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Sample records for 2d nmr ms

  1. Isolation, LC-MS/MS and 2D-NMR characterization of alkaline degradants of tenofovir disoproxil fumarate.

    PubMed

    Anandgaonkar, Vaibhav; Gupta, Abhishek; Kona, Srinivas; Talluri, M V N Kumar

    2015-03-25

    The present work describes the preparative isolation and characterization of two alkaline degradation products of tenofovir disoproxil fumarate (TDF). Tenofovir disoproxil is a prodrug of tenofovir (antiviral agent) and co-crystal form of this prodrug with fumaric acid is tenofovir disoproxil fumarate. The drug is subjected to alkaline degradation with 0.1N sodium hydroxide for 2 min at room temperature. The two degradants were detected by high performance liquid chromatography (HPLC) at relative retention of 0.26 and 0.73 with respect to the drug. HPLC method involves gradient elution on Kromasil Eternity column (150 mm × 2.1 mm, 2.5 μm) using ammonium acetate (10mM) - acetonitrile as mobile phase at flow rate of 0.3 mL/min and UV detection at 260 nm. Two degradation products were isolated by preparative HPLC and further characterized by LC-MS, (1)H NMR, (13)C NMR and 2D-NMR. On the basis of this spectral data, the structure of two DPs are confirmed as methyl hydrogen ({[1-(6-amino-9H-purin-9-yl)propan-2-yl]oxy}methyl)phosphonate for DP-I and dimethyl ({[1-(6-amino-9H-purin-9-yl)propan-2-yl]oxy}methyl)phosphonate for DP-II. PMID:25594895

  2. Isolation and characterization of a potential process related impurity of phenazopyridine HCl by preparative HPLC followed by MS-MS and 2D-NMR spectroscopy.

    PubMed

    Rao, R Nageswara; Maurya, Pawan K; Raju, A Narasa

    2009-07-12

    During the process development of phenazopyridine HCl bulk drug, a potential impurity was detected in the routine impurity profiles by HPLC. Using MS-MS and multidimensional NMR techniques, the trace level impurity was unambiguously identified to be 3-phenyl-5-phenylazo-pyridine-2,6-diamine after its isolation from phenazopyridine HCl by semi-preparative HPLC. The formation of the impurity was discussed. To our knowledge, it is a novel impurity not reported elsewhere. PMID:19376664

  3. NMR profiling of biomolecules at natural abundance using 2D 1H-15N and 1H-13C multiplicity-separated (MS) HSQC spectra

    NASA Astrophysics Data System (ADS)

    Chen, Kang; Freedberg, Darón I.; Keire, David A.

    2015-02-01

    2D NMR 1H-X (X = 15N or 13C) HSQC spectra contain cross-peaks for all XHn moieties. Multiplicity-edited1H-13C HSQC pulse sequences generate opposite signs between peaks of CH2 and CH/CH3 at a cost of lower signal-to-noise due to the 13C T2 relaxation during an additional 1/1JCH period. Such CHn-editing experiments are useful in assignment of chemical shifts and have been successfully applied to small molecules and small proteins (e.g. ubiquitin) dissolved in deuterated solvents where, generally, peak overlap is minimal. By contrast, for larger biomolecules, peak overlap in 2D HSQC spectra is unavoidable and peaks with opposite phases cancel each other out in the edited spectra. However, there is an increasing need for using NMR to profile biomolecules at natural abundance dissolved in water (e.g., protein therapeutics) where NMR experiments beyond 2D are impractical. Therefore, the existing 2D multiplicity-edited HSQC methods must be improved to acquire data on nuclei other than 13C (i.e.15N), to resolve more peaks, to reduce T2 losses and to accommodate water suppression approaches. To meet these needs, a multiplicity-separated1H-X HSQC (MS-HSQC) experiment was developed and tested on 500 and 700 MHz NMR spectrometers equipped with room temperature probes using RNase A (14 kDa) and retroviral capsid (26 kDa) proteins dissolved in 95% H2O/5% D2O. In this pulse sequence, the 1/1JXH editing-period is incorporated into the semi-constant time (semi-CT) X resonance chemical shift evolution period, which increases sensitivity, and importantly, the sum and the difference of the interleaved 1JXH-active and the 1JXH-inactive HSQC experiments yield two separate spectra for XH2 and XH/XH3. Furthermore we demonstrate improved water suppression using triple xyz-gradients instead of the more widely used z-gradient only water-suppression approach.

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

    PubMed

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

    2014-01-01

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

  5. Ultrafast 2D NMR: an emerging tool in analytical spectroscopy.

    PubMed

    Giraudeau, Patrick; Frydman, Lucio

    2014-01-01

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

  6. Ultrafast 2D NMR: An Emerging Tool in Analytical Spectroscopy

    NASA Astrophysics Data System (ADS)

    Giraudeau, Patrick; Frydman, Lucio

    2014-06-01

    Two-dimensional nuclear magnetic resonance (2D NMR) spectroscopy is widely used in chemical and biochemical analyses. Multidimensional NMR is also witnessing increased use in quantitative and metabolic screening applications. Conventional 2D NMR experiments, however, are affected by inherently long acquisition durations, arising from their need to sample the frequencies involved along their indirect domains in an incremented, scan-by-scan nature. A decade ago, a so-called ultrafast (UF) approach was proposed, capable of delivering arbitrary 2D NMR spectra involving any kind of homo- or heteronuclear correlation, in a single scan. During the intervening years, the performance of this subsecond 2D NMR methodology has been greatly improved, and UF 2D NMR is rapidly becoming a powerful analytical tool experiencing an expanded scope of applications. This review summarizes the principles and main developments that have contributed to the success of this approach and focuses on applications that have been recently demonstrated in various areas of analytical chemistry—from the real-time monitoring of chemical and biochemical processes, to extensions in hyphenated techniques and in quantitative applications.

  7. A new inversion method for (T2, D) 2D NMR logging and fluid typing

    NASA Astrophysics Data System (ADS)

    Tan, Maojin; Zou, Youlong; Zhou, Cancan

    2013-02-01

    One-dimensional nuclear magnetic resonance (1D NMR) logging technology has some significant limitations in fluid typing. However, not only can two-dimensional nuclear magnetic resonance (2D NMR) provide some accurate porosity parameters, but it can also identify fluids more accurately than 1D NMR. In this paper, based on the relaxation mechanism of (T2, D) 2D NMR in a gradient magnetic field, a hybrid inversion method that combines least-squares-based QR decomposition (LSQR) and truncated singular value decomposition (TSVD) is examined in the 2D NMR inversion of various fluid models. The forward modeling and inversion tests are performed in detail with different acquisition parameters, such as magnetic field gradients (G) and echo spacing (TE) groups. The simulated results are discussed and described in detail, the influence of the above-mentioned observation parameters on the inversion accuracy is investigated and analyzed, and the observation parameters in multi-TE activation are optimized. Furthermore, the hybrid inversion can be applied to quantitatively determine the fluid saturation. To study the effects of noise level on the hybrid method and inversion results, the numerical simulation experiments are performed using different signal-to-noise-ratios (SNRs), and the effect of different SNRs on fluid typing using three fluid models are discussed and analyzed in detail.

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

    ERIC Educational Resources Information Center

    Alonso, David E.; Warren, Steven E.

    2005-01-01

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

  9. In-Cell Protein Structures from 2D NMR Experiments.

    PubMed

    Müntener, Thomas; Häussinger, Daniel; Selenko, Philipp; Theillet, Francois-Xavier

    2016-07-21

    In-cell NMR spectroscopy provides atomic resolution insights into the structural properties of proteins in cells, but it is rarely used to solve entire protein structures de novo. Here, we introduce a paramagnetic lanthanide-tag to simultaneously measure protein pseudocontact shifts (PCSs) and residual dipolar couplings (RDCs) to be used as input for structure calculation routines within the Rosetta program. We employ this approach to determine the structure of the protein G B1 domain (GB1) in intact Xenopus laevis oocytes from a single set of 2D in-cell NMR experiments. Specifically, we derive well-defined GB1 ensembles from low concentration in-cell NMR samples (∼50 μM) measured at moderate magnetic field strengths (600 MHz), thus offering an easily accessible alternative for determining intracellular protein structures. PMID:27379949

  10. Characterization of Porous Medium Properties Using 2D NMR

    NASA Astrophysics Data System (ADS)

    Sun, Boqin; Dunn, Keh-Jim

    2003-03-01

    We have successfully applied the concept of 2D NMR to the characterization of properties of fluid-saturated porous medium. Using a two-windowed modified CPMG pulse sequence, we were able to explore the magnetic internal filed gradient distribution within the pore space of a fluid-saturated porous medium due to magnetic susceptibility contrast between the solid matrix and pore fluid. Similar scheme is used to identify and quantify different types of pore fluids, such as oil, water, and gas, based on the contrast in their diffusion coefficients. The magic angle spinning technique (MAS) can also be applied in the 2D NMR framework for delineating the chemical shift spectra of the pore fluids in a porous medium at different T1 or T2 relaxation times. The results can be displayed in a two-dimensional plot, with one axis being the T1 or T2 relaxation times, the other axis being the internal field gradient, diffusion coefficient, or chemical shift, and the third axis being the proton population. Our preliminary laboratory work indicates that the 2D NMR approach can be a powerful tool for the characterization of properties of fluid-saturated porous medium, such as fluid typing, oil viscosity determination, surface wettability, etc.

  11. 2D NMR-spectroscopic screening reveals polyketides in ladybugs

    PubMed Central

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

    2011-01-01

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

  12. 2D NMR-spectroscopic screening reveals polyketides in ladybugs.

    PubMed

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

    2011-06-14

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

  13. Stereochemistry of 16a-hydroxyfriedelin and 3-Oxo-16-methylfriedel-16-ene established by 2D NMR spectroscopy.

    PubMed

    Duarte, Lucienir Pains; Silva de Miranda, Roqueline Rodrigues; Rodrigues, Salomão Bento Vasconcelos; de Fátima Silva, Grácia Divina; Vieira Filho, Sidney Augusto; Knupp, Vagner Fernandes

    2009-01-01

    Friedelin (1), 3beta-friedelinol (2), 28-hydroxyfriedelin (3), 16alpha-hydroxyfriedelin (4), 30-hydroxyfriedelin (5) and 16alpha,28-dihydroxyfriedelin (6) were isolated through fractionation of the hexane extract obtained from branches of Salacia elliptica. After a week in CDCl(3) solution, 16alpha-hydroxyfriedelin (4) reacted turning into 3-oxo-16-methylfriedel-16-ene (7). This is the first report of a dehydration followed by a Nametkin rearrangement of a pentacyclic triterpene in CDCl(3) solution occurring in the NMR tube. These seven pentacyclic triterpenes was identified through NMR spectroscopy and the stereochemistry of compound 4 and 7 was established by 2D NMR (NOESY) spectroscopy and mass spectrometry (GC-MS). It is also the first time that all the (13)C-NMR and 2D NMR spectral data are reported for compounds 4 and 7. PMID:19214150

  14. Theory for spiralling ions for 2D FT-ICR and comparison with precessing magnetization vectors in 2D NMR.

    PubMed

    Sehgal, Akansha Ashvani; Pelupessy, Philippe; Rolando, Christian; Bodenhausen, Geoffrey

    2016-04-01

    Two-dimensional (2D) Fourier transform ion cyclotron resonance (FT-ICR) offers an approach to mass spectrometry (MS) that pursuits similar objectives as MS/MS experiments. While the latter must focus on one ion species at a time, 2D FT ICR can examine all possible correlations due to ion fragmentation in a single experiment: correlations between precursors, charged and neutral fragments. We revisited the original 2D FT-ICR experiment that has hitherto fallen short of stimulating significant analytical applications, probably because it is technically demanding. These shortcomings can now be overcome by improved FT-ICR instrumentation and computer hard- and software. We seek to achieve a better understanding of the intricacies of the behavior of ions during a basic two-dimensional ICR sequence comprising three simple monochromatic pulses. Through simulations based on Lorentzian equations, we have mapped the ion trajectories for different pulse durations and phases. PMID:26974979

  15. (13)C NMR assignments of regenerated cellulose from solid-state 2D NMR spectroscopy.

    PubMed

    Idström, Alexander; Schantz, Staffan; Sundberg, Johan; Chmelka, Bradley F; Gatenholm, Paul; Nordstierna, Lars

    2016-10-20

    From the assignment of the solid-state (13)C NMR signals in the C4 region, distinct types of crystalline cellulose, cellulose at crystalline surfaces, and disordered cellulose can be identified and quantified. For regenerated cellulose, complete (13)C assignments of the other carbon regions have not previously been attainable, due to signal overlap. In this study, two-dimensional (2D) NMR correlation methods were used to resolve and assign (13)C signals for all carbon atoms in regenerated cellulose. (13)C-enriched bacterial nanocellulose was biosynthesized, dissolved, and coagulated as highly crystalline cellulose II. Specifically, four distinct (13)C signals were observed corresponding to conformationally different anhydroglucose units: two signals assigned to crystalline moieties and two signals assigned to non-crystalline species. The C1, C4 and C6 regions for cellulose II were fully examined by global spectral deconvolution, which yielded qualitative trends of the relative populations of the different cellulose moieties, as a function of wetting and drying treatments. PMID:27474592

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

    PubMed

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

    1991-04-01

    Six known furanoquinoline alkaloids have been isolated from the wood and trunk bark of COMPTONELLA SESSILIFOLIOLA (Guillaumin) Hartley (Rutaceae). 2D NMR experiments gave the assignment of all the signals for both (1)H- and (13)C-NMR spectra. Pteleine and kokusaginine were used as models. The two-dimensional carbon-proton correlation experiments, performed for the first time on furanoquinoline alkaloids, led us to correct (13)C-NMR assignments previously described in the literature. PMID:17226139

  17. Use of LC-MS/TOF, LC-MS(n), NMR and LC-NMR in characterization of stress degradation products: Application to cilazapril.

    PubMed

    Narayanam, Mallikarjun; Sahu, Archana; Singh, Saranjit

    2015-01-01

    Forced degradation studies on cilazapril were carried out according to ICH and WHO guidelines. Significant degradation of the drug was observed in acid and base conditions, resulting primarily in cilazaprilat. In neutral condition, five degradation products were formed, while under oxidative condition, two degradation products were generated. In total, seven degradation products were formed, which were separated on an Inertsil C-18 column using a stability-indicating HPLC method. Structure elucidation of the degradation products was done by using sophisticated and hyphenated tools like, LC-MS/TOF, LC-MS(n), on-line H/D exchange, LC-NMR and NMR. Initially, comprehensive mass fragmentation pathway of the drug was laid down. Critical comparison of mass fragmentation pathways of the drug and its hydrolytic degradation products allowed structure characterization of the latter. 1D and 2D proton LC-NMR studies further confirmed the proposed structures of hydrolytic degradation products. The oxidative degradation products could not be characterized using LC-MS and LC-NMR tools. Hence, these degradation products were isolated using preparative HPLC and extensive 1D ((1)H, (13)C, DEPT) and 2D (COSY, TOCSY, HETCOR and HMBC) NMR studies were performed to ascertain their structures. Finally, degradation pathways and mechanisms of degradation of the drug were outlined. PMID:25890215

  18. Application of quantitative artificial neural network analysis to 2D NMR spectra of hydrocarbon mixtures.

    PubMed

    Väänänen, Taito; Koskela, Harri; Hiltunen, Yrjö; Ala-Korpela, Mika

    2002-01-01

    Understanding relationships between the structure and composition of molecular mixtures and their chemical properties is a main industrial aim. One central field of research is oil chemistry where the key question is how the molecular characteristics of composite hydrocarbon mixtures can be associated with the macroscopic properties of the oil products. Apparently these relationships are complex and often nonlinear and therefore call for advanced spectroscopic techniques. An informative and an increasingly used approach is two-dimensional nuclear magnetic resonance (2D NMR) spectroscopy. In the case of composite hydrocarbons the application of 2D NMR methodologies in a quantitative manner pose many technical difficulties, and, in any case, the resulting spectra contain many overlapping resonances that challenge the analytical work. Here, we present a general methodology, based on quantitative artificial neural network (ANN) analysis, to resolve overlapping information in 2D NMR spectra and to simultaneously assess the relative importance of multiple spectral variables on the sample properties. The results in a set of 2D NMR spectra of oil samples illustrate, first, that use of ANN analysis for quantitative purposes is feasible also in 2D and, second, that this methodology offers an intrinsic opportunity to assess the complex and nonlinear relationships between the molecular composition and sample properties. The presented ANN methodology is not limited to the analysis of NMR spectra but can also be applied in a manner similar to other (multidimensional) spectroscopic data. PMID:12444730

  19. Stability-indicating HPLC method development and structural elucidation of novel degradation products in posaconazole injection by LC-TOF/MS, LC-MS/MS and NMR.

    PubMed

    Yang, Yidi; Zhu, Xi; Zhang, Fei; Li, Wei; Wu, Ying; Ding, Li

    2016-06-01

    Stress testing was carried out under acidic, alkaline, oxidative, thermal and photolytic conditions to evaluate the intrinsic stability of posaconazole injection. A total of four degradation products were detected and the drug was found to be susceptible to oxidative and thermal degradations. Three unknown degradants formed under oxidative stress condition were isolated by preparative HPLC and unambiguously elucidated by LC-TOF/MS, LC-MS/MS, (1)H NMR, (13)C NMR and 2D NMR techniques. Based on the spectrometric and spectroscopic information, these novel degradation products were unequivocally assigned as the N-oxides of posaconazole. Probable mechanisms for the formation of the degradants were proposed. A new and selective HPLC method was developed and validated to separate, detect and quantify all the degradants in posaconazole injection. PMID:27023129

  20. Numerical simulation of ( T 2, T 1) 2D NMR and fluid responses

    NASA Astrophysics Data System (ADS)

    Tan, Mao-Jin; Zou, You-Long; Zhang, Jin-Yan; Zhao, Xin

    2012-12-01

    One-dimensional nuclear magnetic resonance (1D NMR) logging technology is limited for fluid typing, while two-dimensional nuclear magnetic resonance (2D NMR) logging can provide more parameters including longitudinal relaxation time ( T 1) and transverse relaxation time ( T 2) relative to fluid types in porous media. Based on the 2D NMR relaxation mechanism in a gradient magnetic field, echo train simulation and 2D NMR inversion are discussed in detail. For 2D NMR inversion, a hybrid inversion method is proposed based on the damping least squares method (LSQR) and an improved truncated singular value decomposition (TSVD) algorithm. A series of spin echoes are first simulated with multiple waiting times ( T W s) in a gradient magnetic field for given fluid models and these synthesized echo trains are inverted by the hybrid method. The inversion results are consistent with given models. Moreover, the numerical simulation of various fluid models such as the gas-water, light oil-water, and vicious oil-water models were carried out with different echo spacings ( T E s) and T W s by this hybrid method. Finally, the influences of different signal-to-noise ratios (SNRs) on inversion results in various fluid models are studied. The numerical simulations show that the hybrid method and optimized observation parameters are applicable to fluid typing of gas-water and oil-water models.

  1. Gated cardiac NMR imaging and 2D echocardiography in the detection of intracardial neoplasm

    SciTech Connect

    Go, R.T.; O'Donnell, J.K.; Salcedo, E.E.; Feiglin, D.H.; Underwood, D.A.; MacIntyre, W.J.; Meaney, T.F.

    1985-05-01

    Noninvasive 2D echocardiography has replaced contrast angiography as the procedure of choice in the diagnosis of intracardiac neoplasm. The purpose of this study was to determine whether intracardiac neoplasm can be detected as well by gated cardiac NMR. Four patients with known intracardiac neoplasm previously diagnosed by 2D echocardiography had gated cardiac NMR imaging using a superconductive 0.6 Tesla magnet. All patients were performed using a Tl weighted spin echo pulse sequence with a TE of 30 msec and TR of one R-R interval. Two-dimensional planar single or multiple slice techniques were used. In one patient, imaging at different times along the R-R interval were performed for cine display. The results of the present study show detection of the intracardiac neoplasm in all four cases by gated cardiac NMR imaging and the results were comparable to 2D echocardiography. The former imaging technique showed superior spatial resolution. Despite its early stage of development, gated cardiac NMR imaging appears at least equal to 2D echocardiography in the detection of intracardiac neoplasm. The availability of multislice coupled with multiframe acquisition techniques now being developed will provide a cinematic display that will be more effective in the display of the tumor in motion within the cardiac chamber involved and facilitate visualization of the relationship of the tumor to adjacent cardiac structures.

  2. 2D NMR spectroscopic analyses of archangelicin from the seeds of Angelica archangelica.

    PubMed

    Muller, Melanie; Byres, Maureenx; Jaspars, Marcel; Kumarasamy, Yashodharan; Middleton, Moira; Nahar, Lutfun; Shoeb, Mohammad; Sarker, Satyajit D

    2004-12-01

    A total of six coumarins, bergapten (1), xanthotoxin (2), imperatorin (3), isoimperatorin (4), phellopterin (5) and archangelicin (6), have been isolated from an n-hexane extract of the seeds of Angelica archangelica. The results of comprehensive 2D NMR analyses of archangelicin are discussed. PMID:15634612

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

    PubMed

    Sun, Boqin

    2007-05-01

    In situ nuclear magnetic resonance (NMR) fluid typing has recently gained momentum due to data acquisition and inversion algorithm enhancement of NMR logging tools. T(2) distributions derived from NMR logging contain information on bulk fluids and pore size distributions. However, the accuracy of fluid typing is greatly overshadowed by the overlap between T(2) peaks arising from different fluids with similar apparent T(2) relaxation times. Nevertheless, the shapes of T(2) distributions from different fluid components are often different and can be predetermined. Inversion with predetermined T(2) distributions allows us to perform fluid component decomposition to yield individual fluid volume ratios. Another effective method for in situ fluid typing is two-dimensional (2D) NMR logging, which results in proton population distribution as a function of T(2) relaxation time and fluid diffusion coefficient (or T(1) relaxation time). Since diffusion coefficients (or T(1) relaxation time) for different fluid components can be very different, it is relatively easy to separate oil (especially heavy oil) from water signal in a 2D NMR map and to perform accurate fluid typing. Combining NMR logging with resistivity and/or neutron/density logs provides a third method for in situ fluid typing. We shall describe these techniques with field examples. PMID:17466778

  4. NMR/MS Translator for the Enhanced Simultaneous Analysis of Metabolomics Mixtures by NMR Spectroscopy and Mass Spectrometry: Application to Human Urine.

    PubMed

    Bingol, Kerem; Brüschweiler, Rafael

    2015-06-01

    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. PMID:25881480

  5. Enhancement of MS2D Bartington point measurement of soil magnetic susceptibility

    NASA Astrophysics Data System (ADS)

    Fabijańczyk, Piotr; Zawadzki, Jarosław

    2015-04-01

    Field magnetometry is fast method used to assess the potential soil pollution. The most popular device used to measure the soil magnetic susceptibility on the soil surface is a MS2D Bartington. Single reading using MS2D device of soil magnetic susceptibility is low time-consuming but often characterized by considerable errors related to the instrument or environmental and lithogenic factors. Typically, in order to calculate the reliable average value of soil magnetic susceptibility, a series of MS2D readings is performed in the sample point. As it was analyzed previously, such methodology makes it possible to significantly reduce the nugget effect of the variograms of soil magnetic susceptibility that is related to the micro-scale variance and measurement errors. The goal of this study was to optimize the process of taking a series of MS2D readings, whose average value constitutes a single measurement, in order to take into account micro-scale variations of soil magnetic susceptibility in proper determination of this parameter. This was done using statistical and geostatistical analyses. The analyses were performed using field MS2D measurements that were carried out in the study area located in the direct vicinity of the Katowice agglomeration. At 150 sample points 10 MS2D readings of soil magnetic susceptibility were taken. Using this data set, series of experimental variograms were calculated and modeled. Firstly, using single random MS2D reading for each sample point, and next using the data set increased by adding one more MS2D reading, until their number reached 10. The parameters of variogram: nugget effect, sill and range of correlation were used to determine the most suitable number of MS2D readings at sample point. The distributions of soil magnetic susceptibility at sample point were also analyzed in order to determine adequate number of readings enabling to calculate reliable average soil magnetic susceptibility. The research leading to these results has

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

    NASA Astrophysics Data System (ADS)

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

    2016-03-01

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

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

    PubMed

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

    2016-03-01

    A recent study explored the use of hyperpolarized water, to enhance the sensitivity of nuclei in biomolecules thanks to rapid proton exchanges with labile amide backbone and sidechain groups. Further optimizations of this approach have now allowed us to achieve proton polarizations approaching 25% in the water transferred into the NMR spectrometer, effective water T1 times approaching 40s, and a reduction in the dilution demanded for the cryogenic dissolution process. Further hardware developments have allowed us to perform these experiments, repeatedly and reliably, in 5mm NMR tubes. All these ingredients--particularly the ⩾ 3000× (1)H polarization enhancements over 11.7T thermal counterparts, long T1 times and a compatibility with high-resolution biomolecular NMR setups - augur well for hyperpolarized 2D NMR studies of peptides, unfolded proteins and intrinsically disordered systems undergoing fast exchanges of their protons with the solvent. This hypothesis is here explored by detailing the provisions that lead to these significant improvements over previous reports, and demonstrating 1D coherence transfer experiments and 2D biomolecular HMQC acquisitions delivering NMR spectral enhancements of 100-500× over their optimized, thermally-polarized, counterparts. PMID:26920830

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-05-01

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

  10. Gint2D-T2 correlation NMR of porous media

    NASA Astrophysics Data System (ADS)

    Zhang, Yan; Blümich, Bernhard

    2015-03-01

    The internal magnetic field gradient induced in porous media by magnetic susceptibility differences at material interfaces impacts diffusion measurements in particular at high magnetic field and can be used to probe the pore structure. Insight about the relationship between pore space and internal gradient Gint can be obtained from 2D Laplace NMR experiments. When measuring distributions of transverse relaxation times T2 in fluid filled porous media, relaxation and diffusion in internal gradients arise simultaneously and data are often interpreted with the assumption that one or the other parameter be constant throughout the sample. To examine this assumption we measure correlations of the distributions of Gint2D and T2 by 2D Laplace NMR for three different kinds of samples, glass beads with different bead diameters saturated with water, glass beads filled with oil and water, and a wet mortar sample. For the first two samples the cases where either the internal gradient or diffusion dominates were examined separately in order to better understand the relationship between Gint and D. These results are useful for assessing the impact of internal gradients and diffusion in unknown samples, such as the mortar sample. The experiments were performed at different magnetic field strengths corresponding to 300 MHz and 700 MHz 1H Larmor frequency to identify the impact of the magnetic field on the internal gradient. Subsequently, spatially resolved Gint2D-T2 maps were obtained to study the sample heterogeneity.

  11. Gint2D-T2 correlation NMR of porous media.

    PubMed

    Zhang, Yan; Blümich, Bernhard

    2015-03-01

    The internal magnetic field gradient induced in porous media by magnetic susceptibility differences at material interfaces impacts diffusion measurements in particular at high magnetic field and can be used to probe the pore structure. Insight about the relationship between pore space and internal gradient G(int) can be obtained from 2D Laplace NMR experiments. When measuring distributions of transverse relaxation times T(2) in fluid filled porous media, relaxation and diffusion in internal gradients arise simultaneously and data are often interpreted with the assumption that one or the other parameter be constant throughout the sample. To examine this assumption we measure correlations of the distributions of G(int)(2)D and T(2) by 2D Laplace NMR for three different kinds of samples, glass beads with different bead diameters saturated with water, glass beads filled with oil and water, and a wet mortar sample. For the first two samples the cases where either the internal gradient or diffusion dominates were examined separately in order to better understand the relationship between G(int) and D. These results are useful for assessing the impact of internal gradients and diffusion in unknown samples, such as the mortar sample. The experiments were performed at different magnetic field strengths corresponding to 300 MHz and 700 MHz (1)H Larmor frequency to identify the impact of the magnetic field on the internal gradient. Subsequently, spatially resolved Gint(2)D-T(2) maps were obtained to study the sample heterogeneity. PMID:25723135

  12. Real-time reaction monitoring by ultrafast 2D NMR on a benchtop spectrometer.

    PubMed

    Gouilleux, Boris; Charrier, Benoît; Danieli, Ernesto; Dumez, Jean-Nicolas; Akoka, Serge; Felpin, François-Xavier; Rodriguez-Zubiri, Mireia; Giraudeau, Patrick

    2015-12-01

    Reaction monitoring is widely used to follow chemical processes in a broad range of application fields. Recently, the development of robust benchtop NMR spectrometers has brought NMR under the fume hood, making it possible to monitor chemical reactions in a safe and accessible environment. However, these low-field NMR approaches suffer from limited resolution leading to strong peak overlaps, which can limit their application range. Here, we propose an approach capable of recording ultrafast 2D NMR spectra on a compact spectrometer and of following in real time reactions in the synthetic chemistry laboratory. This approach--whose potential is shown here on a Heck-Matsuda reaction--is highly versatile; the duration of the measurement can be optimized to follow reactions whose time scale ranges from between a few tens of seconds to a few hours. It makes it possible to monitor complex reactions in non-deuterated solvents, and to confirm in real time the molecular structure of the compounds involved in the reaction while giving access to relevant kinetic parameters. PMID:26501887

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

    NASA Astrophysics Data System (ADS)

    Ruan, Qing-Xia; Zhou, Ping

    2008-07-01

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

  14. 2D NMR Methods for Structural Delineation of Copper(II) Complexes of Penicillin and Pilocarpine

    PubMed Central

    Gaggelli, Elena; Gaggelli, Nicola

    1994-01-01

    A method was developed for delineating the structure of paramagnetic metal complexes. The selective disappearance of cross-peaks in proton-carbon shift correlated 2D NMR maps was shown to uniquely depend upon the scalar and/or dipolar interaction between ligand nuclei and the unpaired electron(s), thus providing a means of identifying binding sites. Copper(II) was shown to form metal complexes with both Penicillin (PNC) and Pilocarpine (PLC) and the structure of the two 1:2 complexes in water solution at physiological pH were determined. PMID:18476239

  15. Differential Analysis of 2D NMR Spectra: New Natural Products from a Pilot-Scale Fungal Extract Library

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Using a newly developed protocol for the differential analysis of arrays of 2D NMR spectra, we were able to rapidly identify two previously unreported indole alkaloids from a library of unfractionated fungal extracts. Differential analyses of NMR spectra thus constitute an effective tool for the non...

  16. Identification of Acetaminophen Adducts of Rat Liver Microsomal Proteins using 2D-LC-MS/MS.

    PubMed

    Golizeh, Makan; LeBlanc, André; Sleno, Lekha

    2015-11-16

    Xenobiotic metabolism in the liver can give rise to reactive metabolites that covalently bind to proteins, and determining which proteins are targeted is important in drug discovery and molecular toxicology. However, there are difficulties in the analysis of these modified proteins in complex biological matrices due to their low abundance. In this study, an analytical approach was developed to systematically identify target proteins of acetaminophen (APAP) in rat liver microsomes (RLM) using two-dimensional chromatography and high-resolution tandem mass spectrometry. In vitro microsomal incubations, with and without APAP, were digested and subjected to strong cation exchange (SCX) fractionation prior to reverse-phase UHPLC-MS/MS. Four data processing strategies were combined into an efficient label-free workflow meant to eliminate potential false positives, using peptide spectral matching, statistical differential analysis, product ion screening, and a custom-built delta-mass filtering tool to pinpoint potential modified peptides. This study revealed four proteins, involved in important cellular processes, to be covalently modified by APAP. Data are available via ProteomeXchange with identifier PXD002590. PMID:26510387

  17. 2D NMR Barcoding and Differential Analysis of Complex Mixtures for Chemical Identification: The Actaea Triterpenes

    PubMed Central

    2015-01-01

    The interpretation of NMR spectroscopic information for structure elucidation involves decoding of complex resonance patterns that contain valuable molecular information (δ and J), which is not readily accessible otherwise. We introduce a new concept of 2D-NMR barcoding that uses clusters of fingerprint signals and their spatial relationships in the δ−δ coordinate space to facilitate the chemical identification of complex mixtures. Similar to widely used general barcoding technology, the structural information of individual compounds is encoded as a specifics pattern of their C,H correlation signals. Software-based recognition of these patterns enables the structural identification of the compounds and their discrimination in mixtures. Using the triterpenes from various Actaea (syn. Cimicifuga) species as a test case, heteronuclear multiple-bond correlation (HMBC) barcodes were generated on the basis of their structural subtypes from a statistical investigation of their δH and δC data in the literature. These reference barcodes allowed in silico identification of known triterpenes in enriched fractions obtained from an extract of A. racemosa (black cohosh). After dereplication, a differential analysis of heteronuclear single-quantum correlation (HSQC) spectra even allowed for the discovery of a new triterpene. The 2D barcoding concept has potential application in a natural product discovery project, allowing for the rapid dereplication of known compounds and as a tool in the search for structural novelty within compound classes with established barcodes. PMID:24673652

  18. 2D NMR barcoding and differential analysis of complex mixtures for chemical identification: the Actaea triterpenes.

    PubMed

    Qiu, Feng; McAlpine, James B; Lankin, David C; Burton, Ian; Karakach, Tobias; Chen, Shao-Nong; Pauli, Guido F

    2014-04-15

    The interpretation of NMR spectroscopic information for structure elucidation involves decoding of complex resonance patterns that contain valuable molecular information (δ and J), which is not readily accessible otherwise. We introduce a new concept of 2D-NMR barcoding that uses clusters of fingerprint signals and their spatial relationships in the δ-δ coordinate space to facilitate the chemical identification of complex mixtures. Similar to widely used general barcoding technology, the structural information of individual compounds is encoded as a specifics pattern of their C,H correlation signals. Software-based recognition of these patterns enables the structural identification of the compounds and their discrimination in mixtures. Using the triterpenes from various Actaea (syn. Cimicifuga) species as a test case, heteronuclear multiple-bond correlation (HMBC) barcodes were generated on the basis of their structural subtypes from a statistical investigation of their δH and δC data in the literature. These reference barcodes allowed in silico identification of known triterpenes in enriched fractions obtained from an extract of A. racemosa (black cohosh). After dereplication, a differential analysis of heteronuclear single-quantum correlation (HSQC) spectra even allowed for the discovery of a new triterpene. The 2D barcoding concept has potential application in a natural product discovery project, allowing for the rapid dereplication of known compounds and as a tool in the search for structural novelty within compound classes with established barcodes. PMID:24673652

  19. Dolphin: a tool for automatic targeted metabolite profiling using 1D and 2D (1)H-NMR data.

    PubMed

    Gómez, Josep; Brezmes, Jesús; Mallol, Roger; Rodríguez, Miguel A; Vinaixa, Maria; Salek, Reza M; Correig, Xavier; Cañellas, Nicolau

    2014-12-01

    One of the main challenges in nuclear magnetic resonance (NMR) metabolomics is to obtain valuable metabolic information from large datasets of raw NMR spectra in a high throughput, automatic, and reproducible way. To date, established software packages used to match and quantify metabolites in NMR spectra remain mostly manually operated, leading to low resolution results and subject to inconsistencies not attributable to the NMR technique itself. Here, we introduce a new software package, called Dolphin, able to automatically quantify a set of target metabolites in multiple sample measurements using an approach based on 1D and 2D NMR techniques to overcome the inherent limitations of 1D (1)H-NMR spectra in metabolomics. Dolphin takes advantage of the 2D J-resolved NMR spectroscopy signal dispersion to avoid inconsistencies in signal position detection, enhancing the reliability and confidence in metabolite matching. Furthermore, in order to improve accuracy in quantification, Dolphin uses 2D NMR spectra to obtain additional information on all neighboring signals surrounding the target metabolite. We have compared the targeted profiling results of Dolphin, recorded from standard biological mixtures, with those of two well established approaches in NMR metabolomics. Overall, Dolphin produced more accurate results with the added advantage of being a fully automated and high throughput processing package. PMID:25370160

  20. 1D and 2D NMR studies of isobornyl acrylate - Methyl methacrylate copolymers

    NASA Astrophysics Data System (ADS)

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

    2011-10-01

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

  1. Novel 2D Triple-Resonance NMR Experiments for Sequential Resonance Assignments of Proteins

    NASA Astrophysics Data System (ADS)

    Ding, Keyang; Gronenborn, Angela M.

    2002-06-01

    We present 2D versions of the popular triple resonance HN(CO) CACB, HN(COCA)CACB, HN(CO)CAHA, and HN(COCA) CAHA experiments, commonly used for sequential resonance assignments of proteins. These experiments provide information about correlations between amino proton and nitrogen chemical shifts and the α- and β-carbon and α-proton chemical shifts within and between amino acid residues. Using these 2D spectra, sequential resonance assignments of H N, N, C α, C β, and H α nuclei are easily achieved. The resolution of these spectra is identical to the well-resolved 2D 15N- 1H HSQC and H(NCO)CA spectra, with slightly reduced sensitivity compared to their 3D and 4D versions. These types of spectra are ideally suited for exploitation in automated assignment procedures and thereby constitute a fast and efficient means for NMR structural determination of small and medium-sized proteins in solution in structural genomics programs.

  2. Differentiation of enantiomers by 2D NMR spectroscopy at 1 T using residual dipolar couplings.

    PubMed

    Koos, Martin R M; Danieli, Ernesto; Casanova, Federico; Blümich, Bernhard; Luy, Burkhard

    2016-06-01

    Differentiating enantiomers using 2D bench-top NMR spectroscopy. Spectrometers working with permanent magnets at 1 T field strength allow the acquisition of 2D data sets. In conjunction with previously reported chiral alignment media, this setup allows the measurement of enantiomeric excess via residual dipolar couplings in stretched gelatine as a result of the reduced line width obtained by 2D J-resolved spectroscopy. PMID:25773020

  3. Reproducibility of an Integrated Quantitation Method Coupling 2D GeLC-MS/MS with the emPAI for Comparative Proteomics

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In 2D gel mapping, most protein spots consist of multiple proteins posing a significant challenge for the proper interpretation of gel-based comparative experiments. Previously we introduced an approach integrating 2-D difference gel electrophoresis and LC-MS/MS analysis with the exponentially modif...

  4. Structural description of acid-denatured cytochrome c by hydrogen exchange and 2D NMR

    SciTech Connect

    Jeng, Meifen; Englander, S.W.; Elove, G.A.; Wand, A.J.; Roder, H. )

    1990-11-01

    Hydrogen exchange and two-dimensional nuclear magnetic resonance (2D NMR) techniques were used to characterize the structure of oxidized horse cytochrome c at acid pH and high ionic strength. Under these conditions, cytochrome c is known to assume a globular conformation (A state) with properties resembling those of the molten globule state described for other proteins. In order to measure the rate of hydrogen-deuterium exchange for individual backbone amide protons in the A state, samples of oxidized cytochrome c were incubated at 20 {degree}C in D{sub 2}O buffer for time periods ranging from 2 min to 500 h. The exchange reaction was then quenched by transferring the protein to native conditions. The extent of exchange for 44 amide protons trapped in the refolded protein was measured by 2D NMR spectroscopy. The results show that this approach can provide detailed information on H-bonded secondary and tertiary structure in partially folded equilibrium forms of a protein. All of the slowly exchanging amide protons in the three major helices of native cytochrome c are strongly protected from exchange at acid pH, indicating that the A state contains native-like elements of helical secondary structure. By contrast, a number of amide protons involved in irregular tertiary H-bonds of the native structure are only marginally protected in the A state, indicating that these H-bonds are unstable or absent. The H-exchange results suggest that the major helices of cytochrome c and their common hydrophobic domain are largely preserved in the globular acidic form while the loop region of the native structure is flexible and partly disordered.

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

    DOE PAGESBeta

    Khatun, Sufia; Castner, Edward W.

    2014-11-26

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

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

    SciTech Connect

    Khatun, Sufia; Castner, Edward W.

    2014-11-26

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

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

    PubMed

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

    2015-12-15

    Identifying cellular processes in terms of metabolic pathways is one of the avowed goals of metabolomics studies. Currently, this is done after relevant metabolites are identified to allow their mapping onto specific pathways. This task is daunting due to the complex nature of cellular processes and the difficulty in establishing the identity of individual metabolites. We propose here a new method: ChemSMP (Chemical Shifts to Metabolic Pathways), which facilitates rapid analysis by identifying the active metabolic pathways directly from chemical shifts obtained from a single two-dimensional (2D) [(13)C-(1)H] correlation NMR spectrum without the need for identification and assignment of individual metabolites. ChemSMP uses a novel indexing and scoring system comprised of a "uniqueness score" and a "coverage score". Our method is demonstrated on metabolic pathways data from the Small Molecule Pathway Database (SMPDB) and chemical shifts from the Human Metabolome Database (HMDB). Benchmarks show that ChemSMP has a positive prediction rate of >90% in the presence of decluttered data and can sustain the same at 60-70% even in the presence of noise, such as deletions of peaks and chemical shift deviations. The method tested on NMR data acquired for a mixture of 20 amino acids shows a success rate of 93% in correct recovery of pathways. When used on data obtained from the cell lysate of an unexplored oncogenic cell line, it revealed active metabolic pathways responsible for regulating energy homeostasis of cancer cells. Our unique tool is thus expected to significantly enhance analysis of NMR-based metabolomics data by reducing existing impediments. PMID:26556218

  8. Simulation of 2D NMR Spectra of Carbohydrates Using GODESS Software.

    PubMed

    Kapaev, Roman R; Toukach, Philip V

    2016-06-27

    Glycan Optimized Dual Empirical Spectrum Simulation (GODESS) is a web service, which has been recently shown to be one of the most accurate tools for simulation of (1)H and (13)C 1D NMR spectra of natural carbohydrates and their derivatives. The new version of GODESS supports visualization of the simulated (1)H and (13)C chemical shifts in the form of most 2D spin correlation spectra commonly used in carbohydrate research, such as (1)H-(1)H TOCSY, COSY/COSY-DQF/COSY-RCT, and (1)H-(13)C edHSQC, HSQC-COSY, HSQC-TOCSY, and HMBC. Peaks in the simulated 2D spectra are color-coded and labeled according to the signal assignment and can be exported in JCAMP-DX format. Peak widths are estimated empirically from the structural features. GODESS is available free of charge via the Internet at the platform of the Carbohydrate Structure Database project ( http://csdb.glycoscience.ru ). PMID:27227420

  9. Acid epimerization of 20-keto pregnane glycosides is determined by 2D-NMR spectroscopy.

    PubMed

    García, Víctor P

    2011-05-01

    Carbohydrates influence many essential biological events such as apoptosis, differentiation, tumor metastasis, cancer, neurobiology, immunology, development, host-pathogen interactions, diabetes, signal transduction, protein folding, and many other contexts. We now report on the structure determination of pregnane glycosides isolated from the aerial parts of Ceropegia fusca Bolle (Asclepiadaceae). The observation of cicatrizant, vulnerary and cytostatic activities in some humans and animals of Ceropegia fusca Bolle, a species endemic to the Canary Islands, encouraged us to begin a pharmacological study to determine their exact therapeutic properties. High resolution (1)H-NMR spectra of pregnane glycosides very often display well-resolved signals that can be used as starting points in several selective NMR experiments to study scalar (J coupling), and dipolar (NOE) interactions. ROESY is especially suited for molecules such that ωτ(c) ~ 1, where τ(c) are the motional correlation times and ω is the angular frequency. In these cases the NOE is nearly zero, while the rotating-frame Overhauser effect spectroscopy (ROESY) is always positive and increases monotonically for increasing values of τ(c). The ROESY shows dipolar interactions cross peaks even in medium-sized molecules which are helpful in unambiguous assignment of all the interglycosidic linkages. Selective excitation was carried out using a double pulsed-field gradient spin-echo sequence (DPFGSE) in which 180° Gaussian pulses are sandwiched between sine shaped z-gradients. Scalar interactions were studied by homonuclear DPFGSE-COSY and DPFGSE-TOCSY experiments, while DPFGSE-ROESY was used to monitor the spatial environment of the selectively excited proton. Dipolar interactions between nuclei close in space can be detected by the 1D GROESY experiment, which is a one-dimensional counterpart of the 2D ROESY method. The C-12 and C-17 configurations were determined by ROESY experiments. PMID:21431831

  10. Determination and removal of impurities in 2-D LC-MS of peptides.

    PubMed

    Mihailova, Albena; Lundanes, Elsa; Greibrokk, Tyge

    2006-03-01

    Problems occurring during operation of a 2-D LC-MS system for separation and identification of neuropeptides, such as contamination of the used salts and column bleed, are described. When using polysulfoethyl aspartamide, which is widely used as a strong cation exchange stationary phase in the first dimension, interfering peaks were observed in the second-dimension reversed-phase chromatograms. The observed peaks, found to be caused by column bleeding, had abundance above the threshold value and influenced the quality of the analyses. The origin of the peaks was verified and appropriate measures are proposed. Additionally, peaks caused by polyethylene glycols (PEGs), covering approximately 5 min of feasible chromatographic time in every fraction, were observed. The commercial ammonium formate salts used to prepare the first-dimension mobile phase were found to contain PEG impurities, and in subsequent work the salt solutions were prepared from formic acid and ammonia to avoid any additional contaminations. PMID:16583696

  11. Metabolite Fingerprinting of Eugenia jambolana Fruit Pulp Extracts using NMR, HPLC-PDA-MS, GC-MS, MALDI-TOF-MS and ESI-MS/MS Spectrometry.

    PubMed

    Sharma, Ram Jee; Gupta, Ramesh C; Bansal, Arvind Kumar; Singh, Inder Pal

    2015-06-01

    Eugenia jambolana, commonly known as 'jamun' or Indian blackberry, is an important source of bioactive compounds. All parts of the plant like stem bark, leaves, flower, fruit pulp and seeds are traditionally used for many diseases. Metabolite profiling in medicinally important plants is critical to resolve the problems associated with standardization and quality control. Metabolite profiling of the fruit pulp of Jamun was performed by NMR, HPLC, MS, GC-MS and MALDI-TOF mass spectrometry. These hyphenated techniques helped in the identification of 68 chemically-diverse metabolites of the fruit pulp. These include anthocyanins, anthocyanidins, sugars, phenolics and volatile compounds. Five extracts of fruit pulp were prepared i.e. hexane, chloroform, ethylacetate, butanol and aqueous methanolic. Twenty-five metabolites identified and quantified in the n-butanol and aqueous-methanolic extracts of ripe jamun fruit by qNMR. LC-PDA-MS and MALDI-TOF spectrometry helped in deciphering thirty-nine metabolites out of which thirteen were quantified. PMID:26197529

  12. Combined analysis of C-18 unsaturated fatty acids using natural abundance deuterium 2D NMR spectroscopy in chiral oriented solvents.

    PubMed

    Lesot, Philippe; Baillif, Vincent; Billault, Isabelle

    2008-04-15

    The quantitative determination of isotopic (2H/1H)i ratios at natural abundance using the SNIF-NMR protocol is a well-known method for understanding the enzymatic biosynthesis of metabolites. However, this approach is not always successful for analyzing large solutes and, specifically, is inadequate for prochiral molecules such as complete essential unsaturated fatty acids. To overcome these analytical limitations, we use the natural abundance deuterium 2D NMR (NAD 2D NMR) spectroscopy on solutes embedded in polypeptide chiral liquid crystals. This approach, recently explored for measuring (2H/1H)i ratios of small analytes (Lesot, P.; Aroulanda, C.; Billault, I. Anal. Chem. 2004, 76, 2827-2835), is a powerful way to separate the 2H signals of all nonequivalent enantioisotopomers on the basis both of the 2H quadrupolar interactions and of the 2H chemical shift. Two significant advances over our previous work are presented here and allow the complete isotopic analysis of four mono- and polyunsaturated fatty acid methyl esters: methyl oleate (1), methyl linoleate (2), methyl linolenate (3), and methyl vernoleate (4). The first consists of using NMR spectrometers operating at higher magnetic field strength (14.1 T) and equipped with a selective cryoprobe optimized for deuterium nuclei. The second is the development of Q-COSY Fz 2D NMR experiments able to produce phased 2H 2D maps after a double Fourier transformation. This combination of modern hardware and efficient NMR sequences provides a unique tool to analyze the (2H/1H)i ratios of large prochiral molecules (C-18) dissolved in organic solutions of poly(gamma-benzyl-L-glutamate) and requires smaller amounts of solute than previous study on fatty acids. For each compound (1-4), all 2H quadrupolar doublets visible in the 2D spectra have been assigned on the basis of 2H chemical shifts, isotopic data obtained from isotropic quantitative NAD NMR, and by an interspectral comparison of the anisotropic NAD spectra of four

  13. Interactions of sialic acid with phosphatidylcholine liposomes studied by 2D NMR spectroscopy.

    PubMed

    Timoszyk, Anna; Latanowicz, Lidia

    2013-01-01

    Biological membranes are complex systems which have attracted scientific interest for a long time and for various reasons. The sialic acid-liposome interactions at the molecular level depend on their hydro-lipophilic characteristics. The aim of the present study was to investigate the changes of conformation of the phospholipid (1,2-Diacyl-sn-glycero-3-phosphocholine) and sialic acid (2,8-(N-acetylneuraminic acid)) molecules and the type of interactions induced by the sialic acid molecules on membrane-like systems (liposomes) by 2D NMR (TOCSY, HETCOR, ROESY). The nature of the interaction of sialic acid with the model membrane depends on the structure of the phospholipid headgroups and the hydration of membrane. In ROESY spectra was observed the absence of dipole-dipole couplings within the choline head, between headgroups and glycerol, and between glycerol and fatty acid chains. It indicates an increase of the membrane dynamics in the presence of sialic acid. Moreover, the conformation of sialic acid molecule is changed in the presence of liposomes, which depends on stereochemistry of the chemical groups of the carbon atoms C7 and C8, and oxygen O8. The observed differences between the ROESY spectra of free and liposome bound sialic acid may be a consequence of a changed orientation of the pyranose ring from trans to gauche in the presence of liposomes. The sialic acid penetrate into the phospholipid bilayer to a sufficient depth to allow the dipole interaction. The present result that the correlation signal was found only between the methyl protons from the acetyl group of sialic acid and the methylene tail of phospholipid molecule in the ROESY spectrum indicates that the opposite end of the sialic acid molecule stays in the aqueous phase without interacting with membrane molecules. PMID:24364043

  14. Characterization of novel isobenzofuranones by DFT calculations and 2D NMR analysis.

    PubMed

    Teixeira, Milena G; Alvarenga, Elson S

    2016-08-01

    Phthalides are frequently found in naturally occurring substances and exhibit a broad spectrum of biological activities. In the search for compounds with insecticidal activity, phthalides have been used as versatile building blocks for the syntheses of novel potential agrochemicals. In our work, the Diels-Alder reaction between furan-2(5H)-one and cyclopentadiene was used successfully to obtain (3aR,4S,7R,7aS)-3a,4,7,7a-tetrahydro-4,7-methanoisobenzofuran-1(3H)-one and (3aS,4R,7S,7aR)-3a,4,7,7a-tetrahydro-4,7-methanoisobenzofuran-1(3H)-one (2) and (3aS,4S,7R,7aR)-3a,4,7,7a-tetrahydro-4,7-methanoisobenzofuran-1(3H)-one and (3aR,4R,7S,7aS)-3a,4,7,7a-tetrahydro-4,7-methanoisobenzofuran-1(3H)-one (3). The endo adduct (2) was brominated to afford (3aR,4R,5R,7R,7aS,8R)-5,8-dibromohexahydro-4,7-methanoisobenzofuran-1(3H)-one and (3aS,4S,5S,7S,7aR,8S)-5,8-dibromohexahydro-4,7-methanoisobenzofuran-1(3H)-one (4) and (3aS,4R,5R,6S,7S,7aR)-5,6-dibromohexahydro-4,7-methanoisobenzofuran-1(3H)-one and (3aR,4S,5S,6R,7R,7aS)-5,6-dibromohexahydro-4,7-methanoisobenzofuran-1(3H)-one (5). Following the initial analysis of the NMR spectra and the proposed two novel unforeseen products, we have decided to fully analyze the classical and non-classical assay structures with the aid of computational calculations. Computation to predict the (13) C and (1) H chemical shifts for mean absolute error analyses have been carried out by gauge-including atomic orbital method at M06-2X/6-31+G(d,p) and B3LYP/6-311+G(2d,p) levels of theory for all viable conformers. Characterization of the novel unforeseen compounds (4) and (5) were not possible by employing only the experimental NMR data; however, a more conclusive structural identification was performed by comparing the experimental and theoretical (1) H and (13) C chemical shifts by mean absolute error and DP4 probability analyses. Copyright © 2016 John Wiley & Sons, Ltd. PMID:26811211

  15. Off-resonance effects on 2D NMR nutation spectra of I = 3/2 quadrupolar nuclei in static samples.

    PubMed

    Xia, Y; Deng, F; Ye, C

    1995-12-01

    The off-resonance effects on 2D NMR nutation of I = 3/2 quadrupolar nuclei are demonstrated with perturbation theory and numerical calculation in static samples. The off-resonant (delta omega) rf field (omega 1) enlarges a nutation frequency and consequently increases the measurement range of nuclear quadrupolar interaction parameters. When omega e > omega Qmax, and arctg(omega 1/delta omega) = +/- 54.7 degrees (magic angle), the satellite lines (produced by coherence transfers) in a nutation spectrum are superimposed with the line of central transition, and hence the nutation spectrum is simplified and its sensitivity is enhanced. The nuclear quadrupolar interaction parameters of 23Na nuclei in Na omega molecular sieve are obtained using 2D NMR nutation. PMID:9053113

  16. Structural analysis of photo-degradation in thiazole-containing compounds by LC-MS/MS and NMR.

    PubMed

    Wu, Lianming; Hong, Tricia Y; Vogt, Frederick G

    2007-07-27

    The photo-degradation behavior of a pharmaceutical compound previously under development for treatment of overactive bladder was studied. Samples of {4-(4-chloro-3-fluorophenyl)-2-[4-(methyloxy)phenyl]-1,3-thiazol-5-yl} acetic acid were stressed with visible light and were observed to degrade into a single primary photo-degradation product. This unknown product was analyzed by liquid chromatography tandem mass spectrometry (LC-MS/MS) with accurate mass measurement and hydrogen/deuterium exchange to determine its molecular weight and formula, isotope distribution patterns and exchangeable protons, and product ion structures. By comparison of the fragmentation pathways of the protonated and sodiated species, the charge was found to locate in the electron-rich part of the molecule after fragmentation. MS-derived structural information combined with stopped-flow 1H LC-nuclear magnetic resonance (NMR) analysis suggested that the degradation product was 4-chloro-N-(4-methoxybenzoyl)-3-fluorobenzamide. This unique photo-degradation product was subsequently isolated using preparative-scale chromatography, and its structure was confirmed using 1D and 2D NMR techniques involving the 1H, 13C, 15N and 19F nuclei. The structure of this product suggests that {4-(4-chloro-3-fluorophenyl)-2-[4-(methyloxy)phenyl]-1,3-thiazol-5-yl} acetic acid has reacted with singlet oxygen (1Deltag) via a [4+2] Diels-Alder cycloaddition upon photo-irradiation to cause photo-oxygenation in the solid-state (as is common in solution phase), resulting in an unstable endoperoxide that rearranges to the final degradation product structure. Photo-degradation of a structurally related thiazole, 4-(4-Chlorophenyl)thiazol-2-amine, proceeded via a similar process but in a less reactive manner. However, when exposed to the same conditions, sulfathiazole did not degrade, indicating that this photo-degradation process may only occur for thiazole-containing compounds with specific substituents, such as aryl

  17. Biodegradation pathway of mesotrione: complementarities of NMR, LC-NMR and LC-MS for qualitative and quantitative metabolic profiling.

    PubMed

    Durand, Stéphanie; Sancelme, Martine; Besse-Hoggan, Pascale; Combourieu, Bruno

    2010-09-01

    Enhanced knowledge of pesticide transformation products formed in the environment could lead to both accurate estimates of the overall effects of these compounds on environmental ecosystems and human health and improved removal processes. These compounds can present chemical and environmental behaviours completely different from the starting active ingredient. The difficulty lies on their identification or/and their quantification due to the lack of analytical reference standards. In this context, ex situ Nuclear Magnetic Resonance (NMR) and Liquid Chromatography-NMR (LC-NMR) were used as complementary tools to LC-Mass Spectrometry (MS) to define the metabolic pathway of mesotrione, an emergent herbicide, by the bacterial strain Bacillus sp. 3B6. The complementarities of ex situ and LC-NMR allowed us to unambiguously identify six metabolites whereas the structures of only four metabolites were suggested by LC-MS. The presence of a new metabolic pathway was evidenced by NMR. These results demonstrate that NMR and LC-NMR spectroscopy provided unambiguous structural information for xenobiotic metabolic profiling, even at moderate magnetic field and allowed direct absolute quantification despite the lack of commercial or synthetic standards, required for LC-MS techniques. PMID:20692682

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

    NASA Astrophysics Data System (ADS)

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

    2016-01-01

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

  19. 2D FT-ICR MS of Calmodulin: A Top-Down and Bottom-Up Approach.

    PubMed

    Floris, Federico; van Agthoven, Maria; Chiron, Lionel; Soulby, Andrew J; Wootton, Christopher A; Lam, Yuko P Y; Barrow, Mark P; Delsuc, Marc-André; O'Connor, Peter B

    2016-09-01

    Two-dimensional Fourier transform ion cyclotron resonance mass spectrometry (2D FT-ICR MS) allows data-independent fragmentation of all ions in a sample and correlation of fragment ions to their precursors through the modulation of precursor ion cyclotron radii prior to fragmentation. Previous results show that implementation of 2D FT-ICR MS with infrared multi-photon dissociation (IRMPD) and electron capture dissociation (ECD) has turned this method into a useful analytical tool. In this work, IRMPD tandem mass spectrometry of calmodulin (CaM) has been performed both in one-dimensional and two-dimensional FT-ICR MS using a top-down and bottom-up approach. 2D IRMPD FT-ICR MS is used to achieve extensive inter-residue bond cleavage and assignment for CaM, using its unique features for fragment identification in a less time- and sample-consuming experiment than doing the same thing using sequential MS/MS experiments. Graphical Abstract ᅟ. PMID:27431513

  20. 2D FT-ICR MS of Calmodulin: A Top-Down and Bottom-Up Approach

    NASA Astrophysics Data System (ADS)

    Floris, Federico; van Agthoven, Maria; Chiron, Lionel; Soulby, Andrew J.; Wootton, Christopher A.; Lam, Yuko P. Y.; Barrow, Mark P.; Delsuc, Marc-André; O'Connor, Peter B.

    2016-09-01

    Two-dimensional Fourier transform ion cyclotron resonance mass spectrometry (2D FT-ICR MS) allows data-independent fragmentation of all ions in a sample and correlation of fragment ions to their precursors through the modulation of precursor ion cyclotron radii prior to fragmentation. Previous results show that implementation of 2D FT-ICR MS with infrared multi-photon dissociation (IRMPD) and electron capture dissociation (ECD) has turned this method into a useful analytical tool. In this work, IRMPD tandem mass spectrometry of calmodulin (CaM) has been performed both in one-dimensional and two-dimensional FT-ICR MS using a top-down and bottom-up approach. 2D IRMPD FT-ICR MS is used to achieve extensive inter-residue bond cleavage and assignment for CaM, using its unique features for fragment identification in a less time- and sample-consuming experiment than doing the same thing using sequential MS/MS experiments.

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

  2. High field and 2D-nmr studies with the aporphine alkaloid glaucine.

    PubMed

    Kerr, K M; Kook, A M; Davis, P J

    1986-01-01

    The aporphine alkaloid glaucine (1) was examined by comparison of the high field (600 MHz) 1H-nmr spectra of 1 vs. racemic 6a,7,7-trideutereoglaucine (4,5), by computer-simulated 1H-nmr spectra at 600 MHz, by using decoupled proton spectra, and two-dimensional COSY and HETCOR experiments with 1 at 500 and 360 MHz, respectively, and using high field (90 MHZ) 13C-nmr of S-(+)-glaucine (1). Emphasis was placed on the resolution of the chemical shifts and coupling constants for the H-4 alpha, H-4 beta, H-5 alpha, H-5 beta, H-6 alpha, H-7 alpha, and H-7 beta alicyclic protons of the molecule, which were previously unassigned. The complete assignment of the alicyclic protons of 1 by 1H-nmr was required for the structural elucidation of deuterated analogs of glaucine, which will be used in microbial transformation studies to determine the stereochemical course of aporphine dehydrogenation by the fungi Fusarium solani (ATCC 12823) and Aspergillus flavipes (ATCC 1030). PMID:3783155

  3. A high-resolution 2D J-resolved NMR detection technique for metabolite analyses of biological samples

    PubMed Central

    Huang, Yuqing; Zhang, Zhiyong; Chen, Hao; Feng, Jianghua; Cai, Shuhui; Chen, Zhong

    2015-01-01

    NMR spectroscopy is a commonly used technique for metabolite analyses. Due to the observed macroscopic magnetic susceptibility in biological tissues, current NMR acquisitions in measurements of biological tissues are generally performed on tissue extracts using liquid NMR or on tissues using magic-angle spinning techniques. In this study, we propose an NMR method to achieve high-resolution J-resolved information for metabolite analyses directly from intact biological samples. A dramatic improvement in spectral resolution is evident in our contrastive demonstrations on a sample of pig brain tissue. Metabolite analyses for a postmortem fish from fresh to decayed statuses are presented to further reveal the capability of the proposed method. This method is a previously-unreported high-resolution 2D J-resolved spectroscopy for biological applications without specialised hardware requirements or complicated sample pretreatments. It provides a significant contribution to metabolite analyses of biological samples, and may be potentially applicable to in vivo samples. Furthermore, this method also can be applied to measurements of semisolid and viscous samples. PMID:25670027

  4. A high-resolution 2D J-resolved NMR detection technique for metabolite analyses of biological samples.

    PubMed

    Huang, Yuqing; Zhang, Zhiyong; Chen, Hao; Feng, Jianghua; Cai, Shuhui; Chen, Zhong

    2015-01-01

    NMR spectroscopy is a commonly used technique for metabolite analyses. Due to the observed macroscopic magnetic susceptibility in biological tissues, current NMR acquisitions in measurements of biological tissues are generally performed on tissue extracts using liquid NMR or on tissues using magic-angle spinning techniques. In this study, we propose an NMR method to achieve high-resolution J-resolved information for metabolite analyses directly from intact biological samples. A dramatic improvement in spectral resolution is evident in our contrastive demonstrations on a sample of pig brain tissue. Metabolite analyses for a postmortem fish from fresh to decayed statuses are presented to further reveal the capability of the proposed method. This method is a previously-unreported high-resolution 2D J-resolved spectroscopy for biological applications without specialised hardware requirements or complicated sample pretreatments. It provides a significant contribution to metabolite analyses of biological samples, and may be potentially applicable to in vivo samples. Furthermore, this method also can be applied to measurements of semisolid and viscous samples. PMID:25670027

  5. Targeted Molecular Imaging of Cancer Cells Using MS2-Based (129)Xe NMR.

    PubMed

    Jeong, Keunhong; Netirojjanakul, Chawita; Munch, Henrik K; Sun, Jinny; Finbloom, Joel A; Wemmer, David E; Pines, Alexander; Francis, Matthew B

    2016-08-17

    We have synthesized targeted, selective, and highly sensitive (129)Xe NMR nanoscale biosensors using a spherical MS2 viral capsid, Cryptophane A molecules, and DNA aptamers. The biosensors showed strong binding specificity toward targeted lymphoma cells (Ramos line). Hyperpolarized (129)Xe NMR signal contrast and hyper-CEST (129)Xe MRI image contrast indicated its promise as highly sensitive hyperpolarized (129)Xe NMR nanoscale biosensor for future applications in cancer detection in vivo. PMID:27454679

  6. Influence of anthraquinone scaffold on E/Z isomer distribution of two thiosemicarbazone derivatives. 2D NMR and DFT studies

    NASA Astrophysics Data System (ADS)

    Marković, Violeta; Joksović, Milan D.; Marković, Svetlana; Jakovljević, Ivan

    2014-01-01

    A distribution of possible isomeric and tautomeric forms of two tautomerizable anthraquinone-thiosemicarbazones with pronounced cytotoxic potential was investigated using 2D NMR and DFT studies. Conformational analysis of the E and Z isomers of both thiosemicarbazones was performed to find out the most stable conformation for each molecule. It was found that superior stability of E-isomers results from ten-membered intramolecular hydrogen bond between thiosemicarbazone N2H and anthraquinone carbonyl group. This hydrogen bond is stronger than that between thiosemicarbazone N2H and ester oxygen, owing to the large partial negative charge on the anthraquinone oxygen.

  7. Unraveling the heterogeneity in N butyl-N-methylpiperidinium trifluromethanesulfonimide ionic liquid by 1D and 2D NMR spectroscopy

    NASA Astrophysics Data System (ADS)

    Tripathi, Neha; Saha, Satyen

    2014-06-01

    Room temperature ionic liquids are one of the most exciting classes of materials in the last decade. In particular piperidinium (PIP) cation based ionic liquid (IL) (such as PIP14NTf2) have found application in electrochemistry/batteries. In this Letter, 2D NMR (NOESY and HOESY) is employed for studying the interactions present between cations and anions. HOESY spectrum shows that fluorine of NTf2 unusually interacts with all proton of the cation (PIP14). Combined HOESY and NOESY indicate that NTf2 anion is distributed heterogeneously in liquid. Existence of micro heterogeneity in this important class of IL is proposed.

  8. Combining DI-ESI–MS and NMR datasets for metabolic profiling

    PubMed Central

    Marshall, Darrell D.; Lei, Shulei; Worley, Bradley; Huang, Yuting; Garcia-Garcia, Aracely; Franco, Rodrigo; Dodds, Eric D.; Powers, Robert

    2014-01-01

    Metabolomics datasets are commonly acquired by either mass spectrometry (MS) or nuclear magnetic resonance spectroscopy (NMR), despite their fundamental complementarity. In fact, combining MS and NMR datasets greatly improves the coverage of the metabolome and enhances the accuracy of metabolite identification, providing a detailed and high-throughput analysis of metabolic changes due to disease, drug treatment, or a variety of other environmental stimuli. Ideally, a single metabolomics sample would be simultaneously used for both MS and NMR analyses, minimizing the potential for variability between the two datasets. This necessitates the optimization of sample preparation, data collection and data handling protocols to effectively integrate direct-infusion MS data with one-dimensional (1D) 1H NMR spectra. To achieve this goal, we report for the first time the optimization of (i) metabolomics sample preparation for dual analysis by NMR and MS, (ii) high throughput, positive-ion direct infusion electrospray ionization mass spectrometry (DI-ESI-MS) for the analysis of complex metabolite mixtures, and (iii) data handling protocols to simultaneously analyze DI-ESI-MS and 1D 1H NMR spectral data using multiblock bilinear factorizations, namely multiblock principal component analysis (MB-PCA) and multiblock partial least squares (MB-PLS). Finally, we demonstrate the combined use of backscaled loadings, accurate mass measurements and tandem MS experiments to identify metabolites significantly contributing to class separation in MB-PLS-DA scores. We show that integration of NMR and DI-ESI-MS datasets yields a substantial improvement in the analysis of neurotoxin involvement in dopaminergic cell death. PMID:25774104

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

    PubMed

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

    2006-06-01

    To remove uremic octapeptide from the blood stream of uremic patients, various modified polyacylamide cross-linked absorbents were prepared. Adsorption experiments showed these absorbents have significant differences in adsorption capacity to the target peptide. In this paper, two-dimension proton nuclear magnetic resonance (2D 1H NMR) spectroscopy was used to investigate the interaction mechanism between the peptide and the adsorbents. Because of the insolubility of the absorbent, some soluble linear polymers with the same functional groups as the absorbents were employed as the model adsorbents in 2D 1H NMR. The preferred binding site for the peptide and polymers was identified to be at the C-terminal carboxyl group of the octapeptide via chemical shift perturbation effects. In this study, we found that hydrogen bonding, electrostatic, and hydrophobic interactions all play a role in the interaction force but had different contributions. Especially, the great chemical shift changes of the aromatic amino acid residues (Trp) during the interaction between butyl-modified polyacrylamide and octapeptide suggested the hydrophobic interaction, incorporated with the electrostatic force, played an important role in the binding reaction in aqueous solutions. This information not only rationally explained the results of the adsorption experiments, but also identified the effective binding site and mechanism, and shall provide a structural basis for designing better affinity-type adsorbents for the target peptide. PMID:16768402

  10. Computer-assisted assignment of 2D 1H NMR spectra of proteins: basic algorithms and application to phoratoxin B.

    PubMed

    Kleywegt, G J; Boelens, R; Cox, M; Llinás, M; Kaptein, R

    1991-05-01

    A suite of computer programs (CLAIRE) is described which can be of assistance in the process of assigning 2D 1H NMR spectra of proteins. The programs embody a software implementation of the sequential assignment approach first developed by Wüthrich and co-workers (K. Wüthrich, G. Wider, G. Wagner and W. Braun (1982) J. Mol. Biol. 155, 311). After data-abstraction (peakpicking), the software can be used to detect patterns (spin systems), to find cross peaks between patterns in 2D NOE data sets and to generate assignments that are consistent with all available data and which satisfy a number of constraints imposed by the user. An interactive graphics program called CONPAT is used to control the entire assignment process as well as to provide the essential feedback from the experimental NMR spectra. The algorithms are described in detail and the approach is demonstrated on a set of spectra from the mistletoe protein phoratoxin B, a homolog of crambin. The results obtained compare well with those reported earlier based entirely on a manual assignment process. PMID:1841687

  11. 2D exchange 31P NMR spectroscopy of bacteriophage M13 and tobacco mosaic virus.

    PubMed Central

    Magusin, P C; Hemminga, M A

    1995-01-01

    Two-dimensional (2D) exchange 31P nuclear magnetic resonance spectroscopy is used to study the slow overall motion of the rod-shaped viruses M13 and tobacco mosaic virus in concentrated gels. Even for short mixing times, observed diagonal spectra differ remarkably from projection spectra and one-dimensional spectra. Our model readily explains this to be a consequence of the T2e anisotropy caused by slow overall rotation of the viruses about their length axis. 2D exchange spectra recorded for 30% (w/w) tobacco mosaic virus with mixing times < 1 s do not show any off-diagonal broadening, indicating that its overall motion occurs in the sub-Hz frequency range. In contrast, the exchange spectra obtained for 30% M13 show significant off-diagonal intensity for mixing times of 0.01 s and higher. A log-gaussian distribution around 25 Hz of overall diffusion coefficients mainly spread between 1 and 10(3) Hz faithfully reproduces the 2D exchange spectra of 30% M13 recorded at various mixing times in a consistent way. A small but notable change in diagonal spectra at increasing mixing time is not well accounted for by our model and is probably caused by 31P spin diffusion. PMID:7756532

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

    PubMed

    Vergara, Fredd; Shino, Amiu; Kikuchi, Jun

    2016-01-01

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

  13. HyperSPASM NMR: A new approach to single-shot 2D correlations on DNP-enhanced samples

    NASA Astrophysics Data System (ADS)

    Donovan, Kevin J.; Frydman, Lucio

    2012-12-01

    Dissolution DNP experiments are limited to a single or at most a few scans, before the non-Boltzmann magnetization has been consumed. This makes it impractical to record 2D NMR data by conventional, t1-incremented schemes. Here a new approach termed HyperSPASM to establish 2D heteronuclear correlations in a single scan is reported, aimed at dealing with this kind of challenge. The HyperSPASM experiment relies on imposing an amplitude-modulation of the data by a single Δt1 indirect-domain evolution time, and subsequently monitoring the imparted encoding on separate echo and anti-echo pathway signals within a single continuous acquisition. This is implemented via the use of alternating, switching, coherence selection gradients. As a result of these manipulations the phase imparted by a heteronucleus over its indirect domain evolution can be accurately extracted, and 2D data unambiguously reconstructed with a single-shot excitation. The nature of this sequence makes the resulting experiment particularly well suited for collecting indirectly-detected HSQC data on hyperpolarized samples. The potential of the ensuing HyperSPASM method is exemplified with natural-abundance hyperpolarized correlations on model systems.

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

    NASA Astrophysics Data System (ADS)

    Topcu, Gulacti; Ulubelen, Ayhan

    2007-05-01

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

  15. Improvement of Capture Compound Mass Spectrometry Technology (CCMS) for the Profiling of Human Kinases by Combination with 2D LC-MS/MS

    PubMed Central

    Fischer, Jenny J.; Graebner, Olivia; Dreger, Mathias; Glinski, Mirko; Baumgart, Sabine; Koester, Hubert

    2011-01-01

    An increasingly popular and promising field in functional proteomics is the isolation of proteome subsets based on small molecule-protein interactions. One platform approach in this field are Capture Compounds that contain a small molecule of interest to bind target proteins, a photo-activatable reactivity function to covalently trap bound proteins, and a sorting function to isolate captured protein conjugates from complex biological samples for direct protein identification by liquid chromatography/mass spectrometry (nLC-MS/MS). In this study we used staurosporine as a selectivity group for analysis in HepG2 cells derived from human liver. In the present study, we combined the functional isolation of kinases with different separation workflows of automated split-free nanoflow liquid chromatography prior to mass spectrometric analysis. Two different CCMS setups, CCMS technology combined with 1D LC-MS and 2D LC-MS, were compared regarding the total number of kinase identifications. By extending the chromatographic separation of the tryptic digested captured proteins from 1D LC linear gradients to 2D LC we were able to identify 97 kinases. This result is similar to the 1D LC setup we previously reported but this time 4 times less input material was needed. This makes CCMS of kinases an even more powerful tool for the proteomic profiling of this important protein family. PMID:21941435

  16. Analysis of the extracts of Isatis tinctoria by new analytical approaches of HPLC, MS and NMR.

    PubMed

    Zhou, Jue; Qu, Fan

    2011-01-01

    The methods of extraction, separation and analysis of alkaloids and indole glucosinolates (GLs) ofIsatis tinctoria were reviewed. Different analytical approaches such as High-pressure Liquid Chromatography (HPLC), Liquid Chromatography with Electrospray Ionization Mass Spectrometry (LC/ESI/MS), Electrospray Ionization Time-Of-Flight Mass Spectrometry (ESI-TOF-MS), and Nuclear Magnetic Resonance (NMR) were used to validate and identity of these constituents. These methods provide rapid separation, identification and quantitative measurements of alkaloids and GLs of Isatis tinctoria. By connection with different detectors to HPLC such as PDA, ELSD, ESI- and APCI-MS in positive and negative ion modes, complicated compounds could be detected with at least two independent detection modes. The molecular formula can be derived in a second step of ESI-TOF-MS data. But for some constituents, UV and MS cannot provide sufficient structure identification. After peak purification, NMR by semi-preparative HPLC can be used as a complementary method. PMID:22754056

  17. Conformational studies of [Nphe5]SFTI-1 by means of 2D NMR spectroscopy in conjunction with molecular dynamics calculations

    NASA Astrophysics Data System (ADS)

    Brzozowski, K.; Stawikowski, M.; Ślusarz, R.; Sikorska, E.; Lesner, A.; Łęgowska, A.; Rolka, K.

    2015-11-01

    Trypsin inhibitor SFTI-1 is the smallest and the most potent among BBI inhibitors. It is also an interesting object for SAR studies since it is cyclic 14 amino acid molecule which additionally contains disulfide bridge. We showed that elimination of head-to-tail cycliztion did not influence its activity. Moreover peptoid monomers of Nlys and Nphe introduced in the substrate specificity P1 position of monocyclic SFTI-1 preserved trypsin and chymotripsin inhibitory activity respectively and made P1-P1‧ bond proteolytically stable. These findings motivated us to perform conformational analysis of [Nphe5]SFTI-1 by means of 2D NMR spectroscopy and molecular dynamics calculations. Obtained structure occurred to be in a good agreement with published structures for wild-type SFTI-1, its monocyclic analog with disulfide bridge only as well as one containing Nlys peptoid monomer in P1 position.

  18. In-Depth Characterization and Spectral Library Building of Glycopeptides in the Tryptic Digest of a Monoclonal Antibody Using 1D and 2D LC-MS/MS.

    PubMed

    Dong, Qian; Yan, Xinjian; Liang, Yuxue; Stein, Stephen E

    2016-05-01

    This work presents a detailed analysis of glycopeptides produced in the tryptic digestion of an IgG1 reference material. Analysis was done by nanospray ESI LC-MS/MS over a wide range of HCD collision energies with both conventional 1D separation for various digestion conditions and a 20 fraction 2D-LC study of a single digest. An extended version of NIST-developed software for analysis of "shotgun" proteomics served to identify the glycopeptides from their precursor masses and product ions for peptides with up to three missed cleavages. A peptide with a single missed cleavage, TKPREEQYNSTYR, was dominant and led to the determination of almost all glycans reported in this study. The 2D studies found a total of 247 glycopeptide ions and 60 glycans of different masses, including 30 glycans found in the 1D studies. This significantly larger number of glycans than found in any other glycoanalysis of therapeutic glycoproteins is due to both the improved separation of sialylated versus asialylated species in the first (high-pH) dimension and the ability to inject large amounts of glycosylated peptides in the 2D studies. Systematic variations in retention with glycan size were also noted. Energy-dependent changes in HCD fragmentation confirmed the proposed glycan structures and led to a peak-annotated mass spectral library to aid the analysis of glycopeptides derived from IgG1 drugs. PMID:26990841

  19. Dihydrofolate reductase: Sequential resonance assignments using 2D and 3D NMR and secondary structure determination in solution

    SciTech Connect

    Carr, M.D.; Birdsall, B.; Jimenez-Barbero, J.; Polshakov, V.I.; McCormick, J.E.; Feeney, J.; Frenkiel, T.A.; Bauer, C.J. ); Roberts, G.C.K. )

    1991-06-25

    Three-dimensional (3D) heteronuclear NMR techniques have been used to make sequential {sup 1}H and {sup 15}H resonance assignments for most of the residues of Lactobacillus casei dihydrofolate reductase (DHFR), a monomeric protein of molecular mass 18,300 Da. A uniformly {sup 15}N-labeled sample of the protein was prepared and its complex with methotrexate (MTX) studied by 3D {sup 15}N/{sup 1}H nuclear Overhauserheteronuclear multiple quantum coherence (NOESY-HMQC), Harmann-Hahn-heteronuclear multiple quantum coherence (HOHAHA-HMQC), and HMQC-NOESY-HMQC experiments. These experiments overcame most of the spectral overlap problems caused by chemical shift degeneracies in 2D spectra and allowed the {sup 1}H-{sup 1}H through-space and through-bond connectivities to be identified unambiguously, leading to the resonance assignments. The novel HMQC-NOESY-HMQC experiment allows NOE cross peaks to be detected between NH protons even when their {sup 1}H chemical shifts are degenerate as long as the amide {sup 15}N chemical shifts are nondegenerate. The 3D experiments, in combination with conventional 2D NOESY, COSY, and HOHAHA experiments on unlabelled and selectively deuterated DHFR, provide backbone assignments for 146 of the 162 residues and side-chain assignments for 104 residues of the protein. Data from the NOE-based experiments and identification of the slowly exchanging amide protons provide detailed information about the secondary structure of the binary complex of the protein with methotrexate.

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

    PubMed

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

    2007-08-01

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

  1. Proton zero-quantum 2D NMR of 2-propenenitrile aligned by an electric field. Determination of the 2H and 14N quadrupole coupling constants

    NASA Astrophysics Data System (ADS)

    Ruessink, B. H.; De Kanter, F. J. J.; MaClean, C.

    Zero-quantum NMR, selectively detected by 2D NMR, is applied to observe small 1H- 1H dipolar couplings in a polar liquid partially oriented by a strong electric field. The normal (single-quantum) 1H spectrum is severely broadened, which prevents the observation of small couplings. The results from the zero-quantum proton spectrum are used to calculate the 2H and 14N quadrupole coupling constants of 2-deutero-2-propenenitrile from the 2H and 14N NMR spectra.

  2. Identification and quantification of flavonoids and ellagic acid derivatives in therapeutically important Drosera species by LC-DAD, LC-NMR, NMR, and LC-MS.

    PubMed

    Zehl, Martin; Braunberger, Christina; Conrad, Jürgen; Crnogorac, Marija; Krasteva, Stanimira; Vogler, Bernhard; Beifuss, Uwe; Krenn, Liselotte

    2011-06-01

    Droserae herba is a drug commonly used for treatment of convulsive or whooping cough since the seventeenth century. Because of the contribution of flavonoids and ellagic acid derivatives to the therapeutic activity of Droserae herba, an LC-DAD method has been developed for quantification of these analytes in four Drosera species used in medicine (Drosera anglica, D. intermedia, D. madagascariensis, and D. rotundifolia). During elaboration of the method 13 compounds, including three substances not previously described for Drosera species, were detected and unambiguously identified by means of extensive LC-MS and LC-NMR experiments and by off-line heteronuclear 2D NMR after targeted isolation. The most prominent component of D. rotundifolia and D. anglica, 2″-O-galloylhyperoside, with myricetin-3-O-β-glucopyranoside and kaempferol-3-O-(2″-O-galloyl)-β-galactopyranoside, were identified for the very first time in this genus. The LC-DAD method for quantification was thoroughly validated, and enables, for the first time, separation and precise analysis of these analytes in Droserae herba. Simple sample preparation and use of a narrow-bore column guarantee low cost and simplicity of the suggested system, which is excellently suited to quality control of the drug or herbal medicinal products containing this drug. PMID:21298259

  3. Large structure rearrangement of colicin ia channel domain after membrane binding from 2D 13C spin diffusion NMR.

    PubMed

    Luo, Wenbin; Yao, Xiaolan; Hong, Mei

    2005-05-01

    One of the main mechanisms of membrane protein folding is by spontaneous insertion into the lipid bilayer from the aqueous environment. The bacterial toxin, colicin Ia, is one such protein. To shed light on the conformational changes involved in this dramatic transfer from the polar to the hydrophobic milieu, we carried out 2D magic-angle spinning (13)C NMR experiments on the water-soluble and membrane-bound states of the channel-forming domain of colicin Ia. Proton-driven (13)C spin diffusion spectra of selectively (13)C-labeled protein show unequivocal attenuation of cross-peaks after membrane binding. This attenuation can be assigned to distance increases but not reduction of the diffusion coefficient. Analysis of the statistics of the interhelical and intrahelical (13)C-(13)C distances in the soluble protein structure indicates that the observed cross-peak reduction is well correlated with a high percentage of short interhelical contacts in the soluble protein. This suggests that colicin Ia channel domain becomes open and extended upon membrane binding, thus lengthening interhelical distances. In comparison, cross-peaks with similar intensities between the two states are dominated by intrahelical contacts in the soluble state. This suggests that the membrane-bound structure of colicin Ia channel domain may be described as a "molten globule", in which the helical secondary structure is retained while the tertiary structure is unfolded. This study demonstrates that (13)C spin diffusion NMR is a valuable tool for obtaining qualitative long-range distance constraints on membrane protein folding. PMID:15853348

  4. Analysis of pharmaceutical impurities using multi-heartcutting 2D LC coupled with UV-charged aerosol MS detection.

    PubMed

    Zhang, Kelly; Li, Yi; Tsang, Midco; Chetwyn, Nik P

    2013-09-01

    To overcome challenges in HPLC impurity analysis of pharmaceuticals, we developed an automated online multi-heartcutting 2D HPLC system with hyphenated UV-charged aerosol MS detection. The first dimension has a primary column and the second dimension has six orthogonal columns to enhance flexibility and selectivity. The two dimensions were interfaced by a pair of switching valves equipped with six trapping loops that allow multi-heartcutting of peaks of interest in the first dimension and also allow "peak parking." The hyphenated UV-charged aerosol MS detection provides comprehensive detection for compounds with and without UV chromophores, organics, and inorganics. It also provides structural information for impurity identification. A hidden degradation product that co-eluted with the drug main peak was revealed by RP × RP separation and thus enabled the stability-indicating method development. A poorly retained polar component with no UV chromophores was analyzed by RP × hydrophilic interaction liquid chromatography separation with charged aerosol detection. Furthermore, using this system, the structures of low-level impurities separated by a method using nonvolatile phosphate buffer were identified and tracked by MS in the second dimension. PMID:23821312

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

    PubMed

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

    2010-10-01

    Solid-state NMR (SSNMR) can provide detailed structural information about amorphous solid dispersions of pharmaceutical small molecules. In this study, the ability of SSNMR experiments based on dipolar correlation, spin diffusion, and relaxation measurements to characterize the structure of solid dispersions is explored. Observation of spin diffusion effects using the 2D (1)H-(13)C cross-polarization heteronuclear correlation (CP-HETCOR) experiment is shown to be a useful probe of association between the amorphous drug and polymer that is capable of directly proving glass solution formation. Dispersions of acetaminophen and indomethacin in different polymers are examined using this approach, as well as (1)H double-quantum correlation experiments to probe additional structural features. (1)H-(19)F CP-HETCOR serves a similar role for fluorinated drug molecules such as diflunisal in dispersions, providing a rapid means to prove the formation of a glass solution. Phase separation is detected using (13)C, (19)F, and (23)Na-detected (1)H T(1) experiments in crystalline and amorphous solid dispersions that contain small domains. (1)H T(1) measurements of amorphous nanosuspensions of trehalose and dextran illustrate the ability of SSNMR to detect domain size effects in dispersions that are not glass solutions via spin diffusion effects. Two previously unreported amorphous solid dispersions involving up to three components and containing voriconazole and telithromycin are analyzed using these experiments to demonstrate the general applicability of the approach. PMID:20681586

  6. An omics approach to rational feed: Enhancing growth in CHO cultures with NMR metabolomics and 2D-DIGE proteomics.

    PubMed

    Blondeel, Eric J M; Ho, Raymond; Schulze, Steffen; Sokolenko, Stanislav; Guillemette, Simon R; Slivac, Igor; Durocher, Yves; Guillemette, J Guy; McConkey, Brendan J; Chang, David; Aucoin, Marc G

    2016-09-20

    Expression of recombinant proteins exerts stress on cell culture systems, affecting the expression of endogenous proteins, and contributing to the depletion of nutrients and accumulation of waste metabolites. In this work, 2D-DIGE proteomics was employed to analyze differential expression of proteins following stable transfection of a Chinese Hamster Ovary (CHO) cell line to constitutively express a heavy-chain monoclonal antibody. Thirty-four proteins of significant differential expression were identified and cross-referenced with cellular functions and metabolic pathways to identify points of cell stress. Subsequently, 1D-(1)H NMR metabolomics experiments analyzed cultures to observe nutrient depletion and waste metabolite accumulations to further examine these cell stresses and pathways. From among fifty metabolites tracked in time-course, eight were observed to be completely depleted from the production media, including: glucose, glutamine, proline, serine, cystine, asparagine, choline, and hypoxanthine, while twenty-three excreted metabolites were also observed to accumulate. The differentially expressed proteins, as well as the nutrient depletion and accumulation of these metabolites corresponded with upregulated pathways and cell systems related to anaplerotic TCA-replenishment, NADH/NADPH replenishment, tetrahydrofolate cycle C1 cofactor conversions, limitations to lipid synthesis, and redox modulation. A nutrient cocktail was assembled to improve the growth medium and alleviate these cell stresses to achieve a ∼75% improvement to peak cell densities. PMID:27496566

  7. Automated structure verification based on a combination of 1D (1)H NMR and 2D (1)H - (13)C HSQC spectra.

    PubMed

    Golotvin, Sergey S; Vodopianov, Eugene; Pol, Rostislav; Lefebvre, Brent A; Williams, Antony J; Rutkowske, Randy D; Spitzer, Timothy D

    2007-10-01

    A method for structure validation based on the simultaneous analysis of a 1D (1)H NMR and 2D (1)H - (13)C single-bond correlation spectrum such as HSQC or HMQC is presented here. When compared with the validation of a structure by a 1D (1)H NMR spectrum alone, the advantage of including a 2D HSQC spectrum in structure validation is that it adds not only the information of (13)C shifts, but also which proton shifts they are directly coupled to, and an indication of which methylene protons are diastereotopic. The lack of corresponding peaks in the 2D spectrum that appear in the 1D (1)H spectrum, also gives a clear picture of which protons are attached to heteroatoms. For all these benefits, combined NMR verification was expected and found by all metrics to be superior to validation by 1D (1)H NMR alone. Using multiple real-life data sets of chemical structures and the corresponding 1D and 2D data, it was possible to unambiguously identify at least 90% of the correct structures. As part of this test, challenging incorrect structures, mostly regioisomers, were also matched with each spectrum set. For these incorrect structures, the false positive rate was observed as low as 6%. PMID:17694570

  8. A new approach to the optimisation of non-uniform sampling schedules for use in the rapid acquisition of 2D NMR spectra of small molecules.

    PubMed

    Sidebottom, Philip J

    2016-08-01

    Non-uniform sampling allows the routine, rapid acquisition of 2D NMR data. When the number of points in the NUS schedule is low, the quality of the data obtained is very dependent of the schedule used. A simple proceedure for finding optimium schedules has been developed and is demonstrated for the multiplicity edited HSQC experiment. PMID:27160788

  9. The novel acid degradation products of losartan: Isolation and characterization using Q-TOF, 2D-NMR and FTIR.

    PubMed

    Kumar Pandey, Avadhesh; Rapolu, Ravi; Raju, Ch Krishnam; Sasalamari, Gururaj; Kumar Goud, Sanath; Awasthi, Atul; Navalgund, Sameer G; Surendranath, Koduru V

    2016-02-20

    Forced degradation of losartan potassium in acidic condition resulted into three potential unknown impurities. These unknown degradation products marked as LD-I, LD-II and LD-III were analyzed using a new reverse-phase high performance liquid chromatography (HPLC), eluting at 3.63, 3.73 and 3.91 relative retention times with respect to losartan potassium (LOS) peak. All three were isolated from reaction mass using preparative HPLC and their structures were elucidated using LC-MS/MS, multidimensional NMR and FTIR spectroscopic techniques, as 5(2),11(2)-dibutyl-5(4),11(4)-dichloro-1(1)H,5(1)H,7(1)H,11(1)H-1(5,1),7(1,5)-ditetrazola-5,11(1,5)-diimidazola-2,8(1,2),3,9(1,4)-tetrabenzenacyclododecaphane,(Z)-5(2),11(2)-dibutyl-5(4),11(4)-dichloro-1(1)H,5(1)H,7(2)H,11(1)H-1(5,1),7(2,5)-ditetrazola-5,11(1,5)-diimidazola-2,8(1,2),3,9(1,4)-tetrabenzenacyclododecaphane, and 5(2),11(2)-dibutyl-5(4),11(4)-dichloro-1(2)H,5(1)H,7(2)H,11(1)H-1(5,2),7(2,5)-ditetrazola-5,11(1,5)-diimidazola-2,8(1,2),3,9(1,4)-tetrabenzenacyclododecaphane, respectively. To best of our knowledge, all three degradation products are novel impurities which are not discussed at any form of publication yet. PMID:26704631

  10. Quantitative metabolite profiling of edible onion species by NMR and HPLC-MS.

    PubMed

    Soininen, Tuula H; Jukarainen, Niko; Auriola, Seppo O K; Julkunen-Tiitto, Riitta; Karjalainen, Reijo; Vepsäläinen, Jouko J

    2014-12-15

    Allium genus is a treasure trove of valuable bioactive compounds with potentially therapeutically important properties. This work utilises HPLC-MS and a constrained total-line-shape (CTLS) approach applied to (1)H NMR spectra to quantify metabolites present in onion species to reveal important inter-species differences. Extensive differences were detected between the sugar concentrations in onion species. Yellow onion contained the highest and red onion the lowest amounts of amino acids. The main flavonol-glucosides were quercetin 3,4'-diglucoside and quercetin 4'-glucoside. In general, the levels of flavonols were, higher in yellow onions than in red onions, and garlic and leek contained a lower amount of flavonols than the other Allium species. Our results highlight how (1)H NMR together with HPLC-MS can be useful in the quantification and the identification of the most abundant metabolites, representing an efficient means to pinpoint important functional food ingredients from Allium species. PMID:25038704

  11. Examination of the structures of several glycerolipids from marine macroalgae by NMR and GC-MS.

    PubMed

    Logvinov, Stepan; Gerasimenko, Natalia; Esipov, Andrey; Denisenko, Vladimir A

    2015-12-01

    Several classes of glycerolipids were isolated from the total lipids of the algae Saccharina cichorioides, Eualaria fistulosa, Fucus evanescens, Sargassum pallidum, Silvetia babingtonii (Ochrophyta, Phaeophyceae), Tichocarpus crinitus, and Neorhodomela larix (Rhodophyta, Florideophyceae). The structures of these lipids were examined by nuclear magnetic resonance (NMR) spectroscopy, including 1D ((1) H and (13) C) and 2D (COSY, HSQC and HMBC) experiments. All of the investigated algae included common galactolipids and sulfonoglycolipids as the major glycolipids. Minor glycolipids isolated from S. cichorioides, T. crinitus, and N. laris were identified as lyso-galactolipids with a polar group consisted of the galactose. Comparison of the (1) H NMR data of minor nonpolar lipids isolated from the extracts of the brown algae S. pallidum and F. evanescens with the (1) H NMR data of other lipids allowed them to be identified as diacylglycerols. The structures of betaine lipids isolated from brown algae were confirmed by NMR for the first time. The fatty acid compositions of the isolated lipids were determined by gas chromatography-mass spectrometry. PMID:26987002

  12. Mapping and Identification of the Urine Proteome of Prostate Cancer Patients by 2D PAGE/MS

    PubMed Central

    Kiprijanovska, Sanja; Stavridis, Sotir; Stankov, Oliver; Komina, Selim; Petrusevska, Gordana; Polenakovic, Momir; Davalieva, Katarina

    2014-01-01

    Proteome analysis of the urine has shown that urine contains disease-specific information for a variety of urogenital system disorders, including prostate cancer (PCa). The aim of this study was to determine the protein components of urine from PCa patients. Urine from 8 patients with clinically and histologically confirmed PCa was analyzed by conventional 2D PAGE. The MS identification of the most prominent 125 spots from the urine map revealed 45 distinct proteins. According to Gene Ontology, the identified proteins are involved in a variety of biological processes, majority of them are secreted (71%), and half of them are enzymes or transporters. Comparison with the normal urine proteome revealed 11 proteins distinctive for PCa. Using Ingenuity Pathways Analysis, we have found 3 proteins (E3 ubiquitin-protein ligase rififylin, tumor protein D52, and thymidine phosphorylase) associated with cellular growth and proliferation (p = 8.35 × 10−4 − 3.41 × 10−2). The top network of functional associations between 11 proteins was Cell Death and Survival, Cell-To-Cell Signaling and Interaction, and System Development and Function (p = 10−30). In summary, we have created an initial proteomic map of PCa patient's urine. The results from this study provide some leads to understand the molecular bases of prostate cancer. PMID:25215235

  13. A Group of Novel Serum Diagnostic Biomarkers for Multidrug-Resistant Tuberculosis by iTRAQ-2D LC-MS/MS and Solexa Sequencing

    PubMed Central

    Wang, Chong; Liu, Chang-Ming; Wei, Li-Liang; Shi, Li-Ying; Pan, Zhi-Fen; Mao, Lian-Gen; Wan, Xiao-Chen; Ping, Ze-Peng; Jiang, Ting-Ting; Chen, Zhong-Liang; Li, Zhong-Jie; Li, Ji-Cheng

    2016-01-01

    The epidemic of pulmonary tuberculosis (TB), especially multidrug-resistance tuberculosis (MDR-TB) presented a major challenge for TB treatment today. We performed iTRAQ labeling coupled with two-dimensional liquid chromatography-tandem mass spectrometry (2D LC-MS/MS) and Solexa sequencing among MDR-TB patients, drug-sensitive tuberculosis (DS-TB) patients, and healthy controls. A total of 50 differentially expressed proteins and 43 differentially expressed miRNAs (fold change >1.50 or <0.60, P<0.05) were identified in the MDR-TB patients compared to both DS-TB patients and healthy controls. We found that 22.00% of differentially expressed proteins and 32.56% of differentially expressed miRNAs were related, and could construct a network mainly in complement and coagulation cascades. Significant differences in CD44 antigen (CD44), coagulation factor XI (F11), kininogen-1 (KNG1), miR-4433b-5p, miR-424-5p, and miR-199b-5p were found among MDR-TB patients, DS-TB patients and healthy controls (P<0.05) by enzyme-linked immunosorbent assay (ELISA) and SYBR green qRT-PCR validation. A strong negative correlation, consistent with the target gene prediction, was found between miR-199b-5p and KNG1 (r=-0.232, P=0.017). Moreover, we established the MDR-TB diagnostic model based on five biomarkers (CD44, KNG1, miR-4433b-5p, miR-424-5p, and miR-199b-5p). Our study proposes potential biomarkers for MDR-TB diagnosis, and also provides a new experimental basis to understand the pathogenesis of MDR-TB. PMID:26884721

  14. Comparative proteome analysis of brown adipose tissue in obese C57BL/6J mice using iTRAQ-coupled 2D LC-MS/MS.

    PubMed

    Li, Juan; Zhao, Wei-Gang; Shen, Zhu-Fang; Yuan, Tao; Liu, Shuai-Nan; Liu, Quan; Fu, Yong; Sun, Wei

    2015-01-01

    High-fat diet (HFD) leads to the development of obesity accompanied by insulin resistance, which increases the risk of type 2 diabetes mellitus and cardiovascular disease. Brown adipose tissue (BAT) plays an essential role in energy metabolism, thus it will give us promising treatment targets through elucidating underlying mechanisms of BAT in obesity. In this study, female C57BL/6J mice were fed HFD or normal diet (ND) for 22 weeks. Hyperinsulinemic-euglycemic clamp was performed to evaluate insulin sensitivity, which was independently correlated with obesity. Using isobaric tag for relative and absolute quantification (iTRAQ) coupled with 2D LC-MS/MS, we quantitated 3048 proteins in BAT. As compared HFD with ND, we obtained 727 differentially expressed proteins. Functional analysis found that those proteins were mainly assigned to the pathway of mitochondrial function. In this pathway, carnitine O-palmitoyltransferase 2 (CPT2), uncoupling protein 1 (UCP1) and apoptosis-inducing factor 1 (AIF1) were up-regulated significantly by HFD, and they were confirmed by western blotting. The results indicated that HFD might induce the apoptosis of brown adipocytes via the up-regulated AIF1. Meanwhile, HFD also stimulated fatty acid β-oxidation and raised compensatory energy consuming through the increases of CPT2 and UCP1, respectively. However, the apoptosis of brown adipocytes might weaken the compensatory energy expenditure, and finally contribute to overweight/obesity. So, preventing the apoptosis of brown adipocytes may be the key target to treat obesity. PMID:25747866

  15. Structural environments of carboxyl groups in natural organic molecules from terrestrial systems. Part 2: 2D NMR spectroscopy

    NASA Astrophysics Data System (ADS)

    Deshmukh, Ashish P.; Pacheco, Carlos; Hay, Michael B.; Myneni, Satish C. B.

    2007-07-01

    Carboxyl groups are abundant in natural organic molecules (NOM) and play a major role in their reactivity. The structural environments of carboxyl groups in IHSS soil and river humic samples were investigated using 2D NMR (heteronuclear and homonuclear correlation) spectroscopy. Based on the 1H- 13C heteronuclear multiple-bond correlation (HMBC) spectroscopy results, the carboxyl environments in NOM were categorized as Type I (unsubstituted and alkyl-substituted aliphatic/alicyclic), Type II (functionalized carbon substituted), Type IIIa, b (heteroatom and olefin substituted), and Type IVa, b (5-membered heterocyclic aromatic and 6-membered aromatic). The most intense signal in the HMBC spectra comes from the Type I carboxyl groups, including the 2JCH and 3JCH couplings of unsubstituted aliphatic and alicyclic acids, though this spectral region also includes the 3JCH couplings of Type II and III structures. Type II and III carboxyls have small but detectable 2JCH correlations in all NOM samples except for the Suwannee River humic acid. Signals from carboxyls bonded to 5-membered aromatic heterocyclic fragments (Type IVa) are observed in the soil HA and Suwannee River FA, while correlations to 6-membered aromatics (Type IVb) are only observed in Suwannee River HA. In general, aromatic carboxylic acids may be present at concentrations lower than previously imagined in these samples. Vibrational spectroscopy results for these NOM samples, described in an accompanying paper [Hay M. B. and Myneni S. C. B. (2007) Structural environments of carboxyl groups in natural organic molecules from terrestrial systems. Part 1: Infrared spectroscopy. Geochim. Cosmochim. Acta (in press)], suggest that Type II and Type III carboxylic acids with α substituents (e.g., -OH, -OR, or -CO 2H) constitute the majority of carboxyl structures in all humic substances examined. Furoic and salicylic acid structures (Type IV) are also feasible fragments, albeit as minor constituents. The

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

    DOE PAGESBeta

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

    2016-04-26

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

  17. 2D 1H and 3D 1H-15N NMR of zinc-rubredoxins: contributions of the beta-sheet to thermostability.

    PubMed Central

    Richie, K. A.; Teng, Q.; Elkin, C. J.; Kurtz, D. M.

    1996-01-01

    Based on 2D 1H-1H and 2D and 3D 1H-15N NMR spectroscopies, complete 1H NMR assignments are reported for zinc-containing Clostridium pasteurianum rubredoxin (Cp ZnRd). Complete 1H NMR assignments are also reported for a mutated Cp ZnRd, in which residues near the N-terminus, namely, Met 1, Lys 2, and Pro 15, have been changed to their counterparts, (-), Ala and Glu, respectively, in rubredoxin from the hyperthermophilic archaeon, Pyrococcus furiosus (Pf Rd). The secondary structure of both wild-type and mutated Cp ZnRds, as determined by NMR methods, is essentially the same. However, the NMR data indicate an extension of the three-stranded beta-sheet in the mutated Cp ZnRd to include the N-terminal Ala residue and Glu 15, as occurs in Pf Rd. The mutated Cp Rd also shows more intense NOE cross peaks, indicating stronger interactions between the strands of the beta-sheet and, in fact, throughout the mutated Rd. However, these stronger interactions do not lead to any significant increase in thermostability, and both the mutated and wild-type Cp Rds are much less thermostable than Pf Rd. These correlations strongly suggest that, contrary to a previous proposal [Blake PR et al., 1992, Protein Sci 1:1508-1521], the thermostabilization mechanism of Pf Rd is not dominated by a unique set of hydrogen bonds or electrostatic interactions involving the N-terminal strand of the beta-sheet. The NMR results also suggest that an overall tighter protein structure does not necessarily lead to increased thermostability. PMID:8732760

  18. Determination of lipid content of oleaginous microalgal biomass by NMR spectroscopic and GC-MS techniques.

    PubMed

    Sarpal, Amarijt S; Teixeira, Claudia M L L; Silva, Paulo R M; Lima, Gustavo M; Silva, Samantha R; Monteiro, Thays V; Cunha, Valnei S; Daroda, Romeu J

    2015-05-01

    Direct methods based on (1)H NMR spectroscopic techniques have been developed for the determination of neutral lipids (triglycerides and free fatty acids) and polar lipids (glyceroglycolipids/phospholipids) in the solvent extracts of oleaginous microalgal biomasses cultivated on a laboratory scale with two species in different media. The chemical shift assignments observed in the (1)H and (13)C NMR spectra corresponding to unsaturated (C18:N, N = 1-3, C20:3, C20:5, C22:6, epoxy) and saturated (C14-C18) fatty acid ester components in a complex matrix involving overlapped resonances have been unambiguously confirmed by the application of 2D NMR spectroscopy (total correlation spectroscopy and heteronuclear single quantum coherence-total correlation spectroscopy). The study of the effect of a polar lipid matrix on the determination of neutral lipids by an internal reference blending process by a systematic designed experimental protocol has provided absolute quantification. The fatty acid composition of algal extracts was found to be similar to that of vegetable oils containing saturated (C16-C18:0) and unsaturated (C18:N, N = 1-3, C20:N, N = 3-4, C22:6) fatty acids as confirmed by NMR spectroscopy and gas chromatography-mass spectrometry analyses. The NMR methods developed offer great potential for rapid screening of algal strains for generation of algal biomass with the desired lipid content, quality, and potential for biodiesel and value-added polyunsaturated fatty acids in view of the cost economics of the overall cost of generation of the biomass. PMID:25801382

  19. NMR Investigations of Nitrophorin 2 Belt Side Chain Effects on Heme Orientation and Seating of Native N-terminus NP2 and NP2(D1A)

    PubMed Central

    Muthu, Dhanasekaran; Shokhireva, Tatiana K.; Garrett, Sarah A.; Goren, Allena M.; Zhang, Hongjun

    2014-01-01

    Nitrophorin 2, one of the four NO–storing and –releasing proteins found in the saliva of the blood-sucking bug Rhodnius prolixus, has a more ruffled heme and a high preference for a particular heme orientation (B), compared to those of NP1 and NP4, which show no preference (A:B ~ 1:1), suggesting that it fits more tightly in the β-barrel protein. In this work we have prepared a series of “Belt” mutants of NP2(D1A) and (ΔM0)NP2 aimed at reducing the size of aromatic or other residues that surround the heme, and investigated them as the high-spin aqua and low-spin N-methylimidazole (NMeIm) complexes. The “Belt” mutants included Y38A, Y38F, F42A, F66A, Y85A, Y85F, Y104A, I120T and a triple mutant of NP2(D1A), the F42L,L106F,I120T mutant. Although I120 has been mainly considered to be a distal pocket residue, the CδH3 of I120 lies directly above the heme 3-methyl, at 2.67 Å, of heme orientation B, or 2-vinyl of A, and it thus plays a role as a “Belt” mutant, a role that turns out to be extremely important in creating the strong favoring of the B heme orientation (A:B = 1:14) for NP2(D1A) or 1:12 for (ΔM0)NP2. The results show that the 1D 1H NMR spectra of the high-spin forms are quite sensitive to changes in the shape of the heme binding cavity. The single mutation I120T eliminates the favorability of the B heme orientation by producing a heme A:B orientation of 1:1, while the single mutation F42A reverses the heme orientation from A:B = 1:14 seen for NP2(D1A) to 10:1 for NP2(D1A,F42A). The most extreme ratio was found for the triple mutant of NP2(D1A), NP2(D1A,F42L,L105F,I120T), in which A:B ~25:1, a ΔG change of about −3.5 kcal/mol or −14.1 kJ/mol with respect to NP2(D1A). The seating of the heme is modified as well in that mutant and several others, by rotations of the heme by up to 4° from the seating observed in NP2(D1A), in order to relieve steric interactions between a vinyl β-carbon and a protein side chain, or to fill a cavity

  20. Using NMR, SIP, and MS measurements for monitoring subsurface biogeochemical reactions at the Rifle IFRC site

    NASA Astrophysics Data System (ADS)

    Rosier, C. L.; Keating, K.; Williams, K. H.; Robbins, M.; Ntarlagiannis, D.; Grunewald, E.; Walsh, D. O.

    2013-12-01

    The Rifle Integrated Field Research Challenge (IFRC) site is located on a former uranium ore-processing facility in Rifle, Colorado (USA). Although removal of tailings and contaminated surface materials was completed in 1996, residual uranium contamination of groundwater and subsurface sediments remains. Since 2002, research at the site has primarily focused on quantifying uranium mobility associated with stimulated and natural biogeochemical processes. Uranium mobility at the Rifle IFRC site is typically quantified through direct sampling of groundwater; however, direct sampling does not provide information about the solid phase material outside of the borehole and continuous measurements are not always possible due to multiple constraints. Geophysical methods have been suggested as a minimally invasive alternative approach for long term monitoring of biogeochemical reactions associated with uranium remediation. In this study, nuclear magnetic resonance (NMR), spectral induced polarization (SIP), and magnetic susceptibility (MS) are considered as potential geophysical methods for monitoring the biogeochemical reactions occurring at the Rifle IFRC site. Additionally, a pilot field study using an NMR borehole-logging tool was carried out at the Rifle IFRC site. These methods are sensitive to changes in the chemical and physical subsurface properties that occur as a result of bioremediation efforts; specifically, changes in the redox state and chemical form of iron, production of iron sulfide minerals, production of the magnetic mineral magnetite, and associated changes in the pore geometry. Laboratory experiments consisted of monitoring changes in the NMR, SIP and MS response of an acetate-amended columns packed with sediments from the Rifle IFRC site over the course of two months. The MS values remained relatively stable throughout the course of the experiment suggesting negligible production of magnetic phases (e.g. magnetite, pyrrhotite) as a result of enhanced

  1. Comprehensive Chemical Profiling of Picrorhiza kurroa Royle ex Benth Using NMR, HPTLC and LC-MS/MS Techniques.

    PubMed

    Kumar, Dinesh; Kumar, Rakesh; Singh, Bikram; Ahuja, Paramvir Singh

    2016-01-01

    Picrorhiza kurroa is an important herb in Indian medicine and contains cucurbitacins, flavonoids, phenolics, iridoid-glucoside and their derivatives as active constituents for the treatment of indigestion, fever, hepatitis, cancer, liver and respiratory diseases. Extensive use of P. kurroa needs detailed analysis and recognition of chemical diversity, is of great importance to evaluate their role as quality control markers. In the present study, comprehensive metabolic profiling of crude extracts of leaves and rhizomes of P. kurroa was carried out using NMR, HPTLC and LC-MS/MS. Primary and secondary metabolites were unambiguously identified along with a new report of monoterpenic glycoside (1-β-D-glucopyranosyl)-8-hydroxy-3,7-dimethyl-oct-2(E),6(E)-dienoate) in P. Kurroa. Significant qualitative differences with respect to the secondary metabolites were noticed between the leaves and rhizomes tissues. Leaves contained more cucurbitacins and flavonoids while iridoids were present more in rhizomes. The comprehensive chemical profiling is expected to give an idea of chemical diversity and quality of P. kurroa, for their ultimate utilisation in various applications. PMID:26777484

  2. Orthogonal analytical methods for botanical standardization: Determination of green tea catechins by qNMR and LC-MS/MS

    PubMed Central

    Napolitano, José G.; Gödecke, Tanja; Lankin, David C.; Jaki, Birgit U.; McAlpine, James B.; Chen, Shao-Nong; Pauli, Guido F.

    2013-01-01

    The development of analytical methods for parallel characterization of multiple phytoconstituents is essential to advance the quality control of herbal products. While chemical standardization is commonly carried out by targeted analysis using gas or liquid chromatography-based methods, more universal approaches based on quantitative 1H NMR (qHNMR) measurements are being used increasingly in the multi-targeted assessment of these complex mixtures. The present study describes the development of a 1D qHNMR-based method for simultaneous identification and quantification of green tea constituents. This approach utilizes computer-assisted 1H iterative Full Spin Analysis (HiFSA) and enables rapid profiling of seven catechins in commercial green tea extracts. The qHNMR results were cross-validated against quantitative profiles obtained with an orthogonal LC-MS/MS method. The relative strengths and weaknesses of both approaches are discussed, with special emphasis on the role of identical reference standards in qualitative and quantitative analyses. PMID:23870106

  3. Combining NMR and LC/MS Using Backward Variable Elimination: Metabolomics Analysis of Colorectal Cancer, Polyps, and Healthy Controls.

    PubMed

    Deng, Lingli; Gu, Haiwei; Zhu, Jiangjiang; Nagana Gowda, G A; Djukovic, Danijel; Chiorean, E Gabriela; Raftery, Daniel

    2016-08-16

    Both nuclear magnetic resonance (NMR) spectroscopy and mass spectrometry (MS) play important roles in metabolomics. The complementary features of NMR and MS make their combination very attractive; however, currently the vast majority of metabolomics studies use either NMR or MS separately, and variable selection that combines NMR and MS for biomarker identification and statistical modeling is still not well developed. In this study focused on methodology, we developed a backward variable elimination partial least-squares discriminant analysis algorithm embedded with Monte Carlo cross validation (MCCV-BVE-PLSDA), to combine NMR and targeted liquid chromatography (LC)/MS data. Using the metabolomics analysis of serum for the detection of colorectal cancer (CRC) and polyps as an example, we demonstrate that variable selection is vitally important in combining NMR and MS data. The combined approach was better than using NMR or LC/MS data alone in providing significantly improved predictive accuracy in all the pairwise comparisons among CRC, polyps, and healthy controls. Using this approach, we selected a subset of metabolites responsible for the improved separation for each pairwise comparison, and we achieved a comprehensive profile of altered metabolite levels, including those in glycolysis, the TCA cycle, amino acid metabolism, and other pathways that were related to CRC and polyps. MCCV-BVE-PLSDA is straightforward, easy to implement, and highly useful for studying the contribution of each individual variable to multivariate statistical models. On the basis of these results, we recommend using an appropriate variable selection step, such as MCCV-BVE-PLSDA, when analyzing data from multiple analytical platforms to obtain improved statistical performance and a more accurate biological interpretation, especially for biomarker discovery. Importantly, the approach described here is relatively universal and can be easily expanded for combination with other analytical

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

    NASA Astrophysics Data System (ADS)

    Gopinath, T.; Veglia, Gianluigi

    2013-05-01

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

  5. Homo- and heteronuclear 2D NMR approaches to analyse a mixture of deuterated unlike/like stereoisomers using weakly ordering chiral liquid crystals

    NASA Astrophysics Data System (ADS)

    Ben Ali, Karim; Lafon, Olivier; Zimmermann, Herbert; Guittet, Eric; Lesot, Philippe

    2007-08-01

    We describe several homo- and heteronuclear 2D NMR strategies dedicated to the analysis of anisotropic 2H spectra of a mixture of dideuterated unlike/like stereoisomers with two remote stereogenic centers, using weakly orienting chiral liquid crystals. To this end, we propose various 2D correlation experiments, denoted "D(H) nD" or "D(H) nC" (with n = 1, 2), that involve two heteronuclear polarization transfers of INEPT-type with one or two proton relays. The analytical expressions of correlation signals for four pulse sequences reported here were calculated using the product-operators formalism for spin I = 1 and S = 1/2. The features and advantages of each scheme are presented and discussed. The efficiency of these 2D sequences is illustrated using various deuterated model molecules, dissolved in organic solutions of polypeptides made of poly- γ-benzyl- L-glutamate (PBLG) or poly- ɛ-carbobenzyloxy- L-lysine (PCBLL) and NMR numerical simulations.

  6. Reduced dimensionality (3,2)D NMR experiments and their automated analysis: implications to high-throughput structural studies on proteins.

    PubMed

    Reddy, Jithender G; Kumar, Dinesh; Hosur, Ramakrishna V

    2015-02-01

    Protein NMR spectroscopy has expanded dramatically over the last decade into a powerful tool for the study of their structure, dynamics, and interactions. The primary requirement for all such investigations is sequence-specific resonance assignment. The demand now is to obtain this information as rapidly as possible and in all types of protein systems, stable/unstable, soluble/insoluble, small/big, structured/unstructured, and so on. In this context, we introduce here two reduced dimensionality experiments – (3,2)D-hNCOcanH and (3,2)D-hNcoCAnH – which enhance the previously described 2D NMR-based assignment methods quite significantly. Both the experiments can be recorded in just about 2-3 h each and hence would be of immense value for high-throughput structural proteomics and drug discovery research. The applicability of the method has been demonstrated using alpha-helical bovine apo calbindin-D9k P43M mutant (75 aa) protein. Automated assignment of this data using AUTOBA has been presented, which enhances the utility of these experiments. The backbone resonance assignments so derived are utilized to estimate secondary structures and the backbone fold using Web-based algorithms. Taken together, we believe that the method and the protocol proposed here can be used for routine high-throughput structural studies of proteins. PMID:25178811

  7. Topotecan dynamics, tautomerism and reactivity--1H/13C NMR and ESI MS study.

    PubMed

    Hyz, Karolina; Kawecki, Robert; Bednarek, Elzbieta; Bocian, Wojciech; Sitkowski, Jerzy; Kozerski, Lech

    2010-08-01

    Topotecan (TPT) is in clinical use as an antitumor agent, hycamtin. Because of this, it requires both biologically and chemically useful information to be available. TPT acts by binding to the covalent complex formed by nicked DNA and topoisomerase I. This has a poisonous effect since inserted into the single-strand nick and TPT inhibits its religation. We used NMR to trace TPT dynamics, tautomerism and solvolysis products in various solvents and conditions. Chemical stability was assessed in methanol and DMSO as compared to water, and the regioselectivity of the N- and O-methylation was studied using various alkylating agents. The reaction products of quaternization of the nitrogen atom and methylation of the oxygen atom were characterized by means of ESI MS, (1)H/(13)C-HMBC and -HSQCAD NMR. We have focused on the NMR characterization of TPT with an anticipation that its aggregation, tumbling properties and the intramolecular dipolar interactions will be a common feature for other compounds described in this article. These features can also be useful in tracing the interactions of this class of topoisomerase I (TopoI) poisons with DNA. Moreover, the results explained shed light on the recently disclosed problem of lack of stability of TPT in the heart tissue homogenate samples using the analytical assays developed for this class of compounds carried out in the presence of methanol. PMID:20623719

  8. Analytical contribution of NAD 2D-NMR spectroscopy in polypeptide mesophases to the investigation of triglycerides.

    PubMed

    Lesot, Philippe; Serhan, Zeinab; Aroulanda, Christie; Billault, Isabelle

    2012-12-01

    In this work, we report and discuss on the use and limitations of the natural abundance deuterium two-dimensional NMR spectroscopy in polypeptide chiral and achiral aligning media in the studies of homogenous triglycerides at 14.1 T. As illustrative examples, two triglycerides with short and long alkyl chains were investigated: the 1,3-di(butanoyloxy)propan-2-yl butanoate or tributyrin (TB) and the 1,3-di(tetradecanoyloxy)propan-2-yl tetradecanoate or trimyristin (TM). If both flexible compounds are theoretically of C(s) symmetry on average, according to the Altmann's definition (Proc. Roy. Soc., 1967, A298, 184.), the analysis of spectral data in terms of enantiotopic and diastereotopic discriminations shows noticeable differences related to their orientational ordering behavior inside the mesophases. Although from NMR analysis viewpoint, TB behaves as a C(s) symmetry molecule as expected, the NMR results obtained for TM suggest a behavior that could be formally predicted for a C(3v) symmetry molecule on average. This conclusion was nicely supported by the comparison with the tri-n-propylorthoformate, a real C(3v) symmetry solute on average on the NMR timescale. This difference of effective orientational behavior could originate from the difference of size and shape between lateral and central alkyl chains of the solute molecule. PMID:23280656

  9. Study of the cyclodextrin and its complexation with 2,4-dinitrobenzoic acid through photophysical properties and 2D NMR spectroscopy

    NASA Astrophysics Data System (ADS)

    Stalin, T.; Srinivasan, K.; Sivakumar, K.

    2014-02-01

    The host-guest inclusion complex formation of 2,4-dinitrobenzoic acid (2,4-DNB) with nano-hydrophobic cavity of β-cyclodextrin (β-CD) in solution phase were studied by UV-visible spectrophotometer and electrochemical method (cyclic voltammetry, CV). The prototropic behaviors of 2,4-DNB with and without β-CD and the ground state acidity constant (pKa) of host-guest inclusion complex (2,4-DNB-β-CD) was studied. The binding constant of the inclusion complex at 303 K was calculated using Benesi-Hildebrand plot. The solid inclusion complex formation between β-CD and 2,4-DNB was confirmed by 1H NMR, 2D 1H NMR (ROESY), FT-IR, XRD and SEM analysis. A schematic representation of this inclusion process is proposed by molecular docking studies using the patch dock server.

  10. Chemical prospection of important ayurvedic plant Tinospora cordifolia by UPLC-DAD-ESI-QTOF-MS/MS and NMR.

    PubMed

    Bala, Manju; Verma, Praveen Kumar; Awasthi, Shiv; Kumar, Neeraj; Lal, Brij; Singh, Bikram

    2015-01-01

    A rapid, sensitive, and accurate ultra-performance liquid chromatography coupled with mass spectrometric method (UPLC-MS) was developed and validated for simultaneous determination of four bioactive compounds, syringin (3), cordifolioside A (4), magnoflorine (6) and tinocordiside (10) in the stem of Tinospora cordifolia. The analysis was performed using an Acquity C18 column and gradient elution of 0.05% formic acid in water and acetonitrile at a detection wavelength of 267 nm in 5 min. A high correlation coefficient (r2 > 0.998) indicated good correlation between investigated compounds concentration and their peak area within the test ranges. The LODs for compounds 3, 4, 6 and 10 were 1.95, 0.97, 3.90 and 0.97 ng/mL, respectively, and LOQs were 6.64, 3.20, 12.87 and 3.20 ng/mL, respectively. The overall intra- and inter-day variations of the four compounds were less than 1%. The variation of these four bioactive compounds in T. cordifolia hosted on fifteen different trees was also determined. The compounds (3, 4, 6 and 10) were found in high amount in the T. cordifolia hosted on Azadirachta indica and Mangifera indica as compared with other plants. Twelve compounds were identified on the basis of their mass and UV-vis spectra. The NMR fingerprinting of the extract revealed the presence of alkaloids, fatty acid methyl esters, polysaccharides and marker components of T. cordifolia. PMID:25920217

  11. Structural and conformational study of the aluminum-thymulin complex using 1-D and 2-D NMR techniques

    SciTech Connect

    Laussac, J.P.; Lefrancier, P.; Dardenne, M.; Bach, J.F.; Marraud, M.; Cung, M.T.

    1988-11-16

    The interaction between aluminum and thymulin, a linear nonapeptide of thymic origin isolated from serum, was investigated by means of one- and two-dimensional NMR experiments. These experiments were performed in dimethyl-d/sub 6/ sulfoxide solution at different metal:peptide ratios. The results lead the following conclusions: (i) the Al(III) complexation corresponds to a fast exchange on the NMR time scale; (ii) the evolution of /sup 1/H and /sup 13/C NMR chemical shifts indicates the existence of one type of complex with a 1:2 stoichiometry, associating two peptide molecules and one Al(III) ion; (iii) analysis of the spectra suggests that Al(III) has a specific binding site involving the Asn/sup 9/COO/sup /minus// terminal group and the hydroxyl group of the Ser/sup 4/ residue; (iv) from the NOESY data a conformation has been proposed and compared to the biologically active Zn(II)-thymulin complex. 23 refs., 6 figs., 1 tab.

  12. The application of NMR and MS methods for detection of adulteration of wine, fruit juices, and olive oil. A review.

    PubMed

    Ogrinc, N; Kosir, I J; Spangenberg, J E; Kidric, J

    2003-06-01

    This review covers two important techniques, high resolution nuclear magnetic resonance (NMR) spectroscopy and mass spectrometry (MS), used to characterize food products and detect possible adulteration of wine, fruit juices, and olive oil, all important products of the Mediterranean Basin. Emphasis is placed on the complementary use of SNIF-NMR (site-specific natural isotopic fractionation nuclear magnetic resonance) and IRMS (isotope-ratio mass spectrometry) in association with chemometric methods for detecting the adulteration. PMID:12819845

  13. Simultaneous Acquisition of 2D and 3D Solid-State NMR Experiments for Sequential Assignment of Oriented Membrane Protein Samples

    PubMed Central

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

    2016-01-01

    We present a new method called DAISY (Dual Acquisition orIented ssNMR spectroScopY) for the simultaneous acquisition of 2D and 3D oriented solid-state NMR experiments for membrane proteins aligned in mechanically or magnetically lipid bilayers. DAISY utilizes dual acquisition of sine and cosine dipolar or chemical shift coherences and long living 15N longitudinal polarization to obtain two multi-dimensional spectra, simultaneously. In these new experiments, the first acquisition gives the polarization inversion spin exchange at the magic angle (PISEMA) or heteronuclear correlation (HETCOR) spectra, the second acquisition gives PISEMA-mixing or HETCOR-mixing spectra, where the mixing element enables inter-residue correlations through 15N-15N homonuclear polarization transfer. The analysis of the two 2D spectra (first and second acquisitions) enables one to distinguish 15N-15N inter-residue correlations for sequential assignment of membrane proteins. DAISY can be implemented in 3D experiments that include the polarization inversion spin exchange at magic angle via I spin coherence (PISEMAI) sequence, as we show for the simultaneous acquisition of 3D PISEMAI-HETCOR and 3D PISEMAI-HETCOR-mixing experiments. PMID:25749871

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

    PubMed

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

    2015-05-01

    We present a new method called DAISY (Dual Acquisition orIented ssNMR spectroScopY) for the simultaneous acquisition of 2D and 3D oriented solid-state NMR experiments for membrane proteins reconstituted in mechanically or magnetically aligned lipid bilayers. DAISY utilizes dual acquisition of sine and cosine dipolar or chemical shift coherences and long living (15)N longitudinal polarization to obtain two multi-dimensional spectra, simultaneously. In these new experiments, the first acquisition gives the polarization inversion spin exchange at the magic angle (PISEMA) or heteronuclear correlation (HETCOR) spectra, the second acquisition gives PISEMA-mixing or HETCOR-mixing spectra, where the mixing element enables inter-residue correlations through (15)N-(15)N homonuclear polarization transfer. The analysis of the two 2D spectra (first and second acquisitions) enables one to distinguish (15)N-(15)N inter-residue correlations for sequential assignment of membrane proteins. DAISY can be implemented in 3D experiments that include the polarization inversion spin exchange at magic angle via I spin coherence (PISEMAI) sequence, as we show for the simultaneous acquisition of 3D PISEMAI-HETCOR and 3D PISEMAI-HETCOR-mixing experiments. PMID:25749871

  15. Digit (2D:4D) ratio is associated with muscle mass (MM) and strength (MS) in older adults: possible effect of in utero androgen exposure.

    PubMed

    Halil, Meltem; Gurel, Esin Ileri; Kuyumcu, Mehmet Emin; Karaismailoglu, Serkan; Yesil, Yusuf; Ozturk, Zeynel Abidin; Yavuz, Burcu Balam; Cankurtaran, Mustafa; Ariogul, Servet

    2013-01-01

    Decline in MM and MS with aging, defined as sarcopenia, is related with physical disability, poor quality of life and death. Its mechanisms are not fully understood. Testosterone increases muscle protein synthesis. However, the effects of in utero androgen exposure to MM and MS in older adults have not been studied. In utero androgen exposure is inversely related with 2D:4D ratio. The aim of this study was to investigate the relationship between 2D:4D ratio as an indicator of in utero androgen exposure and MM and MS in elderly patients. A total of 151 older adults were included. Calf-circumference (CC) and skeletal muscle mass index (SMI) were used for the assessment of MM and hand grip strength for the assessment of MS. Mean age ± SD of the patients was 73.72 ± 6.23. Fifty-two (34.4%) of patients were male, 99 (65.6%) were female. Right and left 2D:4D were significantly and negatively correlated with hand grip strength (r=-0.365, p=0.018 and r=-0.434, p=0.005, respectively), CC (r=-0.422, p=0.002 and r=-0.459, p=0.001, respectively) and SMI (r=-0.354, p=0.018 and r=-0.348, p=0.022, respectively) in men. In women, right and left 2D:4D were significantly and negatively correlated with hand grip strength (r=-0.252, p=0.022 and r=-0.234, p=0.033, respectively), CC (r=-0.229, p=0.024 and r=-0.302, p=0.003, respectively) and SMI (r=-0.382, p<0.001 and r=-0.431, p<0.001, respectively). In this study, we found that 2D:4D ratio was significantly and negatively correlated with parameters depicting MM and MS which may suggest the possible role of in utero androgen exposure in the development of MM and MS loss in the elderly. PMID:23219021

  16. NMR- and GC/MS-based metabolomics of sulfur mustard exposed individuals: a pilot study.

    PubMed

    Nobakht, B Fatemeh; Aliannejad, Rasoul; Rezaei-Tavirani, Mostafa; Arefi Oskouie, Afsaneh; Naseri, Mohammad Taghi; Parastar, Hadi; Aliakbarzadeh, Ghazaleh; Fathi, Fariba; Taheri, Salman

    2016-09-01

    Sulfur mustard (SM) is a potent alkylating agent and its effects on cells and tissues are varied and complex. Due to limitations in the diagnostics of sulfur mustard exposed individuals (SMEIs) by noninvasive approaches, there is a great necessity to develop novel techniques and biomarkers for this condition. We present here the first nuclear magnetic resonance (NMR) and gas chromatography-mass spectrometry (GC/MS) metabolic profiling of serum from and healthy controls to identify novel biomarkers in blood serum for better diagnostics. Of note, SMEIs were exposed to SM 30 years ago and that differences between two groups could still be found. Pathways in which differences between SMEIs and healthy controls are observed are related to lipid metabolism, ketogenesis, tricarboxylic acid (TCA) cycle and amino acid metabolism. PMID:26984270

  17. Spin-coated and PECVD low dielectric constant porous organosilicate films studied by 1D and 2D solid-state NMR.

    PubMed

    Gerbaud, Guillaume; Hediger, Sabine; Bardet, Michel; Favennec, Laurent; Zenasni, Aziz; Beynet, Julien; Gourhant, Olivier; Jousseaume, Vincent

    2009-11-14

    In the research field of the sub-65 nm semiconductor industry, organosilicate SiOCH films with low dielectric constant (k < 2.4) need to be developed in order to improve the performance of integrated circuits [International Roadmap for Semiconductors (ITRS), San Jose, CA, 2004]. One way to produce SiOCH films of low dielectric constant is to introduce pores into the film. This is usually obtained in two steps. Firstly, co-deposition of a matrix precursor, with a sacrificial organic porogen, either by plasma enhanced chemical vapor deposition (PECVD) or spin-coating. Secondly, application of a specific thermal treatment to remove the porogen and create the porosity. This last step can be improved by adding to the thermal process a super-critical CO(2) treatment, an UV irradiation or an electronic bombardment (e-beam). In this study, the two deposition processes as well as the various treatments applied to eliminate the porogens were evaluated and compared using high-resolution solid-state NMR. For this purpose, hybrid (containing porogens) and porous films were extensively characterized on the basis of their (1)H, (13)C and (29)Si high-resolution NMR spectra. Information was obtained concerning the crosslinking of the Si skeleton. Spectral features could be correlated to the processes used. Isotropic chemical shift analyses and 2D correlation NMR experiments were used to show the existence and nature of the interactions between the matrix precursor and the organic porogen. PMID:19851550

  18. Solution-state 2D NMR of ball-milled plant cell wall gels in DMSO-d6/pyridine-d5†

    PubMed Central

    Ralph, John

    2014-01-01

    NMR fingerprinting of the components of finely divided plant cell walls swelled in DMSO has been recently described. Cell wall gels, produced directly in the NMR tube with perdeutero-dimethylsulfoxide, allowed the acquisition of well resolved/dispersed 2D 13C–1H correlated solution-state NMR spectra of the entire array of wall polymers, without the need for component fractionation. That is, without actual solubilization, and without apparent structural modification beyond that inflicted by the ball milling and ultrasonication steps, satisfactorily interpretable spectra can be acquired that reveal compositional and structural details regarding the polysaccharide and lignin components in the wall. Here, the profiling method has been improved by using a mixture of perdeuterated DMSO and pyridine (4:1, v/v). Adding pyridine provided not only easier sample handling because of the better mobility compared to the DMSO-d6-only system but also considerably elevated intensities and improved resolution of the NMR spectra due to the enhanced swelling of the cell walls. This modification therefore provides a more rapid method for comparative structural evaluation of plant cell walls than is currently available. We examined loblolly pine (Pinus taeda, a gymnosperm), aspen (Populus tremuloides, an angiosperm), kenaf (Hibiscus cannabinus, an herbaceous plant), and corn (Zea mays L., a grass, i.e., from the Poaceae family). In principle, lignin composition (notably, the syringyl : guaiacyl : p-hydroxyphenyl ratio) can be quantified without the need for lignin isolation. Correlations for p-coumarate units in the corn sample are readily seen, and a variety of the ferulate correlations are also well resolved; ferulates are important components responsible for cell wall cross-linking in grasses. Polysaccharide anomeric correlations were tentatively assigned for each plant sample based on standard samples and various literature data. With the new potential for chemometric analysis

  19. Hartmann-Hahn 2D-map to optimize the RAMP-CPMAS NMR experiment for pharmaceutical materials.

    PubMed

    Suzuki, Kazuko; Martineau, Charlotte; Fink, Gerhard; Steuernagel, Stefan; Taulelle, Francis

    2012-02-01

    Cross polarization-magic angle spinning (CPMAS) is the most used experiment for solid-state NMR measurements in the pharmaceutical industry, with the well-known variant RAMP-CPMAS its dominant implementation. The experimental work presented in this contribution focuses on the entangled effects of the main parameters of such an experiment. The shape of the RAMP-CP pulse has been considered as well as the contact time duration, and a particular attention also has been devoted to the radio-frequency (RF) field inhomogeneity. (13)C CPMAS NMR spectra have been recorded with a systematic variation of (13)C and (1)H constant radiofrequency field pair values and represented as a Hartmann-Hahn matching two-dimensional map. Such a map yields a rational overview of the intricate optimal conditions necessary to achieve an efficient CP magnetization transfer. The map also highlights the effects of sweeping the RF by the RAMP-CP pulse on the number of Hartmann-Hahn matches crossed and how RF field inhomogeneity helps in increasing the CP efficiency by using a larger fraction of the sample. In the light of the results, strategies for optimal RAMP-CPMAS measurements are suggested, which lead to a much higher efficiency than constant amplitude CP experiment. PMID:22367881

  20. Removal of t1 noise from metabolomic 2D 1H- 13C HSQC NMR spectra by Correlated Trace Denoising

    NASA Astrophysics Data System (ADS)

    Poulding, Simon; Charlton, Adrian J.; Donarski, James; Wilson, Julie C.

    2007-12-01

    The presence of t1 noise artefacts in 2D phase-cycled Heteronuclear Single Quantum Coherence (HSQC) spectra constrains the use of this experiment despite its superior sensitivity. This paper proposes a new processing algorithm, working in the frequency-domain, for reducing t1 noise. The algorithm has been developed for use in contexts, such as metabolomic studies, where existing denoising techniques cannot always be applied. Two test cases are presented that show the algorithm to be effective in improving the SNR of peaks embedded within t1 noise by a factor of more than 2, while retaining the intensity and shape of genuine peaks.

  1. Study of inclusion complex between 2,6-dinitrobenzoic acid and β-cyclodextrin by 1H NMR, 2D 1H NMR (ROESY), FT-IR, XRD, SEM and photophysical methods.

    PubMed

    Srinivasan, Krishnan; Stalin, Thambusamy

    2014-09-15

    The formation of host-guest inclusion complex of 2,6-dinitrobenzoic acid (2,6-DNB) with nano-hydrophobic cavity of β-cyclodextrin (β-CD) in solution phase has been studied by UV-visible spectroscopy and electrochemical analysis (cyclic voltammetry, CV). The effect of acid-base concentrations of 2,6-DNB has been studied in presence and absence of β-CD to determination for the ground state acidity constant (pKa). The binding constant of inclusion complex at 303 K was calculated using Benesi-Hildebrand plot and thermodynamic parameter (ΔG) was also calculated. The solid inclusion complex formation between β-CD and 2,6-DNB was confirmed by 1H NMR, 2D 1H NMR (ROESY), FT-IR, XRD and SEM analysis. A schematic representation of this inclusion process was proposed by molecular docking studies using patch dock server. PMID:24769381

  2. Study of inclusion complex between 2,6-dinitrobenzoic acid and β-cyclodextrin by 1H NMR, 2D 1H NMR (ROESY), FT-IR, XRD, SEM and photophysical methods

    NASA Astrophysics Data System (ADS)

    Srinivasan, Krishnan; Stalin, Thambusamy

    2014-09-01

    The formation of host-guest inclusion complex of 2,6-dinitrobenzoic acid (2,6-DNB) with nano-hydrophobic cavity of β-cyclodextrin (β-CD) in solution phase has been studied by UV-visible spectroscopy and electrochemical analysis (cyclic voltammetry, CV). The effect of acid-base concentrations of 2,6-DNB has been studied in presence and absence of β-CD to determination for the ground state acidity constant (pKa). The binding constant of inclusion complex at 303 K was calculated using Benesi-Hildebrand plot and thermodynamic parameter (ΔG) was also calculated. The solid inclusion complex formation between β-CD and 2,6-DNB was confirmed by 1H NMR, 2D 1H NMR (ROESY), FT-IR, XRD and SEM analysis. A schematic representation of this inclusion process was proposed by molecular docking studies using patch dock server.

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

    PubMed

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

    2008-09-16

    The earliest steps in the folding of proteins are complete on an extremely rapid time scale that is difficult to access experimentally. We have used rapid-mixing quench-flow methods to extend the time resolution of folding studies on apomyoglobin and elucidate the structural and dynamic features of members of the ensemble of intermediate states that are populated on a submillisecond time scale during this process. The picture that emerges is of a continuum of rapidly interconverting states. Even after only 0.4 ms of refolding time a compact state is formed that contains major parts of the A, G, and H helices, which are sufficiently well folded to protect amides from exchange. The B, C, and E helix regions fold more slowly and fluctuate rapidly between open and closed states as they search docking sites on this core; the secondary structure in these regions becomes stabilized as the refolding time is increased from 0.4 to 6 ms. No further stabilization occurs in the A, G, H core at 6 ms of folding time. These studies begin to time-resolve a progression of compact states between the fully unfolded and native folded states and confirm the presence an ensemble of intermediates that interconvert in a hierarchical sequence as the protein searches conformational space on its folding trajectory. PMID:18779573

  4. 13C and 1H chemical shift assignments and conformation confirmation of trimedlure-Y via 2-D NMR

    NASA Astrophysics Data System (ADS)

    Warthen, J. D.; Waters, R. M.; McGovern, T. P.

    The conformation of 1,1-dimethylethyl 5-chloro- cis-2-methylcyclohexane-1-carboxylate (trimedlure-Y) was confirmed as 1,2,5 equatorial, axial, equatorial via 13C, 1H, APT, CSCM and COSY NMR analyses. The carbon and proton nuclei in trimedlure-Y and the previously unassigned eight cyclohexyl protons (1.50-2.60 ppm) in 1,1-dimethylethyl 5-chloro- trans-2-methylcyclohexane-1-carboxylate (trimedlure-B 1; 1,2,5 equatorial, equatorial, equatorial) were also characterized by these methods. The effects of the 2-CH 3 in the axial or equatorial conformation upon the chemical shifts of the other nuclei in the molecule are discussed.

  5. 2D 31P solid state NMR spectroscopy, electronic structure and thermochemistry of PbP7

    NASA Astrophysics Data System (ADS)

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

    2016-03-01

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

  6. An insight on the alkaloid content of Capparis spinosa L. root by HPLC-DAD-MS, MS/MS and (1)H qNMR.

    PubMed

    Khatib, Mohamad; Pieraccini, Giuseppe; Innocenti, Marzia; Melani, Fabrizio; Mulinacci, Nadia

    2016-05-10

    The Capparis spinosa L. has a wide distribution in the Old World from South Europe, North and East Africa, Madagascar, Southwest and Central Asia to Australia and Oceania. The consolidated traditional use of C. spinosa root as remedy against different pains in human is well known since the antiquity. Various secondary metabolites have been found in caper plant, nevertheless, few studies have been focused to the analysis of root constituents. To date, several free and glycosilated spermidine alkaloids and a more polar alkaloid, the stachydrine, have been isolated from the root of C. spinosa. Aim of this work was to improve the knowledge on the alkaloid content of the root of a Syrian sample of C. spinosa by HPLC-DAD-MS(n) and to propose methods to quantify these molecules in different raw extracts. A decoction, an hydroalcoholic extraction and a fractionation process to selectively recover the spermidine alkaloids were applied. To our knowledge, this is the first HPLC-DAD-MS(n) profile that pointed out the co-presence of stachydrine, several isobaric forms of capparispine and/or capparisine in free and glycosylated forms and some isobars of isocodonocarpine or codonocarpine as monoglycosides in extracts of C. spinosa root. The determination by HPLC/DAD for the spermidine alkaloids expressed as p-OH-coumaric acid gave values up to 3.5mg/g dried root and the stachydrine evaluated by (1)H NMR was close to 12.5mg/g dried root. Overall, the total alkaloids were almost doubled in hydroalcoholic extract with respect to the decoction, and the stachydrine in the cortex was almost double than in the whole root. PMID:26874255

  7. Isolation and Identification of Dipeptidyl Peptidase IV-Inhibitory Peptides from Trypsin/Chymotrypsin-Treated Goat Milk Casein Hydrolysates by 2D-TLC and LC-MS/MS.

    PubMed

    Zhang, Ying; Chen, Ran; Ma, Huiqin; Chen, Shangwu

    2015-10-14

    New dipeptidyl peptidase IV (DPP-IV)-inhibitory peptides from trypsin/chymotrypsin-treated goat milk casein hydrolysates were isolated and identified by two-dimensional silica thin-layer chromatography (2D-TLC) combined to nano LC-MS/MS. 2D-TLC with chloroform/methanol/25% ammonia (2:2:1) and n-butanol/acetic acid/water (4:1:1) as the first- and second-dimension eluents, respectively, in analytical and semipreparative scales, was set up and verified by reversed-phase high-performance liquid chromatography (RP-HPLC) to be feasible and efficient to separate the hydrolysates. Five new DPP-IV-inhibitory peptides, four relatively large oligopeptides (MHQPPQPL, SPTVMFPPQSVL, VMFPPQSVL, and INNQFLPYPY), and AWPQYL were identified, and INNQFLPYPY showed a notable IC50 value of 40.08 μM as an uncompetitive inhibitor. Interactive effects on DPP-IV inhibition were also observed among separated fractions and pure synthetic peptide mixtures with concentration-dependent activity. The study gives new insights into goat casein hydrolysates with identified DPP-IV-inhibitory peptides efficiently isolated by 2D-TLC, which provides a simple and cost-efficient separation process and is compatible with liquid chromatography-tandem mass spectrometry (LC-MS/MS) identification. PMID:26323964

  8. LC-MS and 1H NMR as an improved dereplication tool to identify antifungal diterpenoids from Sagittaria latifolia

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A dereplication strategy using a combination of liquid chromatography-mass spectrometry (LC-MS) and proton nuclear magnetic resonance spectroscopy (1H NMR) to facilitate compound identification towards antifungal natural product discovery is presented. This analytical approach takes advantage of th...

  9. 1H NMR-based metabolomics combined with HPLC-PDA-MS-SPE-NMR for investigation of standardized Ginkgo biloba preparations

    PubMed Central

    Agnolet, Sara; Jaroszewski, Jerzy W.; Verpoorte, Robert

    2010-01-01

    Commercial preparations of Ginkgo biloba are very complex mixtures prepared from raw leaf extracts by a series of extraction and prepurification steps. The pharmacological activity is attributed to a number of flavonoid glycosides and unique terpene trilactones (TTLs), with largely uncharacterized pharmacological profiles on targets involved in neurological disorders. It is therefore important to complement existing targeted analytical methods for analysis of Ginkgo biloba preparations with alternative technology platforms for their comprehensive and global characterization. In this work, 1H NMR-based metabolomics and hyphenation of high-performance liquid chromatography, photo-diode array detection, mass spectrometry, solid-phase extraction, and nuclear magnetic resonance spectroscopy (HPLC-PDA-MS-SPE-NMR) were used for investigation of 16 commercially available preparations of Ginkgo biloba. The standardized extracts originated from Denmark, Italy, Sweden, and United Kingdom, and the results show that 1H NMR spectra allow simultaneous assessment of the content as well as identity of flavonoid glycosides and TTLs based on a very simple sample-preparation procedure consisting of extraction, evaporation and reconstitution in acetone-d6. Unexpected or unwanted extract constituents were also easily identified in the 1H NMR spectra, which contrasts traditional methods that depend on UV absorption or MS ionizability and usually require availability of reference standards. Automated integration of 1H NMR spectral segments (buckets or bins of 0.02 ppm width) provides relative distribution plots of TTLs based on their H-12 resonances. The present study shows that 1H NMR-based metabolomics is an attractive method for non-selective and comprehensive analysis of Ginkgo extracts. Electronic supplementary material The online version of this article (doi:10.1007/s11306-009-0195-x) contains supplementary material, which is available to authorized users. PMID:20526353

  10. Synthesis of new thiazolo-celecoxib analogues as dual cyclooxygenase-2/15-lipoxygenase inhibitors: Determination of regio-specific different pyrazole cyclization by 2D NMR.

    PubMed

    Abdelall, Eman K A; Kamel, Gehan M

    2016-08-01

    Two new series of 1,5-diaryl pyrazoles (5a, 5b, 7a, 7b and 10) and 1,5-diaryl pyrazoline (12a and 12b) were prepared as both Cyclooxygenase-2 and 15-lipoxygenase inhibitors. Carrageenan-induced rat paw edema, ulcer index and anti-COX-1/COX-2 and 15-LOX inhibition assays were also included. Cyclization of different pyrazoles was discussed using 2D NMR such as HSQC, HMBC and NOSEY determinations. Compound 5a is more effective with ED50 = 0.98 and 3.98 μM against COX-2 and 15-lipoxygenase respectively, than the references celecoxib (1.54 μM) and meclofenamate sodium (5.64 μM). PMID:27131067

  11. Carbon-proton scalar couplings in RNA. 3D heteronuclear and 2D isotope-edited NMR of a [sup 13]C-labeled extra-stable hairpin

    SciTech Connect

    Hines, J.V.; Landry, S.M.; Varani, G.; Tinoco, I. Jr. Lawrence Berkeley Lab., CA )

    1994-06-29

    Long range carbon-proton scalar couplings were measured for an RNA hairpin of 12 nucleotides using 3D and [sup 13]C-edited 2D NMR. The large one-bond carbon-proton scalar couplings ([sup 1]J[sub CH]) and small n-bond couplings ([sup 1]J[sub CH]) produce ECOSY type cross-peaks, thus facilitating the determination of the sign and magnitude of the smaller [sup 2]J[sub CH] or [sup 3]J[sub CH]. The UUCGRNA hairpin (5[prime]-rGGACUUCGGUCC-3[prime]), whose structure has been determined by our laboratory, was uniformly [sup 13]C-labeled at 30% isotopic enrichment. The observed [sup 1]J[sub CH] couplings were then correlated to the known structure. The signs of [sup 2]J[sub C4[prime]H5[prime

  12. A direct sensitivity comparison between flow-modulated comprehensive 2D and 1D GC in untargeted and targeted MS-based experiments.

    PubMed

    Tranchida, Peter Q; Franchina, Flavio A; Zoccali, Mariosimone; Bonaccorsi, Ivana; Cacciola, Francesco; Mondello, Luigi

    2013-09-01

    The present contribution is focused on the measurement of the analytical sensitivity attained in untargeted/targeted MS/MS experiments, performed using flow-modulator comprehensive 2D and 1D GC. The comprehensive 2D experiment was performed by diverting part of the high flow (circa 80%) to flush the accumulation loop (about 28 mL/min) to waste, to reduce the gas flow entering the ion source. 1D analyses were performed through: (i) unmodulated and (ii) single column applications. An equivalent temperature program was applied in the modulated and unmodulated analyses, while a faster one was employed in the single column one. In all application types, the (same) triple quadrupole instrument was operated in the full-scan and multiple reaction monitoring modes. A genuine sweet orange oil and the same sample spiked with 20 phytosanitary compounds were employed to reach the research objective. The results highlight the problems related to the flow modulation-MS combination. Specifically, it was found that sensitivity was on average three to four times higher in unmodulated and optimized single-column applications. PMID:23868497

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

    NASA Astrophysics Data System (ADS)

    Zhang, Rongchun; Ramamoorthy, Ayyalusamy

    2016-01-01

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

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

    PubMed

    Zhang, Rongchun; Ramamoorthy, Ayyalusamy

    2016-01-21

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

  15. Characterization of Fatty Acids in Crenarchaeota by GC-MS and NMR

    PubMed Central

    Hamerly, Timothy; Tripet, Brian; Wurch, Louie; Hettich, Robert L.; Podar, Mircea; Bothner, Brian; Copié, Valérie

    2015-01-01

    Lipids composed of condensed isoprenyl units connected to glycerol backbones by ether linkages are a distinguishing feature of Archaea. Data suggesting that fatty acids with linear hydrocarbon chains are present in some Archaea have been available for decades. However, lack of genomic and biochemical evidence for the metabolic machinery required to synthesize and degrade fatty acids has left the field unclear on this potentially significant biochemical aspect. Because lipids are energy currency and cell signaling molecules, their presence in Archaea is significant for understanding archaeal biology. A recent large-scale bioinformatics analysis reignited the debate as to the importance of fatty acids in Archaea by presenting genetic evidence for the presence of enzymes required for anabolic and catabolic fatty acid metabolism across the archaeal domain. Here, we present direct biochemical evidence from gas chromatography-mass spectrometry (GC-MS) and nuclear magnetic resonance (NMR) spectroscopy for the presence of fatty acids in two members of the Crenarchaeota, Sulfolobus solfataricus and Ignicoccus hospitalis. This is the first report providing biochemical data for the existence of fatty acids in these Crenarchaeota, opening new discussions on energy balance and the potential for the discovery of new thermostable enzymes for industry. PMID:26880868

  16. Pyrolysis GC-MS and NMR studies of humics in contaminated sediments

    SciTech Connect

    Higashi, R.M.; Fan, T.W.M.; Lane, A.N.

    1994-12-31

    Sediment ``humics`` play a major role in sorption and chemical reactions of organic and metal pollutants, as well as of nutrients, detritus, and other naturally-occurring chemicals. Not surprisingly, the chemical structure of humics is very important in this regard. The problem is, humics are among the most complex and least-understood substances in the world. This is because the primary structure is heterologous, unlike most other macromolecules which are polymeric; thus, researchers could not obtain coherent structures to identify with properties. However, recent advances in NMR spectroscopy and pyrolysis GC-MS have enabled researchers to begin relating primary and higher order structural motifs germane to the chemistry of the refractory humics. The authors have explored various means of sediment extraction for humics analysis by these techniques, including direct analysis of unextracted sediments. Marine sediments from near produced water discharges, salt marshes, and dredge material were surveyed. The study has revealed interpretive pitfalls, depending on the method of humic extraction. These difficulties are expected since the approach is at its infancy, but the overall approach is clearly useful in probing the humic structure profile of marine sediments.

  17. Characterization of Fatty Acids in Crenarchaeota by GC-MS and NMR

    DOE PAGESBeta

    Hamerly, Timothy; Tripet, Brian; Wurch, Louie; Hettich, Robert L.; Podar, Mircea; Bothner, Brian; Copié, Valérie

    2015-01-01

    Lipids composed of condensed isoprenyl units connected to glycerol backbones by ether linkages are a distinguishing feature of Archaea. Data suggesting that fatty acids with linear hydrocarbon chains are present in some Archaea have been available for decades. However, lack of genomic and biochemical evidence for the metabolic machinery required to synthesize and degrade fatty acids has left the field unclear on this potentially significant biochemical aspect. Because lipids are energy currency and cell signaling molecules, their presence in Archaea is significant for understanding archaeal biology. A recent large-scale bioinformatics analysis reignited the debate as to the importance ofmore » fatty acids in Archaea by presenting genetic evidence for the presence of enzymes required for anabolic and catabolic fatty acid metabolism across the archaeal domain. Here, we present direct biochemical evidence from gas chromatography-mass spectrometry (GC-MS) and nuclear magnetic resonance (NMR) spectroscopy for the presence of fatty acids in two members of the Crenarchaeota, Sulfolobus solfataricus and Ignicoccus hospitalis . This is the first report providing biochemical data for the existence of fatty acids in these Crenarchaeota, opening new discussions on energy balance and the potential for the discovery of new thermostable enzymes for industry.« less

  18. Accurate GM atrophy quantification in MS using lesion-filling with co-registered 2D lesion masks☆

    PubMed Central

    Popescu, V.; Ran, N.C.G.; Barkhof, F.; Chard, D.T.; Wheeler-Kingshott, C.A.; Vrenken, H.

    2014-01-01

    Background In multiple sclerosis (MS), brain atrophy quantification is affected by white matter lesions. LEAP and FSL-lesion_filling, replace lesion voxels with white matter intensities; however, they require precise lesion identification on 3DT1-images. Aim To determine whether 2DT2 lesion masks co-registered to 3DT1 images, yield grey and white matter volumes comparable to precise lesion masks. Methods 2DT2 lesion masks were linearly co-registered to 20 3DT1-images of MS patients, with nearest-neighbor (NNI), and tri-linear interpolation. As gold-standard, lesion masks were manually outlined on 3DT1-images. LEAP and FSL-lesion_filling were applied with each lesion mask. Grey (GM) and white matter (WM) volumes were quantified with FSL-FAST, and deep gray matter (DGM) volumes using FSL-FIRST. Volumes were compared between lesion mask types using paired Wilcoxon tests. Results Lesion-filling with gold-standard lesion masks compared to native images reduced GM overestimation by 1.93 mL (p < .001) for LEAP, and 1.21 mL (p = .002) for FSL-lesion_filling. Similar effects were achieved with NNI lesion masks from 2DT2. Global WM underestimation was not significantly influenced. GM and WM volumes from NNI, did not differ significantly from gold-standard. GM segmentation differed between lesion masks in the lesion area, and also elsewhere. Using the gold-standard, FSL-FAST quantified as GM on average 0.4% of the lesion area with LEAP and 24.5% with FSL-lesion_filling. Lesion-filling did not influence DGM volumes from FSL-FIRST. Discussion These results demonstrate that for global GM volumetry, precise lesion masks on 3DT1 images can be replaced by co-registered 2DT2 lesion masks. This makes lesion-filling a feasible method for GM atrophy measurements in MS. PMID:24567908

  19. Comparative Proteomics Profile of Lipid-Cumulating Oleaginous Yeast: An iTRAQ-Coupled 2-D LC-MS/MS Analysis

    PubMed Central

    Shi, Jiahua; Feng, Huixing; Lee, Jaslyn; Ning Chen, Wei

    2013-01-01

    Accumulation of intracellular lipid in oleaginous yeast cells has been studied for providing an alternative supply for energy, biofuel. Numerous studies have been conducted on increasing lipid content in oleaginous yeasts. However, few explore the mechanism of the high lipid accumulation ability of oleaginous yeast strains at the proteomics level. In this study, a time-course comparative proteomics analysis was introduced to compare the non-oleaginous yeast Saccharomyces cerevisiae, with two oleaginous yeast strains, Cryptococcus albidus and Rhodosporidium toruloides at different lipid accumulation stages. Two dimensional LC-MS/MS approach has been applied for protein profiling together with isobaric tag for relative and absolute quantitation (iTRAQ) labelling method. 132 proteins were identified when three yeast strains were all at early lipid accumulation stage; 122 and 116 proteins were found respectively within cells of three strains collected at middle and late lipid accumulation stages. Significantly up-regulation or down-regulation of proteins were experienced among comparison. Essential proteins correlated to lipid synthesis and regulation were detected. Our approach provides valuable indication and better understanding for lipid accumulation mechanism from proteomics level and would further contribute to genetic engineering of oleaginous yeasts. PMID:24386479

  20. Isolation and Identification of the Antimicrobial Agent Beauvericin from the Endophytic Fusarium oxysporum 5-19 with NMR and ESI-MS/MS

    PubMed Central

    Ruan, Chuanfen; Bai, Xuelian; Zhang, Miao; Zhu, Shuangshuang; Jiang, Yingying

    2016-01-01

    Endophytic microbe has been proved to be one of rich sources of bioactive natural products with potential application for new drug and pesticide discovery. One cyclodepsipeptide, beauvericin, was firstly isolated from the fermentation broth of Fusarium oxysporum 5-19 endophytic on Edgeworthia chrysantha Linn. Its chemical structure was unambiguously identified by a combination of spectroscopic methods, such as HRESI-MS and 1H and 13C NMR. ESI-MS/MS was successfully used to elucidate the splitting decomposition route of the positive molecule ion of beauvericin. Antimicrobial results showed that this cyclodepsipeptide had inhibitory effect on three human pathogenic microbes, Candida albicans, Escherichia coli, and Staphylococcus aureus. In particular, beauvericin exhibited the strongest antimicrobial activity against S. aureus with MIC values of 3.91 μM, which had similar effect with that of the positive control amoxicillin. PMID:27413733

  1. Isolation and Identification of the Antimicrobial Agent Beauvericin from the Endophytic Fusarium oxysporum 5-19 with NMR and ESI-MS/MS.

    PubMed

    Zhang, Huawei; Ruan, Chuanfen; Bai, Xuelian; Zhang, Miao; Zhu, Shuangshuang; Jiang, Yingying

    2016-01-01

    Endophytic microbe has been proved to be one of rich sources of bioactive natural products with potential application for new drug and pesticide discovery. One cyclodepsipeptide, beauvericin, was firstly isolated from the fermentation broth of Fusarium oxysporum 5-19 endophytic on Edgeworthia chrysantha Linn. Its chemical structure was unambiguously identified by a combination of spectroscopic methods, such as HRESI-MS and (1)H and (13)C NMR. ESI-MS/MS was successfully used to elucidate the splitting decomposition route of the positive molecule ion of beauvericin. Antimicrobial results showed that this cyclodepsipeptide had inhibitory effect on three human pathogenic microbes, Candida albicans, Escherichia coli, and Staphylococcus aureus. In particular, beauvericin exhibited the strongest antimicrobial activity against S. aureus with MIC values of 3.91 μM, which had similar effect with that of the positive control amoxicillin. PMID:27413733

  2. Development of quantitative plasma N-glycoproteomics using label-free 2-D LC-MALDI MS and its applicability for biomarker discovery in hepatocellular carcinoma.

    PubMed

    Ishihara, Takeshi; Fukuda, Isao; Morita, Atsushi; Takinami, Yoshihiko; Okamoto, Hiroyuki; Nishimura, Shin-Ichiro; Numata, Yoshito

    2011-09-01

    There has been rapid progress in the development of clinical proteomic methodologies with improvements in mass spectrometric technologies and bioinformatics, leading to many new methodologies for biomarker discovery from human plasma. However, it is not easy to find new biomarkers because of the wide dynamic range of plasma proteins and the need for their quantification. Here, we report a new methodology for relative quantitative proteomic analysis combining large-scale glycoproteomics with label-free 2-D LC-MALDI MS. In this method, enrichment of glycopeptides using hydrazide resin enables focusing on plasma proteins with lower abundance corresponding to the tissue leakage region. On quantitative analysis, signal intensities by 2-D LC-MALDI MS were normalized using a peptide internal control, and the values linked to LC data were treated with DeView™ software. Our proteomic method revealed that the quantitative dynamic ranged from 10² to 10⁶ pg/mL of plasma proteins with good reproducibility, and the limit of detection was of the order of a few ng/mL of proteins in biological samples. To evaluate the applicability of our method for biomarker discovery, we performed a feasibility study using plasma samples from patients with hepatocellular carcinoma, and identified biomarker candidates, including ceruloplasmin, alpha-1 antichymotrypsin, and multimerin-1. PMID:21704746

  3. [Comparative proteomics study of different processing technology for pilose antler using iTRAQ technology coupled with 2D LC-MS].

    PubMed

    Jin, Meng-ya; Dong, Ling; Luo, Yuan-ming; Yu, Li; Mo, Mei; Hou, Cheng-bo; Li, Zhi-yuan

    2015-12-01

    This study was designed to use iTRAQ technology coupled with 2D LC-MS/MS to study the comparative proteomics of different processing technology for pilose antler. 1015 proteins were identified with 2D LC combined with MOLDI TOF/TOF mass spectrometry. Comparative analysis with Protein Pilot (Version 4.5) revealed that 87 proteins were changed (P ≤ 0.05, the ratio of > 1.50 or < 0.60 as the threshold selection of difference proteins), of which 24 were up regulated and 33 were down regulated in the traditional frying process (TFP) compared with the fresh pilose antler (P ≤ 0.05). 7 significant different proteins (P ≤ 0.001), most of these significantly changed proteins were found to be involved in calcium ion binding and ATP binding associated with human healthy. Freeze drying with protective agent (FDP) (Trehalose) can improve the content of significantly different proteins (P ≤ 0.001) including Collagen alpha-1 (XII) chain (COL12A1) and Collagen alpha-1 (II) chain (COL2A1). The significant function involves in platelets activating, maintenance of spermatogonium, and disorder expression in tumor cells. The functional annotation by Hierarchical clustering and GO (gene ontology) showed that the main molecule functions of the proteins significantly changed in these processes were involved in binding (52.7%), catalytic (25.3%), structural molecule and transporter (6.6%). PMID:27169289

  4. Proton-detected 2D radio frequency driven recoupling solid-state NMR studies on micelle-associated cytochrome-b5

    NASA Astrophysics Data System (ADS)

    Pandey, Manoj Kumar; Vivekanandan, Subramanian; Yamamoto, Kazutoshi; Im, Sangchoul; Waskell, Lucy; Ramamoorthy, Ayyalusamy

    2014-05-01

    Solid-state NMR spectroscopy is increasingly used in the high-resolution structural studies of membrane-associated proteins and peptides. Most such studies necessitate isotopically labeled (13C, 15N and 2H) proteins/peptides, which is a limiting factor for some of the exciting membrane-bound proteins and aggregating peptides. In this study, we report the use of a proton-based slow magic angle spinning (MAS) solid-state NMR experiment that exploits the unaveraged 1H-1H dipolar couplings from a membrane-bound protein. We have shown that the difference in the buildup rates of cross-peak intensities against the mixing time - obtained from 2D 1H-1H radio frequency-driven recoupling (RFDR) and nuclear Overhauser effect spectroscopy (NOESY) experiments on a 16.7-kDa micelle-associated full-length rabbit cytochrome-b5 (cytb5) - can provide insights into protein dynamics and could be useful to measure 1H-1H dipolar couplings. The experimental buildup curves compare well with theoretical simulations and are used to extract relaxation parameters. Our results show that due to fast exchange of amide protons with water in the soluble heme-containing domain of cyb5, coherent 1H-1H dipolar interactions are averaged out for these protons while alpha and side chain protons show residual dipolar couplings that can be obtained from 1H-1H RFDR experiments. The appearance of resonances with distinct chemical shift values in 1H-1H RFDR spectra enabled the identification of residues (mostly from the transmembrane region) of cytb5 that interact with micelles.

  5. Proton-Detected 2D Radio Frequency Driven Recoupling Solid-state NMR Studies on Micelle-associated Cytochrome-b5

    PubMed Central

    Pandey, Manoj Kumar; Vivekanandan, Subramanian; Yamamoto, Kazutoshi; Im, Sangchoul; Waskell, Lucy; Ramamoorthy, Ayyalusamy

    2014-01-01

    Solid-state NMR spectroscopy is increasingly used in the high-resolution structural studies of membrane-associated proteins and peptides. Most such studies necessitate isotopically labeled (13C, 15N and 2H) proteins/peptides, which is a limiting factor for some of the exciting membrane-bound proteins and aggregating peptides. In this study, we report the use of a proton-based slow magic angle spinning (MAS) solid-state NMR experiment that exploits the unaveraged 1H-1H dipolar couplings from a membrane-bound protein. We have shown that the difference in the buildup rates of cross peak intensities against the mixing time - obtained from 2D 1H-1H radio frequency-driven recoupling (RFDR) and nuclear Overhauser effect spectroscopy (NOESY) experiments on a 16.7-kDa micelle-associated full-length rabbit cytochrome-b5 (cytb5) - can provide insights into protein dynamics and could be useful to measure 1H-1H dipolar couplings. The experimental buildup curves compare well with theoretical simulations and are used to extract relaxation parameters. Our results show that due to fast exchange of amide protons with water in the soluble heme-containing domain of cyb5, coherent 1H-1H dipolar interactions are averaged out for these protons while alpha and side chain protons show residual dipolar couplings that can be obtained from 1H-1H RFDR experiments. The appearance of resonances with distinct chemical shift values in 1H-1H RFDR spectra enabled the identification of residues (mostly from the transmembrane region) of cytb5 that interact with micelles. PMID:24657390

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

    PubMed

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

    2016-06-13

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

  7. Assessment of peeling of Astragalus roots using 1H NMR- and UPLC-MS-based metabolite profiling.

    PubMed

    Jung, Jee-Youn; Jung, Youngae; Kim, Jin-Sup; Ryu, Do Hyun; Hwang, Geum-Sook

    2013-10-30

    A metabolomic analysis was performed to examine the postharvest processing of Astragalus membranaceus roots with a focus on the peeling procedure using (1)H NMR and UPLC-MS analyses. Principal component analysis (PCA) score plots from the (1)H NMR and UPLC-MS data showed clear separation between peeled and unpeeled Astragalus roots. Peeled roots exhibited significant losses of several primary metabolites, including acetate, alanine, arginine, caprate, fumarate, glutamate, histidine, N-acetylaspartate, malate, proline, sucrose, trigonelline, and valine. In contrast, the peeled roots contained higher levels of asparagine, aspartate, and xylose, which are xylem-related compounds, and formate, which is produced in response to wound stress incurred during postharvest processing. In addition, the levels of isoflavonoids and astragalosides were significantly reduced in peeled Astragalus root. These results demonstrate that metabolite profiling based on a combination of (1)H NMR and UPLC-MS analyses can be used to evaluate peeling procedures used in the postharvest processing of herbal medicines. PMID:24073592

  8. The use of LC/MS, GC/MS, and LC/NMR hyphenated techniques to identify a drug degradation product in pharmaceutical development.

    PubMed

    Pan, Changkang; Liu, Frances; Ji, Qin; Wang, Wei; Drinkwater, Donald; Vivilecchia, Richard

    2006-02-24

    Understanding drug degradation in the formulated product is critical in pharmaceutical development as it has significant impacts on drug efficacy, safety profile and storage conditions. As a result, identification of degradation compounds has taken an important role in the drug development process. In this study, various hyphenated analytical techniques, such as liquid chromatography mass spectrometry (LC/MS), gas chromatography mass spectrometry (GC/MS), and liquid chromatography nuclear magnetic resonance with a solid phase extraction interface (LC/SPE/NMR), have been applied to the identification of a drug degradation product which grew over time in the stability study of the drug product. The target unknown is less polar and more unsaturated than the drug substance based upon reverse phase HPLC relative retention time and UV spectra. It is not ionizable by electrospray ionization (ESI) or atmospheric pressure chemical ionization (APCI) in either a positive or a negative mode. The unknown was isolated by an HPLC fraction collector and enriched by solid phase extraction. GC/MS with chemical ionization (CI) was employed to determine the molecular weight of this compound. Its fragmentation pattern was determined by CI-MS/MS using an ion trap mass spectrometer. The isolated material was also analyzed by LC/SPE/NMR, from which the structure of this compound was further characterized. The study utilizes a combination of various hyphenated analytical techniques to obtain complimentary information for structure elucidation of the unknown. The combination approach is critical for unambiguous impurity structure elucidation in drug degradation studies of pharmaceutical drug products. PMID:16242883

  9. Determination of substitution positions in hyaluronic acid hydrogels using NMR and MS based methods.

    PubMed

    Wende, Frida J; Gohil, Suresh; Mojarradi, Hotan; Gerfaud, Thibaud; Nord, Lars I; Karlsson, Anders; Boiteau, Jean-Guy; Kenne, Anne Helander; Sandström, Corine

    2016-01-20

    In hydrogels of cross-linked polysaccharides, the total amount of cross-linker and the degree of cross-linking influence the properties of the hydrogel. The substitution position of the cross-linker on the polysaccharide is another parameter that can influence hydrogel properties; hence methods for detailed structural analysis of the substitution pattern are required. NMR and LC-MS methods were developed to determine the positions and amounts of substitution of 1,4-butanediol diglycidyl ether (BDDE) on hyaluronic acid (HA), and for the first time it is shown that BDDE can react with any of the four available hydroxyl groups of the HA disaccharide repeating unit. This was achieved by studying di-, tetra-, and hexasaccharides obtained from degradation of BDDE cross-linked HA hydrogel by chondroitinase. Furthermore, amount of linker substitution at each position was shown to be dependent on the size of the oligosaccharides. For the disaccharide, substitutions were predominantly at ΔGlcA-OH2 and GlcNAc-OH6 while in the tetra- and hexasaccharides, it was mainly at the reducing end GlcNAc-OH4. In the disaccharide there was no substitution at this position. Since chondroitinase is able to completely hydrolyse non-substituted HA into unsaturated disaccharides, these results indicate that the enzyme is prevented to cleave on the non-reducing side of an oligosaccharide substituted at the reducing end GlcNAc-OH4. The procedure can be adopted for the determination of substitution positions in other types of polymers. PMID:26572480

  10. Spectrally edited 2D 13Csbnd 13C NMR spectra without diagonal ridge for characterizing 13C-enriched low-temperature carbon materials

    NASA Astrophysics Data System (ADS)

    Johnson, Robert L.; Anderson, Jason M.; Shanks, Brent H.; Fang, Xiaowen; Hong, Mei; Schmidt-Rohr, Klaus

    2013-09-01

    Two robust combinations of spectral editing techniques with 2D 13Csbnd 13C NMR have been developed for characterizing the aromatic components of 13C-enriched low-temperature carbon materials. One method (exchange with protonated and nonprotonated spectral editing, EXPANSE) selects cross peaks of protonated and nearby nonprotonated carbons, while the other technique, dipolar-dephased double-quantum/single-quantum (DQ/SQ) NMR, selects signals of bonded nonprotonated carbons. Both spectra are free of a diagonal ridge, which has many advantages: Cross peaks on the diagonal or of small intensity can be detected, and residual spinning sidebands or truncation artifacts associated with the diagonal ridge are avoided. In the DQ/SQ experiment, dipolar dephasing of the double-quantum coherence removes protonated-carbon signals; this approach also eliminates the need for high-power proton decoupling. The initial magnetization is generated with minimal fluctuation by combining direct polarization, cross polarization, and equilibration by 13C spin diffusion. The dipolar dephased DQ/SQ spectrum shows signals from all linkages between aromatic rings, including a distinctive peak from polycondensed aromatics. In EXPANSE NMR, signals of protonated carbons are selected in the first spectral dimension by short cross polarization combined with dipolar dephasing difference. This removes ambiguities of peak assignment to overlapping signals of nonprotonated and protonated aromatic carbons, e.g. near 125 ppm. Spin diffusion is enhanced by dipolar-assisted rotational resonance. Before detection, Csbnd H dipolar dephasing by gated decoupling is applied, which selects signals of nonprotonated carbons. Thus, only cross peaks due to magnetization originating from protonated C and ending on nearby nonprotonated C are retained. Combined with the chemical shifts deduced from the cross-peak position, this double spectral editing defines the bonding environment of aromatic, COO, and Cdbnd O carbons

  11. Forced degradation study of racecadotril: Effect of co-solvent, characterization of degradation products by UHPLC-Q-TOF-MS/MS, NMR and cytotoxicity assay.

    PubMed

    Chiguru, Vishnuvardhan; Lingesh, Allakonda; R, Srinivas; N, Satheeshkumar

    2016-09-01

    Racecadotril, an enkephalinase inhibitor, was subjected to hydrolysis (acidic and alkaline), oxidation, photolysis and thermal stress, as per ICH specified conditions. The drug showed extensive degradation under acidic, basic hydrolysis and oxidative stress conditions whereas, it was stable under other stress conditions. A total of seven degradation products (DPs) were observed. The chromatographic separation was optimized on Acquity HSS Cyano (100×2.1mm, 1.8μ) column using 0.1% formic acid and acetonitrile as mobile phase in gradient mode. Six DPs were characterised by LC-MS/MS and DP1 by GC-MS. The major DPs (DP 2 and DP 5) were isolated and characterised by NMR. This is a typical case of degradation where co solvent methanol reacts with racecadotril leading to the formation of pseudo DPs, DP 6 and DP 5. Interestingly the MS/MS spectra of protonated drug, DP 4 and DP 7 showed product ions which were formed due to intramolecular benzyl migrations. In vitro cytotoxic activity studies on isolated DP 2 and DP 5 revealed that the former has no cytotoxic nature, whereas the latter has potential pulmonary and hepatic toxicity. PMID:27209450

  12. Identification of Metabolites from LC-EC Profiling: GC-MS and Re-Fractionation Provide Essential Information Orthogonal to LCMS/microNMR

    PubMed Central

    Gathungu, Rose M.; Bird, Susan S.; Sheldon, Diane P.; Kautz, Roger; Vouros, Paul; Matson, Wayne R.; Kristal, Bruce S.

    2014-01-01

    HPLC-coulometric electrode-array detection (LC-EC) is a sensitive, quantitative and robust metabolomics profiling tool that complements the commonly used MS and NMR-based approaches. However, LC-EC provides little structural information. We recently demonstrated a workflow for the structural characterization of metabolites detected by LC-EC profiling, combined with LC-ESI-MS and microNMR. This methodology is now extended to include: (i) GC-EI-MS analysis to fill structural gaps left by LC-ESI-MS and NMR, and (ii) secondary fractionation of LC-collected fractions containing multiple co-eluting analytes. GC-EI-MS spectra have more informative fragment ions that are reproducible for database searches. Secondary fractionation provides enhanced metabolite characterization by reducing spectral overlap in NMR and ion-suppression in LC-ESI-MS. The need for these additional methods in the analysis of the broad chemical classes and concentration ranges found in plasma is illustrated with discussion of four specific examples, including: (i) characterization of compounds for which one or more of the detectors is insensitive (e.g., positional isomers in LC-MS, the direct detection of carboxylic groups and sulfonic groups in 1H NMR, or non-volatile species in GC-MS).; (ii) detection of labile compounds, (iii) resolution of closely eluting and/or co-eluting compounds and, (iv) the capability to harness structural similarities common in many biologically-related, LC-EC detectable compounds. PMID:24657819

  13. 15N-Cholamine – A Smart Isotope Tag for Combining NMR- and MS-Based Metabolite Profiling

    PubMed Central

    Tayyari, Fariba; Nagana Gowda, G. A.; Gu, Haiwei; Raftery, Daniel

    2013-01-01

    Recently, the enhanced resolution and sensitivity offered by chemoselective isotope tags have enabled new and enhanced methods for detecting hundreds of quantifiable metabolites in biofluids using nuclear magnetic resonance (NMR) spectroscopy or mass spectrometry. However, the inability to effectively detect the same metabolites using both complementary analytical techniques has hindered the correlation of data derived from the two powerful platforms and thereby the maximization of their combined strengths for applications such as biomarker discovery of the identification of unknown metabolites. With the goal of alleviating this bottleneck, we describe a smart isotope tag, 15N-cholamine, which possesses two important properties: an NMR sensitive isotope, and a permanent charge for MS sensitivity. Using this tag, we demonstrate the detection of carboxyl group containing metabolites in both human serum and urine. By combining the individual strengths of the 15N label and permanent charge, the smart isotope tag facilitates effective detection of the carboxyl-containing metabolome by both analytical methods. This study demonstrates a unique approach to exploit the combined strength of MS and NMR in the field of metabolomics. PMID:23930664

  14. Quality assessment of fluoxetine and fluvoxamine pharmaceutical formulations purchased in different countries or via the Internet by 19F and 2D DOSY 1H NMR.

    PubMed

    Trefi, Saleh; Gilard, Véronique; Balayssac, Stéphane; Malet-Martino, Myriam; Martino, Robert

    2008-03-13

    A simple and selective (19)F NMR method has been validated for the quantitation of fluoxetine (FLX) and fluvoxamine (FLV) in methanol solutions and in human plasma and urine. The regression equations for FLX and FLV showed a good linearity in the range of 1.4-620 microg mL(-1) (3.3 x 10(-6)-1.8 x 10(-3) mol L(-1)) with a limit of detection of approximately 0.5 microg mL(-1) (1.3 x 10(-6) mol L(-1)) and a limit of quantification of approximately 2 microg mL(-1) (4.6 x 10(-6) mol L(-1)). The precision of the assay depends on the concentrations and is comprised between 1.5 and 9.5% for a range of concentrations between 1.2 x 10(-3) and 3.2 x 10(-6) mol L(-1). The accuracy evaluated through recovery studies ranged from approximately 96 to 103% in methanol solutions and in urine, and from approximately 93 to 104% in plasma, with standard deviations <7.5%. The low sensitivity of the method precludes its use for the assay of these antidepressants in biofluids at least at therapeutic doses as the ranges of FLX and FLV plasma levels are 0.15-0.5 microg mL(-1) and 0.15-0.25 microg mL(-1), respectively. The method was applied successfully to the determination of FLX and FLV contents in pharmaceutical samples (brand-named and generic) purchased in several countries or via the Internet. All the commercial formulations contain the active ingredient in the range 94-103% of stated concentration. A "signature" of the formulations (solid and liquid) was obtained with 2D Diffusion-Ordered SpectroscopY (DOSY) (1)H NMR which allowed the characterisation of the active ingredient and excipients present in the formulations studied. Finally, the DOSY separation of FLX and FLV whose molecular weights are very close was obtained by using beta-cyclodextrin as host-guest complexing agent. PMID:18206329

  15. Classification of Coffee Beans by GC-C-IRMS, GC-MS, and (1)H-NMR.

    PubMed

    Arana, Victoria Andrea; Medina, Jessica; Esseiva, Pierre; Pazos, Diego; Wist, Julien

    2016-01-01

    In a previous work using (1)H-NMR we reported encouraging steps towards the construction of a robust expert system for the discrimination of coffees from Colombia versus nearby countries (Brazil and Peru), to assist the recent protected geographical indication granted to Colombian coffee in 2007. This system relies on fingerprints acquired on a 400 MHz magnet and is thus well suited for small scale random screening of samples obtained at resellers or coffee shops. However, this approach cannot easily be implemented at harbour's installations, due to the elevated operational costs of cryogenic magnets. This limitation implies shipping the samples to the NMR laboratory, making the overall approach slower and thereby more expensive and less attractive for large scale screening at harbours. In this work, we report on our attempt to obtain comparable classification results using alternative techniques that have been reported promising as an alternative to NMR: GC-MS and GC-C-IRMS. Although statistically significant information could be obtained by all three methods, the results show that the quality of the classifiers depends mainly on the number of variables included in the analysis; hence NMR provides an advantage since more molecules are detected to obtain a model with better predictions. PMID:27516919

  16. Classification of Coffee Beans by GC-C-IRMS, GC-MS, and 1H-NMR

    PubMed Central

    Arana, Victoria Andrea; Esseiva, Pierre; Pazos, Diego

    2016-01-01

    In a previous work using 1H-NMR we reported encouraging steps towards the construction of a robust expert system for the discrimination of coffees from Colombia versus nearby countries (Brazil and Peru), to assist the recent protected geographical indication granted to Colombian coffee in 2007. This system relies on fingerprints acquired on a 400 MHz magnet and is thus well suited for small scale random screening of samples obtained at resellers or coffee shops. However, this approach cannot easily be implemented at harbour's installations, due to the elevated operational costs of cryogenic magnets. This limitation implies shipping the samples to the NMR laboratory, making the overall approach slower and thereby more expensive and less attractive for large scale screening at harbours. In this work, we report on our attempt to obtain comparable classification results using alternative techniques that have been reported promising as an alternative to NMR: GC-MS and GC-C-IRMS. Although statistically significant information could be obtained by all three methods, the results show that the quality of the classifiers depends mainly on the number of variables included in the analysis; hence NMR provides an advantage since more molecules are detected to obtain a model with better predictions. PMID:27516919

  17. The intact muscle lipid composition of bulls: an investigation by MALDI-TOF MS and 31P NMR.

    PubMed

    Dannenberger, Dirk; Süss, Rosmarie; Teuber, Kristin; Fuchs, Beate; Nuernberg, Karin; Schiller, Jürgen

    2010-02-01

    The analysis of beef lipids is normally based on chromatographic techniques and/or gas chromatography in combination with mass spectrometry (GC/MS). Modern techniques of soft-ionization MS were so far scarcely used to investigate the intact lipids in muscle tissues of beef. The objective of the study was to investigate whether matrix-assisted laser desorption and ionization time-of-flight (MALDI-TOF) mass spectrometry and (31)P nuclear magnetic resonance (NMR) spectroscopy are useful tools to study the intact lipid composition of beef. For the MALDI-TOF MS and (31)P NMR investigations muscle samples were selected from a feeding experiment with German Simmental bulls fed different diets. Beside the triacylglycerols (TAGs), phosphatidylethanolamine (PE), phosphatidylcholine (PC) and phosphatidylinositol (PI) species the MALDI-TOF mass spectra of total muscle lipids gave also intense signals of cardiolipin (CL) species. The application of different matrix compounds, 2,5-dihydroxybenzoic acid (DHB) and 9-aminoacridine (9-AA), leads to completely different mass spectra: 9-AA is particularly useful for the detection of (polar) phospholipids, whereas apolar lipids, such as cholesterol and triacylglycerols, are exclusively detected if DHB is used. Finally, the quality of the negative ion mass spectra is much higher if 9-AA is used. PMID:19900429

  18. Metabolic flux and metabolic network analysis of Penicillium chrysogenum using 2D [13C, 1H] COSY NMR measurements and cumulative bondomer simulation.

    PubMed

    van Winden, Wouter A; van Gulik, Walter M; Schipper, Dick; Verheijen, Peter J T; Krabben, Preben; Vinke, Jacobus L; Heijnen, Joseph J

    2003-07-01

    At present two alternative methods are available for analyzing the fluxes in a metabolic network: (1) combining measurements of net conversion rates with a set of metabolite balances including the cofactor balances, or (2) leaving out the cofactor balances and fitting the resulting free fluxes to measured (13)C-labeling data. In this study these two approaches are applied to the fluxes in the glycolysis and pentose phosphate pathway of Penicillium chrysogenum growing on either ammonia or nitrate as the nitrogen source, which is expected to give different pentose phosphate pathway fluxes. The presented flux analyses are based on extensive sets of 2D [(13)C, (1)H] COSY data. A new concept is applied for simulation of this type of (13)C-labeling data: cumulative bondomer modeling. The outcomes of the (13)C-labeling based flux analysis substantially differ from those of the pure metabolite balancing approach. The fluxes that are determined using (13)C-labeling data are shown to be highly dependent on the chosen metabolic network. Extending the traditional nonoxidative pentose phosphate pathway with additional transketolase and transaldolase reactions, extending the glycolysis with a fructose 6-phosphate aldolase/dihydroxyacetone kinase reaction sequence or adding a phosphoenolpyruvate carboxykinase reaction to the model considerably improves the fit of the measured and the simulated NMR data. The results obtained using the extended version of the nonoxidative pentose phosphate pathway model show that the transketolase and transaldolase reactions need not be assumed reversible to get a good fit of the (13)C-labeling data. Strict statistical testing of the outcomes of (13)C-labeling based flux analysis using realistic measurement errors is demonstrated to be of prime importance for verifying the assumed metabolic model. PMID:12740935

  19. LC/MS/NMR analysis of isomeric divanilloylquinic acids from the root bark of Fagara zanthoxyloides Lam.

    PubMed

    Ouattara, Badioré; Angenot, Luc; Guissou, Pierre; Fondu, Pierre; Dubois, Jacques; Frédérich, Michel; Jansen, Olivia; van Heugen, Jean-Claude; Wauters, Jean-Noël; Tits, Monique

    2004-04-01

    Gradient HPLC coupled to DAD/UV, MS/MS and NMR has been applied to the rapid structure determination of three new isomeric divanilloylquinic acids from Fagara zanthoxyloides collected in Burkina Faso: 3,4-O-divanilloylquinic acid, 3,5-O-divanilloylquinic acid and 4,5-O-divanilloylquinic acid. Furthermore these new compounds named burkinabins A-C could play a useful role in sickle cell disease, as the active agents of Fagara zanthoxyloïdes are said to be unidentified aromatic compounds with carboxylic acid grouping (Adesanya, S.A., Sofowora, A., 1983. Biological standardisation of Zanthoxylum roots for antisickling activity. Planta Med. 48, 27-33). PMID:15110696

  20. LC-NMR, NMR, and LC-MS identification and LC-DAD quantification of flavonoids and ellagic acid derivatives in Drosera peltata.

    PubMed

    Braunberger, Christina; Zehl, Martin; Conrad, Jürgen; Fischer, Sonja; Adhami, Hamid-Reza; Beifuss, Uwe; Krenn, Liselotte

    2013-08-01

    The herb of Drosera peltata, commonly named the shield sundew, is used as an antitussive in phytotherapy, although the plants' composition has not been determined in detail so far. Hence, in this study, we present a validated, sensitive, reliable, and cheap narrow-bore LC-DAD method for the simultaneous quantification of flavonoids and ellagic acid derivatives in this herbal drug. In addition, the structures of 13 compounds have been elucidated by LC-MS, LC-NMR, and offline NMR experiments after isolation: herbacetin-3-O-glucoside (1), gossypitrin (2), ellagic acid (3), quercetin-7-O-glucoside (4), isoquercitrin (5), kaempferol-3-O-(6″-O-galloyl)-glucoside (6), herbacetin-7-O-glucoside (7), astragalin (8), gossypetin (9), herbacetin (10), quercetin (11), 3,3'-di-O-methyl ellagic acid (12), and kaempferol (13). Compounds 1, 2, 4, 5, 6, 7, and 10 have been identified in D. peltata for the first time, and compounds 1, 4, 6, 7, and 10 have not been detected in any Drosera species before. PMID:23831703

  1. Four process-related potential new impurities in ticagrelor: Identification, isolation, characterization using HPLC, LC/ESI-MS(n), NMR and their synthesis.

    PubMed

    Kumar, Neeraj; Devineni, Subba Rao; Gajjala, Prasad Reddy; Gupta, Dharmendra Kumar; Bhat, Sandesh; Kumar, Rajesh; Dubey, Shailendra Kumar; Kumar, Pramod

    2016-02-20

    Five process-related impurities were detected in the range of 0.08-0.22% in ticagrelor laboratory batches by HPLC and LC-MS methods. These impurities were named as TIC Imp-I, -II, -III, -IV and -V. Four of these impurities, TIC Imp-I to -IV were unknown and have not been reported previously. Based on LC-ESI/MS(n) study, the chemical structures of new impurities were presumed as (1S,2S,3S,5S)-3-(2-hydroxyethoxy)-5-(7-amino-5-(propylthio)-3H-[1,2,3]triazolo[4,5-d] pyrimidin-3-yl)cyclopentane-1,2-diol (TIC Imp-I), (1S,2S,3S,5S)-3-(7-((1R,2S)-2-(3,4-difluorophenyl)cyclopropylamino)-5-(propylsulfinyl)-3H-[1,2,3]triazolo [4,5-d]pyrimidin-3-yl)-5-(2-hydroxyethoxy)cyclopentane-1,2-diol (TIC Imp-II), (1S,2R,3S,4S)-4-(7-((1R,2S)-2-(3,4-difluorophenyl)cyclopropylamino)-5-(propylthio)-3H-[1,2,3]triazolo[4,5-d]pyrimidin-3-yl)cyclopentane-1,2,3-triol (TIC Imp-III) and (3S,5S)-3-(7-((1R,2S)-2-(3,4-difluorophenyl)cyclopropylamino)-5-(propylthio)-3H-[1,2,3]triazolo[4,5-d]pyrimidin-3-yl)-5-(2-hydroxyethoxy)cyclopentane-1,2-diol (TIC Imp-IV). The unknown impurities were isolated from enriched crude sample by column chromatography and preparative HPLC. The complete spectral analysis, MS, 1D NMR ((1)H, (13)C and DEPT), 2D NMR (HSQC and HMBC) and IR confirmed the proposed chemical structures of impurities. Identification, isolation, structural characterization, prospects for the formation of impurities and their synthesis were first reported in this paper. PMID:26760243

  2. Metabolic fingerprinting of Leontopodium species (Asteraceae) by means of 1H NMR and HPLC–ESI-MS

    PubMed Central

    Safer, Stefan; Cicek, Serhat S.; Pieri, Valerio; Schwaiger, Stefan; Schneider, Peter; Wissemann, Volker; Stuppner, Hermann

    2011-01-01

    The genus Leontopodium, mainly distributed in Central and Eastern Asia, consists of ca. 34–58 different species. The European Leontopodium alpinum, commonly known as Edelweiss, has a long tradition in folk medicine. Recent research has resulted in the identification of prior unknown secondary metabolites, some of them with interesting biological activities. Despite this, nearly nothing is known about the Asian species of the genus. In this study, we applied proton nuclear magnetic resonance (1H NMR) spectroscopy and liquid chromatography–mass spectrometry (LC–MS) metabolic fingerprinting to reveal insights into the metabolic patterns of 11 different Leontopodium species, and to conclude on their taxonomic relationship. Principal component analysis (PCA) of 1H NMR fingerprints revealed two species groups. Discriminators for these groups were identified as fatty acids and sucrose for group A, and ent-kaurenoic acid and derivatives thereof for group B. Five diterpenes together with one sesquiterpene were isolated from Leontopodium franchetii roots; the compounds were described for the first time for L. franchetii: ent-kaur-16-en-19-oic acid, methyl-15α-angeloyloxy-ent-kaur-16-en-19-oate, methyl-ent-kaur-16-en-19-oate, 8-acetoxymodhephene, 19-acetoxy-ent-kaur-16-ene, methyl-15β–angeloyloxy-16,17-epoxy-ent-kauran-19-oate. In addition, differences in the metabolic profile between collected and cultivated species could be observed using a partial least squares-discriminant analysis (PLS-DA). PCA of the LC–MS fingerprints revealed three groups. Discriminating signals were compared to literature data and identified as two bisabolane derivatives responsible for discrimination of group A and C, and one ent-kaurenoic acid derivative, discriminating group B. A taxonomic relationship between a previously unidentified species and L. franchetii and Leontopodium sinense could be determined by comparing NMR fingerprints. This finding supports recent molecular data

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

    ERIC Educational Resources Information Center

    Mak, Kendrew K. W.

    2004-01-01

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

  4. α-Glucosidase inhibition and antioxidant activity of an oenological commercial tannin. Extraction, fractionation and analysis by HPLC/ESI-MS/MS and (1)H NMR.

    PubMed

    Muccilli, Vera; Cardullo, Nunzio; Spatafora, Carmela; Cunsolo, Vincenzo; Tringali, Corrado

    2017-01-15

    Two batches of the oenological tannin Tan'Activ R, (toasted oak wood - Quercus robur), were extracted with ethanol. A fractionation on XAD-16 afforded four fractions for each extract. Extracts and fractions were evaluated for antioxidant activity (DPPH), polyphenol content (GAE) and yeast α-glucosidase inhibitory activity. Comparable results were obtained for both columns, fractions X1B and X2B showing the highest antioxidant activity. Fractions X1C and X2C notably inhibited α-glucosidase, with IC50=9.89 and 8.05μg/mL, respectively. Fractions were subjected to HPLC/ESI-MS/MS and (1)H NMR analysis. The main phenolic constituents of both X1B and X2B were a monogalloylglucose isomer (1), a HHDP-glucose isomer (2), castalin (3) gallic acid (4), vescalagin (5), and grandinin (or its isomer roburin E, 6). X1C and X2C showed a complex composition, including non-phenolic constituents. Fractionation of X2C gave a subfraction, with enhanced α-glucosidase inhibitory activity (IC50=6.15μg/mL), with castalagin (7) as the main constituent. PMID:27542449

  5. Identification of metabolites from liquid chromatography-coulometric array detection profiling: gas chromatography-mass spectrometry and refractionation provide essential information orthogonal to LC-MS/microNMR.

    PubMed

    Gathungu, Rose M; Bird, Susan S; Sheldon, Diane P; Kautz, Roger; Vouros, Paul; Matson, Wayne R; Kristal, Bruce S

    2014-06-01

    Liquid chromatography-coulometric array detection (LC-EC) is a sensitive, quantitative, and robust metabolomics profiling tool that complements the commonly used mass spectrometry (MS) and nuclear magnetic resonance (NMR)-based approaches. However, LC-EC provides little structural information. We recently demonstrated a workflow for the structural characterization of metabolites detected by LC-EC profiling combined with LC-electrospray ionization (ESI)-MS and microNMR. This methodology is now extended to include (i) gas chromatography (GC)-electron ionization (EI)-MS analysis to fill structural gaps left by LC-ESI-MS and NMR and (ii) secondary fractionation of LC-collected fractions containing multiple coeluting analytes. GC-EI-MS spectra have more informative fragment ions that are reproducible for database searches. Secondary fractionation provides enhanced metabolite characterization by reducing spectral overlap in NMR and ion suppression in LC-ESI-MS. The need for these additional methods in the analysis of the broad chemical classes and concentration ranges found in plasma is illustrated with discussion of four specific examples: (i) characterization of compounds for which one or more of the detectors is insensitive (e.g., positional isomers in LC-MS, the direct detection of carboxylic groups and sulfonic groups in (1)H NMR, or nonvolatile species in GC-MS), (ii) detection of labile compounds, (iii) resolution of closely eluting and/or coeluting compounds, and (iv) the capability to harness structural similarities common in many biologically related, LC-EC-detectable compounds. PMID:24657819

  6. Moving pieces in a taxonomic puzzle: venom 2D-LC/MS and data clustering analyses to infer phylogenetic relationships in some scorpions from the Buthidae family (Scorpiones).

    PubMed

    Nascimento, Danielle G; Rates, Breno; Santos, Daniel M; Verano-Braga, Thiago; Barbosa-Silva, Adriano; Dutra, Alexandre A A; Biondi, Ilka; Martin-Eauclaire, Marie France; De Lima, Maria Elena; Pimenta, Adriano M C

    2006-05-01

    The Buthidae is the most clinically important scorpion family, with over 500 species distributed worldwide. Taxonomical positions and phylogenetic relationships concerning the representative genera and species of this family have been mostly inferred based upon comparisons between morphological characters. Yet, some authors have performed such inferences by comparing some structural properties of a few selected molecules found in the venoms from these scorpions. Here, we propose a novel methodology pipeline designed to address these issues. We have analyzed the whole venoms from some species that exemplify peculiar cases in the Buthidae family (Tityus stigmurus, Tityus serrulatus, Tityus bahiensis, Leiurus quinquestriatus quinquestriatus and Leiurus quinquestriatus hebraeus), by means of a proteomic approach using a 2D-LC/MS technique. The molecules found in these venoms were clustered according to their physicochemical properties (molecular mass and hydrophobicity), by using the machine learning-based Weka software. The clusters assessment, along with the number of molecules found in a given cluster for each scorpion, which assigns for the venom and structural family complexities, respectively, was used to generate a phenetic correlation tree for positioning these species. Our results were in accordance with the classical taxonomy viewpoint, which places T. serrulatus and T. stigmurus as very close species, T. bahiensis as a less related species in the Tityus genus and L. q. quinquestriatus and L. q. hebraeus with small differences within the same species (L. quinquestriatus). Therefore, we believe that this is a well-suited method to determine venom complexities that reflect the scorpions' evolutionary history, which can be crucial to reconstruct their phylogeny through the molecular evolution of their venoms. PMID:16551474

  7. Simultaneous Structural Identification of Natural Products in Fractions of Crude Extract of the Rare Endangered Plant Anoectochilus roxburghii Using 1H NMR/RRLC-MS Parallel Dynamic Spectroscopy

    PubMed Central

    Wang, Xiao-Xue; He, Jiu-Ming; Wang, Chun-Lan; Zhang, Rui-Ping; He, Wen-Yi; Guo, Shun-Xing; Sun, Rui-Xiang; Abliz, Zeper

    2011-01-01

    Nuclear magnetic resonance/liquid chromatography-mass spectroscopy parallel dynamic spectroscopy (NMR/LC-MS PDS) is a method aimed at the simultaneous structural identification of natural products in complex mixtures. In this study, the method is illustrated with respect to 1H NMR and rapid resolution liquid chromatography-mass spectroscopy (RRLC-MS) data, acquired from the crude extract of Anoectochilus roxburghii, which was separated into a series of fractions with the concentration of constituent dynamic variation using reversed-phase preparative chromatography. Through fraction ranges and intensity changing profiles in 1H NMR/RRLC–MS PDS spectrum, 1H NMR and the extracted ion chromatogram (XIC) signals deriving from the same individual constituent, were correlated due to the signal amplitude co-variation resulting from the concentration variation of constituents in a series of incompletely separated fractions. 1H NMR/RRLC-MS PDS was then successfully used to identify three types of natural products, including eight flavonoids, four organic acids and p-hydroxybenzaldehyde, five of which have not previously been reported in Anoectochilus roxburghii. In addition, two groups of co-eluted compounds were successfully identified. The results prove that this approach should be of benefit in the unequivocal structural determination of a variety of classes of compounds from extremely complex mixtures, such as herbs and biological samples, which will lead to improved efficiency in the identification of new potential lead compounds. PMID:21731458

  8. Simultaneous structural identification of natural products in fractions of crude extract of the rare endangered plant Anoectochilus roxburghii using H NMR/RRLC-MS parallel dynamic spectroscopy.

    PubMed

    Wang, Xiao-Xue; He, Jiu-Ming; Wang, Chun-Lan; Zhang, Rui-Ping; He, Wen-Yi; Guo, Shun-Xing; Sun, Rui-Xiang; Abliz, Zeper

    2011-01-01

    Nuclear magnetic resonance/liquid chromatography-mass spectroscopy parallel dynamic spectroscopy (NMR/LC-MS PDS) is a method aimed at the simultaneous structural identification of natural products in complex mixtures. In this study, the method is illustrated with respect to (1)H NMR and rapid resolution liquid chromatography-mass spectroscopy (RRLC-MS) data, acquired from the crude extract of Anoectochilus roxburghii, which was separated into a series of fractions with the concentration of constituent dynamic variation using reversed-phase preparative chromatography. Through fraction ranges and intensity changing profiles in (1)H NMR/RRLC-MS PDS spectrum, (1)H NMR and the extracted ion chromatogram (XIC) signals deriving from the same individual constituent, were correlated due to the signal amplitude co-variation resulting from the concentration variation of constituents in a series of incompletely separated fractions. 1H NMR/RRLC-MS PDS was then successfully used to identify three types of natural products, including eight flavonoids, four organic acids and p-hydroxybenzaldehyde, five of which have not previously been reported in Anoectochilus roxburghii. In addition, two groups of co-eluted compounds were successfully identified. The results prove that this approach should be of benefit in the unequivocal structural determination of a variety of classes of compounds from extremely complex mixtures, such as herbs and biological samples, which will lead to improved efficiency in the identification of new potential lead compounds. PMID:21731458

  9. Bioautography with TLC-MS/NMR for Rapid Discovery of Anti-tuberculosis Lead Compounds from Natural Sources

    PubMed Central

    Grzelak, Edyta M.; Hwang, Changhwa; Cai, Geping; Nam, Joo-Won; Choules, Mary P.; Gao, Wei; Lankin, David C.; McAlpine, James B.; Mulugeta, Surafel G.; Napolitano, José G.; Suh, Joo-Won; Yang, Seung Hwan; Cheng, Jinhua; Lee, Hanki; Kim, Jin-Yong; Cho, Sang-Hyun; Pauli, Guido F.; Franzblau, Scott G.; Jaki, Birgit U.

    2016-01-01

    While natural products constitute an established source of lead compounds, the classical iterative bioassay-guided isolation process is both time- and labor-intensive and prone to failing to identify active minor constituents. (HP)TLC-bioautography-MS/NMR, which combines cutting-edge microbiological, chromatographic, and spectrometric technologies, was developed to accelerate anti-tuberculosis (TB) drug discovery from natural sources by acquiring structural information at a very early stage of the isolation process. Using the avirulent, bioluminescent Mtb strain mc27000 luxABCDE, three variations of bioautography were evaluated and optimized for sensitivity in detecting anti-TB agents, including established clinical agents and new leads with novel mechanisms of action. Several exemplary applications of this approach to microbial extracts demonstrate its potential as a routine method in anti-TB drug discovery from natural sources.

  10. NMR and MALDI-TOF MS based characterization of exopolysaccharides in anaerobic microbial aggregates from full-scale reactors.

    PubMed

    Gonzalez-Gil, Graciela; Thomas, Ludivine; Emwas, Abdul-Hamid; Lens, Piet N L; Saikaly, Pascal E

    2015-01-01

    Anaerobic granular sludge is composed of multispecies microbial aggregates embedded in a matrix of extracellular polymeric substances (EPS). Here we characterized the chemical fingerprint of the polysaccharide fraction of EPS in anaerobic granules obtained from full-scale reactors treating different types of wastewater. Nuclear magnetic resonance (NMR) signals of the polysaccharide region from the granules were very complex, likely as a result of the diverse microbial population in the granules. Using nonmetric multidimensional scaling (NMDS), the (1)H NMR signals of reference polysaccharides (gellan, xanthan, alginate) and those of the anaerobic granules revealed that there were similarities between the polysaccharides extracted from granules and the reference polysaccharide alginate. Further analysis of the exopolysaccharides from anaerobic granules, and reference polysaccharides using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) revealed that exopolysaccharides from two of the anaerobic granular sludges studied exhibited spectra similar to that of alginate. The presence of sequences related to the synthesis of alginate was confirmed in the metagenomes of the granules. Collectively these results suggest that alginate-like exopolysaccharides are constituents of the EPS matrix in anaerobic granular sludge treating different industrial wastewater. This finding expands the engineered environments where alginate has been found as EPS constituent of microbial aggregates. PMID:26391984

  11. NMR and MALDI-TOF MS based characterization of exopolysaccharides in anaerobic microbial aggregates from full-scale reactors

    PubMed Central

    Gonzalez-Gil, Graciela; Thomas, Ludivine; Emwas, Abdul-Hamid; Lens, Piet N. L.; Saikaly, Pascal E.

    2015-01-01

    Anaerobic granular sludge is composed of multispecies microbial aggregates embedded in a matrix of extracellular polymeric substances (EPS). Here we characterized the chemical fingerprint of the polysaccharide fraction of EPS in anaerobic granules obtained from full-scale reactors treating different types of wastewater. Nuclear magnetic resonance (NMR) signals of the polysaccharide region from the granules were very complex, likely as a result of the diverse microbial population in the granules. Using nonmetric multidimensional scaling (NMDS), the 1H NMR signals of reference polysaccharides (gellan, xanthan, alginate) and those of the anaerobic granules revealed that there were similarities between the polysaccharides extracted from granules and the reference polysaccharide alginate. Further analysis of the exopolysaccharides from anaerobic granules, and reference polysaccharides using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) revealed that exopolysaccharides from two of the anaerobic granular sludges studied exhibited spectra similar to that of alginate. The presence of sequences related to the synthesis of alginate was confirmed in the metagenomes of the granules. Collectively these results suggest that alginate-like exopolysaccharides are constituents of the EPS matrix in anaerobic granular sludge treating different industrial wastewater. This finding expands the engineered environments where alginate has been found as EPS constituent of microbial aggregates. PMID:26391984

  12. Pyridinoacridine alkaloids of marine origin: NMR and MS spectral data, synthesis, biosynthesis and biological activity

    PubMed Central

    Kuete, Victor; Biavatti, Maique W

    2015-01-01

    Summary This review focuses on pyridoacridine-related metabolites as one biologically interesting group of alkaloids identified from marine sources. They are produced by marine sponges, ascidians and tunicates, and they are structurally comprised of four to eight fused rings including heterocycles. Acridine, acridone, dihydroacridine, and quinolone cores are features regularly found in these alkaloid skeletons. The lack of hydrogen atoms next to quaternary carbon atoms for two or three rings makes the chemical shift assignment a difficult task. In this regard, one of the aims of this review is the compilation of previously reported, pyridoacridine 13C NMR data. Observations have been made on the delocalization of electrons and the presence of some functional groups that lead to changes in the chemical shift of some carbon resonances. The lack of mass spectra information for these alkaloids due to the compactness of their structures is further discussed. Moreover, the biosynthetic pathways of some of these metabolites have been shown since they could inspire biomimetic synthesis. The synthesis routes used to prepare members of these marine alkaloids (as well as their analogues), which are synthesized for biological purposes are also discussed. Pyridoacridines were found to have a large spectrum of bioactivity and this review highlights and compares the pharmacophores that are responsible for the observed bioactivity. PMID:26664587

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

    PubMed

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

    2016-05-10

    Improved signal identification for biological small molecules (BSMs) in a mixture was demonstrated by using multidimensional NMR on samples from (13) C-enriched Rhododendron japonicum (59.5 atom%) cultivated in air containing (13) C-labeled carbon dioxide for 14 weeks. The resonance assignment of 386 carbon atoms and 380 hydrogen atoms in the mixture was achieved. 42 BSMs, including eight that were unlisted in the spectral databases, were identified. Comparisons between the experimental values and the (13) C chemical shift values calculated by density functional theory supported the identifications of unlisted BSMs. Tracing the (13) C/(12) C ratio by multidimensional NMR spectra revealed faster and slower turnover ratios of BSMs involved in central metabolism and those categorized as secondary metabolites, respectively. The identification of BSMs and subsequent flow analysis provided insight into the metabolic systems of the plant. PMID:27060701

  14. Distinctive features of complexation of anthracycline antibiotic daunomycin with deoxyhexanucleotide d(GCATGC) in aqueous solution: 1D- and 2D-NMR analysis

    NASA Astrophysics Data System (ADS)

    Pahomov, Valery I.; Rogova, Olga V.; Volynkin, Vladimir S.; Veselkov, Kyrill A.; Hernandez Santiago, Adrian A.; Semanin, Alexander V.; Djimant, Leonid N.; Veselkov, Alexei N.

    2004-07-01

    Complexation of anthracycline antibiotic daunomycin (DAU) with self-complementary deoxyhexanucleotide d(GCATGC) in aqueous solution has been investigated by one-dimensional and two-dimensional homonuclear 'H NMR spectroscopy (TOCSY and NOESY) and heteronuclear 'H-31P NMR spectroscopy (HMBC). Quantitative determination of parameters of oligonucleotide self-association and its complexation with DAU was based on the analysis of the dependences of proton chemical shifts on concentration and temperature. Experimental results were analysed in terms of the equilibrium reaction constants, limiting proton chemical shifts and thermodynamical parameters (enthalpies AN, entropies AS) of the formation of hexamer duplex and different drug-DNA complexes. The most favourable structures of the single-stranded form of d(GCATGC) and the intercalated DAU-hexamer complex have been determined using X-PLOR software taking into consideration both intra- and intermolecular NOE contacts.

  15. Hydrogen bonding induced distortion of CO3 units and kinetic stabilization of amorphous calcium carbonate: results from 2D (13)C NMR spectroscopy.

    PubMed

    Sen, Sabyasachi; Kaseman, Derrick C; Colas, Bruno; Jacob, Dorrit E; Clark, Simon M

    2016-07-27

    Systematic correlation in alkaline-earth carbonate compounds between the deviation of the CO3 units from the perfect D3h symmetry and their (13)C nuclear magnetic resonance (NMR) chemical shift anisotropy (CSA) parameters is established. The (13)C NMR CSA parameters of amorphous calcium carbonate (ACC) are measured using two-dimensional (13)C phase adjusted spinning sidebands (PASS) NMR spectroscopy and are analyzed on the basis of this correlation. The results indicate a distortion of the CO3 units in ACC in the form of an in-plane displacement of the C atom away from the centroid of the O3 triangle, resulting from hydrogen bonding with the surrounding H2O molecules, without significant out-of-plane displacement. Similar distortion for all C atoms in the structure of ACC suggests a uniform spatial disposition of H2O molecules around the CO3 units forming a hydrogen-bonded amorphous network. This amorphous network is stabilized against crystallization by steric frustration, while additives such as Mg presumably provide further stabilization by increasing the energy of dehydration. PMID:27276013

  16. Structural studies of an arabinan from the stems of Ephedra sinica by methylation analysis and 1D and 2D NMR spectroscopy.

    PubMed

    Xia, Yong-Gang; Liang, Jun; Yang, Bing-You; Wang, Qiu-Hong; Kuang, Hai-Xue

    2015-05-01

    Plant arabinan has important biological activity. In this study, a water-soluble arabinan (Mw∼6.15kDa) isolated from the stems of Ephedra sinica was found to consist of (1→5)-Araƒ, (1→3,5)-Araƒ, T-Araƒ, (1→3)-Araƒ and (1→2,5)-Araƒ residues at proportions of 10:2:3:2:1. A tentative structure was proposed by methylation analysis, nuclear magnetic resonance (NMR) spectroscopy ((1)H NMR, (13)C NMR, DEPT-135, (1)H-(1)H COSY, HSQC, HMBC and ROESY) and literature. The structure proposed includes a branched (1→5)-α-Araf backbone where branching occurs at the O-2 and O-3 positions of the residues with 7.7% and 15.4% of the 1,5-linked α-Araf substituted at the O-2 and O-3 positions. The presence of a branched structure was further observed by atomic force microscopy. This polymer was characterized as having a much longer linear (1→5)-α-Araf backbone as a repeating unit. In particular, the presence of α-Araf→3)-α-Araf-(1→3)-α-Araf-(1→ attached at the O-2 is a new finding. This study may facilitate a deeper understanding of structure-activity relationships of biological polysaccharides from the stems of E. sinica. PMID:25659720

  17. GC-MS, LC-MS(n), LC-high resolution-MS(n), and NMR studies on the metabolism and toxicological detection of mesembrine and mesembrenone, the main alkaloids of the legal high "Kanna" isolated from Sceletium tortuosum.

    PubMed

    Meyer, Golo M J; Wink, Carina S D; Zapp, Josef; Maurer, Hans H

    2015-01-01

    Mesembrine and mesembrenone are the main alkaloids of Sceletium tortuosum, a plant species that was used for sedation and analgesia by the KhoiSan, previously known as Hottentots, a tribe in South Africa. After fermentation, the obtained preparation called "Kanna" or "Kougoed" was used by chewing, smoking, or sniffing. Today, Kanna gains popularity by drug users as legal high. For monitoring such consumption, metabolism studies are mandatory because the metabolites are mostly the analytical targets, especially in urine. Therefore, the metabolism of both alkaloids was investigated in rat urine and pooled human liver preparations after several sample work-up procedures. As both alkaloids were not commercially available, they were isolated from plant material by Soxhlet extraction, and their identity confirmed by NMR. The metabolites were identified using gas chromatography-mass spectrometry (GC-MS) and liquid chromatography coupled to linear ion trap high resolution mass spectrometry (LC-HR-MS(n)). Both alkaloids were O- and N-demethylated, dihydrated, and/or hydroxylated at different positions. The phenolic metabolites were partly excreted as glucuronides and/or sulfates. Most of the phase I metabolites identified in rat urine could be detected also in the human liver preparations. After a common user's low dose application of mesembrine, mainly the O- and N demethyl-dihydro, hydroxy, and bis-demethyl-dihydro metabolites, and in case of mesembrenone only the N-demethyl and the N-demethyl-dihydro metabolite could be detected in rat urine using the authors' standard urine screening approaches (SUSA) by GC-MS or LC-MS(n). Thus, it should be possible to monitor a consumption of mesembrine and/or mesembrenone assuming similar pharmacokinetics in humans. PMID:25240931

  18. Chemical Profiling (HPLC-NMR & HPLC-MS), Isolation, and Identification of Bioactive Meroditerpenoids from the Southern Australian Marine Brown Alga Sargassum paradoxum

    PubMed Central

    Brkljača, Robert; Urban, Sylvia

    2014-01-01

    A phytochemical investigation of a southern Australian marine brown alga, Sargassum paradoxum, resulted in the isolation and identification of four new (5, 9, 10, and 15) and nine previously reported (1, 2, 6–8, and 11–14) bioactive meroditerpenoids. HPLC-NMR and HPLC-MS were central to the identification of a new unstable compound, sargahydroquinal (9), and pivotal in the deconvolution of eight (1, 2, 5–7, and 10–12) other meroditerpenoids. In particular, the complete characterization and identification of the two main constituents (1 and 2) in the crude dichloromethane extract was achieved using stop-flow HPLC-NMR and HPLC-MS. This study resulted in the first acquisition of gHMBCAD NMR spectra in the stop-flow HPLC-NMR mode for a system solely equipped with a 60 μL HPLC-NMR flow cell without the use of a cold probe, microcoil, or any pre-concentration. PMID:25551779

  19. The nature and fate of natural resins in the geosphere - VIII - NMR and Py-GC-MS characterization of soluble labdanoid polymers isolated from holocene class I resins.

    SciTech Connect

    Clifford, D. J.; Hatcher, P. G.; Botto, R. E.; Muntean, J. V.; Michaels, B.; Anderson, K. B.; Chemistry; Pennsylvania State Univ.; Amoco Oil Co.

    1997-01-01

    Soluble polylabdanoids isolated by sequential solvent extraction have been characterized by liquid-state {sup 13}C- and {sup 1}H NMR and {sup 13}C-{sup 1}H HMQC (heteronuclear correlation) NMR spectroscopy in addition to solid-state NMR and Py-GC-MS techniques. Two Holocene resins originating from Santander, Colombia and Mombasa, Kenya were analyzed. Soluble polymers were isolated by extraction with a 1:1 (v/v) methylene chloride-methanol mixture following sequential extractions with methylene chloride and methanol. The molecular weight of polymer extracts was shown by GPC analyses to exceed that of non-polymeric occluded terpenoids. Py-GC-MS, solid-state {sup 13}C CP/MAS and {sup 13}C cross-polarization/depolarization NMR spectroscopy results indicated that chemical compositions of soluble polymers isolated from immature resins are highly representative of the structure of corresponding insoluble polymers, i.e. polylabdatrienes. These data provide evidence for cross-linking or cyclization of side-chain olefinic carbons during or shortly after polymerization. Generally, the characterization of soluble resin polymers by liquid-state NMR spectroscopy has proven to be an excellent means for investigating the maturation mechanism of polylabdanoid resinites, and has potential for furthering the application of Class I resinites as geothermal indicators.

  20. Comparative structural profiling of trichome specialized metabolites in tomato (Solanum lycopersicum) and S. habrochaites: acylsugar profiles revealed by UHPLC/MS and NMR.

    PubMed

    Ghosh, Banibrata; Westbrook, Thomas C; Jones, A Daniel

    2014-01-01

    Many plants accumulate large quantities of specialized metabolites in secretory glandular trichomes (SGTs), which are specialized epidermal cells. In the genus Solanum, SGTs store a diverse collection of glucose and sucrose esters. Profiling of extracts from two accessions (LA1777 and LA1392) of Solanum habrochaites using ultra-high performance liquid chromatography-mass spectrometry (UHPLC/MS) revealed wide acylsugar diversity, with up to 11 isomers annotated for each individual elemental formula. These isomers arise from differences in ester chain lengths and their positions of substitution or branching. Since fragment ion masses were not sufficient to distinguish all isomers, 24 acylsucroses were purified from S. habrochaites accessions and cultivated tomato (Solanum lycopersicum M82) and characterized using NMR spectroscopy. Two-dimensional NMR spectra yielded assignments of positions of substitution of specific acyl groups, and locations of branching. The range of substitution was wider than reported earlier, and in contrast to previous reports, tetra- and penta-acylsucroses were substituted at position 2 with acyl groups other than acetate. Because UHPLC/MS fails to yield sufficient information about structure diversity, and quantitative NMR of acylsugar mixtures is confounded by structural redundancy, the strategic combination of NMR and UHPLC/MS provides a powerful approach for profiling a class of metabolites with great structural diversity across genotypes. PMID:24772058

  1. Inclusion complex of a new propiconazole derivative with β-cyclodextrin: NMR, ESI–MS and preliminary pharmacological studies

    PubMed Central

    Marangoci, Narcisa; Mares, Mihai; Silion, Mihaela; Fifere, Adrian; Varganici, Cristian; Nicolescu, Alina; Deleanu, Calin; Coroaba, Adina; Pinteala, Mariana; Simionescu, Bogdan C.

    2011-01-01

    A novel inclusion complex of the propiconazole nitrate (NO3PCZ) with β-cyclodextrin (β-CD) was prepared by treatment of propiconazole (PCZ) with an acidic nitrating agent. The formation of NO3PCZ and its inclusion complex with β-CD has been studied by NMR, ESI–MS, TGA, DSC methods. Using the undecoupled signal in the HMBC correlation spectra, almost identical coupling constants of CH from trizolic ring of PCZ and NO3PCZ compounds (1J(HC)3=207 Hz, 1J(CH)5=214 Hz, for PCZ; 1J(HC)3=208 Hz and 1J(CH)5=215 Hz, for NO3PCZ) were determined, confirming that the geometry of the heterocyclic skeleton is identical in both the forms. The 1:1 stoichiometry of the complex was determined by ESI–MS and was confirmed using Scott's equation in DMSO and Higuchi and Connors equation in water. The solubility curve obtained for NO3PCZ in presence of β-CD in distilled water was constructed, resulting in a solubility diagram of AL type. Solubility of NO3PCZ in water was determined by DLS studies. The results showed that NO3PCZ was encapsulated within the β-CD cavity with a binding constant of 330 M-1 in DMSO and 975 M-1 in water. Preliminary pharmacological studies showed higher antifungal activities for NO3PCZ and its inclusion complex, compared with its PCZ analog. The acute toxicity of the complex is smaller than the pure or modified drug, recommending the inclusion complex as future promising therapeutic agents. PMID:25755979

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

    PubMed

    Keum, Sam-Rok; Lim, Hyun-Woo

    2016-02-01

    We report the synthesis of a series of novel stilbene-based (St) Fischer base analogs of leuco-triarylmethane (LTAM) dyes by treating Fischer base with (E)-4-styrylbenzaldehyde derivatives. All St-LTAM molecules examined herein are characterized by 1D and 2D NMR. They were found to exhibit ZE configuration and isomerize to their diastereomers EE and ZZ in 2-3 h. They exhibit type I behavior of diastereomeric isomerization. PMID:26448377

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

    NASA Astrophysics Data System (ADS)

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

    2013-06-01

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

  4. Determination of optimal protein quantity required to identify abundant and less abundant soybean seed proteins by 2D-PAGE and MS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Optimizing the amounts of proteins required to separate and characterize both abundant and less abundant proteins by two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) is critical for conducting proteomic research. In this study, we tested five different levels of soybean seed proteins (7...

  5. Intercalation complex of imidazoacridinone C-1311, a potential anticancer drug, with DNA helix d(CGATCG)2: stereostructural studies by 2D NMR spectroscopy.

    PubMed

    Laskowski, Tomasz; Czub, Jacek; Sowiński, Paweł; Mazerski, Jan

    2016-03-01

    Imidazoacridinone C-1311 (Symadex®) is a powerful antitumor agent, which successfully made its way through the Phase I clinical trials and has been recommended for Phase II few a years ago. It has been shown experimentally that during the initial stage of its action C-1311 forms a relatively stable intercalation complex with DNA, yet it has shown no base-sequence specificity while binding to DNA. In this paper, the d(CGATCG)2:C-1311 intercalation complex has been studied by means of two-dimensional NMR spectroscopy, yielding a full assignment of the resonance lines observed in (1)H NMR spectra. The observation of the intermolecular NOE contacts between C-1311 and DNA allowed locating the ligand between the guanine and adenine moieties. Formation of a symmetric complex was pointed out on the basis of the lack of a second set of the (1)H resonances. The resulting stereostructure of the complex was then improved by means of molecular dynamics, using the CHARMM force field and GROMACS software. To this end, distance restraints derived from the NOESY cross-peak volumes were applied to the atomistic model of the d(CGATCG)2:C-1311 complex. Obtained results are in full agreement with biochemical data on the mechanism of action of C-1311, in particular with the previously postulated post-intercalation enzymatic activation of the studied drug. PMID:26211888

  6. LC-MS- and (1)H NMR-Based Metabolomic Analysis and in Vitro Toxicological Assessment of 43 Aristolochia Species.

    PubMed

    Michl, Johanna; Kite, Geoffrey C; Wanke, Stefan; Zierau, Oliver; Vollmer, Guenter; Neinhuis, Christoph; Simmonds, Monique S J; Heinrich, Michael

    2016-01-22

    Species of Aristolochia are used as herbal medicines worldwide. They cause aristolochic acid nephropathy (AAN), a devastating disease associated with kidney failure and renal cancer. Aristolochic acids I and II (1 and 2) are considered to be responsible for these nephrotoxic and carcinogenic effects. A wide range of other aristolochic acid analogues (AAAs) exist, and their implication in AAN may have been overlooked. An LC-MS- and (1)H NMR-based metabolomic analysis was carried out on 43 medicinally used Aristolochia species. The cytotoxicity and genotoxicity of 28 Aristolochia extracts were measured in human kidney (HK-2) cells. Compounds 1 and 2 were found to be the most common AAAs. However, AA IV (3), aristolactam I (4), and aristolactam BI (5) were also widespread. No correlation was found between the amounts of 1 or 2 and extract cytotoxicity against HK-2 cells. The genotoxicity and cytotoxicity of the extracts could be linked to their contents of 5, AA D (8), and AA IIIa (10). These results undermine the assumption that 1 and 2 are exclusively responsible for the toxicity of Aristolochia species. Other analogues are likely to contribute to their toxicity and need to be considered as nephrotoxic agents. These findings facilitate understanding of the nephrotoxic mechanisms of Aristolochia and have significance for the regulation of herbal medicines. PMID:26706944

  7. Lactonization and protonation of gluconic acid: a thermodynamicand kinetic study by potentiometry, nmr and esi-ms

    SciTech Connect

    Zhang, Z.; Gibson, P.; Clark, S.B.; Tian, G.; Zanonato, P.; Rao, L.

    2007-01-10

    In acidic aqueous solutions, gluconate protonation is coupled with lactonization of gluconic acid. With the decrease of pC{sub H}, two lactones ({delta}/{gamma}) are sequentially formed. The {delta}-lactone forms more readily than the {gamma}-lactone. In 0.1 M gluconate solutions, if pC{sub H} is above 2.5, only the {delta}-lactone is generated. When pC{sub H} is decreased below 2.0, the formation of the {gamma}-lactone is observable although the {delta}-lactone predominates. At I = 0.1 M NaClO{sub 4} and room temperature, the deprotonation constant of the carboxylic group, using the NMR technique, was determined to be log K{sub a} = 3.30 {+-} 0.02; the {delta}-lactonization constant, by the batch potentiometric titrations, was obtained to be log K{sub L} = - (0.54 {+-} 0.04). Using ESI-MS, the rate constants of the {delta}-lactonization and the hydrolysis at pC{sub H} {approx} 5.0 were estimated to be k{sub 1} = 3.2 x 10{sup -5} s{sup -1} and k{sup -1} = 1.1 x 10{sup -4} s{sup -1}, respectively.

  8. NMR and LC/MS-based global metabolomics to identify serum biomarkers differentiating hepatocellular carcinoma from liver cirrhosis.

    PubMed

    Liu, Yue; Hong, Zhanying; Tan, Guangguo; Dong, Xin; Yang, Genjin; Zhao, Liang; Chen, Xiaofei; Zhu, Zhenyu; Lou, Ziyang; Qian, Baohua; Zhang, Guoqing; Chai, Yifeng

    2014-08-01

    Hepatocellular carcinoma (HCC) is one of the most common malignant tumors in the world. However, current biomarkers that discriminate HCC from liver cirrhosis (LC) are important but are limited. More reliable biomarkers for HCC diagnosis are therefore needed. Serum from HCC patients, LC patients and healthy volunteers were analyzed using NMR and LC/MS-based approach in conjunction with random forest (RF) analysis to discriminate their serum metabolic profiles. Thirty-two potential biomarkers have been identified, and the feasibility of using these biomarkers for the diagnosis of HCC was evaluated, where 100% sensitivity was achieved in detecting HCC patients even with AFP values lower than 20 ng/mL. The metabolic alterations induced by HCC showed perturbations in synthesis of ketone bodies, citrate cycle, phospholipid metabolism, sphingolipid metabolism, fatty acid oxidation, amino acid catabolism and bile acid metabolism in HCC patients. Our results suggested that these potential biomarkers identified appeared to have diagnostic and/or prognostic values for HCC, which deserve to be further investigated. In addition, it also suggested that RF is a classification algorithm well suited for selection of biologically relevant features in metabolomics. PMID:24382646

  9. Identifying Three Ecological Chemotypes of Xanthium strumarium Glandular Trichomes Using a Combined NMR and LC-MS Method

    PubMed Central

    Gou, Junbo; Lu, Dayan; Gong, Fujun; Tang, Huiru; Zhang, Yansheng

    2013-01-01

    Xanthanolides, as the sesquiterpene lactones, are reportedly the major components for the pharmacological properties of X. strumarium L. species. Phytochemical studies indicated that the glandular structures on the surface of plant tissues would form the primary sites for the accumulation of this class of the compounds. As the interface between plants and their natural enemies, glandular trichomes may vary with respect to which of their chemicals are sequestered against different herbivores in different ecologies. However, to date, no data are available on the chemical characterisation of X. strumarium glandular cells. In this study, the trichome secretions of the X. strumarium species originating from nineteen unique areas across eleven provinces in China, were analysed by HPLC, LC-ESI-MS and NMR. For the first time three distinct chemotypes of X. strumarium glandular trichomes were discovered along with the qualitative and quantitative evaluations of their presence of xanthanolides; these were designated glandular cell Types I, II, and III, respectively. The main xanthanolides in Type I cells were 8-epi-xanthatin and xanthumin while no xanthatin was detected. Xanthatin, 8-epi-xanthatin, and xanthumin dominated in Type II cells with comparable levels of each being present. For Type III cells, significantly higher concentrations of 8-epi-xanthatin or xanthinosin (relative to xanthatin) were detected with xanthinosin only being observed in this type. Further research will focus on understanding the ecological and molecular mechanism causing these chemotype differences in X. strumarium glandular structures. PMID:24098541

  10. Identifying three ecological chemotypes of Xanthium strumarium glandular trichomes using a combined NMR and LC-MS method.

    PubMed

    Chen, Fangfang; Hao, Fuhua; Li, Changfu; Gou, Junbo; Lu, Dayan; Gong, Fujun; Tang, Huiru; Zhang, Yansheng

    2013-01-01

    Xanthanolides, as the sesquiterpene lactones, are reportedly the major components for the pharmacological properties of X. strumarium L. species. Phytochemical studies indicated that the glandular structures on the surface of plant tissues would form the primary sites for the accumulation of this class of the compounds. As the interface between plants and their natural enemies, glandular trichomes may vary with respect to which of their chemicals are sequestered against different herbivores in different ecologies. However, to date, no data are available on the chemical characterisation of X. strumarium glandular cells. In this study, the trichome secretions of the X. strumarium species originating from nineteen unique areas across eleven provinces in China, were analysed by HPLC, LC-ESI-MS and NMR. For the first time three distinct chemotypes of X. strumarium glandular trichomes were discovered along with the qualitative and quantitative evaluations of their presence of xanthanolides; these were designated glandular cell Types I, II, and III, respectively. The main xanthanolides in Type I cells were 8-epi-xanthatin and xanthumin while no xanthatin was detected. Xanthatin, 8-epi-xanthatin, and xanthumin dominated in Type II cells with comparable levels of each being present. For Type III cells, significantly higher concentrations of 8-epi-xanthatin or xanthinosin (relative to xanthatin) were detected with xanthinosin only being observed in this type. Further research will focus on understanding the ecological and molecular mechanism causing these chemotype differences in X. strumarium glandular structures. PMID:24098541

  11. 2D NMR studies of aminoglycoside antibiotics. Use of relayed coherence transfer for /sub 1/H resonance assignment and in situ structure elucidation of amikacin derivatives in reaction mixtures

    SciTech Connect

    Andersen, N.H.; Eaton, H.L.; Nguyen, K.T.; Hartzell, C.; Nelson, R.J.; Priest, J.H.

    1988-04-19

    Phase-sensitive 2D /sup 1/H//sup 1/H COSY spectra can be used to identify the structures of individual pure specimens of the aminoglycoside antibiotic amikacin and its N-hemisuccinyl derivatives. However, even at 500 MHz the 2D chemical shift dispersion does not allow for unambiguous assignment of all cross-peaks. By use of 2D relayed coherence transfer experiments (RELAY) optimized to detect two-step /sup 1/H//sup 1/H scalar interactions in which one of the J-values is small, sufficient additional correlations can be obtained from the frequency-isolated resonances to allow facile tracing of all scalar connectivities. Complete assignments of the /sup 1/H NMR spectra of amikacin, its 6'-N-hemisuccinamide, and a novel bis(acylate) (..gamma..-N-(p-vinylbenzoyl)amikacin 6'-N-hemisuccinamide) were obtained for aqueous media. The NMR spectrum of amikacin free base was also assigned in dimethyl sulfoxide solution. The RELAY experiment can be extended to the analysis of reaction mixtures, which allows for the identification and resonance assignment of regioisomeric amikacin haptens in the mixture state. All of the N-monohemisuccinyl isomers of amikacin have been identified in reaction mixtures through the RELAY experiment. The relative reactivities of the amino functions of amikacin toward acylating agents were found to be 6'-N > 3-N greater than or equal to 3''-N greater than or equal to ..gamma..-N. However, this reactivity order is altered after the initial acylation event.

  12. 13C and 15N—Chemical Shift Anisotropy of Ampicillin and Penicillin-V Studied by 2D-PASS and CP/MAS NMR

    NASA Astrophysics Data System (ADS)

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

    1998-11-01

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

  13. 31P NMR 2D Mapping of Creatine Kinase Forward Flux Rate in Hearts with Postinfarction Left Ventricular Remodeling in Response to Cell Therapy.

    PubMed

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

    2016-01-01

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

  14. Soft Corals Biodiversity in the Egyptian Red Sea: A Comparative MS and NMR Metabolomics Approach of Wild and Aquarium Grown Species.

    PubMed

    Farag, Mohamed A; Porzel, Andrea; Al-Hammady, Montasser A; Hegazy, Mohamed-Elamir F; Meyer, Achim; Mohamed, Tarik A; Westphal, Hildegard; Wessjohann, Ludger A

    2016-04-01

    Marine life has developed unique metabolic and physiologic capabilities and advanced symbiotic relationships to survive in the varied and complex marine ecosystems. Herein, metabolite composition of the soft coral genus Sarcophyton was profiled with respect to its species and different habitats along the coastal Egyptian Red Sea via (1)H NMR and ultra performance liquid chromatography-mass spectrometry (UPLC-MS) large-scale metabolomics analyses. The current study extends the application of comparative secondary metabolite profiling from plants to corals revealing for metabolite compositional differences among its species via a comparative MS and NMR approach. This was applied for the first time to investigate the metabolism of 16 Sarcophyton species in the context of their genetic diversity or growth habitat. Under optimized conditions, we were able to simultaneously identify 120 metabolites including 65 diterpenes, 8 sesquiterpenes, 18 sterols, and 15 oxylipids. Principal component analysis (PCA) and orthogonal projection to latent structures-discriminant analysis (OPLS) were used to define both similarities and differences among samples. For a compound based classification of coral species, UPLC-MS was found to be more effective than NMR. The main differentiations emanate from cembranoids and oxylipids. The specific metabolites that contribute to discrimination between soft corals of S. ehrenbergi from the three different growing habitats also belonged to cembrane type diterpenes, with aquarium S. ehrenbergi corals being less enriched in cembranoids compared to sea corals. PCA using either NMR or UPLC-MS data sets was found equally effective in predicting the species origin of unknown Sarcophyton. Cyclopropane containing sterols observed in abundance in corals may act as cellular membrane protectant against the action of coral toxins, that is, cembranoids. PMID:26892921

  15. Identification of endogenous metabolites in human sperm cells using proton nuclear magnetic resonance ((1) H-NMR) spectroscopy and gas chromatography-mass spectrometry (GC-MS).

    PubMed

    Paiva, C; Amaral, A; Rodriguez, M; Canyellas, N; Correig, X; Ballescà, J L; Ramalho-Santos, J; Oliva, R

    2015-05-01

    The objective of this study was to contribute to the first comprehensive metabolomic characterization of the human sperm cell through the application of two untargeted platforms based on proton nuclear magnetic resonance ((1) H-NMR) spectroscopy and gas chromatography coupled to mass spectrometry (GC-MS). Using these two complementary strategies, we were able to identify a total of 69 metabolites, of which 42 were identified using NMR, 27 using GC-MS and 4 by both techniques. The identity of some of these metabolites was further confirmed by two-dimensional (1) H-(1) H homonuclear correlation spectroscopy (COSY) and (1) H-(13) C heteronuclear single-quantum correlation (HSQC) spectroscopy. Most of the metabolites identified are reported here for the first time in mature human spermatozoa. The relationship between the metabolites identified and the previously reported sperm proteome was also explored. Interestingly, overrepresented pathways included not only the metabolism of carbohydrates, but also of lipids and lipoproteins. Of note, a large number of the metabolites identified belonged to the amino acids, peptides and analogues super class. The identification of this initial set of metabolites represents an important first step to further study their function in male gamete physiology and to explore potential reasons for dysfunction in future studies. We also demonstrate that the application of NMR and MS provides complementary results, thus constituting a promising strategy towards the completion of the human sperm cell metabolome. PMID:25854681

  16. 1H-NMR and MS Based Metabolomics Study of the Intervention Effect of Curcumin on Hyperlipidemia Mice Induced by High-Fat Diet

    PubMed Central

    Li, Ze-Yun; Ding, Li-Li; Li, Jin-Mei; Xu, Bao-Li; Yang, Li; Bi, Kai-Shun; Wang, Zheng-Tao

    2015-01-01

    Curcumin, a principle bioactive component of Curcuma longa L, is well known for its anti-hyperlipidemia effect. However, no holistic metabolic information of curcumin on hyperlipidemia models has been revealed, which may provide us an insight into the underlying mechanism. In the present work, NMR and MS based metabolomics was conducted to investigate the intervention effect of curcumin on hyperlipidemia mice induced by high-fat diet (HFD) feeding for 12 weeks. The HFD induced animals were orally administered with curcumin (40, 80 mg/kg) or lovastatin (30 mg/kg, positive control) once a day during the inducing period. Serum biochemistry assay of TC, TG, LDL-c, and HDL-c was conducted and proved that treatment of curcumin or lovastatin can significantly improve the lipid profiles. Subsequently, metabolomics analysis was carried out for urine samples. Orthogonal Partial Least Squares-Discriminant analysis (OPLS-DA) was employed to investigate the anti-hyperlipidemia effect of curcumin and to detect related potential biomarkers. Totally, 35 biomarkers were identified, including 31 by NMR and nine by MS (five by both). It turned out that curcumin treatment can partially recover the metabolism disorders induced by HFD, with the following metabolic pathways involved: TCA cycle, glycolysis and gluconeogenesis, synthesis of ketone bodies and cholesterol, ketogenesis of branched chain amino acid, choline metabolism, and fatty acid metabolism. Besides, NMR and MS based metabolomics proved to be powerful tools in investigating pharmacodynamics effect of natural products and underlying mechanisms. PMID:25786031

  17. Identification of histidine tautomers in proteins by 2D 1H/13C(delta2) one-bond correlated NMR.

    PubMed

    Sudmeier, James L; Bradshaw, Elizabeth M; Haddad, Kristin E Coffman; Day, Regina M; Thalhauser, Craig J; Bullock, Peter A; Bachovchin, William W

    2003-07-16

    If the 13Cdelta2 chemical shift of neutral ("high pH") histidine is >122 ppm, primarily Ndelta1-H tautomer (2) is indicated; if it is <122 ppm, primarily Nepsilon2-H tautomer (1) is indicated. His resonances from the catalytic triad of active serine proteases, for example, are readily distinguished from those of denatured enzyme. The 13Cdelta2 chemical shifts increased by 6.2 ppm for the catalytic histidines in both alpha-lytic protease and subtilisin BPN' in raising the pH from that of imidazolium cation to that of tautomer 2. This tautomer identification method is easy to implement, requiring only bioincorporation of [U-13C] (or the more readily available [U-13C,15N])-histidine. Standard 1H/13C correlation HMQC or HSQC NMR pulse programs then yield the 13Cdelta2 chemical shifts with the benefit of high 1H sensitivity. Because of large one-bond spin-couplings (1JCH approximately 200 Hz), the method should extend to proteins having large 1H and 13C line widths, including very high molecular weights. PMID:12848537

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

    SciTech Connect

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

    2014-11-15

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

  19. Isoxazole derivatives of alpha-pinene isomers: Synthesis, crystal structure, spectroscopic characterization (FT-IR/NMR/GC-MS) and DFT studies

    NASA Astrophysics Data System (ADS)

    Eryılmaz, Serpil; Gül, Melek; İnkaya, Ersin; Taş, Murat

    2016-03-01

    In this paper, the alpha-pinene isoxazole derivatives (3a-b-c, 4a-b) were synthesized via 1,3-dipolar cycloaddition and characterized with FT-IR, 1H NMR, 13C NMR and GC-MS. Isoxazole (C21H23NO) compound (4a) 6,6,7a,-trimethyl-3-(naphthalen-2-yl)-3a,4,5,6,7,7a-hexahydro-5,7-methanobenzo[d] was characterized by X-ray single crystal diffraction technique. The compound crystallizes in the monoclinic space group P 212121, with Z = 4. The molecular geometry of the compound was optimized by applying Density Functional Theory (DFT/B3LYP) method with 6-31G(d,p) and 6-311 + G(d,p) basis sets in the ground state and geometric parameters were compared with the X-ray analysis results of the structure. Results of the experimental FT-IR and NMR spectral analysis were examined in order to determine the compliance with vibrational frequencies, 1H NMR and 13C NMR chemical shifts values by using the Gauge-Independent Atomic Orbital (GIAO) method calculated over the optimized structure. Besides molecular electrostatic potential (MEP), frontier molecular orbitals (FMOs), some global reactivity descriptors, thermodynamic properties, non-linear optical (NLO) behaviour and Mulliken charge analysis of the (4a) compound were computed with the same method in gas phase, theoretically.

  20. 2D-NMR, X-ray crystallography and theoretical studies of the reaction mechanism for the synthesis of 1,5-benzodiazepines from dehydroacetic acid derivatives and o-phenylenediamines

    NASA Astrophysics Data System (ADS)

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

    2014-03-01

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

  1. 2D-DIGE and MALDI TOF/TOF MS analysis reveal that small GTPase signaling pathways may play an important role in cadmium-induced colon cell malignant transformation.

    PubMed

    Lu, Jian; Zhou, Zhongping; Zheng, Jianzhou; Zhang, Zhuyi; Lu, Rongzhu; Liu, Hanqing; Shi, Haifeng; Tu, Zhigang

    2015-10-01

    Cadmium is a toxic heavy metal present in the environment and in industrial materials. Cadmium has demonstrated carcinogenic activity that induces cell transformation, but how this occurs is unclear. We used 2D-DIGE and MALDI TOF/TOF MS combined with bioinformatics and immunoblotting to investigate the molecular mechanism of cadmium transformation. We found that small GTPases were critical for transformation. Additionally, proteins involved in mitochondrial transcription, DNA repair, and translation also had altered expression patterns in cadmium treated cells. Collectively, our results suggest that activation of small GTPases contributes to cadmium-induced transformation of colon cells. PMID:26220685

  2. UPLC-MS metabolic profiling of second trimester amniotic fluid and maternal urine and comparison with NMR spectral profiling for the identification of pregnancy disorder biomarkers.

    PubMed

    Graça, Gonçalo; Goodfellow, Brian J; Barros, António S; Diaz, Sílvia; Duarte, Iola F; Spagou, Konstantina; Veselkov, Kirill; Want, Elizabeth J; Lindon, John C; Carreira, Isabel M; Galhano, Eulália; Pita, Cristina; Gil, Ana M

    2012-04-01

    We report on the first untargeted UPLC-MS study of 2nd trimester maternal urine and amniotic fluid (AF), to investigate the possible metabolic effects of fetal malformations (FM), gestational diabetes mellitus (GDM) and preterm delivery (PTD). For fetal malformations, considerable metabolite variations were identified in AF and, to a lesser extent, in urine. Using validated PLS-DA models and statistical correlations between UPLC-MS data and previously acquired NMR data, a metabolic picture of fetal hypoxia, enhanced gluconeogenesis, TCA activity and hindered kidney development affecting FM pregnancies was reinforced. Moreover, changes in carnitine, pyroglutamate and polyols were newly noted, respectively, reflecting lipid oxidation, altered placental amino acid transfer and alterations in polyol pathways. Higher excretion of conjugated products in maternal urine was seen suggesting alterations in conjugation reactions. For the pre-diagnostic GDM group, no significant changes were observed, either considering amniotic fluid or maternal urine, whereas, for the pre-PTD group, some newly observed changes were noted, namely, the decrease of particular amino acids and the increase of an hexose (possibly glucose), suggesting alteration in placental amino acid fluxes and a possible tendency for hyperglycemia. This work shows the potential of UPLC-MS for the study of fetal and maternal biofluids, particularly when used in tandem with comparable NMR data. The important roles played by sampling characteristics (e.g. group dimensions) and the specific experimental conditions chosen for MS methods are discussed. PMID:22294348

  3. Identification of Differential Protein Expression in Hepatocellular Carcinoma Induced Wistar Albino Rats by 2D Electrophoresis and MALDI-TOF-MS Analysis.

    PubMed

    Vedarethinam, Vadanasundari; Dhanaraj, Karthik; Soundherrajan, Ilavenil; Sivanesan, Ravikumar

    2016-04-01

    Hepato cellular carcinoma (HCC) is a type of malignant tumor. To investigate the proteins in cancer molecular mechanism and its role in HCC, we have used proteomic tools such as 2DE and MALDI-TOF-MS. Our investigation ravels that, plasma α-fetoprotein and carcinoembryonic antigen levels were elevated in DEN induced rats and gradually decreased after the treatment with 1,3BPMU. 2DE and MALDI-TOF-MS tool offers to identify the up and down regulation of proteins in HCC. Proteomic study reveals that, five differentially expressed proteins were identified in DEN induced rats and 1,3BPMU treated rats i.e. three up regulated protein such as T kininogen, NDPKB, PRMT1 (DEN induced rats), RGS19 and PAF (1,3BPMU treated rats) in 3BPMU treated rats, activation of transcription of a single gene from multiple promoters provides flexibility in the controlled gene expression. The regulations of hepatocyte stimulating factor were slow down the proliferation of hepatic cell and uncontrolled hepatic cell growth and also molecular signals strongly argue for a patho-physiological role in liver metastasis to control the cell aggression. This indicates that, anti cancer property of 1,3BPMU can be used as potent anti cancer agent. The present study also shows the proteomic approach helps to elucidate the tumor maker as well as regulatory marker proteins in HCC. PMID:27069327

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

    NASA Astrophysics Data System (ADS)

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

    2007-09-01

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

  5. Qualitative and quantitative analysis of the unsaponifiable fraction of vegetable oils by using comprehensive 2D GC with dual MS/FID detection.

    PubMed

    Tranchida, Peter Q; Salivo, Simona; Franchina, Flavio A; Bonaccorsi, Ivana; Dugo, Paola; Mondello, Luigi

    2013-05-01

    The present investigation is focused on the development of a comprehensive two-dimensional GC (GC × GC) method, with dual MS/FID detection, for the qualitative and quantitative analysis of the entire unsaponifiable fraction of vegetable oils. The unsaponifiable fraction forms a minor, highly specific part of a vegetable oil, and can be used as an indicator of genuineness. The column set used consisted of a low-polarity first dimension, and a medium-polarity secondary one, both characterized by a high thermal stability. The use of dual detection enabled the attainment of both mass spectral information and relative % FID data. The complexity of the fingerprint, generated by the unsaponifiable fraction, fully justified the employment of the two-dimensional GC technology. Furthermore, two other GC × GC benefits contributed greatly to the attainment of promising results, namely sensitivity enhancement and the formation of group-type patterns. The method herein proposed could potentially open a new opportunity for the more in-depth knowledge of the unsaponifiable fraction of vegetable oils. PMID:23334257

  6. The structure investigations of dehydroacetic acid and 1,8-diaminonaphthalene condensation product by NMR, MS, and X-ray measurements

    NASA Astrophysics Data System (ADS)

    Kołodziej, B.; Morawiak, M.; Kamieński, B.; Schilf, W.

    2016-05-01

    A new unexpected product of condensation reaction of 1,8-diaminonaphthalene (DAN) and carbonyl compound (here: dehydroacetic acid (dha)) was synthesized. Discussion about the molecular structure of possible products of this reaction was done on the base of NMR studies. The structure of the titled product in both DMSO solution and in the solid state was resolved by analysis of its spectral data (X-ray structure analysis, multinuclear NMR in solution and solid state spectra) and MS measurements. The presented studies provided clear evidence that the titled product exists in diluted DMSO solution as the mixture of two kinetic free ionic species whereas in concentrated DMSO solution as well as in the solid state this system forms associated ionic pairs bonded together by hydrogen bonds.

  7. Combined analysis by GC (RI), GC-MS and 13C NMR of the supercritical fluid extract of Abies alba twigs.

    PubMed

    Duquesnoy, Emilie; Marongiu, Bruno; Castola, Vincent; Piras, Alessandra; Porcedda, Silvia; Casanova, Joseph

    2010-12-01

    Two samples (leaves and twigs) of Abies alba Miller from Corsica were extracted using supercritical CO2 and their chemical compositions were compared with those of the essential oils obtained from the same batch of plant material. In total 45 components were identified using combined analysis by GC (RI), GC-MS and 13C NMR. It was observed that the contents of monoterpenes (mainly represented by limonene, alpha-pinene and camphene) were significantly lower in the supercritical fluid extract (SFE) than in the essential oil (EO). Conversely, the proportions of sesquiterpenes were much higher in CO2 extracts than in essential oils (around 30% vs 4%). Cis-abienol, a diterpene alcohol, was identified only in SFE, and the proportions of this constituent (7.5% and 17.3%) were determined using quantitative 13C NMR since it was under estimated using the standard conditions of GC. PMID:21299139

  8. (1)H NMR and GC-MS Based Metabolomics Reveal Defense and Detoxification Mechanism of Cucumber Plant under Nano-Cu Stress.

    PubMed

    Zhao, Lijuan; Huang, Yuxiong; Hu, Jerry; Zhou, Hongjun; Adeleye, Adeyemi S; Keller, Arturo A

    2016-02-16

    Because copper nanoparticles are being increasingly used in agriculture as pesticides, it is important to assess their potential implications for agriculture. Concerns have been raised about the bioaccumulation of nano-Cu and their toxicity to crop plants. Here, the response of cucumber plants in hydroponic culture at early development stages to two concentrations of nano-Cu (10 and 20 mg/L) was evaluated by proton nuclear magnetic resonance spectroscopy ((1)H NMR) and gas chromatography-mass spectrometry (GC-MS) based metabolomics. Changes in mineral nutrient metabolism induced by nano-Cu were determined by inductively coupled plasma-mass spectrometry (ICP-MS). Results showed that nano-Cu at both concentrations interferes with the uptake of a number of micro- and macro-nutrients, such as Na, P, S, Mo, Zn, and Fe. Metabolomics data revealed that nano-Cu at both levels triggered significant metabolic changes in cucumber leaves and root exudates. The root exudate metabolic changes revealed an active defense mechanism against nano-Cu stress: up-regulation of amino acids to sequester/exclude Cu/nano-Cu; down-regulation of citric acid to reduce the mobilization of Cu ions; ascorbic acid up-regulation to combat reactive oxygen species; and up-regulation of phenolic compounds to improve antioxidant system. Thus, we demonstrate that nontargeted (1)H NMR and GC-MS based metabolomics can successfully identify physiological responses induced by nanoparticles. Root exudates metabolomics revealed important detoxification mechanisms. PMID:26751164

  9. Comparative metabolite profiling and fingerprinting of genus Passiflora leaves using a multiplex approach of UPLC-MS and NMR analyzed by chemometric tools.

    PubMed

    Farag, Mohamed A; Otify, Asmaa; Porzel, Andrea; Michel, Camilia George; Elsayed, Aly; Wessjohann, Ludger A

    2016-05-01

    Passiflora incarnata as well as some other Passiflora species are reported to possess anxiolytic and sedative activity and to treat various CNS disorders. The medicinal use of only a few Passiflora species has been scientifically verified. There are over 400 species in the Passiflora genus worldwide, most of which have been little characterized in terms of phytochemical or pharmacological properties. Herein, large-scale multi-targeted metabolic profiling and fingerprinting techniques were utilized to help gain a broader insight into Passiflora species leaves' chemical composition. Nuclear magnetic resonance spectroscopy (NMR) and mass spectrometry (MS) spectra of extracted components derived from 17 Passiflora accessions and from different geographical origins were analyzed using multivariate data analyses. A total of 78 metabolites were tentatively identified, that is, 20 C-flavonoids, 8 O-flavonoids, 21 C, O-flavonoids, 2 cyanogenic glycosides, and 23 fatty acid conjugates, of which several flavonoid conjugates are for the first time to be reported in Passiflora spp. To the best of our knowledge, this study provides the most complete map for secondary metabolite distribution within that genus. Major signals in (1)H-NMR and MS spectra contributing to species discrimination were assigned to those of C-flavonoids including isovitexin-2″-O-xyloside, luteolin-C-deoxyhexoside-O-hexoside, schaftoside, isovitexin, and isoorientin. P. incarnata was found most enriched in C-flavonoids, justifying its use as an official drug within that genus. Compared to NMR, LC-MS was found more effective in sample classification based on genetic and/ or geographical origin as revealed from derived multivariate data analyses. Novel insight on metabolite candidates to mediate for Passiflora CNS sedative effects is also presented. PMID:26883968

  10. On-line 1D and 2D porous layer open tubular/LC-ESI-MS using 10-microm-i.d. poly(styrene-divinylbenzene) columns for ultrasensitive proteomic analysis.

    PubMed

    Luo, Quanzhou; Yue, Guihua; Valaskovic, Gary A; Gu, Ye; Wu, Shiaw-Lin; Karger, Barry L

    2007-08-15

    Following on our recent work, on-line one-dimensional (1D) and two-dimensional (2D) porous layer open tubular/liquid chromatography-electrospray ionization-mass spectrometry (PLOT/LC-ESI-MS) platforms using 3.2 mx10 microm i.d. poly(styrene-divinylbenzene) (PS-DVB) PLOT columns have been developed to provide robust, high-performance, and ultrasensitive proteomic analysis. With the use of a PicoClear tee, the dead volume connection between a 50 microm i.d. PS-DVB monolithic micro-SPE column and the PLOT column was minimized. The micro-SPE/PLOT column assembly provided a separation performance similar to that obtained with direct injection onto the PLOT column at a mobile phase flow rate of 20 nL/min. The trace analysis potential of the platform was evaluated using an in-gel tryptic digest sample of a gel fraction (15-40 kDa) of a cervical cancer (SiHa) cell line. As an example of the sensitivity of the system, approximately 2.5 ng of protein in 2 microL of solution, an amount corresponding to 20 SiHa cells, was subjected to on-line micro-SPE-PLOT/LC-ESI-MS/MS analysis using a linear ion trap MS. A total of 237 peptides associated with 163 unique proteins were identified from a single analysis when using stringent criteria associated with a false positive rate of less than 1%. The number of identified peptides and proteins increased to 638 and 343, respectively, as the injection amount was raised to approximately 45 ng of protein, an amount corresponding to 350 SiHa cells. In comparison, only 338 peptides and 231 unique proteins were identified (false positive rate again less than 1%) from 750 ng of protein from the identical gel fraction, an amount corresponding to 6000 SiHa cells, using a typical 15 cmx75 microm i.d. packed capillary column. The greater sensitivity, higher recovery, and higher resolving power of the PLOT column resulted in the increased number of identifications from only approximately 5% of the injected sample amount. The resolving power of the

  11. Combination of UHPLC/Q-TOF-MS, NMR spectroscopy, and ECD calculation for screening and identification of reactive metabolites of gentiopicroside in humans.

    PubMed

    Han, Han; Xiong, Ai-Zhen; He, Chun-Yong; Liu, Qing; Yang, Li; Wang, Zheng-Tao

    2014-02-01

    The metabolic investigation of natural products is a great challenge because of unpredictable metabolic pathways, little knowledge on metabolic effects, and lack of recommended analytical methodology. Herein, a combined strategy based on ultrahigh-performance liquid chromatography coupled with electrospray ionization quadrupole time-of-flight tandem mass spectrometry (UHPLC/Q-TOF-MS), nuclear magnetic resonance (NMR) spectroscopy, and electronic circular dichroism (ECD) calculation was developed and employed for the human metabolism study of gentiopicroside (GPS), a naturally hepato-protective iridoid glycoside. The whole metabolic study consisted of three major procedures. First, an improved UHPLC/Q-TOF-MS method was used to separate and detect a total of 15 GPS metabolites that were obtained from urine samples (0 to 72 h) of 12 healthy male participants after a single 50-mg oral dose of GPS. Second, a developed "MS-NMR-MS" method was applied to accurately identify molecular structures of the observed metabolites. Finally, given that the associated stereochemistry may be a crucial factor of the metabolic activation, the absolute configuration of the reactive metabolites was revealed through chemical calculations. Based on the combined use, a pair of diastereoisomers (G05 and G06) were experimentally addressed as the bioreactive metabolites of GPS, and the stereochemical determination was completed. Whereas several novel metabolic transformations, occurring via oxidation, N-heterocyclization and glucuronidation after deglycosylation, were also observed. The results indicated that GPS has to undergo in vivo metabolism-based activation to generate reactive molecules capable of processing its hepato-protective activity. PMID:24408300

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

    PubMed Central

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

    2015-01-01

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

  13. A 430 mW 16 b 170 MS/s CMOS pipelined ADC with 77.2 dB SNR and 97.6 dB SFDR

    NASA Astrophysics Data System (ADS)

    Hui, Zhang; Dan, Li; Lei, Wan; Hui, Zhang; Haijun, Wang; Yuan, Gao; Feili, Zhu; Ziqi, Wang; Xuexin, Ding

    2016-03-01

    A 16-bit 170 MS/s pipelined ADC implemented in 0.18 μm CMOS process is presented in this paper. An improved digital calibration method and a linearized sampling front-end are employed to achieve a high SFDR. The enlarged full scale range makes it possible to obtain a high SNR with smaller sampling capacitors, thus achieving higher speed and low power. This ADC attains an SNR of 77.2 dBFS, an SFDR of 97.6 dBc for a 10 MHz input signal, while preserving an SFDR > 80 dBc up to 300 MHz input frequency. The ADC consumes 430 mW from a 1.8 V supply and occupies a 17 mm2 active area. Project supported by the National Science and Technology Major Project (No. 2009ZX01034-002-001-016).

  14. Comparison of Flow Injection MS, NMR, and DNA Sequencing: Methods for Identification and Authentication of Black Cohosh (Actaea racemosa)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Flow injection mass spectrometry (FIMS) and proton nuclear magnetic resonance spectrometry (1H-NMR), two metabolic fingerprinting methods, and DNA sequencing were used to identify and authenticate Actaea species. Initially, samples of Actaea racemosa L. from a single source were distinguished from ...

  15. Glyphosate complexation to aluminium(III). An equilibrium and structural study in solution using potentiometry, multinuclear NMR, ATR-FTIR, ESI-MS and DFT calculations.

    PubMed

    Purgel, Mihály; Takács, Zoltán; Jonsson, Caroline M; Nagy, Lajos; Andersson, Ingegärd; Bányai, István; Pápai, Imre; Persson, Per; Sjöberg, Staffan; Tóth, Imre

    2009-11-01

    The stoichiometries and stability constants of a series of Al(3+)-N-phosponomethyl glycine (PMG/H(3)L) complexes have been determined in acidic aqueous solution using a combination of precise potentiometric titration data, quantitative (27)Al and (31)P NMR spectra, ATR-FTIR spectrum and ESI-MS measurements (0.6M NaCl, 25 degrees C). Besides the mononuclear AlH(2)L(2+), Al(H(2)L)(HL), Al(HL)(2)(-) and Al(HL)L(2-), dimeric Al(2)(HL)L(+) and trinuclear Al(3)H(5)L(4)(2+) complexes have been postulated. (1)H and (31)P NMR data show that different isomers co-exist in solution and the isomerization reactions are slow on the (31)P NMR time scale. The geometries of monomeric and dimeric complexes likely double hydroxo bridged and double phosphonate bridged isomers have been optimized using DFT ab initio calculations starting from rational structural proposals. Energy calculations using the PCM solvation method also support the co-existence of isomers in solutions. PMID:19766319

  16. Interpretation of combined 2H SNIF/NMR and 13C SIRA/MS analyses of fruit juices to detect added sugar.

    PubMed

    Martin, G G; Hanote, V; Lees, M; Martin, Y L

    1996-01-01

    The site-specific natural isotopic fractionation studied by nuclear magnetic resonance (SNIF/NMR) method measures site-specific isotope contents in a variety of organic compounds by deuterium nuclear magnetic resonance spectroscopy. This technique, together with SIRA/MS (stable isotope ratio analysis/mass spectrometry) provides a powerful tool for food authentication and characterization. By using the ethanol resulting from sugar fermentation as a molecular probe, SNIF/NMR (deuterium) and SIRA/MS (13C) have been used together for authentication of fruit juices. The influence of deuterium content of the fermentation water on the isotopic parameters is shown and a means for normalizing the results is proposed. A large number of authentic juices have been analyzed to define the variation of isotopic ratios in natural juices. On the basis of these data, a set of rules was designed to enable interpretation of isotopic parameters in terms of possible adulteration of fruit juices by sugar addition. Results of analyses of Florida orange juice are presented. Orange juice samples from Brazil and Israel are included as 2 extreme cases. Assignment limits for a sample of orange juice of unknown origin also are given. These assignment limits are also provided for apple and grapefruit juices. PMID:8620113

  17. Determination of astaxanthin and astaxanthin esters in the microalgae Haematococcus pluvialis by LC-(APCI)MS and characterization of predominant carotenoid isomers by NMR spectroscopy.

    PubMed

    Holtin, Karsten; Kuehnle, Maximilian; Rehbein, Jens; Schuler, Paul; Nicholson, Graeme; Albert, Klaus

    2009-11-01

    The oily product ZANTHIN consists of natural astaxanthin, which is manufactured from the microalgae Haematococcus pluvialis by supercritical CO(2) extraction. An HPLC method was developed to separate all of the components of the complex astaxanthin extract using a C(30) column. The separation resulted in different isomers of astaxanthin accompanied by two other carotenoids. The main component consisted of astaxanthin singly esterified with several different fatty acids. C18:3, C18:2, C18:1 and C16:0 were identified as the most commonly occurring fatty acids. Doubly esterified astaxanthin was also found, although in lower concentrations compared to singly esterified astaxanthin. After performing a detailed fatty acid analysis by GC-MS, the peaks from the extract were assigned via HPLC-MS. A trans to cis transmutation of the all-trans compound was performed by thermal treatment in order to obtain an enrichment of cis isomers as the basis for unambiguous identification via NMR experiments. The all-trans as well as the 9- and 13-cis isomers of astaxanthin were characterized in detail by UV/Vis, (1)H, and (1)H,(1)H COSY NMR spectroscopy. PMID:19466394

  18. Nuclear Magnetic Resonance (NMR), Infrared (IR) and Mass Spectrometry (MS) study of keto-enol tautomerism of isobenzofuran-1(3H)-one derivatives

    NASA Astrophysics Data System (ADS)

    Pires, Diego Arantes Teixeira; Pereira, Wagner Luiz; Teixeira, Róbson Ricardo; Figueroa-Villar, José Daniel; Nascimento, Claudia Jorge do

    2016-06-01

    The keto-enol tautomerism of 3-(2-hydroxy-4,4-dimethyl-6-oxo-cyclohexen-1-yl)isobenzofuran-1(3H-one (1), 3-(2-hydroxy-6-oxocyclohex-1-enyl)isobenzofuran-1(3H)-one (2), 3-(2-hydroxy-4-methyl-6-oxocyclohex-1-enyl)isobenzofuran-1(3H)-one (3), 3-(2-hydroxy-5-oxocyclopent-1-enyl)isobenzofuran-1(3H)-one (4) and 2-(3-oxo-1,3-dihydroisobenzofuran-1-yl)-1H-indene-1,3(2H)-dione (5) were investigated. We noticed that for compounds 1 to 4 only the enol form is observed in solid, in solution or in the gas phase. Their tautomeric equilibria are not affected by the solvent, temperature or physical state. Compound 5 was observed in its keto form in solution (NMR) and solid state (IR). The enol species of 5 was also observed upon Mass Spectrometry analysis. These findings were supported by NMR, IR, MS/MS and molecular modeling analyses.

  19. NMR and GC-MS based metabolic profiling and free-radical scavenging activities of Cordyceps pruinosa mycelia cultivated under different media and light conditions.

    PubMed

    Oh, Taek-Joo; Hyun, Sun-Hee; Lee, Seul-Gi; Chun, Young-Jin; Sung, Gi-Ho; Choi, Hyung-Kyoon

    2014-01-01

    Variation of metabolic profiles in Cordyceps pruinosa mycelia cultivated under various media and light conditions was investigated using 1H nuclear magnetic resonance (NMR) analysis and gas chromatography mass spectrometry (GC-MS) with multivariate statistical analysis. A total of 71 metabolites were identified (5 alcohols, 21 amino acids, 15 organic acids, 4 purines, 3 pyrimidines, 7 sugars, 11 fatty acids, and 5 other metabolites) by NMR and GC-MS analysis. The mycelia grown in nitrogen media and under dark conditions showed the lowest growth and ergosterol levels, essential to a functional fungal cell membrane; these mycelia, however, had the highest levels of putrescine, which is involved in abiotic stress tolerance. In contrast, mycelia cultivated in sabouraud dextrose agar with yeast extract (SDAY) media and under light conditions contained relatively higher levels of fatty acids, including valeric acid, stearic acid, lignoceric acid, myristic acid, oleic acid, palmitoleic acid, hepadecenoic acid, and linoleic acid. These mycelia also had the highest phenolic content and antioxidant activity, and did not exhibit growth retardation due to enhanced asexual development caused by higher levels of linoleic acid. Therefore, we suggested that a light-enriched environment with SDAY media was more optimal than dark condition for cultivation of C. pruinosa mycelia as biopharmaceutical or nutraceutical resources. PMID:24608751

  20. Determination of [{sup 13}C]pyrene sequestration in sediment microcosms using flash pyrolysis--GC--MS and {sup 13}C NMR

    SciTech Connect

    Guthrie, E.A.; Bortiatynski, J.M.; Hardy, K.S.; Kovach, E.M.; Van Heemst, J.D.H.; Hatcher, P.G.; Richman, J.E.

    1999-01-01

    In this study, the use of a {sup 13}C-labeled pollutant probe, [{sup 13}C]pyrene, and the application of flash pyrolysis--GC--MS and CPMAS {sup 13}C NMR provided analytical capabilities to study pyrene interactions with soluble and insoluble compartments of sedimentary organic matter (S{sub D}OM) during whole sediments incubations in aerated microcosms. Surface sediments were collected from a site of previous hydrocarbon contamination in New Orleans, LA. Over a period of 60 days, humic acid and humin fractions of S{sub D}OM accumulated increasing amounts of pyrene that were resistant to exhaustive extraction with organic solvents. The sequestered pyrene was evident in CPMAS {sup 13}C NMR spectra of humin fractions. The amount of sequestered pyrene in humic materials was quantified by flash pyrolysis--GC--MS, a technique that destroys the three-dimensional structure of macromolecular S{sub D}OM. Noncovalent binding of pyrene to humic materials in S{sub D}OM was greater in sediments incubated with biological activity than biocide-treated sediments. The combined analytical approaches demonstrate that the sequestered pyrene, or bound residue, is noncovalently associated with S{sub D}OM and has not undergone structural alteration. Implications of these data are discussed in reference to S{sub D}OM diagenesis and long-term availability of bound pollutant residues in sediments.

  1. Water-soluble organic compounds in biomass burning aerosols over Amazonia1. Characterization by NMR and GC-MS

    NASA Astrophysics Data System (ADS)

    Graham, Bim; Mayol-Bracero, Olga L.; Guyon, Pascal; Roberts, Gregory C.; Decesari, Stefano; Facchini, M. Cristina; Artaxo, Paulo; Maenhaut, Willy; Köll, Peter; Andreae, Meinrat O.

    2002-09-01

    As part of the European contribution to the Large-Scale Atmosphere-Biosphere Experiment in Amazonia (LBA-EUSTACH), aerosols were sampled at representative pasture and primary rainforest sites in Rondônia, Brazil, during the 1999 ``burning season'' and dry-to-wet season transition (September-October). Water-soluble organic compounds (WSOCs) within the samples were characterized using a combination of 1H Nuclear Magnetic Resonance (NMR) spectroscopy for chemical functional group analysis, and Gas Chromatography-Mass Spectrometry (GC-MS) for identification and quantification of individual low-molecular-weight compounds. The 1H NMR analysis indicates that WSOCs are predominantly aliphatic or oxygenated aliphatic compounds (alcohols, carboxylic acids, etc.), with a minor content of aromatic rings carrying carboxylic and phenolic groups. Levoglucosan (1,6-anhydro-β-D-glucose), a well-known cellulose combustion product, was the most abundant individual compound identified by GC-MS (0.04-6.90 μg m-3), accounting for 1-6% of the total carbon (TC) and 2-8% of the water-soluble organic carbon (WSOC). Other anhydrosugars, produced by hemicellulose breakdown, were detected in much smaller amounts, in addition to series of acids, hydroxyacids, oxoacids, and polyalcohols (altogether 2-5% of TC, 3-6% of WSOC). Most correlated well with organic carbon, black carbon, and potassium, indicating biomass burning to be the major source. A series of sugar alcohols (mannitol, arabitol, erythritol) and sugars (glucose, fructose, mannose, galactose, sucrose, trehalose) were identified as part of the natural background aerosol and are probably derived from airborne microbes and other biogenic material. The bulk of the WSOCs (86-91% WSOC) eluded analysis by GC-MS and may be predominantly high-molecular weight in nature.

  2. Valorization of agroindustrial wastes: Identification by LC-MS and NMR of benzylglucosinolate from papaya (Carica papaya L.) seeds, a protective agent against lipid oxidation in edible oils.

    PubMed

    Castro-Vargas, Henry I; Baumann, Wolfram; Parada-Alfonso, Fabián

    2016-07-01

    In the present study we report the characterization of benzylglucosinolate (BG) isolated from papaya (Carica papaya L.) seeds. A methanolic extract was fractionated and further purified by solid phase extraction (SPE). It was analyzed by liquid chromatography-electrospray ionization-mass spectrometry (LC-ESI-MS), and nuclear magnetic resonance spectroscopy ((1) H and (13) C-NMR) as well, and the target compound BG was identified by these two techniques. The effect of BG on lipid oxidation in edible vegetable oil (EO) was shown by observing some lipid oxidation products (linoleic acid hydroperoxides, LHP; hexanal, HEX; nonanal, NON; thiobarbituric acid reactives species, TBARS). BG reduced lipid oxidation production in EO by over 80%, as compared to a control sample and in this way has proved to be a useful antioxidant, even more effective than some antioxidants used by food industry. PMID:26756135

  3. On-line identification of the bioactive compounds from Blumea gariepina by HPLC-UV-MS and HPLC-UV-NMR, combined with HPLC-micro-fractionation.

    PubMed

    Queiroz, E F; Ioset, J R; Ndjoko, K; Guntern, A; Foggin, C M; Hostettmann, K

    2005-01-01

    The dichloromethane extract of the aerial parts of Blumea gariepina (Asteraceae) was shown to be active against the phytopathogenic fungus Cladosporium cucumerinum and to inhibit acetylcholinesterase. In order rapidly to identify the active principles, the crude extract was analysed by on-flow HPLC-1H-NMR. HPLC-micro-fractionation was performed and all peaks collected were submitted to assays against C. cucumerinum and acetylcholinesterase. By this means, the biological activities could be efficiently associated with selected HPLC peaks. Complementary on-line structural data for all peaks of interest in the crude extract were obtained from HPLC-MS and from HPLC-UV with post-column addition of UV shift reagents. This chemical screening strategy with integrated bioassays permitted the on-line identification of a number of constituents and gave useful information for an efficient isolation procedure. PMID:15997849

  4. High-performance liquid chromatographic separation of natural and synthetic desulphoglucosinolates and their chemical validation by UV, NMR and chemical ionisation-MS methods.

    PubMed

    Kiddle, G; Bennett, R N; Botting, N P; Davidson, N E; Robertson, A A; Wallsgrove, R M

    2001-01-01

    Methods are described for the optimised extraction, desulphation and HPLC separation of desulphoglucosinolates. These methods provide rapid separation, identification and quantitative measurements of glucosinolates extracted from Brassica napus L and related crops, of unusual glucosinolates found in crucifer weed species, and also of synthetic alkylglucosinolates. The desulphoglucosinolates used in these studies were either chemically synthesised (at least one example from each major structural class), or purified from various plant sources. Validation of the identities of the desulphoglucosinolates was by comparison of retention times with standards, and by UV, 1H- and 13C-NMR and chemical ionisation MS analysis. A list of useful species, and the specific tissues, from which high concentrations of standards can be extracted is included. PMID:11705329

  5. FT-IR, 1H, 13C NMR, ESI-MS and semiempirical investigation of the structures of Monensin phenyl urethane complexes with the sodium cation.

    PubMed

    Huczyński, Adam

    2013-06-01

    In this paper three forms of phenyl urethane of Monensin i.e. its acid form (H-MU) and its 1:1 complex with NaClO4 (H-MU-Na) and its sodium salt (Na-MU) were obtained and their structures were studied by FT-IR, (1)H and (13)C NMR, ESI MS and PM5 methods. The FT-IR data of Na-MU complexes demonstrate that the C=O urethane group is not engaged in the complexation of the sodium cation. However spectroscopic studies of H-MU-Na complex show that the structure in which this C=O urethane groups participate in the complexation is also present, but it is in the minority. The PM5 semiempirical calculations allow visualisation of all structures and determination of the hydrogen bond parameters. PMID:23578536

  6. Stability-indicating reversed-phase HPLC method development and characterization of impurities in vortioxetine utilizing LC-MS, IR and NMR.

    PubMed

    Liu, Lei; Cao, Na; Ma, Xingling; Xiong, Kaihe; Sun, Lili; Zou, Qiaogen; Yao, Lili

    2016-01-01

    The current study reports the development and validation of a stability-indicating reversed phase HPLC method for the separation and identification of potential impurities in vortioxetine, a recently developed antidepressant. The structures of a new compound and four process-related impurities formed during the synthesis were characterized and confirmed by NMR, MS, and IR spectroscopy analyses. The most probable formation mechanisms of the impurities identified were proposed. Based on the characterization data, the new compound was proposed to be 1-[4-[(2,4-dimethylphenyl)thio]phenyl]-piperazine. In addition, an efficient chromatographic method was optimized to separate and quantify the impurities, which were obtained in the 0.05-0.75 μg/mL range. The developed HPLC method was validated with respect to accuracy, precision, linearity, robustness, and limits of detection and quantitation. PMID:26412721

  7. Forced degradation of fingolimod: effect of co-solvent and characterization of degradation products by UHPLC-Q-TOF-MS/MS and 1H NMR.

    PubMed

    Patel, Prinesh N; Kalariya, Pradipbhai D; Gananadhamu, S; Srinivas, R

    2015-11-10

    Fingolimod (FGL), an immunomodulator drug for treating multiple sclerosis, was subjected to hydrolysis (acidic, alkaline and neutral), oxidation, photolysis and thermal stress, as per International Conference on Harmonization specified conditions. The drug showed extensive degradation under base hydrolysis, however, it was stable under all other conditions. A total of three degradation products (DPs) were observed. The chromatographic separation of the drug and its degradation products was achieved on a Fortis C18 (100×2.1mm, 1.7μm) column with a mobile phase composed of 0.1% formic acid (Solvent A) and acetonitrile (Solvent B) in gradient mode. All the DPs were identified and characterized by liquid chromatography-quadrupole time of flight-mass spectrometry (LC-Q-TOF-MS) in combination with accurate mass measurements. The major DP was isolated and characterized by Nuclear Magnetic resonance spectroscopy. This is a typical case of degradation where acetonitrile used as co-solvent in stress studies, reacts with FGL in base hydrolytic conditions to produce acetylated DPs. Hence, it can be suggested that acetonitrile is not preferable as a co-solvent for stress degradation of FGL. The developed UHPLC method was validated as per ICH guidelines. PMID:26279369

  8. Prediction of variability in CYP3A4 induction using a combined 1H NMR metabonomics and targeted UPLC-MS approach.

    PubMed

    Rahmioglu, Nilufer; Le Gall, Gwénaëlle; Heaton, James; Kay, Kristine L; Smith, Norman W; Colquhoun, Ian J; Ahmadi, Kourosh R; Kemsley, E Kate

    2011-06-01

    The activity of Cytochrome P450 3A4 (CYP3A4) enzyme is associated with many adverse or poor therapeutic responses to drugs. We used (1)H NMR-based metabonomics to identify a metabolic signature associated with variation in induced CYP3A4 activity. A total of 301 female twins, aged 45--84, participated in this study. Each volunteer was administered a potent inducer of CYP3A4 (St. John's Wort) for 14 days and the activity of CYP3A4 was quantified through the metabolism of the exogenously administered probe drug quinine sulfate (300 mg). Pre- and postintervention fasting urine samples were used to obtain metabolite profiles, using (1)H NMR spectroscopy, and were analyzed using UPLC--MS to obtain a marker for CYP3A4 induction, via the ratio of 3-hydroxyquinine to quinine (3OH-Q:Q). Multiple linear regression was used to build a predictive model for 3OH-Q:Q values based on the preintervention metabolite profiles. A combination of seven metabolites and seven covariates showed a strong (r = 0.62) relationship with log(3OH-Q:Q). This regression model demonstrated significant (p < 0.00001) predictive ability when applied to an independent validation set. Our results highlight the promise of metabonomics for predicting CYP3A4-mediated drug response. PMID:21491888

  9. A comprehensive investigation of guaiacyl-pyranoanthocyanin synthesis by one-/two-dimensional NMR and UPLC-DAD-ESI-MS(n).

    PubMed

    Vallverdú-Queralt, Anna; Meudec, Emmanuelle; Ferreira-Lima, Nayla; Sommerer, Nicolas; Dangles, Olivier; Cheynier, Véronique; Le Guernevé, Christine

    2016-05-15

    In red and rosé wines, the grape anthocyanins are progressively converted to more stable pigments, including phenylpyranoanthocyanins. One-/two-dimensional NMR and UPLC-DAD-ESI-MS(n) measurements were used to monitor the synthesis of guaiacylpyranomalvidin 3-O-glucoside from malvidin 3-O-glucoside and vinylguaiacol in model solutions and identify the products formed during the reaction. The highest conversion rates (30%, determined by (1)H qNMR) were obtained with a small excess of vinylguaiacol in methanol/water (70/30) at pH 3 and 35°C. Two reaction pathways competed with the formation of guaiacylpyranomalvidin 3-O-glucoside. The first one only concerns malvidin 3-O-glucoside and consists in C-ring cleavage with formation of malvone and smaller molecular weight breakdown products. This pathway is favored at higher pH and incubation temperature. At lower pH values or in the presence of large vinylguaiacol excess, faster consumption of malvidin 3-O-glucoside resulted from the formation of more complex pyranoanthocyanins substituted by vinylguaiacol oligomers. PMID:26776050

  10. Untargeted metabolomics studies employing NMR and LC–MS reveal metabolic coupling between Nanoarcheum equitans and its archaeal host Ignicoccus hospitalis

    DOE PAGESBeta

    Hamerly, Timothy; Tripet, Brian P.; Tigges, Michelle; Giannone, Richard J.; Wurch, Louie; Hettich, Robert L.; Podar, Mircea; Copié, Valerie; Bothner, Brian

    2014-11-05

    Interactions between species are the basis of microbial community formation and infectious diseases. Systems biology enables the construction of complex models describing such interactions, leading to a better understanding of disease states and communities. However, before interactions between complex organisms can be understood, metabolic and energetic implications of simpler real-world host-microbe systems must be worked out. To this effect, untargeted metabolomics experiments were conducted and integrated with proteomics data to characterize key molecular-level interactions between two hyperthermophilic microbial species, both of which have reduced genomes. Metabolic changes and transfer of metabolites between the archaea Ignicoccus hospitalis and Nanoarcheum equitans weremore » investigated using integrated LC–MS and NMR metabolomics. The study of such a system is challenging, as no genetic tools are available, growth in the laboratory is challenging, and mechanisms by which they interact are unknown. Together with information about relative enzyme levels obtained from shotgun proteomics, the metabolomics data provided useful insights into metabolic pathways and cellular networks of I. hospitalis that are impacted by the presence of N. equitans, including arginine, isoleucine, and CTP biosynthesis. On the organismal level, the data indicate that N. equitans exploits metabolites generated by I. hospitalis to satisfy its own metabolic needs. Lastly, this finding is based on N. equitans’s consumption of a significant fraction of the metabolite pool in I. hospitalis that cannot solely be attributed to increased biomass production for N. equitans. Combining LC–MS and NMR metabolomics datasets improved coverage of the metabolome and enhanced the identification and quantitation of cellular metabolites.« less

  11. Untargeted metabolomics studies employing NMR and LC–MS reveal metabolic coupling between Nanoarcheum equitans and its archaeal host Ignicoccus hospitalis

    SciTech Connect

    Hamerly, Timothy; Tripet, Brian P.; Tigges, Michelle; Giannone, Richard J.; Wurch, Louie; Hettich, Robert L.; Podar, Mircea; Copié, Valerie; Bothner, Brian

    2014-11-05

    Interactions between species are the basis of microbial community formation and infectious diseases. Systems biology enables the construction of complex models describing such interactions, leading to a better understanding of disease states and communities. However, before interactions between complex organisms can be understood, metabolic and energetic implications of simpler real-world host-microbe systems must be worked out. To this effect, untargeted metabolomics experiments were conducted and integrated with proteomics data to characterize key molecular-level interactions between two hyperthermophilic microbial species, both of which have reduced genomes. Metabolic changes and transfer of metabolites between the archaea Ignicoccus hospitalis and Nanoarcheum equitans were investigated using integrated LC–MS and NMR metabolomics. The study of such a system is challenging, as no genetic tools are available, growth in the laboratory is challenging, and mechanisms by which they interact are unknown. Together with information about relative enzyme levels obtained from shotgun proteomics, the metabolomics data provided useful insights into metabolic pathways and cellular networks of I. hospitalis that are impacted by the presence of N. equitans, including arginine, isoleucine, and CTP biosynthesis. On the organismal level, the data indicate that N. equitans exploits metabolites generated by I. hospitalis to satisfy its own metabolic needs. Lastly, this finding is based on N. equitans’s consumption of a significant fraction of the metabolite pool in I. hospitalis that cannot solely be attributed to increased biomass production for N. equitans. Combining LC–MS and NMR metabolomics datasets improved coverage of the metabolome and enhanced the identification and quantitation of cellular metabolites.

  12. New findings on the in vivo antioxidant activity of Curcuma longa extract by an integrated (1)H NMR and HPLC-MS metabolomic approach.

    PubMed

    Dall'Acqua, Stefano; Stocchero, Matteo; Boschiero, Irene; Schiavon, Mariano; Golob, Samuel; Uddin, Jalal; Voinovich, Dario; Mammi, Stefano; Schievano, Elisabetta

    2016-03-01

    Curcuminoids possess powerful antioxidant activity as demonstrated in many chemical in vitro tests and in several in vivo trials. Nevertheless, the mechanism of this activity is not completely elucidated and studies on the in vivo antioxidant effects are still needed. Metabolomics may be used as an attractive approach for such studies and in this paper, we describe the effects of oral administration of a Curcuma longa L. extract (150mg/kg of total curcuminoids) to 12 healthy rats with particular attention to urinary markers of oxidative stress. The experiment was carried out over 33days and changes in the 24-h urine samples metabolome were evaluated by (1)H NMR and HPLC-MS. Both techniques produced similar representations for the collected samples confirming our previous study. Modifications of the urinary metabolome lead to the observation of different variables proving the complementarity of (1)H NMR and HPLC-MS for metabolomic purposes. The urinary levels of allantoin, m-tyrosine, 8-hydroxy-2'-deoxyguanosine, and nitrotyrosine were decreased in the treated group thus supporting an in vivo antioxidant effect of the oral administration of Curcuma extract to healthy rats. On the other hand, urinary TMAO levels were higher in the treated compared to the control group suggesting a role of curcumin supplementation on microbiota or on TMAO urinary excretion. Furthermore, the urinary levels of the sulphur containing compounds taurine and cystine were also changed suggesting a role for such constituents in the biochemical pathways involved in Curcuma extract bioactivity and indicating the need for further investigation on the complex role of antioxidant curcumin effects. PMID:26712080

  13. Application of high-performance liquid chromatography-nuclear magnetic resonance coupling to the identification of limonoids from mahogany tree (Switenia macrophylla, Meliaceae) by stopped-flow 1D and 2D NMR spectroscopy.

    PubMed

    Schefer, Alexandre B; Braumann, Ulrich; Tseng, Li-Hong; Spraul, Manfred; Soares, Marisi G; Fernandes, João B; da Silva, Maria F G F; Vieira, Paulo C; Ferreira, Antonio G

    2006-09-22

    Separation and characterization of limonoids from Switenia macrophylla (Meliaceae) by HPLC-NMR technique has been described. Analyses were carried out using reversed-phase gradient HPLC elution coupled to NMR (600 MHz) spectrometer in stopped-flow mode. Separated peaks were collected into an interface unit prior to NMR measurements, which were performed with suppression of solvent signals by shaped pulses sequences. Structure elucidation of the limonoids was attained by data obtained from 1H NMR, TOCSY, gHSQC and gHMBC spectra without conventional isolation that is usually applied in natural products studies. PMID:16904679

  14. Molecular characterization of dissolved organic matter from subtropical wetlands: a comparative study through the analysis of optical properties, NMR and FTICR/MS

    NASA Astrophysics Data System (ADS)

    Hertkorn, N.; Harir, M.; Cawley, K. M.; Schmitt-Kopplin, P.; Jaffé, R.

    2015-08-01

    unsaturated protons (δH > 5 ppm). The larger discrimination observed between 1H NMR spectra of DOM from different wetlands in comparison with the intrinsic variance among DOM within each wetland readily suggests the presence of an individual molecular signature, characteristic of each particular wetland. 2-D NMR spectroscopy for a particular sample revealed a large richness of aliphatic and unsaturated substructures, likely derived from microbial sources such as periphyton in the Everglades. In contrast, the chemical diversity of aromatic wetland DOM likely originates from a combination of higher plant sources, progressive microbial and photochemical oxidation, and contributions from combustion-derived products (e.g. black carbon). In addition, FT-ICRMS spectra allowed far-reaching classifications of wetland DOM. While DOM of both Okavango and Pantanal showed near 57 ± 2 % CHO, 8 ± 2 % CHOS, 33 ± 2 CHNO, and < 1 % CHNOS molecules, the mass spectra of Everglades samples were fundamentally different compared to those as well as among long and short hydroperiod samples, as they were markedly enriched in CHOS and CHNOS at the expense of CHO and CHNO compounds. Here, four groups of CHOS molecules were differentiated as (a) saturated sulfolipids, (b) unsaturated sulfolipids, (c) molecularly diverse DOM-type CHOS molecules, (d) and particularly enriched in the Everglades short hydroperiod site, a large set of aromatic and oxygen-deficient "black sulphur" compounds. The significantly higher proportion of CHOS compounds in general for the Everglades samples is likely the result of higher inputs of agriculture-derived and sea spray derived sulphate to this wetland compared to the others. Although wetland DOM samples were found to share many molecular features, each sample was unique in its composition, which reflected specific environmental drivers and/or specific biogeochemical processes.

  15. Development and validation of a RP-HPLC method for stability-indicating assay of gemifloxacin mesylate including identification of related substances by LC-ESI-MS/MS, 1H and 13C NMR spectroscopy.

    PubMed

    Rao, R Nageswara; Naidu, Ch Gangu; Prasad, K Guru; Narasimha, R

    2011-11-01

    A validated stability indicating RP-HPLC assay of gemifloxacin mesylate was developed by separating its related substances on an Inertsil-ODS3V-C18 (4.6 × 250 mm; 5 μm) column using 0.1% trifluoroaceticacid (pH 2.5) and methanol as a mobile phase in a gradient elution mode at a flow rate of 1.0 mL/min at 27°C. The column effluents were monitored by a photodiode array detector set at 287 nm. The method was validated in terms of accuracy, precision and linearity as per ICH guidelines. Forced degradation of gemifloxacin (GFX) was carried out under acidic, basic, thermal, photolysis and peroxide conditions and the degradation products were separated and characterized by ESI-MS/MS, (1) H and (13) C NMR spectroscopy. The method was successfully applied to the analysis of bulk drugs and the recoveries of gemifloxacin and impurities were in the range of 97.60-102.90 and 96.99-102.10%, respectively. No previous reports were found in the literature on identification of degradation products of gemifloxacin. PMID:21370250

  16. Rapid discovery and identification of anti-inflammatory constituents from traditional Chinese medicine formula by activity index, LC-MS, and NMR

    PubMed Central

    Wang, Shufang; Wang, Haiqiang; Liu, Yining; Wang, Yi; Fan, Xiaohui; Cheng, Yiyu

    2016-01-01

    The traditional activity-guided approach has the shortcoming of low accuracy and efficiency in discovering active compounds from TCM. In this work, an approach was developed by integrating activity index (AI), liquid chromatography – mass spectrometry (LC-MS), and nuclear magnetic resonance (NMR) to rapidly predict and identify the potential active constituents from TCM. This approach was used to discover and identify the anti-inflammatory constituents from a TCM formula, Gui-Zhi-Jia-Shao-Yao-Tang (GZJSYT). The AI results indicated that, among the 903 constituents detected in GZJSYT by LC-MS, 61 constituents with higher AI values were very likely to have anti-inflammatory activities. And eight potential active constituents of them were isolated and validated to have significant inhibitory effects against NO production on LPS-induced RAW 264.7 cell model. Among them, glycyrrhisoflavone (836), glisoflavanone (893) and isoangustone A (902) were reported to have anti-inflammatory effects for the first time. The proposed approach could be generally applicable for rapid and high efficient discovery of anti-inflammatory constituents from other TCM formulae or natural products. PMID:27499135

  17. Rapid discovery and identification of anti-inflammatory constituents from traditional Chinese medicine formula by activity index, LC-MS, and NMR.

    PubMed

    Wang, Shufang; Wang, Haiqiang; Liu, Yining; Wang, Yi; Fan, Xiaohui; Cheng, Yiyu

    2016-01-01

    The traditional activity-guided approach has the shortcoming of low accuracy and efficiency in discovering active compounds from TCM. In this work, an approach was developed by integrating activity index (AI), liquid chromatography - mass spectrometry (LC-MS), and nuclear magnetic resonance (NMR) to rapidly predict and identify the potential active constituents from TCM. This approach was used to discover and identify the anti-inflammatory constituents from a TCM formula, Gui-Zhi-Jia-Shao-Yao-Tang (GZJSYT). The AI results indicated that, among the 903 constituents detected in GZJSYT by LC-MS, 61 constituents with higher AI values were very likely to have anti-inflammatory activities. And eight potential active constituents of them were isolated and validated to have significant inhibitory effects against NO production on LPS-induced RAW 264.7 cell model. Among them, glycyrrhisoflavone (836), glisoflavanone (893) and isoangustone A (902) were reported to have anti-inflammatory effects for the first time. The proposed approach could be generally applicable for rapid and high efficient discovery of anti-inflammatory constituents from other TCM formulae or natural products. PMID:27499135

  18. Data from mass spectrometry, NMR spectra, GC-MS of fatty acid esters produced by Lasiodiplodia theobromae.

    PubMed

    Uranga, Carla C; Beld, Joris; Mrse, Anthony; Córdova-Guerrero, Iván; Burkart, Michael D; Hernández-Martínez, Rufina

    2016-09-01

    The data described herein is related to the article with the title "Fatty acid esters produced by Lasiodiplodia theobromae function as growth regulators in tobacco seedlings" C.C. Uranga, J. Beld, A. Mrse, I. Cordova-Guerrero, M.D. Burkart, R. Hernandez-Martinez (2016) [1]. Data includes nuclear magnetic resonance spectroscopy and GC-MS data used for the identification and characterization of fatty acid esters produced by L. theobromae. GC-MS traces are also shown for incubations in defined substrate, consisting in Vogel׳s salts supplemented with either 5% grapeseed oil or 5% glucose, the two combined, or 5% fructose. Traces for incubations in the combination of 5% grapeseed oil and 5% glucose for different fungal species are also included. Images of mycelium morphology when grown in 5% glucose with or without 5% grapeseed oil are shown due to the stark difference in mycelial pigmentation in the presence of triglycerides. High concentration gradient data for the plant model Nicotiana tabacum germinated in ethyl stearate (SAEE) and ethyl linoleate (LAEE) is included to show the transition between growth inhibition and growth induction in N. tabacum by these compounds. PMID:27274528

  19. Two dimensional NMR spectroscopic approaches for exploring plant metabolome: A review

    PubMed Central

    Mahrous, Engy A.; Farag, Mohamed A.

    2014-01-01

    Today, most investigations of the plant metabolome tend to be based on either nuclear magnetic resonance (NMR) spectroscopy or mass spectrometry (MS), with or without hyphenation with chromatography. Although less sensitive than MS, NMR provides a powerful complementary technique for the identification and quantification of metabolites in plant extracts. NMR spectroscopy, well appreciated by phytochemists as a particularly information-rich method, showed recent paradigm shift for the improving of metabolome(s) structural and functional characterization and for advancing the understanding of many biological processes. Furthermore, two dimensional NMR (2D NMR) experiments and the use of chemometric data analysis of NMR spectra have proven highly effective at identifying novel and known metabolites that correlate with changes in genotype or phenotype. In this review, we provide an overview of the development of NMR in the field of metabolomics with special focus on 2D NMR spectroscopic techniques and their applications in phytomedicines quality control analysis and drug discovery from natural sources, raising more attention at its potential to reduce the gap between the pace of natural products research and modern drug discovery demand. PMID:25685540

  20. Molecular characterization of dissolved organic matter from subtropical wetlands: a comparative study through the analysis of optical properties, NMR and FTICR/MS

    NASA Astrophysics Data System (ADS)

    Hertkorn, Norbert; Harir, Mourad; Cawley, Kaelin M.; Schmitt-Kopplin, Philippe; Jaffé, Rudolf

    2016-04-01

    Wetlands provide quintessential ecosystem services such as maintenance of water quality, water supply and biodiversity, among others; however, wetlands are also among the most threatened ecosystems worldwide. Natural dissolved organic matter (DOM) is an abundant and critical component in wetland biogeochemistry. This study describes the first detailed, comparative, molecular characterization of DOM in subtropical, pulsed, wetlands, namely the Everglades (USA), the Pantanal (Brazil) and the Okavango Delta (Botswana), using optical properties, high-field nuclear magnetic resonance (NMR) and ultrahigh-resolution mass spectrometry (FT-ICRMS), and compares compositional features to variations in organic matter sources and flooding characteristics (i.e., differences in hydroperiod). While optical properties showed a high degree of variability within and between the three wetlands, analogies in DOM fluorescence properties were such that an established excitation emission matrix fluorescence parallel factor analysis (EEM-PARAFAC) model for the Everglades was perfectly applicable to the other two wetlands. Area-normalized 1H NMR spectra of selected samples revealed clear distinctions of samples while a pronounced congruence within the three pairs of wetland DOM readily suggested the presence of an individual wetland-specific molecular signature. Within sample pairs (long- vs. short-hydroperiod sites), internal differences mainly referred to intensity variations (denoting variable abundance) rather than to alterations of NMR resonances positioning (denoting diversity of molecules). The relative disparity was largest between the Everglades long- and short-hydroperiod samples, whereas Pantanal and Okavango samples were more alike among themselves. Otherwise, molecular divergence was most obvious in the case of unsaturated protons (δH > 5 ppm). 2-D NMR spectroscopy for a particular sample revealed a large richness of aliphatic and unsaturated substructures, likely derived from

  1. Metabolomic analysis of glycerophospholipid signatures of inflammation treated with non-steroidal anti-inflammatory drugs-induced-RAW264.7 cells using (1)H NMR and U-HPLC/Q-TOF-MS.

    PubMed

    Wu, Xia; Cao, Han; Zhao, Lifang; Song, Jianao; She, Yuqi; Feng, Yifan

    2016-08-15

    Non-destructive proton nuclear magnetic resonance ((1)H NMR) spectroscopy and highly sensitive ultra-performance liquid chromatography quadrupole time-of-flight mass spectrometry (U-HPLC/Q-TOF-MS) coupled to data processing methods were applied to analyze the metabolic profiling changes of glycerophospholipids (GPLs) in RAW264.7 cells from inflammation to prognosis. Analysis of (1)H NMR was shown that the models were grouped successfully, illustrating that all of them had significant differences. Based on the highly simple, accurate, non-targeted and non-destructively advantages of (1)H NMR, it could be used as a new screening tool of anti-inflammatory drugs in the metabolic profiling of GPLs. 58 GPLs were identified by U-HPLC/Q-TOF-MS, and 19 components were firstly identified in this study compared with our previous results. In addition, ten potential biomarkers were proved, of which phosphatidylcholine (PC) (16:0/18:1) and (18:0/18:1) changed consistently in three drug-induced groups and might be the important biomarkers. Compared with (1)H NMR, U-HPLC/Q-TOF-MS showed higher sensitivity and specificity and was more suitable for the determination of biomarkers apart from the deficiency of time-consuming sample preparation steps and unambiguous metabolite identification. Therefore, it is feasible to analyze the changes of GPLs during inflammation by combining (1)H NMR spectroscopy with U-HPLC/Q-TOF-MS. The metabolic profiling of GPLs provides valuable evidence for inflammation diagnosis and prognosis, and might unravel the mechanisms involved in inflammation progression. PMID:27371817

  2. Dereplication of antioxidant compounds in Bene (Pistacia atlantica subsp. mutica) hull using a multiplex approach of HPLC-DAD, LC-MS and (1)H NMR techniques.

    PubMed

    Rezaie, Mitra; Farhoosh, Reza; Pham, Ngoc; Quinn, Ronald J; Iranshahi, Mehrdad

    2016-01-01

    Bene is an edible fruit from the tree Pistacia atlantica subsp. mutica, and is of steadily growing interest in recent years due to its significant antioxidant properties and potential health benefits. An antioxidant activity-guided fractionation of the methanol extract from Bene hull together with an integrated approach of HPLC-DAD, LC-MS and (1)H NMR techniques led to the identification of main antioxidant phenolic compounds for the first time. Radical scavenging activity of each fraction/compound was tested using DPPH and FRAP assays. The phenolic content of the fractions was also determined by Folin-Ciocalteu's method. The main identified antioxidant compounds were luteolin (46.53% w/w of total extract), gallic acid (9.84% w/w), 2″-O-galloylisoquercitrin (0.53% w/w), quercetin 3-rutinoside (0.34% w/w) and 2″-O-cis-caffeoylquercitrin (0.26% w/w). The minor antioxidant compounds were also identified by liquid chromatography-positive/negative electrospray ionization tandem mass spectrometry. The structure-antioxidant activity relationship of identified phenolics are also discussed in this paper. PMID:26432386

  3. [UPLC/Q-TOF MS and NMR plant metabolomics approach in studying the effect of growth year on the quality of Polygala tenuifolia].

    PubMed

    Xue, Ying; Li, Xiao-wei; Li, Zhen-yu; Zeng, Zu-ping; Zhang, Fu-sheng; Li, Ai-ping; Qin, Xue-mei; Peng, Bing

    2015-03-01

    Growth year is one of the important factors for the quality of Polygala tenufolia. In this study, primary metabolites and secondary metabolites were compared in 1, 2 and 3 years old P. tenufolia cultivated in Shaanxi Heyang. The samples were subjected to ultra-high performance liquid chromatography (UPLC)-quadrupole time-of-flight mass spectrometry (Q-TOF MS) and nuclear magnetic resonance (NMR) analysis, and the obtained data were analyzed using principal component analysis (PCA) and other statistical analysis methods. In addition, content and correlation of different metabolites were also calculated. The results showed no significance between main component contents in 2 year-old and 3 year-old P. Tenufolia, but 1 year-old was statistically different. The contents of primary metabolites, such as fructose, sucrose, and choline increased as time goes on, while glycine and raffinose decreased. The contents of secondary metabolites, such as onjisaponin Fg, polygalasaponin XXVIII, polygalasaponin XXXII increased, while polygalaxanthone III and parts of oligosaccharide multi-ester including tenuifoliose A, tenuifoliose C, tenuifoliose C2 and tenuifoliose H decreased with the extension of the growth years. Growth years has important impact on the quality of P. tenuifolia and the existing growing years of commodity P. tenuifolia have its scientific evidence. This study supplied a new method for the quality evaluation of Chinese medicinal materials. PMID:26118115

  4. Thin-layer chromatography combined with MALDI-TOF-MS and 31P-NMR to study possible selective bindings of phospholipids to silica gel.

    PubMed

    Teuber, Kristin; Riemer, Thomas; Schiller, Jürgen

    2010-12-01

    High-performance thin-layer chromatography (HPTLC) is a highly established separation method in the field of lipid and (particularly) phospholipid (PL) research. HPTLC is not only used to identify certain lipids in a mixture but also to isolate lipids (preparative TLC). To do this, the lipids are separated and subsequently re-eluted from the silica gel. Unfortunately, it is not yet known whether all PLs are eluted to the same extent or whether some lipids bind selectively to the silica gel. It is also not known whether differences in the fatty acyl compositions affect the affinities to the stationary phase. We have tried to clarify these questions by using a readily available extract from hen egg yolk as a selected example of a lipid mixture. After separation, the complete lanes or selected spots were eluted from the silica gel and investigated by a combination of MALDI-TOF MS and (31)P NMR spectroscopy. The data obtained were compared with the composition of the total extract (without HPTLC). Although there were significant, solvent-dependent losses in the amount of each lipid, the relative composition of the mixture remained constant; there were also only very slight changes in the fatty acyl compositions of the individual PL classes. Therefore, lipid isolation by TLC may be used without any risk of major sample alterations. PMID:20694807

  5. Characterization of potential degradation products in a PEGylating reagent 20 kDa monomethoxy polyethylene glycol propionaldehyde by RP-HPLC, APCI-MS and NMR.

    PubMed

    Zhang, Heidi; Wilson, John; Zhang, Jifeng; Luo, Ying

    2014-02-01

    Ensuring quality of PEGylating reagents is essential for the successful development and manufacturing of PEGylated biopharmaceuticals. However, little is known about how to maintain and verify the quality of PEG raw materials for PEGylated protein manufacturing. In this study, monomethoxy polyethylene glycol propionaldehyde (mPEG-aldehyde) was subjected to conditions that mimic accelerated stability conditions. Separation of trace-level degradation products in the presence of mPEG-aldehyde was achieved by derivatization with 2,4-dinitrophenylhydrazine (DNPH), followed by reversed phase high performance liquid chromatography with ultraviolet detection (RP-HPLC-UV) at 355nm. Structural characterization by atmospheric pressure chemical ionization mass spectrometry (APCI-MS) identified formaldehyde, acetaldehyde, crotonaldehyde, acrolein, benzaldehyde, and tolualdehyde as major degradation products or process-related impurities. The presence of formaldehyde and acrolein was confirmed by (1)H NMR in the forced degraded mPEG-aldehyde samples without derivatization of mPEG-aldehyde. Findings from this study imply that reactive impurities could form as a result of inappropriate mPEG-aldehyde handling or storage. Further, a rapid screening method based on reversed phase HPLC was shown to be an effective screening assay used for routine screening of mPEG-aldehyde to ensure consistent PEGylated protein product quality. PMID:24316423

  6. NMR investigation of acrolein stability in hydroalcoholic solution as a foundation for the valid HS-SPME/GC-MS quantification of the unsaturated aldehyde in beverages.

    PubMed

    Kächele, Martin; Monakhova, Yulia B; Kuballa, Thomas; Lachenmeier, Dirk W

    2014-04-11

    Acrolein (propenal) is found in many foods and beverages and may pose a health hazard due to its cytotoxicity. Considerable knowledge gaps regarding human exposure to acrolein exist, and there is a lack of reliable analytical methods. Hydroalcoholic dilutions prepared for calibration purposes from pure acrolein show considerable degradation of the compound and nuclear magnetic resonance (NMR) spectroscopy showed that 1,3,3-propanetriol and 3-hydroxypropionaldehyde are formed. The degradation can be prevented by addition of hydroquinone as stabilizer to the calibration solutions, which then show linear concentration-response behaviour required for quantitative analysis. The stabilized calibration solutions were used for quantitative headspace solid-phase microextraction/gas chromatography-mass spectrometry (HS-SPME/GC-MS) determination of acrolein in alcoholic beverages with a detection limit of 14 μg L(-1). Of 117 tested alcoholic beverages, 64 were tested positive with the highest incidence in grape marc spirits and whiskey (100%, mean 252 μg L(-1)), followed by fruit spirits (86%, mean 591 μg/L(-1)), tequila (86%, mean 404 μg L(-1)), Asian spirits (43%, mean 54 μg L(-1)) and wine (9%, mean 0.7 μg L(-1)). Acrolein could not be detected in beer, vodka, absinthe and bottled water. Six of the fruit and grape marc spirits had acrolein levels above the World Health Organization (WHO) provisional tolerable concentration of 1.5 mg L(-1). PMID:24745744

  7. Two dimensional NMR spectroscopy

    SciTech Connect

    Schram, J.; Bellama, J.M.

    1988-01-01

    Two dimensional NMR represents a significant achievement in the continuing effort to increase solution in NMR spectroscopy. This book explains the fundamentals of this new technique and its analytical applications. It presents the necessary information, in pictorial form, for reading the ''2D NMR,'' and enables the practicing chemist to solve problems and run experiments on a commercial spectrometer by using the software provided by the manufacturer.

  8. Cross Gradient Based Joint Inversion of 2D Wide Angle Seismic Reflection/Refraction and Gravity Data Along the Profile Through the 2010 Ms 7.1 Yushu Earthquake, China

    NASA Astrophysics Data System (ADS)

    Xiang, S.; Zhang, H.

    2015-12-01

    2D wide-angle seismic reflection/refraction survey has been widely used to investigate crustal structure and Moho topography. Similarly gravity survey is also very important in the study of local and regional earth features. Seismic survey is sensitive to the seismic velocity parameters and interface variations. For gravity survey, it is sensitive to density parameters of the medium but the resolution along the vertical direction is relatively poor. In this study, we have developed a strategy to jointly invert for seismic velocity model, density model and interface positions using the gravity observations and seismic arrival times from different phases. For the joint inversion of seismic and gravity data, it often relies on the empirical relationship between seismic velocity and density. In comparison, our joint inversion strategy also includes the cross-gradient based structure constraint for seismic velocity and density models in addition to the empirical relationship between them. The objective function for the joint inversion includes data misfit terms for seismic travel times and gravity observations, the cross-gradient constraint, the smoothness terms for two models, and the data misfit term between predicted gravity data based on density model converted from velocity model using the empirical relationship. Each term has its respective weight. We have applied the new joint inversion method to the Riwoqe-Yushu-Maduo profile in northwest China. The profile crosses through the Qiangtang block and Bayan Har block from southwest to northeast, respectively. The 2010 Ms 7.1 Yushu earthquake is located on the profile, around the Ganzi-Yushu fault zone. The joint inversion produces the velocity and density models that are similar in structure and at the same time fit their respective data sets well. Compared to separate seismic inversion using seismic travel times, the joint inversion with gravity data gives a velocity model that better delineates the fault zones. Low

  9. Combined analysis of the essential oil of Chenopodium ambrosioides by GC, GC-MS and 13C-NMR spectroscopy: quantitative determination of ascaridole, a heat-sensitive compound.

    PubMed

    Cavalli, Jean-François; Tomi, Félix; Bernardini, Antoine-François; Casanova, Joseph

    2004-01-01

    A commercial sample of the essential oil of Chenopodium ambrosioides L. from Madagascar was analysed by GC, GC-MS and 13C-NMR. By GC analysis, the major constituents were found to be ascaridole (1) (41.8%), isoascaridole (2) (18.1%), p-cymene (16.2%), alpha-terpinene (9.7%) and limonene (3.8%). However, ascaridole undergoes a partial thermal isomerisation to 2 and hence the amount of 1 is under-estimated by GC analysis. The actual contents of 1 and 2 (55.3 and 4.6%, respectively) were obtained following combined analysis of the sample by GC and 13C-NMR. Several hydroxy- and polyhydroxy-menthanes were identified by 13C-NMR. PMID:15508830

  10. Off-line TMAH-GC/MS and NMR characterization of humic substances extracted from river sediments of northwestern São Paulo under different soil uses.

    PubMed

    Tadini, Amanda Maria; Pantano, Glaucia; de Toffoli, Ana Lúcia; Fontaine, Barbara; Spaccini, Riccardo; Piccolo, Alessandro; Moreira, Altair Benedito; Bisinoti, Márcia Cristina

    2015-02-15

    Humic substances (HS) vary according to the physical and chemical factors present in the environment. Thus, the characterization of HS is very important because it improves the understanding of the groups that comprise the chemical structure. Sediment HS were extracted from four locations representative of sugar cane cultivation, pasture, urban area and the impoundment of the Água Vermelha Hydroelectric Power Plant. Characterization using nuclear magnetic resonance (NMR) allowed us to infer that the HS from an area predominantly characterized by sugar cane cultivation (41.9%) and a typical rural area (35.0%) showed the highest aromaticity percentage. Using the off-line TMAH-thermochemolysis-GC-MS, we inferred that the HS of a typical rural area had a structure rich in plant waxes, plant biopolyester and a large amount of fatty acid methyl ester, which are related to the large amount of humic acid in the structure. The HS samples from the sugar cane cultivation area and the impoundment receiving all of the pollution load from the Turvo/Grande Hydrographic Basin (Bacia Hidrográfica do Turvo/Grande-BHTG) contained contributions from compounds rich in lipids and fatty acid methyl esters, highlighting the presence of the breakdown of petroleum-derived hydrocarbons in the area receiving the entire pollution load. We conclude that the HS extracted from the sediments of the Preto, Turvo and Grande rivers showed well-defined characteristics that varied depending on soil use and occupation, especially the HS extracted from sediments sampled in areas typically planted with sugar cane and rural areas, whose structures contained more aromatic groups. PMID:25460956

  11. Soils, Pores, and NMR

    NASA Astrophysics Data System (ADS)

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

    2010-05-01

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

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

    SciTech Connect

    Millar, J.M.

    1986-02-01

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

  13. 2D NMR analysis of highly restricted internal rotation in 2-methylthio-3H-4- p-bromophenyl)-7-[( ortho- and para-substituted)-phenylthio]-1,5-benzodiazepines

    NASA Astrophysics Data System (ADS)

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

    2000-08-01

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

  14. Aniso2D

    2005-07-01

    Aniso2d is a two-dimensional seismic forward modeling code. The earth is parameterized by an X-Z plane in which the seismic properties Can have monoclinic with x-z plane symmetry. The program uses a user define time-domain wavelet to produce synthetic seismograms anrwhere within the two-dimensional media.

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

    SciTech Connect

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

    1992-06-17

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

  16. Mesh2d

    SciTech Connect

    Greg Flach, Frank Smith

    2011-12-31

    Mesh2d is a Fortran90 program designed to generate two-dimensional structured grids of the form [x(i),y(i,j)] where [x,y] are grid coordinates identified by indices (i,j). The x(i) coordinates alone can be used to specify a one-dimensional grid. Because the x-coordinates vary only with the i index, a two-dimensional grid is composed in part of straight vertical lines. However, the nominally horizontal y(i,j0) coordinates along index i are permitted to undulate or otherwise vary. Mesh2d also assigns an integer material type to each grid cell, mtyp(i,j), in a user-specified manner. The complete grid is specified through three separate input files defining the x(i), y(i,j), and mtyp(i,j) variations.

  17. Mesh2d

    2011-12-31

    Mesh2d is a Fortran90 program designed to generate two-dimensional structured grids of the form [x(i),y(i,j)] where [x,y] are grid coordinates identified by indices (i,j). The x(i) coordinates alone can be used to specify a one-dimensional grid. Because the x-coordinates vary only with the i index, a two-dimensional grid is composed in part of straight vertical lines. However, the nominally horizontal y(i,j0) coordinates along index i are permitted to undulate or otherwise vary. Mesh2d also assignsmore » an integer material type to each grid cell, mtyp(i,j), in a user-specified manner. The complete grid is specified through three separate input files defining the x(i), y(i,j), and mtyp(i,j) variations.« less

  18. Determinants of the substrate specificity of human cytochrome P-450 CYP2D6: design and construction of a mutant with testosterone hydroxylase activity.

    PubMed Central

    Smith, G; Modi, S; Pillai, I; Lian, L Y; Sutcliffe, M J; Pritchard, M P; Friedberg, T; Roberts, G C; Wolf, C R

    1998-01-01

    , the CYP2D6F483I mutant acquired the ability to metabolize testosterone to a novel product, which was identified by MS and proton NMR spectroscopy as 15alpha-hydroxytestosterone. NMR spin relaxation experiments were used to measure distances between the haem iron and protons of testosterone bound to the CYP2D6F483I mutant. These experiments demonstrate that very minor modifications to the active site structure of CYP2D6 can have a profound influence on the substrate specificity of the enzyme. PMID:9560305

  19. Push-through Direction Injectin NMR Automation

    EPA Science Inventory

    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...

  20. Vertical 2D Heterostructures

    NASA Astrophysics Data System (ADS)

    Lotsch, Bettina V.

    2015-07-01

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

  1. Synthesis, characterization and dynamic NMR studies of a novel chalcone based N-substituted morpholine derivative

    NASA Astrophysics Data System (ADS)

    Baskar, R.; Baby, C.; Moni, M. S.; Subramanian, K.

    2013-05-01

    The synthesis of a novel chalcone based N-substituted morpholine derivative namely, (E)-1-(biphenyl-4-yl)-3-(4-(5-morpholinopentyloxy) phenyl) prop-2-en-1-one (BMPP), using a two step protocol is reported. The compound is characterized by FTIR, GC-MS and FTNMR spectroscopy techniques. Advanced 2D NMR techniques such as gradient enhanced COSY, HSQC, HMBC and NOESY were employed to establish through-bond and through-space correlations. Dynamic NMR measurements were carried out to obtain the energy barrier to ring inversion of the morpholine moiety.

  2. Integration of 1H NMR and UPLC-Q-TOF/MS for a Comprehensive Urinary Metabonomics Study on a Rat Model of Depression Induced by Chronic Unpredictable Mild Stress

    PubMed Central

    Jia, Hong-mei; Feng, Yu-fei; Liu, Yue-tao; Chang, Xing; Chen, Lin; Zhang, Hong-wu; Ding, Gang; Zou, Zhong-mei

    2013-01-01

    Depression is a type of complex psychiatric disorder with long-term, recurrent bouts, and its etiology remains largely unknown. Here, an integrated approach utilizing 1H NMR and UPLC-Q-TOF/MS together was firstly used for a comprehensive urinary metabonomics study on chronic unpredictable mild stress (CUMS) treated rats. More than twenty-nine metabolic pathways were disturbed after CUMS treatment and thirty-six potential biomarkers were identified by using two complementary analytical technologies. Among the identified biomarkers, nineteen (10, 11, 16, 17, 21–25, and 27–36) were firstly reported as potential biomarkers of CUMS-induced depression. Obviously, this paper presented a comprehensive map of the metabolic pathways perturbed by CUMS and expanded on the multitude of potential biomarkers that have been previously reported in the CUMS model. Four metabolic pathways, including valine, leucine and isoleucine biosynthesis; phenylalanine, tyrosine and tryptophan biosynthesis; tryptophan metabolism; synthesis and degradation of ketone bodies had the deepest influence in the pathophysiologic process of depression. Fifteen potential biomarkers (1–2, 4–6, 15, 18, 20–23, 27, 32, 35–36) involved in the above four metabolic pathways might become the screening criteria in clinical diagnosis and predict the development of depression. Moreover, the results of Western blot analysis of aromatic L-amino acid decarboxylase (DDC) and indoleamine 2, 3-dioxygenase (IDO) in the hippocampus of CUMS-treated rats indicated that depletion of 5-HT and tryptophan, production of 5-MT and altered expression of DDC and IDO together played a key role in the initiation and progression of depression. In addition, none of the potential biomarkers were detected by NMR and LC-MS simultaneously which indicated the complementary of the two kinds of detection technologies. Therefore, the integration of 1H NMR and UPLC-Q-TOF/MS in metabonomics study provided an approach to identify the

  3. Two-dimensional NMR spectroscopy

    SciTech Connect

    Croasmun, W.R.; Carlson, R.M.K.

    1987-01-01

    Written for chemists and biochemists who are not NMR spectroscopists, but who wish to use the new techniques of two-dimensional NMR spectroscopy, this book brings together for the first time much of the practical and experimental data needed. It also serves as information source for industrial, academic, and graduate student researchers who already use NMR spectroscopy, but not yet in two dimensions. The authors describe the use of 2-D NMR in a wide variety of chemical and biochemical fields, among them peptides, steroids, oligo- and poly-saccharides, nucleic acids, natural products (including terpenoids, alkaloids, and coal-derived heterocyclics), and organic synthetic intermediates. They consider throughout the book both the advantages and limitations of using 2-D NMR.

  4. Moving NMR

    NASA Astrophysics Data System (ADS)

    Blümich, Bernhard; Casanova, Federico; Danieli, Ernesto; Gong, Qingxia; Greferath, Marcus; Haber, Agnes; Kolz, Jürgen; Perlo, Juan

    2008-12-01

    Initiated by the use of NMR for well logging, portable NMR instruments are being developed for a variety of novel applications in materials testing and process analysis and control. Open sensors enable non-destructive testing of large objects, and small, cup-size magnets become available for high throughput analysis by NMR relaxation and spectroscopy. Some recent developments of mobile NMR are reviewed which delineate the direction into which portable NMR is moving.

  5. LC-MS guided isolation of ent-kaurane diterpenoids from Nouelia insignis.

    PubMed

    Sun, Chang-Li; Geng, Chang-An; Chen, Xing-Long; Yang, Tong-Hua; Yin, Xiu-Juan; Huang, Xiao-Yan; Peng, Hua; Chen, Ji-Jun

    2016-06-01

    The preliminary LC-MS investigation on the stems of Nouelia insignis manifested the existence of diterpenoids. As a result, 15 ent-kaurane diterpenoids, including 7 new glycosides (nouelosides A-G, 1-7), were isolated under the direction of LC-MS analysis. The new compounds were determined by extensive spectroscopic analysis including HRESIMS, 1D and 2D NMR data and chemical methods. Compounds 6 and 15 with the exo-methylene cyclopentanone functional group exhibited obvious nitric oxide production inhibitory activity with IC50 values of 3.84±0.20 and 3.19±0.25μM. PMID:27094114

  6. Efficient 2D MRI relaxometry using compressed sensing

    NASA Astrophysics Data System (ADS)

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

    2015-06-01

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

  7. NMR Methods, Applications and Trends for Groundwater Evaluation and Management

    NASA Astrophysics Data System (ADS)

    Walsh, D. O.; Grunewald, E. D.

    2011-12-01

    Nuclear magnetic resonance (NMR) measurements have a tremendous potential for improving groundwater characterization, as they provide direct detection and measurement of groundwater and unique information about pore-scale properties. NMR measurements, commonly used in chemistry and medicine, are utilized in geophysical investigations through non-invasive surface NMR (SNMR) or downhole NMR logging measurements. Our recent and ongoing research has focused on improving the performance and interpretation of NMR field measurements for groundwater characterization. Engineering advancements have addressed several key technical challenges associated with SNMR measurements. Susceptibility of SNMR measurements to environmental noise has been dramatically reduced through the development of multi-channel acquisition hardware and noise-cancellation software. Multi-channel instrumentation (up to 12 channels) has also enabled more efficient 2D and 3D imaging. Previous limitations in measuring NMR signals from water in silt, clay and magnetic geology have been addressed by shortening the instrument dead-time from 40 ms to 4 ms, and increasing the power output. Improved pulse sequences have been developed to more accurately estimate NMR relaxation times and their distributions, which are sensitive to pore size distributions. Cumulatively, these advancements have vastly expanded the range of environments in which SNMR measurements can be obtained, enabling detection of groundwater in smaller pores, in magnetic geology, in the unsaturated zone, and nearby to infrastructure (presented here in case studies). NMR logging can provide high-resolution estimates of bound and mobile water content and pore size distributions. While NMR logging has been utilized in oil and gas applications for decades, its use in groundwater investigations has been limited by the large size and high cost of oilfield NMR logging tools and services. Recently, engineering efforts funded by the US Department of

  8. Development and validation of a stability indicating assay of doxofylline by RP-HPLC: ESI-MS/MS, ¹H and ¹³C NMR spectroscopic characterization of degradation products and process related impurities.

    PubMed

    Rao, R Nageswara; Naidu, Ch Gangu; Prasad, K Guru; Santhakumar, B; Saida, Shaik

    2013-05-01

    A validated stability indicating RP-HPLC assay of doxofylline was developed by separating its related substances and degradants on LichrocartC18 (250 mm × 4.6 mm; 5 μm) column using 10 mM ammonium acetate and acetonitrile as a mobile phase in a gradient mode of elution at a flow rate of 1.0 mL/min at 30 °C. The column effluents were monitored by a photo diode array detector set at 274 nm. The method was validated in terms of accuracy, precision and linearity as per ICH guidelines. The limits of quantification of doxofylline and impurities were obtained in the range of 0.19-0.36 μg/mL. Forced degradation of doxofylline was carried out under acidic, basic, thermal, photo, peroxide conditions and the degradation products were isolated and characterized by ESI-MS/MS, (1)H and (13)C spectroscopy. The method was successfully applied not only to quantify related substances and degradation products but also assay of doxofylline in bulk drugs. The recoveries of doxofylline and impurities were in the range of 99.00-100.05% and 97.83-99.86% respectively. PMID:23466440

  9. Molecular Characterization of Dissolved Organic Matter from Subtropical Wetlands: A Comparative Study Through the Analysis of Optical Properties, NMR and FTICR/MS

    NASA Astrophysics Data System (ADS)

    Jaffe, R.; Hertkorn, N.; Harir, M.; Cawley, K.; Schmitt-Kopplin, P.

    2014-12-01

    Dissolved organic matter (DOM) is a critical component of the carbon cycle in freshwater systems and its elemental composition and molecular features determine its reactivity and thus its stability in the environment. DOM is particularly prominent in wetland ecosystems and can be exported through drainage into streams and ultimately the ocean. While DOM has been characterized through a great variety of analytical techniques, much focus has been placed on characterizations in oceanic environments and large river systems. In addition, multi-analytical approaches using advanced analytical techniques for the characterization of DOM in wetlands have been sparse. Here we present a comparative study of DOM from three, large, subtropical wetlands, the Everglades (USA), the Pantanal (Brazil) and the Okavango Delta (Botswana), applying a combination of optical properties (EEM-PARAFAC), high field NMR and FT-ICRMS. We basically confirm findings of other reports that many of the bulk molecular characteristics in freshwater DOM are shared by diverse aquatic ecosystems that can be very different in their environmental character. However, detailed analyses reveal significant variations in the molecular composition that can in most cases be controlled by site-specific ecological processes and watershed dynamics including fire regimes, external sources of sulphur, and hydrological drivers such as hydroperiod or degree of inundation. Differences and similarities between selected sites from the three abovementioned wetland systems will be presented in relation to their specific environmental characteristics.

  10. High divergent 2D grating

    NASA Astrophysics Data System (ADS)

    Wang, Jin; Ma, Jianyong; Zhou, Changhe

    2014-11-01

    A 3×3 high divergent 2D-grating with period of 3.842μm at wavelength of 850nm under normal incidence is designed and fabricated in this paper. This high divergent 2D-grating is designed by the vector theory. The Rigorous Coupled Wave Analysis (RCWA) in association with the simulated annealing (SA) is adopted to calculate and optimize this 2D-grating.The properties of this grating are also investigated by the RCWA. The diffraction angles are more than 10 degrees in the whole wavelength band, which are bigger than the traditional 2D-grating. In addition, the small period of grating increases the difficulties of fabrication. So we fabricate the 2D-gratings by direct laser writing (DLW) instead of traditional manufacturing method. Then the method of ICP etching is used to obtain the high divergent 2D-grating.

  11. Realistic and efficient 2D crack simulation

    NASA Astrophysics Data System (ADS)

    Yadegar, Jacob; Liu, Xiaoqing; Singh, Abhishek

    2010-04-01

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

  12. Structure Elucidation of the Metabolites of 2', 3', 5'-Tri-O-Acetyl-N6-(3-Hydroxyphenyl) Adenosine in Rat Urine by HPLC-DAD, ESI-MS and Off-Line Microprobe NMR

    PubMed Central

    Miao, Zhaoxia; Qu, Kai; Liu, Xia; Zhang, Peicheng; Qin, Hailin; Zhu, Haibo; Wang, Yinghong

    2015-01-01

    2', 3', 5'-tri-O-acetyl-N6-(3-hydroxyphenyl) adenosine (also known as WS070117) is a new adenosine analog that displays anti-hyperlipidemic activity both in vitro and in vivo experiments as shown in many preliminary studies. Due to its new structure, little is known about the metabolism of WS070117. Hence, the in vivo metabolites of WS070117 in rat urine following oral administration were investigated. Identification of the metabolites was conducted using the combination of high-performance liquid chromatography (HPLC) coupled with diode array detector (DAD), ion trap electrospray ionization-mass spectrometry (ESI-MS), and off-line microprobe nuclear magnetic resonance (NMR) measurements. Seven metabolites were obtained as pure compounds at the sub-milligram to milligram levels. Results of structure elucidation unambiguously revealed that the phase I metabolite, N6-(3-hydroxyphenyl) adenosine (M8), was a hydrolysate of WS070117 by hydrolysis on the three ester groups. N6-(3-hydr-oxyphenyl) adenine (M7), also one of the phase I metabolites, was the derivative of M8 by the loss of ribofuranose. In addition to two phase I metabolites, there were five phase II metabolites of WS070117 found in rat urine. 8-hydroxy-N6-(3-hydroxy-phenyl) adenosine (M6) was the product of M7 by hydrolysis at position 8. The other four were elucidated to be N6-(3-O-β-D-glucuronyphenyl) adenine (M2), N8-hydroxy-N6-(3-O-sulfophenyl) adenine (M3), N6-(3-O-β-D-glucuronyphenyl) adenosine (M4), and N6-(3-O- sulfophenyl) adenosine (M5). Phase II metabolic pathways were proven to consist of hydroxylation, glucuronidation and sulfation. This study provides new and valuable information on the metabolism of WS070117, and also demonstrates the HPLC/MS/off-line microprobe NMR approach as a robust means for rapid identification of metabolites. PMID:26029929

  13. Metabolomic Assessment of Key Maize Resources: GC-MS and NMR Profiling of Grain from B73 Hybrids of the Nested Association Mapping (NAM) Founders and of Geographically Diverse Landraces.

    PubMed

    Venkatesh, Tyamagondlu V; Chassy, Alexander W; Fiehn, Oliver; Flint-Garcia, Sherry; Zeng, Qin; Skogerson, Kirsten; Harrigan, George G

    2016-03-16

    The present study expands metabolomic assessments of maize beyond commercial lines to include two sets of hybrids used extensively in the scientific community. One set included hybrids derived from the nested association mapping (NAM) founder lines, a collection of 25 inbreds selected on the basis of genetic diversity and used to investigate the genetic basis of complex plant traits. A second set included 24 hybrids derived from a collection of landraces representative of native diversity from North and South America that may serve as a source of new alleles for improving modern maize hybrids. Metabolomic analysis of grain harvested from these hybrids utilized gas chromatography-time-of-flight mass spectrometry (GC-TOF-MS) and (1)H nuclear magnetic resonance spectroscopy ((1)H NMR) techniques. Results highlighted extensive metabolomic variation in grain from both hybrid sets, but also demonstrated that, within each hybrid set, subpopulations could be differentiated in a pattern consistent with the known genetic and compositional variation of these lines. Correlation analysis did not indicate a strong association of the metabolomic data with grain nutrient composition, although some metabolites did show moderately strong correlations with agronomic features such as plant and ear height. Overall, this study provides insights into the extensive metabolomic diversity associated with conventional maize germplasm. PMID:26923484

  14. 1H, 13C NMR, FT-IR, ESI MS and PM5 studies of a new 3,6,9-trioxadecylamide of monensin A and its complexes with Li +, Na + and K + cations

    NASA Astrophysics Data System (ADS)

    Łowicki, Daniel; Huczyński, Adam; Brzezinski, Bogumil; Bartl, Franz

    2011-03-01

    A new 3,6,9-trioxadecylamide of monensin A (M-AM4) has been synthesised and its ability to form complexes with Li +, Na + and K + cations has been studied by ESI mass spectrometry, 1H and 13C NMR, FT-IR spectroscopy and PM5 semiempirical method. The ESI MS data indicate that M-AM4 forms complexes with Li +, Na + and K + of exclusively 1:1 stoichiometry which are stable up to cv = 70 V. The formation of the M-AM4-Na + is strongly favoured. Above cv = 70 the fragmentation process is observed. The spectroscopic studies show that the structures of the M-AM4 and its complexes with the cations of 1:1 stoichiometry are stabilized by intramolecular hydrogen bonds in which the OH groups are always involved. The C dbnd O amide group is engaged in the complexation process of each cation. The M-AM4-K + complex can also assume a structure in which the C dbnd O amide group does not participate in the complexation but the complexes of such structure do not dominate.

  15. Quantitating Metabolites in Protein Precipitated Serum Using NMR Spectroscopy

    PubMed Central

    2015-01-01

    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,” 15N-cholamine for further resolution enhancement, which resulted in the detection of a number of additional metabolites. 1H 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. PMID:24796490

  16. Binding of copper(II) ions to the polyproline II helices of PEVK modules of the giant elastic protein titin as revealed by ESI-MS, CD, and NMR.

    PubMed

    Ma, Kan; Wang, Kuan

    2003-10-01

    Titin, a family of giant elastic proteins, constitutes an elastic sarcomere matrix in striated muscle. In the I-band region of the sarcomere, the titin PEVK segment acts as a molecular spring to generate elasticity as well as sites of adhesion with parallel thin filaments. Previously, we reported that PEVK consists of tandem repeats of 28 residue modules and that the "polyproline II-coil" motif is the fundamental conformational motif of the PEVK module. In order to characterize the factors that may affect and alter the PPII-coil conformational motifs, we have initiated a systematic study of the interaction with divalent cations (Cu2+, Ca2+, Zn2+, and Ni2+) and a conformational profile of PEVK peptides (a representative 28-mer peptide PR: PEPPKEVVPEKKAPVAPPKKPEVPPVKV and its subfragments PR1: kvPEPPKEVVPE, PR2: VPEKKAPVAPPK, PR3: KPEVPPVKV). UV-Vis absorption difference spectra and CD spectra showed that Cu2+ bound to PR1 with high affinity (20 microM), while its binding to PR2 and PR3 as well as the binding of other cations to all four peptides were of lower affinity (>100 microM). Conformational studies by CD revealed that Cu2+ binding to PR1 resulted in a polyproline II to turn transition up to a 1:2 PR1/Cu2+ ratio and a coil to turn transition at higher Cu2+ concentration. ESI-MS provided the stoichiometry of PEVK peptide-Cu2+ complexes at both low and high ion strength, confirming the specific high affinity binding of Cu2+ to PR1 and PR. Furthermore, NMR and ESI-MS/MS fragmentation analysis elucidated the binding sites of the PEVK peptide-Cu2+ complexes at (-2)KVPE2, 8VPE10, 13APV15, and 22EVP24. A potential application of Cu2+ binding in peptide sequencing by mass spectrometry was also revealed. We conclude that Cu2+ binds and bends PEVK peptides to a beta-turn-like structure at specific sites. The specific targeting of Cu2+ towards PPII is likely to be of significant value in elucidating the roles of PPII in titin elasticity as well as in interactions of

  17. AnisWave 2D

    2004-08-01

    AnisWave2D is a 2D finite-difference code for a simulating seismic wave propagation in fully anisotropic materials. The code is implemented to run in parallel over multiple processors and is fully portable. A mesh refinement algorithm has been utilized to allow the grid-spacing to be tailored to the velocity model, avoiding the over-sampling of high-velocity materials that usually occurs in fixed-grid schemes.

  18. Pediatric MS

    MedlinePlus

    ... of the oral medications in the pediatric population. Network of Pediatric MS Centers The National MS Society ... MS Study Group (2004) and established a nationwide network of six Pediatric MS Centers of Excellence (2006) ...

  19. CD4+NKG2D+ T Cells Exhibit Enhanced Migratory and Encephalitogenic Properties in Neuroinflammation

    PubMed Central

    Ruck, Tobias; Bittner, Stefan; Gross, Catharina C.; Breuer, Johanna; Albrecht, Stefanie; Korr, Sabrina; Göbel, Kerstin; Pankratz, Susann; Henschel, Christian M.; Schwab, Nicholas; Staszewski, Ori; Prinz, Marco; Kuhlmann, Tanja

    2013-01-01

    Migration of encephalitogenic CD4+ T lymphocytes across the blood-brain barrier is an essential step in the pathogenesis of multiple sclerosis (MS). We here demonstrate that expression of the co-stimulatory receptor NKG2D defines a subpopulation of CD4+ T cells with elevated levels of markers for migration, activation, and cytolytic capacity especially when derived from MS patients. Furthermore, CD4+NKG2D+ cells produce high levels of proinflammatory IFN-γ and IL-17 upon stimulation. NKG2D promotes the capacity of CD4+NKG2D+ cells to migrate across endothelial cells in an in vitro model of the blood-brain barrier. CD4+NKG2D+ T cells are enriched in the cerebrospinal fluid of MS patients, and a significant number of CD4+ T cells in MS lesions coexpress NKG2D. We further elucidated the role of CD4+NKG2D+ T cells in the mouse system. NKG2D blockade restricted central nervous system migration of T lymphocytes in vivo, leading to a significant decrease in the clinical and pathologic severity of experimental autoimmune encephalomyelitis, an animal model of MS. Blockade of NKG2D reduced killing of cultivated mouse oligodendrocytes by activated CD4+ T cells. Taken together, we identify CD4+NKG2D+ cells as a subpopulation of T helper cells with enhanced migratory, encephalitogenic and cytotoxic properties involved in inflammatory CNS lesion development. PMID:24282598

  20. Chromatographic NMR in NMR solvents

    NASA Astrophysics Data System (ADS)

    Carrara, Caroline; Viel, Stéphane; Delaurent, Corinne; Ziarelli, Fabio; Excoffier, Grégory; Caldarelli, Stefano

    2008-10-01

    Recently, it was demonstrated that pseudo-chromatographic NMR experiments could be performed using typical chromatographic solids and solvents. This first setup yielded improved separation of the spectral components of the NMR spectra of mixtures using PFG self-diffusion measurements. The method (dubbed Chromatographic NMR) was successively shown to possess, in favorable cases, superior resolving power on non-functionalized silica, compared to its LC counterpart. To further investigate the applicability of the method, we studied here the feasibility of Chromatographic NMR in common deuterated solvents. Two examples are provided, using deuterated chloroform and water, for homologous compounds soluble in these solvents, namely aromatic molecules and alcohols, respectively.

  1. Stacking up 2D materials

    NASA Astrophysics Data System (ADS)

    Mayor, Louise

    2016-05-01

    Graphene might be the most famous example, but there are other 2D materials and compounds too. Louise Mayor explains how these atomically thin sheets can be layered together to create flexible “van der Waals heterostructures”, which could lead to a range of novel applications.

  2. MOSS2D V1

    2001-01-31

    This software reduces the data from two-dimensional kSA MOS program, k-Space Associates, Ann Arbor, MI. Initial MOS data is recorded without headers in 38 columns, with one row of data per acquisition per lase beam tracked. The final MOSS 2d data file is reduced, graphed, and saved in a tab-delimited column format with headers that can be plotted in any graphing software.

  3. Competing coexisting phases in 2D water

    PubMed Central

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

    2016-01-01

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

  4. Competing coexisting phases in 2D water

    NASA Astrophysics Data System (ADS)

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

    2016-05-01

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

  5. Competing coexisting phases in 2D water.

    PubMed

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

    2016-01-01

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

  6. Nanoimprint lithography: 2D or not 2D? A review

    NASA Astrophysics Data System (ADS)

    Schift, Helmut

    2015-11-01

    Nanoimprint lithography (NIL) is more than a planar high-end technology for the patterning of wafer-like substrates. It is essentially a 3D process, because it replicates various stamp topographies by 3D displacement of material and takes advantage of the bending of stamps while the mold cavities are filled. But at the same time, it keeps all assets of a 2D technique being able to pattern thin masking layers like in photon- and electron-based traditional lithography. This review reports about 20 years of development of replication techniques at Paul Scherrer Institut, with a focus on 3D aspects of molding, which enable NIL to stay 2D, but at the same time enable 3D applications which are "more than Moore." As an example, the manufacturing of a demonstrator for backlighting applications based on thermally activated selective topography equilibration will be presented. This technique allows generating almost arbitrary sloped, convex and concave profiles in the same polymer film with dimensions in micro- and nanometer scale.

  7. Rapid characterization of molecular diffusion by NMR spectroscopy.

    PubMed

    Pudakalakatti, Shivanand M; Chandra, Kousik; Thirupathi, Ravula; Atreya, Hanudatta S

    2014-11-24

    An NMR-based approach for rapid characterization of translational diffusion of molecules has been developed. Unlike the conventional method of acquiring a series of 2D (13)C and (1)H spectra, the proposed approach involves a single 2D NMR spectrum, which can be acquired in minutes. Using this method, it was possible to detect the presence of intermediate oligomeric species of diphenylalanine in solution during the process of its self-assembly to form nanotubular structures. PMID:25331210

  8. 3,4-DEHYDRODEBRISOQUINE, A NOVEL DEBRISOQUINE METABOLITE FORMED FROM 4-HYDROXYDEBRISOQUINE THAT IMPACTS THE CYP2D6 METABOLIC RATIO

    PubMed Central

    Zhen, Yueying; Slanař, Ondřej; Krausz, Kristopher W.; Chen, Chi; Slavík, Josef; McPhail, Kerry L.; Zabriskie, T. Mark; Perlík, František; Gonzalez, Frank J.; Idle, Jeffrey R.

    2006-01-01

    Considerable unexplained inter-subject variability in the debrisoquine metabolic ratio (urinary debrisoquine/4-hydroxydebrisoquine) exists within individual CYP2D6 genotypes. We speculated that debrisoquine was converted to as yet undisclosed metabolites. Thirteen healthy young volunteers, nine CYP2D6*1 homozygotes (EMs) and four CYP2D6*4 homozygotes (PMs) took 12.8 mg debrisoquine hemisulfate by mouth and collected 0–8 and 8–24 h urines, which were analyzed by GCMS before and after treatment with β-glucuronidase. Authentic 3,4-dehydrodebrisoquine was synthesized and characterized by GCMS, LC-MS/MS and 1H NMR. 3,4-Dehydrodebrisoquine is a novel metabolite of debrisoquine excreted variably in 0–24 h urine, both in EMs (3.1–27.6% dose) and PMs (0–2.1% dose). This metabolite is produced from 4-hydroxydebrisoquine in vitro by human and rat liver microsomes. A single CYP2D6*1 homozygote was administered 10.2 mg 4-hydroxydebrisoquine orally and also excreted 3,4-dehydrodebrisoquine. EMs excreted 6-hydroxydebrisoquine (0–4.8%), 8-hydroxydebrisoquine (0–1.3%) but these phenolic metabolites were not detected in PM urine. Debrisoquine and 4-hydroxydebrisoquine glucuronides were excreted in a highly genotype-dependent manner. A non-cytochrome P450 microsomal activity participates in the further metabolism of 4-hydroxydebrisoquine, which we speculate may also lead to the formation of 1- and 3-hydroxydebrisoquine and their ring-opened products. In conclusion, this study suggests that the traditional metabolic ratio is not a true measure of the debrisoquine 4-hydroxylation capacity of an individual and thus may, in part, explain the wide intragenotype variation in metabolic ratio. PMID:16782768

  9. MS Based Metabonomics

    SciTech Connect

    Want, Elizabeth J.; Metz, Thomas O.

    2010-03-01

    Metabonomics is the latest and least mature of the systems biology triad, which also includes genomics and proteomics, and has its origins in the early orthomolecular medicine work pioneered by Linus Pauling and Arthur Robinson. It was defined by Nicholson and colleagues in 1999 as the quantitative measurement of perturbations in the metabolite complement of an integrated biological system in response to internal or external stimuli, and is often used today to describe many non-global types of metabolite analyses. Applications of metabonomics are extensive and include toxicology, nutrition, pharmaceutical research and development, physiological monitoring and disease diagnosis. For example, blood samples from millions of neonates are tested routinely by mass spectrometry (MS) as a diagnostic tool for inborn errors of metabolism. The metabonome encompasses a wide range of structurally diverse metabolites; therefore, no single analytical platform will be sufficient. Specialized sample preparation and detection techniques are required, and advances in NMR and MS technologies have led to enhanced metabonome coverage, which in turn demands improved data analysis approaches. The role of MS in metabonomics is still evolving as instrumentation and software becomes more sophisticated and as researchers realize the strengths and limitations of current technology. MS offers a wide dynamic range, high sensitivity, and reproducible, quantitative analysis. These attributes are essential for addressing the challenges of metabonomics, as the range of metabolite concentrations easily exceeds nine orders of magnitude in biofluids, and the diversity of molecular species ranges from simple amino and organic acids to lipids and complex carbohydrates. Additional challenges arise in generating a comprehensive metabolite profile, downstream data processing and analysis, and structural characterization of important metabolites. A typical workflow of MS-based metabonomics is shown in Figure

  10. Two-dimensional NMR spectroscopy. Applications for chemists and biochemists

    SciTech Connect

    Croasmun, W.R.; Carlson, R.M.K.

    1987-01-01

    Two-dimensional nuclear magnetic resonance spectroscopy (2-D NMR) has become a very powerful class of experiments (in the hands of an adept scientist) with broad adaptability to new situations. It is the product of a happy marriage between modern pulse FT-NMR technology, with its large memory and high-speed computers, and the physicists and chemists who love to manipulate spin systems. Basic 2-D experiments are now a standard capability of modern NMR spectrometers, and this timely book intends to make 2-D NMR users of those who are familiar with normal 1-D NMR. The 2-D NMR goal is correlation of the lines of the observed NMR spectrum with other properties of the system. This book deals with applications to high-resolution spectrum analysis, utilizing either coupling between the NMR-active nuclei or chemical exchange to perform the correlation. The coupling can be scalar (through bonds) or direct through space (within 5 A). The coupling may be homonuclear (between like nuclei) or heteronuclear.

  11. Analysis of Amino Acid Isotopomers using FT-ICR MS

    SciTech Connect

    Pingitore, Francesco; Tang, Yinjie; Kruppa, Gary H.; Keasling,Jay D.

    2006-10-08

    Fluxes through known metabolic pathways and the presence ofnovel metabolic reactions are often determined by feedingisotopically-labeled substrate to an organism and then determining theisotopomer distribution in amino acids in proteins. However, commonlyused techniques to measure the isotopomer distributions requirederivatization prior to analysis (gas chromatography-mass spectrometry(GC-MS)) or large sample sizes (nuclear magnetic resonance (NMR)spectroscopy). Here, we demonstrate the use of Fourier Transform-IonCyclotron Resonance Mass Spectrometry (FT-ICR MS) with direct infusionvia electrospray ionization to rapidly measure the amino acid isotopomerdistribution in a biomass hydrolysate of the soil bacterium Desulfovibriovulgaris Hildenborough. By applying high front-end resolution for theprecursor ion selection followed by sustained off-resonance irradiation -collision-induced dissociation (SORI-CID), it was possible to determineexactly and unambiguously the specific locations of the labeled atoms inthe amino acids, which usually requires a combination of 2-D 13C NMRspectroscopy and GC-MS. This method should be generally applicable toallbiomass samples and will allow more accurate determination of metabolicfluxes with less work and less sample.

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

    ERIC Educational Resources Information Center

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

    2015-01-01

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

  13. NKG2D ligands as therapeutic targets

    PubMed Central

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

    2013-01-01

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

  14. UPLC-MS, HPLC-radiometric, and NMR-spectroscopic studies on the metabolic fate of 3-fluoro-[U-14C]-aniline in the bile-cannulated rat.

    PubMed

    Athersuch, T J; Castro-Perez, J; Rodgers, C; Nicholson, J K; Wilson, Ian D

    2010-07-01

    1. A study of the rates and routes of excretion of 3-fluoro-[U-(14)C]aniline following intraperitoneal administration to male bile-cannulated rats by liquid scintillation counting (LSC) gave a total recovery of approximately 90% in the 48 h following dosing, with the majority of the dose being excreted in the urine during the first 24 h (approximately 49%). 2. The total recovery as determined by (19)F-nuclear magnetic resonance ((19)F-NMR) was approximately 49%, with the majority of the dose excreted in the first 24 h (approximately 41%). The comparatively low recovery in comparison to that obtained from LSC was due to matrix effects in bile and a contribution from metabolic defluorination. 3. High-performance liquid chromatography with radiometric profiling of urine and bile revealed a complex pattern of metabolites with the bulk of the dose excreted as a single peak. 4. Ultra-performance liquid chromatography-orthogonal acceleration time of flight mass spectrometry profiling also showed a complex pattern of metabolites, detecting approximately 21 metabolites of 3-fluoroaniline (3-FA) with six of these detected only in urine and four solely in bile. 5. (19)F-NMR revealed the presence of the parent compound and 15 metabolites in urine collected during the first 24 h after -dosing. The matrix effects of bile on (19)F-NMR spectroscopy made metabolite profiling impractical for this biofluid. The major metabolite of 3-FA was identified as 2-fluoro-4-acetamidophenol-sulfate. PMID:20443683

  15. Slow motions in microcrystalline proteins as observed by MAS-dependent 15N rotating-frame NMR relaxation

    NASA Astrophysics Data System (ADS)

    Krushelnitsky, Alexey; Zinkevich, Tatiana; Reif, Bernd; Saalwächter, Kay

    2014-11-01

    15N NMR relaxation rate R1ρ measurements reveal that a substantial fraction of residues in the microcrystalline chicken alpha-spectrin SH3 domain protein undergoes dynamics in the μs-ms timescale range. On the basis of a comparison of 2D site-resolved with 1D integrated 15N spectral intensities, we demonstrate that the significant fraction of broad signals in the 2D spectrum exhibits the most pronounced slow mobility. We show that 15N R1ρ's in proton-diluted protein samples are practically free from the coherent spin-spin contribution even at low MAS rates, and thus can be analysed quantitatively. Moderate MAS rates (10-30 kHz) can be more advantageous in comparison with the rates >50-60 kHz when slow dynamics are to be identified and quantified by means of R1ρ experiments.

  16. Perspectives for spintronics in 2D materials

    NASA Astrophysics Data System (ADS)

    Han, Wei

    2016-03-01

    The past decade has been especially creative for spintronics since the (re)discovery of various two dimensional (2D) materials. Due to the unusual physical characteristics, 2D materials have provided new platforms to probe the spin interaction with other degrees of freedom for electrons, as well as to be used for novel spintronics applications. This review briefly presents the most important recent and ongoing research for spintronics in 2D materials.

  17. Studies of organic paint binders by NMR spectroscopy

    NASA Astrophysics Data System (ADS)

    Spyros, A.; Anglos, D.

    2006-06-01

    Nuclear magnetic resonance spectroscopy is applied to the study of aged binding media used in paintings, namely linseed oil, egg tempera and an acrylic medium. High resolution 1D and 2D NMR experiments establish the state of hydrolysis and oxidation of the linseed and egg tempera binders after five years of aging, by determining several markers sensitive to the hydrolytic and oxidative processes of the binder lipid fraction. The composition of the acrylic binder co-polymer is determined by 2D NMR spectroscopy, while the identification of a surfactant, poly(ethylene glycol), found in greater amounts in aged acrylic medium, is reported. The non-destructive nature of the proposed analytical NMR methodology, and minimization of the amount of binder material needed through the use of sophisticated cryoprobes and hyphenated LC-NMR techniques, make NMR attractive for the arts analyst, in view of its rapid nature and experimental simplicity.

  18. Structure determination and sensory analysis of bitter-tasting 4-vinylcatechol oligomers and their identification in roasted coffee by means of LC-MS/MS.

    PubMed

    Frank, Oliver; Blumberg, Simone; Kunert, Christof; Zehentbauer, Gerhard; Hofmann, Thomas

    2007-03-01

    Aimed at elucidating intense bitter-tasting molecules in coffee, various bean ingredients were thermally treated in model experiments and evaluated for their potential to produce bitter compounds. As caffeic acid was found to generate intense bitterness reminiscent of the bitter taste of a strongly roasted espresso-type coffee, the reaction products formed were screened for bitter compounds by means of taste dilution analysis, and the most bitter tastants were isolated and purified. LC-MS/MS as well as 1-D/2-D NMR experiments enabled the identification of 10 bitter compounds with rather low recognition threshold concentrations ranging between 23 and 178 micromol/L. These bitter compounds are the previously unreported 1,3-bis(3',4'-dihydroxyphenyl) butane, trans-1,3-bis(3',4'-dihydroxyphenyl)-1-butene, and eight multiply hydroxylated phenylindanes, among which five derivatives are reported for the first time. In addition, the occurrence of each of these bitter compounds in a coffee brew was verified by means of LC-MS/MS (ESI-) operating in the multiple reaction monitoring (MRM) mode. The structures of these bitter compounds show strong evidence that they are generated by oligomerization of 4-vinylcatechol released from caffeic acid moieties upon roasting. PMID:17269788

  19. Annotated Bibliography of EDGE2D Use

    SciTech Connect

    J.D. Strachan and G. Corrigan

    2005-06-24

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

  20. Staring 2-D hadamard transform spectral imager

    DOEpatents

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

    2006-02-07

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

  1. Light field morphing using 2D features.

    PubMed

    Wang, Lifeng; Lin, Stephen; Lee, Seungyong; Guo, Baining; Shum, Heung-Yeung

    2005-01-01

    We present a 2D feature-based technique for morphing 3D objects represented by light fields. Existing light field morphing methods require the user to specify corresponding 3D feature elements to guide morph computation. Since slight errors in 3D specification can lead to significant morphing artifacts, we propose a scheme based on 2D feature elements that is less sensitive to imprecise marking of features. First, 2D features are specified by the user in a number of key views in the source and target light fields. Then the two light fields are warped view by view as guided by the corresponding 2D features. Finally, the two warped light fields are blended together to yield the desired light field morph. Two key issues in light field morphing are feature specification and warping of light field rays. For feature specification, we introduce a user interface for delineating 2D features in key views of a light field, which are automatically interpolated to other views. For ray warping, we describe a 2D technique that accounts for visibility changes and present a comparison to the ideal morphing of light fields. Light field morphing based on 2D features makes it simple to incorporate previous image morphing techniques such as nonuniform blending, as well as to morph between an image and a light field. PMID:15631126

  2. 2D materials for nanophotonic devices

    NASA Astrophysics Data System (ADS)

    Xu, Renjing; Yang, Jiong; Zhang, Shuang; Pei, Jiajie; Lu, Yuerui

    2015-12-01

    Two-dimensional (2D) materials have become very important building blocks for electronic, photonic, and phononic devices. The 2D material family has four key members, including the metallic graphene, transition metal dichalcogenide (TMD) layered semiconductors, semiconducting black phosphorous, and the insulating h-BN. Owing to the strong quantum confinements and defect-free surfaces, these atomically thin layers have offered us perfect platforms to investigate the interactions among photons, electrons and phonons. The unique interactions in these 2D materials are very important for both scientific research and application engineering. In this talk, I would like to briefly summarize and highlight the key findings, opportunities and challenges in this field. Next, I will introduce/highlight our recent achievements. We demonstrated atomically thin micro-lens and gratings using 2D MoS2, which is the thinnest optical component around the world. These devices are based on our discovery that the elastic light-matter interactions in highindex 2D materials is very strong. Also, I would like to introduce a new two-dimensional material phosphorene. Phosphorene has strongly anisotropic optical response, which creates 1D excitons in a 2D system. The strong confinement in phosphorene also enables the ultra-high trion (charged exciton) binding energies, which have been successfully measured in our experiments. Finally, I will briefly talk about the potential applications of 2D materials in energy harvesting.

  3. Inertial solvation in femtosecond 2D spectra

    NASA Astrophysics Data System (ADS)

    Hybl, John; Albrecht Ferro, Allison; Farrow, Darcie; Jonas, David

    2001-03-01

    We have used 2D Fourier transform spectroscopy to investigate polar solvation. 2D spectroscopy can reveal molecular lineshapes beneath ensemble averaged spectra and freeze molecular motions to give an undistorted picture of the microscopic dynamics of polar solvation. The transition from "inhomogeneous" to "homogeneous" 2D spectra is governed by both vibrational relaxation and solvent motion. Therefore, the time dependence of the 2D spectrum directly reflects the total response of the solvent-solute system. IR144, a cyanine dye with a dipole moment change upon electronic excitation, was used to probe inertial solvation in methanol and propylene carbonate. Since the static Stokes' shift of IR144 in each of these solvents is similar, differences in the 2D spectra result from solvation dynamics. Initial results indicate that the larger propylene carbonate responds more slowly than methanol, but appear to be inconsistent with rotational estimates of the inertial response. To disentangle intra-molecular vibrations from solvent motion, the 2D spectra of IR144 will be compared to the time-dependent 2D spectra of the structurally related nonpolar cyanine dye HDITCP.

  4. Internal Photoemission Spectroscopy of 2-D Materials

    NASA Astrophysics Data System (ADS)

    Nguyen, Nhan; Li, Mingda; Vishwanath, Suresh; Yan, Rusen; Xiao, Shudong; Xing, Huili; Cheng, Guangjun; Hight Walker, Angela; Zhang, Qin

    Recent research has shown the great benefits of using 2-D materials in the tunnel field-effect transistor (TFET), which is considered a promising candidate for the beyond-CMOS technology. The on-state current of TFET can be enhanced by engineering the band alignment of different 2D-2D or 2D-3D heterostructures. Here we present the internal photoemission spectroscopy (IPE) approach to determine the band alignments of various 2-D materials, in particular SnSe2 and WSe2, which have been proposed for new TFET designs. The metal-oxide-2-D semiconductor test structures are fabricated and characterized by IPE, where the band offsets from the 2-D semiconductor to the oxide conduction band minimum are determined by the threshold of the cube root of IPE yields as a function of photon energy. In particular, we find that SnSe2 has a larger electron affinity than most semiconductors and can be combined with other semiconductors to form near broken-gap heterojunctions with low barrier heights which can produce a higher on-state current. The details of data analysis of IPE and the results from Raman spectroscopy and spectroscopic ellipsometry measurements will also be presented and discussed.

  5. Attaining 2D Black Phosphorus and Investigations into Floating-Electrode Dielectric Barrier Discharge Treatment of Solutions

    NASA Astrophysics Data System (ADS)

    Smith, Joshua Benjamin

    -ray diffraction, transmission electron microscopy, and Raman spectroscopy have confirmed successful growth of 2D black phosphorus from red phosphorus thin films for potential uses in 2D semiconductor applications. Additionally, this work discusses some of the chemistry occurring in solution as a result of nonthermal plasma treatment from a floating-electrode dielectric barrier discharge (FE-DBD) configuration. Nonthermal plasma generation allows for the treatment of heat sensitive materials. This has opened up the field to numerous clinical applications of nonthermal plasma treatment including sterilization and wound healing along with potentials in dentistry, dermatology, and even food industries. FE-DBD plasma treatment of water was found to provide a wide-range antimicrobial solution that remained active following 2 years of aging. This plasma-treated water was found to generate a number of ROS/RNS and the formation of these components was studied and verified with UV/Vis and ESR spectroscopy. Enhanced effects were observed when cell culture medium was plasma treated, suggesting the formation of additional reactive species from the plasma treatment of a variety of biomolecules. It is essential to understand these effects for a number of reasons. The possibility to generate a wide range of antimicrobial solutions from air, water, and basic biomolecules could provide a solution for those bacteria that have developed antibiotic resistances. Simultaneously, information into the reaction mechanisms of this FE-DBD plasma treatment can be investigated. All of the applications mentioned above involve complex networks of basic biomolecules, from skin tissue to bacteria cell walls. This work analyzes the effects of plasma treatment on several biomolecule solutions and simultaneously takes aim at understanding some of the potential mechanisms of plasma treatment. Studies were carried out using NMR and GC/MS. This information was used to investigate the possible targeted areas for FE

  6. Brittle damage models in DYNA2D

    SciTech Connect

    Faux, D.R.

    1997-09-01

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

  7. Matrix models of 2d gravity

    SciTech Connect

    Ginsparg, P.

    1991-01-01

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

  8. Matrix models of 2d gravity

    SciTech Connect

    Ginsparg, P.

    1991-12-31

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

  9. 2D electronic materials for army applications

    NASA Astrophysics Data System (ADS)

    O'Regan, Terrance; Perconti, Philip

    2015-05-01

    The record electronic properties achieved in monolayer graphene and related 2D materials such as molybdenum disulfide and hexagonal boron nitride show promise for revolutionary high-speed and low-power electronic devices. Heterogeneous 2D-stacked materials may create enabling technology for future communication and computation applications to meet soldier requirements. For instance, transparent, flexible and even wearable systems may become feasible. With soldier and squad level electronic power demands increasing, the Army is committed to developing and harnessing graphene-like 2D materials for compact low size-weight-and-power-cost (SWAP-C) systems. This paper will review developments in 2D electronic materials at the Army Research Laboratory over the last five years and discuss directions for future army applications.

  10. 2-d Finite Element Code Postprocessor

    1996-07-15

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

  11. Chemical Approaches to 2D Materials.

    PubMed

    Samorì, Paolo; Palermo, Vincenzo; Feng, Xinliang

    2016-08-01

    Chemistry plays an ever-increasing role in the production, functionalization, processing and applications of graphene and other 2D materials. This special issue highlights a selection of enlightening chemical approaches to 2D materials, which nicely reflect the breadth of the field and convey the excitement of the individuals involved in it, who are trying to translate graphene and related materials from the laboratory into a real, high-impact technology. PMID:27478083

  12. Knight shift and spin relaxation in the single band 2D Hubbard model

    NASA Astrophysics Data System (ADS)

    Leblanc, James; Chen, Xi; Gull, Emanuel

    We study in detail the roles of spin and charge fluctuations in the single band 2D Hubbard model. Using dynamical mean field theory and cluster extensions such as the dynamical cluster approximation (DCA), we compute the full two particle susceptibilities in the spin and charge representations. By performing analytic continuations we obtain the temperature and doping dependence of the spin-lattice relaxation (T1- 1) and knight shift in the 2D Hubbard model relevant to NMR results on doped cuprates and connect these to RPA results in weak coupling limits.

  13. Extended 2D generalized dilaton gravity theories

    NASA Astrophysics Data System (ADS)

    de Mello, R. O.

    2008-09-01

    We show that an anomaly-free description of matter in (1+1) dimensions requires a deformation of the 2D relativity principle, which introduces a non-trivial centre in the 2D Poincaré algebra. Then we work out the reduced phase space of the anomaly-free 2D relativistic particle, in order to show that it lives in a noncommutative 2D Minkowski space. Moreover, we build a Gaussian wave packet to show that a Planck length is well defined in two dimensions. In order to provide a gravitational interpretation for this noncommutativity, we propose to extend the usual 2D generalized dilaton gravity models by a specific Maxwell component, which guages the extra symmetry associated with the centre of the 2D Poincaré algebra. In addition, we show that this extension is a high energy correction to the unextended dilaton theories that can affect the topology of spacetime. Further, we couple a test particle to the general extended dilaton models with the purpose of showing that they predict a noncommutativity in curved spacetime, which is locally described by a Moyal star product in the low energy limit. We also conjecture a probable generalization of this result, which provides strong evidence that the noncommutativity is described by a certain star product which is not of the Moyal type at high energies. Finally, we prove that the extended dilaton theories can be formulated as Poisson Sigma models based on a nonlinear deformation of the extended Poincaré algebra.

  14. MS Detectors

    SciTech Connect

    Koppenaal, David W.; Barinaga, Charles J.; Denton, M Bonner B.; Sperline, Roger P.; Hieftje, Gary M.; Schilling, G. D.; Andrade, Francisco J.; Barnes IV., James H.

    2005-11-01

    Good eyesight is often taken for granted, a situation that everyone appreciates once vision begins to fade with age. New eyeglasses or contact lenses are traditional ways to improve vision, but recent new technology, i.e. LASIK laser eye surgery, provides a new and exciting means for marked vision restoration and improvement. In mass spectrometry, detectors are the 'eyes' of the MS instrument. These 'eyes' have also been taken for granted. New detectors and new technologies are likewise needed to correct, improve, and extend ion detection and hence, our 'chemical vision'. The purpose of this report is to review and assess current MS detector technology and to provide a glimpse towards future detector technologies. It is hoped that the report will also serve to motivate interest, prompt ideas, and inspire new visions for ion detection research.

  15. The solubilisation of boar sperm membranes by different detergents - a microscopic, MALDI-TOF MS, 31P NMR and PAGE study on membrane lysis, extraction efficiency, lipid and protein composition

    PubMed Central

    2009-01-01

    Background Detergents are often used to isolate proteins, lipids as well as "detergent-resistant membrane domains" (DRMs) from cells. Different detergents affect different membrane structures according to their physico-chemical properties. However, the effects of different detergents on membrane lysis of boar spermatozoa and the lipid composition of DRMs prepared from the affected sperm membranes have not been investigated so far. Results Spermatozoa were treated with the selected detergents Pluronic F-127, sodium cholate, CHAPS, Tween 20, Triton X-100 and Brij 96V. Different patterns of membrane disintegration were observed by light and electron microscopy. In accordance with microscopic data, different amounts of lipids and proteins were released from the cells by the different detergents. The biochemical methods to assay the phosphorus and cholesterol contents as well as 31P NMR to determine the phospholipids were not influenced by the presence of detergents since comparable amounts of lipids were detected in the organic extracts from whole cell suspensions after exposure to each detergent. However, matrix-assisted laser desorption and ionization time-of-flight mass spectrometry applied to identify phospholipids was essentially disturbed by the presence of detergents which exerted particular suppression effects on signal intensities. After separation of the membrane fractions released by detergents on a sucrose gradient only Triton X-100 and sodium cholate produced sharp turbid DRM bands. Only membrane solubilisation by Triton X-100 leads to an enrichment of cholesterol, sphingomyelin, phosphatidylinositol and phosphatidylethanolamine in a visible DRM band accompanied by a selective accumulation of proteins. Conclusion The boar sperm membranes are solubilised to a different extent by the used detergents. Particularly, the very unique DRMs isolated after Triton X-100 exposure are interesting candidates for further studies regarding the architecture of sperm. PMID

  16. Isolation and Identification of a New Phenylpropanoid Derivative from the Fruits of Pimpinella Haussknechtii Rech. f. & Riedl and GC-MS Analysis of the Essential Oil

    PubMed Central

    Sajjadi, Seyed Ebrahim; Ghanadian, Mustafa; Ahmadi, Shahla; Shafiyan, Sorour

    2015-01-01

    The chemical composition of the essential oil of fruits of Pimpinella haussknechtii. was studied by GC-MS. After GC-MS analysis, one unknown component (56.7%) was observed, which was not characterized in the GC-MS library. The essential oil of P.haussknechtii was injected to HPLC using YMC-Pak-Sil column (250 × 20 mm) with gradient system of hexane (A), and hexane: ethyl acetate, 9:1 (B) to yield the interested compound as a new phenylpropanoid derivative. Its structure was elucidated as 4-(prop-2-enyl)-phenyl-3'-methylbutanoate based on 13C- and 1H-NMR as well as 2D-NMR, IR and different MS spectra. In the essential oil analysis, thirty-six components, comprising 94.9% of the total oil, were identified. 4-(2-propenyl)-phenyl 3'-methylbutyrate (56.7%), bicyclogermacrene (8.9%), germacrene D (7.6%), perilla aldehyde (3.5%) and β-caryophyllene (2.9%) were found to be the major constituents of the oil. The oil of the fruits of P. haussknechtii consisted of eight monoterpene hydrocarbons (1.7%), two oxygenated monoterpenes (3.9%), sixteen sesquiterpene hydrocarbons (26.8%), two oxygenated sesquiterpenes (2.1%) and five phenylpropanoids (58.7%). Three other nonterpenic compounds also comprised 1.7% of the oil. PMID:26664391

  17. Isolation and Identification of a New Phenylpropanoid Derivative from the Fruits of Pimpinella Haussknechtii Rech. f. & Riedl and GC-MS Analysis of the Essential Oil.

    PubMed

    Sajjadi, Seyed Ebrahim; Ghanadian, Mustafa; Ahmadi, Shahla; Shafiyan, Sorour

    2015-01-01

    The chemical composition of the essential oil of fruits of Pimpinella haussknechtii. was studied by GC-MS. After GC-MS analysis, one unknown component (56.7%) was observed, which was not characterized in the GC-MS library. The essential oil of P.haussknechtii was injected to HPLC using YMC-Pak-Sil column (250 × 20 mm) with gradient system of hexane (A), and hexane: ethyl acetate, 9:1 (B) to yield the interested compound as a new phenylpropanoid derivative. Its structure was elucidated as 4-(prop-2-enyl)-phenyl-3'-methylbutanoate based on (13)C- and (1)H-NMR as well as 2D-NMR, IR and different MS spectra. In the essential oil analysis, thirty-six components, comprising 94.9% of the total oil, were identified. 4-(2-propenyl)-phenyl 3'-methylbutyrate (56.7%), bicyclogermacrene (8.9%), germacrene D (7.6%), perilla aldehyde (3.5%) and β-caryophyllene (2.9%) were found to be the major constituents of the oil. The oil of the fruits of P. haussknechtii consisted of eight monoterpene hydrocarbons (1.7%), two oxygenated monoterpenes (3.9%), sixteen sesquiterpene hydrocarbons (26.8%), two oxygenated sesquiterpenes (2.1%) and five phenylpropanoids (58.7%). Three other nonterpenic compounds also comprised 1.7% of the oil. PMID:26664391

  18. Optical modulators with 2D layered materials

    NASA Astrophysics Data System (ADS)

    Sun, Zhipei; Martinez, Amos; Wang, Feng

    2016-04-01

    Light modulation is an essential operation in photonics and optoelectronics. With existing and emerging technologies increasingly demanding compact, efficient, fast and broadband optical modulators, high-performance light modulation solutions are becoming indispensable. The recent realization that 2D layered materials could modulate light with superior performance has prompted intense research and significant advances, paving the way for realistic applications. In this Review, we cover the state of the art of optical modulators based on 2D materials, including graphene, transition metal dichalcogenides and black phosphorus. We discuss recent advances employing hybrid structures, such as 2D heterostructures, plasmonic structures, and silicon and fibre integrated structures. We also take a look at the future perspectives and discuss the potential of yet relatively unexplored mechanisms, such as magneto-optic and acousto-optic modulation.

  19. Large Area Synthesis of 2D Materials

    NASA Astrophysics Data System (ADS)

    Vogel, Eric

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

  20. 2D microwave imaging reflectometer electronics

    SciTech Connect

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

    2014-11-15

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

  1. 2D microwave imaging reflectometer electronics

    NASA Astrophysics Data System (ADS)

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

    2014-11-01

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

  2. 2D microwave imaging reflectometer electronics.

    PubMed

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

    2014-11-01

    A 2D microwave imaging reflectometer system has been developed to visualize electron density fluctuations on the DIII-D tokamak. Simultaneously illuminated at four probe frequencies, large aperture optics image reflections from four density-dependent cutoff surfaces in the plasma over an extended region of the DIII-D plasma. Localized density fluctuations in the vicinity of the plasma cutoff surfaces modulate the plasma reflections, yielding a 2D image of electron density fluctuations. Details are presented of the receiver down conversion electronics that generate the in-phase (I) and quadrature (Q) reflectometer signals from which 2D density fluctuation data are obtained. Also presented are details on the control system and backplane used to manage the electronics as well as an introduction to the computer based control program. PMID:25430247

  3. 2D-Crystal-Based Functional Inks.

    PubMed

    Bonaccorso, Francesco; Bartolotta, Antonino; Coleman, Jonathan N; Backes, Claudia

    2016-08-01

    The possibility to produce and process graphene, related 2D crystals, and heterostructures in the liquid phase makes them promising materials for an ever-growing class of applications as composite materials, sensors, in flexible optoelectronics, and energy storage and conversion. In particular, the ability to formulate functional inks with on-demand rheological and morphological properties, i.e., lateral size and thickness of the dispersed 2D crystals, is a step forward toward the development of industrial-scale, reliable, inexpensive printing/coating processes, a boost for the full exploitation of such nanomaterials. Here, the exfoliation strategies of graphite and other layered crystals are reviewed, along with the advances in the sorting of lateral size and thickness of the exfoliated sheets together with the formulation of functional inks and the current development of printing/coating processes of interest for the realization of 2D-crystal-based devices. PMID:27273554

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

    ERIC Educational Resources Information Center

    Alty, Lisa T.

    2005-01-01

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

  5. Review of NMR characterization of pyrolysis oils

    DOE PAGESBeta

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

    2016-08-24

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

  6. The 2D lingual appliance system.

    PubMed

    Cacciafesta, Vittorio

    2013-09-01

    The two-dimensional (2D) lingual bracket system represents a valuable treatment option for adult patients seeking a completely invisible orthodontic appliance. The ease of direct or simplified indirect bonding of 2D lingual brackets in combination with low friction mechanics makes it possible to achieve a good functional and aesthetic occlusion, even in the presence of a severe malocclusion. The use of a self-ligating bracket significantly reduces chair-side time for the orthodontist, and the low-profile bracket design greatly improves patient comfort. PMID:24005953

  7. Inkjet printing of 2D layered materials.

    PubMed

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

    2014-11-10

    Inkjet printing of 2D layered materials, such as graphene and MoS2, has attracted great interests for emerging electronics. However, incompatible rheology, low concentration, severe aggregation and toxicity of solvents constitute critical challenges which hamper the manufacturing efficiency and product quality. Here, we introduce a simple and general technology concept (distillation-assisted solvent exchange) to efficiently overcome these challenges. By implementing the concept, we have demonstrated excellent jetting performance, ideal printing patterns and a variety of promising applications for inkjet printing of 2D layered materials. PMID:25169938

  8. Measurement of 2D birefringence distribution

    NASA Astrophysics Data System (ADS)

    Noguchi, Masato; Ishikawa, Tsuyoshi; Ohno, Masahiro; Tachihara, Satoru

    1992-10-01

    A new measuring method of 2-D birefringence distribution has been developed. It has not been an easy job to get a birefringence distribution in an optical element with conventional ellipsometry because of its lack of scanning means. Finding an analogy between the rotating analyzer method in ellipsometry and the phase-shifting method in recently developed digital interferometry, we have applied the phase-shifting algorithm to ellipsometry, and have developed a new method that makes the measurement of 2-D birefringence distribution easy and possible. The system contains few moving parts, assuring reliability, and measures a large area of a sample at one time, making the measuring time very short.

  9. Inferences on the nature of a Cr(V) or Cr(IV) species formed by reduction of dichromate by a bovine liver homogenate: NMR and mass-spectrometric studies.

    PubMed

    Gaggelli, Elena; D'Amelio, Nicola; Gaggelli, Nicola; Valensin, Gianni; Bovalini, Lucia; Paffetti, Alessandro; Trabalzini, Lorenza

    2003-01-01

    A low-molecular weight chromium-containing fraction of the material resulting from dichromate reduction by bovine liver homogenate was investigated by NMR and ES-MS. The ES-MS spectrum showed a readily detectable peak at m/z = 786.1. The same molecular weight reasonably agreed with the relatively low diffusion coefficient measured by NMR-DOSY experiments on the main species observed in the (1)H NMR spectrum. At least two downfield shifted and broad paramagnetic signals were apparent in the (1)H NMR spectrum. Temperature dependence of chemical shift was exploited in order to estimate the diamagnetic shift of the signals in the diamagnetic region of the spectrum. 2D TOCSY, NOESY, COSY and (1)H-(3)C HMQC spectra revealed the presence of aromatic protons (which were assigned as His residues), Gly and some other short chain amino-acids. Combinations of the molecular masses of such components together with acetate (which is present in the solution) and chromium atoms allowed a tentative proposal of a model for the compound. PMID:18365060

  10. NMR analysis of biodiesel

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  11. Highly resolved measurements of atmospheric turbulence with the new 2d-Atmospheric Laser Cantilever Anemometer

    NASA Astrophysics Data System (ADS)

    Jeromin, A.; Schaffarczyk, A. P.; Puczylowski, J.; Peinke, J.; Hölling, M.

    2014-12-01

    For the investigation of atmospheric turbulent flows on small scales a new anemometer was developed, the so-called 2d-Atmospheric Laser Cantilever Anemometer (2d-ALCA). It performs highly resolved measurements with a spatial resolution in millimeter range and temporal resolution in kHz range, thus detecting very small turbulent structures. The anemometer is a redesign of the successfully operating 2d-LCA for laboratory application. The new device was designed to withstand hostile operating environments (rain and saline, humid air). In February 2012, the 2d-ALCA was used for the first time in a test field. The device was mounted in about 53 m above ground level on a lattice tower near the German North Sea coast. Wind speed was measured by the 2d-ALCA at 10 kHz sampling rate and by cup anemometers at 1 Hz. The instantaneous wind speed ranged from 8 m/s to 19 m/s at an average turbulence level of about 7 %. Wind field characteristics were analyzed based on cup anemometer as well as 2d-ALCA. The combination of both devices allowed the study of atmospheric turbulence over several magnitudes in turbulent scales.

  12. Parallel stitching of 2D materials

    DOE PAGESBeta

    Ling, Xi; Wu, Lijun; Lin, Yuxuan; Ma, Qiong; Wang, Ziqiang; Song, Yi; Yu, Lili; Huang, Shengxi; Fang, Wenjing; Zhang, Xu; et al

    2016-01-27

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

  13. Parallel Stitching of 2D Materials.

    PubMed

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

    2016-03-01

    Diverse parallel stitched 2D heterostructures, including metal-semiconductor, semiconductor-semiconductor, and insulator-semiconductor, are synthesized directly through selective "sowing" of aromatic molecules as the seeds in the chemical vapor deposition (CVD) method. The methodology enables the large-scale fabrication of lateral heterostructures, which offers tremendous potential for its application in integrated circuits. PMID:26813882

  14. Baby universes in 2d quantum gravity

    NASA Astrophysics Data System (ADS)

    Ambjørn, Jan; Jain, Sanjay; Thorleifsson, Gudmar

    1993-06-01

    We investigate the fractal structure of 2d quantum gravity, both for pure gravity and for gravity coupled to multiple gaussian fields and for gravity coupled to Ising spins. The roughness of the surfaces is described in terms of baby universes and using numerical simulations we measure their distribution which is related to the string susceptibility exponent γstring.

  15. Propagator-resolved 2D exchange in porous media in the inhomogeneous magnetic field.

    PubMed

    Burcaw, Lauren M; Hunter, Mark W; Callaghan, Paul T

    2010-08-01

    We present a propagator-resolved 2D exchange spectroscopy technique for observing fluid motion in a porous medium. The susceptibility difference between the matrix and the fluid is exploited to produce an inhomogeneous internal magnetic field, causing the Larmor frequency to change as molecules migrate. We test our method using a randomly packed monodisperse 100 microm diameter glass bead matrix saturated with distilled water. Building upon previous 2D exchange spectroscopy work we add a displacement dimension which allows us to obtain 2D exchange spectra that are defined by both mixing time and spatial displacement rather than by mixing time alone. We also simulate our system using a Monte Carlo process in a random nonpenetrating monodisperse bead pack, finding good agreement with experiment. A simple analytic model is used to interpret the NMR data in terms of a characteristic length scale over which molecules must diffuse to sample the inhomogeneous field distribution. PMID:20554230

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

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

    2016-01-01

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

  18. Traceability of Italian garlic (Allium sativum L.) by means of HRMAS-NMR spectroscopy and multivariate data analysis.

    PubMed

    Ritota, Mena; Casciani, Lorena; Han, Bei-Zhong; Cozzolino, Sara; Leita, Liviana; Sequi, Paolo; Valentini, Massimiliano

    2012-11-15

    (1)H High Resolution Magic Angle Spinning-Nuclear Magnetic Resonance (HRMAS-NMR) spectroscopy was used to analyse garlic (Allium sativum L.) belonging to red and white varieties and collected in different Italian regions, in order to address the traceability issue. 1D and 2D NMR spectra, performed directly on untreated small pieces of garlic, so without any sample manipulation, allowed the assignment of several compounds: organic acids, sugars, fatty acids, amino acids and the nutritionally important fructo-oligosaccharides and allyl-organosulphur compounds. Application of Partial Least Squares projections to latent structures-Discrimination Analysis provided an excellent model for the discrimination of both the variety and, most important, the place origin, allowing the identification of the metabolites contributing to such classifications. The presence of organosulphurs, allicin and some allyl-organosulphurs found by HRMAS-NMR, was confirmed also by SPME-GC-MS; 11 molecules were identified, containing from one up to three sulphur atoms and with and without allyl moieties. PMID:22868146

  19. Standardization of solvent extracts from Onopordum acanthium fruits by GC-MS, HPLC-UV/DAD, HPLC-TQMS and 1H-NMR and evaluation of their inhibitory effects on the expression of IL-8 and E-selectin in immortalized endothelial cells (HUVECtert).

    PubMed

    Daci, Armond; Gold-Binder, Markus; Garzon, Davide; Patea, Alessio; Beretta, Giangiacomo

    2014-07-01

    In this work we have characterized and standardized the solvent extracts of the fruits of Onopordum acanthium, a plant widely distributed from Europe to Asia and used in different traditional medicines. Fruits were extracted with methanol (ME) and n-hexane (HE) and the extract compositions determined by GC-MS, HPLC-UV/DAD, HPLC-TQMS and 1H NMR spectroscopy. Anti-inflammatory activity (IL-8 and E-selectin, qPCR and ELISA) was investigated in HUVECtert cells stimulated with TNF-alpha and LPS. Arctiin and isochlorogenic acid were found in ME (87 +/- 2%, w/w, and 10.2 +/- 0.2%, w/w; 38.0 +/- 3.2 mg/gFRUITS and 3.5 +/- 0.4 mg/gFRUITS) and (ii) paraffins in the HE (195.6 +/- 5.6 mg/g). A dose dependent (from 15 to 40 microgME/mL corresponding to 20-75 microM arctiin) inhibition of E-selectin and of the induction of IL-8 was induced by LPS. The results of this study support the use of O. acanthium fruits in traditional medicine as an anti-inflammatory agent and for cancer prevention and treatment. PMID:25230500

  20. Theoretical NMR correlations based Structure Discussion

    PubMed Central

    2011-01-01

    The constitutional assignment of natural products by NMR spectroscopy is usually based on 2D NMR experiments like COSY, HSQC, and HMBC. The actual difficulty of the structure elucidation problem depends more on the type of the investigated molecule than on its size. The moment HMBC data is involved in the process or a large number of heteroatoms is present, a possibility of multiple solutions fitting the same data set exists. A structure elucidation software can be used to find such alternative constitutional assignments and help in the discussion in order to find the correct solution. But this is rarely done. This article describes the use of theoretical NMR correlation data in the structure elucidation process with WEBCOCON, not for the initial constitutional assignments, but to define how well a suggested molecule could have been described by NMR correlation data. The results of this analysis can be used to decide on further steps needed to assure the correctness of the structural assignment. As first step the analysis of the deviation of carbon chemical shifts is performed, comparing chemical shifts predicted for each possible solution with the experimental data. The application of this technique to three well known compounds is shown. Using NMR correlation data alone for the description of the constitutions is not always enough, even when including 13C chemical shift prediction. PMID:21797997

  1. Stable Isotope Labeled Tracers for Metabolic Pathway Elucidation by GC-MS and FT-MS

    PubMed Central

    Higashi, Richard M.; Fan, Teresa W-M.; Lorkiewicz, Pawel K.; Moseley, Hunter N.B.; Lane, Andrew N.

    2015-01-01

    Advances in analytical methodologies, principally nuclear magnetic resonance spectroscopy (NMR) and mass spectrometry (MS), over the last decade have made large-scale analysis of the human metabolome a reality. This is leading to the reawakening of the importance of metabolism in human diseases, particularly widespread metabolic diseases such as cancer, diabetes, and obesity. Emerging NMR and MS atom-tracking technologies and informatics is poised to revolutionize metabolomics-based research because they deliver the high information throughput (HIT) that is needed for deciphering systems biochemistry. In particular, Stable Isotope Resolved Metabolomics (SIRM) enables unambiguous tracking of individual atoms through compartmentalized metabolic networks, in a wide range of experimental systems, including human subjects. MS offers a wide range of initial capital outlay and operating costs, ranging from gas-chromatography (GC) MS affordable by many individual laboratories, to the HIT-supporting Fourier-transform (FT) class of MS that rivals NMR in cost and infrastructure support. This chapter will focus on sample preparation, instrument, and data processing procedures for these two extremes of MS instrumentation used in SIRM. PMID:25270929

  2. Static & Dynamic Response of 2D Solids

    1996-07-15

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

  3. Stochastic Inversion of 2D Magnetotelluric Data

    2010-07-01

    The algorithm is developed to invert 2D magnetotelluric (MT) data based on sharp boundary parametrization using a Bayesian framework. Within the algorithm, we consider the locations and the resistivity of regions formed by the interfaces are as unknowns. We use a parallel, adaptive finite-element algorithm to forward simulate frequency-domain MT responses of 2D conductivity structure. Those unknown parameters are spatially correlated and are described by a geostatistical model. The joint posterior probability distribution function ismore » explored by Markov Chain Monte Carlo (MCMC) sampling methods. The developed stochastic model is effective for estimating the interface locations and resistivity. Most importantly, it provides details uncertainty information on each unknown parameter. Hardware requirements: PC, Supercomputer, Multi-platform, Workstation; Software requirements C and Fortan; Operation Systems/version is Linux/Unix or Windows« less

  4. Stochastic Inversion of 2D Magnetotelluric Data

    SciTech Connect

    Chen, Jinsong

    2010-07-01

    The algorithm is developed to invert 2D magnetotelluric (MT) data based on sharp boundary parametrization using a Bayesian framework. Within the algorithm, we consider the locations and the resistivity of regions formed by the interfaces are as unknowns. We use a parallel, adaptive finite-element algorithm to forward simulate frequency-domain MT responses of 2D conductivity structure. Those unknown parameters are spatially correlated and are described by a geostatistical model. The joint posterior probability distribution function is explored by Markov Chain Monte Carlo (MCMC) sampling methods. The developed stochastic model is effective for estimating the interface locations and resistivity. Most importantly, it provides details uncertainty information on each unknown parameter. Hardware requirements: PC, Supercomputer, Multi-platform, Workstation; Software requirements C and Fortan; Operation Systems/version is Linux/Unix or Windows

  5. Explicit 2-D Hydrodynamic FEM Program

    1996-08-07

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

  6. Schottky diodes from 2D germanane

    NASA Astrophysics Data System (ADS)

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

    2016-07-01

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

  7. Layer Engineering of 2D Semiconductor Junctions.

    PubMed

    He, Yongmin; Sobhani, Ali; Lei, Sidong; Zhang, Zhuhua; Gong, Yongji; Jin, Zehua; Zhou, Wu; Yang, Yingchao; Zhang, Yuan; Wang, Xifan; Yakobson, Boris; Vajtai, Robert; Halas, Naomi J; Li, Bo; Xie, Erqing; Ajayan, Pulickel

    2016-07-01

    A new concept for junction fabrication by connecting multiple regions with varying layer thicknesses, based on the thickness dependence, is demonstrated. This type of junction is only possible in super-thin-layered 2D materials, and exhibits similar characteristics as p-n junctions. Rectification and photovoltaic effects are observed in chemically homogeneous MoSe2 junctions between domains of different thicknesses. PMID:27136275

  8. 2dF mechanical engineering

    NASA Astrophysics Data System (ADS)

    Smith, Greg; Lankshear, Allan

    1998-07-01

    2dF is a multi-object instrument mounted at prime focus at the AAT capable of spectroscopic analysis of 400 objects in a single 2 degree field. It also prepares a second 2 degree 400 object field while the first field is being observed. At its heart is a high precision robotic positioner that places individual fiber end magnetic buttons on one of two field plates. The button gripper is carried on orthogonal gantries powered by linear synchronous motors and contains a TV camera which precisely locates backlit buttons to allow placement in user defined locations to 10 (mu) accuracy. Fiducial points on both plates can also be observed by the camera to allow repeated checks on positioning accuracy. Field plates rotate to follow apparent sky rotation. The spectrographs both analyze light from the 200 observing fibers each and back- illuminate the 400 fibers being re-positioned during the observing run. The 2dF fiber position and spectrograph system is a large and complex instrument located at the prime focus of the Anglo Australian Telescope. The mechanical design has departed somewhat from the earlier concepts of Gray et al, but still reflects the audacity of those first ideas. The positioner is capable of positioning 400 fibers on a field plate while another 400 fibers on another plate are observing at the focus of the telescope and feeding the twin spectrographs. When first proposed it must have seemed like ingenuity unfettered by caution. Yet now it works, and works wonderfully well. 2dF is a system which functions as the result of the combined and coordinated efforts of the astronomers, the mechanical designers and tradespeople, the electronic designers, the programmers, the support staff at the telescope, and the manufacturing subcontractors. The mechanical design of the 2dF positioner and spectrographs was carried out by the mechanical engineering staff of the AAO and the majority of the manufacture was carried out in the AAO workshops.

  9. Compact 2-D graphical representation of DNA

    NASA Astrophysics Data System (ADS)

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

    2003-05-01

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

  10. 2D materials: Graphene and others

    NASA Astrophysics Data System (ADS)

    Bansal, Suneev Anil; Singh, Amrinder Pal; Kumar, Suresh

    2016-05-01

    Present report reviews the recent advancements in new atomically thick 2D materials. Materials covered in this review are Graphene, Silicene, Germanene, Boron Nitride (BN) and Transition metal chalcogenides (TMC). These materials show extraordinary mechanical, electronic and optical properties which make them suitable candidates for future applications. Apart from unique properties, tune-ability of highly desirable properties of these materials is also an important area to be emphasized on.

  11. TACO (2D AND 3D). Taco

    SciTech Connect

    Mason, W.E.

    1983-03-01

    A set of finite element codes for the solution of nonlinear, two-dimensional (TACO2D) and three-dimensional (TACO3D) heat transfer problems. Performs linear and nonlinear analyses of both transient and steady state heat transfer problems. Has the capability to handle time or temperature dependent material properties. Materials may be either isotropic or orthotropic. A variety of time and temperature dependent boundary conditions and loadings are available including temperature, flux, convection, radiation, and internal heat generation.

  12. Tomosynthesis imaging with 2D scanning trajectories

    NASA Astrophysics Data System (ADS)

    Khare, Kedar; Claus, Bernhard E. H.; Eberhard, Jeffrey W.

    2011-03-01

    Tomosynthesis imaging in chest radiography provides volumetric information with the potential for improved diagnostic value when compared to the standard AP or LAT projections. In this paper we explore the image quality benefits of 2D scanning trajectories when coupled with advanced image reconstruction approaches. It is intuitively clear that 2D trajectories provide projection data that is more complete in terms of Radon space filling, when compared with conventional tomosynthesis using a linearly scanned source. Incorporating this additional information for obtaining improved image quality is, however, not a straightforward problem. The typical tomosynthesis reconstruction algorithms are based on direct inversion methods e.g. Filtered Backprojection (FBP) or iterative algorithms that are variants of the Algebraic Reconstruction Technique (ART). The FBP approach is fast and provides high frequency details in the image but at the same time introduces streaking artifacts degrading the image quality. The iterative methods can reduce the image artifacts by using image priors but suffer from a slow convergence rate, thereby producing images lacking high frequency details. In this paper we propose using a fast converging optimal gradient iterative scheme that has advantages of both the FBP and iterative methods in that it produces images with high frequency details while reducing the image artifacts. We show that using favorable 2D scanning trajectories along with the proposed reconstruction method has the advantage of providing improved depth information for structures such as the spine and potentially producing images with more isotropic resolution.

  13. MAGNUM-2D computer code: user's guide

    SciTech Connect

    England, R.L.; Kline, N.W.; Ekblad, K.J.; Baca, R.G.

    1985-01-01

    Information relevant to the general use of the MAGNUM-2D computer code is presented. This computer code was developed for the purpose of modeling (i.e., simulating) the thermal and hydraulic conditions in the vicinity of a waste package emplaced in a deep geologic repository. The MAGNUM-2D computer computes (1) the temperature field surrounding the waste package as a function of the heat generation rate of the nuclear waste and thermal properties of the basalt and (2) the hydraulic head distribution and associated groundwater flow fields as a function of the temperature gradients and hydraulic properties of the basalt. MAGNUM-2D is a two-dimensional numerical model for transient or steady-state analysis of coupled heat transfer and groundwater flow in a fractured porous medium. The governing equations consist of a set of coupled, quasi-linear partial differential equations that are solved using a Galerkin finite-element technique. A Newton-Raphson algorithm is embedded in the Galerkin functional to formulate the problem in terms of the incremental changes in the dependent variables. Both triangular and quadrilateral finite elements are used to represent the continuum portions of the spatial domain. Line elements may be used to represent discrete conduits. 18 refs., 4 figs., 1 tab.

  14. Engineering light outcoupling in 2D materials.

    PubMed

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

    2015-02-11

    When light is incident on 2D transition metal dichalcogenides (TMDCs), it engages in multiple reflections within underlying substrates, producing interferences that lead to enhancement or attenuation of the incoming and outgoing strength of light. Here, we report a simple method to engineer the light outcoupling in semiconducting TMDCs by modulating their dielectric surroundings. We show that by modulating the thicknesses of underlying substrates and capping layers, the interference caused by substrate can significantly enhance the light absorption and emission of WSe2, resulting in a ∼11 times increase in Raman signal and a ∼30 times increase in the photoluminescence (PL) intensity of WSe2. On the basis of the interference model, we also propose a strategy to control the photonic and optoelectronic properties of thin-layer WSe2. This work demonstrates the utilization of outcoupling engineering in 2D materials and offers a new route toward the realization of novel optoelectronic devices, such as 2D LEDs and solar cells. PMID:25602462

  15. Hyperpolarized NMR of plant and cancer cell extracts at natural abundance.

    PubMed

    Dumez, Jean-Nicolas; Milani, Jonas; Vuichoud, Basile; Bornet, Aurélien; Lalande-Martin, Julie; Tea, Illa; Yon, Maxime; Maucourt, Mickaël; Deborde, Catherine; Moing, Annick; Frydman, Lucio; Bodenhausen, Geoffrey; Jannin, Sami; Giraudeau, Patrick

    2015-09-01

    Natural abundance (13)C NMR spectra of biological extracts are recorded in a single scan provided that the samples are hyperpolarized by dissolution dynamic nuclear polarization combined with cross polarization. Heteronuclear 2D correlation spectra of hyperpolarized breast cancer cell extracts can also be obtained in a single scan. Hyperpolarized NMR of extracts opens many perspectives for metabolomics. PMID:26215673

  16. 2D superconductivity by ionic gating

    NASA Astrophysics Data System (ADS)

    Iwasa, Yoshi

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

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

    NASA Astrophysics Data System (ADS)

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

    1997-11-01

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

  18. Pulse methods in 1D and 2D liquid-phase NMR

    SciTech Connect

    Brey, W.S.

    1988-01-01

    State-of-the-art nuclear magnetic resonance spectrometers are capable of performing an array of multiple-pulse one-dimensional and two-dimensional experiments. These experiments can provide detailed information about the structure, dynamics, and reactions of molecules. However, their successful application to chemical problems requires that the chemist have some knowledge of the various experiments and the information they can provide. This book, written by authorities in the field, provides such information for both the specialist and the nonspecialist.

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

    NASA Astrophysics Data System (ADS)

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

    2005-02-01

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

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

    ERIC Educational Resources Information Center

    Caes, Benjamin; Jensen, Dell, Jr.

    2008-01-01

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

  1. DFT Calculations and ROESY NMR Data for the Diastereochemical Characterization of Cytotoxic Tetraterpenoids from the Oleoresin of Abies balsamea.

    PubMed

    Lavoie, Serge; Gauthier, Charles; Mshvildadze, Vakhtang; Legault, Jean; Roger, Benoit; Pichette, André

    2015-12-24

    Eight non-carotenoid tetraterpenoids, abibalsamins C-J (3-10), were isolated from the oleoresin of Abies balsamea. Their chemical structures were determined based on analysis of 1D/2D NMR and MS data. The assignment of their relative configurations was accomplished using homonuclear coupling constants in tandem with ROESY data. However, the presence of two stereogenic centers on a flexible side chain complicated the characterization. In silico models and ROESY data were analyzed in order to assign relative configurations of the isolated tetraterpenoids. Abibalsamins B and H-J showed moderate cytotoxicity against human A549 lung carcinoma cells, with IC50 values ranging between 6.7 and 10 μM. PMID:26592897

  2. GBL-2D Version 1.0: a 2D geometry boolean library.

    SciTech Connect

    McBride, Cory L. (Elemental Technologies, American Fort, UT); Schmidt, Rodney Cannon; Yarberry, Victor R.; Meyers, Ray J.

    2006-11-01

    This report describes version 1.0 of GBL-2D, a geometric Boolean library for 2D objects. The library is written in C++ and consists of a set of classes and routines. The classes primarily represent geometric data and relationships. Classes are provided for 2D points, lines, arcs, edge uses, loops, surfaces and mask sets. The routines contain algorithms for geometric Boolean operations and utility functions. Routines are provided that incorporate the Boolean operations: Union(OR), XOR, Intersection and Difference. A variety of additional analytical geometry routines and routines for importing and exporting the data in various file formats are also provided. The GBL-2D library was originally developed as a geometric modeling engine for use with a separate software tool, called SummitView [1], that manipulates the 2D mask sets created by designers of Micro-Electro-Mechanical Systems (MEMS). However, many other practical applications for this type of software can be envisioned because the need to perform 2D Boolean operations can arise in many contexts.

  3. 2D Seismic Reflection Data across Central Illinois

    SciTech Connect

    Smith, Valerie; Leetaru, Hannes

    2014-09-30

    In a continuing collaboration with the Midwest Geologic Sequestration Consortium (MGSC) on the Evaluation of the Carbon Sequestration Potential of the Cambro-Ordovician Strata of the Illinois and Michigan Basins project, Schlumberger Carbon Services and WesternGeco acquired two-dimensional (2D) seismic data in the Illinois Basin. This work included the design, acquisition and processing of approximately 125 miles of (2D) seismic reflection surveys running west to east in the central Illinois Basin. Schlumberger Carbon Services and WesternGeco oversaw the management of the field operations (including a pre-shoot planning, mobilization, acquisition and de-mobilization of the field personnel and equipment), procurement of the necessary permits to conduct the survey, post-shoot closure, processing of the raw data, and provided expert consultation as needed in the interpretation of the delivered product. Three 2D seismic lines were acquired across central Illinois during November and December 2010 and January 2011. Traversing the Illinois Basin, this 2D seismic survey was designed to image the stratigraphy of the Cambro-Ordovician sections and also to discern the basement topography. Prior to this survey, there were no regionally extensive 2D seismic data spanning this section of the Illinois Basin. Between the NW side of Morgan County and northwestern border of Douglas County, these seismic lines ran through very rural portions of the state. Starting in Morgan County, Line 101 was the longest at 93 miles in length and ended NE of Decatur, Illinois. Line 501 ran W-E from the Illinois Basin – Decatur Project (IBDP) site to northwestern Douglas County and was 25 miles in length. Line 601 was the shortest and ran N-S past the IBDP site and connected lines 101 and 501. All three lines are correlated to well logs at the IBDP site. Originally processed in 2011, the 2D seismic profiles exhibited a degradation of signal quality below ~400 millisecond (ms) which made

  4. Interparticle Attraction in 2D Complex Plasmas

    NASA Astrophysics Data System (ADS)

    Kompaneets, Roman; Morfill, Gregor E.; Ivlev, Alexei V.

    2016-03-01

    Complex (dusty) plasmas allow experimental studies of various physical processes occurring in classical liquids and solids by directly observing individual microparticles. A major problem is that the interaction between microparticles is generally not molecularlike. In this Letter, we propose how to achieve a molecularlike interaction potential in laboratory 2D complex plasmas. We argue that this principal aim can be achieved by using relatively small microparticles and properly adjusting discharge parameters. If experimentally confirmed, this will make it possible to employ complex plasmas as a model system with an interaction potential resembling that of conventional liquids.

  5. Periodically sheared 2D Yukawa systems

    SciTech Connect

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

    2015-10-15

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

  6. ENERGY LANDSCAPE OF 2D FLUID FORMS

    SciTech Connect

    Y. JIANG; ET AL

    2000-04-01

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

  7. A scalable 2-D parallel sparse solver

    SciTech Connect

    Kothari, S.C.; Mitra, S.

    1995-12-01

    Scalability beyond a small number of processors, typically 32 or less, is known to be a problem for existing parallel general sparse (PGS) direct solvers. This paper presents a parallel general sparse PGS direct solver for general sparse linear systems on distributed memory machines. The algorithm is based on the well-known sequential sparse algorithm Y12M. To achieve efficient parallelization, a 2-D scattered decomposition of the sparse matrix is used. The proposed algorithm is more scalable than existing parallel sparse direct solvers. Its scalability is evaluated on a 256 processor nCUBE2s machine using Boeing/Harwell benchmark matrices.

  8. 2D stepping drive for hyperspectral systems

    NASA Astrophysics Data System (ADS)

    Endrödy, Csaba; Mehner, Hannes; Grewe, Adrian; Sinzinger, Stefan; Hoffmann, Martin

    2015-07-01

    We present the design, fabrication and characterization of a compact 2D stepping microdrive for pinhole array positioning. The miniaturized solution enables a highly integrated compact hyperspectral imaging system. Based on the geometry of the pinhole array, an inch-worm drive with electrostatic actuators was designed resulting in a compact (1 cm2) positioning system featuring a step size of about 15 µm in a 170 µm displacement range. The high payload (20 mg) as required for the pinhole array and the compact system design exceed the known electrostatic inch-worm-based microdrives.

  9. The application of 2-D dual nanoscale liquid chromatography and triple quadrupole-linear ion trap system for the identification of proteins.

    PubMed

    Tschäppät, Viviane; Varesio, Emmanuel; Signor, Luca; Hopfgartner, Gérard

    2005-09-01

    2-D nanoscale LC combined with a triple quadrupole-linear ion trap mass spectrometer was applied to the analysis of a complex peptide mixture. A 2-D dual nanoscale LC-MS/MS system was compared to a conventional one. Peptides were separated with a strong cation exchange (SCX) microcolumn in the first dimension and two C18 nanocolumns were used as second dimension. MS experiments were performed using information-dependent data acquisition, where two precursor ions were selected from an enhanced MS (EMS) or an enhanced multicharged ion (EMC) as survey scan. The major benefit of EMC instead of EMS was a two-fold reduction of the data file and a 15% increase of characterized proteins. The advantage of the 2-D dual nanoscale LC-MS/MS system versus the conventional 2-D nanoscale LC-MS/MS system was reflected in the significant increase of peptides which were successfully identified within the same time frame. The first factor contributing to this increase was that the mass spectrometer was collecting twice the number of relevant MS/MS data. The second factor is the use of twice the number of SCX salt fractions in the first dimension, allowing a better sample fractionation, thereby reducing the number of peptides transferred to the second chromatographic dimension per salt fraction. PMID:16224964

  10. Combining high-throughput MALDI-TOF mass spectrometry and isoelectric focusing gel electrophoresis for virtual 2D gel-based proteomics.

    PubMed

    Lohnes, Karen; Quebbemann, Neil R; Liu, Kate; Kobzeff, Fred; Loo, Joseph A; Ogorzalek Loo, Rachel R

    2016-07-15

    The virtual two-dimensional gel electrophoresis/mass spectrometry (virtual 2D gel/MS) technology combines the premier, high-resolution capabilities of 2D gel electrophoresis with the sensitivity and high mass accuracy of mass spectrometry (MS). Intact proteins separated by isoelectric focusing (IEF) gel electrophoresis are imaged from immobilized pH gradient (IPG) polyacrylamide gels (the first dimension of classic 2D-PAGE) by matrix-assisted laser desorption/ionization (MALDI) MS. Obtaining accurate intact masses from sub-picomole-level proteins embedded in 2D-PAGE gels or in IPG strips is desirable to elucidate how the protein of one spot identified as protein 'A' on a 2D gel differs from the protein of another spot identified as the same protein, whenever tryptic peptide maps fail to resolve the issue. This task, however, has been extremely challenging. Virtual 2D gel/MS provides access to these intact masses. Modifications to our matrix deposition procedure improve the reliability with which IPG gels can be prepared; the new procedure is described. Development of this MALDI MS imaging (MSI) method for high-throughput MS with integrated 'top-down' MS to elucidate protein isoforms from complex biological samples is described and it is demonstrated that a 4-cm IPG gel segment can now be imaged in approximately 5min. Gel-wide chemical and enzymatic methods with further interrogation by MALDI MS/MS provide identifications, sequence-related information, and post-translational/transcriptional modification information. The MSI-based virtual 2D gel/MS platform may potentially link the benefits of 'top-down' and 'bottom-up' proteomics. PMID:26826592

  11. WFR-2D: an analytical model for PWAS-generated 2D ultrasonic guided wave propagation

    NASA Astrophysics Data System (ADS)

    Shen, Yanfeng; Giurgiutiu, Victor

    2014-03-01

    This paper presents WaveFormRevealer 2-D (WFR-2D), an analytical predictive tool for the simulation of 2-D ultrasonic guided wave propagation and interaction with damage. The design of structural health monitoring (SHM) systems and self-aware smart structures requires the exploration of a wide range of parameters to achieve best detection and quantification of certain types of damage. Such need for parameter exploration on sensor dimension, location, guided wave characteristics (mode type, frequency, wavelength, etc.) can be best satisfied with analytical models which are fast and efficient. The analytical model was constructed based on the exact 2-D Lamb wave solution using Bessel and Hankel functions. Damage effects were inserted in the model by considering the damage as a secondary wave source with complex-valued directivity scattering coefficients containing both amplitude and phase information from wave-damage interaction. The analytical procedure was coded with MATLAB, and a predictive simulation tool called WaveFormRevealer 2-D was developed. The wave-damage interaction coefficients (WDICs) were extracted from harmonic analysis of local finite element model (FEM) with artificial non-reflective boundaries (NRB). The WFR-2D analytical simulation results were compared and verified with full scale multiphysics finite element models and experiments with scanning laser vibrometer. First, Lamb wave propagation in a pristine aluminum plate was simulated with WFR-2D, compared with finite element results, and verified by experiments. Then, an inhomogeneity was machined into the plate to represent damage. Analytical modeling was carried out, and verified by finite element simulation and experiments. This paper finishes with conclusions and suggestions for future work.

  12. Microwave Assisted 2D Materials Exfoliation

    NASA Astrophysics Data System (ADS)

    Wang, Yanbin

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

  13. Photocurrent spectroscopy of 2D materials

    NASA Astrophysics Data System (ADS)

    Cobden, David

    Confocal photocurrent measurements provide a powerful means of studying many aspects of the optoelectronic and electrical properties of a 2D device or material. At a diffraction-limited point they can provide a detailed absorption spectrum, and they can probe local symmetry, ultrafast relaxation rates and processes, electron-electron interaction strengths, and transport coefficients. We illustrate this with several examples, once being the photo-Nernst effect. In gapless 2D materials, such as graphene, in a perpendicular magnetic field a photocurrent antisymmetric in the field is generated near to the free edges, with opposite sign at opposite edges. Its origin is the transverse thermoelectric current associated with the laser-induced electron temperature gradient. This effect provides an unambiguous demonstration of the Shockley-Ramo nature of long-range photocurrent generation in gapless materials. It also provides a means of investigating quasiparticle properties. For example, in the case of graphene on hBN, it can be used to probe the Lifshitz transition that occurs due to the minibands formed by the Moire superlattice. We also observe and discuss photocurrent generated in other semimetallic (WTe2) and semiconducting (WSe2) monolayers. Work supported by DoE BES and NSF EFRI grants.

  14. Multienzyme Inkjet Printed 2D Arrays.

    PubMed

    Gdor, Efrat; Shemesh, Shay; Magdassi, Shlomo; Mandler, Daniel

    2015-08-19

    The use of printing to produce 2D arrays is well established, and should be relatively facile to adapt for the purpose of printing biomaterials; however, very few studies have been published using enzyme solutions as inks. Among the printing technologies, inkjet printing is highly suitable for printing biomaterials and specifically enzymes, as it offers many advantages. Formulation of the inkjet inks is relatively simple and can be adjusted to a variety of biomaterials, while providing nonharmful environment to the enzymes. Here we demonstrate the applicability of inkjet printing for patterning multiple enzymes in a predefined array in a very straightforward, noncontact method. Specifically, various arrays of the enzymes glucose oxidase (GOx), invertase (INV) and horseradish peroxidase (HP) were printed on aminated glass surfaces, followed by immobilization using glutardialdehyde after printing. Scanning electrochemical microscopy (SECM) was used for imaging the printed patterns and to ascertain the enzyme activity. The successful formation of 2D arrays consisting of enzymes was explored as a means of developing the first surface confined enzyme based logic gates. Principally, XOR and AND gates, each consisting of two enzymes as the Boolean operators, were assembled, and their operation was studied by SECM. PMID:26214072

  15. Can NMR solve some significant challenges in metabolomics?

    NASA Astrophysics Data System (ADS)

    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.

  16. Qualitative determination of β-acids and their transformation products in beer and hop using HR/AM-LC-MS/MS.

    PubMed

    Dušek, Martin; Olšovská, Jana; Krofta, Karel; Jurková, Marie; Mikyška, Alexandr

    2014-08-01

    Hops represent an important source of β-acids with antimicrobial and sensory properties. Transformation products of β-acids formed during their oxidation, mainly hulupones, have been shown to have an interesting kind of bitterness. Their structures were recently elucidated using LC-TOFMS and 1D/2D NMR in solution after thermal treatment of the hop β-acids. This study demonstrates the advantages of MS detection with high resolution and accurate mass measurements. The structure of transformation products in an experimental solution of oxidized β-acids was elucidated using a newly developed method by hybrid quadrupole-Orbitrap MS. In addition to already known structures, two new ones were identified and named epoxycohulupone and epoxyhulupone. The method was verified on real samples; the profiles of these products in Sládek hops harvested in 2008 and 2012 and in corresponding beers were compared. For this purpose, a new QuEChERS assay was used for the preparation of beer samples. PMID:25099125

  17. 2-D or not 2-D, that is the question: A Northern California test

    SciTech Connect

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

    2005-06-06

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

  18. Lectures on pulsed NMR

    SciTech Connect

    Pines, A.

    1988-08-01

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

  19. Lectures on pulsed NMR

    SciTech Connect

    Pines, A.

    1986-09-01

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

  20. NMR logging apparatus

    DOEpatents

    Walsh, David O; Turner, Peter

    2014-05-27

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

  1. Silver and Gold NMR

    PubMed Central

    Zangger, Klaus

    1999-01-01

    Silver and gold, together with copper, form the transition metal group IB elements in the periodic table and possess very different nuclear magnetic resonance (NMR) spectroscopic properties. While there is only one gold isotope (197Au), which has a spin of 3/2 and therefore a quadrupole moment, silver occurs in two isotopic forms (109Ag and 109Au), both of which have a spin 1/2 and similar NMR spectroscopic properties. The unfavorable properties of gold have prevented its NMR spectroscopic investigation thus far. On the other hand, there are several reports of silver NMR. However, the low sensitivity of silver, combined with its long relaxation times have rendered the direct detection of silver possible only with concentrations greater than a few tenth molar. Reviewed here are the general limitations of silver NMR and some techniques to partially overcome these limitations, as well as a summary of currently available chemical shift and scalar coupling data on 109Ag. PMID:18475898

  2. Numerical Evaluation of 2D Ground States

    NASA Astrophysics Data System (ADS)

    Kolkovska, Natalia

    2016-02-01

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

  3. Canard configured aircraft with 2-D nozzle

    NASA Technical Reports Server (NTRS)

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

    1978-01-01

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

  4. 2D Electrostatic Actuation of Microshutter Arrays

    NASA Technical Reports Server (NTRS)

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

    2015-01-01

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

  5. 2D Electrostatic Actuation of Microshutter Arrays

    NASA Technical Reports Server (NTRS)

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

    2015-01-01

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

  6. Graphene suspensions for 2D printing

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

  7. Metrology for graphene and 2D materials

    NASA Astrophysics Data System (ADS)

    Pollard, Andrew J.

    2016-09-01

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

  8. The mouse ruby-eye 2(d) (ru2(d) /Hps5(ru2-d) ) allele inhibits eumelanin but not pheomelanin synthesis.

    PubMed

    Hirobe, Tomohisa; Ito, Shosuke; Wakamatsu, Kazumasa

    2013-09-01

    The novel mutation named ru2(d) /Hps5(ru2-d) , characterized by light-colored coats and ruby-eyes, prohibits differentiation of melanocytes by inhibiting tyrosinase (Tyr) activity, expression of Tyr, Tyr-related protein 1 (Tyrp1), Tyrp2, and Kit. However, it is not known whether the ru2(d) allele affects pheomelanin synthesis in recessive yellow (e/Mc1r(e) ) or in pheomelanic stage in agouti (A) mice. In this study, effects of the ru2(d) allele on pheomelanin synthesis were investigated by chemical analysis of melanin present in dorsal hairs of 5-week-old mice from F2 generation between C57BL/10JHir (B10)-co-isogenic ruby-eye 2(d) and B10-congenic recessive yellow or agouti. Eumelanin content was decreased in ruby-eye 2(d) and ruby-eye 2(d) agouti mice, whereas pheomelanin content in ruby-eye 2(d) recessive yellow and ruby-eye 2(d) agouti mice did not differ from the corresponding Ru2(d) /- mice, suggesting that the ru2(d) allele inhibits eumelanin but not pheomelanin synthesis. PMID:23672590

  9. Correlating nuclear frequencies by two-dimensional ELDOR-detected NMR spectroscopy

    NASA Astrophysics Data System (ADS)

    Kaminker, Ilia; Wilson, Tiffany D.; Savelieff, Masha G.; Hovav, Yonatan; Zimmermann, Herbert; Lu, Yi; Goldfarb, Daniella

    2014-03-01

    ELDOR (Electron Double Resonance)-detected NMR (EDNMR) is a pulse EPR experiment that is used to measure the transition frequencies of nuclear spins coupled to electron spins. These frequencies are further used to determine hyperfine and quadrupolar couplings, which are signatures of the electronic and spatial structures of paramagnetic centers. In recent years, EDNMR has been shown to be particularly useful at high fields/high frequencies, such as W-band (∼95 GHz, ∼3.5 T), for low γ quadrupolar nuclei. Although at high fields the nuclear Larmor frequencies are usually well resolved, the limited resolution of EDNMR still remains a major concern. In this work we introduce a two dimensional, triple resonance, correlation experiment based on the EDNMR pulse sequence, which we term 2D-EDNMR. This experiment allows circumventing the resolution limitation by spreading the signals in two dimensions and the observed correlations help in the assignment of the signals. First we demonstrate the utility of the 2D-EDNMR experiment on a nitroxide spin label, where we observe correlations between 14N nuclear frequencies. Negative cross-peaks appear between lines belonging to different MS electron spin manifolds. We resolved two independent correlation patterns for nuclear frequencies arising from the EPR transitions corresponding to the 14N mI = 0 and mI = -1 nuclear spin states, which severely overlap in the one dimensional EDNMR spectrum. The observed correlations could be accounted for by considering changes in the populations of energy levels that S = 1/2, I = 1 spin systems undergo during the pulse sequence. In addition to these negative cross-peaks, positive cross-peaks appear as well. We present a theoretical model based on the Liouville equation and use it to calculate the time evolution of populations of the various energy levels during the 2D-EDNMR experiment and generated simulated 2D-EDMR spectra. These calculations show that the positive cross-peaks appear due

  10. Correlating nuclear frequencies by two-dimensional ELDOR-detected NMR spectroscopy.

    PubMed

    Kaminker, Ilia; Wilson, Tiffany D; Savelieff, Masha G; Hovav, Yonatan; Zimmermann, Herbert; Lu, Yi; Goldfarb, Daniella

    2014-03-01

    ELDOR (Electron Double Resonance)-detected NMR (EDNMR) is a pulse EPR experiment that is used to measure the transition frequencies of nuclear spins coupled to electron spins. These frequencies are further used to determine hyperfine and quadrupolar couplings, which are signatures of the electronic and spatial structures of paramagnetic centers. In recent years, EDNMR has been shown to be particularly useful at high fields/high frequencies, such as W-band (∼95 GHz, ∼3.5 T), for low γ quadrupolar nuclei. Although at high fields the nuclear Larmor frequencies are usually well resolved, the limited resolution of EDNMR still remains a major concern. In this work we introduce a two dimensional, triple resonance, correlation experiment based on the EDNMR pulse sequence, which we term 2D-EDNMR. This experiment allows circumventing the resolution limitation by spreading the signals in two dimensions and the observed correlations help in the assignment of the signals. First we demonstrate the utility of the 2D-EDNMR experiment on a nitroxide spin label, where we observe correlations between (14)N nuclear frequencies. Negative cross-peaks appear between lines belonging to different MS electron spin manifolds. We resolved two independent correlation patterns for nuclear frequencies arising from the EPR transitions corresponding to the (14)N mI=0 and mI=-1 nuclear spin states, which severely overlap in the one dimensional EDNMR spectrum. The observed correlations could be accounted for by considering changes in the populations of energy levels that S=1/2, I=1 spin systems undergo during the pulse sequence. In addition to these negative cross-peaks, positive cross-peaks appear as well. We present a theoretical model based on the Liouville equation and use it to calculate the time evolution of populations of the various energy levels during the 2D-EDNMR experiment and generated simulated 2D-EDMR spectra. These calculations show that the positive cross-peaks appear due to

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

    PubMed

    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. PMID:26081575

  12. ADAPT-NMR 3.0: utilization of BEST-type triple-resonance NMR experiments to accelerate the process of data collection and assignment

    PubMed Central

    Dashti, Hesam; Tonelli, Marco

    2015-01-01

    ADAPT-NMR (Assignment-directed Data collection Algorithm utilizing a Probabilistic Toolkit in NMR) is a software package whose Bayesian core uses on-the-fly chemical shift assignments to guide data acquisition by non-uniform sampling from a panel of through-bond NMR experiments. The new version of ADAPT-NMR (ADAPT-NMR v3.0) has the option of utilizing 2D tilted-plane versions of 3D fast spectral acquisition with BEST-type pulse sequences, while also retaining the capability of acquiring and processing data from tilted-plane versions of conventional sensitivity-enhanced experiments. The use of BEST experiments significantly reduces data collection times and leads to enhanced performance by ADAPT-NMR. PMID:26021595

  13. ADAPT-NMR 3.0: utilization of BEST-type triple-resonance NMR experiments to accelerate the process of data collection and assignment.

    PubMed

    Dashti, Hesam; Tonelli, Marco; Markley, John L

    2015-07-01

    ADAPT-NMR (Assignment-directed Data collection Algorithm utilizing a Probabilistic Toolkit in NMR) is a software package whose Bayesian core uses on-the-fly chemical shift assignments to guide data acquisition by non-uniform sampling from a panel of through-bond NMR experiments. The new version of ADAPT-NMR (ADAPT-NMR v3.0) has the option of utilizing 2D tilted-plane versions of 3D fast spectral acquisition with BEST-type pulse sequences, while also retaining the capability of acquiring and processing data from tilted-plane versions of conventional sensitivity-enhanced experiments. The use of BEST experiments significantly reduces data collection times and leads to enhanced performance by ADAPT-NMR. PMID:26021595

  14. Decorating the Edges of a 2D Polymer with a Fluorescence Label.

    PubMed

    Zhao, Yingjie; Bernitzky, Richard H M; Kory, Max J; Hofer, Gregor; Hofkens, Johan; Schlüter, A Dieter

    2016-07-20

    This work proves the existence and chemical addressability of defined edge groups of a 2D polymer. Pseudohexagonally prismatic single crystals consisting of layered stacks of a 2D polymer are used. They should expose anthracene-based edge groups at the six (100) but not at the two pseudohexagonal (001) and (001̅) faces. The crystals are reacted with the isotopically enriched dienophiles maleic anhydride and a C18-alkyl chain-modified maleimide. In both cases the corresponding Diels-Alder adducts between these reagents and the edge groups are formed as confirmed by solid state NMR spectroscopy. The same applies to a maleimide derivative carrying a BODIPY dye which was chosen for its fluorescence to be out of the range of the self-fluorescence of the 2D polymer crystals stemming from contained template molecules. If the crystals are excited at λ = 633 nm, their (100) faces and thus their rims fluoresce brightly, while the pseudohexagonal faces remain silent. This is visible when the crystals lie on a pseudohexagonal face. Lambda-mode laser scanning microscopy confirms this fluorescence to originate from the BODIPY dye. Micromechanical exfoliation of the dye-modified crystals results in thinner sheet packages which still exhibit BODIPY fluorescence right at the rim of these packages. This work establishes the chemical nature of the edge groups of a 2D polymer and is also the first implementation of an edge group modification similar to end group modifications of linear polymers. PMID:27347597

  15. Structural features of a bituminous coal and their changes during low-temperature oxidation and loss of volatiles investigated by advanced solid-state NMR spectroscopy

    USGS Publications Warehouse

    Mao, J.-D.; Schimmelmann, A.; Mastalerz, Maria; Hatcher, P.G.; Li, Y.

    2010-01-01

    Quantitative and advanced 13C solid-state NMR techniques were employed to investigate (i) the chemical structure of a high volatile bituminous coal, as well as (ii) chemical structural changes of this coal after evacuation of adsorbed gases, (iii) during oxidative air exposure at room temperature, and (iv) after oxidative heating in air at 75 ??C. The solid-state NMR techniques employed in this study included quantitative direct polarization/magic angle spinning (DP/MAS) at a high spinning speed of 14 kHz, cross polarization/total sideband suppression (CP/TOSS), dipolar dephasing, CH, CH2, and CHn selection, 13C chemical shift anisotropy (CSA) filtering, two-dimensional (2D) 1H-13C heteronuclear correlation NMR (HETCOR), and 2D HETCOR with 1H spin diffusion. With spectral editing techniques, we identified methyl CCH 3, rigid and mobile methylene CCH2C, methine CCH, quaternary Cq, aromatic CH, aromatic carbons bonded to alkyls, small-sized condensed aromatic moieties, and aromatic C-O groups. With direct polarization combined with spectral-editing techniques, we quantified 11 different types of functional groups. 1H-13C 2D HETCOR NMR experiments indicated spatial proximity of aromatic and alkyl moieties in cross-linked structures. The proton spin diffusion experiments indicated that the magnetization was not equilibrated at a 1H spin diffusion time of 5 ms. Therefore, the heterogeneity in spatial distribution of different functional groups should be above 2 nm. Recoupled C-H long-range dipolar dephasing showed that the fraction of large charcoal-like clusters of polycondensed aromatic rings was relatively small. The exposure of this coal to atmospheric oxygen at room temperature for 6 months did not result in obvious chemical structural changes of the coal, whereas heating at 75 ??C in air for 10 days led to oxidation of coal and generated some COO groups. Evacuation removed most volatiles and caused a significant reduction in aliphatic signals in its DP

  16. High resolution NMR measurements using a 400 MHz NMR with an (RE)Ba2Cu3O7-x high-temperature superconducting inner coil: Towards a compact super-high-field NMR

    NASA Astrophysics Data System (ADS)

    Piao, R.; Iguchi, S.; Hamada, M.; Matsumoto, S.; Suematsu, H.; Saito, A. T.; Li, J.; Nakagome, H.; Takao, T.; Takahashi, M.; Maeda, H.; Yanagisawa, Y.

    2016-02-01

    Use of high-temperature superconducting (HTS) inner coils in combination with conventional low-temperature superconducting (LTS) outer coils for an NMR magnet, i.e. a LTS/HTS NMR magnet, is a suitable option to realize a high-resolution NMR spectrometer with operating frequency >1 GHz. From the standpoint of creating a compact magnet, (RE: Rare earth) Ba2Cu3O7-x (REBCO) HTS inner coils which can tolerate a strong hoop stress caused by a Lorentz force are preferred. However, in our previous work on a first-generation 400 MHz LTS/REBCO NMR magnet, the NMR resolution and sensitivity were about ten times worse than that of a conventional LTS NMR magnet. The result was caused by a large field inhomogeneity in the REBCO coil itself and the shielding effect of a screening current induced in that coil. In the present paper, we describe the operation of a modified 400 MHz LTS/REBCO NMR magnet with an advanced field compensation technology using a combination of novel ferromagnetic shimming and an appropriate procedure for NMR spectrum line shape optimization. We succeeded in obtaining a good NMR line shape and 2D NOESY spectrum for a lysozyme aqueous sample. We believe that this technology is indispensable for the realization of a compact super-high-field high-resolution NMR.

  17. Radiofrequency Spectroscopy and Thermodynamics of Fermi Gases in the 2D to Quasi-2D Dimensional Crossover

    NASA Astrophysics Data System (ADS)

    Cheng, Chingyun; Kangara, Jayampathi; Arakelyan, Ilya; Thomas, John

    2016-05-01

    We tune the dimensionality of a strongly interacting degenerate 6 Li Fermi gas from 2D to quasi-2D, by adjusting the radial confinement of pancake-shaped clouds to control the radial chemical potential. In the 2D regime with weak radial confinement, the measured pair binding energies are in agreement with 2D-BCS mean field theory, which predicts dimer pairing energies in the many-body regime. In the qausi-2D regime obtained with increased radial confinement, the measured pairing energy deviates significantly from 2D-BCS theory. In contrast to the pairing energy, the measured radii of the cloud profiles are not fit by 2D-BCS theory in either the 2D or quasi-2D regimes, but are fit in both regimes by a beyond mean field polaron-model of the free energy. Supported by DOE, ARO, NSF, and AFOSR.

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

    PubMed

    Cobas, Carlos; Iglesias, Isaac; Seoane, Felipe

    2015-08-01

    Touch-screen computers are emerging as a popular platform for many applications, including those in chemistry and analytical sciences. In this work, we present our implementation of a new NMR 'app' designed for hand-held and portable touch-controlled devices, such as smartphones and tablets. It features a flexible architecture formed by a powerful NMR processing and analysis kernel and an intuitive user interface that makes full use of the smart devices haptic capabilities. Routine 1D and 2D NMR spectra acquired in most NMR instruments can be processed in a fully unattended way. More advanced experiments such as non-uniform sampled NMR spectra are also supported through a very efficient parallelized Modified Iterative Soft Thresholding algorithm. Specific technical development features as well as the overall feasibility of using NMR software apps will also be discussed. All aspects considered the functionalities of the app allowing it to work as a stand-alone tool or as a 'companion' to more advanced desktop applications such as Mnova NMR. PMID:25924947

  19. 2D Radiative Processes Near Cloud Edges

    NASA Technical Reports Server (NTRS)

    Varnai, T.

    2012-01-01

    Because of the importance and complexity of dynamical, microphysical, and radiative processes taking place near cloud edges, the transition zone between clouds and cloud free air has been the subject of intense research both in the ASR program and in the wider community. One challenge in this research is that the one-dimensional (1D) radiative models widely used in both remote sensing and dynamical simulations become less accurate near cloud edges: The large horizontal gradients in particle concentrations imply that accurate radiative calculations need to consider multi-dimensional radiative interactions among areas that have widely different optical properties. This study examines the way the importance of multidimensional shortwave radiative interactions changes as we approach cloud edges. For this, the study relies on radiative simulations performed for a multiyear dataset of clouds observed over the NSA, SGP, and TWP sites. This dataset is based on Microbase cloud profiles as well as wind measurements and ARM cloud classification products. The study analyzes the way the difference between 1D and 2D simulation results increases near cloud edges. It considers both monochromatic radiances and broadband radiative heating, and it also examines the influence of factors such as cloud type and height, and solar elevation. The results provide insights into the workings of radiative processes and may help better interpret radiance measurements and better estimate the radiative impacts of this critical region.

  20. Simulation of Yeast Cooperation in 2D.

    PubMed

    Wang, M; Huang, Y; Wu, Z

    2016-03-01

    Evolution of cooperation has been an active research area in evolutionary biology in decades. An important type of cooperation is developed from group selection, when individuals form spatial groups to prevent them from foreign invasions. In this paper, we study the evolution of cooperation in a mixed population of cooperating and cheating yeast strains in 2D with the interactions among the yeast cells restricted to their small neighborhoods. We conduct a computer simulation based on a game theoretic model and show that cooperation is increased when the interactions are spatially restricted, whether the game is of a prisoner's dilemma, snow drifting, or mutual benefit type. We study the evolution of homogeneous groups of cooperators or cheaters and describe the conditions for them to sustain or expand in an opponent population. We show that under certain spatial restrictions, cooperator groups are able to sustain and expand as group sizes become large, while cheater groups fail to expand and keep them from collapse. PMID:26988702

  1. Phase Engineering of 2D Tin Sulfides.

    PubMed

    Mutlu, Zafer; Wu, Ryan J; Wickramaratne, Darshana; Shahrezaei, Sina; Liu, Chueh; Temiz, Selcuk; Patalano, Andrew; Ozkan, Mihrimah; Lake, Roger K; Mkhoyan, K A; Ozkan, Cengiz S

    2016-06-01

    Tin sulfides can exist in a variety of phases and polytypes due to the different oxidation states of Sn. A subset of these phases and polytypes take the form of layered 2D structures that give rise to a wide host of electronic and optical properties. Hence, achieving control over the phase, polytype, and thickness of tin sulfides is necessary to utilize this wide range of properties exhibited by the compound. This study reports on phase-selective growth of both hexagonal tin (IV) sulfide SnS2 and orthorhombic tin (II) sulfide SnS crystals with diameters of over tens of microns on SiO2 substrates through atmospheric pressure vapor-phase method in a conventional horizontal quartz tube furnace with SnO2 and S powders as the source materials. Detailed characterization of each phase of tin sulfide crystals is performed using various microscopy and spectroscopy methods, and the results are corroborated by ab initio density functional theory calculations. PMID:27099950

  2. Ion Transport in 2-D Graphene Nanochannels

    NASA Astrophysics Data System (ADS)

    Xie, Quan; Foo, Elbert; Duan, Chuanhua

    2015-11-01

    Graphene membranes have recently attracted wide attention due to its great potential in water desalination and selective molecular sieving. Further developments of these membranes, including enhancing their mass transport rate and/or molecular selectivity, rely on the understanding of fundamental transport mechanisms through graphene membranes, which has not been studied experimentally before due to fabrication and measurement difficulties. Herein we report the fabrication of the basic constituent of graphene membranes, i.e. 2-D single graphene nanochannels (GNCs) and the study of ion transport in these channels. A modified bonding technique was developed to form GNCs with well-defined geometry and uniform channel height. Ion transport in such GNCs was studied using DC conductance measurement. Our preliminary results showed that the ion transport in GNCs is still governed by surface charge at low concentrations (10-6M to 10-4M). However, GNCs exhibits much higher ionic conductances than silica nanochannels with the same geometries in the surface-charge-governed regime. This conductance enhancement can be attributed to the pre-accumulation of charges on graphene surfaces. The work is supported by the Faculty Startup Fund (Boston University, USA).

  3. Parallel map analysis on 2-D grids

    SciTech Connect

    Berry, M.; Comiskey, J.; Minser, K.

    1993-12-31

    In landscape ecology, computer modeling is used to assess habitat fragmentation and its ecological iMPLications. Specifically, maps (2-D grids) of habitat clusters must be analyzed to determine number, sizes and geometry of clusters. Models prior to this study relied upon sequential Fortran-77 programs which limited the sizes of maps and densities of clusters which could be analyzed. In this paper, we present more efficient computer models which can exploit recursion or parallelism. Significant improvements over the original Fortran-77 programs have been achieved using both recursive and nonrecursive C implementations on a variety of workstations such as the Sun Sparc 2, IBM RS/6000-350, and HP 9000-750. Parallel implementations on a 4096-processor MasPar MP-1 and a 32-processor CM-5 are also studied. Preliminary experiments suggest that speed improvements for the parallel model on the MasPar MP-1 (written in MPL) and on the CM-5 (written in C using CMMD) can be as much as 39 and 34 times faster, respectively, than the most efficient sequential C program on a Sun Sparc 2 for a 512 map. An important goal in this research effort is to produce a scalable map analysis algorithm for the identification and characterization of clusters for relatively large maps on massively-parallel computers.

  4. 2D Turbulence with Complicated Boundaries

    NASA Astrophysics Data System (ADS)

    Roullet, G.; McWilliams, J. C.

    2014-12-01

    We examine the consequences of lateral viscous boundary layers on the 2D turbulence that arises in domains with complicated boundaries (headlands, bays etc). The study is carried out numerically with LES. The numerics are carefully designed to ensure all global conservation laws, proper boundary conditions and a minimal range of dissipation scales. The turbulence dramatically differs from the classical bi-periodic case. Boundary layer separations lead to creation of many small vortices and act as a continuing energy source exciting the inverse cascade of energy throughout the domain. The detachments are very intermittent in time. In free decay, the final state depends on the effective numerical resolution: laminar with a single dominant vortex for low Re and turbulent with many vortices for large enough Re. After very long time, the turbulent end-state exhibits a striking tendency for the emergence of shielded vortices which then interact almost elastically. In the forced case, the boundary layers allow the turbulence to reach a statistical steady state without any artificial hypo-viscosity or other large-scale dissipation. Implications are discussed for the oceanic mesoscale and submesoscale turbulence.

  5. 2-D wavelet with position controlled resolution

    NASA Astrophysics Data System (ADS)

    Walczak, Andrzej; Puzio, Leszek

    2005-09-01

    Wavelet transformation localizes all irregularities in the scene. It is most effective in the case when intensities in the scene have no sharp details. It is the case often present in a medical imaging. To identify the shape one has to extract it from the scene as typical irregularity. When the scene does not contain sharp changes then common differential filters are not efficient tool for a shape extraction. The new 2-D wavelet for such task has been proposed. Described wavelet transform is axially symmetric and has varied scale in dependence on the distance from the centre of the wavelet symmetry. The analytical form of the wavelet has been presented as well as its application for details extraction in the scene. Most important feature of the wavelet transform is that it gives a multi-scale transformation, and if zoom is on the wavelet selectivity varies proportionally to the zoom step. As a result, the extracted shape does not change during zoom operation. What is more the wavelet selectivity can be fit to the local intensity gradient properly to obtain best extraction of the irregularities.

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

    ERIC Educational Resources Information Center

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

    2010-01-01

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

  7. Metabolomic profiling of the phytomedicinal constituents of Carica papaya L. leaves and seeds by 1H NMR spectroscopy and multivariate statistical analysis.

    PubMed

    Gogna, Navdeep; Hamid, Neda; Dorai, Kavita

    2015-11-10

    Extracts from the Carica papaya L. plant are widely reported to contain metabolites with antibacterial, antioxidant and anticancer activity. This study aims to analyze the metabolic profiles of papaya leaves and seeds in order to gain insights into their phytomedicinal constituents. We performed metabolite fingerprinting using 1D and 2D 1H NMR experiments and used multivariate statistical analysis to identify those plant parts that contain the most concentrations of metabolites of phytomedicinal value. Secondary metabolites such as phenyl propanoids, including flavonoids, were found in greater concentrations in the leaves as compared to the seeds. UPLC-ESI-MS verified the presence of significant metabolites in the papaya extracts suggested by the NMR analysis. Interestingly, the concentration of eleven secondary metabolites namely caffeic, cinnamic, chlorogenic, quinic, coumaric, vanillic, and protocatechuic acids, naringenin, hesperidin, rutin, and kaempferol, were higher in young as compared to old papaya leaves. The results of the NMR analysis were corroborated by estimating the total phenolic and flavonoid content of the extracts. Estimation of antioxidant activity in leaves and seed extracts by DPPH and ABTS in-vitro assays and antioxidant capacity in C2C12 cell line also showed that papaya extracts exhibit high antioxidant activity. PMID:26163870

  8. Real-time 2D separation by LC × differential ion mobility hyphenated to mass spectrometry.

    PubMed

    Varesio, Emmanuel; Le Blanc, J C Yves; Hopfgartner, Gérard

    2012-03-01

    The liquid chromatography-mass spectrometry (LC-MS) analysis of complex samples such as biological fluid extracts is widespread when searching for new biomarkers as in metabolomics. The success of this hyphenation resides in the orthogonality of both separation techniques. However, there are frequent cases where compounds are co-eluting and the resolving power of mass spectrometry (MS) is not sufficient (e.g., isobaric compounds and interfering isotopic clusters). Different strategies are discussed to solve these cases and a mixture of eight compounds (i.e., bromazepam, chlorprothixene, clonapzepam, fendiline, flusilazol, oxfendazole, oxycodone, and pamaquine) with identical nominal mass (i.e., m/z 316) is taken to illustrate them. Among the different approaches, high-resolution mass spectrometry or liquid chromatography (i.e., UHPLC) can easily separate these compounds. Another technique, mostly used with low resolving power MS analyzers, is differential ion mobility spectrometry (DMS), where analytes are gas-phase separated according to their size-to-charge ratio. Detailed investigations of the addition of different polar modifiers (i.e., methanol, ethanol, and isopropanol) into the transport gas (nitrogen) to enhance the peak capacity of the technique were carried out. Finally, a complex urine sample fortified with 36 compounds of various chemical properties was analyzed by real-time 2D separation LC×DMS-MS(/MS). The addition of this orthogonal gas-phase separation technique in the LC-MS(/MS) hyphenation greatly improved data quality by resolving composite MS/MS spectra, which is mandatory in metabolomics when performing database generation and search. PMID:22006241

  9. 2-D Animation's Not Just for Mickey Mouse.

    ERIC Educational Resources Information Center

    Weinman, Lynda

    1995-01-01

    Discusses characteristics of two-dimensional (2-D) animation; highlights include character animation, painting issues, and motion graphics. Sidebars present Silicon Graphics animations tools and 2-D animation programs for the desktop computer. (DGM)

  10. MAZE96. Generates 2D Input for DYNA NIKE & TOPAZ

    SciTech Connect

    Sanford, L.; Hallquist, J.O.

    1992-02-24

    MAZE is an interactive program that serves as an input and two-dimensional mesh generator for DYNA2D, NIKE2D, TOPAZ2D, and CHEMICAL TOPAZ2D. MAZE also generates a basic template for ISLAND input. MAZE has been applied to the generation of input data to study the response of two-dimensional solids and structures undergoing finite deformations under a wide variety of large deformation transient dynamic and static problems and heat transfer analyses.

  11. On 2D graphical representation of DNA sequence of nondegeneracy

    NASA Astrophysics Data System (ADS)

    Zhang, Yusen; Liao, Bo; Ding, Kequan

    2005-08-01

    Some two-dimensional (2D) graphical representations of DNA sequences have been given by Gates, Nandy, Leong and Mogenthaler, Randić, and Liao et al., which give visual characterizations of DNA sequences. In this Letter, we introduce a nondegeneracy 2D graphical representation of DNA sequence, which is different from Randić's novel 2D representation and Liao's 2D representation. We also present the nondegeneracy forms corresponding to the representations of Gates, Nandy, Leong and Mogenthaler.

  12. Generates 2D Input for DYNA NIKE & TOPAZ

    1996-07-15

    MAZE is an interactive program that serves as an input and two-dimensional mesh generator for DYNA2D, NIKE2D, TOPAZ2D, and CHEMICAL TOPAZ2D. MAZE also generates a basic template for ISLAND input. MAZE has been applied to the generation of input data to study the response of two-dimensional solids and structures undergoing finite deformations under a wide variety of large deformation transient dynamic and static problems and heat transfer analyses.

  13. 2d PDE Linear Symmetric Matrix Solver

    1983-10-01

    ICCG2 (Incomplete Cholesky factorized Conjugate Gradient algorithm for 2d symmetric problems) was developed to solve a linear symmetric matrix system arising from a 9-point discretization of two-dimensional elliptic and parabolic partial differential equations found in plasma physics applications, such as resistive MHD, spatial diffusive transport, and phase space transport (Fokker-Planck equation) problems. These problems share the common feature of being stiff and requiring implicit solution techniques. When these parabolic or elliptic PDE''s are discretized withmore » finite-difference or finite-element methods,the resulting matrix system is frequently of block-tridiagonal form. To use ICCG2, the discretization of the two-dimensional partial differential equation and its boundary conditions must result in a block-tridiagonal supermatrix composed of elementary tridiagonal matrices. The incomplete Cholesky conjugate gradient algorithm is used to solve the linear symmetric matrix equation. Loops are arranged to vectorize on the Cray1 with the CFT compiler, wherever possible. Recursive loops, which cannot be vectorized, are written for optimum scalar speed. For matrices lacking symmetry, ILUCG2 should be used. Similar methods in three dimensions are available in ICCG3 and ILUCG3. A general source containing extensions and macros, which must be processed by a pre-compiler to obtain the standard FORTRAN source, is provided along with the standard FORTRAN source because it is believed to be more readable. The pre-compiler is not included, but pre-compilation may be performed by a text editor as described in the UCRL-88746 Preprint.« less

  14. 2d PDE Linear Asymmetric Matrix Solver

    1983-10-01

    ILUCG2 (Incomplete LU factorized Conjugate Gradient algorithm for 2d problems) was developed to solve a linear asymmetric matrix system arising from a 9-point discretization of two-dimensional elliptic and parabolic partial differential equations found in plasma physics applications, such as plasma diffusion, equilibria, and phase space transport (Fokker-Planck equation) problems. These equations share the common feature of being stiff and requiring implicit solution techniques. When these parabolic or elliptic PDE''s are discretized with finite-difference or finite-elementmore » methods, the resulting matrix system is frequently of block-tridiagonal form. To use ILUCG2, the discretization of the two-dimensional partial differential equation and its boundary conditions must result in a block-tridiagonal supermatrix composed of elementary tridiagonal matrices. A generalization of the incomplete Cholesky conjugate gradient algorithm is used to solve the matrix equation. Loops are arranged to vectorize on the Cray1 with the CFT compiler, wherever possible. Recursive loops, which cannot be vectorized, are written for optimum scalar speed. For problems having a symmetric matrix ICCG2 should be used since it runs up to four times faster and uses approximately 30% less storage. Similar methods in three dimensions are available in ICCG3 and ILUCG3. A general source, containing extensions and macros, which must be processed by a pre-compiler to obtain the standard FORTRAN source, is provided along with the standard FORTRAN source because it is believed to be more readable. The pre-compiler is not included, but pre-compilation may be performed by a text editor as described in the UCRL-88746 Preprint.« less

  15. Ultrasonic 2D matrix PVDF transducer

    NASA Astrophysics Data System (ADS)

    Ptchelintsev, A.; Maev, R. Gr.

    2000-05-01

    During the past decade a substantial amount of work has been done in the area of ultrasonic imaging technology using 2D arrays. The main problems arising for the two-dimensional matrix transducers at megahertz frequencies are small size and huge count of the elements, high electrical impedance, low sensitivity, bad SNR and slower data acquisition rate. The major technological difficulty remains the high density of the interconnect. To solve these problems numerous approaches have been suggested. In the present work, a 24×24 elements (24 transmit+24 receive) matrix and a switching board were developed. The transducer consists of two 52 μm PVDF layers each representing a linear array of 24 elements placed one on the top of the other. Electrodes in these two layers are perpendicular and form the grid of 0.5×0.5 mm pitch. The layers are bonded together with the ground electrode being monolithic and located between the layers. The matrix is backed from the rear surface with an epoxy composition. During the emission, a linear element from the emitting layer generates a longitudinal wave pulse propagating inside the test object. Reflected pulses are picked-up by the receiving layer. During one transmit-receive cycle one transmit element and one receive element are selected by corresponding multiplexers. These crossed elements emulate a small element formed by their intersection. The present design presents the following advantages: minimizes number of active channels and density of the interconnect; reduces the electrical impedance of the element improving electrical matching; enables the transmit-receive mode; due to the efficient backing provides bandwidth and good time resolution; and, significantly reduces the electronics complexity. The matrix can not be used for the beam steering and focusing. Owing to this impossibility of focusing, the penetration depth is limited as well by the diffraction phenomena.

  16. NMR ANALYSIS OF MALE FATHEAD MINNOW URINARY METABOLITES: A POTENTIAL APPROACH FOR STUDYING IMPACTS OF CHEMICAL EXPOSURES

    EPA Science Inventory

    The potential for profiling endogenous metabolites in urine from male fathead minnows (Pimephales promelas) to assess chemical exposures was explored using nuclear magnetic resonance (NMR) spectroscopy. Both one dimensional (1D) and two dimensional (2D) NMR spectroscopy w...

  17. A Planar Quantum Transistor Based on 2D-2D Tunneling in Double Quantum Well Heterostructures

    SciTech Connect

    Baca, W.E.; Blount, M.A.; Hafich, M.J.; Lyo, S.K.; Moon, J.S.; Reno, J.L.; Simmons, J.A.; Wendt, J.R.

    1998-12-14

    We report on our work on the double electron layer tunneling transistor (DELTT), based on the gate-control of two-dimensional -- two-dimensional (2D-2D) tunneling in a double quantum well heterostructure. While previous quantum transistors have typically required tiny laterally-defined features, by contrast the DELTT is entirely planar and can be reliably fabricated in large numbers. We use a novel epoxy-bond-and-stop-etch (EBASE) flip-chip process, whereby submicron gating on opposite sides of semiconductor epitaxial layers as thin as 0.24 microns can be achieved. Because both electron layers in the DELTT are 2D, the resonant tunneling features are unusually sharp, and can be easily modulated with one or more surface gates. We demonstrate DELTTs with peak-to-valley ratios in the source-drain I-V curve of order 20:1 below 1 K. Both the height and position of the resonant current peak can be controlled by gate voltage over a wide range. DELTTs with larger subband energy offsets ({approximately} 21 meV) exhibit characteristics that are nearly as good at 77 K, in good agreement with our theoretical calculations. Using these devices, we also demonstrate bistable memories operating at 77 K. Finally, we briefly discuss the prospects for room temperature operation, increases in gain, and high-speed.

  18. Correlated Electron Phenomena in 2D Materials

    NASA Astrophysics Data System (ADS)

    Lambert, Joseph G.

    In this thesis, I present experimental results on coherent electron phenomena in layered two-dimensional materials: single layer graphene and van der Waals coupled 2D TiSe2. Graphene is a two-dimensional single-atom thick sheet of carbon atoms first derived from bulk graphite by the mechanical exfoliation technique in 2004. Low-energy charge carriers in graphene behave like massless Dirac fermions, and their density can be easily tuned between electron-rich and hole-rich quasiparticles with electrostatic gating techniques. The sharp interfaces between regions of different carrier densities form barriers with selective transmission, making them behave as partially reflecting mirrors. When two of these interfaces are set at a separation distance within the phase coherence length of the carriers, they form an electronic version of a Fabry-Perot cavity. I present measurements and analysis of multiple Fabry-Perot modes in graphene with parallel electrodes spaced a few hundred nanometers apart. Transition metal dichalcogenide (TMD) TiSe2 is part of the family of materials that coined the term "materials beyond graphene". It contains van der Waals coupled trilayer stacks of Se-Ti-Se. Many TMD materials exhibit a host of interesting correlated electronic phases. In particular, TiSe2 exhibits chiral charge density waves (CDW) below TCDW ˜ 200 K. Upon doping with copper, the CDW state gets suppressed with Cu concentration, and CuxTiSe2 becomes superconducting with critical temperature of T c = 4.15 K. There is still much debate over the mechanisms governing the coexistence of the two correlated electronic phases---CDW and superconductivity. I will present some of the first conductance spectroscopy measurements of proximity coupled superconductor-CDW systems. Measurements reveal a proximity-induced critical current at the Nb-TiSe2 interfaces, suggesting pair correlations in the pure TiSe2. The results indicate that superconducting order is present concurrently with CDW in

  19. Ultrafast multidimensional Laplace NMR for a rapid and sensitive chemical analysis

    NASA Astrophysics Data System (ADS)

    Ahola, Susanna; Zhivonitko, Vladimir V.; Mankinen, Otto; Zhang, Guannan; Kantola, Anu M.; Chen, Hsueh-Ying; Hilty, Christian; Koptyug, Igor V.; Telkki, Ville-Veikko

    2015-09-01

    Traditional nuclear magnetic resonance (NMR) spectroscopy relies on the versatile chemical information conveyed by spectra. To complement conventional NMR, Laplace NMR explores diffusion and relaxation phenomena to reveal details on molecular motions. Under a broad concept of ultrafast multidimensional Laplace NMR, here we introduce an ultrafast diffusion-relaxation correlation experiment enhancing the resolution and information content of corresponding 1D experiments as well as reducing the experiment time by one to two orders of magnitude or more as compared with its conventional 2D counterpart. We demonstrate that the method allows one to distinguish identical molecules in different physical environments and provides chemical resolution missing in NMR spectra. Although the sensitivity of the new method is reduced due to spatial encoding, the single-scan approach enables one to use hyperpolarized substances to boost the sensitivity by several orders of magnitude, significantly enhancing the overall sensitivity of multidimensional Laplace NMR.

  20. Ultrafast multidimensional Laplace NMR for a rapid and sensitive chemical analysis

    PubMed Central

    Ahola, Susanna; Zhivonitko, Vladimir V; Mankinen, Otto; Zhang, Guannan; Kantola, Anu M.; Chen, Hsueh-Ying; Hilty, Christian; Koptyug, Igor V.; Telkki, Ville-Veikko

    2015-01-01

    Traditional nuclear magnetic resonance (NMR) spectroscopy relies on the versatile chemical information conveyed by spectra. To complement conventional NMR, Laplace NMR explores diffusion and relaxation phenomena to reveal details on molecular motions. Under a broad concept of ultrafast multidimensional Laplace NMR, here we introduce an ultrafast diffusion-relaxation correlation experiment enhancing the resolution and information content of corresponding 1D experiments as well as reducing the experiment time by one to two orders of magnitude or more as compared with its conventional 2D counterpart. We demonstrate that the method allows one to distinguish identical molecules in different physical environments and provides chemical resolution missing in NMR spectra. Although the sensitivity of the new method is reduced due to spatial encoding, the single-scan approach enables one to use hyperpolarized substances to boost the sensitivity by several orders of magnitude, significantly enhancing the overall sensitivity of multidimensional Laplace NMR. PMID:26381101

  1. CYP2D7 Sequence Variation Interferes with TaqMan CYP2D6*15 and *35 Genotyping

    PubMed Central

    Riffel, Amanda K.; Dehghani, Mehdi; Hartshorne, Toinette; Floyd, Kristen C.; Leeder, J. Steven; Rosenblatt, Kevin P.; Gaedigk, Andrea

    2016-01-01

    TaqMan™ genotyping assays are widely used to genotype CYP2D6, which encodes a major drug metabolizing enzyme. Assay design for CYP2D6 can be challenging owing to the presence of two pseudogenes, CYP2D7 and CYP2D8, structural and copy number variation and numerous single nucleotide polymorphisms (SNPs) some of which reflect the wild-type sequence of the CYP2D7 pseudogene. The aim of this study was to identify the mechanism causing false-positive CYP2D6*15 calls and remediate those by redesigning and validating alternative TaqMan genotype assays. Among 13,866 DNA samples genotyped by the CompanionDx® lab on the OpenArray platform, 70 samples were identified as heterozygotes for 137Tins, the key SNP of CYP2D6*15. However, only 15 samples were confirmed when tested with the Luminex xTAG CYP2D6 Kit and sequencing of CYP2D6-specific long range (XL)-PCR products. Genotype and gene resequencing of CYP2D6 and CYP2D7-specific XL-PCR products revealed a CC>GT dinucleotide SNP in exon 1 of CYP2D7 that reverts the sequence to CYP2D6 and allows a TaqMan assay PCR primer to bind. Because CYP2D7 also carries a Tins, a false-positive mutation signal is generated. This CYP2D7 SNP was also responsible for generating false-positive signals for rs769258 (CYP2D6*35) which is also located in exon 1. Although alternative CYP2D6*15 and *35 assays resolved the issue, we discovered a novel CYP2D6*15 subvariant in one sample that carries additional SNPs preventing detection with the alternate assay. The frequency of CYP2D6*15 was 0.1% in this ethnically diverse U.S. population sample. In addition, we also discovered linkage between the CYP2D7 CC>GT dinucleotide SNP and the 77G>A (rs28371696) SNP of CYP2D6*43. The frequency of this tentatively functional allele was 0.2%. Taken together, these findings emphasize that regardless of how careful genotyping assays are designed and evaluated before being commercially marketed, rare or unknown SNPs underneath primer and/or probe regions can impact

  2. CYP2D7 Sequence Variation Interferes with TaqMan CYP2D6 (*) 15 and (*) 35 Genotyping.

    PubMed

    Riffel, Amanda K; Dehghani, Mehdi; Hartshorne, Toinette; Floyd, Kristen C; Leeder, J Steven; Rosenblatt, Kevin P; Gaedigk, Andrea

    2015-01-01

    TaqMan™ genotyping assays are widely used to genotype CYP2D6, which encodes a major drug metabolizing enzyme. Assay design for CYP2D6 can be challenging owing to the presence of two pseudogenes, CYP2D7 and CYP2D8, structural and copy number variation and numerous single nucleotide polymorphisms (SNPs) some of which reflect the wild-type sequence of the CYP2D7 pseudogene. The aim of this study was to identify the mechanism causing false-positive CYP2D6 (*) 15 calls and remediate those by redesigning and validating alternative TaqMan genotype assays. Among 13,866 DNA samples genotyped by the CompanionDx® lab on the OpenArray platform, 70 samples were identified as heterozygotes for 137Tins, the key SNP of CYP2D6 (*) 15. However, only 15 samples were confirmed when tested with the Luminex xTAG CYP2D6 Kit and sequencing of CYP2D6-specific long range (XL)-PCR products. Genotype and gene resequencing of CYP2D6 and CYP2D7-specific XL-PCR products revealed a CC>GT dinucleotide SNP in exon 1 of CYP2D7 that reverts the sequence to CYP2D6 and allows a TaqMan assay PCR primer to bind. Because CYP2D7 also carries a Tins, a false-positive mutation signal is generated. This CYP2D7 SNP was also responsible for generating false-positive signals for rs769258 (CYP2D6 (*) 35) which is also located in exon 1. Although alternative CYP2D6 (*) 15 and (*) 35 assays resolved the issue, we discovered a novel CYP2D6 (*) 15 subvariant in one sample that carries additional SNPs preventing detection with the alternate assay. The frequency of CYP2D6 (*) 15 was 0.1% in this ethnically diverse U.S. population sample. In addition, we also discovered linkage between the CYP2D7 CC>GT dinucleotide SNP and the 77G>A (rs28371696) SNP of CYP2D6 (*) 43. The frequency of this tentatively functional allele was 0.2%. Taken together, these findings emphasize that regardless of how careful genotyping assays are designed and evaluated before being commercially marketed, rare or unknown SNPs underneath primer

  3. Suramin blocks interaction between human FGF1 and FGFR2 D2 domain and reduces downstream signaling activity.

    PubMed

    Wu, Zong-Sian; Liu, Che Fu; Fu, Brian; Chou, Ruey-Hwang; Yu, Chin

    2016-09-01

    The extracellular portion of the human fibroblast growth factor receptor2 D2 domain (FGFR2 D2) interacts with human fibroblast growth factor 1 (hFGF1) to activate a downstream signaling cascade that ultimately affects mitosis and differentiation. Suramin is an antiparasiticdrug and a potent inhibitor of FGF-induced angiogenesis. Suramin has been shown to bind to hFGF1, and might block the interaction between hFGF1 and FGFR2 D2. Here, we titrated hFGF1 with FGFR2 D2 and suramin to elucidate their interactions using the detection of NMR. The docking results of both hFGF1-FGFR2 D2 domain and hFGF1-suramin complex were superimposed. The results indicate that suramin blocks the interaction between hFGF1 and FGFR2 D2. We used the PyMOL software to show the hydrophobic interaction of hFGF1-suramin. In addition, we used a Water-soluble Tetrazolium salts assay (WST1) to assess hFGF1 bioactivity. The results will be useful for the development of new antimitogenic activity drugs. PMID:27387234

  4. NMR imaging microscopy

    SciTech Connect

    Not Available

    1986-10-01

    In the past several years, proton nuclear magnetic resonance (NMR) imaging has become an established technique in diagnostic medicine and biomedical research. Although much of the work in this field has been directed toward development of whole-body imagers, James Aguayo, Stephen Blackband, and Joseph Schoeninger of the Johns Hopkins University School of Medicine working with Markus Hintermann and Mark Mattingly of Bruker Medical Instruments, recently developed a small-bore NMR microscope with sufficient resolution to image a single African clawed toad cell (Nature 1986, 322, 190-91). This improved resolution should lead to increased use of NMR imaging for chemical, as well as biological or physiological, applications. The future of NMR microscopy, like that of many other newly emerging techniques, is ripe with possibilities. Because of its high cost, however, it is likely to remain primarily a research tool for some time. ''It's like having a camera,'' says Smith. ''You've got a way to look at things at very fine levels, and people are going to find lots of uses for it. But it is a very expensive technique - it costs $100,000 to add imaging capability once you have a high-resolution NMR, which itself is at least a $300,000 instrument. If it can answer even a few questions that can't be answered any other way, though, it may be well worth the cost.''

  5. Statistical filtering for NMR based structure generation

    PubMed Central

    2011-01-01

    The constitutional assignment of natural products by NMR spectroscopy is usually based on 2D NMR experiments like COSY, HSQC, and HMBC. The difficulty of a structure elucidation problem depends more on the type of the investigated molecule than on its size. Saturated compounds can usually be assigned unambiguously by hand using only COSY and 13C-HMBC data, whereas condensed heterocycles are problematic due to their lack of protons that could show interatomic connectivities. Different computer programs were developed to aid in the structural assignment process, one of them COCON. In the case of unsaturated and substituted molecules structure generators frequently will generate a very large number of possible solutions. This article presents a "statistical filter" for the reduction of the number of results. The filter works by generating 3D conformations using smi23d, a simple MD approach. All molecules for which the generation of constitutional restraints failed were eliminated from the result set. Some structural elements removed by the statistical filter were analyzed and checked against Beilstein. The automatic removal of molecules for which no MD parameter set could be created was included into WEBCOCON. The effect of this filter varies in dependence of the NMR data set used, but in no case the correct constitution was removed from the resulting set. PMID:21835037

  6. DFT and NMR parameterized conformation of valeranone.

    PubMed

    Torres-Valencia, J Martín; Meléndez-Rodríguez, Myriam; Alvarez-García, Rocío; Cerda-García-Rojas, Carlos M; Joseph-Nathan, Pedro

    2004-10-01

    A Monte Carlo random search using molecular mechanics, followed by geometry optimization of each minimum energy structure employing density functional theory (DFT) calculations at the B3LYP/6-31G* level and a Boltzmann analysis of the total energies, generated accurate molecular models which describe the conformational behavior of the antispasmodic bicyclic sesquiterpene valeranone (1). The theoretical H-C-C-H dihedral angles gave the corresponding 1H, 1H vicinal coupling constants using a generalized Karplus-type equation. In turn, the 3J(H,H) values were used as initial input data for the spectral simulation of 1, which after iteration provided an excellent correlation with the experimental 1H NMR spectrum. The calculated 3J(H,H) values closely predicted the experimental values, excepting the coupling constant between the axial hydrogen alpha to the carbonyl group and the equatorial hydrogen beta to the carbonyl group (J(2beta, 3beta)). The difference is explained in terms of the electron density distribution found in the highest occupied molecular orbital (HOMO) of 1. The simulated spectrum, together with 2D NMR experiments, allowed the total assignment of the 1H and 13C NMR spectra of 1. PMID:15366065

  7. Development of a 2D precision cryogenic chopper for METIS

    NASA Astrophysics Data System (ADS)

    Paalvast, Sander L.; Janssen, Huub; Teuwen, Maurice; Huisman, Robert; Brandl, Bernhard; Molster, Frank; Venema, Lars

    2012-09-01

    The Mid-infrared E-ELT Imager and Spectrograph, or METIS, is foreseen as the third instrument for the European Extremely Large Telescope (E-ELT). A key part of METIS is the Cold Chopper (MCC) which switches the optical beam between the target and a nearby reference sky during observation for elimination of the fluctuating IR background signal in post-processing. This paper discusses the development of the MCC demonstrator. The chopper mirror (Ø64mm) has to tip/tilt in 2D with a combined angle of up to 13.6mrad with 1.7μrad stability and repeatability within 5ms (95% duty cycle at 5Hz) at 80K. As these requirements cannot be met in the presence of friction or backlash, the mirror is guided by a monolithically integrated flexure mechanism. The angular position is actuated by three linear actuators and measured by three linear position sensors, resulting in a fast tip, tilt, and focus mirror. Using the third actuator to introduce symmetry, homogeneity in forces and heat flux is obtained. Both the actuators and the sensors are key components. A voice coil actuator had to be custom designed, to achieve the required acceleration force within the specified 1W heat load. The requirements for the displacement measurement can be met with a commercially available, fiber interferometry system. For integration of this system, stray light elimination is a critical design aspect and retro-reflectors have been used to reflect sufficient power into the fiber at large tip/tilt angles.

  8. Differential CYP 2D6 Metabolism Alters Primaquine Pharmacokinetics

    PubMed Central

    Potter, Brittney M. J.; Xie, Lisa H.; Vuong, Chau; Zhang, Jing; Zhang, Ping; Duan, Dehui; Luong, Thu-Lan T.; Bandara Herath, H. M. T.; Dhammika Nanayakkara, N. P.; Tekwani, Babu L.; Walker, Larry A.; Nolan, Christina K.; Sciotti, Richard J.; Zottig, Victor E.; Smith, Philip L.; Paris, Robert M.; Read, Lisa T.; Li, Qigui; Pybus, Brandon S.; Sousa, Jason C.; Reichard, Gregory A.

    2015-01-01

    Primaquine (PQ) metabolism by the cytochrome P450 (CYP) 2D family of enzymes is required for antimalarial activity in both humans (2D6) and mice (2D). Human CYP 2D6 is highly polymorphic, and decreased CYP 2D6 enzyme activity has been linked to decreased PQ antimalarial activity. Despite the importance of CYP 2D metabolism in PQ efficacy, the exact role that these enzymes play in PQ metabolism and pharmacokinetics has not been extensively studied in vivo. In this study, a series of PQ pharmacokinetic experiments were conducted in mice with differential CYP 2D metabolism characteristics, including wild-type (WT), CYP 2D knockout (KO), and humanized CYP 2D6 (KO/knock-in [KO/KI]) mice. Plasma and liver pharmacokinetic profiles from a single PQ dose (20 mg/kg of body weight) differed significantly among the strains for PQ and carboxy-PQ. Additionally, due to the suspected role of phenolic metabolites in PQ efficacy, these were probed using reference standards. Levels of phenolic metabolites were highest in mice capable of metabolizing CYP 2D6 substrates (WT and KO/KI 2D6 mice). PQ phenolic metabolites were present in different quantities in the two strains, illustrating species-specific differences in PQ metabolism between the human and mouse enzymes. Taking the data together, this report furthers understanding of PQ pharmacokinetics in the context of differential CYP 2D metabolism and has important implications for PQ administration in humans with different levels of CYP 2D6 enzyme activity. PMID:25645856

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

    NASA Astrophysics Data System (ADS)

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

    2015-08-01

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

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

    PubMed Central

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

    2015-01-01

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

  11. Dual Species NMR Oscillator

    NASA Astrophysics Data System (ADS)

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

    2016-05-01

    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 π 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 details of the apparatus and measurements of dual species co-magnetometry using this method. Research supported by the NSF and Northrop-Grumman Corp.

  12. 2D to 3D to 2D Dimensionality Crossovers in Thin BSCCO Films

    NASA Astrophysics Data System (ADS)

    Williams, Gary A.

    2003-03-01

    With increasing temperature the superfluid fraction in very thin BSCCO films undergoes a series of dimensionality crossovers. At low temperatures the strong anisotropy causes the thermal excitations to be 2D pancake-antipancake pairs in uncoupled layers. At higher temperatures where the c-axis correlation length becomes larger than a layer there is a crossover to 3D vortex loops. These are initially elliptical, but as the 3D Tc is approached they become more circular as the anisotropy scales away, as modeled by Shenoy and Chattopadhyay [1]. Close to Tc when the correlation length becomes comparable to the film thickness there is a further crossover to a 2D Kosterlitz-Thouless transition, with a drop of the superfluid fraction to zero at T_KT which can be of the order of 1 K below T_c. Good agreement with this model is found for experiments on thin BSCCO 2212 films [2]. 1. S. R. Shenoy and B. Chattopadhyay, Phys. Rev. B 51, 9129 (1995). 2. K. Osborn et al., cond-mat/0204417.

  13. Mechanical characterization of 2D, 2D stitched, and 3D braided/RTM materials

    NASA Technical Reports Server (NTRS)

    Deaton, Jerry W.; Kullerd, Susan M.; Portanova, Marc A.

    1993-01-01

    Braided composite materials have potential for application in aircraft structures. Fuselage frames, floor beams, wing spars, and stiffeners are examples where braided composites could find application if cost effective processing and damage tolerance requirements are met. Another important consideration for braided composites relates to their mechanical properties and how they compare to the properties of composites produced by other textile composite processes being proposed for these applications. Unfortunately, mechanical property data for braided composites do not appear extensively in the literature. Data are presented in this paper on the mechanical characterization of 2D triaxial braid, 2D triaxial braid plus stitching, and 3D (through-the-thickness) braid composite materials. The braided preforms all had the same graphite tow size and the same nominal braid architectures, (+/- 30 deg/0 deg), and were resin transfer molded (RTM) using the same mold for each of two different resin systems. Static data are presented for notched and unnotched tension, notched and unnotched compression, and compression after impact strengths at room temperature. In addition, some static results, after environmental conditioning, are included. Baseline tension and compression fatigue results are also presented, but only for the 3D braided composite material with one of the resin systems.

  14. Development and validation of sensitive LC-MS/MS assays for quantification of HP-β-CD in human plasma and CSF

    PubMed Central

    Jiang, Hui; Sidhu, Rohini; Fujiwara, Hideji; De Meulder, Marc; de Vries, Ronald; Gong, Yong; Kao, Mark; Porter, Forbes D.; Yanjanin, Nicole M.; Carillo-Carasco, Nuria; Xu, Xin; Ottinger, Elizabeth; Woolery, Myra; Ory, Daniel S.; Jiang, Xuntian

    2014-01-01

    2-Hydroxypropyl-β-cyclodextrin (HP-β-CD), a widely used excipient for drug formulation, has emerged as an investigational new drug for the treatment of Niemann-Pick type C1 (NPC1) disease, a neurodegenerative cholesterol storage disorder. Development of a sensitive quantitative LC-MS/MS assay to monitor the pharmacokinetics (PKs) of HP-β-CD required for clinical trials has been challenging owing to the dispersity of the HP-β-CD. To support a phase 1 clinical trial for ICV delivery of HP-β-CD in NPC1 patients, novel methods for quantification of HP-β-CD in human plasma and cerebrospinal fluid (CSF) using LC-MS/MS were developed and validated: a 2D-LC-in-source fragmentation-MS/MS (2D-LC-IF-MS/MS) assay and a reversed phase ultra performance LC-MS/MS (RP-UPLC-MS/MS) assay. In both assays, protein precipitation and “dilute and shoot” procedures were used to process plasma and CSF, respectively. The assays were fully validated and in close agreement, and allowed determination of PK parameters for HP-β-CD. The LC-MS/MS methods are ∼100-fold more sensitive than the current HPLC assay, and were successfully employed to analyze HP-β-CD in human plasma and CSF samples to support the phase 1 clinical trial of HP-β-CD in NPC1 patients. PMID:24868096

  15. Characterization of zebrafish cardiac proteome using online pH gradient SCX-RP HPLC-MS/MS platform.

    PubMed

    Zhang, Jiang; Lanham, Kevin A; Heideman, Warren; Peterson, Richard E; Li, Lingjun

    2013-01-01

    Two-dimensional HPLC coupled with tandem MS (MS/MS) has become a mainstream technique in the shotgun proteomics for large-scale identification of proteins from biological samples. This powerful technology provides speed, sensitivity, and dynamic range which are essential to probe complex peptide mixtures from proteomic samples. Herein we present a pH gradient SCX-RP 2D HPLC-MS/MS method designed to improve the peptide resolution and protein identification from complex proteomic samples. The comparison between the pH gradient SCX-RP 2D HPLC method and traditional salt gradient SCX-RP method was presented. A two-step sample prefractionation method utilizing microwave-assisted tryptic digestion to improve the identification of insoluble proteins was also introduced. This novel 2D HPLC-MS/MS method was applied to the heart proteomic sample of the zebrafish, Danio rerio, to provide comprehensive cardiac proteomic profiling of this important model organism for cardiovascular and environmental toxicology studies. PMID:23606253

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

    NASA Astrophysics Data System (ADS)

    Lee, Woonghee; Hu, Kaifeng; Tonelli, Marco; Bahrami, Arash; Neuhardt, Elizabeth; Glass, Karen C.; Markley, John L.

    2013-11-01

    ADAPT-NMR (Assignment-directed Data collection Algorithm utilizing a Probabilistic Toolkit in NMR) supports automated NMR data collection and backbone and side chain assignment for [U-13C, U-15N]-labeled proteins. Given the sequence of the protein and data for the orthogonal 2D 1H-15N and 1H-13C planes, the algorithm automatically directs the collection of tilted plane data from a variety of triple-resonance experiments so as to follow an efficient pathway toward the probabilistic assignment of 1H, 13C, and 15N signals to specific atoms in the covalent structure of the protein. Data collection and assignment calculations continue until the addition of new data no longer improves the assignment score. ADAPT-NMR was first implemented on Varian (Agilent) spectrometers [A. Bahrami, M. Tonelli, S.C. Sahu, K.K. Singarapu, H.R. Eghbalnia, J.L. Markley, PLoS One 7 (2012) e33173]. Because of broader interest in the approach, we present here a version of ADAPT-NMR for Bruker spectrometers. We have developed two AU console programs (ADAPT_ORTHO_run and ADAPT_NMR_run) that run under TOPSPIN Versions 3.0 and higher. To illustrate the performance of the algorithm on a Bruker spectrometer, we tested one protein, chlorella ubiquitin (76 amino acid residues), that had been used with the Varian version: the Bruker and Varian versions achieved the same level of assignment completeness (98% in 20 h). As a more rigorous evaluation of the Bruker version, we tested a larger protein, BRPF1 bromodomain (114 amino acid residues), which yielded an automated assignment completeness of 86% in 55 h. Both experiments were carried out on a 500 MHz Bruker AVANCE III spectrometer equipped with a z-gradient 5 mm TCI probe. ADAPT-NMR is available at http://pine.nmrfam.wisc.edu/ADAPT-NMR in the form of pulse programs, the two AU programs, and instructions for installation and use.

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

    PubMed

    Lee, Woonghee; Hu, Kaifeng; Tonelli, Marco; Bahrami, Arash; Neuhardt, Elizabeth; Glass, Karen C; Markley, John L

    2013-11-01

    ADAPT-NMR (Assignment-directed Data collection Algorithm utilizing a Probabilistic Toolkit in NMR) supports automated NMR data collection and backbone and side chain assignment for [U-(13)C, U-(15)N]-labeled proteins. Given the sequence of the protein and data for the orthogonal 2D (1)H-(15)N and (1)H-(13)C planes, the algorithm automatically directs the collection of tilted plane data from a variety of triple-resonance experiments so as to follow an efficient pathway toward the probabilistic assignment of (1)H, (13)C, and (15)N signals to specific atoms in the covalent structure of the protein. Data collection and assignment calculations continue until the addition of new data no longer improves the assignment score. ADAPT-NMR was first implemented on Varian (Agilent) spectrometers [A. Bahrami, M. Tonelli, S.C. Sahu, K.K. Singarapu, H.R. Eghbalnia, J.L. Markley, PLoS One 7 (2012) e33173]. Because of broader interest in the approach, we present here a version of ADAPT-NMR for Bruker spectrometers. We have developed two AU console programs (ADAPT_ORTHO_run and ADAPT_NMR_run) that run under TOPSPIN Versions 3.0 and higher. To illustrate the performance of the algorithm on a Bruker spectrometer, we tested one protein, chlorella ubiquitin (76 amino acid residues), that had been used with the Varian version: the Bruker and Varian versions achieved the same level of assignment completeness (98% in 20 h). As a more rigorous evaluation of the Bruker version, we tested a larger protein, BRPF1 bromodomain (114 amino acid residues), which yielded an automated assignment completeness of 86% in 55 h. Both experiments were carried out on a 500 MHz Bruker AVANCE III spectrometer equipped with a z-gradient 5 mm TCI probe. ADAPT-NMR is available at http://pine.nmrfam.wisc.edu/ADAPT-NMR in the form of pulse programs, the two AU programs, and instructions for installation and use. PMID:24091140

  18. Differential Cytochrome P450 2D Metabolism Alters Tafenoquine Pharmacokinetics

    PubMed Central

    Vuong, Chau; Xie, Lisa H.; Potter, Brittney M. J.; Zhang, Jing; Zhang, Ping; Duan, Dehui; Nolan, Christina K.; Sciotti, Richard J.; Zottig, Victor E.; Nanayakkara, N. P. Dhammika; Tekwani, Babu L.; Walker, Larry A.; Smith, Philip L.; Paris, Robert M.; Read, Lisa T.; Li, Qigui; Pybus, Brandon S.; Sousa, Jason C.; Reichard, Gregory A.; Smith, Bryan

    2015-01-01

    Cytochrome P450 (CYP) 2D metabolism is required for the liver-stage antimalarial efficacy of the 8-aminoquinoline molecule tafenoquine in mice. This could be problematic for Plasmodium vivax radical cure, as the human CYP 2D ortholog (2D6) is highly polymorphic. Diminished CYP 2D6 enzyme activity, as in the poor-metabolizer phenotype, could compromise radical curative efficacy in humans. Despite the importance of CYP 2D metabolism for tafenoquine liver-stage efficacy, the exact role that CYP 2D metabolism plays in the metabolism and pharmacokinetics of tafenoquine and other 8-aminoquinoline molecules has not been extensively studied. In this study, a series of tafenoquine pharmacokinetic experiments were conducted in mice with different CYP 2D metabolism statuses, including wild-type (WT) (reflecting extensive metabolizers for CYP 2D6 substrates) and CYPmouse 2D knockout (KO) (reflecting poor metabolizers for CYP 2D6 substrates) mice. Plasma and liver pharmacokinetic profiles from a single 20-mg/kg of body weight dose of tafenoquine differed between the strains; however, the differences were less striking than previous results obtained for primaquine in the same model. Additionally, the presence of a 5,6-ortho-quinone tafenoquine metabolite was examined in both mouse strains. The 5,6-ortho-quinone species of tafenoquine was observed, and concentrations of the metabolite were highest in the WT extensive-metabolizer phenotype. Altogether, this study indicates that CYP 2D metabolism in mice affects tafenoquine pharmacokinetics and could have implications for human tafenoquine pharmacokinetics in polymorphic CYP 2D6 human populations. PMID:25870069

  19. Characterization of Seed Storage Proteins from Chickpea Using 2D Electrophoresis Coupled with Mass Spectrometry.

    PubMed

    Singh, Pramod Kumar; Shrivastava, Nidhi; Chaturvedi, Krishna; Sharma, Bechan; Bhagyawant, Sameer S

    2016-01-01

    Proteomic analysis was employed to map the seed storage protein network in landrace and cultivated chickpea accessions. Protein extracts were separated by two-dimensional gel electrophoresis (2D-GE) across a broad range 3.0-10.0 immobilized pH gradient (IPG) strips. Comparative elucidation of differentially expressed proteins between two diverse geographically originated chickpea accessions was carried out using 2D-GE coupled with mass spectrometry. A total of 600 protein spots were detected in these accessions. In-gel protein expression patterns revealed three protein spots as upregulated and three other as downregulated. Using trypsin in-gel digestion, these differentially expressed proteins were identified by matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF-MS) which showed 45% amino acid homology of chickpea seed storage proteins with Arabidopsis thaliana. PMID:27144024

  20. Characterization of Seed Storage Proteins from Chickpea Using 2D Electrophoresis Coupled with Mass Spectrometry

    PubMed Central

    Singh, Pramod Kumar; Shrivastava, Nidhi; Chaturvedi, Krishna

    2016-01-01

    Proteomic analysis was employed to map the seed storage protein network in landrace and cultivated chickpea accessions. Protein extracts were separated by two-dimensional gel electrophoresis (2D-GE) across a broad range 3.0–10.0 immobilized pH gradient (IPG) strips. Comparative elucidation of differentially expressed proteins between two diverse geographically originated chickpea accessions was carried out using 2D-GE coupled with mass spectrometry. A total of 600 protein spots were detected in these accessions. In-gel protein expression patterns revealed three protein spots as upregulated and three other as downregulated. Using trypsin in-gel digestion, these differentially expressed proteins were identified by matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF-MS) which showed 45% amino acid homology of chickpea seed storage proteins with Arabidopsis thaliana. PMID:27144024

  1. NMR Mechanisms and Fluid Typing Based on Numerical Simulation in Gas-Bearing Shale

    NASA Astrophysics Data System (ADS)

    Tan, M.; Xu, J.; Wang, X.

    2013-12-01

    In Nuclear Magnetic Resonance (NMR) survey of oil- or gas-bearing shales, the relaxation is so fast and the diffusion is so low, and oil or gas typing is difficult to distinguish from each other using the previous analysis method. To study the NMR responses in gas-bearing shale, we supposed an ideal shale model including incredible water, free and adsorbed gas, and kerogen. Firstly, we supposed a series of ideal shale models with incredible water, free and adsorbed gas, and kerogen. Then, some simulations are performed for two-dimensional T2-D plots, and NMR characteristics are summarized successfully. Then, a series of simulations of different models with different adsorbed gas fractions are made, and the NMR responses are analyzed, from which we can identify the adsorbed gas and free gas. In inversion, a hybrid method with LSQR and TSVD is proved suitable for D-T2 NMR of gas shale with slow and fast diffusion, and short and long relaxation. It is noticed that the activation sequence of NMR is also important for accurate fluid typing in gas-bearing shale. We design a series of activation sequences, and simulate the corresponding NMR echo decays, and invert the fluid properties to search for an optimal activation sequence for fluid typing purpose. Figure 1 SEM picture and petrophysical model of organic shale. (a) 2D SEM shows pore and kerogen within shale. Black deposits pore, and dark gray is kerogen, light grey is matrix including clay and silica; (b) Petrophysical model Figure 2 Comparison of 2D-NMR simulations with different adsorbed gas fractions, (a) ɛ =0.0, (b) ɛ =0.2, (c) ɛ=0.4, t (d) ɛ =0.6, (e) ɛ =0.8, and (f) ɛ=1.0. From D-T2 plots, the position and amplitude of signals in T2-D plots indicate the fluid typing and fraction of the gas or adsorbed gas.

  2. A Geometric Boolean Library for 2D Objects

    2006-01-05

    The 2D Boolean Library is a collection of C++ classes -- which primarily represent 2D geometric data and relationships, and routines -- which contain algorithms for 2D geometric Boolean operations and utility functions. Classes are provided for 2D points, lines, arcs, edgeuses, loops, surfaces and mask sets. Routines are provided that incorporate the Boolean operations Union(OR), XOR, Intersection and Difference. Various analytical geometry routines and routines for importing and exporting the data in various filemore » formats, are also provided in the library.« less

  3. A Geometric Boolean Library for 2D Objects

    SciTech Connect

    McBride, Corey L.; Yarberry, Victor; Jorgensen, Craig

    2006-01-05

    The 2D Boolean Library is a collection of C++ classes -- which primarily represent 2D geometric data and relationships, and routines -- which contain algorithms for 2D geometric Boolean operations and utility functions. Classes are provided for 2D points, lines, arcs, edgeuses, loops, surfaces and mask sets. Routines are provided that incorporate the Boolean operations Union(OR), XOR, Intersection and Difference. Various analytical geometry routines and routines for importing and exporting the data in various file formats, are also provided in the library.

  4. Screening proteins for NMR suitability

    PubMed Central

    Yee, Adelinda A.; Semesi, Anthony; Garcia, Maite; Arrowsmith, Cheryl H.

    2014-01-01

    Summary NMR spectroscopy is an invaluable tool in structural genomics. Identification of protein samples that are amenable to structure determination by NMR spectroscopy requires efficient screening. Here, we describe how we prepare multiple samples in parallel and screen by NMR. The method described here is applicable to large structural genomics projects but can easily be scaled down for application to small structural biology projects since all the equipments used are those commonly found in any NMR structural biology laboratory. PMID:24590717

  5. Modern NMR Spectroscopy.

    ERIC Educational Resources Information Center

    Jelinski, Lynn W.

    1984-01-01

    Discusses direct chemical information that can be obtained from modern nuclear magnetic resonance (NMR) methods, concentrating on the types of problems that can be solved. Shows how selected methods provide information about polymers, bipolymers, biochemistry, small organic molecules, inorganic compounds, and compounds oriented in a magnetic…

  6. Enantiodiscrimination by NMR spectroscopy.

    PubMed

    Uccello-Barretta, Gloria; Balzano, Federica; Salvadori, Piero

    2006-01-01

    The analysis of enantiorecognition processes involves the detection of enantiomeric species as well as the study of chiral discrimination mechanisms. In both fields Nuclear Magnetic Resonance (NMR) spectroscopy plays a fundamental role, providing several tools, based on the use of suitable chiral auxiliaries, for observing distinct signals of enantiomers and for investigating the complexation phenomena involved in enantiodiscrimination processes. PMID:17100610

  7. NMR studies of bond arrangements in alkali phosphate glasses

    SciTech Connect

    Alam, T.M.; Brow, R.K.

    1998-01-01

    Solid-state magic angle spinning (MAS) nuclear magnetic resonance (NMR) spectroscopy has become a powerful tool for the investigation of local structure and medium range order in glasses. Previous {sup 31}P MAS NMR studies have detailed the local structure for a series of phosphate glasses. Phosphate tetrahedra within the glass network are commonly described using the Q{sup n} notation, where n = 0, 1, 2, 3 and represents the number of bridging oxygens attached to the phosphate. Using {sup 31}P MAS NMR different phosphate environments are readily identified and quantified. In this paper, the authors present a brief description of recent one dimensional (1D) {sup 6}Li, {sup 7}Li and {sup 31}P MAS experiments along with two-dimensional (2D) {sup 31}P exchange NMR experiments for a series of lithium ultraphosphate glasses. From the 2D exchange experiments the connectivities between different Q{sup n} phosphate tetrahedra were directly measured, while the 1D experiments provided a measure of the P-O-P bond angle distribution and lithium coordination number as a function of Li{sub 2}O concentration.

  8. AnisWave2D: User's Guide to the 2d Anisotropic Finite-DifferenceCode

    SciTech Connect

    Toomey, Aoife

    2005-01-06

    This document describes a parallel finite-difference code for modeling wave propagation in 2D, fully anisotropic materials. The code utilizes a mesh refinement scheme to improve computational efficiency. Mesh refinement allows the grid spacing to be tailored to the velocity model, so that fine grid spacing can be used in low velocity zones where the seismic wavelength is short, and coarse grid spacing can be used in zones with higher material velocities. Over-sampling of the seismic wavefield in high velocity zones is therefore avoided. The code has been implemented to run in parallel over multiple processors and allows large-scale models and models with large velocity contrasts to be simulated with ease.

  9. Klassifikation von Standardebenen in der 2D-Echokardiographie mittels 2D-3D-Bildregistrierung

    NASA Astrophysics Data System (ADS)

    Bergmeir, Christoph; Subramanian, Navneeth

    Zum Zweck der Entwicklung eines Systems, das einen unerfahrenen Anwender von Ultraschall (US) zur Aufnahme relevanter anatomischer Strukturen leitet, untersuchen wir die Machbarkeit von 2D-US zu 3D-CT Registrierung. Wir verwenden US-Aufnahmen von Standardebenen des Herzens, welche zu einem 3D-CT-Modell registriert werden. Unser Algorithmus unterzieht sowohl die US-Bilder als auch den CT-Datensatz Vorverarbeitungsschritten, welche die Daten durch Segmentierung auf wesentliche Informationen in Form von Labein für Muskel und Blut reduzieren. Anschließend werden diese Label zur Registrierung mittels der Match-Cardinality-Metrik genutzt. Durch mehrmaliges Registrieren mit verschiedenen Initialisierungen ermitteln wir die im US-Bild sichtbare Standardebene. Wir evaluierten die Methode auf sieben US-Bildern von Standardebenen. Fünf davon wurden korrekt zugeordnet.

  10. NMR Studies of Dynamic Biomolecular Conformational Ensembles

    PubMed Central

    Torchia, Dennis A.

    2015-01-01

    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. PMID:25669739

  11. Depth-selective 2D-ACAR studies on low- k dielectric thin films

    NASA Astrophysics Data System (ADS)

    Eijt, S. W. H.; van Veen, A.; Falub, C. V.; Galindo, R. Escobar; Schut, H.; Mijnarends, P. E.; de Theije, F. K.; Balkenende, A. R.

    2003-10-01

    Depth-selective 2D-ACAR investigations on ordered mesoporous silica thin films provide direct evidence that para-positronium ( p-Ps) created deep in the films can escape through a network of interconnected pores. The depth dependence of the escape fraction and of the average kinetic energy of non-thermally excited p-Ps is in quantitative agreement with Monte Carlo modeling, assuming classical collisions of p-Ps with the pore walls. The model provides insight in the shape of the angular correlation distributions and their sensitivity to, e.g., the effective wall mass Ms and pore dimensions.

  12. Functional characterization of CYP2D6 enhancer polymorphisms

    PubMed Central

    Wang, Danxin; Papp, Audrey C.; Sun, Xiaochun

    2015-01-01

    CYP2D6 metabolizes nearly 25% of clinically used drugs. Genetic polymorphisms cause large inter-individual variability in CYP2D6 enzyme activity and are currently used as biomarker to predict CYP2D6 metabolizer phenotype. Previously, we had identified a region 115 kb downstream of CYP2D6 as enhancer for CYP2D6, containing two completely linked single nucleotide polymorphisms (SNPs), rs133333 and rs5758550, associated with enhanced transcription. However, the enhancer effect on CYP2D6 expression, and the causative variant, remained to be ascertained. To characterize the CYP2D6 enhancer element, we applied chromatin conformation capture combined with the next-generation sequencing (4C assays) and chromatin immunoprecipitation with P300 antibody, in HepG2 and human primary culture hepatocytes. The results confirmed the role of the previously identified enhancer region in CYP2D6 expression, expanding the number of candidate variants to three highly linked SNPs (rs133333, rs5758550 and rs4822082). Among these, only rs5758550 demonstrated regulating enhancer activity in a reporter gene assay. Use of clustered regularly interspaced short palindromic repeats mediated genome editing in HepG2 cells targeting suspected enhancer regions decreased CYP2D6 mRNA expression by 70%, only upon deletion of the rs5758550 region. These results demonstrate robust effects of both the enhancer element and SNP rs5758550 on CYP2D6 expression, supporting consideration of rs5758550 for CYP2D6 genotyping panels to yield more accurate phenotype prediction. PMID:25381333

  13. An Incompressible 2D Didactic Model with Singularity and Explicit Solutions of the 2D Boussinesq Equations

    NASA Astrophysics Data System (ADS)

    Chae, Dongho; Constantin, Peter; Wu, Jiahong

    2014-09-01

    We give an example of a well posed, finite energy, 2D incompressible active scalar equation with the same scaling as the surface quasi-geostrophic equation and prove that it can produce finite time singularities. In spite of its simplicity, this seems to be the first such example. Further, we construct explicit solutions of the 2D Boussinesq equations whose gradients grow exponentially in time for all time. In addition, we introduce a variant of the 2D Boussinesq equations which is perhaps a more faithful companion of the 3D axisymmetric Euler equations than the usual 2D Boussinesq equations.

  14. Nested data independent MS/MS acquisition.

    PubMed

    Kaufmann, Anton; Walker, Stephan

    2016-07-01

    Data independent acquisition (DIA) attempts to provide comprehensive MS/MS data while providing a cycle time that is capable of following the elution profile of chromatographic peaks. Currently available MS technology is not yet fully capable of fulfilling these expectations. This paper suggests a new multiplex-based approach to more closely achieve this objective. Customized scans have been programmed for a Q Orbitrap instrument. Multiple nonadjacent mass range segments are sequentially collected (cut out) by the quadrupole. These combined mass ranges undergo fragmentation, and the resulting product ions are analyzed as a whole by the Orbitrap analyzer. The systematical variation of the mass range segments (nested design) permits the mathematical assignment of the observed product ions within a narrow precursor mass range. The proposed approach allows the use of mass windows that are narrower than those in conventional DIA (SWATH). A unique aspect of the proposed approach is the fact that halving the mass window width requires the addition of only a single multiplexed scan. This is different from conventional DIA, which requires the number of mass windows to be doubled in order to achieve the same objective. This paper shows that for a given cycle time, the proposed nested DIA technique produces significantly less chimeric product ion spectra than conventional DIA. However, further improvements from the programming, and most likely the hardware side, are still required in order to achieve the aim of comprehensive MS/MS. Graphical Abstract Schematic of nested design. PMID:27188447

  15. Stable isotope-enhanced two- and three-dimensional diffusion ordered 13C-NMR spectroscopy (SIE-DOSY 13C-NMR)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Stable Isotope-Enhanced Diffusion Ordered (SIE-DOSY) 13C-NMR has been applied to 13C-enriched carbohydrates and has been used to determine diffusion coefficients for pentose and hexose monosaccharides, a disaccharide and a trisaccharide. These 2D spectra were obtained with as little as 8 min of acq...

  16. Efficient Visible Quasi-2D Perovskite Light-Emitting Diodes.

    PubMed

    Byun, Jinwoo; Cho, Himchan; Wolf, Christoph; Jang, Mi; Sadhanala, Aditya; Friend, Richard H; Yang, Hoichang; Lee, Tae-Woo

    2016-09-01

    Efficient quasi-2D-structure perovskite light-emitting diodes (4.90 cd A(-1) ) are demonstrated by mixing a 3D-structured perovskite material (methyl ammonium lead bromide) and a 2D-structured perovskite material (phenylethyl ammonium lead bromide), which can be ascribed to better film uniformity, enhanced exciton confinement, and reduced trap density. PMID:27334788

  17. Integrating Mobile Multimedia into Textbooks: 2D Barcodes

    ERIC Educational Resources Information Center

    Uluyol, Celebi; Agca, R. Kagan

    2012-01-01

    The major goal of this study was to empirically compare text-plus-mobile phone learning using an integrated 2D barcode tag in a printed text with three other conditions described in multimedia learning theory. The method examined in the study involved modifications of the instructional material such that: a 2D barcode was used near the text, the…

  18. LC-MS and GC-MS metabolite profiling of nickel(II) complexes in the latex of the nickel-hyperaccumulating tree Sebertia acuminata and identification of methylated aldaric acid as a new nickel(II) ligand.

    PubMed

    Callahan, Damien L; Roessner, Ute; Dumontet, Vincent; Perrier, Nicolas; Wedd, Anthony G; O'Hair, Richard A J; Baker, Alan J M; Kolev, Spas D

    2008-01-01

    Targeted liquid chromatography-mass spectrometry (LC-MS) technology using size exclusion chromatography and metabolite profiling based on gas chromatography-mass spectrometry (GC-MS) were used to study the nickel-rich latex of the hyperaccumulating tree Sebertia acuminata. More than 120 compounds were detected, 57 of these were subsequently identified. A methylated aldaric acid (2,4,5-trihydroxy-3-methoxy-1,6-hexan-dioic acid) was identified for the first time in biological extracts and its structure was confirmed by 1D and 2D nuclear magnetic resonance (NMR) spectroscopy. After citric acid, it appears to be one of the most abundant small organic molecules present in the latex studied. Nickel(II) complexes of stoichiometry NiII:acid=1:2 were detected for these two acids as well as for malic, itaconic, erythronic, galacturonic, tartaric, aconitic and saccharic acids. These results provide further evidence that organic acids may play an important role in the transport and possibly in the storage of metal ions in hyperaccumulating plants. PMID:17765935

  19. Solution structural characteristics of cyanometmyoglobin: resonance assignment of heme cavity residues by two-dimensional NMR.

    PubMed

    Emerson, S D; La Mar, G

    1990-02-13

    Steady-state nuclear Overhauser effects (NOE), two-dimensional (2D) nuclear Overhauser effect spectroscopy (NOESY), and 2D spin correlation spectroscopy (COSY) have been applied to the fully paramagnetic low-spin, cyanide-ligated complex of sperm whale ferric myoglobin to assign the majority of the heme pocket side-chain proton signals and the remainder of the heme signals. It is shown that the 2D NOESY map reveals essentially all dipolar connectivities observed in ordinary 1D NOE experiments and expected on the basis of crystal coordinates, albeit often more weakly than in a diamagnetic analogue. For extremely broad (approximately 600-Hz) and rapidly relaxing (Tf1 approximately 3 ms) signals which show no NEOSY peaks, we demonstrate that conventional steady-state NOEs obtained under very rapid pulsing conditions still allow detection of the critical dipoar connectivities that allow unambiguous assignments. The COSY map was found to be generally less useful for the hyperfine-shifted residues, with cross peaks detected only for protons greater than 6 A from the iron. Nevertheless, numerous critical COSY cross peaks between strongly hyperfine-shifted peaks were resolved and assigned. In all, 95% (53 of 56 signals) of the total proton sets within approximately 7.5 A of the iron, the region experiencing the strongest hyperfine shifts and paramagnetic relaxation, are now unambiguously assigned. Hence it is clear that the 2D methods can be profitably applied to paramagnetic proteins. The scope and limitations of such application are discussed. The resulting hyperfine shift pattern for the heme confirmed expectations based on model compounds. In contrast, while exhibiting fortuitous 1H NMR spectral similarities, a major discrepancy was uncovered between the hyperfine shift pattern of the axially bound (F8 histidyl) imidazole in the protein and that of the imidazole in a relevant model compound [Chacko, V.P., & La Mar, G. N. (1982) J. Am. Chem. Soc. 104, 7002

  20. Van der Waals stacked 2D layered materials for optoelectronics

    NASA Astrophysics Data System (ADS)

    Zhang, Wenjing; Wang, Qixing; Chen, Yu; Wang, Zhuo; Wee, Andrew T. S.

    2016-06-01

    The band gaps of many atomically thin 2D layered materials such as graphene, black phosphorus, monolayer semiconducting transition metal dichalcogenides and hBN range from 0 to 6 eV. These isolated atomic planes can be reassembled into hybrid heterostructures made layer by layer in a precisely chosen sequence. Thus, the electronic properties of 2D materials can be engineered by van der Waals stacking, and the interlayer coupling can be tuned, which opens up avenues for creating new material systems with rich functionalities and novel physical properties. Early studies suggest that van der Waals stacked 2D materials work exceptionally well, dramatically enriching the optoelectronics applications of 2D materials. Here we review recent progress in van der Waals stacked 2D materials, and discuss their potential applications in optoelectronics.

  1. Unitary quantum lattice gas representation of 2D quantum turbulence

    NASA Astrophysics Data System (ADS)

    Zhang, Bo; Vahala, George; Vahala, Linda; Soe, Min

    2011-05-01

    Quantum vortex structures and energy cascades are examined for two dimensional quantum turbulence (2D QT) using a special unitary evolution algorithm. The qubit lattice gas (QLG) algorithm, is employed to simulate the weakly-coupled Bose-Einstein condensate (BEC) governed by the Gross-Pitaevskii (GP) equation. A parameter regime is uncovered in which, as in 3D QT, there is a very short Poincare recurrence time. This short recurrence time is destroyed as the nonlinear interaction energy is increased. Energy cascades for 2D QT are considered to examine whether 2D QT exhibits the inverse cascades of 2D classical turbulence. In the parameter regime considered, the spectra analysis reveals no such dual cascades---dual cascades being a hallmark of 2D classical turbulence.

  2. CYP2D6 polymorphism in patients with eating disorders.

    PubMed

    Peñas-Lledó, E M; Dorado, P; Agüera, Z; Gratacós, M; Estivill, X; Fernández-Aranda, F; Llerena, A

    2012-04-01

    CYP2D6 polymorphism is associated with variability in drug response, endogenous metabolism (that is, serotonin), personality, neurocognition and psychopathology. The relationship between CYP2D6 genetic polymorphism and the risk of eating disorders (ED) was analyzed in 267 patients with ED and in 285 controls. A difference in the CYP2D6 active allele distribution was found between these groups. Women carrying more than two active genes (ultrarapid metabolizers) (7.5 vs 4.6%) or two (67 vs 58.9%) active genes were more frequent among patients with ED, whereas those with one (20.6 vs 30.2%) or zero active genes (4.9 vs 6.3%) were more frequent among controls (P<0.05). Although further research is needed, present findings suggest an association between CYP2D6 and ED. CYP2D6 allele distribution in patients with ED seems related to increased enzyme activity. PMID:20877302

  3. 2D materials and van der Waals heterostructures.

    PubMed

    Novoselov, K S; Mishchenko, A; Carvalho, A; Castro Neto, A H

    2016-07-29

    The physics of two-dimensional (2D) materials and heterostructures based on such crystals has been developing extremely fast. With these new materials, truly 2D physics has begun to appear (for instance, the absence of long-range order, 2D excitons, commensurate-incommensurate transition, etc.). Novel heterostructure devices--such as tunneling transistors, resonant tunneling diodes, and light-emitting diodes--are also starting to emerge. Composed from individual 2D crystals, such devices use the properties of those materials to create functionalities that are not accessible in other heterostructures. Here we review the properties of novel 2D crystals and examine how their properties are used in new heterostructure devices. PMID:27471306

  4. Access to experimentally infeasible spectra by pure-shift NMR covariance.

    PubMed

    Fredi, André; Nolis, Pau; Cobas, Carlos; Parella, Teodor

    2016-09-01

    Covariance processing is a versatile processing tool to generate synthetic NMR spectral representations without the need to acquire time-consuming experimental datasets. Here we show that even experimentally prohibited NMR spectra can be reconstructed by introducing key features of a reference 1D CHn-edited spectrum into standard 2D spectra. This general procedure is illustrated with the calculation of experimentally infeasible multiplicity-edited pure-shift NMR spectra of some very popular homonuclear (ME-psCOSY and ME-psTOCSY) and heteronuclear (ME-psHSQC-TOCSY and ME-psHMBC) experiments. PMID:27494746

  5. RUBIDIUM, a program for computer-aided assignment of two-dimensional NMR spectra of polypeptides.

    PubMed

    Yu, C; Hwang, J F; Chen, T B; Soo, V W

    1992-01-01

    Taking advantage of the rule-based expert system technology, a program named RUBIDIUM (Rule-Based Identification In 2D NMR Spectrum) was developed to accomplish the automatic 1H NMR resonance assignments of polypeptides. Besides noise elimination and peak selection capabilities, RUBIDIUM detects the cross-peak patterns of amino acid residues in the COSY spectrum, assigning these patterns to amino acid types, performing sequential assignments using combined COSY/NOESY spectra, and finally, achieving the total assignment of the 1H NMR spectrum. PMID:1607394

  6. Access to experimentally infeasible spectra by pure-shift NMR covariance

    NASA Astrophysics Data System (ADS)

    Fredi, André; Nolis, Pau; Cobas, Carlos; Parella, Teodor

    2016-09-01

    Covariance processing is a versatile processing tool to generate synthetic NMR spectral representations without the need to acquire time-consuming experimental datasets. Here we show that even experimentally prohibited NMR spectra can be reconstructed by introducing key features of a reference 1D CHn-edited spectrum into standard 2D spectra. This general procedure is illustrated with the calculation of experimentally infeasible multiplicity-edited pure-shift NMR spectra of some very popular homonuclear (ME-psCOSY and ME-psTOCSY) and heteronuclear (ME-psHSQC-TOCSY and ME-psHMBC) experiments.

  7. Digital NMR profiles as building blocks: assembling ¹H fingerprints of steviol glycosides.

    PubMed

    Napolitano, José G; Simmler, Charlotte; McAlpine, James B; Lankin, David C; Chen, Shao-Nong; Pauli, Guido F

    2015-04-24

    This report describes a fragment-based approach to the examination of congeneric organic compounds by NMR spectroscopy. The method combines the classic interpretation of 1D- and 2D-NMR data sets with contemporary computer-assisted NMR analysis. Characteristic NMR profiles of key structural motifs were generated by (1)H iterative full spin analysis and then joined together as building blocks to recreate the (1)H NMR spectra of increasingly complex molecules. To illustrate the methodology described, a comprehensive analysis of steviol (1), seven steviol glycosides (2-8) and two structurally related isosteviol compounds (9, 10) was carried out. The study also assessed the potential impact of this method on relevant aspects of natural product research including structural verification, chemical dereplication, and mixture analysis. PMID:25714117

  8. Digital NMR Profiles as Building Blocks: Assembling 1H Fingerprints of Steviol Glycosides

    PubMed Central

    Napolitano, José G.; Simmler, Charlotte; McAlpine, James B.; Lankin, David C.; Chen, Shao-Nong; Pauli, Guido F.

    2015-01-01

    This report describes a fragment-based approach to the examination of congeneric organic compounds by NMR spectroscopy. The method combines the classic interpretation of 1D- and 2D-NMR data sets with contemporary computer-assisted NMR analysis. Characteristic NMR profiles of key structural motifs were generated by 1H iterative full spin analysis and then joined together as building blocks to recreate the 1H NMR spectra of increasingly complex molecules. To illustrate the methodology described, a comprehensive analysis of steviol (1), seven steviol glycosides (2–8) and two structurally related isosteviol compounds (9, 10) was carried out. The study also assessed the potential impact of this method on relevant aspects of natural product research including structural verification, chemical dereplication, and mixture analysis. PMID:25714117

  9. Preparation of RNA samples with narrow line widths for solid state NMR investigations

    NASA Astrophysics Data System (ADS)

    Huang, Wei; Bardaro, Michael F.; Varani, Gabriele; Drobny, Gary P.

    2012-10-01

    Solid state NMR can provide detailed structural and dynamic information on biological systems that cannot be studied under solution conditions, and can investigate motions which occur with rates that cannot be fully studied by solution NMR. This approach has successfully been used to study proteins, but the application of multidimensional solid state NMR to RNA has been limited because reported line widths have been too broad to execute most multidimensional experiments successfully. A reliable method to generate spectra with narrow line widths is necessary to apply the full range of solid state NMR spectroscopic approaches to RNA. Using the HIV-1 transactivation response (TAR) RNA as a model, we present an approach based on precipitation with polyethylene glycol that improves the line width of 13C signals in TAR from >6 ppm to about 1 ppm, making solid state 2D NMR studies of selectively enriched RNAs feasible at ambient temperature.

  10. NMR-based analysis of the chemical composition of Japanese persimmon aqueous extracts.

    PubMed

    Ryu, Shoraku; Furihata, Kazuo; Koda, Masanori; Wei, Feifei; Miyakawa, Takuya; Tanokura, Masaru

    2016-03-01

    Japanese persimmon (Diospyros kaki L.) is recognized as an outstanding source of biologically active compounds relating to many health benefits. In the present study, NMR spectroscopy provided a comprehensive metabolic overview of Japanese persimmon juice. Detailed signal assignments of Japanese persimmon juice were carried out using various 2D NMR techniques incorporated with broadband water suppression enhanced through T1 effects (BB-WET) or WET sequences, and 26 components, including minor components, were identified. In addition, most components were quantitatively evaluated by the integration of signals using conventional (1) H NMR and BB-WET NMR. This is the first detailed analysis combined with quantitative characterization of chemical components using NMR for Japanese persimmon. Copyright © 2015 John Wiley & Sons, Ltd. PMID:26482562

  11. Primary-Progressive MS (PPMS)

    MedlinePlus

    ... MS? Types of MS Primary progressive MS (PPMS) Primary progressive MS (PPMS) Share Smaller Text Larger Text Print In this article Overview PPMS is characterized by worsening neurologic function ( ...

  12. 224} studied by NMR

    SciTech Connect

    Furukawa, Y; Fang, X; Kögerler, P

    2014-05-14

    7Li nuclear magnetic resonance (NMR) studies have been performed to investigate magnetic properties and spin dynamics of Mn3+ (S = 2) spins in the giant polyoxometalate molecule {Mn40W224}. The 7Li-NMR line width is proportional to the external magnetic field H as expected in a paramagnetic state above 3 K. Below this temperature the line width shows a sudden increase and is almost independent of H, which indicates freezing of the local Mn3+ spins. The temperature dependence of T1 for both 1H and 7Li reveals slow spin dynamics at low temperatures, consistent with spin freezing. The slow spin dynamics is also evidenced by the observation of a peak of 1/T2 around 3 K, where the fluctuation frequency of spins is of the order of ~200 kHz. An explicit form of the temperature dependence of the fluctuation frequency of Mn3+ spins is derived from the nuclear relaxation data.

  13. Sensitivity of GC-EI/MS, GC-EI/MS/MS, LC-ESI/MS/MS, LC-Ag(+) CIS/MS/MS, and GC-ESI/MS/MS for analysis of anabolic steroids in doping control.

    PubMed

    Cha, Eunju; Kim, Sohee; Kim, Ho Jun; Lee, Kang Mi; Kim, Ki Hun; Kwon, Oh-Seung; Lee, Jaeick

    2015-01-01

    This study compared the sensitivity of various separation and ionization methods, including gas chromatography with an electron ionization source (GC-EI), liquid chromatography with an electrospray ionization source (LC-ESI), and liquid chromatography with a silver ion coordination ion spray source (LC-Ag(+) CIS), coupled to a mass spectrometer (MS) for steroid analysis. Chromatographic conditions, mass spectrometric transitions, and ion source parameters were optimized. The majority of steroids in GC-EI/MS/MS and LC-Ag(+) CIS/MS/MS analysis showed higher sensitivities than those obtained with other analytical methods. The limits of detection (LODs) of 65 steroids by GC-EI/MS/MS, 68 steroids by LC-Ag(+) CIS/MS/MS, 56 steroids by GC-EI/MS, 54 steroids by LC-ESI/MS/MS, and 27 steroids by GC-ESI/MS/MS were below cut-off value of 2.0 ng/mL. LODs of steroids that formed protonated ions in LC-ESI/MS/MS analysis were all lower than the cut-off value. Several steroids such as unconjugated C3-hydroxyl with C17-hydroxyl structure showed higher sensitivities in GC-EI/MS/MS analysis relative to those obtained using the LC-based methods. The steroids containing 4, 9, 11-triene structures showed relatively poor sensitivities in GC-EI/MS and GC-ESI/MS/MS analysis. The results of this study provide information that may be useful for selecting suitable analytical methods for confirmatory analysis of steroids. PMID:26489966

  14. The NMR phased array.

    PubMed

    Roemer, P B; Edelstein, W A; Hayes, C E; Souza, S P; Mueller, O M

    1990-11-01

    We describe methods for simultaneously acquiring and subsequently combining data from a multitude of closely positioned NMR receiving coils. The approach is conceptually similar to phased array radar and ultrasound and hence we call our techniques the "NMR phased array." The NMR phased array offers the signal-to-noise ratio (SNR) and resolution of a small surface coil over fields-of-view (FOV) normally associated with body imaging with no increase in imaging time. The NMR phased array can be applied to both imaging and spectroscopy for all pulse sequences. The problematic interactions among nearby surface coils is eliminated (a) by overlapping adjacent coils to give zero mutual inductance, hence zero interaction, and (b) by attaching low input impedance preamplifiers to all coils, thus eliminating interference among next nearest and more distant neighbors. We derive an algorithm for combining the data from the phased array elements to yield an image with optimum SNR. Other techniques which are easier to implement at the cost of lower SNR are explored. Phased array imaging is demonstrated with high resolution (512 x 512, 48-cm FOV, and 32-cm FOV) spin-echo images of the thoracic and lumbar spine. Data were acquired from four-element linear spine arrays, the first made of 12-cm square coils and the second made of 8-cm square coils. When compared with images from a single 15 x 30-cm rectangular coil and identical imaging parameters, the phased array yields a 2X and 3X higher SNR at the depth of the spine (approximately 7 cm). PMID:2266841

  15. NMR imaging of materials

    SciTech Connect

    Vinegar, H.J.; Rothwell, W.P.

    1988-03-01

    A method for obtaining at least one petrophysical property of a porous material containing therein at least one preselected fluid, is described, comprising: NMR imaging the material to generate signals dependent upon both M(0) and T/sub 1/ and M(0) and T/sub 2/, generating separate M(0), T/sub 1/ and T/sub 2/ images from the signals, and determining at least one petrophysical property from at least one of the images.

  16. NMR Studies of Peroxidases.

    NASA Astrophysics Data System (ADS)

    Veitch, Nigel Charles

    Available from UMI in association with The British Library. Requires signed TDF. Peroxidases are a haem-containing group of enzymes with a wide diversity of function within biological systems. While a common characteristic is the ability to catalyse the conversion of hydrogen peroxide to water, it is the accompanying processes of hormone synthesis and degradation which have generated such a high level of interest. However, information at the molecular level is limited to a single well-resolved crystal structure, that of yeast cytochrome c peroxidase. This thesis presents a strategy for the investigation of peroxidase structure and function based on proton nuclear magnetic resonance spectroscopy, a technique which has the ability to address aspects of both protein structure and protein dynamics in solution. The application of one- and two-dimensional NMR techniques has been developed in the context of plant peroxidases, notably the isoenzyme HRP-C derived from the horseradish root. Characterisation of the proton NMR spectra of HRP -C in resting and ligated states provided new information enabling the structure of the binding site for aromatic donor molecules, such as indole-3-propionic, ferulic and benzhydroxamic acids, to be resolved. In order to overcome difficulties encountered with a protein of the complexity of peroxidase, additional information was obtained from chemical shift parameters and the use of peroxidase variants produced by site-directed mutagenesis. A comparative study using NMR spectroscopy was undertaken for wild-type recombinant HRP-C expressed in Escherichia coli, and two protein variants with substitutions made to residues located on the distal side of the haem pocket, Phe41 to Val and Arg38 to Lys. NMR analyses of a plant peroxidase from barley grains and the fungal peroxidase from Coprinus cinereus were also successful using methods conceived with HRP-C. Examination of three specifically constructed recombinant protein variants of C. cinereus

  17. Targeted fluorescence imaging enhanced by 2D materials: a comparison between 2D MoS2 and graphene oxide.

    PubMed

    Xie, Donghao; Ji, Ding-Kun; Zhang, Yue; Cao, Jun; Zheng, Hu; Liu, Lin; Zang, Yi; Li, Jia; Chen, Guo-Rong; James, Tony D; He, Xiao-Peng

    2016-08-01

    Here we demonstrate that 2D MoS2 can enhance the receptor-targeting and imaging ability of a fluorophore-labelled ligand. The 2D MoS2 has an enhanced working concentration range when compared with graphene oxide, resulting in the improved imaging of both cell and tissue samples. PMID:27378648

  18. GFT projection NMR spectroscopy for proteins in the solid state

    PubMed Central

    Franks, W. Trent; Atreya, Hanudatta S.; Szyperski, Thomas

    2011-01-01

    Recording of four-dimensional (4D) spectra for proteins in the solid state has opened new avenues to obtain virtually complete resonance assignments and three-dimensional (3D) structures of proteins. As in solution state NMR, the sampling of three indirect dimensions leads per se to long minimal measurement time. Furthermore, artifact suppression in solid state NMR relies primarily on radio-frequency pulse phase cycling. For an n-step phase cycle, the minimal measurement times of both 3D and 4D spectra are increased n times. To tackle the associated ‘sampling problem’ and to avoid sampling limited data acquisition, solid state G-Matrix Fourier Transform (SS GFT) projection NMR is introduced to rapidly acquire 3D and 4D spectral information. Specifically, (4,3)D (HA)CANCOCX and (3,2)D (HACA)NCOCX were implemented and recorded for the 6 kDa protein GB1 within about 10% of the time required for acquiring the conventional congeners with the same maximal evolution times and spectral widths in the indirect dimensions. Spectral analysis was complemented by comparative analysis of expected spectral congestion in conventional and GFT NMR experiments, demonstrating that high spectral resolution of the GFT NMR experiments enables one to efficiently obtain nearly complete resonance assignments even for large proteins. PMID:21052779

  19. CC2D2A mutations in Meckel and Joubert syndromes indicate a genotype-phenotype correlation

    PubMed Central

    Mougou-Zerelli, Soumaya; Thomas, Sophie; Szenker, Emmanuelle; Audollent, Sophie; Elkhartoufi, Nadia; Babarit, Candice; Romano, Stéphane; Salomon, Rémi; Amiel, Jeanne; Esculpavit, Chantal; Gonzales, Marie; Escudier, Estelle; Leheup, Bruno; Loget, Philippe; Odent, Sylvie; Roume, Joëlle; Gérard, Marion; Delezoide, Anne-Lise; Khung, Suonavy; Patrier, Sophie; Cordier, Marie-Pierre; Bouvier, Raymonde; Martinovic, Jéléna; Gubler, Marie-Claire; Boddaert, Nathalie; Munnich, Arnold; Encha-Razavi, Férechté; Valente, Enza Maria; Saad, Ali; Saunier, Sophie; Vekemans, Michel; Attié-Bitach, Tania

    2009-01-01

    The Meckel syndrome (MKS) is a lethal fetal disorder characterized by diffuse renal cystic dysplasia, polydactyly, a brain malformation that is usually occipital encephalocele and/or vermian agenesis, with intrahepatic biliary duct proliferation. Joubert syndrome (JBS) is a viable neurological disorder with a characteristic “molar tooth sign” (MTS) on axial images reflecting cerebellar vermian hypoplasia/dysplasia. Both conditions are classified as ciliopathies with an autosomal recessive mode of inheritance. Allelism of MS and JBS has been reported for TMEM67/MKS3, CEP290/MKS4, and RPGRIP1L/MKS5. Recently, one homozygous splice mutation with a founder effect was reported in the CC2D2A gene in Finnish fetuses with MKS, defining the 6th locus for MKS. Shortly thereafter, CC2D2A mutations were reported in JBS also. The analysis of the CC2D2A gene in our series of MKS fetuses, identified 14 novel truncating mutations in 11 cases. These results confirm the involvement of CC2D2A in MKS and reveal a major contribution of CC2D2A to the disease. We also identified three missense CC2D2A mutations in two JBS cases. Therefore and in accordance with the data reported regarding RPGRIP1L, our results indicate phenotype-genotype correlations, as missense and presumably hypomorphic mutations lead to JBS while all null alleles lead to MKS. PMID:19777577

  20. 2D vs. 3D mammography observer study

    NASA Astrophysics Data System (ADS)

    Fernandez, James Reza F.; Hovanessian-Larsen, Linda; Liu, Brent

    2011-03-01

    Breast cancer is the most common type of non-skin cancer in women. 2D mammography is a screening tool to aid in the early detection of breast cancer, but has diagnostic limitations of overlapping tissues, especially in dense breasts. 3D mammography has the potential to improve detection outcomes by increasing specificity, and a new 3D screening tool with a 3D display for mammography aims to improve performance and efficiency as compared to 2D mammography. An observer study using a mammography phantom was performed to compare traditional 2D mammography with this ne 3D mammography technique. In comparing 3D and 2D mammography there was no difference in calcification detection, and mass detection was better in 2D as compared to 3D. There was a significant decrease in reading time for masses, calcifications, and normals in 3D compared to 2D, however, as well as more favorable confidence levels in reading normal cases. Given the limitations of the mammography phantom used, however, a clearer picture in comparing 3D and 2D mammography may be better acquired with the incorporation of human studies in the future.

  1. Giant, Hollow 2D Metalloarchitecture: Stepwise Self-Assembly of a Hexagonal Supramolecular Nut.

    PubMed

    Li, Yiming; Jiang, Zhilong; Wang, Ming; Yuan, Jie; Liu, Die; Yang, Xiaoyu; Chen, Mingzhao; Yan, Jun; Li, Xiaopeng; Wang, Pingshan

    2016-08-10

    A polyterpyridinyl building block-based nutlike hexagonal bismetallo architecture with a central hollow Star of David was assembled by a stepwise strategy. This nanoarchitecture can be viewed as a recursive mathematical form that possesses a supramolecular corner-connected cyclic structure, i.e., a triangle or rhombus at various levels of scale or detail. The key metallo-organic ligand (MOL) with four uncomplexed free terpyridines was obtained by a final Suzuki cross-coupling reaction with a tetrabromoterpyridine Ru dimer. The molecular metallorhombus was prepared by reacting the MOL with a 60° bis-terpyridine and Fe(2+). The giant hollow hexagonal nut with a diameter of more than 11 nm and a molecular weight of ca. 33 kDa was obtained in near-quantitative yield by mixing the two types of multi-terpyridine ligands with Fe(2+). The supramolecular architecture was characterized by NMR ((1)H and (13)C), 2D NMR (COSY and ROESY), and DOSY spectroscopies, high-resolution electrospray ionization mass spectrometry, traveling-wave ion mobility mass spectrometry, and transmission electron microscopy. PMID:27447878

  2. Accelerated 2D magnetic resonance spectroscopy of single spins using matrix completion

    PubMed Central

    Scheuer, Jochen; Stark, Alexander; Kost, Matthias; Plenio, Martin B.; Naydenov, Boris; Jelezko, Fedor

    2015-01-01

    Two dimensional nuclear magnetic resonance (NMR) spectroscopy is one of the major tools for analysing the chemical structure of organic molecules and proteins. Despite its power, this technique requires long measurement times, which, particularly in the recently emerging diamond based single molecule NMR, limits its application to stable samples. Here we demonstrate a method which allows to obtain the spectrum by collecting only a small fraction of the experimental data. Our method is based on matrix completion which can recover the full spectral information from randomly sampled data points. We confirm experimentally the applicability of this technique by performing two dimensional electron spin echo envelope modulation (ESEEM) experiments on a two spin system consisting of a single nitrogen vacancy (NV) centre in diamond coupled to a single 13C nuclear spin. The signal to noise ratio of the recovered 2D spectrum is compared to the Fourier transform of randomly subsampled data, where we observe a strong suppression of the noise when the matrix completion algorithm is applied. We show that the peaks in the spectrum can be obtained with only 10% of the total number of the data points. We believe that our results reported here can find an application in all types of two dimensional spectroscopy, as long as the measured matrices have a low rank. PMID:26631593

  3. Accelerated 2D magnetic resonance spectroscopy of single spins using matrix completion

    NASA Astrophysics Data System (ADS)

    Scheuer, Jochen; Stark, Alexander; Kost, Matthias; Plenio, Martin B.; Naydenov, Boris; Jelezko, Fedor

    2015-12-01

    Two dimensional nuclear magnetic resonance (NMR) spectroscopy is one of the major tools for analysing the chemical structure of organic molecules and proteins. Despite its power, this technique requires long measurement times, which, particularly in the recently emerging diamond based single molecule NMR, limits its application to stable samples. Here we demonstrate a method which allows to obtain the spectrum by collecting only a small fraction of the experimental data. Our method is based on matrix completion which can recover the full spectral information from randomly sampled data points. We confirm experimentally the applicability of this technique by performing two dimensional electron spin echo envelope modulation (ESEEM) experiments on a two spin system consisting of a single nitrogen vacancy (NV) centre in diamond coupled to a single 13C nuclear spin. The signal to noise ratio of the recovered 2D spectrum is compared to the Fourier transform of randomly subsampled data, where we observe a strong suppression of the noise when the matrix completion algorithm is applied. We show that the peaks in the spectrum can be obtained with only 10% of the total number of the data points. We believe that our results reported here can find an application in all types of two dimensional spectroscopy, as long as the measured matrices have a low rank.

  4. NKG2D receptor and its ligands in host defense

    PubMed Central

    Lanier, Lewis L.

    2015-01-01

    NKG2D is an activating receptor expressed on the surface of natural killer (NK) cells, CD8+ T cells, and subsets of CD4+ T cells, iNKT cells, and γδ T cells. In humans NKG2D transmits signals by its association with the DAP10 adapter subunit and in mice alternatively spliced isoforms transmit signals either using DAP10 or DAP12 adapter subunits. Although NKG2D is encoded by a highly conserved gene (KLRK1) with limited polymorphism, the receptor recognizes an extensive repertoire of ligands, encoded by at least 8 genes in humans (MICA, MICB, RAET1E, RAET1G, RAET1H, RAET1I, RAET1L, and RAET1N), some with extensive allelic polymorphism. Expression of the NKG2D ligands is tightly regulated at the level of transcription, translation, and post-translation. In general healthy adult tissues do not express NKG2D glycoproteins on the cell surface, but these ligands can be induced by hyper-proliferation and transformation, as well as when cells are infected by pathogens. Thus, the NKG2D pathway serves a mechanism for the immune system to detect and eliminate cells that have undergone “stress”. Viruses and tumor cells have devised numerous strategies to evade detection by the NKG2D surveillance system and diversification of the NKG2D ligand genes likely has been driven by selective pressures imposed by pathogens. NKG2D provides an attractive target for therapeutics in the treatment of infectious diseases, cancer, and autoimmune diseases. PMID:26041808

  5. Bayesian reconstruction of projection reconstruction NMR (PR-NMR).

    PubMed

    Yoon, Ji Won

    2014-11-01

    Projection reconstruction nuclear magnetic resonance (PR-NMR) is a technique for generating multidimensional NMR spectra. A small number of projections from lower-dimensional NMR spectra are used to reconstruct the multidimensional NMR spectra. In our previous work, it was shown that multidimensional NMR spectra are efficiently reconstructed using peak-by-peak based reversible jump Markov chain Monte Carlo (RJMCMC) algorithm. We propose an extended and generalized RJMCMC algorithm replacing a simple linear model with a linear mixed model to reconstruct close NMR spectra into true spectra. This statistical method generates samples in a Bayesian scheme. Our proposed algorithm is tested on a set of six projections derived from the three-dimensional 700 MHz HNCO spectrum of a protein HasA. PMID:25218584

  6. 1H and 13C NMR signal assignment of cucurbitacin derivatives from Citrullus colocynthis (L.) Schrader and Ecballium elaterium L. (Cucurbitaceae).

    PubMed

    Seger, Christoph; Sturm, Sonja; Mair, Maria-Elisabeth; Ellmerer, Ernst P; Stuppner, Hermann

    2005-06-01

    2D NMR-derived 1H and 13C NMR signal assignments of six structurally closely related cucurbitacin derivatives are presented. The investigated 2-O-beta-D-glucopyranosylcucurbitacins I, J, K, and L were obtained from Citrullus colocynthis (L.) Schrader whereas the aglyca cucurbitacin E and I were isolated from Ecballium elaterium L. PMID:15772995

  7. 2D constant-loss taper for mode conversion

    NASA Astrophysics Data System (ADS)

    Horth, Alexandre; Kashyap, Raman; Quitoriano, Nathaniel J.

    2015-03-01

    Proposed in this manuscript is a novel taper geometry, the constant-loss taper (CLT). This geometry is derived with 1D slabs of silicon embedded in silicon dioxide using coupled-mode theory (CMT). The efficiency of the CLT is compared to both linear and parabolic tapers using CMT and 2D finite-difference time-domain simulations. It is shown that over a short 2D, 4.45 μm long taper the CLT's mode conversion efficiency is ~90% which is 10% and 18% more efficient than a 2D parabolic or linear taper, respectively.

  8. Recent advances in 2D materials for photocatalysis

    NASA Astrophysics Data System (ADS)

    Luo, Bin; Liu, Gang; Wang, Lianzhou

    2016-03-01

    Two-dimensional (2D) materials have attracted increasing attention for photocatalytic applications because of their unique thickness dependent physical and chemical properties. This review gives a brief overview of the recent developments concerning the chemical synthesis and structural design of 2D materials at the nanoscale and their applications in photocatalytic areas. In particular, recent progress on the emerging strategies for tailoring 2D material-based photocatalysts to improve their photo-activity including elemental doping, heterostructure design and functional architecture assembly is discussed.

  9. Comparison of 2D and 3D gamma analyses

    SciTech Connect

    Pulliam, Kiley B.; Huang, Jessie Y.; Howell, Rebecca M.; Followill, David; Kry, Stephen F.; Bosca, Ryan; O’Daniel, Jennifer

    2014-02-15

    Purpose: As clinics begin to use 3D metrics for intensity-modulated radiation therapy (IMRT) quality assurance, it must be noted that these metrics will often produce results different from those produced by their 2D counterparts. 3D and 2D gamma analyses would be expected to produce different values, in part because of the different search space available. In the present investigation, the authors compared the results of 2D and 3D gamma analysis (where both datasets were generated in the same manner) for clinical treatment plans. Methods: Fifty IMRT plans were selected from the authors’ clinical database, and recalculated using Monte Carlo. Treatment planning system-calculated (“evaluated dose distributions”) and Monte Carlo-recalculated (“reference dose distributions”) dose distributions were compared using 2D and 3D gamma analysis. This analysis was performed using a variety of dose-difference (5%, 3%, 2%, and 1%) and distance-to-agreement (5, 3, 2, and 1 mm) acceptance criteria, low-dose thresholds (5%, 10%, and 15% of the prescription dose), and data grid sizes (1.0, 1.5, and 3.0 mm). Each comparison was evaluated to determine the average 2D and 3D gamma, lower 95th percentile gamma value, and percentage of pixels passing gamma. Results: The average gamma, lower 95th percentile gamma value, and percentage of passing pixels for each acceptance criterion demonstrated better agreement for 3D than for 2D analysis for every plan comparison. The average difference in the percentage of passing pixels between the 2D and 3D analyses with no low-dose threshold ranged from 0.9% to 2.1%. Similarly, using a low-dose threshold resulted in a difference between the mean 2D and 3D results, ranging from 0.8% to 1.5%. The authors observed no appreciable differences in gamma with changes in the data density (constant difference: 0.8% for 2D vs 3D). Conclusions: The authors found that 3D gamma analysis resulted in up to 2.9% more pixels passing than 2D analysis. It must

  10. Materials for Flexible, Stretchable Electronics: Graphene and 2D Materials

    NASA Astrophysics Data System (ADS)

    Kim, Sang Jin; Choi, Kyoungjun; Lee, Bora; Kim, Yuna; Hong, Byung Hee

    2015-07-01

    Recently, 2D materials have been intensively studied as emerging materials for future electronics, including flexible electronics, photonics, and electrochemical energy storage devices. Among representative 2D materials (such as graphene, boron nitride, and transition metal dichalcogenides) that exhibit extraordinary properties, graphene stands out in the flexible electronics field due to its combination of high electron mobility, high thermal conductivity, high specific surface area, high optical transparency, excellent mechanical flexibility, and environmental stability. This review covers the synthesis, transfer, and characterization methods of graphene and 2D materials and graphene's application to flexible devices as well as comparison with other competing materials.

  11. Ms. Mentor Unmasked

    ERIC Educational Resources Information Center

    Krebs, Paula

    2008-01-01

    This article presents an interview with Emily Toth, who writes the monthly "Ms. Mentor" academic advice column in the "Chronicle of Higher Education" and teaches in the English department at Louisiana State University, in Baton Rouge. She is the author of "Ms. Mentor's Impeccable Advice for Women in Academia" (1997), "Inside Peyton Place: The Life…

  12. A cyclo‐P6 Ligand Complex for the Formation of Planar 2D Layers

    PubMed Central

    Heindl, Claudia; Peresypkina, Eugenia V.; Lüdeker, David; Brunklaus, Gunther; Virovets, Alexander V.

    2016-01-01

    Abstract The all‐phosphorus analogue of benzene, stabilized as middle deck in triple‐decker complexes, is a promising building block for the formation of graphene‐like sheet structures. The reaction of [(CpMo)2(μ,η6:η6‐P6)] (1) with CuX (X=Br, I) leads to self‐assembly into unprecedented 2D networks of [{(CpMo)2P6}(CuBr)4]n (2) and [{(CpMo)2P6}(CuI)2]n (3). X‐ray structural analyses show a unique deformation of the previously planar cyclo‐P6 ligand. This includes bending of one P atom in an envelope conformation as well as a bisallylic distortion. Despite this, 2 and 3 form planar layers. Both polymers were furthermore analyzed by 31P{1H} magic angle spinning (MAS) NMR spectroscopy, revealing signals corresponding to six non‐equivalent phosphorus sites. A peak assignment is achieved by 2D correlation spectra as well as by DFT chemical shift computations. PMID:26711699

  13. A cyclo-P6 Ligand Complex for the Formation of Planar 2D Layers.

    PubMed

    Heindl, Claudia; Peresypkina, Eugenia V; Lüdeker, David; Brunklaus, Gunther; Virovets, Alexander V; Scheer, Manfred

    2016-02-01

    The all-phosphorus analogue of benzene, stabilized as middle deck in triple-decker complexes, is a promising building block for the formation of graphene-like sheet structures. The reaction of [(CpMo)2 (μ,η(6) :η(6) -P6 )] (1) with CuX (X=Br, I) leads to self-assembly into unprecedented 2D networks of [{(CpMo)2 P6 }(CuBr)4 ]n (2) and [{(CpMo)2 P6 }(CuI)2 ]n (3). X-ray structural analyses show a unique deformation of the previously planar cyclo-P6 ligand. This includes bending of one P atom in an envelope conformation as well as a bisallylic distortion. Despite this, 2 and 3 form planar layers. Both polymers were furthermore analyzed by (31) P{(1) H} magic angle spinning (MAS) NMR spectroscopy, revealing signals corresponding to six non-equivalent phosphorus sites. A peak assignment is achieved by 2D correlation spectra as well as by DFT chemical shift computations. PMID:26711699

  14. Recent developments in 2D layered inorganic nanomaterials for sensing

    NASA Astrophysics Data System (ADS)

    Kannan, Padmanathan Karthick; Late, Dattatray J.; Morgan, Hywel; Rout, Chandra Sekhar

    2015-08-01

    Two dimensional layered inorganic nanomaterials (2D-LINs) have recently attracted huge interest because of their unique thickness dependent physical and chemical properties and potential technological applications. The properties of these layered materials can be tuned via both physical and chemical processes. Some 2D layered inorganic nanomaterials like MoS2, WS2 and SnS2 have been recently developed and employed in various applications, including new sensors because of their layer-dependent electrical properties. This article presents a comprehensive overview of recent developments in the application of 2D layered inorganic nanomaterials as sensors. Some of the salient features of 2D materials for different sensing applications are discussed, including gas sensing, electrochemical sensing, SERS and biosensing, SERS sensing and photodetection. The working principles of the sensors are also discussed together with examples.

  15. 2. D Street facade and rear (east) blank wall of ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    2. D Street facade and rear (east) blank wall of parking garage. Farther east is 408 8th Street (National Art And Frame Company). - PMI Parking Garage, 403-407 Ninth Street, Northwest, Washington, District of Columbia, DC

  16. Collective excitations in 2D hard-disc fluid.

    PubMed

    Huerta, Adrian; Bryk, Taras; Trokhymchuk, Andrij

    2015-07-01

    Collective dynamics of a two-dimensional (2D) hard-disc fluid was studied by molecular dynamics simulations in the range of packing fractions that covers states up to the freezing. Some striking features concerning collective excitations in this system were observed. In particular, the short-wavelength shear waves while being absent at low packing fractions were observed in the range of high packing fractions, just before the freezing transition in a 2D hard-disc fluid. In contrast, the so-called "positive sound dispersion" typically observed in dense Lennard-Jones-like fluids, was not detected for the 2D hard-disc fluid. The ratio of specific heats in the 2D hard-disc fluid shows a monotonic increase with density approaching the freezing, resembling in this way the similar behavior in the vicinity of the Widom line in the case of supercritical fluids. PMID:25595625

  17. Alloyed 2D Metal-Semiconductor Atomic Layer Junctions.

    PubMed

    Kim, Ah Ra; Kim, Yonghun; Nam, Jaewook; Chung, Hee-Suk; Kim, Dong Jae; Kwon, Jung-Dae; Park, Sang Won; Park, Jucheol; Choi, Sun Young; Lee, Byoung Hun; Park, Ji Hyeon; Lee, Kyu Hwan; Kim, Dong-Ho; Choi, Sung Mook; Ajayan, Pulickel M; Hahm, Myung Gwan; Cho, Byungjin

    2016-03-01

    Heterostructures of compositionally and electronically variant two-dimensional (2D) atomic layers are viable building blocks for ultrathin optoelectronic devices. We show that the composition of interfacial transition region between semiconducting WSe2 atomic layer channels and metallic NbSe2 contact layers can be engineered through interfacial doping with Nb atoms. WxNb1-xSe2 interfacial regions considerably lower the potential barrier height of the junction, significantly improving the performance of the corresponding WSe2-based field-effect transistor devices. The creation of such alloyed 2D junctions between dissimilar atomic layer domains could be the most important factor in controlling the electronic properties of 2D junctions and the design and fabrication of 2D atomic layer devices. PMID:26839956

  18. Technical Review of the UNET2D Hydraulic Model

    SciTech Connect

    Perkins, William A.; Richmond, Marshall C.

    2009-05-18

    The Kansas City District of the US Army Corps of Engineers is engaged in a broad range of river management projects that require knowledge of spatially-varied hydraulic conditions such as velocities and water surface elevations. This information is needed to design new structures, improve existing operations, and assess aquatic habitat. Two-dimensional (2D) depth-averaged numerical hydraulic models are a common tool that can be used to provide velocity and depth information. Kansas City District is currently using a specific 2D model, UNET2D, that has been developed to meet the needs of their river engineering applications. This report documents a tech- nical review of UNET2D.

  19. From weakly to strongly interacting 2D Fermi gases

    NASA Astrophysics Data System (ADS)

    Dyke, Paul; Fenech, Kristian; Lingham, Marcus; Peppler, Tyson; Hoinka, Sascha; Vale, Chris

    2014-05-01

    We study ultracold 2D Fermi gases of 6Li formed in a highly oblate trapping potential. The potential is generated by a cylindrically focused, blue detuned TEM01 mode laser beam. Weak magnetic field curvature provides highly harmonic confinement in the radial direction and we can readily produce single clouds with an aspect ratio of 230. Our experiments investigate the dimensional crossover from 3D to 2D for a two component Fermi gas in the Bose-Einstein Condensate to Bardeen Cooper Schrieffer crossover. Observation of an elbow in measurements of the cloud width vs. atom number is consistent with populating only the lowest transverse harmonic oscillator state for weak attractive interactions. This measurement is extended to the strongly interacting region using the broad Feshbach resonance at 832 G. We also report our progress towards measurement of the 2D equation of state for an interacting 2D Fermi gas via in-situ absorption imaging.

  20. Chemical vapour deposition: Transition metal carbides go 2D

    NASA Astrophysics Data System (ADS)

    Gogotsi, Yury

    2015-11-01

    The unique properties of 2D materials, such as graphene or transition metal dichalcogenides, have been attracting much attention in the past decade. Now, metallically conductive and even superconducting transition metal carbides are entering the game.