undermines the important objective of establishing a rational metabolic engineering strategy. Metabolic analysis is central to removing this obstacle and currently there is particular interest in harnessing high-throughput and/or large-scale analyses to the task of defining metabolic phenotypes. Nuclear magnetic resonance (NMR) spectroscopy contributes to this objective by providing a versatile suite of analytical techniques for the detection of metabolites and the fluxes between them. The principles that underpin the analysis of plant metabolism by NMR are described, including a discussion of the measurement options for the detection of metabolites in vivo and in vitro, and a description of the stable isotope labelling experiments that provide the basis for metabolic flux analysis. Despite a relatively low sensitivity, NMR is suitable for high-throughput system-wide analyses of the metabolome, providing methods for both metabolite fingerprinting and metabolite profiling, and in these areas NMR can contribute to the definition of plant metabolic phenotypes that are based on metabolic composition. NMR can also be used to investigate the operation of plant metabolic networks. Labelling experiments provide information on the operation of specific pathways within the network, and the quantitative analysis of steady-state labelling experiments leads to the definition of large-scale flux maps for heterotrophic carbon

  16. NMR and transport measurements of copper chalcogenide and clathrate compounds

    Science.gov (United States)

    Sirusi Arvij, Ali

    Due to limited sources of fossil fuels worldwide and a large percentage wasted as heat energy, searching for efficient thermoelectric materials to convert heat to electricity has gained a great deal of attention. Most of the attempts are focused on materials with substantially lower lattice thermal conductivity and narrow band gaps. Among them, inorganic clathrates and copper-based chalcogenides possess intrinsic low thermal conductivity which makes them promising thermoelectrics. In this work, nuclear magnetic resonance (NMR), transport, and magnetic measurements were performed on clathrates and copper-based chalcogenides to investigate their vibrational and electronic charge carrier properties, as well as the unknown structures of Cu2Se and Cu 2Te at low temperatures, and the effect of rattling of guest atoms in the clathrates. The NMR results in Ba8Ga16Ge30 indicate a pseudogap in the Ga electronic density of states, superposed upon a surprisingly large Ba contribution to the conduction band. Meanwhile, the phonon contributions to the Ga relaxation rates are large and increase more rapidly with temperature than typical semiconductors due to enhanced anharmonicity of the propagative phonon modes over a wide range. Moreover, the observed NMR shifts in the Ba8Cu5Si xGe41-x clathrates change in a nonlinear way with increasing Si substitution: from x = 0 to about 20 the shifts are essentially constant, while approaching x = 41 they increase rapidly, demonstrating a significant change in hybridizations vs Si substitution. NMR studies of Cu2Se show an initial appearance of ionic hopping in a narrow temperature range above 100 K, coinciding with the recently observed low-temperature phase transition. At room temperature and above, this goes over to rapid Cu-ion hopping and a single motionally narrowed line both above and below the alpha-beta structural transition. Furthermore, the NMR results on Cu2Te and Cu 1.98Ag0.2Te demonstrate unusually large negative chemical

  17. NMR/MS Translator for the Enhanced Simultaneous Analysis of Metabolomics Mixtures by NMR Spectroscopy and Mass Spectrometry: Application to Human Urine.

    Science.gov (United States)

    Bingol, Kerem; Brüschweiler, Rafael

    2015-06-05

    A novel metabolite identification strategy is presented for the combined NMR/MS analysis of complex metabolite mixtures. The approach first identifies metabolite candidates from 1D or 2D NMR spectra by NMR database query, which is followed by the determination of the masses (m/z) of their possible ions, adducts, fragments, and characteristic isotope distributions. The expected m/z ratios are then compared with the MS(1) spectrum for the direct assignment of those signals of the mass spectrum that contain information about the same metabolites as the NMR spectra. In this way, the mass spectrum can be assigned with very high confidence, and it provides at the same time validation of the NMR-derived metabolites. The method was first demonstrated on a model mixture, and it was then applied to human urine collected from a pool of healthy individuals. A number of metabolites could be detected that had not been reported previously, further extending the list of known urine metabolites. The new analysis approach, which is termed NMR/MS Translator, is fully automated and takes only a few seconds on a computer workstation. NMR/MS Translator synergistically uses the power of NMR and MS, enhancing the accuracy and efficiency of the identification of those metabolites compiled in databases.

  18. The second round of Critical Assessment of Automated Structure Determination of Proteins by NMR: CASD-NMR-2013.

    Science.gov (United States)

    Rosato, Antonio; Vranken, Wim; Fogh, Rasmus H; Ragan, Timothy J; Tejero, Roberto; Pederson, Kari; Lee, Hsiau-Wei; Prestegard, James H; Yee, Adelinda; Wu, Bin; Lemak, Alexander; Houliston, Scott; Arrowsmith, Cheryl H; Kennedy, Michael; Acton, Thomas B; Xiao, Rong; Liu, Gaohua; Montelione, Gaetano T; Vuister, Geerten W

    2015-08-01

    The second round of the community-wide initiative Critical Assessment of automated Structure Determination of Proteins by NMR (CASD-NMR-2013) comprised ten blind target datasets, consisting of unprocessed spectral data, assigned chemical shift lists and unassigned NOESY peak and RDC lists, that were made available in both curated (i.e. manually refined) or un-curated (i.e. automatically generated) form. Ten structure calculation programs, using fully automated protocols only, generated a total of 164 three-dimensional structures (entries) for the ten targets, sometimes using both curated and un-curated lists to generate multiple entries for a single target. The accuracy of the entries could be established by comparing them to the corresponding manually solved structure of each target, which was not available at the time the data were provided. Across the entire data set, 71 % of all entries submitted achieved an accuracy relative to the reference NMR structure better than 1.5 Å. Methods based on NOESY peak lists achieved even better results with up to 100% of the entries within the 1.5 Å threshold for some programs. However, some methods did not converge for some targets using un-curated NOESY peak lists. Over 90% of the entries achieved an accuracy better than the more relaxed threshold of 2.5 Å that was used in the previous CASD-NMR-2010 round. Comparisons between entries generated with un-curated versus curated peaks show only marginal improvements for the latter in those cases where both calculations converged.

  19. The second round of Critical Assessment of Automated Structure Determination of Proteins by NMR: CASD-NMR-2013

    Energy Technology Data Exchange (ETDEWEB)

    Rosato, Antonio [University of Florence, Department of Chemistry and Magnetic Resonance Center (Italy); Vranken, Wim [Vrije Universiteit Brussel, Structural Biology Brussels (Belgium); Fogh, Rasmus H.; Ragan, Timothy J. [University of Leicester, Department of Biochemistry, School of Biological Sciences (United Kingdom); Tejero, Roberto [Universidad de Valencia, Departamento de Química Física (Spain); Pederson, Kari; Lee, Hsiau-Wei; Prestegard, James H. [University of Georgia, Complex Carbohydrate Research Center and Northeast Structural Genomics Consortium (United States); Yee, Adelinda; Wu, Bin; Lemak, Alexander; Houliston, Scott; Arrowsmith, Cheryl H. [University of Toronto, Department of Medical Biophysics, Cancer Genomics and Proteomics, Ontario Cancer Institute, Northeast Structural Genomics Consortium (Canada); Kennedy, Michael [Miami University, Department of Chemistry and Biochemistry, Northeast Structural Genomics Consortium (United States); Acton, Thomas B.; Xiao, Rong; Liu, Gaohua; Montelione, Gaetano T., E-mail: guy@cabm.rutgers.edu [The State University of New Jersey, Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine, Northeast Structural Genomics Consortium, Rutgers (United States); Vuister, Geerten W., E-mail: gv29@le.ac.uk [University of Leicester, Department of Biochemistry, School of Biological Sciences (United Kingdom)

    2015-08-15

    The second round of the community-wide initiative Critical Assessment of automated Structure Determination of Proteins by NMR (CASD-NMR-2013) comprised ten blind target datasets, consisting of unprocessed spectral data, assigned chemical shift lists and unassigned NOESY peak and RDC lists, that were made available in both curated (i.e. manually refined) or un-curated (i.e. automatically generated) form. Ten structure calculation programs, using fully automated protocols only, generated a total of 164 three-dimensional structures (entries) for the ten targets, sometimes using both curated and un-curated lists to generate multiple entries for a single target. The accuracy of the entries could be established by comparing them to the corresponding manually solved structure of each target, which was not available at the time the data were provided. Across the entire data set, 71 % of all entries submitted achieved an accuracy relative to the reference NMR structure better than 1.5 Å. Methods based on NOESY peak lists achieved even better results with up to 100 % of the entries within the 1.5 Å threshold for some programs. However, some methods did not converge for some targets using un-curated NOESY peak lists. Over 90 % of the entries achieved an accuracy better than the more relaxed threshold of 2.5 Å that was used in the previous CASD-NMR-2010 round. Comparisons between entries generated with un-curated versus curated peaks show only marginal improvements for the latter in those cases where both calculations converged.

  20. A 1H/19F minicoil NMR probe for solid-state NMR: application to 5-fluoroindoles.

    Science.gov (United States)

    Graether, Steffen P; DeVries, Jeffrey S; McDonald, Robert; Rakovszky, Melissa L; Sykes, Brian D

    2006-01-01

    We show that it is feasible to use a minicoil for solid-state 19F 1H NMR experiments that has short pulse widths, good RF homogeneity, and excellent signal-to-noise for small samples while using low power amplifiers typical to liquid-state NMR. The closely spaced resonant frequencies of 1H and 19F and the ubiquitous use of fluorine in modern plastics and electronic components present two major challenges in the design of a high-sensitivity, high-field 1H/19F probe. Through the selection of specific components, circuit design, and pulse sequence, we were able to build a probe that has low 19F background and excellent separation of 1H and 19F signals. We determine the principle components of the chemical shift anisotropy tensor of 5-fluoroindole-3-acetic acid (5FIAA) and 5-fluorotryptophan. We also solve the crystal structure of 5FIAA, determine the orientation dependence of the chemical shift of a single crystal of 5FIAA, and predict the 19F chemical shift based on the orientation of the fluorine in the crystal. The results show that this 1H/19F probe is suitable for solid-state NMR experiments with low amounts of biological molecules that have been labeled with 19F.

  1. AEM and NMR: Tools for the Future of Groundwater Management

    Science.gov (United States)

    Abraham, J. D.; Cannia, J. C.; Lawrie, K.

    2012-12-01

    Within the world, understanding groundwater resources and their management are growing in importance to society as groundwater resources are stressed by drought and continued development. To minimize conflicts, tools and techniques need to be applied to support knowledge-based decisions and management. Airborne electromagnetic (AEM) surveys provide high-quality subsurface data not available from any other source for building the complex hydrogeologic frameworks needed by water-resource managers for effective groundwater management. Traditionally, point data, such as borehole logs, borehole geophysics, surface geophysics, and aquifer tests were interpolated over long distances to create hydrogeologic frameworks. These methods have enjoyed a long history of being the best available technology to inform our understanding of groundwater and how it moves. The AEM techniques proivde pathway for geoscientists to follow to develop more accurate descriptions of the hydrogeological framework. However, the critical and challenging measurements in characterizing aquifers include effective porosity and hydraulic conductivity. These parameters are not reliable derived from AEM. Typically, values for effective porosity and hydraulic conductivity are derived by lithological comparisons with published data; direct measurements of hydraulic conductivity acquired by a few constant head aquifer tests or slug tests; and expensive and time consuming laboratory measurements of cores which can be biased by sampling and the difficulty of making measurements on unconsolidated materials. Aquifer tests are considered to be the best method to gather information on hydraulic conductivity but are rare because of cost and difficult logistics. Also they are unique in design and interpretation from site to site. Nuclear Magnetic Resonance (NMR) can provide a direct measurement of the presence of water in the pore space of aquifer materials. Detection and direct measurement is possible due to the

  2. Functional Analysis of the Nitrogen Metabolite Repression Regulator Gene nmrA in Aspergillus flavus

    Directory of Open Access Journals (Sweden)

    Xiaoyun Han

    2016-11-01

    Full Text Available In Aspergillus nidulans, the nitrogen metabolite repression regulator NmrA plays a major role in regulating the activity of the GATA transcription factor AreA during nitrogen metabolism. However, the function of nmrA in Aspergillus flavus has notbeen previously studied. Here, we report the identification and functional analysis of nmrA in A. flavus. Our work showed that the amino acid sequences of NmrA are highly conserved among Aspergillus species and that A. flavus NmrA protein contains a canonical Rossmann fold motif. Deletion of nmrA slowed the growth of A. flavus but significantly increased conidiation and sclerotia production. Moreover, seed infection experiments indicated that nmrA is required for the invasive virulence of A. flavus. In addition, the ΔnmrA mutant showed increased sensitivity to rapamycin and methyl methanesulfonate, suggesting that nmrA could be responsive to target of rapamycin signaling and DNA damage. Furthermore, quantitative real-time reverse transcription polymerase chain reaction analysis suggested that nmrA might interact with other nitrogen regulatory and catabolic genes. Our study provides a better understanding of nitrogen metabolite repression and the nitrogen metabolism network in fungi.

  3. Assessment of (1)H NMR-based metabolomics analysis for normalization of urinary metals against creatinine.

    Science.gov (United States)

    Cassiède, Marc; Nair, Sindhu; Dueck, Meghan; Mino, James; McKay, Ryan; Mercier, Pascal; Quémerais, Bernadette; Lacy, Paige

    2017-01-01

    Proton nuclear magnetic resonance ((1)H NMR, or NMR) spectroscopy and inductively coupled plasma-mass spectrometry (ICP-MS) are commonly used for metabolomics and metal analysis in urine samples. However, creatinine quantification by NMR for the purpose of normalization of urinary metals has not been validated. We assessed the validity of using NMR analysis for creatinine quantification in human urine samples in order to allow normalization of urinary metal concentrations. NMR and ICP-MS techniques were used to measure metabolite and metal concentrations in urine samples from 10 healthy subjects. For metabolite analysis, two magnetic field strengths (600 and 700MHz) were utilized. In addition, creatinine concentrations were determined by using the Jaffe method. Creatinine levels were strongly correlated (R(2)=0.99) between NMR and Jaffe methods. The NMR spectra were deconvoluted with a target database containing 151 metabolites that are present in urine. A total of 50 metabolites showed good correlation (R(2)=0.7-1.0) at 600 and 700MHz. Metal concentrations determined after NMR-measured creatinine normalization were comparable to previous reports. NMR analysis provided robust urinary creatinine quantification, and was sufficient for normalization of urinary metal concentrations. We found that NMR-measured creatinine-normalized urinary metal concentrations in our control subjects were similar to general population levels in Canada and the United Kingdom. Copyright © 2016 Elsevier B.V. All rights reserved.

  4. A review of NMR methods used in the study of the structure and dynamics of ionic liquids.

    Science.gov (United States)

    Nanda, Raju; Damodaran, Krishnan

    2017-09-18

    Recently, NMR spectroscopy has been emerging out as a powerful tool to study the structure and dynamics of ionic liquids (ILs) and ILs-Li(+) salt mixtures. This mini-review primarily focuses on the applications of various NMR spectroscopic techniques such as self-diffusion measurements, NMR relaxometry, two-dimensional NMR and other novel NMR approaches to study the structure and dynamics of ILs and its mixtures with lithium salts. This article is protected by copyright. All rights reserved.

  5. From single-site tantalum complexes to nanoparticles of TaxNy and TaOxNy supported on silica: elucidation of synthesis chemistry by dynamic nuclear polarization surface enhanced NMR spectroscopy and X-ray absorption spectroscopy

    KAUST Repository

    Mohandas, Janet Chakkamadathil

    2017-06-08

    Air-stable catalysts consisting of tantalum nitride nanoparticles represented as a mixture of TaxNy and TaOxNy with diameters in the range of 0.5 to 3 nm supported on highly dehydroxylated silica were synthesized from TaMe5 (Me = methyl) and dimeric Ta-2(OMe)(10) with guidance by the principles of surface organometallic chemistry (SOMC). Characterization of the supported precursors and the supported nanoparticles formed from them was carried out by IR, NMR, UV-Vis, extended X-ray absorption fine structure, and X-ray photoelectron spectroscopies complemented with XRD and high-resolution TEM, with dynamic nuclear polarization surface enhanced NMR spectroscopy being especially helpful by providing enhanced intensities of the signals of H-1, C-13, Si-29, and N-15 at their natural abundances. The characterization data provide details of the synthesis chemistry, including evidence of (a) O-2 insertion into Ta-CH3 species on the support and (b) a binuclear to mononuclear transformation of species formed from Ta-2(OMe)(10) on the support. A catalytic test reaction, cyclooctene epoxidation, was used to probe the supported nanoparticles, with 30% H2O2 serving as the oxidant. The catalysts gave selectivities up to 98% for the epoxide at conversions as high as 99% with a 3.4 wt% loading of Ta present as TaxNy/TaOxNy.

  6. In-cell NMR of intrinsically disordered proteins in prokaryotic cells.

    Science.gov (United States)

    Ito, Yutaka; Mikawa, Tsutomu; Smith, Brian O

    2012-01-01

    In-cell NMR, i.e., the acquisition of heteronuclear multidimensional NMR of biomacromolecules inside living cells, is, to our knowledge, the only method for investigating the three-dimensional structure and dynamics of proteins at atomic detail in the intracellular environment. Since the inception of the method, intrinsically disordered proteins have been regarded as particular targets for in-cell NMR, due to their expected sensitivity to the molecular crowding in the intracellular environment. While both prokaryotic and eukaryotic cells can be used as host cells for in-cell NMR, prokaryotic in-cell NMR, particularly employing commonly used protein overexpression systems in Escherichia coli cells, is the most accessible approach. In this chapter we describe general procedures for obtaining in-cell NMR spectra in E. coli cells.

  7. Multidimensional NMR approaches towards highly resolved, sensitive and high-throughput quantitative metabolomics.

    Science.gov (United States)

    Marchand, Jérémy; Martineau, Estelle; Guitton, Yann; Dervilly-Pinel, Gaud; Giraudeau, Patrick

    2017-02-01

    Multi-dimensional NMR is an appealing approach for dealing with the challenging complexity of biological samples in metabolomics. This article describes how spectroscopists have recently challenged their imagination in order to make 2D NMR a powerful tool for quantitative metabolomics, based on innovative pulse sequences combined with meticulous analytical chemistry approaches. Clever time-saving strategies have also been explored to make 2D NMR a high-throughput tool for metabolomics, relying on alternative data acquisition schemes such as ultrafast NMR. Currently, much work is aimed at drastically boosting the NMR sensitivity thanks to hyperpolarisation techniques, which have been used in combination with fast acquisition methods and could greatly expand the application potential of NMR metabolomics. Copyright © 2016 Elsevier Ltd. All rights reserved.

  8. Stacked planar micro coils for single-sided NMR applications

    Science.gov (United States)

    Watzlaw, Jan; Glöggler, Stefan; Blümich, Bernhard; Mokwa, Wilfried; Schnakenberg, Uwe

    2013-05-01

    This paper describes planar micro structured coils fabricated in a novel multilayer assembly for single-sided NMR experiments. By arranging the coil's turns in both lateral and vertical directions, all relevant coil parameters can be tailored to a specific application. To this end, we implemented an optimization algorithm based on simulations applying finite element methods (FEMs), which maximizes the coil's sensitivity and thus signal-to-noise ratio (SNR) while incorporating boundary conditions such as the coil's electrical properties and a localized sensitivity needed for single-sided applications. Utilizing thin-film technology and microstructuring techniques, the planar character is kept by a sub-millimeter overall thickness. The coils are adapted to the Profile NMR-MOUSE® magnet with a homogeneous slice of about 200 μm in height and a uniform depth gradient of about 20 T/m. The final design of a coil with 20 turns, separated in four layers with five turns each, and an outer dimension of 4 × 4 mm2 is able to measure a sample volume almost five times smaller than that of a state-of-the-art 14 × 16 mm2 Profile NMR-MOUSE® coil with the same SNR. This allows for volume-limited measurements with high SNR and enables different future developments. The minimal dead time of 4 μs facilitates further improvements of the SNR by echo adding techniques and the characterization of samples with short T2 relaxation times. Measurements on solid polymers like polyethylene (PE) and polypropylene (PP) with T2 components as short as 200 μs approve the overall beneficial coil properties. Furthermore the ability to perform depth profiling with microscopic resolution is demonstrated.

  9. Cellulose Isolation Methodology for NMR Analysis of Cellulose Ultrastructure

    Directory of Open Access Journals (Sweden)

    Art J. Ragauskas

    2011-11-01

    Full Text Available In order to obtain accurate information about the ultrastructure of cellulose from native biomass by 13C cross polarization magic angle spinning (CP/MAS NMR spectroscopy the cellulose component must be isolated due to overlapping resonances from both lignin and hemicellulose. Typically, cellulose isolation has been achieved via holocellulose pulping to remove lignin followed by an acid hydrolysis procedure to remove the hemicellulose components. Using 13C CP/MAS NMR and non-linear line-fitting of the cellulose C4 region, it was observed that the standard acid hydrolysis procedure caused an apparent increase in crystallinity of ~10% or less on the cellulose isolated from Populus holocellulose. We have examined the effect of the cellulose isolation method, particularly the acid treatment time for hemicellulose removal, on cellulose ultrastructural characteristics by studying these effects on cotton, microcrystalline cellulose (MCC and holocellulose pulped Populus. 13C CP/MAS NMR of MCC indicated that holocellulose pulping and acid hydrolysis has little effect on the crystalline ultrastructural components of cellulose. Although any chemical method to isolate cellulose from native biomass will invariably alter substrate characteristics, especially those related to regions accessible to solvents, we found those changes to be minimal and consistent in samples of typical crystallinity and lignin/hemicellulose content. Based on the rate of the hemicellulose removal, as determined by HPLC-carbohydrate analysis and magnitude of cellulose ultrastructural alteration, the most suitable cellulose isolation methodology utilizes a treatment of 2.5 M HCl at 100 °C for a standard residence time between 1.5 and 4 h. However, for the most accurate crystallinity results this residence time should be determined empirically for a particular sample.

  10. Cellulose Isolation Methodology for NMR Analysis of Cellulose Ultrastructure

    Science.gov (United States)

    Foston, Marcus B.; Hubbell, Chistopher A.; Ragauskas, Art J.

    2011-01-01

    In order to obtain accurate information about the ultrastructure of cellulose from native biomass by 13C cross polarization magic angle spinning (CP/MAS) NMR spectroscopy the cellulose component must be isolated due to overlapping resonances from both lignin and hemicellulose. Typically, cellulose isolation has been achieved via holocellulose pulping to remove lignin followed by an acid hydrolysis procedure to remove the hemicellulose components. Using 13C CP/MAS NMR and non-linear line-fitting of the cellulose C4 region, it was observed that the standard acid hydrolysis procedure caused an apparent increase in crystallinity of ~10% or less on the cellulose isolated from Populus holocellulose. We have examined the effect of the cellulose isolation method, particularly the acid treatment time for hemicellulose removal, on cellulose ultrastructural characteristics by studying these effects on cotton, microcrystalline cellulose (MCC) and holocellulose pulped Populus. 13C CP/MAS NMR of MCC indicated that holocellulose pulping and acid hydrolysis has little effect on the crystalline ultrastructural components of cellulose. Although any chemical method to isolate cellulose from native biomass will invariably alter substrate characteristics, especially those related to regions accessible to solvents, we found those changes to be minimal and consistent in samples of typical crystallinity and lignin/hemicellulose content. Based on the rate of the hemicellulose removal, as determined by HPLC-carbohydrate analysis and magnitude of cellulose ultrastructural alteration, the most suitable cellulose isolation methodology utilizes a treatment of 2.5 M HCl at 100 °C for a standard residence time between 1.5 and 4 h. However, for the most accurate crystallinity results this residence time should be determined empirically for a particular sample. PMID:28824119

  11. High pressure {sup 31}P NMR spectroscopy on guanine nucleotides

    Energy Technology Data Exchange (ETDEWEB)

    Spoerner, Michael; Karl, Matthias; Lopes, Pedro; Hoering, Marcus; Loeffel, Karoline; Nuehs, Andrea; Adelsberger, Joseph; Kremer, Werner; Kalbitzer, Hans Robert, E-mail: hans-robert.kalbitzer@ur.de [University of Regensburg, Centre of Magnetic Resonance in Chemistry and Biomedicine, Institute of Biophysics and Physical Biochemistry (Germany)

    2017-01-15

    The {sup 31}P NMR pressure response of guanine nucleotides bound to proteins has been studied in the past for characterizing the pressure perturbation of conformational equilibria. The pressure response of the {sup 31}P NMR chemical shifts of the phosphate groups of GMP, GDP, and GTP as well as the commonly used GTP analogs GppNHp, GppCH{sub 2}p and GTPγS was measured in the absence and presence of Mg{sup 2+}-ions within a pressure range up to 200 MPa. The pressure dependence of chemical shifts is clearly non-linear. For all nucleotides a negative first order pressure coefficient B{sub 1} was determined indicating an upfield shift of the resonances with pressure. With exception of the α-phosphate group of Mg{sup 2+}·GMP and Mg{sup 2+}·GppNHp the second order pressure coefficients are positive. To describe the data of Mg{sup 2+}·GppCH{sub 2}p and GTPγS a Taylor expansion of 3rd order is required. For distinguishing pH effects from pressure effects a complete pH titration set is presented for GMP, as well as GDP and GTP in absence and presence of Mg{sup 2+} ions using indirect referencing to DSS under identical experimental conditions. By a comparison between high pressure {sup 31}P NMR data on free Mg{sup 2+}-GDP and Mg{sup 2+}-GDP in complex with the proto-oncogene Ras we demonstrate that pressure induced changes in chemical shift are clearly different between both forms.

  12. Some double resonance and multiple quantum NMR studies in solids

    Energy Technology Data Exchange (ETDEWEB)

    Wemmer, D.E.

    1978-08-01

    The first section of this work presents the theory and experimental applications to analysis of molecular motion of chemical shielding lineshapes obtained with high resolution double resonance NMR techniques. Analysis of /sup 13/C powder lineshapes in hexamethylbenzene (HMB) and decamethylferrocene (DMFe) show that these molecules reorient in a jumping manner about the symmetry axis. Analysis of proton chemical shielding lineshapes of residual protons in heavy ice (D/sub 2/O) show that protons are exchanged among the tetrahedral positions of neighboring oxygen atoms, consistent with motion expected from defect migration. The second section describes the application of Fourier Transform Double Quantum NMR to measurement of chemical shielding of deuterium in powder samples. Studies of partially deuterated benzene and ferrocene give equal shielding anisotropies, ..delta..sigma = -6.5 ppM. Theoretical predictions and experimental measurements of dipolar couplings between deuterons using FTDQ NMR are presented. Crystals of BaClO/sub 3/.D/sub 2/O, ..cap alpha..,..beta.. d-2 HMB and ..cap alpha..,..beta..,..gamma.. d-3 HMB were studied, as were powders of d-2 HMB and anisic acid. The third section discusses general multiple quantum spectroscopy in dipolar coupled spin systems. Theoretical description is made for creation and detection of coherences between states without quantum number selection rules ..delta..m = +-1. Descriptions of techniques for partial selectivity of order in preparation and detection of multiple quantum coherences are made. The effects on selectivity and resolution of echo pulses during multiple quantum experiments are discussed. Experimental observation of coherences up to order 6 have been made in a sample of benzene dissolved in a liquid crystal. Experimental verifications of order selection and echo generation have been made.

  13. Tungsten(VI) Carbyne/Bis(carbene) Tautomerization Enabled by N-Donor SBA15 Surface Ligands: A Solid-State NMR and DFT Study

    KAUST Repository

    Bendjeriou-Sedjerari, Anissa

    2016-08-11

    Designing supported well-defined bis(carbene) complexes remains a key challenge in heterogeneous catalysis. The reaction of W(CtBu)(CH(2)tBu)(3) with amine-modified mesoporous SBA15 silica, which has vicinal silanol/silylamine pairs [(SiOH)(SiNH2)], leads to [(SiNH2-)(SiO-)W(CHtBu)(CH(2)tBu)(2)] and [(SiNH2-)(SiO-)W(=CHtBu)(2)(CH(2)tBu). Variable temperature, H-1-H-1 2D double-quantum, H-1-C-13 HETCOR, and HETCOR with spin diffusion solid-state NMR spectroscopy demonstrate tautomerization between the alkyl alkylidyne and the bis(alkylidene) on the SBA15 surface. Such equilibrium is possible through the coordination of W to the surface [(Si-OH)(Si-NH2)] groups, which act as a [N,O] pincer ligand. DFT calculations provide a rationalization for the surface-complex tautomerization and support the experimental results. This direct observation of such a process shows the strong similarity between molecular mechanisms in homogeneous and heterogeneous catalysis. In propane metathesis (at 150 degrees C), the tungsten bis(carbene) tautomer is favorable, with a turnover number (TON) of 262. It is the highest TON among all the tungsten alkyl-supported catalysts.

  14. Development and applications of NMR (nuclear magnetic resonance) in low fields and zero field

    Energy Technology Data Exchange (ETDEWEB)

    Bielecki, A.

    1987-05-01

    This dissertation is about nuclear magnetic resonance (NMR) spectroscopy in the absence of applied magnetic fields. NMR is usually done in large magnetic fields, often as large as can be practically attained. The motivation for going the opposite way, toward zero field, is that for certain types of materials, particularly powdered or polycrystalline solids, the NMR spectra in zero field are easier to interpret than those obtained in high field. 92 refs., 60 figs., 1 tab.

  15. NMR studies of non-freezing water in randomly packed beds of porous particles

    Science.gov (United States)

    Hills, B. P.; Le Floc'h, G.

    NMR water proton transverse relaxation time distributions are shown to provide valuable information about the distribution of ice and nonfreezing water in complex heterogeneous systems. In a model system consisting of randomly packed Sephadex beads the NMR data confirm that ice inside the porous Sephadex beads coexists as a two phase system with unfrozen dextran gel. The NMR relaxation technique is shown to provide complementary information to both differential scanning calorimetry and cryomicroscopy.

  16. Development of an NMR microprobe procedure for high-throughput environmental metabolomics of Daphnia magna.

    Science.gov (United States)

    Nagato, Edward G; Lankadurai, Brian P; Soong, Ronald; Simpson, André J; Simpson, Myrna J

    2015-09-01

    Nuclear magnetic resonance (NMR) is the primary platform used in high-throughput environmental metabolomics studies because its non-selectivity is well suited for non-targeted approaches. However, standard NMR probes may limit the use of NMR-based metabolomics for tiny organisms because of the sample volumes required for routine metabolic profiling. Because of this, keystone ecological species, such as the water flea Daphnia magna, are not commonly studied because of the analytical challenges associated with NMR-based approaches. Here, the use of a 1.7-mm NMR microprobe in analyzing tissue extracts from D. magna is tested. Three different extraction procedures (D2O-based buffer, Bligh and Dyer, and acetonitrile : methanol : water) were compared in terms of the yields and breadth of polar metabolites. The D2O buffer extraction yielded the most metabolites and resulted in the best reproducibility. Varying amounts of D. magna dry mass were extracted to optimize metabolite isolation from D. magna tissues. A ratio of 1-1.5-mg dry mass to 40 µl of extraction solvent provided excellent signal-to-noise and spectral resolution using (1)H NMR. The metabolite profile of a single daphnid was also investigated (approximately 0.2 mg). However, the signal-to-noise of the (1)H NMR was considerably lower, and while feasible for select applications would likely not be appropriate for high-throughput NMR-based metabolomics. Two-dimensional NMR experiments on D. magna extracts were also performed using the 1.7-mm NMR probe to confirm (1)H NMR metabolite assignments. This study provides an NMR-based analytical framework for future metabolomics studies that use D. magna in ecological and ecotoxicity studies. Copyright © 2015 John Wiley & Sons, Ltd.

  17. Dataset on metabolomics profile of acute leukemia blood obtained by the NMR methods

    OpenAIRE

    Bogaychuk, Alexander; Zyubin, Andrey; Lavrova, Anastasiya; Kupriyanova, Galina; Babak, Svetlana; Dambieva, Mariya; Demin, Maksim; Borisova, Anastasiya; Opryshko, Nikita

    2017-01-01

    This article contains NMR (nuclear magnetic resonance) experimental data, obtained by the NMR Varian 400?MHz spectrometer (USA) which can be used for the metabolites identification in human blood. Data include analyzed NMR spectra of plasma proteins extracted from human blood of 24 patients (0?5 years old) with the confirmed acute leukemia diagnosis. Data can provide information about metabolites and their concentration in blood.

  18. Dataset on metabolomics profile of acute leukemia blood obtained by the NMR methods.

    Science.gov (United States)

    Bogaychuk, Alexander; Zyubin, Andrey; Lavrova, Anastasiya; Kupriyanova, Galina; Babak, Svetlana; Dambieva, Mariya; Demin, Maksim; Borisova, Anastasiya; Opryshko, Nikita

    2017-04-01

    This article contains NMR (nuclear magnetic resonance) experimental data, obtained by the NMR Varian 400 MHz spectrometer (USA) which can be used for the metabolites identification in human blood. Data include analyzed NMR spectra of plasma proteins extracted from human blood of 24 patients (0-5 years old) with the confirmed acute leukemia diagnosis. Data can provide information about metabolites and their concentration in blood.

  19. Dataset on metabolomics profile of acute leukemia blood obtained by the NMR methods

    Directory of Open Access Journals (Sweden)

    Alexander Bogaychuk

    2017-04-01

    Full Text Available This article contains NMR (nuclear magnetic resonance experimental data, obtained by the NMR Varian 400 MHz spectrometer (USA which can be used for the metabolites identification in human blood. Data include analyzed NMR spectra of plasma proteins extracted from human blood of 24 patients (0–5 years old with the confirmed acute leukemia diagnosis. Data can provide information about metabolites and their concentration in blood.

  20. NMR-Studien an grenzflächenaktiven Verbindungen in kosmetisch relevanten Systemen

    OpenAIRE

    Plaß, Jan Thomas Nikolaus

    2001-01-01

    In this work surfactant systems of cosmetically interest are examined by static and dynamic NMR-methods in order to get more insight in stabilization mechanisms of emulsions used for cosmetic products. Cosmetic oil in water emulsions with a stearyl phosphate emulsifier were examined by means of static and dynamic 31P NMR techniques in order to characterize the molecular properties of the emulsifier in situ. The interfacially bound emulsifier can be detected by high resolution NMR spectroscopy...