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Sample records for 2-d nmr techniques

  1. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2015-02-01

    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.

  3. Quantitative 2D liquid-state NMR.

    PubMed

    Giraudeau, Patrick

    2014-06-01

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

  4. 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

  5. Experimental identification of diffusive coupling using 2D NMR.

    PubMed

    Song, Y-Q; Carneiro, G; Schwartz, L M; Johnson, D L

    2014-12-01

    Spin relaxation based nuclear magnetic resonance (NMR) methods have been used extensively to determine pore size distributions in a variety of materials. This approach is based on the assumption that each pore is in the fast diffusion limit but that diffusion between pores can be neglected. However, in complex materials these assumptions may be violated and the relaxation time distribution is not easily interpreted. We present a 2D NMR technique and an associated data analysis that allow us to work directly with the time dependent experimental data without Laplace inversion to identify the signature of diffusive coupling between different pores. Measurements on microporous glass beads and numerical simulations are used to illustrate the technique. PMID:25526135

  6. 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.

  7. 2D-Cosy NMR Spectroscopy as a Quantitative Tool in Biological Matrix: Application to Cyclodextrins.

    PubMed

    Dufour, Gilles; Evrard, Brigitte; de Tullio, Pascal

    2015-11-01

    Classical analytical quantifications in biological matrices require time-consuming sample pre-treatments and extractions. Nuclear magnetic resonance (NMR) analysis does not require heavy sample treatments or extractions which therefore increases its accuracy in quantification. In this study, even if quantitative (q)NMR could not be applied to 2D spectra, we demonstrated that cross-correlations and diagonal peak intensities have a linear relationship with the analyzed pharmaceutical compound concentration. This work presents the validation process of a 2D-correlation spectroscopy (COSY) NMR quantification of 2-hydroxypropyl-β-cyclodextrin in plasma. Specificity, linearity, precision (repeatability and intermediate precision), trueness, limits of quantification (LOQs), and accuracy were used as validation criteria. 2D-NMR could therefore be used as a valuable and accurate analytical technique for the quantification of pharmaceutical compounds, including hardly detectable compounds such as cyclodextrins or poloxamers, in complex biological matrices based on a calibration curve approach.

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

    PubMed Central

    Giraudeau, Patrick; Frydman, Lucio

    2016-01-01

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

  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. 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

  11. 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

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

    NASA Astrophysics Data System (ADS)

    Kirwan, Gemma M.; Adams, Michael J.

    2008-12-01

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

  13. 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

  14. 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.

  15. Real-time separation of natural products by ultrafast 2D NMR coupled to on-line HPLC.

    PubMed

    Queiroz, Luiz H K; Queiroz, Darlene P K; Dhooghe, Liene; Ferreira, Antonio G; Giraudeau, Patrick

    2012-05-21

    Hyphenated HPLC-NMR is an extremely efficient analytical tool, which makes it possible to perform on-flow experiments where 1D NMR spectra are obtained in real time as the analytes are separated and eluted from the chromatographic column. However, it is incompatible with multidimensional NMR methods that form an indispensible tool for the study of complex mixtures. Recently, Frydman and co-workers have proposed an ultrafast 2D NMR approach, where a complete 2D NMR correlation can be recorded in a single scan, thus providing a solution to the irreversibility of hyphenated techniques. This paper presents the first implementation of on-line ultrafast HPLC-NMR. Ultrafast COSY spectra are acquired every 12 s in the course of a chromatographic run performed on a mixture of natural aromatic compounds. The results, obtained on a commercial HPLC-NMR setup, highlight the generality of the ultrafast HPLC-NMR methodology, thus opening the way to a number of applications in the numerous fields in which HPLC-NMR forms a routine analytical tool.

  16. (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

  17. High-resolution 2D NMR spectra in inhomogeneous fields via 3D acquisition

    NASA Astrophysics Data System (ADS)

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

    2014-04-01

    High-resolution nuclear magnetic resonance (NMR) spectroscopy plays an important role in chemical studies. Here, a pulse sequence, based on coherence transfer module of tracking differences of precession frequencies of two spins and spin echo module, is proposed to obtain two dimension (2D) high-resolution NMR spectra via 3D acquisition under large field inhomogeneity. The proposed scheme composes of simple hard pulses and rectangle gradients. Resulting 2D spectra exhibit chemical shift differences and J coupling splittings in two orthogonal dimensions. The method developed here may offer a promising way for in situ high-resolution NMR studies on combinatorial chemistry.

  18. Study of aging in oil paintings by 1D and 2D NMR spectroscopy.

    PubMed

    Spyros, Apostolos; Anglos, Demetrios

    2004-09-01

    Nuclear magnetic resonance spectroscopy is proposed as an efficient analytical tool in the study of painted artworks. The binding medium from two original oil paintings, dated from the early 20th and the late 17th century, was studied via high-resolution 1D and 2D NMR, establishing the advanced state of hydrolysis and oxidation of the oil paint. Studies of the solvent-extractable component from model samples of various drying oils, raw oil paints, and aged oil paints allowed the definition of several markers based on the integral ratios of various chemical species present in the 1H and 13C NMR spectra. These markers are sensitive to hydrolytic and oxidative processes that reflect the extent of aging in oil paintings. The rapidity, simplicity, and nondestructive nature of the proposed analytical NMR methodology represents a great advantage, since the usually minute sample quantities available from original artwork can be subsequently analyzed further by other analytical techniques, if necessary. PMID:15373425

  19. Single Scan 2D NMR Spectroscopy on a 25 T Bitter Magnet.

    PubMed

    Shapira, Boaz; Shetty, Kiran; Brey, William W; Gan, Zhehong; Frydman, Lucio

    2007-07-16

    2D NMR relies on monitoring systematic changes in the phases incurred by spin coherences as a function of an encoding time t(1), whose value changes over the course of independent experiments. The intrinsic multiscan nature of such protocols implies that resistive and/or hybrid magnets, capable of delivering the highest magnetic field strengths but possessing poor temporal stabilities, become unsuitable for 2D NMR acquisitions. It is here shown with a series of homo- and hetero-nuclear examples that such limitations can be bypassed using recently proposed 2D "ultrafast" acquisition schemes, which correlate interactions along all spectral dimensions within a single scan.

  20. Single Scan 2D NMR Spectroscopy on a 25 T Bitter Magnet

    PubMed Central

    Shapira, Boaz; Shetty, Kiran; Brey, William W.; Gan, Zhehong; Frydman, Lucio

    2007-01-01

    2D NMR relies on monitoring systematic changes in the phases incurred by spin coherences as a function of an encoding time t1, whose value changes over the course of independent experiments. The intrinsic multiscan nature of such protocols implies that resistive and/or hybrid magnets, capable of delivering the highest magnetic field strengths but possessing poor temporal stabilities, become unsuitable for 2D NMR acquisitions. It is here shown with a series of homo- and hetero-nuclear examples that such limitations can be bypassed using recently proposed 2D “ultrafast” acquisition schemes, which correlate interactions along all spectral dimensions within a single scan. PMID:18037970

  1. 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.

  2. 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.

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

    DOE PAGES

    Khatun, Sufia; Castner, Edward W.

    2014-11-26

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

  4. MATCAKE: a flexible toolbox for 2D NMR spectra integration by CAKE algorithm

    NASA Astrophysics Data System (ADS)

    Romano, Rocco; Acernese, Fausto; Vilasi, Silvia; Paris, Debora; Motta, Andrea; Barone, Fabrizio

    2011-04-01

    MatCAKE (www.cake.unisa.it) is a toolbox for integrating 2D NMR spectra by the CAKE (Monte CArlo peaK volume Estimation)1 algorithm within the Matlab environment (www.mathworks.com). Quantitative information from multidimensional NMR experiments can be obtained by peak volume integration. The standard procedure (selection of a region around the chosen peak and addition of all values) is often biased by poor peak definition because of peak overlap. CAKE is a simple algorithm designed for volume integration of (partially) overlapping peaks. Assuming the axial symmetry of two-dimensional NMR peaks, as it occurs in NOESY and TOCSY when Lorentz-Gauss transformation of the signals is carried out, CAKE estimates the peak volume by multiplying a volume fraction by a factor R. It represents a proportionality ratio between the total and the fractional volume, which is identified as a slice in an exposed region of the overlapping peaks. The volume fraction is obtained via Monte Carlo Hit-or-Miss technique, which proved to be the most efficient because of the small region and the limited number of points within the selected area. Due to the large number of software packages available for processing nuclear magnetic resonance data, MatCAKE is designed just for implementing the new CAKE algorithm. In MatCAKe, in fact, only already processed bidimensional spectra are imported and, at the moment, the only volume integration (by CAKE and by the most simple standard procedure) are allowed. MatCAKE is a free software at disposal for the scientific community and can be obtained on line at the web address cake.unisa.it.

  5. 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

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

    PubMed

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

    2004-02-01

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

  7. Structure and Coordination Determination of Peptide-metal Complexes Using 1D and 2D 1H NMR

    PubMed Central

    Shoshan, Michal S.; Tshuva, Edit Y.; Shalev, Deborah E.

    2013-01-01

    Copper (I) binding by metallochaperone transport proteins prevents copper oxidation and release of the toxic ions that may participate in harmful redox reactions. The Cu (I) complex of the peptide model of a Cu (I) binding metallochaperone protein, which includes the sequence MTCSGCSRPG (underlined is conserved), was determined in solution under inert conditions by NMR spectroscopy. NMR is a widely accepted technique for the determination of solution structures of proteins and peptides. Due to difficulty in crystallization to provide single crystals suitable for X-ray crystallography, the NMR technique is extremely valuable, especially as it provides information on the solution state rather than the solid state. Herein we describe all steps that are required for full three-dimensional structure determinations by NMR. The protocol includes sample preparation in an NMR tube, 1D and 2D data collection and processing, peak assignment and integration, molecular mechanics calculations, and structure analysis. Importantly, the analysis was first conducted without any preset metal-ligand bonds, to assure a reliable structure determination in an unbiased manner. PMID:24378924

  8. 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

  9. 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...

  10. Compressed Sensing Reconstruction of Ultrafast 2D NMR Data: Principles and Biomolecular Applications

    PubMed Central

    Shrot, Yoav; Frydman, Lucio

    2016-01-01

    A topic of active investigation in 2D NMR relates to the minimum number of scans required for acquiring this kind of spectra, particularly when these are dictated by sampling rather than by sensitivity considerations. Reductions in this minimum number of scans have been achieved by departing from the regular sampling used to monitor the indirect domain, and relying instead on non-uniform sampling and iterative reconstruction algorithms. Alternatively, so-called “ultrafast” methods can compress the minimum number of scans involved in 2D NMR all the way to a minimum number of one, by spatially encoding the indirect domain information and subsequently recovering it via oscillating field gradients. Given ultrafast NMR’s simultaneous recording of the indirect- and direct-domain data, this experiment couples the spectral constraints of these orthogonal domains –often calling for the use of strong acquisition gradients and large filter widths to fulfill the desired bandwidth and resolution demands along all spectral dimensions. This study discusses a way to alleviate these demands, and thereby enhance the method’s performance and applicability, by combining spatial encoding with iterative reconstruction approaches. Examples of these new principles are given based on the compressed-sensed reconstruction of biomolecular 2D HSQC ultrafast NMR data, an approach that we show enables a decrease of the gradient strengths demanded in this type of experiments by up to 80%. PMID:21316276

  11. 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.

  12. 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

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

    PubMed

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

    2015-04-10

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

  14. 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.

  15. Quantitative Analysis of Metabolic Mixtures by 2D 13C-Constant-Time TOCSY NMR Spectroscopy

    PubMed Central

    Bingol, Kerem; Zhang, Fengli; Bruschweiler-Li, Lei; Brüschweiler, Rafael

    2013-01-01

    An increasing number of organisms can be fully 13C-labeled, which has the advantage that their metabolomes can be studied by high-resolution 2D NMR 13C–13C constant-time (CT) TOCSY experiments. Individual metabolites can be identified via database searching or, in the case of novel compounds, through the reconstruction of their backbone-carbon topology. Determination of quantitative metabolite concentrations is another key task. Because significant peak overlaps in 1D NMR spectra prevents straightforward quantification through 1D peak integrals, we demonstrate here the direct use of 13C–13C CT-TOCSY spectra for metabolite quantification. This is accomplished through the quantum-mechanical treatment of the TOCSY magnetization transfer at short and long mixing times or by the use of analytical approximations, which are solely based on the knowledge of the carbon-backbone topologies. The methods are demonstrated for carbohydrate and amino-acid mixtures. PMID:23773204

  16. 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.

  17. Hetero Diels-Alder Reaction with Aqueous Glyoxylic Acid: An Experiment in Organic Synthesis and 2-D NMR Analysis for Advanced Undergraduate Students

    NASA Astrophysics Data System (ADS)

    Augé, Jacques; Lubin-Germain, Nadège

    1998-10-01

    As an application of the use of water as solvent in organic synthesis, a convenient synthesis of a-hydroxy-g-lactones from an aqueous solution of glyoxylic acid is described. The mechanism of the reaction leading to the lactones goes through cycloadducts which rearrange in situ. The NMR analysis of the diastereomeric lactones is particularly interesting; such an analysis illustrates the importance of modern techniques including 2-D NMR spectroscopy. Complete assignments of the signals are mentioned and NOESY spectra are enclosed. The full experiment is addressed to advanced undergraduate students who are trained in organic synthesis and NMR spectroscopy.

  18. 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...

  19. A New Microcell Technique for NMR Analysis.

    ERIC Educational Resources Information Center

    Yu, Sophia J.

    1987-01-01

    Describes a new laboratory technique for working with small samples of compounds used in nuclear magnetic resonance (NMR) analysis. Demonstrates how microcells can be constructed for each experiment and samples can be recycled. (TW)

  20. NMR Hyperpolarization Techniques for Biomedicine

    PubMed Central

    Nikolaou, Panayiotis; Goodson, Boyd M.

    2015-01-01

    Recent developments in NMR hyperpolarization have enabled a wide array of new in vivo molecular imaging modalities—ranging from functional imaging of the lungs to metabolic imaging of cancer. This Concept article explores selected advances in methods for the preparation and use of hyperpolarized contrast agents, many of which are already at or near the phase of their clinical validation in patients. PMID:25470566

  1. 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.

  2. 1-D and 2-D NMR-based metabolomics of earthworms exposed to endosulfan and endosulfan sulfate in soil.

    PubMed

    Yuk, Jimmy; Simpson, Myrna J; Simpson, André J

    2013-04-01

    One-dimensional (1-D) and two-dimensional (2-D) nuclear magnetic resonance (NMR)-based metabolomics was used to investigate the toxic mode of action (MOA) of endosulfan, an organochlorine pesticide, and its degradation product, endosulfan sulfate, to Eisenia fetida earthworms in soil. Three soil concentrations (0.1, 1.0 and 10.0 mg/kg) were used for both endosulfan and endosulfan sulfate. Both earthworm coelomic fluid (CF) and tissues were extracted and then analyzed using (1)H and (1)H-(13)C NMR techniques. A similar separation trajectory was observed for endosulfan and endosulfan sulfate-exposed earthworms in the mean principal component analysis (PCA) scores plot for both the earthworm CF and tissue extracts. A neurotoxic and apoptotic MOA was postulated for both endosulfan and endosulfan sulfate exposed earthworms as significant fluctuations in glutamine/GABA-glutamate cycle metabolites and spermidine were detected respectively. This study highlights the application of NMR-based metabolomics to understand molecular-level toxicity of persistent organochlorine pesticides and their degradation products directly in soil.

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

    NASA Astrophysics Data System (ADS)

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

    2016-11-01

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

  4. High-resolution 2D NMR spectroscopy of bicelles to measure the membrane interaction of ligands.

    PubMed

    Dvinskikh, Sergey V; Dürr, Ulrich H N; Yamamoto, Kazutoshi; Ramamoorthy, Ayyalusamy

    2007-01-31

    Magnetically aligned bicelles are increasingly being used as model membranes in solution- and solid-state NMR studies of the structure, dynamics, topology, and interaction of membrane-associated peptides and proteins. These studies commonly utilize the PISEMA pulse sequence to measure dipolar coupling and chemical shift, the two key parameters used in subsequent structural analysis. In the present study, we demonstrate that the PISEMA and other rotating-frame pulse sequences are not suitable for the measurement of long-range heteronuclear dipolar couplings, and that they provide inaccurate values when multiple protons are coupled to a 13C nucleus. Furthermore, we demonstrate that a laboratory-frame separated-local-field experiment is capable of overcoming these difficulties in magnetically aligned bicelles. An extension of this approach to accurately measure 13C-31P and 1H-31P couplings from phospholipids, which are useful to understand the interaction of molecules with the membrane, is also described. In these 2D experiments, natural abundance 13C was observed from bicelles containing DMPC and DHPC lipid molecules. As a first application, these solid-state NMR approaches were utilized to probe the membrane interaction of an antidepressant molecule, desipramine, and its location in the membrane.

  5. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2016-10-01

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

  7. 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.

  8. NMR techniques in the study of cardiovascular structure and functions

    SciTech Connect

    Osbakken, M.; Haselgrove, J.

    1987-01-01

    The chapter titles of this book are: Introduction to NMR Techniques;Theory of NMR Probe Design;Overview of Magnetic Resonance Imaging to Study the Cardiovascular System;Vascular Anatomy and Physiology Studied with NMR Techniques;Assessment of Myocardial Ischemia and Infarction by Nuclear Magnetic Resonance Imaging;The Use of MRI in Congenital Heart Disease;Cardiomyopathies and Myocarditis Studied with NMR Techniques;Determination of Myocardial Mechanical Function with Magnetic Resonance Imaging Techniques;Determination of Flow Using NMR Techniques;The Use of Contrast Agents in Cardiac MRI;Can Cardiovascular Disease Be Effectively Evaluated with NMR Spectroscopy. NMR Studies of ATP Synthesis Reactions in the Isolated Heart;Studies of Intermediary Metabolism in the Heart by 13C NMR Spectroscopy;23Na and 39K NMR Spectroscopic Studies of the Intact Beating Heart;and Evaluation of Skeletal Muscle Metabolism in Patients with Congestive Heart Failure Using Phosphorus Nuclear Magnetic Resonance.

  9. Automated compound verification using 2D-NMR HSQC data in an open-access environment.

    PubMed

    Keyes, Philip; Hernandez, Gonzalo; Cianchetta, Giovanni; Robinson, James; Lefebvre, Brent

    2009-01-01

    Since the introduction of NMR prediction software, medicinal chemists have imagined submitting their compounds to corporate compound registration systems that would ultimately display a simplified pass/fail result. We initially implemented such a system based on HPLC and liquid chromatography mass spectrometry (LCMS) data that is embedded within our industry standard sample submission and registration process. By using gradient-heteronuclear single quantum coherence (HSQC) experiments, we have extended this concept to NMR data through a comparison of experimentally acquired data against predicted (1)H and (13)C NMR data. Integration of our compound registration system with our analytical instruments now provides our chemists unattended and automated NMR verification for collections of submitted compounds. The benefits achieved from automated processing and interpretation of results produced enhanced confidence in our compound library and released the chemists from the tedium of manipulating large amounts of data. This allows scientists to focus more of their attention to the drug discovery process.

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

    PubMed Central

    Gopinath, T.; Veglia, Gianluigi

    2013-01-01

    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. PMID:23676036

  11. 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.

  12. Hyphenated low-field NMR techniques: combining NMR with NIR, GPC/SEC and rheometry.

    PubMed

    Räntzsch, Volker; Wilhelm, Manfred; Guthausen, Gisela

    2016-06-01

    Hyphenated low-field NMR techniques are promising characterization methods for online process analytics and comprehensive offline studies of soft materials. By combining different analytical methods with low-field NMR, information on chemical and physical properties can be correlated with molecular dynamics and complementary chemical information. In this review, we present three hyphenated low-field NMR techniques: a combination of near-infrared spectroscopy and time-domain NMR (TD-NMR) relaxometry, online (1) H-NMR spectroscopy measured directly after size exclusion chromatographic (SEC, also known as GPC) separation and a combination of rheometry and TD-NMR relaxometry for highly viscous materials. Case studies are reviewed that underline the possibilities and challenges of the different hyphenated low-field NMR methods. Copyright © 2015 John Wiley & Sons, Ltd.

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

    PubMed

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

    2016-01-01

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

  14. 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.

  15. 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.

  16. 2D multinuclear NMR, hyperpolarized xenon and gas storage in organosilica nanochannels with crystalline order in the walls.

    PubMed

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

    2007-07-11

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

  17. 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

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

    PubMed Central

    Vergara, Fredd; Shino, Amiu; Kikuchi, Jun

    2016-01-01

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

  19. 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

  20. 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

  1. HyperSPASM NMR: A New Approach to Single-Shot 2D Correlations on DNP-Enhanced Samples

    PubMed Central

    Donovan, Kevin J.; Frydman, Lucio

    2016-01-01

    Dissolution DNP experiments are limited to a single or at most a few scan, before the non-Boltzmann magnetization has been. 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 the 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 the 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. PMID:23159821

  2. Improvements in Technique of NMR Imaging and NMR Diffusion Measurements in the Presence of Background Gradients.

    NASA Astrophysics Data System (ADS)

    Lian, Jianyu

    In this work, modification of the cosine current distribution rf coil, PCOS, has been introduced and tested. The coil produces a very homogeneous rf magnetic field, and it is inexpensive to build and easy to tune for multiple resonance frequency. The geometrical parameters of the coil are optimized to produce the most homogeneous rf field over a large volume. To avoid rf field distortion when the coil length is comparable to a quarter wavelength, a parallel PCOS coil is proposed and discussed. For testing rf coils and correcting B _1 in NMR experiments, a simple, rugged and accurate NMR rf field mapping technique has been developed. The method has been tested and used in 1D, 2D, 3D and in vivo rf mapping experiments. The method has been proven to be very useful in the design of rf coils. To preserve the linear relation between rf output applied on an rf coil and modulating input for an rf modulating -amplifying system of NMR imaging spectrometer, a quadrature feedback loop is employed in an rf modulator with two orthogonal rf channels to correct the amplitude and phase non-linearities caused by the rf components in the rf system. The modulator is very linear over a large range and it can generate an arbitrary rf shape. A diffusion imaging sequence has been developed for measuring and imaging diffusion in the presence of background gradients. Cross terms between the diffusion sensitizing gradients and background gradients or imaging gradients can complicate diffusion measurement and make the interpretation of NMR diffusion data ambiguous, but these have been eliminated in this method. Further, the background gradients has been measured and imaged. A dipole random distribution model has been established to study background magnetic fields Delta B and background magnetic gradients G_0 produced by small particles in a sample when it is in a B_0 field. From this model, the minimum distance that a spin can approach a particle can be determined by measuring

  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. 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.

  5. The structural identification of a methyl analog of methaqualone via 2-dimensional NMR techniques.

    PubMed

    Angelos, S A; Lankin, D C; Meyers, J A; Raney, J K

    1993-03-01

    A submission to the Drug Enforcement Administration North Central Laboratory of a substance believed to be a structural analog of methaqualone hydrochloride precipitated an interest in being able to obtain a rapid and positive identification of such compounds. Both mass spectrometry and proton NMR spectroscopy (1-dimensional) provided evidence to suggest that the structural analog possessed a second methyl group in the molecule, relative to methaqualone, and that the methyl group was attached to the existing methyl-substituted phenyl ring. By application of proton 2-dimensional (2-D) NMR techniques, specifically the homonuclear shift correlation spectroscopy (COSY) and 2-D NOE (NOESY), the precise location of the methyl group in this unknown methaqualone analog was established and shown to have the structure 2.

  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. 2H NMR study of 2D melting and dynamic behaviour of CDCl3 confined in ACF nanospace.

    PubMed

    Ueda, Takahiro; Omichi, Hiroaki; Chen, Yu; Kobayashi, Hirokazu; Kubota, Osamu; Miyakubo, Keisuke; Eguchi, Taro

    2010-08-28

    Two-dimensional melting of trichloromethane (chloroform) confined in activated carbon fibre was investigated using differential thermal analysis and (2)H NMR techniques. Differential thermal analysis revealed a thermal anomaly with an endothermic peak at 269 K, which was distributed from 250 K to 287 K on the heating direction. This anomaly was also observed upon cooling at the same temperature. Furthermore, (2)H NMR revealed that slow motion such as molecular hopping and/or diffusion of CDCl(3) in ACF affected the spectral line width. The temperature dependence (Arrhenius plot) of the spectral line width showed an inflection point at 227 K. The activation energy of molecular motion of CDCl(3) in ACF was 4 kJ mol(-1) at temperatures greater than 227 K and 7.7 kJ mol(-1) at temperatures less than 227 K. Reduction of the activation energy suggests that the average intermolecular distance between CDCl(3) molecules enlarges above the inflection point. The difference of activation energy (3.7 kJ mol(-1)) is close to the enthalpy of fusion in typical plastic crystals. These results reveal that the thermal anomaly and the transition of dynamic process correspond respectively to melting of CHCl(3) in ACF and the pre-melting phenomenon.

  8. 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

  9. A functional technique based on the Euclidean algorithm with applications to 2-D acoustic diffractal diffusers

    NASA Astrophysics Data System (ADS)

    Cortés-Vega, Luis

    2015-09-01

    We built, based on the Euclidean algorithm, a functional technique, which allows to discover a direct proof of Chinese Remainder Theorem. Afterwards, by using this functional approach, we present some applications to 2-D acoustic diffractal diffusers. The novelty of the method is their functional algorithmic character, which improves ideas, as well as, other results of the author and his collaborators in a previous work.

  10. Comparing and visualizing titanium implant integration in rat bone using 2D and 3D techniques.

    PubMed

    Arvidsson, Anna; Sarve, Hamid; Johansson, Carina B

    2015-01-01

    The aim was to compare the osseointegration of grit-blasted implants with and without a hydrogen fluoride treatment in rat tibia and femur, and to visualize bone formation using state-of-the-art 3D visualization techniques. Grit-blasted implants were inserted in femur and tibia of 10 Sprague-Dawley rats (4 implants/rat). Four weeks after insertion, bone implant samples were retrieved. Selected samples were imaged in 3D using Synchrotron Radiation-based μCT (SRμCT). The 3D data was quantified and visualized using two novel visualization techniques, thread fly-through and 2D unfolding. All samples were processed to cut and ground sections and 2D histomorphometrical comparisons of bone implant contact (BIC), bone area (BA), and mirror image area (MI) were performed. BA values were statistically significantly higher for test implants than controls (p < 0.05), but BIC and MI data did not differ significantly. Thus, the results partly indicate improved bone formation at blasted and hydrogen fluoride treated implants, compared to blasted implants. The 3D analysis was a valuable complement to 2D analysis, facilitating improved visualization. However, further studies are required to evaluate aspects of 3D quantitative techniques, with relation to light microscopy that traditionally is used for osseointegration studies.

  11. Comparing and visualizing titanium implant integration in rat bone using 2D and 3D techniques.

    PubMed

    Arvidsson, Anna; Sarve, Hamid; Johansson, Carina B

    2015-01-01

    The aim was to compare the osseointegration of grit-blasted implants with and without a hydrogen fluoride treatment in rat tibia and femur, and to visualize bone formation using state-of-the-art 3D visualization techniques. Grit-blasted implants were inserted in femur and tibia of 10 Sprague-Dawley rats (4 implants/rat). Four weeks after insertion, bone implant samples were retrieved. Selected samples were imaged in 3D using Synchrotron Radiation-based μCT (SRμCT). The 3D data was quantified and visualized using two novel visualization techniques, thread fly-through and 2D unfolding. All samples were processed to cut and ground sections and 2D histomorphometrical comparisons of bone implant contact (BIC), bone area (BA), and mirror image area (MI) were performed. BA values were statistically significantly higher for test implants than controls (p < 0.05), but BIC and MI data did not differ significantly. Thus, the results partly indicate improved bone formation at blasted and hydrogen fluoride treated implants, compared to blasted implants. The 3D analysis was a valuable complement to 2D analysis, facilitating improved visualization. However, further studies are required to evaluate aspects of 3D quantitative techniques, with relation to light microscopy that traditionally is used for osseointegration studies. PMID:24711247

  12. Product operator descriptions of the 2D DEPT J-resolved NMR experiment for weakly coupled ISn (I=\\frac{1}{2}, S=\\frac{3}{2}; n=1, 2, 3) spin systems

    NASA Astrophysics Data System (ADS)

    Tokatlı, Ahmet; Bahçeli, Semiha

    2010-02-01

    There are a variety of multi-pulse nuclear magnetic resonance (NMR) experiments for spectral assignment of complex molecules in a solution. The two-dimensional (2D) distortionless enhancement by polarization transfer (DEPT) J-resolved NMR experiment is a 13C-detected, spectral editing polarization transfer technique. The product operator theory is widely used for an analytical description of the multi-pulse NMR experiment for weakly coupled spin systems. In this study, analytical descriptions of the 2D DEPT J-resolved NMR experiment for weakly coupled ISn (I=\\textstyle{\\frac{1}{2}}, S=\\textstyle{\\frac{3}{2}} ; n=1, 2, 3) spin systems using the product operator theory have been introduced for the first time. The calculated intensities and positions of the observable signals are simulated for molecules containing [13C (I=\\textstyle{\\frac{1}{2}}) , 81Br (S=\\textstyle{\\frac{3}{2}})] nuclei by using a MAPLE program on a computer. Finally, we present a theoretical discussion and experimental suggestions.

  13. Application Of Metric Space Technique (mst) In 2-d And 3-d To Sdss Dr5

    NASA Astrophysics Data System (ADS)

    Wu, Yongfeng; Batuski, D. J.; Khalil, A.

    2009-01-01

    The Metric Space Technique (MST) is a 2-D analysis method using multiple measures for quantitative analysis of any type of structure in an `image'. All potential values of the measures for such distributions are thus coordinates in a multi-parameter space, and the analysis is based on considering a sample's measures (called `output functions'), and their distance from the origin, which corresponds to the measures of the observed SDSS sample, in this multi-parameter space. Applications of this method to thin (approximately 2-D) slices of SDSS DR5 have yielded a detailed comparison of numerical models (Berlind et al. 2006, Croton et al. 2005) against the SDSS galaxy 2-D distribution structure in multi-parameter space. We present those results, including discussion of the effects of transforming from physical space to redshift space on the statistics at different scales. We also extended this 2-D method into 3-D, and we present comparisons of the SDSS galaxy 3-D distribution versus the same numerical simulations.

  14. Solution structure of GCCAAT recognition motif by 2D NMR, spectral simulation, molecular modeling, and distance geometry calculations.

    PubMed

    Nibedita, R; Kumar, R A; Majumdar, A; Hosur, R V; Govil, G; Majumder, K; Chauhan, V S

    1993-09-01

    Solution conformation of a self-complementary 14-mer DNA duplex (d-GGATTGGCCAATCC) containing the GCCAAT recognition motif of several transcription factors has been investigated by NMR spectroscopy. Complete resonance assignment of all the protons (except H5',H5'' protons) has been obtained following standard procedures based on two-dimensional NMR techniques. Three-bond coupling constants have been determined by spectral simulation procedures. New strategies have been described and employed for quantifying NOE intensities from the structural point of view. Approximate ranges of gamma torsion angles have been obtained from a selective NOESY experiment, by estimating the J(4'-5'), J(4'-5''), or their sum in the H1'-H4' cross peaks of the spectrum. Likewise, ranges of epsilon torsion angles have been obtained by monitoring the H3' multiplicities in the H8/H6-H3' cross peaks in selective NOESY spectra. With the help of such a total of 73 coupling constraints, 79 NOE intensity constraints, and 108 H-bond constraints, model building has been carried out to obtain a structure which satisfies the constraints. Starting from such a structure, an expanded distance constraint set has been created which has been used for the distance geometry calculations using the program TANDY. In the best structure thus derived, interesting irregularities similar to a BI-BII transition have been observed in the center. The molecule exhibits a bend. The overall base stacking is different from that in either B- or A-DNA models. The base pairs are tilted with respect to the local helix axes. The observed structural features are likely to have important implications for the recognition mechanism of the GCCAAT motif.

  15. A quantitative damage imaging technique based on enhanced CCRTM for composite plates using 2D scan

    NASA Astrophysics Data System (ADS)

    He, Jiaze; Yuan, Fuh-Gwo

    2016-10-01

    A two-dimensional (2D) non-contact areal scan system was developed to image and quantify impact damage in a composite plate using an enhanced zero-lag cross-correlation reverse-time migration (E-CCRTM) technique. The system comprises a single piezoelectric wafer mounted on the composite plate and a laser Doppler vibrometer (LDV) for scanning a region in the vicinity of the PZT to capture the scattered wavefield. The proposed damage imaging technique takes into account the amplitude, phase, geometric spreading, and all of the frequency content of the Lamb waves propagating in the plate; thus, a reflectivity coefficients of the delamination is calculated and potentially related to damage severity. Comparisons are made in terms of damage imaging quality between 2D areal scans and 1D line scans as well as between the proposed and existing imaging conditions. The experimental results show that the 2D E-CCRTM performs robustly when imaging and quantifying impact damage in large-scale composites using a single PZT actuator with a nearby areal scan using LDV.

  16. Monoplane 3D Overlay Roadmap versus Conventional Biplane 2D Roadmap Technique for Neurointervenional Procedures

    PubMed Central

    Jang, Dong-Kyu; Stidd, David A.; Schafer, Sebastian; Chen, Michael; Moftakhar, Roham

    2016-01-01

    Purpose We investigated whether a 3D overlay roadmap using monoplane fluoroscopy offers advantages over a conventional 2D roadmap using biplane fluoroscopy during endovascular aneurysm treatment. Materials and Methods A retrospective chart review was conducted for 131 consecutive cerebral aneurysm embolizations by three neurointerventionalists at a single institution. Allowing for a transition period, the periods from January 2012 to August 2012 (Time Period 1) and February 2013 to July 2013 (Time Period 2) were analyzed for radiation exposure, contrast administration, fluoroscopy time, procedure time, angiographic results, and perioperative complications. Two neurointerventionalists (Group 1) used a conventional 2D roadmap for both Time Periods, and one neurointerventionalist (Group 2) transitioned from a 2D roadmap during Time Period 1 to a 3D overlay roadmap during Time Period 2. Results During Time Period 2, Group 2 demonstrated reduced fluoroscopy time (p<0.001), procedure time (P=0.023), total radiation dose (p=0.001), and fluoroscopy dose (P=0.017) relative to Group 1. During Time Period 2, there was no difference of immediate angiographic results and procedure complications between the two groups. Through the transition from Time Period 1 to Time Period 2, Group 2 demonstrated decreased fluoroscopy time (p< 0.001), procedure time (p=0.022), and procedure complication rate (p=0.041) in Time Period 2 relative to Time Period 1. Conclusion The monoplane 3D overlay roadmap technique reduced fluoroscopy dose and fluoroscopy time during neurointervention of cerebral aneurysms with similar angiographic occlusions and complications rate relative to biplane 2D roadmap, which implies possible compensation of limitations of monoplane fluoroscopy by 3D overlay technique. PMID:27621947

  17. Monoplane 3D Overlay Roadmap versus Conventional Biplane 2D Roadmap Technique for Neurointervenional Procedures

    PubMed Central

    Jang, Dong-Kyu; Stidd, David A.; Schafer, Sebastian; Chen, Michael; Moftakhar, Roham

    2016-01-01

    Purpose We investigated whether a 3D overlay roadmap using monoplane fluoroscopy offers advantages over a conventional 2D roadmap using biplane fluoroscopy during endovascular aneurysm treatment. Materials and Methods A retrospective chart review was conducted for 131 consecutive cerebral aneurysm embolizations by three neurointerventionalists at a single institution. Allowing for a transition period, the periods from January 2012 to August 2012 (Time Period 1) and February 2013 to July 2013 (Time Period 2) were analyzed for radiation exposure, contrast administration, fluoroscopy time, procedure time, angiographic results, and perioperative complications. Two neurointerventionalists (Group 1) used a conventional 2D roadmap for both Time Periods, and one neurointerventionalist (Group 2) transitioned from a 2D roadmap during Time Period 1 to a 3D overlay roadmap during Time Period 2. Results During Time Period 2, Group 2 demonstrated reduced fluoroscopy time (p<0.001), procedure time (P=0.023), total radiation dose (p=0.001), and fluoroscopy dose (P=0.017) relative to Group 1. During Time Period 2, there was no difference of immediate angiographic results and procedure complications between the two groups. Through the transition from Time Period 1 to Time Period 2, Group 2 demonstrated decreased fluoroscopy time (p< 0.001), procedure time (p=0.022), and procedure complication rate (p=0.041) in Time Period 2 relative to Time Period 1. Conclusion The monoplane 3D overlay roadmap technique reduced fluoroscopy dose and fluoroscopy time during neurointervention of cerebral aneurysms with similar angiographic occlusions and complications rate relative to biplane 2D roadmap, which implies possible compensation of limitations of monoplane fluoroscopy by 3D overlay technique.

  18. 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

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

    DOE PAGES

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

  20. An on-line NMR technique with a programmable processor

    SciTech Connect

    Razazian, K.; Dieckman, S.L.; Raptis, A.C.

    1995-07-01

    Nuclear magnetic resonance (NMR) spectroscopy is used to determine molecular content of materials, mainly in laboratory measurements. The reduced cost of fast computer processors, together with recent break throughs in digital signal processor technology, has facilitated the on-line use of NMR by allowing modifications of the available technology. This paper describes a system and an algorithm for improving the on-line operations. It is base on the time-domain NMR signal detected by the controller and some prior knowledge of chemical signal patterns. The desired signal can be separated from a composite signal by using an adaptive line enhancer (ALE) filter. This technique would be useful for upgrading process procedures in on-line manufacturing.

  1. 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

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

    SciTech Connect

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

    1998-12-04

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

  3. 2-D array for 3-D Ultrasound Imaging Using Synthetic Aperture Techniques

    PubMed Central

    Daher, Nadim M.; Yen, Jesse T.

    2010-01-01

    A 2-D array of 256 × 256 = 65,536 elements, with total area 4 × 4 = 16 cm2, serves as a flexible platform for developing acquisition schemes for 3-D rectilinear ultrasound imaging at 10 MHz using synthetic aperture techniques. This innovative system combines a simplified interconnect scheme and synthetic aperture techniques with a 2-D array for 3-D imaging. A row-column addressing scheme is used to access different elements for different transmit events. This addressing scheme is achieved through a simple interconnect, consisting of one top, one bottom single layer flex circuits, which, compared to multi-layer flex circuits, are simpler to design, cheaper to manufacture and thinner so their effect on the acoustic response is minimized. We present three designs that prioritize different design objectives: volume acquisiton time, resolution, and sensitivity, while maintaining acceptable figures for the other design objectives. For example, one design overlooks time acquisition requirements, assumes good noise conditions, and optimizes for resolution, achieving −6 dB and −20 dB beamwidths of less than 0.2 and 0.5 millimeters, respectively, for an F/2 aperture. Another design can acquire an entire volume in 256 transmit events, with −6dB and −20 dB beamwidths in the order of 0.4 and 0.8 millimeters, respectively. PMID:16764446

  4. Chloride molecular doping technique on 2D materials: WS2 and MoS2.

    PubMed

    Yang, Lingming; Majumdar, Kausik; Liu, Han; Du, Yuchen; Wu, Heng; Hatzistergos, Michael; Hung, P Y; Tieckelmann, Robert; Tsai, Wilman; Hobbs, Chris; Ye, Peide D

    2014-11-12

    Low-resistivity metal-semiconductor (M-S) contact is one of the urgent challenges in the research of 2D transition metal dichalcogenides (TMDs). Here, we report a chloride molecular doping technique which greatly reduces the contact resistance (Rc) in the few-layer WS2 and MoS2. After doping, the Rc of WS2 and MoS2 have been decreased to 0.7 kΩ·μm and 0.5 kΩ·μm, respectively. The significant reduction of the Rc is attributed to the achieved high electron-doping density, thus a significant reduction of Schottky barrier width. As a proof-of-concept, high-performance few-layer WS2 field-effect transistors (FETs) are demonstrated, exhibiting a high drain current of 380 μA/μm, an on/off ratio of 4 × 10(6), and a peak field-effect mobility of 60 cm(2)/(V·s). This doping technique provides a highly viable route to diminish the Rc in TMDs, paving the way for high-performance 2D nanoelectronic devices.

  5. 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

  6. High resolution 2D-NMR studies indicating complete assignments and conformational characteristics of the NF-kappa B binding enhancer element of HIV-LTR.

    PubMed

    Singh, M P; Fregeau, N L; Pon, R T; Lown, J W

    1995-10-01

    The asymmetrical DNA duplex [5'd(AAGGGACTTTCC)].[5'-d(GGAAAGTCCCTT)] has been studied by one- and two-dimensional NMR techniques. The sequence is comprised of the actual 10 base-pair long binding site for the transcription factor NF-kappa B in the enhancer sequence of the long term repeat (LTR) region of HIV and SIV types of retroviruses associated with the AIDS syndrome. Two additional A.T base-pairs are also included on one end for an added interest in the 12-bp duplex sequence with a pseudo dyad-symmetric disposition of the oligopurine and oligopyrimidine segments, as it appears in the HIV-1 genome. Phase-sensitive two-dimensional spectra (NOESY, ROESY, COSY and TOCSY) were obtained at three different temperatures (5, 15 and 25 degrees C) for a complete assignment of the non-exchangeable protons by tracing through sequence specific intra- and internucleotide connectivities. 2D-NOESY spectra were also acquired in aqueous (90% H2O-D2O) solutions, with two different methods of water signal suppression, to assign the exchangeable protons from specific NOE correlations. Adenine H2 protons were assigned by the use of NOE correlations and from T1 relaxation time measurements. The general spectral features and semi-quantitative interproton distance estimates indicate a B-DNA type conformation. However, some distinctly unusual features associated with the nucleotides at and immediately adjacent to both the 5'-and 3'-ends of AAA/TTT and GGG/CCC segments were noted. The complete assignments, and the observed characteristics, will be of significant value in studying the complexes of this transcriptionally active DNA domain with the protein and other rationally designed DNA binding agents.

  7. A New Method for Detecting Goaf Area of Coal Mine :2D Microtremor Profiling Technique

    NASA Astrophysics Data System (ADS)

    Xu, P.; Ling, S.; Guo, H.; Shi, W.; Li, S.; Tian, B.

    2012-12-01

    A goaf area is referred to as a cavity where coal has been removed or mined out. These cavities will change the original geostress equilibrium of stratigraphic system and cause local geostress focusing or concentration. Consequently, the surrounding rock of a goaf may be deformed, fractured, displaced and caved resulting from the combined effect of gravity and geostress. In the cases of little or no effective mining control, widespread cracks, fractures and even subsidence of the rock mass above the goaf will not only lead to groundwater depletion, farmland destruction and deterioration of ecological environment, but also present a serious threat to the mining safety, engineering construction, and even people's lives and property. So, it is important to locate the boundary of the goaf and to evaluate its stability in order to provide the basis for comprehensive control in the latter period of mining. This article attempts to explore a new geophysical method - 2D microtremor profiling technique for goaf detection and mapping. 2D microtremor profiling technique is based on the microtremor array theory (Aki, 1957; Ling, 1994; Okada, 2003) utilizing spatial autocorrelation analysis to obtain Rayleigh-wave dispersion curves for apparent S-wave velocity (Vx) calculation (Ling & Miwa, 2006;Xu et al.,2012). A laterally continuous S-wave velocity section can then be obtained through data interpolation. The final result will be used for interpreting lateral changes in lithology and geological structures. Let's take a case study in Henan Province of China as an example. The coal seams in the survey area were about 150 ~ 250m deep. A triple-circular array was adopted for acquiring microtremor data, with the observation radius in 20, 40 and 80m, respectively, and a sampling the interval of 50m. We observed the following characteristics of the goaf area from the microtremor Vx section: (1) obvious low pseudo velocity anomaly corresponding to limestone layer below the goaf; (2

  8. Synthesis and structure elucidation of a series of pyranochromene chalcones and flavanones using 1D and 2D NMR spectroscopy and X-ray crystallography.

    PubMed

    Pawar, Sunayna S; Koorbanally, Neil A

    2014-06-01

    A series of novel pyranochromene chalcones and corresponding flavanones were synthesized. This is the first report on the confirmation of the absolute configuration of chromene-based flavanones using X-ray crystallography. These compounds were characterized by 2D NMR spectroscopy, and their assignments are reported herein. The 3D structure of the chalcone 3b and flavanone 4g was determined by X-ray crystallography, and the structure of the flavanone was confirmed to be in the S configuration at C-2.

  9. 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

  10. 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

  11. Fast and high-resolution stereochemical analysis by nonuniform sampling and covariance processing of anisotropic natural abundance 2D 2H NMR datasets.

    PubMed

    Lafon, Olivier; Hu, Bingwen; Amoureux, Jean-Paul; Lesot, Philippe

    2011-06-01

    Natural abundance deuterium (NAD) 2D NMR spectroscopy using chiral or achiral liquid crystals is an efficient analytical tool for the stereochemical analysis of enantio- or diastereomers by the virtue of proton-to-deuterium substitution. In particular, it allows the measurement of enantiopurity of organic synthetic molecules or the determination of the natural isotopic (1)H/(2)H fractionation in biological molecules, such as fatty acid methyl esters (FAME). So far, the NAD 2D spectra of solutes were acquired by using uniform sampling (US) and processed by conventional 2D Fourier transform (FT), which could result in long measurement times for medium-sized analytes or low solute concentrations. Herein, we demonstrate that this conventional approach can be advantageously replaced by nonuniform sampling (NUS) processed by covariance (Cov) transform. This original spectral reconstruction provides a significant enhancement of spectral resolution, as well as a reduction of measurement times. The application of Cov to NUS data has required the introduction of a regularization procedure in the time domain for the indirect dimension. The analytical potential of combining Cov and NUS is demonstrated by measuring the enantiomeric excess of a scalemic mixture of 2-ethyloxirane and by determining the diastereomeric excess of methyl vernoleate, a natural FAME. These two organic compounds were aligned in a polypeptide (poly(γ-benzyl-L-glutamate)) mesophase. In the case of NAD 2D NMR spectroscopy, we show that Cov and NUS methods allow a decrease in measurement time by a factor of two compared with Cov applied to US data and a factor of four compared with FT applied to US data.

  12. Performance analysis of the Microsoft Kinect sensor for 2D Simultaneous Localization and Mapping (SLAM) techniques.

    PubMed

    Kamarudin, Kamarulzaman; Mamduh, Syed Muhammad; Shakaff, Ali Yeon Md; Zakaria, Ammar

    2014-12-05

    This paper presents a performance analysis of two open-source, laser scanner-based Simultaneous Localization and Mapping (SLAM) techniques (i.e., Gmapping and Hector SLAM) using a Microsoft Kinect to replace the laser sensor. Furthermore, the paper proposes a new system integration approach whereby a Linux virtual machine is used to run the open source SLAM algorithms. The experiments were conducted in two different environments; a small room with no features and a typical office corridor with desks and chairs. Using the data logged from real-time experiments, each SLAM technique was simulated and tested with different parameter settings. The results show that the system is able to achieve real time SLAM operation. The system implementation offers a simple and reliable way to compare the performance of Windows-based SLAM algorithm with the algorithms typically implemented in a Robot Operating System (ROS). The results also indicate that certain modifications to the default laser scanner-based parameters are able to improve the map accuracy. However, the limited field of view and range of Kinect's depth sensor often causes the map to be inaccurate, especially in featureless areas, therefore the Kinect sensor is not a direct replacement for a laser scanner, but rather offers a feasible alternative for 2D SLAM tasks.

  13. Fabrication of Capacitive Acoustic Resonators Combining 3D Printing and 2D Inkjet Printing Techniques

    PubMed Central

    Haque, Rubaiyet Iftekharul; Ogam, Erick; Loussert, Christophe; Benaben, Patrick; Boddaert, Xavier

    2015-01-01

    A capacitive acoustic resonator developed by combining three-dimensional (3D) printing and two-dimensional (2D) printed electronics technique is described. During this work, a patterned bottom structure with rigid backplate and cavity is fabricated directly by a 3D printing method, and then a direct write inkjet printing technique has been employed to print a silver conductive layer. A novel approach has been used to fabricate a diaphragm for the acoustic sensor as well, where the conductive layer is inkjet-printed on a pre-stressed thin organic film. After assembly, the resulting structure contains an electrically conductive diaphragm positioned at a distance from a fixed bottom electrode separated by a spacer. Measurements confirm that the transducer acts as capacitor. The deflection of the diaphragm in response to the incident acoustic single was observed by a laser Doppler vibrometer and the corresponding change of capacitance has been calculated, which is then compared with the numerical result. Observation confirms that the device performs as a resonator and provides adequate sensitivity and selectivity at its resonance frequency. PMID:26473878

  14. Performance analysis of the Microsoft Kinect sensor for 2D Simultaneous Localization and Mapping (SLAM) techniques.

    PubMed

    Kamarudin, Kamarulzaman; Mamduh, Syed Muhammad; Shakaff, Ali Yeon Md; Zakaria, Ammar

    2014-01-01

    This paper presents a performance analysis of two open-source, laser scanner-based Simultaneous Localization and Mapping (SLAM) techniques (i.e., Gmapping and Hector SLAM) using a Microsoft Kinect to replace the laser sensor. Furthermore, the paper proposes a new system integration approach whereby a Linux virtual machine is used to run the open source SLAM algorithms. The experiments were conducted in two different environments; a small room with no features and a typical office corridor with desks and chairs. Using the data logged from real-time experiments, each SLAM technique was simulated and tested with different parameter settings. The results show that the system is able to achieve real time SLAM operation. The system implementation offers a simple and reliable way to compare the performance of Windows-based SLAM algorithm with the algorithms typically implemented in a Robot Operating System (ROS). The results also indicate that certain modifications to the default laser scanner-based parameters are able to improve the map accuracy. However, the limited field of view and range of Kinect's depth sensor often causes the map to be inaccurate, especially in featureless areas, therefore the Kinect sensor is not a direct replacement for a laser scanner, but rather offers a feasible alternative for 2D SLAM tasks. PMID:25490595

  15. Performance Analysis of the Microsoft Kinect Sensor for 2D Simultaneous Localization and Mapping (SLAM) Techniques

    PubMed Central

    Kamarudin, Kamarulzaman; Mamduh, Syed Muhammad; Shakaff, Ali Yeon Md; Zakaria, Ammar

    2014-01-01

    This paper presents a performance analysis of two open-source, laser scanner-based Simultaneous Localization and Mapping (SLAM) techniques (i.e., Gmapping and Hector SLAM) using a Microsoft Kinect to replace the laser sensor. Furthermore, the paper proposes a new system integration approach whereby a Linux virtual machine is used to run the open source SLAM algorithms. The experiments were conducted in two different environments; a small room with no features and a typical office corridor with desks and chairs. Using the data logged from real-time experiments, each SLAM technique was simulated and tested with different parameter settings. The results show that the system is able to achieve real time SLAM operation. The system implementation offers a simple and reliable way to compare the performance of Windows-based SLAM algorithm with the algorithms typically implemented in a Robot Operating System (ROS). The results also indicate that certain modifications to the default laser scanner-based parameters are able to improve the map accuracy. However, the limited field of view and range of Kinect's depth sensor often causes the map to be inaccurate, especially in featureless areas, therefore the Kinect sensor is not a direct replacement for a laser scanner, but rather offers a feasible alternative for 2D SLAM tasks. PMID:25490595

  16. Fabrication of capacitive acoustic resonators combining 3D printing and 2D inkjet printing techniques.

    PubMed

    Haque, Rubaiyet Iftekharul; Ogam, Erick; Loussert, Christophe; Benaben, Patrick; Boddaert, Xavier

    2015-10-14

    A capacitive acoustic resonator developed by combining three-dimensional (3D) printing and two-dimensional (2D) printed electronics technique is described. During this work, a patterned bottom structure with rigid backplate and cavity is fabricated directly by a 3D printing method, and then a direct write inkjet printing technique has been employed to print a silver conductive layer. A novel approach has been used to fabricate a diaphragm for the acoustic sensor as well, where the conductive layer is inkjet-printed on a pre-stressed thin organic film. After assembly, the resulting structure contains an electrically conductive diaphragm positioned at a distance from a fixed bottom electrode separated by a spacer. Measurements confirm that the transducer acts as capacitor. The deflection of the diaphragm in response to the incident acoustic single was observed by a laser Doppler vibrometer and the corresponding change of capacitance has been calculated, which is then compared with the numerical result. Observation confirms that the device performs as a resonator and provides adequate sensitivity and selectivity at its resonance frequency.

  17. 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…

  18. Development of solid-state NMR techniques for the characterisation of pharmaceutical compounds

    NASA Astrophysics Data System (ADS)

    Tatton, Andrew S.

    Structural characterisation in the solid state is an important step in understanding the physical and chemical properties of a material. Solid-state NMR techniques applied to solid delivery forms are presented as an alternative to more established structural characterisation methods. The effect of homonuclear decoupling upon heteronuclear couplings is investigated using a combination of experimental and density-matrix simulation results acquired from a 13C-1H spinecho pulse sequence, modulated by scalar couplings. It is found that third-order cross terms under MAS and homonuclear decoupling contribute to strong dephasing effects in the NMR signal. Density-matrix simulations allow access to parameters currently unattainable in experiment, and demonstrate that higher homonuclear decoupling rf nutation frequencies reduce the magnitude of third-order cross terms. 15N-1H spinecho experiments were applied to pharmaceutically relevant samples to differentiate between the number of directly attached protons. Using this method, proton transfer in an acid-base reaction is proven in pharmaceutical salts. The indirect detection of 14N lineshapes via protons obtained using 2D 14N-1H HMQC experiments is presented, where coherence transfer is achieved via heteronuclear through-space dipolar couplings. The importance of fast MAS frequencies is demonstrated, and it is found that increasing the recoupling duration reveals longer range NH proximities. The 2D 14N-1H HMQC method is used to demonstrate the presence of specific hydrogen bonding interactions, and thus aid in identifying molecular association in a cocrystal and an amorphous dispersion. In addition, hydrogen bonding motifs were identified by observing the changes in the 14N quadrupolar parameters between individual molecular components relative to the respective solid delivery form. First-principles calculations of NMR chemical shifts and quadrupolar parameters using the GIPAW method were combined with 14N-1H experimental

  19. 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

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

    PubMed Central

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

    2014-01-01

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

  1. High-resolution GPR imaging using a nonstandard 2D EEMD technique

    NASA Astrophysics Data System (ADS)

    Chen, Chih-Sung; Jeng*, Yih; Yu, Hung-Ming

    2013-04-01

    Ground Penetrating Radar (GPR) data are affected by a variety of factors. Linear and nonlinear data processing methods each have been widely applied to the GPR use in geophysical and engineering investigations. For complicated data such as the shallow earth image of urban area, a better result can be achieved by integrating both approaches. In this study, we introduce a nonstandard 2D EEMD approach, which integrates the natural logarithm transformed (NLT) ensemble empirical mode decomposition (EEMD) method with the linear filtering technique to process GPR images. The NLT converts the data into logarithmic values; therefore, it permits a wide dynamic range for the recorded GPR data to be presented. The EEMD dyadic filter bank decomposes the data into multiple components ready for image reconstruction. Consequently, the NLT EEMD method provides a new way of nonlinear energy compensating and noise filtering with results having minimal artifacts. However, horizontal noise in the GPR time-distance section may be enhanced after NLT process in some cases. To solve the dilemma, we process the data two dimensionally. At first, the vertical background noise of each GPR trace is removed by using a standard linear method, the background noise removal algorithm, or simply by performing the sliding background removal filter. After that, the NLT is applied to the data for examining the horizontal coherent energy. Next, we employ the EEMD filter bank horizontally at each time step to remove the horizontal coherent energy. After removing the vertical background noise and horizontal coherent energy, a vertical EEMD method is then applied to generate a filter bank of the GPR time-distance section for final image reconstruction. Two buried models imitating common shallow earth targets are used to verify the effectiveness of the proposed scheme. One model is a brick cistern buried in a disturbed site of poor reflection quality. The other model is a buried two-stack metallic target

  2. 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.

  3. Studies of magnetism using nuclear orientation and related NMR techniques

    NASA Astrophysics Data System (ADS)

    Pond, James F.

    2001-09-01

    Nuclear Orientation and related NMR techniques have been used to study three magnetic insulators: Mn(COOCH3)2·4H2O, MnCl2·4H2O and CoCl2·6H 2O. Continuous wave NMR thermally detected by Nuclear Orientation has been used to investigate the magnetic properties and spin dynamics of the quasi-2-dimensional ferromagnet 54Mn-Mn(COOCH3)2·4H 2O. The system exhibits a frequency pulling effect due to the indirect Suhl-Nakamura interaction between nuclear spins and the electronic spin excitation spectrum is related to the coupling strength of the nuclear spins. The temperature dependence of the frequency pulling effect was measured for the two crystalline sublattices Mn1 and Mn2 in low magnetic field. The spectra show a structure not predicted theoretically. The current theory is valid only for I = 1/2 with uniaxial crystalline anisotropy fields. The theory of frequency pulling has been extended here to the case of I ≥ 1/2 and non-uniaxial crystalline anisotropy fields and the resonant frequencies and linewidths have been calculated as a function of temperature. The new theory and data agree well in terms of the magnitude and temperature dependence of the frequency pulling. Discrepancies are likely due to simplifying assumptions when calculating the electronic magnon spectrum. Classical and quantum numerical simulations confirm qualitatively the predictions of the model. The first Low Temperature Nuclear Orientation experiments on isotopes implanted into insulators is reported. Radioactive 56Mn ions have been implanted into insulating, antiferromagnetic crystals of MnCl 2·4H2O and CoCl2·6H2O. In MnCl2·4H2O, comparison of the gamma-ray anisotropy of the 56Mn nuclei with that of 54Mn, doped into the sample during growth, showed that both the 56Mn and 54Mn spins felt a very similar hyperfine field. The site occupancy factor in a simple, two site model was deduced to be 0.96+0.04-0.07 . In CoCl2·6H2O, the average hyperfine field for the implanted 56Mn was significantly

  4. 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.

  5. Proton 2D NMR and distance geometry study of the folding of Ecballium elaterium trypsin inhibitor, a member of the squash inhibitors family

    SciTech Connect

    Heitz, A.; Chiche, L.; Le-Nguyen, D.; Castro, B. )

    1989-03-21

    The solution conformation of synthetic Ecballium elaterium trypsin inhibitor II, a 28-residue peptide with 3 disulfide bridges, has been studied by {sup 1}H 2D NMR measurements. Secondary structure elements were determined: a miniantiparallel {beta}-sheet Met 7-Cys 9 and Gly 25-Cys 27, a {beta}-hairpin 20-28 with {beta}-turn 22-25, and two tight turns Asp 12-Cys 15 and Leu 16-Cys 19. A set of interproton distance restraints deduced from two-dimensional nuclear Overhauser enhancement spectra and 13 {phi} backbone torsion angles restraints were used as the basis of three-dimensional structure computations including disulfide bridges arrangement by using distance geometry calculations. Computations for the 15 possible S-S linkage combinations lead to the proposal of the array 2-19, 9-21, 15-27 as the most probably structure for EETI II.

  6. Comparative 2D NMR studies of human insulin and des-pentapeptide insulin: Sequential resonance assignment and implications for protein dynamics and receptor recognition

    SciTech Connect

    Hua, Qingxin ); Weiss, M.A. Massachusetts General Hospital, Boston, MA )

    1991-06-04

    The solution structure and dynamics of human insulin are ivestigated by 2D {sup 1}H NMR spectroscopy in reference to a previously analyzed analogue, des-pentapeptide (B26-B30) insulin. This spectroscopic comparison is of interest since (i) the structure of the C-terminal region of the B-chain has not been determined in the monomeric state and (ii) the role of this region in binding to the insulin receptor has been the subject of long-standing speculation. The present NMR studies are conducted in the presence of an organic cosolvent (20% acetic acid), under which conditions both proteins are monomeric and stably folded. Complete sequential assignment of human insulin is obtained and leads to the following conclusions. (1) The secondary structure of the insulin monomer (three {alpha}-helices and B-chain {beta}-turn) is similar to that observed in the 2-Zn crustal state. (2) The folding of DPI is essentially the same as the corresponding portion of intact insulin, in accord with the similarities between their respective crystal structues. (3) residues B24-B28 adopt an extended configuration in the monomer and pack against the hydrophobic core as in crystallographic dimers; residues B29 and B30 are largely disordered. (4) The insulin fold is shown to provide a model for collective motions in a protein with implications for the mechanism of protein-protein recognition. To their knowledge, this paper describes the first detailed analysis of a protein NMR spectrum under conditions of extensive conformational broadening.

  7. 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

  8. 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

  9. SENSASS NMR: New NMR techniques for enhancing the sensitivity and the spectral resolution of polymer supported chemicals

    NASA Astrophysics Data System (ADS)

    Prosa, Nicolò; Scherrmann, Marie-Christine; Merlet, Denis; Farjon, Jonathan

    2013-12-01

    The use of polyethylene glycols (PEGs) as organic polymer soluble supports for synthesis has been receiving growing interest. The main advantages of using PEGs as support are related to their non-toxicity, their commercial availability and their solubility properties allowing easy recovery and analysis of compounds linked to the polymer. The NMR characterization of PEG-branched products could however be difficult due to the presence of huge signals of the polymeric support. In order to overcome this problem, we developed new NMR experiments named SENSitivity increAsed and resolution enhanced by Signal Suppression or SENSASS NMR. These experiments implement either semi-selective pulses or Water Gate sequences for reducing signals of the polymer as well as fast pulsing techniques optimizing the recycling delay for enhancing the sensitivity of signals. They have been successfully implemented in classical NMR characterization experiments namely, COSY, HSQC and HMBC experiments.

  10. 2D electron temperature diagnostic using soft x-ray imaging technique

    SciTech Connect

    Nishimura, K. Sanpei, A. Tanaka, H.; Ishii, G.; Kodera, R.; Ueba, R.; Himura, H.; Masamune, S.; Ohdachi, S.; Mizuguchi, N.

    2014-03-15

    We have developed a two-dimensional (2D) electron temperature (T{sub e}) diagnostic system for thermal structure studies in a low-aspect-ratio reversed field pinch (RFP). The system consists of a soft x-ray (SXR) camera with two pin holes for two-kinds of absorber foils, combined with a high-speed camera. Two SXR images with almost the same viewing area are formed through different absorber foils on a single micro-channel plate (MCP). A 2D T{sub e} image can then be obtained by calculating the intensity ratio for each element of the images. We have succeeded in distinguishing T{sub e} image in quasi-single helicity (QSH) from that in multi-helicity (MH) RFP states, where the former is characterized by concentrated magnetic fluctuation spectrum and the latter, by broad spectrum of edge magnetic fluctuations.

  11. Image Pretreatment Tools II: Normalization Techniques for 2-DE and 2-D DIGE.

    PubMed

    Robotti, Elisa; Marengo, Emilio; Quasso, Fabio

    2016-01-01

    Gel electrophoresis is usually applied to identify different protein expression profiles in biological samples (e.g., control vs. pathological, control vs. treated). Information about the effect to be investigated (a pathology, a drug, a ripening effect, etc.) is however generally confounded with experimental variability that is quite large in 2-DE and may arise from small variations in the sample preparation, reagents, sample loading, electrophoretic conditions, staining and image acquisition. Obtaining valid quantitative estimates of protein abundances in each map, before the differential analysis, is therefore fundamental to provide robust candidate biomarkers. Normalization procedures are applied to reduce experimental noise and make the images comparable, improving the accuracy of differential analysis. Certainly, they may deeply influence the final results, and to this respect they have to be applied with care. Here, the most widespread normalization procedures are described both for what regards the applications to 2-DE and 2D Difference Gel-electrophoresis (2-D DIGE) maps.

  12. 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.

  13. 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

  14. 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

  15. Use of NMR techniques for toxic organophosphorus compound profiling.

    PubMed

    Koskela, Harri

    2010-05-15

    This review presents with selected examples the versatility of nuclear magnetic resonance (NMR) spectroscopy in the analysis of toxic organophosphorus (OP) compounds, i.e. OP pesticides and chemical warfare agents (CWAs). Several NMR applications of biological importance, like studies on inhibition mechanism, metabolism, and exposure determination, are presented. The review also concerns with the environmental analysis of OP compounds by NMR spectroscopy. Residue analysis of environment and food samples as well as characterization of degradation in environment is discussed. Some of the NMR studies that have been done to support the Chemical Weapons Convention, i.e. the development of suitable CWA detoxification means and the method development of verification analysis for CWAs and their degradation products, are outlined. PMID:19939751

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

    PubMed

    Abraham, Anuji; Crull, George

    2014-10-01

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

  17. Analysis of NAD 2D-NMR spectra of saturated fatty acids in polypeptide aligning media by experimental and modeling approaches.

    PubMed

    Serhan, Zeinab; Borgogno, Andrea; Billault, Isabelle; Ferrarini, Alberta; Lesot, Philippe

    2012-01-01

    The overall and detailed elucidation (including the stereochemical aspects) of enzymatic mechanisms requires the access to all reliable information related to the natural isotopic fractionation of both precursors and products. Natural abundance deuterium (NAD) 2D-NMR experiments in polypeptide liquid-crystalline solutions are a new, suitable tool for analyzing site-specific deuterium isotopic distribution profiles. Here this method is utilized for analyzing saturated C14 to C18 fatty acid methyl esters (FAMEs), which are challenging because of the crowding of signals in a narrow spectral region. Experiments in achiral and chiral oriented solutions were performed. The spectral analysis is supplemented by the theoretical prediction of quadrupolar splittings as a function of the geometry and flexibility of FAMEs, based on a novel computational methodology. This allows us to confirm the spectral assignments, while providing insights into the mechanism of solute ordering in liquid-crystalline polypeptide solutions. This is found to be dominated by steric repulsions between FAMEs and polypeptides.

  18. Commissioning a small-field biological irradiator using point, 2D, and 3D dosimetry techniques

    PubMed Central

    Newton, Joseph; Oldham, Mark; Thomas, Andrew; Li, Yifan; Adamovics, John; Kirsch, David G.; Das, Shiva

    2011-01-01

    Purpose: To commission a small-field biological irradiator, the XRad225Cx from Precision x-Ray, Inc., for research use. The system produces a 225 kVp x-ray beam and is equipped with collimating cones that produce both square and circular radiation fields ranging in size from 1 to 40 mm. This work incorporates point, 2D, and 3D measurements to determine output factors (OF), percent-depth-dose (PDD) and dose profiles at multiple depths. Methods: Three independent dosimetry systems were used: ion-chambers (a farmer chamber and a micro-ionisation chamber), 2D EBT2 radiochromic film, and a novel 3D dosimetry system (DLOS/PRESAGE®). Reference point dose rates and output factors were determined from in-air ionization chamber measurements for fields down to ∼13 mm using the formalism of TG61. PDD, profiles, and output factors at three separate depths (0, 0.5, and 2 cm), were determined for all field sizes from EBT2 film measurements in solid water. Several film PDD curves required a scaling correction, reflecting the challenge of accurate film alignment in very small fields. PDDs, profiles, and output factors were also determined with the 3D DLOS/PRESAGE® system which generated isotropic 0.2 mm data, in scan times of 20 min. Results: Surface output factors determined by ion-chamber were observed to gradually drop by ∼9% when the field size was reduced from 40 to 13 mm. More dramatic drops were observed for the smallest fields as determined by EBT∼18% and ∼42% for the 2.5 mm and 1 mm fields, respectively. PRESAGE® and film output factors agreed well for fields <20 mm (where 3D data were available) with mean deviation of 2.2% (range 1%–4%). PDD values at 2 cm depth varied from ∼72% for the 40 mm field, down to ∼55% for the 1 mm field. EBT and PRESAGE® PDDs agreed within ∼3% in the typical therapy region (1–4 cm). At deeper depths the EBT curves were slightly steeper (2.5% at 5 cm). These results indicate good overall consistency between ion-chamber, EBT

  19. A novel 2D silicon nano-mold fabrication technique for linear nanochannels over a 4 inch diameter substrate

    PubMed Central

    Yin, Zhifu; Qi, Liping; Zou, Helin; Sun, Lei

    2016-01-01

    A novel low-cost 2D silicon nano-mold fabrication technique was developed based on Cu inclined-deposition and Ar+ (argon ion) etching. With this technique, sub-100 nm 2D (two dimensional) nano-channels can be etched economically over the whole area of a 4 inch n-type <100> silicon wafer. The fabricating process consists of only 4 steps, UV (Ultraviolet) lithography, inclined Cu deposition, Ar+ sputter etching, and photoresist & Cu removing. During this nano-mold fabrication process, we investigated the influence of the deposition angle on the width of the nano-channels and the effect of Ar+ etching time on their depth. Post-etching measurements showed the accuracy of the nanochannels over the whole area: the variation in width is 10%, in depth it is 11%. However, post-etching measurements also showed the accuracy of the nanochannels between chips: the variation in width is 2%, in depth it is 5%. With this newly developed technology, low-cost and large scale 2D nano-molds can be fabricated, which allows commercial manufacturing of nano-components over large areas. PMID:26752559

  20. 2D and 3D optical diagnostic techniques applied to Madonna dei Fusi by Leonardo da Vinci

    NASA Astrophysics Data System (ADS)

    Fontana, R.; Gambino, M. C.; Greco, M.; Marras, L.; Materazzi, M.; Pampaloni, E.; Pelagotti, A.; Pezzati, L.; Poggi, P.; Sanapo, C.

    2005-06-01

    3D measurement and modelling have been traditionally applied to statues, buildings, archeological sites or similar large structures, but rarely to paintings. Recently, however, 3D measurements have been performed successfully also on easel paintings, allowing to detect and document the painting's surface. We used 3D models to integrate the results of various 2D imaging techniques on a common reference frame. These applications show how the 3D shape information, complemented with 2D colour maps as well as with other types of sensory data, provide the most interesting information. The 3D data acquisition was carried out by means of two devices: a high-resolution laser micro-profilometer, composed of a commercial distance meter mounted on a scanning device, and a laser-line scanner. The 2D data acquisitions were carried out using a scanning device for simultaneous RGB colour imaging and IR reflectography, and a UV fluorescence multispectral image acquisition system. We present here the results of the techniques described, applied to the analysis of an important painting of the Italian Reinassance: `Madonna dei Fusi', attributed to Leonardo da Vinci.

  1. A novel 2D silicon nano-mold fabrication technique for linear nanochannels over a 4 inch diameter substrate.

    PubMed

    Yin, Zhifu; Qi, Liping; Zou, Helin; Sun, Lei

    2016-01-11

    A novel low-cost 2D silicon nano-mold fabrication technique was developed based on Cu inclined-deposition and Ar(+) (argon ion) etching. With this technique, sub-100 nm 2D (two dimensional) nano-channels can be etched economically over the whole area of a 4 inch n-type <100> silicon wafer. The fabricating process consists of only 4 steps, UV (Ultraviolet) lithography, inclined Cu deposition, Ar(+) sputter etching, and photoresist &Cu removing. During this nano-mold fabrication process, we investigated the influence of the deposition angle on the width of the nano-channels and the effect of Ar(+) etching time on their depth. Post-etching measurements showed the accuracy of the nanochannels over the whole area: the variation in width is 10%, in depth it is 11%. However, post-etching measurements also showed the accuracy of the nanochannels between chips: the variation in width is 2%, in depth it is 5%. With this newly developed technology, low-cost and large scale 2D nano-molds can be fabricated, which allows commercial manufacturing of nano-components over large areas.

  2. An enhanced CCRTM (E-CCRTM) damage imaging technique using a 2D areal scan for composite plates

    NASA Astrophysics Data System (ADS)

    He, Jiaze; Yuan, Fuh-Gwo

    2016-04-01

    A two-dimensional (2-D) non-contact areal scan system was developed to image and quantify impact damage in a composite plate using an enhanced zero-lag cross-correlation reverse-time migration (E-CCRTM) technique. The system comprises a single piezoelectric actuator mounted on the composite plate and a laser Doppler vibrometer (LDV) for scanning a region to capture the scattered wavefield in the vicinity of the PZT. The proposed damage imaging technique takes into account the amplitude, phase, geometric spreading, and all of the frequency content of the Lamb waves propagating in the plate; thus, the reflectivity coefficients of the delamination can be calculated and potentially related to damage severity. Comparisons are made in terms of damage imaging quality between 2-D areal scans and linear scans as well as between the proposed and existing imaging conditions. The experimental results show that the 2-D E-CCRTM performs robustly when imaging and quantifying impact damage in large-scale composites using a single PZT actuator with a nearby areal scan using LDV.

  3. Characterization of controlled bone defects using 2D and 3D ultrasound imaging techniques.

    PubMed

    Parmar, Biren J; Longsine, Whitney; Sabonghy, Eric P; Han, Arum; Tasciotti, Ennio; Weiner, Bradley K; Ferrari, Mauro; Righetti, Raffaella

    2010-08-21

    Ultrasound is emerging as an attractive alternative modality to standard x-ray and CT methods for bone assessment applications. As of today, however, there is a lack of systematic studies that investigate the performance of diagnostic ultrasound techniques in bone imaging applications. This study aims at understanding the performance limitations of new ultrasound techniques for imaging bones in controlled experiments in vitro. Experiments are performed on samples of mammalian and non-mammalian bones with controlled defects with size ranging from 400 microm to 5 mm. Ultrasound findings are statistically compared with those obtained from the same samples using standard x-ray imaging modalities and optical microscopy. The results of this study demonstrate that it is feasible to use diagnostic ultrasound imaging techniques to assess sub-millimeter bone defects in real time and with high accuracy and precision. These results also demonstrate that ultrasound imaging techniques perform comparably better than x-ray imaging and optical imaging methods, in the assessment of a wide range of controlled defects both in mammalian and non-mammalian bones. In the future, ultrasound imaging techniques might provide a cost-effective, real-time, safe and portable diagnostic tool for bone imaging applications.

  4. Detection of metallic and plastic landmines using the GPR and 2-D resistivity techniques

    NASA Astrophysics Data System (ADS)

    Metwaly, M.

    2007-12-01

    Low and non-metallic landmines are one of the most difficult subsurface targets to be detected using several geophysical techniques. Ground penetrating radar (GPR) performance at different field sites shows great success in detecting metallic landmines. However significant limitations are taking place in the case of low and non-metallic landmines. Electrical resistivity imaging (ERI) technique is tested to be an alternative or confirmation technique for detecting the metallic and non-metallic landmines in suspicious cleared areas. The electrical resistivity responses using forward modeling for metallic and non-metallic landmines buried in dry and wet environments utilizing the common electrode configurations have been achieved. Roughly all the utilized electrode arrays can establish the buried metallic and plastic mines correctly in dry and wet soil. The accuracy differs from one array to the other based on the relative resistivity contrast to the host soil and the subsurface distribution of current and potential lines as well as the amplitude of the noises in the data. The ERI technique proved to be fast and effective tool for detecting the non-metallic mines especially in the conductive environment whereas the performances of the other metal detector (MD) and GPR techniques show great limitation.

  5. Use of 2D and 3D Imaging Techniques to Understand Fracture Growth

    NASA Astrophysics Data System (ADS)

    Lockner, D. A.

    2004-05-01

    The monitoring of acoustic emissions (AE) is a valuable tool for studying the brittle fracture process in rock. With the improved characterization of transducer response, researchers are able to apply a broad spectrum of seismological techniques to AE catalogues collected in the laboratory; i.e., moment tensor analysis, Vp/Vs ratios, attenuation, event clustering statistics, Gutenberg-Richter b-value and aftershock analysis. Since AE occurs spontaneously as a result of unstable microcrack growth during rock deformation experiments, it provides a non-destructive method to observe damage accumulation. I will give examples of visualization techniques that have proven helpful in the analysis of fracture nucleation and growth based on 3D event locations in granite and sandstone samples. These techniques are useful in interpreting the development of complex fracture systems in lab samples. Complementary measurements of wave speed anisotropy and heterogeneity are used to infer both the development of damage zones and the rate of infiltration of water during fluid injection experiments. Finally, spatial clustering of AE events is evaluated in terms of the surface roughness of reactivated faults during triaxial deformation experiments.

  6. A Beam-Fourier Technique for the Numerical Investigation of 2D Nonlinear Convective Flows

    NASA Astrophysics Data System (ADS)

    Papanicolaou, N. C.

    2011-11-01

    In the current work, we develop a numerical method suitable for treating the problem of nonlinear two-dimensional flows in rectangular domains. For the spatial approximation we employ the Fourier-Galerkin approach. More specifically, our basis functions are products of trigonometric and Beam functions. This choice means that the solutions automatically satisfy the boundary and periodic conditions in the x and y directions respectively. The accuracy of the method is assessed by applying it to model problems which admit exact analytical solutions. The numerical and analytic solutions are found to be in good agreement. The convergence rate of the spectral coefficients is found to be fifth-order algebraic in the x-direction and y-direction, confirming the efficiency and speed of our technique.

  7. Studies of electrolyte penetration in carbon anodes by NMR techniques.

    SciTech Connect

    Sandi, G.

    1998-12-09

    A toroid cavity nuclear magnetic resonance (NMR) detector capable of recording radial concentration profiles, diffusion constants, and displacements of charge carriers was employed to investigate the lithium ion distribution in an electrochemical cell containing a carbonaceous material synthesized from pyrene and pillared clays as inorganic templates. A carbon rod was used in a control experiment to assign the Li{sup +} spectrum and to calibrate the one dimensional radial images.

  8. Application and further development of diffusion based 2D chemical imaging techniques in the rhizosphere

    NASA Astrophysics Data System (ADS)

    Hoefer, Christoph; Santner, Jakob; Borisov, Sergey; Kreuzeder, Andreas; Wenzel, Walter; Puschenreiter, Markus

    2015-04-01

    Two dimensional chemical imaging of root processes refers to novel in situ methods to investigate and map solutes at a high spatial resolution (sub-mm). The visualization of these solutes reveals new insights in soil biogeochemistry and root processes. We derive chemical images by using data from DGT-LA-ICP-MS (Diffusive Gradients in Thin Films and Laser Ablation Inductively Coupled Plasma Mass Spectrometry) and POS (Planar Optode Sensors). Both technologies have shown promising results when applied in aqueous environment but need to be refined and improved for imaging at the soil-plant interface. Co-localized mapping using combined DGT and POS technologies and the development of new gel combinations are in our focus. DGTs are smart and thin (<0.4 mm) hydrogels; containing a binding resin for the targeted analytes (e.g. trace metals, phosphate, sulphide or radionuclides). The measurement principle is passive and diffusion based. The present analytes are diffusing into the gel and are bound by the resin. Thereby, the resin acts as zero sink. After application, DGTs are retrieved, dried, and analysed using LA-ICP-MS. The data is then normalized by an internal standard (e.g. 13C), calibrated using in-house standards and chemical images of the target area are plotted using imaging software. POS are, similar to DGT, thin sensor foils containing a fluorophore coating depending on the target analyte. The measurement principle is based on excitation of the flourophore by a specific wavelength and emission of the fluorophore depending on the presence of the analyte. The emitted signal is captured using optical filters and a DSLR camera. While DGT analysis is destructive, POS measurements can be performed continuously during the application. Both semi-quantitative techniques allow an in situ application to visualize chemical processes directly at the soil-plant interface. Here, we present a summary of results from rhizotron experiments with different plants in metal

  9. 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.

  10. On the potential of 2-D-Video Disdrometer technique to measure micro physical parameters of solid precipitation

    NASA Astrophysics Data System (ADS)

    Bernauer, F.; Hürkamp, K.; Rühm, W.; Tschiersch, J.

    2015-03-01

    Detailed characterization and classification of precipitation is an important task in atmospheric research. Line scanning 2-D-video disdrometer technique is well established for rain observations. The two orthogonal views taken of each hydrometeor passing the sensitive area of the instrument qualify this technique especially for detailed characterization of non symmetric solid hydrometeors. However, in case of solid precipitation problems related to the matching algorithm have to be considered and the user must be aware of the limited spacial resolution when size and shape descriptors are analyzed. This work has the aim of clarifying the potential of 2-D-video disdrometer technique in deriving size, velocity and shape parameters from single recorded pictures. The need of implementing a matching algorithm suitable for mixed and solid phase precipitation is highlighted as an essential step in data evaluation. For this purpose simple reproducible experiments with solid steel spheres and irregularly shaped styrofoam particles are conducted. Self-consistency of shape parameter measurements is tested in 40 cases of real snow fall. As result it was found, that reliable size and shape characterization with a relative standard deviation of less than 5% is only possible for particles larger than 1 mm. For particles between 0.5 and 1.0 mm the relative standard deviation can grow up to 22% for the volume, 17% for size parameters and 14% for shape descriptors. Testing the adapted matching algorithm with a reproducible experiment with styrofoam particles a mismatch probability of less than 2.5% was found. For shape parameter measurements in case of real solid phase precipitation the 2DVD shows self-consistent behavior.

  11. A hybrid experimental-numerical technique for determining 3D velocity fields from planar 2D PIV data

    NASA Astrophysics Data System (ADS)

    Eden, A.; Sigurdson, M.; Mezić, I.; Meinhart, C. D.

    2016-09-01

    Knowledge of 3D, three component velocity fields is central to the understanding and development of effective microfluidic devices for lab-on-chip mixing applications. In this paper we present a hybrid experimental-numerical method for the generation of 3D flow information from 2D particle image velocimetry (PIV) experimental data and finite element simulations of an alternating current electrothermal (ACET) micromixer. A numerical least-squares optimization algorithm is applied to a theory-based 3D multiphysics simulation in conjunction with 2D PIV data to generate an improved estimation of the steady state velocity field. This 3D velocity field can be used to assess mixing phenomena more accurately than would be possible through simulation alone. Our technique can also be used to estimate uncertain quantities in experimental situations by fitting the gathered field data to a simulated physical model. The optimization algorithm reduced the root-mean-squared difference between the experimental and simulated velocity fields in the target region by more than a factor of 4, resulting in an average error less than 12% of the average velocity magnitude.

  12. Grade-2 Teflon (AF1601) PCF for optical communication using 2D FDTD technique: a simplest design

    NASA Astrophysics Data System (ADS)

    Muduli, N.; Achary, J. S. N.; Padhy, Hemanta ku.

    2016-04-01

    A nonlinear ytterbium-doped rectangular proposed PCF structure of inner and outer cladding is used to analyze effective mode field area (Aeff), nonlinear coefficient (γ), dispersion (D), and confinement loss (CL) in a wide range of wavelength. The fabrication of PCF structure is due to different size doped air hole, pitch, and air hole diameter in a regular periodic geometrical array fashion. The various property of PCF structure such as mode field area, nonlinear coefficient, dispersion, and confinement loss are analyzed by implementing 2D FDTD technique. The above PCF property investigated using suitable parameters like Λ1, ?, ?, and ? in three different situations is discussed in simulation. The high nonlinear coefficient and dispersion property of PCF structure are tailored by setting the cladding parameter. However, highly nonlinear fibers with nonzero dispersion at the wavelength of 1.55 μm are very attractive for a range of optical communication application such as laser amplifier, pulse compression, wavelength conversion, all optical switching, and supercontinuum generation. So our newly proposed ytterbium-doped PCF seems to be most suitable exclusively for supercontinuum generation and nonlinear fiber optics. Finally, it is observed that ytterbium-doped Teflon (AF1601) PCF has more nonlinear coefficient (γ(λ) = 65.27 W-1 km-1) as compared to pure silica PCF (γ(λ) = 52 W-1 km-1) design to have same mode field area (Aeff) 1.7 μm2 at an operating wavelength of 1.55 μm.

  13. Difference-NMR techniques for selection of components on the basis of relaxation times

    NASA Astrophysics Data System (ADS)

    Harris, Douglas J.; de Azevedo, Eduardo R.; Bonagamba, Tito J.

    2003-05-01

    This work describes a numerical methodology to obtain more efficient relaxation filters to selectively retain or remove components based on relaxation times. The procedure uses linear combinations of spectra with various recycle or filter delays to obtain components that are both quantitative and pure. Modulation profiles are calculated assuming exponential relaxation behavior. The method is general and can be applied to a wide range of solution or solid-state NMR experiments including direct-polarization (DP), or filtered cross-polarization (CP) spectra. 13C NMR experiments on isotactic poly(1-butene) and dimethyl sulfone showed the utility of the technique for selectively suppressing peaks.

  14. Image-selected in Vivo spectroscopy (ISIS). A new technique for spatially selective nmr spectroscopy

    NASA Astrophysics Data System (ADS)

    Ordidge, R. J.; Connelly, A.; Lohman, J. A. B.

    A method of spatial localization is described which is particularly suitable for the in vivo spectroscopic investigation of biological and medical samples. The technique overcomes most of the technical problems associated with localized NMR spectroscopy and allows the spectrum to be investigated from a cube which can be positioned by reference to an NMR image. The cube can be reduced or enlarged, and can be rapidly moved in space to investigate further volumes of interest within the sample. The first experimental results from a phantom and the human leg are presented.

  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.

  17. Advanced NMR-based techniques for pore structure analysis of coal. Final project report

    SciTech Connect

    Smith, D.M.; Hua, D.W.

    1996-02-01

    During the 3 year term of the project, new methods have been developed for characterizing the pore structure of porous materials such as coals, carbons, and amorphous silica gels. In general, these techniques revolve around; (1) combining multiple techniques such as small-angle x-ray scattering (SAXS) and adsorption of contrast-matched adsorbates or {sup 129}Xe NMR and thermoporometry (the change in freezing point with pore size), (2) combining adsorption isotherms over several pressure ranges to obtain a more complete description of pore filling, or (3) applying NMR ({sup 129}Xe, {sup 14}N{sub 2}, {sup 15}N{sub 2}) techniques with well-defined porous solids with pores in the large micropore size range (>1 nm).

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

    PubMed

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

    1988-05-17

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

  19. Advanced NMR-based techniques for pore structure analysis of coal

    SciTech Connect

    Smith, D.M.

    1992-01-01

    One of the main problems in coal utilization is the inability to properly characterize its complex pore structure. Coals typically have micro/ultra-micro pores but they also exhibit meso and macroporosity. Conventional pore size techniques (adsorption/condensation, mercury porosimetry) are limited because of this broad pore size range, microporosity, reactive nature of coal, samples must be completely dried, and network/percolation effects. Small angle scattering is limited because it probes both open and closed pores. Although one would not expect any single technique to provide a satisfactory description of a coal's structure, it is apparent that better techniques are necessary. We believe that measurement of the NMR parameters of various gas phase and adsorbed phase NMR active probes can provide the resolution to this problem. We will investigate the dependence of the common NMR parameters such as chemical shifts and relaxation times of several different nuclei and compounds on the pore structure of model microporous solids, carbons, and coals. In particular, we will study the interaction between several small molecules and the pore surfaces in coals. These molecules have been selected for their chemical and physical properties. A special NMR probe will be constructed which will allow the concurrent measurement of NMR properties and adsorption uptake at a variety of temperatures. All samples will be subjected to a suite of conventional'' pore structure analyses. These include nitrogen adsorption at 77 K with BET analysis, CO[sub 2] and CH[sub 4] adsorption at 273 K with D-R (Dubinin-Radushkevich) analysis, helium pycnometry, and small angle X-ray scattering as well as gas diffusion measurements.

  20. 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

  1. 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

  2. 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.

  3. Aromatic spectral editing techniques for magic-angle-spinning solid-state NMR spectroscopy of uniformly (13)C-labeled proteins.

    PubMed

    Williams, Jonathan K; Schmidt-Rohr, Klaus; Hong, Mei

    2015-11-01

    The four aromatic amino acids in proteins, namely histidine, phenylalanine, tyrosine, and tryptophan, have strongly overlapping (13)C chemical shift ranges between 100 and 160ppm, and have so far been largely neglected in solid-state NMR determination of protein structures. Yet aromatic residues play important roles in biology through π-π and cation-π interactions. To better resolve and assign aromatic residues' (13)C signals in magic-angle-spinning (MAS) solid-state NMR spectra, we introduce two spectral editing techniques. The first method uses gated (1)H decoupling in a proton-driven spin-diffusion (PDSD) experiment to remove all protonated (13)C signals and retain only non-protonated carbon signals in the aromatic region of the (13)C spectra. The second technique uses chemical shift filters and (1)H-(13)C dipolar dephasing to selectively detect the Cα, Cβ and CO cross peaks of aromatic residues while suppressing the signals of all aliphatic residues. We demonstrate these two techniques on amino acids, a model peptide, and the microcrystalline protein GB1, and show that they significantly simplify the 2D NMR spectra and both reveal and permit the ready assignment of the aromatic residues' signals.

  4. Advanced NMR-based techniques for pore structure analysis of coal

    SciTech Connect

    Smith, D.M.

    1992-01-01

    One of the main problems in coal utilization is the inability to properly characterize its complex pore structure. Coals typically have micro/ultra-micro pores but they also exhibit meso and macroporosity. Conventional pore size techniques (adsorption/condensation, mercury porosimetry) are limited because of this broad pore size range, microporosity, reactive nature of coal, samples must be completely dried, and network/percolation effects. Small angle scattering is limited because it probes both open and closed pores. Although one would not expect any single technique to provide a satisfactory description of a coal's structure, it is apparent that better techniques are necessary. We believe that measurement of the NMR parameters of various gas phase and adsorbed phase NMR active probes can provide the resolution to this problem. We now have two suites of well-characterized microporous materials including oxides (zeolites and silica gel) and activated carbons from our industrial partner, Air Products in Allentown, PA. Our current work may be divided into three areas: small-angle X-ray scattering (SAXS), adsorption, and NMR.

  5. An improved technique for computing permeability from NMR measurements in mudstones

    NASA Astrophysics Data System (ADS)

    Daigle, Hugh; Dugan, Brandon

    2011-08-01

    We develop a technique for extending nuclear magnetic resonance (NMR) permeability estimation to clay-rich sediments. Our technique builds on the Schlumberger-Doll Research (SDR) equation by using porosity, grain size, specific surface, and magnetic susceptibility data to yield more accurate permeability estimation in mudstones with large pore surface areas and complex mineralogies. Based on measurements of natural sediments as well as resedimented laboratory mixtures of silica, bentonite, and kaolinite powders, we find that our method predicts permeability values that match measured values over four orders of magnitude and among lithologies that vary widely in grain size, mineralogy, and surface area. Our results show that the relationship between NMR data and permeability is a function of mineralogy and grain geometry, and that permeability predictions in clay-rich sediments can be improved with insights regarding the nature of the pore system made by the Kozeny theory. This technique extends the utility of NMR measurements beyond typical reservoir-quality rocks to a wide range of lithologies.

  6. 31P NMR 2D Mapping of Creatine Kinase Forward Flux Rate in Hearts with Postinfarction Left Ventricular Remodeling in Response to Cell Therapy

    PubMed Central

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

    2016-01-01

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

  7. 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

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

    PubMed

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

    2013-06-01

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

  9. Identification of the epitopes of calcitonin gene-related peptide (CGRP) for two anti-CGRP monoclonal antibodies by 2D NMR.

    PubMed Central

    Hubbard, J. A.; Raleigh, D. P.; Bonnerjea, J. R.; Dobson, C. M.

    1997-01-01

    The interactions between calcitonin gene-related peptide and FAB fragments prepared from two different high-affinity anti-CGRP monoclonal antibodies (CB3 and CD1) have been studied at physiological pH using the ability of 1H NMR to detect selectively regions of dynamic flexibility. The 37-residue peptide retains considerable flexibility in regions of its sequence when bound to both antibodies; in each case, more than half of the residues can be seen to have linewidths little perturbed from those of the free peptide. However the regions where substantial broadening of resonances occur, attributed to substantially reduced motional freedom of the peptide resulting from interactions within the antibody combining site, differ greatly in the two cases. In the complex with CB3 the results indicate that the restricted residues lie exclusively within the C-terminal half of the peptide, and include residues 25 to 32 and the terminal two residues (36 and 37). By contrast, in the complex with CD1, the conformationally restricted residues appear to lie predominantly within the N-terminal half of the CGRP molecule, particularly residues 4-16, although several residues in the middle section of the sequence (22-31) have reduced conformational freedom. These findings, consistent with the results from immunological assays, add considerably to our knowledge of the epitopes. PMID:9300494

  10. 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.

  11. 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.

  12. Pharmaceutical impurities and degradation products: uses and applications of NMR techniques.

    PubMed

    Maggio, Rubén M; Calvo, Natalia L; Vignaduzzo, Silvana E; Kaufman, Teodoro S

    2014-12-01

    Current standards and regulations demand the pharmaceutical industry not only to produce highly pure drug substances, but to achieve a thorough understanding of the impurities accompanying their manufactured drug substances and products. These challenges have become important goals of process chemistry and have steadily stimulated the search of impurities after accelerated or forced degradation procedures. As a result, impurity profiling is one of the most attractive, active and relevant fields of modern pharmaceutical analysis. This activity includes the identification, structural elucidation and quantitative determination of impurities and degradation products in bulk drugs and their pharmaceutical formulations. Nuclear magnetic resonance (NMR) spectroscopy has evolved into an irreplaceable approach for pharmaceutical quality assessment, currently playing a critical role in unequivocal structure identification as well as structural confirmation (qualitative detection), enabling the understanding of the underlying mechanisms of the formation of process and/or degradation impurities. NMR is able to provide qualitative information without the need of standards of the unknown compounds and multiple components can be quantified in a complex sample without previous separation. When coupled to separative techniques, the resulting hyphenated methodologies enhance the analytical power of this spectroscopy to previously unknown levels. As a result, and by enabling the implementation of rational decisions regarding the identity and level of impurities, NMR contributes to the goal of making better and safer medicines. Herein are discussed the applications of NMR spectroscopy and its hyphenated derivate techniques to the study of a wide range pharmaceutical impurities. Details on the advantages and disadvantages of the methodology and well as specific challenges with regards to the different analytical problems are also presented. PMID:24853620

  13. Assessment of some problematic factors in facial image identification using a 2D/3D superimposition technique.

    PubMed

    Atsuchi, Masaru; Tsuji, Akiko; Usumoto, Yosuke; Yoshino, Mineo; Ikeda, Noriaki

    2013-09-01

    The number of criminal cases requiring facial image identification of a suspect has been increasing because a surveillance camera is installed everywhere in the city and furthermore, the intercom with the recording function is installed in the home. In this study, we aimed to analyze the usefulness of a 2D/3D facial image superimposition system for image identification when facial aging, facial expression, and twins are under consideration. As a result, the mean values of the average distances calculated from the 16 anatomical landmarks between the 3D facial images of the 50s groups and the 2D facial images of the 20s, 30s, and 40s groups were 2.6, 2.3, and 2.2mm, respectively (facial aging). The mean values of the average distances calculated from 12 anatomical landmarks between the 3D normal facial images and four emotional expressions were 4.9 (laughter), 2.9 (anger), 2.9 (sadness), and 3.6mm (surprised), respectively (facial expressions). The average distance obtained from 11 anatomical landmarks between the same person in twins was 1.1mm, while the average distance between different person in twins was 2.0mm (twins). Facial image identification using the 2D/3D facial image superimposition system demonstrated adequate statistical power and identified an individual with high accuracy, suggesting its usefulness. However, computer technology concerning video image processing and superimpose progress, there is a need to keep familiar with the morphology and anatomy as its base. PMID:23886899

  14. Primary style protein expression in the self-incompatible/compatible apricot by the 2D-DIGE technique.

    PubMed

    Cao, Xiaoyan; Feng, Jianrong; Wang, Dajiang; Sun, Junli; Lu, Xiaoyan; Liu, Huaifeng

    2012-07-15

    In order to explore the molecular mechanism underlying self-incompatibility (SI) in the apricot (Prunus armeniaca L.) at the proteome level, we examined the style proteomes at different stages of flower development: small bud, big bud, 24h after self-pollination and 24h after cross-pollination with cultivar Badanshui in the SI apricot cultivar Xinshiji and the self-compatible (SC) apricot cultivar Katy by 2D fluorescence difference gel electrophoresis (2D-DIGE) and mass spectrometry (MS). About 1500 style protein spots were detected; 66 were expressed differently in the four stages in Xinshiji. About 1600 style protein spots were detected; 143 were expressed differently in the four stages of flower development in Katy. In Xinshiji, one protein was expressed specifically, four proteins showed up-regulated expression and twenty-nine proteins showed down-regulated expression in the cross-pollinated style compared to the self-pollinated style. Thirteen proteins were identified unambiguously. In Katy, three proteins were expressed specifically, five proteins showed up-regulated expression and thirteen proteins showed down-regulated expression in the cross-pollinated style compared to self-pollinated style. Seven proteins were identified unambiguously. The different reactions of the style at the proteomic level were triggered in Xinshiji and Katy by self pollen and non-self pollen.

  15. Multigrid techniques for nonlinear eigenvalue probems: Solutions of a nonlinear Schroedinger eigenvalue problem in 2D and 3D

    NASA Technical Reports Server (NTRS)

    Costiner, Sorin; Taasan, Shlomo

    1994-01-01

    This paper presents multigrid (MG) techniques for nonlinear eigenvalue problems (EP) and emphasizes an MG algorithm for a nonlinear Schrodinger EP. The algorithm overcomes the mentioned difficulties combining the following techniques: an MG projection coupled with backrotations for separation of solutions and treatment of difficulties related to clusters of close and equal eigenvalues; MG subspace continuation techniques for treatment of the nonlinearity; an MG simultaneous treatment of the eigenvectors at the same time with the nonlinearity and with the global constraints. The simultaneous MG techniques reduce the large number of self consistent iterations to only a few or one MG simultaneous iteration and keep the solutions in a right neighborhood where the algorithm converges fast.

  16. Structural Characterization of Humic Materials Using ^13C NMR Techniques: A Comparison of Solution- and Solid-State Methods

    NASA Astrophysics Data System (ADS)

    Clewett, Catherine; Alam, Todd; Osantowski, Eric; Pullin, Michael

    2011-10-01

    The analysis of the carbon type distribution and chemical structure of natural organic matter (NOM) by ^13C NMR spectroscopy is an important technique for understanding its origins and reactivity. While prior work has used solution-state NMR techniques, solid-state NMR has the potential to provide this information using less instrument time and sample manipulation, while providing an array of advanced filtering techniques. Analyses of four isolated humic materials with ^13C solid-state magic angle spinning (MAS) NMR techniques are described, including three commercially available samples and one fulvic acid sample isolated from the Rio Grande in New Mexico. This study demonstrates the utility of solid-state ^13C NMR for aquatic NOM structural characterization, comparing these results to the existing solution-state determinations. The solid-state ^13C MAS NMR results are used to determine % carbon distribution, estimates of elemental composition (%C, %H, %(O+N)), aromatic fraction (fa), nonprotonated aromatic fraction (faN), an estimate of aromatic cluster size, and ratio of sp^2 to sp^3 carbons. A Gaussian deconvolution method is introduced that allows for a detailed analysis of carbon type.

  17. Measurement of the intracrystalline self-diffusion of xenon in zeolites by the NMR pulsed field gradient technique

    SciTech Connect

    Heink, W.; Kaerger, J.; Pfeifer, H.; Stallmach, F. )

    1990-03-14

    With use of {sup 129}Xe NMR, the NMR pulsed field gradient technique is applied to study the self-diffusion of xenon adsorbed on zeolites NaX, NaCaA, and ZSM-5. In their dependence on both the type of adsorbent and the sorbate concentration, the self-diffusion coefficients are found to follow the same patterns as previously determined for methane by {sup 1}H NMR. For NaCaA, the comparison of the present results with literature data reveals large discrepancies, while recent computer simulations of xenon self-diffusion in ZSM-5 are found to be in reasonable agreement.

  18. A rapid 2D time-resolved variable-rate k-space sampling MR technique for passive catheter tracking during endovascular procedures.

    PubMed

    Unal, O; Korosec, F R; Frayne, R; Strother, C M; Mistretta, C A

    1998-09-01

    A new, fast, 2D MR imaging technique allowing passive catheter visualization adequate for use as a tool for guiding the movement of a catheter during endovascular procedures is described. This imaging technique samples low spatial frequencies more often than high spatial frequencies; it also uses both k-space view sharing and temporal interpolation. Unlike other techniques for passive visualization that exploit magnetic-susceptibility-induced artifacts, we have adopted a strategy that takes advantage of the T1-shortening effect of paramagnetic contrast agents, such as Gd-DTPA and a projection dephaser. This not only permits visualization of the entire catheter length but also minimizes the risk of intravascular heating. Using this method, a temporal frame rate of up to eight images per second and a tip localization accuracy of +/- 1mm (root mean square difference) can be achieved.

  19. LC-NMR Technique in the Analysis of Phytosterols in Natural Extracts

    PubMed Central

    Horník, Štěpán; Sajfrtová, Marie; Sýkora, Jan; Březinová, Anna; Wimmer, Zdeněk

    2013-01-01

    The ability of LC-NMR to detect simultaneously free and conjugated phytosterols in natural extracts was tested. The advantages and disadvantages of a gradient HPLC-NMR method were compared to the fast composition screening using SEC-NMR method. Fractions of free and conjugated phytosterols were isolated and analyzed by isocratic HPLC-NMR methods. The results of qualitative and quantitative analyses were in a good agreement with the literature data. PMID:24455424

  20. 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

    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.

  1. 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

  2. Aquifer characterisation using Surface NMR jointly with other geophysical techniques at the Nauen/Berlin test site

    NASA Astrophysics Data System (ADS)

    Yaramanci, Ugur; Lange, Gerhard; Hertrich, Marian

    2002-05-01

    The quite new technique of Surface Nuclear Magnetic Resonance (SNMR) has been extensively tested on the test site Nauen near Berlin to yield the geometry, water content and hydraulic conductivity of the aquifer. The test site is composed of an unconfined aquifer consisting of Quaternary sands with glacial till beneath. It is a very favourable site for assessing the suitability and performance of joint geophysical methods for groundwater exploration. Complementary measurements to SNMR were conducted with Ground Penetrating Radar (GPR), 1D-complex resistivity soundings, i.e. Spectral Induced Polarisation (SIP), 2D-geoelectrics and refraction seismics. Laboratory measurements of porosities, grain size distributions and Nuclear Magnetic Resonance (NMR) decay times were carried out on core samples, and hydraulic conductivities were also derived in order to control and interpret the results of field measurements. The SNMR method allowed the detection of the aquifer beyond any doubt and the determination of the approximate aquifer geometry. The aquifer water content found by SNMR fits very well with the independent measurements on core samples. Hydraulic conductivities derived from decay times are well in range with those from laboratory measurements. GPR allowed a very reliable determination of the aquifer geometry. This information, incorporated into inversion of geoelectric data, led to an improved determination of aquifer electrical resistivity. The estimation of water content by GPR and geoelectrics, even under the favourable conditions in Nauen, is by far not as reliable as that by SNMR. Obtaining information about hydraulic conductivity is possible only with SNMR. Thus, in combination with other geophysical methods, SNMR allows a much more detailed and reliable assessment of aquifers than what was possible with other surface geophysical methods before. In fact, it is, by far, the only method that allows direct detection of water and reliable estimations about water

  3. 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.

  4. Unilateral NMR, 13C CPMAS NMR spectroscopy and micro-analytical techniques for studying the materials and state of conservation of an ancient Egyptian wooden sarcophagus.

    PubMed

    Proietti, Noemi; Presciutti, Federica; Di Tullio, Valeria; Doherty, Brenda; Marinelli, Anna Maria; Provinciali, Barbara; Macchioni, Nicola; Capitani, Donatella; Miliani, Costanza

    2011-03-01

    A multi-technique approach was employed to study a decorated Egyptian wooden sarcophagus (XXV-XXVI dynasty, Third Intermediate Period), belonging to the Museo del Vicino Oriente of the Sapienza University of Rome. Portable non-invasive unilateral NMR was applied to evaluate the conservation state of the sarcophagus. Moreover, using unilateral NMR, a non-invasive analytical protocol was established to detect the presence of organic substances on the surface and/or embedded in the wooden matrix. This protocol allowed for an educated sampling campaign aimed at further investigating the state of degradation of the wood and the presence of organic substances by (13)C cross polarization magic angle spinning (CPMAS) NMR spectroscopy. The composition of the painted layer was analysed by optical microscopy (OM), scanning electron microscopy-energy dispersive spectroscopy (SEM-EDS), Raman and surface enhanced (resonance) Raman spectroscopy (SERS/SERRS), infrared and GC-MS techniques, evidencing original components such as clay minerals, Egyptian green, indigo, natural gums, and also highlighting restoration pigments and alteration compounds. The identification of the wood, of great value for the reconstruction of the history of the artwork, was achieved by means of optical microscopy.

  5. Techniques utilized in the simulated altitude testing of a 2D-CD vectoring and reversing nozzle

    NASA Technical Reports Server (NTRS)

    Block, H. Bruce; Bryant, Lively; Dicus, John H.; Moore, Allan S.; Burns, Maureen E.; Solomon, Robert F.; Sheer, Irving

    1988-01-01

    Simulated altitude testing of a two-dimensional, convergent-divergent, thrust vectoring and reversing exhaust nozzle was accomplished. An important objective of this test was to develop test hardware and techniques to properly operate a vectoring and reversing nozzle within the confines of an altitude test facility. This report presents detailed information on the major test support systems utilized, the operational performance of the systems and the problems encountered, and test equipment improvements recommended for future tests. The most challenging support systems included the multi-axis thrust measurement system, vectored and reverse exhaust gas collection systems, and infrared temperature measurement systems used to evaluate and monitor the nozzle. The feasibility of testing a vectoring and reversing nozzle of this type in an altitude chamber was successfully demonstrated. Supporting systems performed as required. During reverser operation, engine exhaust gases were successfully captured and turned downstream. However, a small amount of exhaust gas spilled out the collector ducts' inlet openings when the reverser was opened more than 60 percent. The spillage did not affect engine or nozzle performance. The three infrared systems which viewed the nozzle through the exhaust collection system worked remarkably well considering the harsh environment.

  6. Integration of XAS and NMR techniques for the structure determination of metalloproteins. Examples from the study of copper transport proteins.

    PubMed

    Banci, Lucia; Bertini, Ivano; Mangani, Stefano

    2005-01-01

    Nuclear magnetic resonance (NMR) is a powerful technique for protein structure determination in solution. However, when dealing with metalloproteins, NMR methods are unable to directly determine the structure of the metal site and its coordination geometry. The capability of X-ray absorption spectroscopy (XAS) to provide the structure of a metal ion bound to a protein is then perfectly suited to complement the process of the structure determination. This aspect is particularly relevant in structural genomic projects where high throughput of structural results is the main goal. The synergism of the two techniques has been exploited in the structure determination of bacterial copper transport proteins.

  7. Application of micro-PIV technique to study multiphase flow of water and liquid CO2 in 2D porous media

    NASA Astrophysics Data System (ADS)

    Kazemifar, F.; Blois, G.; Kyritsis, D. C.; Christensen, K. T.

    2014-11-01

    We study the multiphase flow of water and liquid/supercritical CO2 in 2D porous micromodels, with the goal of developing a more complete understanding of pore-scale flow dynamics for the scenario of geological sequestration of carbon dioxide. Fluorescent microscopy and the micro-PIV technique are employed to simultaneously visualize both phases and obtain the velocity field in the aqueous phase. This technique provides a powerful tool for studying such flow systems and the results give valuable insight into flow processes at the pore scale. The fluid-fluid interface curvature from the images can be used to estimate the local capillary pressure. The velocity measurements illustrate active and passive flow pathways and circulation regions near the fluid-fluid interfaces induced by shear. Thin water films observed on the solid surfaces confirm the hydrophilic nature of the micromodels. The velocity of the said films is measured by particle tracking.

  8. 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.

  9. 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…

  10. A neutron-X-ray, NMR and calorimetric study of glassy Probucol synthesized using containerless techniques

    NASA Astrophysics Data System (ADS)

    Weber, J. K. R.; Benmore, C. J.; Tailor, A. N.; Tumber, S. K.; Neuefeind, J.; Cherry, B.; Yarger, J. L.; Mou, Q.; Weber, W.; Byrn, S. R.

    2013-10-01

    Acoustic levitation was used to trap 1-3 mm diameter drops of Probucol and other pharmaceutical materials in containerless conditions. Samples were studied in situ using X-ray diffraction and ex situ using neutron diffraction, NMR and DSC techniques. The materials were brought into non-equilibrium states by supersaturating solutions or by supercooling melts. The glass transition and crystallization temperatures of glassy Probucol were 29 ± 1 and 71 ± 1 °C respectively. The glassy form was stable with a shelf life of at least 8 months. A neutron/X-ray difference function of the glass showed that while molecular sub-groups remain rigid, many of the hydrogen correlations observed in the crystal become smeared out in the disordered material. The glass is principally comprised of slightly distorted Form I Probucol molecules with disordered packing rather than large changes in the individual molecular structure. Avoiding surface contact-induced nucleation provided access to highly non-equilibrium phases and enabled synthesis of phase-pure glasses.

  11. Determination of porosity of lignocellulosic biomass before and after pretreatment by using Simons' stain and NMR techniques.

    PubMed

    Meng, Xianzhi; Foston, Marcus; Leisen, Johannes; DeMartini, Jaclyn; Wyman, Charles E; Ragauskas, Arthur J

    2013-09-01

    To further investigate the effect of dilute acid pretreatment (DAP) and steam explosion pretreatment (SE) on the change in cellulose accessibility, several techniques were applied including a Simons' stain (SS) technique along with several NMR methods (i.e., NMR cryoporometry, (1)H spin-lattice (T1) and (1)H spin-spin (T2) relaxometry, and diffusometry). These methods were utilized to probe biomass porosity and thus assess cellulose accessibility on untreated and pretreated Populus. In general, these techniques indicate that pretreated Populus has larger pore size distributions and specific surface area (SSA) when compared to an untreated sample. The SS method revealed that DAP is more effective than SE in terms of the SSA increase, and that DAP increases SSA as a function of pretreatment severity. Relaxometry and diffusion measurements also suggest pore expansion occurs primarily in the first 10 min of DAP.

  12. 1020MHz single-channel proton fast magic angle spinning solid-state NMR spectroscopy.

    PubMed

    Pandey, Manoj Kumar; Zhang, Rongchun; Hashi, Kenjiro; Ohki, Shinobu; Nishijima, Gen; Matsumoto, Shinji; Noguchi, Takashi; Deguchi, Kenzo; Goto, Atsushi; Shimizu, Tadashi; Maeda, Hideaki; Takahashi, Masato; Yanagisawa, Yoshinori; Yamazaki, Toshio; Iguchi, Seiya; Tanaka, Ryoji; Nemoto, Takahiro; Miyamoto, Tetsuo; Suematsu, Hiroto; Saito, Kazuyoshi; Miki, Takashi; Ramamoorthy, Ayyalusamy; Nishiyama, Yusuke

    2015-12-01

    This study reports a first successful demonstration of a single channel proton 3D and 2D high-throughput ultrafast magic angle spinning (MAS) solid-state NMR techniques in an ultra-high magnetic field (1020MHz) NMR spectrometer comprised of HTS/LTS magnet. High spectral resolution is well demonstrated.

  13. Complete assignments of 1H and 13C NMR data for ten phenylpiperazine derivatives.

    PubMed

    Xiao, Zhihui; Yuan, Mu; Zhang, Si; Wu, Jun; Qi, Shuhua; Li, Qingxin

    2005-10-01

    Ten phenylpiperazine derivatives were designed and synthesized. The first complete assignments of (1)H and (13)C NMR chemical shifts for these phenylpiperazine derivatives were achieved by means of 1D and 2D NMR techniques, including (1)H-(1)H COSY, HSQC and HMBC spectra.

  14. Complete assignments of 1H and 13C NMR data for 10 phenylethanoid glycosides.

    PubMed

    Wu, Jun; Huang, Jianshe; Xiao, Qiang; Zhang, Si; Xiao, Zhihui; Li, Qingxin; Long, Lijuan; Huang, Liangmin

    2004-07-01

    Ten phenylethanoid glycosides, including two new ones, isolated from the aerial parts of the mangrove plant Acanthus ilicifolius were identified. The first complete assignments of the 1H and 13C NMR chemical shifts for these glycosides were achieved by means of 2D NMR techniques, including 1H-1H COSY, TOCSY, HSQC and HMBC spectra.

  15. Perspectives on NMR in drug discovery: a technique comes of age

    PubMed Central

    Pellecchia, Maurizio; Bertini, Ivano; Cowburn, David; Dalvit, Claudio; Giralt, Ernest; Jahnke, Wolfgang; James, Thomas L.; Homans, Steve W.; Kessler, Horst; Luchinat, Claudio; Meyer, Bernd; Oschkinat, Hartmut; Peng, Jeff; Schwalbe, Harald; Siegal, Gregg

    2009-01-01

    In the past decade, the potential of harnessing the ability of nuclear magnetic resonance (NMR) spectroscopy to monitor intermolecular interactions as a tool for drug discovery has been increasingly appreciated in academia and industry. In this Perspective, we highlight some of the major applications of NMR in drug discovery, focusing on hit and lead generation, and provide a critical analysis of its current and potential utility. PMID:19172689

  16. A multiple pulse zero crossing NMR technique, and its application to F-19 chemical shift measurements in solids

    NASA Technical Reports Server (NTRS)

    Burum, D. P.; Elleman, D. D.; Rhim, W.-K.

    1978-01-01

    A simple multiple-pulse 'zero crossing technique' for accurately determining the first moment of a solid-state NMR spectrum is introduced. This technique was applied to obtain the F-19 chemical shift versus pressure curves up to 5 kbar for single crystals of CaF2 (0.29 + or - 0.02 ppm/kbar) and BaF2 (0.62 + or - 0.05 ppm/kbar). Results at ambient temperature and pressure are also reported for a number of other fluorine compounds. Because of its high data rate, this technique is potentially several orders of magnitude more sensitive than similar CW methods.

  17. Inclusion complexes of PBN-type nitrone spin traps and their superoxide spin adducts with cyclodextrin derivatives: parallel determination of the association constants by NMR titrations and 2D-EPR simulations.

    PubMed

    Bardelang, David; Rockenbauer, Antal; Karoui, Hakim; Finet, Jean-Pierre; Tordo, Paul

    2005-05-26

    (1)H NMR and electron paramagnetic resonance (EPR) titrations were used to determine the association constants of the complexes of alpha-phenyl-N-tert-butylnitrone (PBN) analogues and their superoxide spin adducts, respectively, with methylated beta-cyclodextrins. A 1:1 stoichiometry for the nitrones with randomly methylated beta-cyclodextrin and 2,6-di-O-methyl-beta-cyclodextrin and 1:1 and 1:2 stoichiometries for the corresponding cyclodextrin-nitroxide complexes were observed. After the superoxide radical spin trapping reaction, EPR titrations afforded the association constants of the corresponding cyclodextrin-nitroxide complexes. Two-dimensional EPR simulations indicated a bimodal inclusion of the nitroxide free radical spin adducts into the cyclodextrins. For all the nitrone-cyclodextrin and nitroxide-cyclodextrin complexes, the association constants were always higher for the nitroxide complexes than for the nitrone complexes. A cooperative system concerning the complexation of the nitroxide spin adduct with a cyclodextrin was evidenced by EPR titrations. The efficiency of the cyclodextrin inclusion technique to trap superoxide and to resist bioreduction by sodium l-ascorbate was also investigated.

  18. Kinematic Analysis of Healthy Hips during Weight-Bearing Activities by 3D-to-2D Model-to-Image Registration Technique

    PubMed Central

    Hara, Daisuke; Nakashima, Yasuharu; Hamai, Satoshi; Higaki, Hidehiko; Ikebe, Satoru; Shimoto, Takeshi; Hirata, Masanobu; Kanazawa, Masayuki; Kohno, Yusuke; Iwamoto, Yukihide

    2014-01-01

    Dynamic hip kinematics during weight-bearing activities were analyzed for six healthy subjects. Continuous X-ray images of gait, chair-rising, squatting, and twisting were taken using a flat panel X-ray detector. Digitally reconstructed radiographic images were used for 3D-to-2D model-to-image registration technique. The root-mean-square errors associated with tracking the pelvis and femur were less than 0.3 mm and 0.3° for translations and rotations. For gait, chair-rising, and squatting, the maximum hip flexion angles averaged 29.6°, 81.3°, and 102.4°, respectively. The pelvis was tilted anteriorly around 4.4° on average during full gait cycle. For chair-rising and squatting, the maximum absolute value of anterior/posterior pelvic tilt averaged 12.4°/11.7° and 10.7°/10.8°, respectively. Hip flexion peaked on the way of movement due to further anterior pelvic tilt during both chair-rising and squatting. For twisting, the maximum absolute value of hip internal/external rotation averaged 29.2°/30.7°. This study revealed activity dependent kinematics of healthy hip joints with coordinated pelvic and femoral dynamic movements. Kinematics' data during activities of daily living may provide important insight as to the evaluating kinematics of pathological and reconstructed hips. PMID:25506056

  19. A 2-D hybrid technique to model the effect of topography on coseismic displacements. Application to the Umbria-Marche (central Italy) 1997 earthquake sequence

    NASA Astrophysics Data System (ADS)

    Tinti, Stefano; Armigliato, Alberto

    2002-08-01

    We face the problem of modelling the influence of the irregular topography of the Earth's crust on coseismic displacements. The modelling technique we propose is valid for a homogeneous elastic 2-D domain and is based on a two-step approach that uses (1) the traditional analytical results valid for elastic spaces and elastic half-spaces with a flat free surface (FFS) and (2) a finite-element (FE) numerical code to compute the disturbance induced by the local topography. Attention is particularly focused on: (1) the comparison between the results obtained through our method and the analytical formulae valid for FFS geometries, which are used extensively today in both forward and inverse modelling even in the presence of irregular topography and (2) the advantages of our hybrid approach over pure FE models. After discussing the theoretical experiment of a Gaussian topography, we present an application to modelling the displacement fields induced by selected events of the earthquake sequence that hit the Umbria-Marche region in the central Apennines (Italy) in 1997, devoting major attention to the effect of the Apennines chain topography in the source region. In all cases the topography is found to play an important role and to introduce non-negligible corrections to the coseismic surface displacement components computed through the FFS approximation. The main effect is that topography not only affects the magnitude of the surface signal, but it may also lead to high-frequency disturbances that tend to grow with the shallowness of the fault.

  20. "Pulse pair technique in high resolution NMR" a reprint of the historical 1971 lecture notes on two-dimensional spectroscopy.

    PubMed

    Jeener, Jean; Alewaeters, Gerrit

    2016-05-01

    The review articles published in "Progress in NMR Spectroscopy" are usually invited treatments of topics of current interest, but occasionally the Editorial Board may take an initiative to publish important historical material that is not widely available. The present article represents just such a case. Jean Jeener gave a lecture in 1971 at a summer school in Basko Polje, in what was then called Yugoslavia. As is now widely known, Jean Jeener laid down the foundations in that lecture of two - and higher - dimensional NMR spectroscopy by proposing the homonuclear COSY experiment. Jeener realized that the new proposal would open the door towards protein NMR and molecular structure determinations, but he felt that useful versions of such experiments could not be achieved with the NMR, computer and electronics technology available at that time, so that copies of the lecture notes were circulated (the Basko Polje lecture notes by J. Jeener and G. Alewaeters), but no formal publication followed. Fortunately, Ernst, Freeman, Griffin, and many others were more far-sighted and optimistic. An early useful extension was Ernst's proposal to replace the original projection/reconstruction technique of MRI by the widely adopted Fourier transform method inspired by the Basko Polje lecture. Later, the pulse method spread over many fields of spectroscopy as soon as the required technology became available. Jean Jeener, Emeritus professor, Université Libre de Bruxelles. Geoffrey Bodenhausen, Ecole Normale Supérieure, Paris.

  1. Development of 2D band-target entropy minimization and application to the deconvolution of multicomponent 2D nuclear magnetic resonance spectra.

    PubMed

    Guo, Liangfeng; Wiesmath, Anette; Sprenger, Peter; Garland, Marc

    2005-03-15

    Spectral reconstruction from multicomponent spectroscopic data is the frequent primary goal in chemical system identification and exploratory chemometric studies. Various methods and techniques have been reported in the literature. However, few algorithms/methods have been devised for spectral recovery without the use of any a priori information. In the present studies, a higher dimensional entropy minimization method based on the BTEM algorithm (Widjaja, E.; Li, C.; Garland, M. Organometallics 2002, 21, 1991-1997.) and related techniques were extended to large-scale arrays, namely, 2D NMR spectroscopy. The performance of this novel method had been successfully verified on various real experimental mixture spectra from a series of randomized 2D NMR mixtures (COSY NMR and HSQC NMR). With the new algorithm and raw multicomponent NMR alone, it was possible to reconstruct the pure spectroscopic patterns and calculate the relative concentration of each species without recourse to any libraries or any other a priori information. The potential advantages of this novel algorithm and its implications for general chemical system identification of unknown mixtures are discussed. PMID:15762569

  2. Identification of 4-deoxythreonic acid present in human urine by combining HPLC and NMR techniques

    PubMed Central

    Appiah-Amponsah, Emmanuel; Shanaiah, Narasimhamurthy; Nagana Gowda, G. A.; Owusu-Sarfo, Kwadwo; Ye, Tao; Raftery, Daniel

    2010-01-01

    The 1H NMR spectrum of urine exhibits a large number of detectable and quantifiable metabolites and hence urine metabolite profiling is potentially useful for the study of systems biology and the discovery of biomarkers for drug development or clinical applications. While a number of metabolites (50–100) are readily detectable in urine by NMR, a much larger number is potentially available if lower concentration species can be detected unambiguously. Lower concentration metabolites are thought to be more specific to certain disease states and thus it is important to detect these metabolites with certainty. We report the identification of 4-deoxythreonic acid, a relatively low concentration endogenous metabolite that has not been previously identified in the 1H NMR spectrum of human urine. The complimentary use of HPLC and NMR spectroscopy facilitated the unequivocal and non-invasive identification of the molecule in urine which is complicated by extensive peak overlap and multiple, similar resonances from other metabolites such as 3-hydroxybutanoic acid. High-resolution detection and good sensitivity were achieved by the combination of multiple chromatographic fraction collection, sample pre-concentration, and the use of a cryogenically cooled NMR probe. PMID:19615840

  3. New in situ solid-state NMR techniques for probing the evolution of crystallization processes: pre-nucleation, nucleation and growth.

    PubMed

    Hughes, Colan E; Williams, P Andrew; Keast, Victoria L; Charalampopoulos, Vasileios G; Edwards-Gau, Gregory R; Harris, Kenneth D M

    2015-01-01

    The application of in situ techniques for investigating crystallization processes promises to yield significant new insights into fundamental aspects of crystallization science. With this motivation, we recently developed a new in situ solid-state NMR technique that exploits the ability of NMR to selectively detect the solid phase in heterogeneous solid-liquid systems (of the type that exist during crystallization from solution), with the liquid phase "invisible" to the measurement. As a consequence, the technique allows the first solid particles produced during crystallization to be observed and identified, and allows the evolution of different solid phases (e.g., polymorphs) present during the crystallization process to be monitored as a function of time. This in situ solid-state NMR strategy has been demonstrated to be a powerful approach for establishing the sequence of solid phases produced during crystallization and for the discovery of new polymorphs. The most recent advance of the in situ NMR methodology has been the development of a strategy (named "CLASSIC NMR") that allows both solid-state NMR and liquid-state NMR spectra to be measured (essentially simultaneously) during the crystallization process, yielding information on the complementary changes that occur in both the solid and liquid phases as a function of time. In this article, we present new results that highlight the application of our in situ NMR techniques to successfully unravel different aspects of crystallization processes, focusing on: (i) the application of a CLASSIC NMR approach to monitor competitive inclusion processes in solid urea inclusion compounds, (ii) exploiting liquid-state NMR to gain insights into co-crystal formation between benzoic acid and pentafluorobenzoic acid, and (iii) applications of in situ solid-state NMR for the discovery of new solid forms of trimethylphosphine oxide and L-phenylalanine. Finally, the article discusses a number of important fundamental issues

  4. NMR technique for determining the depth of shallow nitrogen-vacancy centers in diamond

    NASA Astrophysics Data System (ADS)

    Pham, Linh M.; DeVience, Stephen J.; Casola, Francesco; Lovchinsky, Igor; Sushkov, Alexander O.; Bersin, Eric; Lee, Junghyun; Urbach, Elana; Cappellaro, Paola; Park, Hongkun; Yacoby, Amir; Lukin, Mikhail; Walsworth, Ronald L.

    2016-01-01

    We demonstrate a robust experimental method for determining the depth of individual shallow nitrogen-vacancy (NV) centers in diamond with ˜1 nm uncertainty. We use a confocal microscope to observe single NV centers and detect the proton nuclear magnetic resonance (NMR) signal produced by objective immersion oil, which has well understood nuclear spin properties, on the diamond surface. We determine the NV center depth by analyzing the NV NMR data using a model that describes the interaction of a single NV center with the statistically polarized proton spin bath. We repeat this procedure for a large number of individual, shallow NV centers and compare the resulting NV depths to the mean value expected from simulations of the ion implantation process used to create the NV centers, with reasonable agreement.

  5. SVD-Based Technique for Interference Cancellation and Noise Reduction in NMR Measurement of Time-Dependent Magnetic Fields.

    PubMed

    Chen, Wenjun; Ma, Hong; Yu, De; Zhang, Hua

    2016-03-04

    A nuclear magnetic resonance (NMR) experiment for measurement of time-dependent magnetic fields was introduced. To improve the signal-to-interference-plus-noise ratio (SINR) of NMR data, a new method for interference cancellation and noise reduction (ICNR) based on singular value decomposition (SVD) was proposed. The singular values corresponding to the radio frequency interference (RFI) signal were identified in terms of the correlation between the FID data and the reference data, and then the RFI and noise were suppressed by setting the corresponding singular values to zero. The validity of the algorithm was verified by processing the measured NMR data. The results indicated that, this method has a significantly suppression of RFI and random noise, and can well preserve the FID signal. At present, the major limitation of the proposed SVD-based ICNR technique is that the threshold value for interference cancellation needs to be manually selected. Finally, the inversion waveform of the applied alternating magnetic field was given by fitting the processed experimental data.

  6. SVD-Based Technique for Interference Cancellation and Noise Reduction in NMR Measurement of Time-Dependent Magnetic Fields

    PubMed Central

    Chen, Wenjun; Ma, Hong; Yu, De; Zhang, Hua

    2016-01-01

    A nuclear magnetic resonance (NMR) experiment for measurement of time-dependent magnetic fields was introduced. To improve the signal-to-interference-plus-noise ratio (SINR) of NMR data, a new method for interference cancellation and noise reduction (ICNR) based on singular value decomposition (SVD) was proposed. The singular values corresponding to the radio frequency interference (RFI) signal were identified in terms of the correlation between the FID data and the reference data, and then the RFI and noise were suppressed by setting the corresponding singular values to zero. The validity of the algorithm was verified by processing the measured NMR data. The results indicated that, this method has a significantly suppression of RFI and random noise, and can well preserve the FID signal. At present, the major limitation of the proposed SVD-based ICNR technique is that the threshold value for interference cancellation needs to be manually selected. Finally, the inversion waveform of the applied alternating magnetic field was given by fitting the processed experimental data. PMID:26959024

  7. Assessment of silicone gel breast implant biodurability by NMR and EDS techniques.

    PubMed

    Taylor, R B; Eldred, D E; Kim, G; Curtis, J M; Brandon, H J; Klykken, P C

    2008-06-01

    In a study using explanted gel breast implants and appropriate nonimplanted controls, we examined silicone biodurability after long-term implantation. Using NMR spectroscopy, as well as NMR relaxometry measurements (T(2)), no evidence of hydrolysis or other chemical degradation of the cross-linked silicone matrix was observed in specimens from an early breast implant model (Cronin) explanted after 32 years in vivo or a more recent Silastic II model after 13 years in vivo. In addition, no appreciable differences were seen in T(2) relaxation times comparing explanted breast implants to suitably-matched nonimplanted controls, further underscoring the biostability of the cross-linked silicone shell and gel. Our T(2) data and resultant interpretations differ from a 2004 report by the NMR lab at the University of Münster, highlighting the importance of suitable nonimplanted controls and sample preparation. Energy dispersive spectroscopy (EDS) was also performed, confirming the persistence of a fluorosilicone layer inside the elastomer shells of Silastic II implants.

  8. New ¹H NMR-Based Technique To Determine Epoxide Concentrations in Oxidized Oil.

    PubMed

    Xia, Wei; Budge, Suzanne M; Lumsden, Michael D

    2015-06-24

    A new method to determine epoxide concentrations in oxidized oils was developed and validated using (1)H NMR. Epoxides derived from lipid oxidation gave signals between 2.90 and 3.24 ppm, well separated from the signals of other lipid oxidation products. To calibrate, soybean oils with a range of epoxide concentrations were synthesized and analyzed using (1)H NMR by taking the sn-1,3 glycerol protons (4.18, 4.33 ppm) as internal references. The (1)H NMR signals were compared to the epoxide content determined by titration with hydrogen bromide (HBr)-acetic acid solution. As expected, the signal response increased with concentration linearly (R(2) = 99.96%), and validation of the method gave results comparable to those of the HBr method. A study of the oxidative stability of soybean oil was performed by applying this method to monitor epoxides during thermal lipid oxidation. The epoxide content increased over time and showed a different trend compared to peroxide value (PV). A phenomenological model was suggested to model epoxides derived from lipid oxidation. PMID:26035119

  9. Gas-phase NMR technique for studying the thermolysis of materials: thermal decomposition of ammonium perfluorooctanoate.

    PubMed

    Krusic, Paul J; Roe, D Christopher

    2004-07-01

    The kinetics of the thermal decomposition of ammonium perfluorooctanoate (APFO) has been studied by high-temperature gas-phase nuclear magnetic resonance spectroscopy over the temperature range 196-234 degrees C. We find that APFO cleanly decomposes by first-order kinetics to give the hydrofluorocarbon 1-H-perfluoroheptane and is completely decomposed (>99%) in a matter of minutes at the upper limit of this temperature range. Based on the temperature dependence of the measured rate constants, we find that the enthalpy and entropy of activation are DeltaH++ = 150 +/- 11 kJ mol(-1) and DeltaS++ = 3 +/- 23 J mol(-)(1) deg(-1). These activation parameters may be used to calculate the rate of APFO decomposition at the elevated temperatures (350-400 degrees C) at which fluoropolymers are processed; for example, at 350 degrees C the half-life for APFO is estimated to be less than 0.2 s. Our studies provide the fundamental parameters involved in the decomposition of the ammonium salt of perfluorooctanoic acid and indicate the utility of gas-phase NMR for thermolysis studies of a variety of materials that release compounds that are volatile at the temperature of decomposition and that contain an NMR-active nucleus.

  10. Synthesis of prostanoids; enantiomeric purity of alcohols by a /sup 31/P NMR technique

    SciTech Connect

    Penning, T.D.

    1985-01-01

    The enone, 2,2-diemthyl-3a..beta.., 6a..beta..-dihydro-4H-cyclopenta-1,3-dioxol-4-one, has been synthesized in six steps from cyclopentadiene, resolved using sulfoximine chemistry, and converted into (-)-prostaglandin E/sub 2/ methyl ester in three steps. Introduction of the optically pure omega side-chain using a conjugate addition of a stabilized organocopper reagent, followed by direct alkylation of the enolate with the ..cap alpha.. side-chain allylic iodide in the presence of hexamethylphosphoramide, afforded a trans, vicinally disubstituted cyclopentanone. Deprotection of the C-15 alcohol, followed by aluminum amalgam reduction of the C-10/oxygen bond, provided (-)-PGE/sub 2/ methyl ester in 47% overall yield from the enone. In an extension of previously described work, 2-chloro-3,4-dimethyl-5-phenyl-1,3,2-oxazaphospholidine 2-sulfide, prepared from l-ephedrine and thiophosphoryl chloride, was used to determine the enantiomeric excess of chiral alcohols in conjunction with /sup 31/P NMR. Chiral primary and secondary alcohols added quantitatively to the phospholidine to give diastereomers which could be analyzed by /sup 31/P NMR and HPLC. A number of other phosphorus heterocycles were also explored as potential chiral derivatizing reagents.

  11. Deteriorated hardened cement paste structure analyzed by XPS and {sup 29}Si NMR techniques

    SciTech Connect

    Kurumisawa, Kiyofumi; Nawa, Toyoharu; Owada, Hitoshi; Shibata, Masahito

    2013-10-15

    In this report, X-ray photoelectron spectroscopy (XPS) and {sup 29}Si-MAS-NMR was used for the evaluation of deteriorated hardened cement pastes. The deterioration by ammonium nitrate solution was accompanied by changes in the pore structure as well as by structural changes in the C–S–H in the hardened cement paste. The CaO/SiO{sub 2} ratio of the C–S–H decreased with the progress of deterioration, there was also polymerization of the silicate in the C–S–H. It was confirmed that the degree of polymerization of silicate of the C–S–H in hardened cement paste can be determined by XPS. It was also shown that the polymerization depends on the structure of the C–S–H. -- Highlights: •The polymerization of silicate of the C–S–H in the HCP can be observed by XPS. •The structure of C–S–H changed with the degree of calcium leaching. •The NMR result about silicate in C–S–H was in good agreement with the XPS result.

  12. Structural characterization of MG and pre-MG states of proteins by MD simulations, NMR, and other techniques.

    PubMed

    Naiyer, Abdullah; Hassan, Md Imtaiyaz; Islam, Asimul; Sundd, Monica; Ahmad, Faizan

    2015-01-01

    Almost all proteins fold via a number of partially structured intermediates such as molten globule (MG) and pre-molten globule states. Understanding the structure of these intermediates at atomic level is often a challenge, as these states are observed under extreme conditions of pH, temperature, and chemical denaturants. Furthermore, several other processes such as chemical modification, site-directed mutagenesis (or point mutation), and cleavage of covalent bond of natural proteins often lead to MG like partially unfolded conformation. However, the dynamic nature of proteins in these states makes them unsuitable for most structure determination at atomic level. Intermediate states studied so far have been characterized mostly by circular dichroism, fluorescence, viscosity, dynamic light scattering measurements, dye binding, infrared techniques, molecular dynamics simulations, etc. There is a limited amount of structural data available on these intermediate states by nuclear magnetic resonance (NMR) and hence there is a need to characterize these states at the molecular level. In this review, we present characterization of equilibrium intermediates by biophysical techniques with special reference to NMR. PMID:25586676

  13. Advanced NMR-based techniques for pore structure analysis of coal

    SciTech Connect

    Smith, D.M.

    1991-01-01

    One of the main problems in coal utilization is the inability to properly characterize its complex pore structure. We propose to investigate the dependence of the common NMR parameters such as chemical shifts and relaxation times of several different nuclei and compounds on the pore structure of model microporous solids, carbons, and coals. In particular, we will study the interaction between several small molecules ({sup 129}Xe, {sup 3}He, {sup 2}H{sub 2}, {sup 14}N{sub 2}, {sup 14}NH{sub 3}, {sup 15}N{sub 2}, {sup 13}CH{sub 4}, {sup 13}CO{sub 2}) and the pore surfaces in coals. These molecules have been selected for their chemical and physical properties.

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

    NASA Astrophysics Data System (ADS)

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

    2016-09-01

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

  15. In situ NMR and electrochemical quartz crystal microbalance techniques reveal the structure of the electrical double layer in supercapacitors.

    PubMed

    Griffin, John M; Forse, Alexander C; Tsai, Wan-Yu; Taberna, Pierre-Louis; Simon, Patrice; Grey, Clare P

    2015-08-01

    Supercapacitors store charge through the electrosorption of ions on microporous electrodes. Despite major efforts to understand this phenomenon, a molecular-level picture of the electrical double layer in working devices is still lacking as few techniques can selectively observe the ionic species at the electrode/electrolyte interface. Here, we use in situ NMR to directly quantify the populations of anionic and cationic species within a working microporous carbon supercapacitor electrode. Our results show that charge storage mechanisms are different for positively and negatively polarized electrodes for the electrolyte tetraethylphosphonium tetrafluoroborate in acetonitrile; for positive polarization charging proceeds by exchange of the cations for anions, whereas for negative polarization, cation adsorption dominates. In situ electrochemical quartz crystal microbalance measurements support the NMR results and indicate that adsorbed ions are only partially solvated. These results provide new molecular-level insight, with the methodology offering exciting possibilities for the study of pore/ion size, desolvation and other effects on charge storage in supercapacitors.

  16. A novel technique for single-shot energy-resolved 2D x-ray imaging of plasmas relevant for the inertial confinement fusion

    SciTech Connect

    Labate, L.; Koester, P.; Levato, T.; Gizzi, L. A.

    2012-10-15

    A novel x-ray diagnostic of laser-fusion plasmas is described, allowing 2D monochromatic images of hot, dense plasmas to be obtained in any x-ray photon energy range, over a large domain, on a single-shot basis. The device (named energy-encoded pinhole camera) is based upon the use of an array of many pinholes coupled to a large area CCD camera operating in the single-photon mode. The available x-ray spectral domain is only limited by the quantum efficiency of scientific-grade x-ray CCD cameras, thus extending from a few keV up to a few tens of keV. Spectral 2D images of the emitting plasma can be obtained at any x-ray photon energy provided that a sufficient number of photons had been collected at the desired energy. Results from recent inertial confinement fusion related experiments will be reported in order to detail the new diagnostic.

  17. New insights from MALDI-ToF MS, NMR, and GC-MS: mass spectrometry techniques applied to palynology.

    PubMed

    Moore, S E M; Hemsley, A R; French, A N; Dudley, E; Newton, R P

    2006-08-01

    The present study for the first time describes the application of matrix-assisted laser desorption ionisation time-of-flight mass spectrometry (MALDI-ToF MS) to palynology. With an accessible mass range of up to about 350,000 Da at subpicomolar range, this technique is ideal for the characterisation of bio-macromolecules, such as sporopollenin, found in fossil and extant pollen and spore walls, which often can only be isolated in very small quantities. At this stage, the limited solubility of sporopollenin allows for the identification of sections of this biopolymer, but with the optimisation of MALDI-ToF matrices, further structure elucidation will become possible. Furthermore, gas chromatography-mass spectrometry (GC-MS) and (1)H nuclear magnetic resonance ((1)H NMR) spectroscopy data obtained from a number of experiments revealed that some previously reported data were misinterpreted. These results add support to the hypothesis that common plasticizers were wrongly described as sporopollenin compounds.

  18. Review of NMR characterization of pyrolysis oils

    DOE PAGES

    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

  19. NMR methods in combinatorial chemistry.

    PubMed

    Shapiro, M J; Wareing, J R

    1998-06-01

    The use of NMR spectroscopy in combinatorial chemistry has provided a versatile tool for monitoring combinatorial chemistry reactions and for assessing ligand-receptor interactions. The application of magic angle spinning NMR is widespread and has allowed structure determination to be performed on compounds attached to solid supports. A variety of two-dimensional NMR techniques have been applied to enhance the usability of the magic angle spinning NMR data. New developments for solution NMR analysis include high performance liquid chromatography, NMR, mass spectroscopy and flow NMR. NMR based methods currently being investigated may prove valuable as compound screening tools.

  20. 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.

  1. Towards 2D nanocomposites

    NASA Astrophysics Data System (ADS)

    Jang, Hyun-Sook; Yu, Changqian; Hayes, Robert; Granick, Steve

    2015-03-01

    Polymer vesicles (``polymersomes'') are an intriguing class of soft materials, commonly used to encapsulate small molecules or particles. Here we reveal they can also effectively incorporate nanoparticles inside their polymer membrane, leading to novel ``2D nanocomposites.'' The embedded nanoparticles alter the capacity of the polymersomes to bend and to stretch upon external stimuli.

  2. An Analytical Technique to Elucidate Field Impurities From Manufacturing Uncertainties of an Double Pancake Type HTS Insert for High Field LTS/HTS NMR Magnets

    PubMed Central

    Hahn, Seung-yong; Ahn, Min Cheol; Bobrov, Emanuel Saul; Bascuñán, Juan; Iwasa, Yukikazu

    2010-01-01

    This paper addresses adverse effects of dimensional uncertainties of an HTS insert assembled with double-pancake coils on spatial field homogeneity. Each DP coil was wound with Bi2223 tapes having dimensional tolerances larger than one order of magnitude of those accepted for LTS wires used in conventional NMR magnets. The paper presents: 1) dimensional variations measured in two LTS/HTS NMR magnets, 350 MHz (LH350) and 700 MHz (LH700), both built and operated at the Francis Bitter Magnet Laboratory; and 2) an analytical technique and its application to elucidate the field impurities measured with the two LTS/HTS magnets. Field impurities computed with the analytical model and those measured with the two LTS/HTS magnets agree quite well, demonstrating that this analytical technique is applicable to design a DP-assembled HTS insert with an improved field homogeneity for a high-field LTS/HTS NMR magnet. PMID:20407595

  3. An Analytical Technique to Elucidate Field Impurities From Manufacturing Uncertainties of an Double Pancake Type HTS Insert for High Field LTS/HTS NMR Magnets.

    PubMed

    Hahn, Seung-Yong; Ahn, Min Cheol; Bobrov, Emanuel Saul; Bascuñán, Juan; Iwasa, Yukikazu

    2009-06-01

    This paper addresses adverse effects of dimensional uncertainties of an HTS insert assembled with double-pancake coils on spatial field homogeneity. Each DP coil was wound with Bi2223 tapes having dimensional tolerances larger than one order of magnitude of those accepted for LTS wires used in conventional NMR magnets. The paper presents: 1) dimensional variations measured in two LTS/HTS NMR magnets, 350 MHz (LH350) and 700 MHz (LH700), both built and operated at the Francis Bitter Magnet Laboratory; and 2) an analytical technique and its application to elucidate the field impurities measured with the two LTS/HTS magnets. Field impurities computed with the analytical model and those measured with the two LTS/HTS magnets agree quite well, demonstrating that this analytical technique is applicable to design a DP-assembled HTS insert with an improved field homogeneity for a high-field LTS/HTS NMR magnet.

  4. A Self-Limiting Electro-Ablation Technique for the Top-Down Synthesis of Large-Area Monolayer Flakes of 2D Materials.

    PubMed

    Das, Saptarshi; Bera, Mrinal K; Tong, Sheng; Narayanan, Badri; Kamath, Ganesh; Mane, Anil; Paulikas, Arvydas P; Antonio, Mark R; Sankaranarayanan, Subramanian K R S; Roelofs, Andreas K

    2016-01-01

    We report the discovery of an electrochemical process that converts two dimensional layered materials of arbitrary thicknesses into monolayers. The lateral dimensions of the monolayers obtained by the process within a few seconds time at room temperature were as large as 0.5 mm. The temporal and spatial dynamics of this physical phenomenon, studied on MoS2 flakes using ex-situ AFM imaging, Raman mapping, and photoluminescence measurements trace the origin of monolayer formation to a substrate-assisted self-limiting electrochemical ablation process. Electronic structure and atomistic calculations point to the interplay between three essential factors in the process: (1) strong covalent interaction of monolayer MoS2 with the substrate; (2) electric-field induced differences in Gibbs free energy of exfoliation; (3) dispersion of MoS2 in aqueous solution of hydrogen peroxide. This process was successful in obtaining monolayers of other 2D transition metal dichalcogenides, like WS2 and MoTe2 as well. PMID:27323877

  5. A Self-Limiting Electro-Ablation Technique for the Top-Down Synthesis of Large-Area Monolayer Flakes of 2D Materials

    PubMed Central

    Das, Saptarshi; Bera, Mrinal K.; Tong, Sheng; Narayanan, Badri; Kamath, Ganesh; Mane, Anil; Paulikas, Arvydas P.; Antonio, Mark R.; Sankaranarayanan, Subramanian K. R. S.; Roelofs, Andreas K.

    2016-01-01

    We report the discovery of an electrochemical process that converts two dimensional layered materials of arbitrary thicknesses into monolayers. The lateral dimensions of the monolayers obtained by the process within a few seconds time at room temperature were as large as 0.5 mm. The temporal and spatial dynamics of this physical phenomenon, studied on MoS2 flakes using ex-situ AFM imaging, Raman mapping, and photoluminescence measurements trace the origin of monolayer formation to a substrate-assisted self-limiting electrochemical ablation process. Electronic structure and atomistic calculations point to the interplay between three essential factors in the process: (1) strong covalent interaction of monolayer MoS2 with the substrate; (2) electric-field induced differences in Gibbs free energy of exfoliation; (3) dispersion of MoS2 in aqueous solution of hydrogen peroxide. This process was successful in obtaining monolayers of other 2D transition metal dichalcogenides, like WS2 and MoTe2 as well. PMID:27323877

  6. A Self-Limiting Electro-Ablation Technique for the Top-Down Synthesis of Large-Area Monolayer Flakes of 2D Materials

    NASA Astrophysics Data System (ADS)

    Das, Saptarshi; Bera, Mrinal K.; Tong, Sheng; Narayanan, Badri; Kamath, Ganesh; Mane, Anil; Paulikas, Arvydas P.; Antonio, Mark R.; Sankaranarayanan, Subramanian K. R. S.; Roelofs, Andreas K.

    2016-06-01

    We report the discovery of an electrochemical process that converts two dimensional layered materials of arbitrary thicknesses into monolayers. The lateral dimensions of the monolayers obtained by the process within a few seconds time at room temperature were as large as 0.5 mm. The temporal and spatial dynamics of this physical phenomenon, studied on MoS2 flakes using ex-situ AFM imaging, Raman mapping, and photoluminescence measurements trace the origin of monolayer formation to a substrate-assisted self-limiting electrochemical ablation process. Electronic structure and atomistic calculations point to the interplay between three essential factors in the process: (1) strong covalent interaction of monolayer MoS2 with the substrate; (2) electric-field induced differences in Gibbs free energy of exfoliation; (3) dispersion of MoS2 in aqueous solution of hydrogen peroxide. This process was successful in obtaining monolayers of other 2D transition metal dichalcogenides, like WS2 and MoTe2 as well.

  7. A Self-Limiting Electro-Ablation Technique for the Top-Down Synthesis of Large-Area Monolayer Flakes of 2D Materials.

    PubMed

    Das, Saptarshi; Bera, Mrinal K; Tong, Sheng; Narayanan, Badri; Kamath, Ganesh; Mane, Anil; Paulikas, Arvydas P; Antonio, Mark R; Sankaranarayanan, Subramanian K R S; Roelofs, Andreas K

    2016-06-21

    We report the discovery of an electrochemical process that converts two dimensional layered materials of arbitrary thicknesses into monolayers. The lateral dimensions of the monolayers obtained by the process within a few seconds time at room temperature were as large as 0.5 mm. The temporal and spatial dynamics of this physical phenomenon, studied on MoS2 flakes using ex-situ AFM imaging, Raman mapping, and photoluminescence measurements trace the origin of monolayer formation to a substrate-assisted self-limiting electrochemical ablation process. Electronic structure and atomistic calculations point to the interplay between three essential factors in the process: (1) strong covalent interaction of monolayer MoS2 with the substrate; (2) electric-field induced differences in Gibbs free energy of exfoliation; (3) dispersion of MoS2 in aqueous solution of hydrogen peroxide. This process was successful in obtaining monolayers of other 2D transition metal dichalcogenides, like WS2 and MoTe2 as well.

  8. 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.

  9. Monitoring biodegradation of poly(butylene sebacate) by Gel Permeation Chromatography, (1)H-NMR and (31)P-NMR techniques.

    PubMed

    Siotto, Michela; Zoia, Luca; Tosin, Maurizio; Degli Innocenti, Francesco; Orlandi, Marco; Mezzanotte, Valeria

    2013-02-15

    The increasing use of new generation plastics has been accompanied by the development of standard methods for studying their biodegradability. Generally, test methods are based on the measurement of CO(2) production, i.e. the mineralization degree of the tested materials. However, in order to describe the biodegradation process, the determination of the residual amount of tested material which remains in the environment and its chemical characterization can be very important. In this study, the biodegradation in soil of a model polyester (poly(butylene sebacate)) was monitored. Gel Permeation Chromatography and Nuclear Magnetic Resonance ((31)P-NMR and (1)H-NMR) were used in order to obtain information about the polyester structure and the possible by-products that can be found in soil during and at the end of the incubation. The polyester mineralization (i.e. the CO(2) production) was tested according to ASTM 5988 standard method for 245 days. When the polyester mineralization was about 21% and 37% (after 78 and 140 days of incubation) and at the end of the process (63% of mineralization, 100% if compared to the cellulose used as reference material), the soil was extracted with chloroform (solvent of the tested substance) and the extracts were analyzed using GPC and NMR acquisitions. The analytical acquisitions showed high molecular weight polyester in soil during the incubation (78 and 140 days): the polyester concentration decreased but its structure remained almost the same with a slow decreasing in molecular weight. At the end of the test (245 days) no film of the polyester could be extracted from the soil: NMR acquisitions and GPC analyses of the extracts suggested a strong degraded structure of the residual polyester. Even if at the end of the process only 63% of carbon had been lost by mineralization, the whole of the added polyester seems to have disappeared after about eight months of incubation, suggesting substantial biomass formation.

  10. Mass spectrometry and NMR spectroscopy: modern high-end detectors for high resolution separation techniques--state of the art in natural product HPLC-MS, HPLC-NMR, and CE-MS hyphenations.

    PubMed

    Seger, Christoph; Sturm, Sonja; Stuppner, Hermann

    2013-07-01

    Current natural product research is unthinkable without the use of high resolution separation techniques as high performance liquid chromatography or capillary electrophoresis (HPLC or CE respectively) combined with mass spectrometers (MS) or nuclear magnetic resonance (NMR) spectrometers. These hyphenated instrumental analysis platforms (CE-MS, HPLC-MS or HPLC-NMR) are valuable tools for natural product de novo identification, as well as the authentication, distribution, and quantification of constituents in biogenic raw materials, natural medicines and biological materials obtained from model organisms, animals and humans. Moreover, metabolic profiling and metabolic fingerprinting applications can be addressed as well as pharmacodynamic and pharmacokinetic issues. This review provides an overview of latest technological developments, discusses the assets and drawbacks of the available hyphenation techniques, and describes typical analytical workflows.

  11. An optical technique for the direct measurement of the 2-D spectral density of a passive scalar in a turbulent flow

    SciTech Connect

    Robey, H.F.; Albrecht, G.F.; Moore, T.R.

    1990-04-06

    A new optical technique for quantitatively measuring the spectral density of passive scalar fluctuations in a turbulent flow has been developed. The technique exploits the photorefractive properties of BaTiO{sub 3} to separate the optical signal of the turbulent field from the coherent illumination background. It is a major improvement over existing techniques in that it is non-intrusive, has excellent frequency response and spatial resolution, and is capable of simultaneously measuring two components of the three-dimensional spectral density, {Phi}{theta}({kappa}). The technique is thus especially well suited to the directly study of anisotropic flows. We have applied this technique to study the spectrum of temperature fluctuations in a fully developed turbulent channel flow with heat addition. The flow is highly anisotropic, yet the spectrum in directions transverse to the flow is seen to exhibit an inertial--convective subrange behavior which is characteristic of isotropic flows. The spectral behavior in the flow direction, due to the direct influence of the mean strain rate, is observed to be markedly different. 17 refs., 7 figs.

  12. 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

  13. 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

  14. A Preliminary Appraisal of the Effect of Pumping on Seawater Intrusion and Upconing in a Small Tropical Island Using 2D Resistivity Technique

    PubMed Central

    Ramli, Mohammad Firuz; Ibrahim, Shaharin; Sulaiman, Wan Nor Azmin; Aris, Ahmad Zaharin

    2014-01-01

    The existing knowledge regarding seawater intrusion and particularly upconing, in which both problems are linked to pumping, entirely relies on theoretical assumptions. Therefore, in this paper, an attempt is made to capture the effects of pumping on seawater intrusion and upconing using 2D resistivity measurement. For this work, two positions, one perpendicular and the other parallel to the sea, were chosen as profile line for resistivity measurement in the coastal area near the pumping wells of Kapas Island, Malaysia. Subsequently, water was pumped out of two pumping wells simultaneously for about five straight hours. Then, immediately after the pumping stopped, resistivity measurements were taken along the two stationed profile lines. This was followed by additional measurements after four and eight hours. The results showed an upconing with low resistivity of about 1–10 Ωm just beneath the pumping well along the first profile line that was taken just after the pumping stopped. The resistivity image also shows an intrusion of saline water (water enriched with diluted salt) from the sea coming towards the pumping well with resistivity values ranging between 10 and 25 Ωm. The subsequent measurements show the recovery of freshwater in the aquifer and how the saline water is gradually diluted or pushed out of the aquifer. Similarly the line parallel to the sea (L2) reveals almost the same result as the first line. However, in the second and third measurements, there were some significant variations which were contrary to the expectation that the freshwater may completely flush out the saline water from the aquifer. These two time series lines show that as the areas with the lowest resistivity (1 Ωm) shrink with time, the low resistivity (10 Ωm) tends to take over almost the entire area implying that the freshwater-saltwater equilibrium zone has already been altered. These results have clearly enhanced our current understanding and add more scientific

  15. beta-Ureidopropionase deficiency: a novel inborn error of metabolism discovered using NMR spectroscopy on urine.

    PubMed

    Moolenaar, S H; Göhlich-Ratmann, G; Engelke, U F; Spraul, M; Humpfer, E; Dvortsak, P; Voit, T; Hoffmann, G F; Bräutigam, C; van Kuilenburg, A B; van Gennip, A; Vreken, P; Wevers, R A

    2001-11-01

    In this work, NMR investigations that led to the discovery of a new inborn error of metabolism, beta-ureidopropionase (UP) deficiency, are reported. 1D (1)H-NMR experiments were performed using a patient's urine. 3-Ureidopropionic acid was observed in elevated concentrations in the urine spectrum. A 1D (1)H-(1)H total correlation spectroscopy (TOCSY) and two heteronuclear 2D NMR techniques (heteronuclear multiple bond correlation (HMBC) and heteronuclear single-quantum correlation (HSQC)) were used to identify the molecular structure of the compound that caused an unknown doublet resonance at 1.13 ppm. Combining the information from the various NMR spectra, this resonance could be assigned to 3-ureidoisobutyric acid. These observations suggested a deficiency of UP. With 1D (1)H-NMR spectroscopy, UP deficiency can be easily diagnosed. The (1)H-NMR spectrum can also be used to diagnose patients suffering from other inborn errors of metabolism in the pyrimidine degradation pathway.

  16. oriGNAI3: a narrow zone of preferential replication initiation in mammalian cells identified by 2D gel and competitive PCR replicon mapping techniques.

    PubMed Central

    Toledo, F; Baron, B; Fernandez, M A; Lachagès, A M; Mayau, V; Buttin, G; Debatisse, M

    1998-01-01

    The nature of mammalian origins of DNA replication remains controversial and this is primarily because two-dimensional gel replicon mapping techniques have identified broad zones of replication initiation whereas several other techniques, such as quantitative PCR, have disclosed more discrete sites of initiation at the same chromosomal loci. In this report we analyze the replication of an amplified genomic region encompassing the 3'-end of the GNAI3 gene, the entire GNAT2 gene and the intergenic region between them in exponentially growing Chinese hamster fibroblasts. These cells express GNAI3 but not GNAT2 . The replication pattern was first analyzed by two-dimensional neutral-alkaline gel electrophoresis. Surprisingly, the results revealed a small preferential zone of replication initiation, of at most 1.7 kb, located in a limited part of the GNAI3 - GNAT2 intergenic region. Mapping of this initiation zone was then confirmed by quantitative PCR. The agreement between the two techniques exploited here strengthens the hypothesis that preferred sites of replication initiation do exist in mammalian genomes. PMID:9580680

  17. Unraveling the complexity of dissolved organic matter with chromatographic and multidimensional NMR applications

    NASA Astrophysics Data System (ADS)

    Woods, G.; Simpson, M. J.; Simpson, A. J.

    2011-12-01

    The elucidation of molecular information in dissolved organic matter (DOM) is largely hindered by successful chromatographic techniques coupled with analytical techniques capable of identifying unknown structural formulas. Nuclear magnetic resonance spectroscopy (NMR) has the capacity to solve bonding inquiries but cannot tackle such complex samples without substantial reduction in heterogeneity. Directly coupled high performance liquid chromatography (HPLC)-NMR, the novel application of hydrophilic interaction chromatography (HILIC) and the application of 2D-HILIC/HILIC have been explored for application with DOM and are reported in this presentation. HILIC is ideal for constituents that are polar and is shown to be ideal for highly oxidized environmental samples. The resulting 1D 1H NMR spectra from HILIC fractions have sharp signals, indicative of individual molecules within DOM, and structural assignments of a number of organic acids are readily identified. The further application of multidimensional NMR experiments to these simplified fractions results in significant structural assignments suggesting that HILIC is a superior HPLC technique for the separation of DOM. Further development with 2D-HILIC/HILIC results in fractions that are substantially homogenized and structurally distinct such that multidimensional NMR permits insight into new structural identifications of unknowns. 2D- and 3D-NMR experiments reveal strong evidence for the presences of highly oxidized sterols as major constituents present in DOM. Continuing research targeted toward the identification of discrete sterols may provide a wealth of information on the parent material and diagenetic processes affecting this material as it moves through the environment.

  18. Magic Angle Spinning NMR Spectroscopy: A Versatile Technique for Structural and Dynamic Analysis of Solid-Phase Systems

    PubMed Central

    Polenova, Tatyana; Gupta, Rupal; Goldbourt, Amir

    2016-01-01

    Magic Angle Spinning (MAS) NMR spectroscopy is a powerful method for analysis of a broad range of systems, including inorganic materials, pharmaceuticals, and biomacromolecules. The recent developments in MAS NMR instrumentation and methodologies opened new vistas to atomic-level characterization of a plethora of chemical environments previously inaccessible to analysis, with unprecedented sensitivity and resolution. PMID:25794311

  19. Diffusion of Paramagnetically Labeled Proteins in Cartilage: Enhancement of the 1-D NMR Imaging Technique

    NASA Astrophysics Data System (ADS)

    Foy, Brent D.; Blake, Joseph

    2001-01-01

    Quantifying the diffusive transport of large molecules in avascular cartilage tissue is important both for planning potential pharamacological treatments and for gaining insight into the molecular-scale structure of cartilage. In this work, the diffusion coefficients of gadolinium-DTPA and Gd-labeled versions of four proteins-lysozyme, trypsinogen, ovalbumin, and bovine serum albumin (BSA) with molecular weights of 14,300, 24,000, 45,000, and 67,000, respectively-have been measured in healthy and degraded calf cartilage. The experimental technique relies on the effect of the paramagnetic on the relaxation properties of the surrounding water, combined with the time course of a 1-dimensional spatial profile of the water signal in the cartilage sample. The enhanced technique presented here does not require a prior measurement of the relaxivity of the paramagnetic compound in the sample of interest. The data are expressed as the ratio of the diffusion coefficient of a compound in cartilage to its diffusion coefficient in water. For healthy cartilage, this ratio was 0.34 ± 0.07 for Gd-DTPA, the smallest compound, and fell to 0.3 ± 0.1 for Gd-lysozyme, 0.08 ± 0.04 for Gd-trypsinogen, and 0.07 ± 0.04 for Gd-ovalbumin. Gd-BSA did not appear to enter healthy cartilage tissue beyond a surface layer. After the cartilage had been degraded by 24-h trypsinization, these ratios were 0.60 ± 0.03 for Gd-DTPA, 0.40 ± 0.08 for Gd-lysozyme, 0.42 ± 0.09 for Gd-trypsinogen, 0.16 ± 0.14 for Gd-ovalbumin, and 0.11 ± 0.05 for Gd-BSA. Thus, degradation of the cartilage led to increases in the diffusion coefficient of up to fivefold for the Gd-labeled proteins. These basic transport parameters yield insights on the nature of pore sizes and chemical-matrix interactions in the cartilage tissue and may prove diagnostically useful for identifying the degree and nature of damage to cartilage.

  20. Experimental characterization of the ISIS technique for volume selected NMR spectroscopy.

    PubMed

    Keevil, S F; Porter, D A; Smith, M A

    1992-01-01

    As clinical applications of MRS grow in number and complexity, there is a need for standardized methods for characterizing the performance of volume selection techniques. The results are presented of a thorough evaluation of a particular implementation of ISIS performed using a procedure which forms the basis of the method adopted by the European Community Concerted Action on MRS and MRI. We have found that ISIS localization is optimal when the volume of interest is slightly smaller than the region we wish to study. Contamination with extraneous signal has little T1 dependence so long as TR greater than T1 and the detection pulse angle is 90 degrees. However, a poorly optimized detection pulse results in T1-weighted contamination unless TR greater than 3T1. In the clinical context, this corresponds to a different degree of contamination for each peak in the spectrum. Adiabatic detection pulses were used in an attempt to overcome this problem without resorting to unacceptable TR values, but these were found to function less well than properly optimized rectangular pulses, even if the power was increased above the level determined by the system for B1 insensitivity. These detailed results pertain only to our system, but illustrate the importance of performing similar measurements as part of clinical spectroscopy programmes at other centres. PMID:1449956

  1. Advanced NMR-based techniques for pore structure analysis of coal. Quarterly report No. 9, October 1, 1993--December 30, 1993

    SciTech Connect

    Smith, D.M.

    1993-12-31

    One of the main problems in coal utilization is the inability to properly characterize its complex pore structure. Coals typically have micro/ultra-micro pores but they also exhibit meso and macroporosity. Conventional pore size techniques (adsorption/condensation, mercury porosimetry) are limited because of this broad pore size range, microporosity, reactive nature of coal, samples must be completely dried, and network/percolation effects. Small angle scattering is limited because it probes both open and dosed pores. Although one would not expect any single technique to provide a satisfactory description of a coal`s structure, it is apparent that better techniques are necessary. Small angle scattering could be improved by combining scattering and adsorption measurements. Also, the measurement of NMR parameters of various gas phase and adsorbed phase NMR active probes can provide pore structure information. We will investigate the dependence of the common NMR parameters such as chemical shifts and relaxation times of several different nuclei and compounds on the pore structure of model microporous solids, carbons, and coals. In particular, we will study the interaction between several small molecules ({sup 129}Xe, {sup 3}He, {sup 14}N{sub 2}, {sup 14}NH{sub 3}, {sup 15}N{sub 2}, {sup 13}CH{sub 4}, {sup 13}CO{sub 2}) and pore surface. Our current work may be divided into three areas: small-angle X-ray scattering (SAXS), adsorption, and NMR.

  2. 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

  3. L-glutamine: Dynamical properties investigation by means of INS, IR, RAMAN, 1H NMR and DFT techniques

    NASA Astrophysics Data System (ADS)

    Pawlukojć, A.; Hołderna-Natkaniec, K.; Bator, G.; Natkaniec, I.

    2014-10-01

    Vibrational spectra of L-glutamine in the solid state were studied using the inelastic neutron scattering (INS), infrared (IR), Raman and 1H NMR spectroscopy techniques. DFT calculation using CASTEP code with the periodic boundary conditions was used to determine and describe the normal modes in the vibrational spectra of pure L-glutamine. An excellent agreement between the calculated and experimental INS, IR and Raman data has been found. Bands assigned to the stretching vibrations of the NH3+ group in hydrogen bonds are observed at 2400, 2618 and 2619 cm-1, while the NH3+ torsion vibration mode is observed at 441 cm-1. The band at 2041 cm-1 is assigned to combinations of the NH3+ bending symmetry vibration and the CO2- rocking vibration and can be used as an "indicator band" for the identification of the NH3+ groups in amino acid. For the L-glutamine an activation energy needed for the NH3+ group reorientation was obtained as 7.4 kcal/mol. It was found, that the combination three spectroscopic methods (INS, IR and Raman) with calculations for the crystal state proved to be an effective tool to investigate dynamical properties of amino acid crystals.

  4. Investigation of kinetics and thermodynamics of DNA hybridization by means of 2-D fluorescence spectroscopy and soft/hard modeling techniques.

    PubMed

    Ebrahimi, Sara; Kompany-Zareh, Mohsen

    2016-02-01

    Reversible hybridization reaction plays a key role in fundamental biological processes, in many laboratory techniques, and also in DNA based sensing devices. Comprehensive investigation of this process is, therefore, essential for the development of more sophisticated applications. Kinetics and thermodynamics of the hybridization reaction, as a second order process, are systematically investigated with the aid of the soft and hard chemometric methods. Labeling two complementary 21 mer DNA single strands with FAM and Texas red fluorophores, enabled recording of the florescence excitation-emission matrices during the experiments which led to three-way data sets. The presence of fluorescence resonance energy transfer in excitation and emission modes and the closure in concentration mode, made the three-way data arrays rank deficient. To acquire primary chemical information, restricted Tucker3 as a soft method was employed. Herein a model-based method, hard restricted trilinear decomposition, is introduced for in depth analysis of rank deficient three-way data sets. By employing proposed hard method, the nonlinear model parameters as well as the correct profiles could be estimated. In addition, a simple constraint is presented to extract chemically reasonable output profiles regarding the core elements of restricted Tucker3 model.

  5. Advanced NMR-based techniques for pore structure analysis of coal. Quarter report No. 4, 1 October 1992--30 December 1992

    SciTech Connect

    Smith, D.M.

    1992-12-31

    One of the main problems in coal utilization is the inability to properly characterize its complex pore structure. Coals typically have micro/ultra-micro pores but they also exhibit meso and macroporosity. Conventional pore size techniques (adsorption/condensation, mercury porosimetry) are limited because of this broad pore size range, microporosity, reactive nature of coal, samples must be completely dried, and network/percolation effects. Small angle scattering is limited because it probes both open and closed pores. Although one would not expect any single technique to provide a satisfactory description of a coal`s structure, it is apparent that better techniques are necessary. We believe that measurement of the NMR parameters of various gas phase and adsorbed phase NMR active probes can provide the resolution to this problem. We will investigate the dependence of the common NMR parameters such as chemical shifts and relaxation times of several different nuclei and compounds on the pore structure of model microporous solids, carbons, and coals. In particular, we will study the interaction between several small molecules and the pore surfaces in coals. These molecules have been selected for their chemical and physical properties. A special NMR probe will be constructed which will allow the concurrent measurement of NMR properties and adsorption uptake at a variety of temperatures. All samples will be subjected to a suite of ``conventional`` pore structure analyses. These include nitrogen adsorption at 77 K with BET analysis, CO{sub 2} and CH{sub 4} adsorption at 273 K with D-R (Dubinin-Radushkevich) analysis, helium pycnometry, and small angle X-ray scattering as well as gas diffusion measurements.

  6. Identification of archaeological triterpenic resins by the non-separative techniques FTIR and 13C NMR: the case of Pistacia resin (mastic) in comparison with frankincense.

    PubMed

    Bruni, Silvia; Guglielmi, Vittoria

    2014-01-01

    The use of spectroscopic techniques such as Fourier-transform infrared (FTIR) spectroscopy and carbon 13 nuclear magnetic resonance ((13)C NMR) using the J-mod experiment is proposed as an effective alternative to gas chromatography-mass spectrometry (GC-MS) for the analysis and identification of natural resin samples found in archaeological environments. The spectral features of the most common diterpenic and triterpenic resins and also two gum-resins are reported and discussed for both techniques. The analytical procedure based on the combined use of FTIR and (13)C NMR is then applied to two archaeological samples from the Milano of the Roman age allowing their identification as Pistacia resin, or mastic, as confirmed by the traditional GC-MS method, and also elucidating some effects of aging on such material.

  7. Advanced NMR-based techniques for pore structure analysis of coal. Quarterly report No. 7, April 1, 1993--June 31, 1993

    SciTech Connect

    Smith, D.M.

    1993-09-01

    One of the main problems in coal utilization is the inability to properly characterize its complex pore structure. Coals typically have micro/ultramicro pores but they also exhibit meso and macroporosity. Conventional pore size techniques (adsorption/condensation, mercury porosimetry) are limited because of this broad pore size range, microporosity, reactive nature of coal, samples must be completely dried, and network/percolation effects. Small angle scattering is limited because it probes both open and closed pores. Although one would not expect any single technique to provide a satisfactory description of a coal`s structure, it is apparent that better techniques are necessary. Small angle scattering could be improved by combining scattering and adsorption measurements. Also, the measurement of NMR parameters of various gas phase and adsorbed phase NMR active probes can provide pore structure information. We will investigate the dependence of the common NMR parameters such as chemical shifts and relaxation times of several different nuclei and compounds on the pore structure of model microporous solids, carbons, and coals. In particular, we will study the interaction between several small molecules ({sup 129}Xe, {sup 3}He, {sup 2}H{sub 2},{sup 14}N{sub 2}, {sup 14}NH{sub 3}, {sup 15}N{sub 2},{sup 13}CH{sub 4}, {sup 13}CO{sub 2}) and the pore surfaces in coals.

  8. Advanced NMR-based techniques for pore structure analysis of coal. Quarterly report No. 3, July 1, 1992--September 30, 1992

    SciTech Connect

    Smith, D.M.

    1992-12-31

    One of the main problems in coal utilization is the inability to properly characterize its complex pore structure. Coals typically have micro/ultra-micro pores but they also exhibit meso and macroporosity. Conventional pore size techniques (adsorption/condensation, mercury porosimetry) are limited because of this broad pore size range, microporosity, reactive nature of coal, samples must be completely dried, and network/percolation effects. Small angle scattering is limited because it probes both open and closed pores. Although one would not expect any single technique to provide a satisfactory description of a coal`s structure, it is apparent that better techniques are necessary. We believe that measurement of the NMR parameters of various gas phase and adsorbed phase NMR active probes can provide the resolution to this problem. We now have two suites of well-characterized microporous materials including oxides (zeolites and silica gel) and activated carbons from our industrial partner, Air Products in Allentown, PA. Our current work may be divided into three areas: small-angle X-ray scattering (SAXS), adsorption, and NMR.

  9. Advanced NMR-based techniques for pore structure analysis of coal. Quarter report {number_sign}8, 7/1/93--9/30/93

    SciTech Connect

    Smith, D.M.

    1993-12-31

    One of the main problems in coal utilization is the inability to properly characterize its complex pore structure. Coals typically have micro/ultramicro pores but they also exhibit meso and macroporosity. Conventional pore size techniques (adsorption/condensation, mercury porosimetry) are limited because of this broad pore size range, microporosity, reactive nature of coal, samples must be completely dried, and network/percolation effects. Small angle scattering is limited because it probes both open and closed pores. Although one would not expect any single technique to provide a satisfactory description of a coal`s structure, it is apparent that better techniques are necessary. Small angle scattering could be improved by combining scattering and adsorption measurements. Also, the measurement of NMR parameters of various gas phase and adsorbed phase NMR active probes can provide pore structure information. The dependence of the common NMR parameters such as chemical shifts and relaxation times of several different nuclei and compounds on the pore structure of model microporous solids, carbons, and coals is investigated. In particular, the interaction between several small molecules ({sup 129}Xe, {sup 3}He, {sup 14}N{sub 2},{sup 14}NH{sub 3},{sup 15}N{sub 2},{sup 13} CH{sub 4}, {sup 13}CO{sub 2}) and pore surface is studied.

  10. Advanced NMR-based techniques for pore structure analysis of coal. Quarterly report No. 6, January 1, 1993--March 31, 1993

    SciTech Connect

    Smith, D.M.

    1993-08-01

    One of the main problems in coal utilization is the inability to properly characterize its complex pore structure. Coals typically have micro/ultra-micro pores but they also exhibit meso and macroporosity. Conventional pore size techniques (adsorption/condensation, mercury porosimetry) are limited because of this broad pore size range, microporosity, reactive nature of coal, samples must be completely dried, and network/percolation effects. Small angle scattering is limited because it probes both open and closed pores. Although one would not expect any single technique to provide a satisfactory description of a coal`s structure, it is apparent that better techniques are necessary. Small angle scattering could be improved by combining scattering and adsorption measurements. Also, the measurement of NMR parameters of various gas phase and adsorbed phase NMR active probes can provide pore structure information. We will investigate the dependence of the common NMR parameters such as chemical shifts and relaxation times of several different nuclei and compounds on the pore structure of model microporous solids, carbons, and coals. In particular, we will study the interaction between several small molecules ({sup 129}Xe, {sup 3}He, {sup 2}H{sub 2}, {sup 14}N{sub 2},{sup 14}NH{sub 3}, {sup 15}N{sup 2}, {sup 13}CH{sub 4}, {sup 13}CO{sub 2}) and the pore surfaces in coals.

  11. 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

  12. 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.

  13. Nonlinear 2D-IR spectroscopy as a tool to study peptide dynamics

    NASA Astrophysics Data System (ADS)

    Hamm, Peter

    2000-03-01

    The structure of bio-macromolecules (peptides, proteins, enzymes and DNA) crucially defines their function and it is the enormous progress in structure-sensitive methods (NMR, x-ray) which has lead to an extremely detailed microscopic understanding of reactions in biological systems. Our knowledge on the dynamics of these structures, which presumably is as important for the function as the structure itself, is essentially based on computer simulations with essentially no or very indirect experimental feedback. Nonlinear 2D vibrational spectroscopy (2D-IR) on the amide I mode of small globular peptides has been demonstrated recently and a detailed relationship between the static 3D structure and the strength of cross peaks has been established (in analogy to COSY in 2D-NMR spectroscopy). An extension of this technique allows to observe equilibrium fluctuations of model helices by incorporating an additional population period (i.e. 'mixing time'), giving rise to spectral diffusion of the diagonal peaks and incoherent population transfer between excitonic states (the latter being equivalent to the nuclear Overhauser effect, NOESY). In contrast to spin transitions, however, the processes are not in the 'motional narrowing limit' (i. e. τ_c>=T_2) so that the timescales of protein fluctuation can be measured directly on a picosecond timescale and in a site specific manner.

  14. Combining 1H NMR spectroscopy and multivariate regression techniques to quantitatively determine falsification of porcine heparin with bovine species.

    PubMed

    Monakhova, Yulia B; Diehl, Bernd W K

    2015-11-10

    (1)H NMR spectroscopy was used to distinguish pure porcine heparin and porcine heparin blended with bovine species and to quantify the degree of such adulteration. For multivariate modelling several statistical methods such as partial least squares regression (PLS), ridge regression (RR), stepwise regression with variable selection (SR), stepwise principal component regression (SPCR) were utilized for modeling NMR data of in-house prepared blends (n=80). The models were exhaustively validated using independent test and prediction sets. PLS and RR showed the best performance for estimating heparin falsification regarding its animal origin with the limit of detection (LOD) and root mean square error of validation (RMSEV) below 2% w/w and 1% w/w, respectively. Reproducibility expressed in coefficients of variation was estimated to be below 10% starting from approximately 5% w/w of bovine adulteration. Acceptable calibration model was obtained by SPCR, by its application range was limited, whereas SR is least recommended for heparin matrix. The developed method was found to be applicable also to heparinoid matrix (not purified heparin). In this case root mean square of prediction (RMSEP) and LOD were approximately 7% w/w and 8% w/w, respectively. The simple and cheap NMR method is recommended for screening of heparin animal origin in parallel with official NMR test of heparin authenticity and purity.

  15. 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.

  16. 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

  17. 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.

  18. 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.

  19. 99Tc NMR as a promising technique for structural investigation of biomolecules: theoretical studies on the solvent and thermal effects of phenylbenzothiazole complex.

    PubMed

    Mancini, Daiana T; Souza, Eugenio F; Caetano, Melissa S; Ramalho, Teodorico C

    2014-04-01

    The phenylbenzothiazole compounds show antitumor properties and are highly selective. In this paper, the (99)Tc chemical shifts based on the ((99m)Tc)(CO)3 (NNO) complex conjugated to the antitumor agent 2-(4'-aminophenyl)benzothiazole are reported. Thermal and solvent effects were studied computationally by quantum-chemical methods, using the density functional theory (DFT) (DFT level BPW91/aug-cc-pVTZ for the Tc and BPW91/IGLO-II for the other atoms) to compute the NMR parameters for the complex. We have calculated the (99)Tc NMR chemical shifts of the complex in gas phase and solution using different solvation models (polarizable continuum model and explicit solvation). To evaluate the thermal effect, molecular dynamics simulations were carried, using the atom-centered density matrix propagation method at the DFT level (BP86/LanL2dz). The results highlight that the (99)Tc NMR spectroscopy can be a promising technique for structural investigation of biomolecules, at the molecular level, in different environments. PMID:24446055

  20. Metabolic characterization of Brassica rapa leaves by NMR spectroscopy.

    PubMed

    Abdel-Farid, Ibrahim Bayoumi; Kim, Hye Kyong; Choi, Young Hae; Verpoorte, Robert

    2007-09-19

    The Brassica has been intensively studied due to the nutritional and beneficial effects. However, many species, varieties, and cultivars of this genus and the resulting large metabolic variation have been obstacles for systematic research of the plant. In order to overcome the problems posed by the biological variation, the metabolomic analysis of various cultivars of Brassica rapa was performed by NMR spectroscopy combined with multivariate data analysis. Discriminating metabolites in different cultivars and development stages were elucidated by diverse 2D-NMR techniques after sorting out different significant signals using (1)H NMR measurements and principal component analysis. Among the elucidated metabolites, several organic and amino acids, carbohydrates, adenine, indole acetic acid (IAA), phenylpropanoids, flavonoids, and glucosinolates were found to be the metabolites contributing to the differentiation between cultivars and age of Brassica rapa. On the basis of these results, the distribution of plant metabolites among different cultivars and development stages of B. rapa is discussed.

  1. 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...

  2. 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.

  3. NMR studies of metalloproteins.

    PubMed

    Li, Hongyan; Sun, Hongzhe

    2012-01-01

    Metalloproteins represent a large share of the proteomes, with the intrinsic metal ions providing catalytic, regulatory, and structural roles critical to protein functions. Structural characterization of metalloproteins and identification of metal coordination features including numbers and types of ligands and metal-ligand geometry, and mapping the structural and dynamic changes upon metal binding are significant for understanding biological functions of metalloproteins. NMR spectroscopy has long been used as an invaluable tool for structure and dynamic studies of macromolecules. Here we focus on the application of NMR spectroscopy in characterization of metalloproteins, including structural studies and identification of metal coordination spheres by hetero-/homo-nuclear metal NMR spectroscopy. Paramagnetic NMR as well as (13)C directly detected protonless NMR spectroscopy will also be addressed for application to paramagnetic metalloproteins. Moreover, these techniques offer great potential for studies of other non-metal binding macromolecules.

  4. Nigericin-mediated transport of cesium ions through phospholipid bilayers studied by a sup 133 Cs magnetization-transfer NMR technique

    SciTech Connect

    Riddell, F.G.; Arumugam, S.; Patel, A. )

    1990-06-27

    The use of Cs-133 NMR spectroscopy to study the nigericin-mediated transport of Cs{sup +} ions through phosphatidylcholine bilayers is reported. A magnetization-transfer technique used involves a compartmentalized system of cells or of vesicles and employs a shift reagent or a relaxation agent to contrast the signals from the intracompartmental and extracompartmental metal ions. A magnetic label is placed at one site by inserting the spin population, and then the signal intensity is followed at the other site as the inverted signal relaxes back. The process was found to be first order in nigericin. 16 refs., 1 fig., 1 tab.

  5. J-Modulation in ID NMR 1H Spectrum of Taurine and Aspartate Using Spin-Echo Technique

    NASA Astrophysics Data System (ADS)

    Oturak, Halil; Sağlam, Adnan; Bahçeli, Semiha

    1999-05-01

    This study reports on a theoretical calculation of Hahn's spin-echo experiment in case of a model A2B2 spin system with a strongly coupling character and gives the experimental results of one-dimension 1H high-resolution NMR spectra of taurine and aspartate. The calculated amplitudes of the spin-echoes for two different proton groups of taurine are given. Using results of our calculations for taurine, the computer simulations of J-modulation are implemented. It is shown that the agreement be-tween the experimental and simulated spectra is good.

  6. Synthesis of 24-phenyl-24-oxo steroids derived from bile acids by palladium-catalyzed cross coupling with phenylboronic acid. NMR characterization and X-ray structures.

    PubMed

    Mayorquín-Torres, Martha C; Romero-Ávila, Margarita; Flores-Álamo, Marcos; Iglesias-Arteaga, Martin A

    2013-11-01

    Palladium-catalyzed cross coupling of phenyboronic acid with acetylated bile acids in which the carboxyl functions have been activated by formation of a mixed anhydride with pivalic anhydride afforded moderate to good yield of 24-phenyl-24-oxo-steroids. Unambiguous assignments of the NMR signals were made with the aid of combined 1D and 2D NMR techniques. X-ray diffraction studies confirmed the obtained structures.

  7. Ultrafast 2D IR microscopy

    PubMed Central

    Baiz, Carlos R.; Schach, Denise; Tokmakoff, Andrei

    2014-01-01

    We describe a microscope for measuring two-dimensional infrared (2D IR) spectra of heterogeneous samples with μm-scale spatial resolution, sub-picosecond time resolution, and the molecular structure information of 2D IR, enabling the measurement of vibrational dynamics through correlations in frequency, time, and space. The setup is based on a fully collinear “one beam” geometry in which all pulses propagate along the same optics. Polarization, chopping, and phase cycling are used to isolate the 2D IR signals of interest. In addition, we demonstrate the use of vibrational lifetime as a contrast agent for imaging microscopic variations in molecular environments. PMID:25089490

  8. Development of a low resolution (1)H NMR spectroscopic technique for the study of matrix mobility in fresh and freeze-thawed hen egg yolk.

    PubMed

    Au, Carmen; Wang, Tong; Acevedo, Nuria C

    2016-08-01

    Three experiments were conducted in developing a low resolution proton nuclear magnetic resonance ((1)H NMR) spectroscopic technique to study matrix mobility in fresh and freeze-thawed gelled yolk. The Carr-Purcell-Meiboom-Gill (CPMG) sequence was used to measure spin-spin relaxation times of proton pools representing major yolk constituents. A component identification test distinguished 3-4 pools. The least mobile pool was assigned to proteins, protein-lipid and protein-water interactions, and the most mobile to unbound water. The remaining pools were assigned to lipids, lipid-protein and lipid-water interactions. A stability test indicated that yolk had varied matrix mobility within the same sample across five days of refrigeration storage. A reproducibility test demonstrated high repeatability of fresh yolk measurements, but significant differences (p<0.05) were found within gelled yolk samples. This research determined that (1)H NMR spectroscopy, a non-destructive technique, can identify yolk components and detect changes in the matrix.

  9. 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.

  10. Reducing acquisition times in multidimensional NMR with a time-optimized Fourier encoding algorithm

    SciTech Connect

    Zhang, Zhiyong; Smith, Pieter E. S.; Frydman, Lucio

    2014-11-21

    Speeding up the acquisition of multidimensional nuclear magnetic resonance (NMR) spectra is an important topic in contemporary NMR, with central roles in high-throughput investigations and analyses of marginally stable samples. A variety of fast NMR techniques have been developed, including methods based on non-uniform sampling and Hadamard encoding, that overcome the long sampling times inherent to schemes based on fast-Fourier-transform (FFT) methods. Here, we explore the potential of an alternative fast acquisition method that leverages a priori knowledge, to tailor polychromatic pulses and customized time delays for an efficient Fourier encoding of the indirect domain of an NMR experiment. By porting the encoding of the indirect-domain to the excitation process, this strategy avoids potential artifacts associated with non-uniform sampling schemes and uses a minimum number of scans equal to the number of resonances present in the indirect dimension. An added convenience is afforded by the fact that a usual 2D FFT can be used to process the generated data. Acquisitions of 2D heteronuclear correlation NMR spectra on quinine and on the anti-inflammatory drug isobutyl propionic phenolic acid illustrate the new method's performance. This method can be readily automated to deal with complex samples such as those occurring in metabolomics, in in-cell as well as in in vivo NMR applications, where speed and temporal stability are often primary concerns.

  11. Reducing acquisition times in multidimensional NMR with a time-optimized Fourier encoding algorithm.

    PubMed

    Zhang, Zhiyong; Smith, Pieter E S; Frydman, Lucio

    2014-11-21

    Speeding up the acquisition of multidimensional nuclear magnetic resonance (NMR) spectra is an important topic in contemporary NMR, with central roles in high-throughput investigations and analyses of marginally stable samples. A variety of fast NMR techniques have been developed, including methods based on non-uniform sampling and Hadamard encoding, that overcome the long sampling times inherent to schemes based on fast-Fourier-transform (FFT) methods. Here, we explore the potential of an alternative fast acquisition method that leverages a priori knowledge, to tailor polychromatic pulses and customized time delays for an efficient Fourier encoding of the indirect domain of an NMR experiment. By porting the encoding of the indirect-domain to the excitation process, this strategy avoids potential artifacts associated with non-uniform sampling schemes and uses a minimum number of scans equal to the number of resonances present in the indirect dimension. An added convenience is afforded by the fact that a usual 2D FFT can be used to process the generated data. Acquisitions of 2D heteronuclear correlation NMR spectra on quinine and on the anti-inflammatory drug isobutyl propionic phenolic acid illustrate the new method's performance. This method can be readily automated to deal with complex samples such as those occurring in metabolomics, in in-cell as well as in in vivo NMR applications, where speed and temporal stability are often primary concerns. PMID:25416883

  12. Reducing acquisition times in multidimensional NMR with a time-optimized Fourier encoding algorithm

    PubMed Central

    Zhang, Zhiyong; Frydman, Lucio

    2014-01-01

    Speeding up the acquisition of multidimensional nuclear magnetic resonance (NMR) spectra is an important topic in contemporary NMR, with central roles in high-throughput investigations and analyses of marginally stable samples. A variety of fast NMR techniques have been developed, including methods based on non-uniform sampling and Hadamard encoding, that overcome the long sampling times inherent to schemes based on fast-Fourier-transform (FFT) methods. Here, we explore the potential of an alternative fast acquisition method that leverages a priori knowledge, to tailor polychromatic pulses and customized time delays for an efficient Fourier encoding of the indirect domain of an NMR experiment. By porting the encoding of the indirect-domain to the excitation process, this strategy avoids potential artifacts associated with non-uniform sampling schemes and uses a minimum number of scans equal to the number of resonances present in the indirect dimension. An added convenience is afforded by the fact that a usual 2D FFT can be used to process the generated data. Acquisitions of 2D heteronuclear correlation NMR spectra on quinine and on the anti-inflammatory drug isobutyl propionic phenolic acid illustrate the new method's performance. This method can be readily automated to deal with complex samples such as those occurring in metabolomics, in in-cell as well as in in vivo NMR applications, where speed and temporal stability are often primary concerns. PMID:25416883

  13. Revealing Potential Biomarkers of Functional Dyspepsia by Combining 1H NMR Metabonomics Techniques and an Integrative Multi-objective Optimization Method

    PubMed Central

    Wu, Qiaofeng; Zou, Meng; Yang, Mingxiao; Zhou, Siyuan; Yan, Xianzhong; Sun, Bo; Wang, Yong; Chang, Shyang; Tang, Yong; Liang, Fanrong; Yu, Shuguang

    2016-01-01

    Metabonomics methods have gradually become important auxiliary tools for screening disease biomarkers. However, recognition of metabolites or potential biomarkers closely related to either particular clinical symptoms or prognosis has been difficult. The current study aims to identify potential biomarkers of functional dyspepsia (FD) by a new strategy that combined hydrogen nuclear magnetic resonance (1H NMR)-based metabonomics techniques and an integrative multi-objective optimization (LPIMO) method. First, clinical symptoms of FD were evaluated using the Nepean Dyspepsia Index (NDI), and plasma metabolic profiles were measured by 1H NMR. Correlations between the key metabolites and the NDI scores were calculated. Then, LPIMO was developed to identify a multi-biomarker panel by maximizing diagnostic ability and correlation with the NDI score. Finally, a KEGG database search elicited the metabolic pathways in which the potential biomarkers are involved. The results showed that glutamine, alanine, proline, HDL, β-glucose, α-glucose and LDL/VLDL levels were significantly altered in FD patients. Among them, phosphatidycholine (PtdCho) and leucine/isoleucine (Leu/Ile) were positively and negatively correlated with the NDI Symptom Index (NDSI) respectively. Our procedure not only significantly improved the credibility of the biomarkers, but also demonstrated the potential of further explorations and applications to diagnosis and treatment of complex disease. PMID:26743458

  14. 4-hydroxyphenylacetic acid derivatives of inositol from dandelion (Taraxacum officinale) root characterised using LC-SPE-NMR and LC-MS techniques.

    PubMed

    Kenny, O; Smyth, T J; Hewage, C M; Brunton, N P; McLoughlin, P

    2014-02-01

    The combination of hyphenated techniques, LC-SPE-NMR and LC-MS, to isolate and identify minor isomeric compounds from an ethyl acetate fraction of Taraxacum officinale root was employed in this study. Two distinct fractions of 4-hydroxyphenylacetic acid derivatives of inositol were isolated and characterised by spectroscopic methods. The (1)H NMR spectra and MS data revealed two groups of compounds, one of which were derivatives of the di-4-hydroxyphenylacetic acid derivative of the inositol compound tetrahydroxy-5-[2-(4-hydroxyphenyl)acetyl] oxycyclohexyl-2-(4-hydroxyphenyl) acetate, while the other group consisted of similar tri-substituted inositol derivatives. For both fractions the derivatives of inositols vary in the number of 4-hydroxyphenylacetic acid groups present and their position and geometry on the inositol ring. In total, three di-substituted and three tri-substituted 4-hydroxyphenylacetic acid inositol derivates were identified for the first time along with a further two previously reported di-substituted inositol derivatives.

  15. Method for determining molar concentrations of metabolites in complex solutions from two-dimensional 1H-13C NMR spectra.

    PubMed

    Lewis, Ian A; Schommer, Seth C; Hodis, Brendan; Robb, Kate A; Tonelli, Marco; Westler, William M; Sussman, Michael R; Markley, John L

    2007-12-15

    One-dimensional (1D) (1)H nuclear magnetic resonance (NMR) spectroscopy is used extensively for high-throughput analysis of metabolites in biological fluids and tissue extracts. Typically, such spectra are treated as multivariate statistical objects rather than as collections of quantifiable metabolites. We report here a two-dimensional (2D) (1)H-(13)C NMR strategy (fast metabolite quantification, FMQ, by NMR) for identifying and quantifying the approximately 40 most abundant metabolites in biological samples. To validate this technique, we prepared mixtures of synthetic compounds and extracts from Arabidopsis thaliana, Saccharomyces cerevisiae, and Medicago sativa. We show that accurate (technical error 2.7%) molar concentrations can be determined in 12 min using our quantitative 2D (1)H-(13)C NMR strategy. In contrast, traditional 1D (1)H NMR analysis resulted in 16.2% technical error under nearly ideal conditions. We propose FMQ by NMR as a practical alternative to 1D (1)H NMR for metabolomics studies in which 50-mg (extract dry weight) samples can be obtained. PMID:17985927

  16. Method for determining molar concentrations of metabolites in complex solutions from two-dimensional 1H-13C NMR spectra.

    PubMed

    Lewis, Ian A; Schommer, Seth C; Hodis, Brendan; Robb, Kate A; Tonelli, Marco; Westler, William M; Sussman, Michael R; Markley, John L

    2007-12-15

    One-dimensional (1D) (1)H nuclear magnetic resonance (NMR) spectroscopy is used extensively for high-throughput analysis of metabolites in biological fluids and tissue extracts. Typically, such spectra are treated as multivariate statistical objects rather than as collections of quantifiable metabolites. We report here a two-dimensional (2D) (1)H-(13)C NMR strategy (fast metabolite quantification, FMQ, by NMR) for identifying and quantifying the approximately 40 most abundant metabolites in biological samples. To validate this technique, we prepared mixtures of synthetic compounds and extracts from Arabidopsis thaliana, Saccharomyces cerevisiae, and Medicago sativa. We show that accurate (technical error 2.7%) molar concentrations can be determined in 12 min using our quantitative 2D (1)H-(13)C NMR strategy. In contrast, traditional 1D (1)H NMR analysis resulted in 16.2% technical error under nearly ideal conditions. We propose FMQ by NMR as a practical alternative to 1D (1)H NMR for metabolomics studies in which 50-mg (extract dry weight) samples can be obtained.

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

    NASA Astrophysics Data System (ADS)

    Gaede, Holly C.; Stark, Ruth E.

    2001-09-01

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

  18. 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.

  19. 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

  20. The role of water in protein's behavior: The two dynamical crossovers studied by NMR and FTIR techniques

    PubMed Central

    Mallamace, Francesco; Corsaro, Carmelo; Mallamace, Domenico; Vasi, Sebastiano; Vasi, Cirino; Dugo, Giacomo

    2014-01-01

    The role the solvent plays in determining the biological activity of proteins is of primary importance. Water is the solvent of life and proteins need at least a water monolayer covering their surface in order to become biologically active. We study how the properties of water and the effect of its coupling with the hydrophilic moieties of proteins govern the regime of protein activity. In particular we follow, by means of Fourier Transform Infrared spectroscopy, the thermal evolution of the amide vibrational modes of hydrated lysozyme in the temperature interval 180 K < T < 350 K. In such a way we are able to observe the thermal limit of biological activity characterizing hydrated lysozyme. Finally we focus on the region of lysozyme thermal denaturation by following the evolution of the proton Nuclear Magnetic Resonance (NMR) spectra for 298 K < T < 366 K with the High-Resolution Magic Angle Spinning probe. Our data suggest that the hydrogen bond coupling between hydration water and protein hydrophilic groups is crucial in triggering the main mechanisms that define the enzymatic activity of proteins. PMID:25750698

  1. The role of water in protein's behavior: The two dynamical crossovers studied by NMR and FTIR techniques.

    PubMed

    Mallamace, Francesco; Corsaro, Carmelo; Mallamace, Domenico; Vasi, Sebastiano; Vasi, Cirino; Dugo, Giacomo

    2015-01-01

    The role the solvent plays in determining the biological activity of proteins is of primary importance. Water is the solvent of life and proteins need at least a water monolayer covering their surface in order to become biologically active. We study how the properties of water and the effect of its coupling with the hydrophilic moieties of proteins govern the regime of protein activity. In particular we follow, by means of Fourier Transform Infrared spectroscopy, the thermal evolution of the amide vibrational modes of hydrated lysozyme in the temperature interval 180 K < T < 350 K. In such a way we are able to observe the thermal limit of biological activity characterizing hydrated lysozyme. Finally we focus on the region of lysozyme thermal denaturation by following the evolution of the proton Nuclear Magnetic Resonance (NMR) spectra for 298 K < T < 366 K with the High-Resolution Magic Angle Spinning probe. Our data suggest that the hydrogen bond coupling between hydration water and protein hydrophilic groups is crucial in triggering the main mechanisms that define the enzymatic activity of proteins.

  2. Advanced solid-state NMR techniques for characterization of membrane protein structure and dynamics: Application to Anabaena Sensory Rhodopsin

    NASA Astrophysics Data System (ADS)

    Ward, Meaghan E.; Brown, Leonid S.; Ladizhansky, Vladimir

    2015-04-01

    Studies of the structure, dynamics, and function of membrane proteins (MPs) have long been considered one of the main applications of solid-state NMR (SSNMR). Advances in instrumentation, and the plethora of new SSNMR methodologies developed over the past decade have resulted in a number of high-resolution structures and structural models of both bitopic and polytopic α-helical MPs. The necessity to retain lipids in the sample, the high proportion of one type of secondary structure, differential dynamics, and the possibility of local disorder in the loop regions all create challenges for structure determination. In this Perspective article we describe our recent efforts directed at determining the structure and functional dynamics of Anabaena Sensory Rhodopsin, a heptahelical transmembrane (7TM) protein. We review some of the established and emerging methods which can be utilized for SSNMR-based structure determination, with a particular focus on those used for ASR, a bacterial protein which shares its 7TM architecture with G-protein coupled receptors.

  3. Advanced solid-state NMR techniques for characterization of membrane protein structure and dynamics: application to Anabaena Sensory Rhodopsin.

    PubMed

    Ward, Meaghan E; Brown, Leonid S; Ladizhansky, Vladimir

    2015-04-01

    Studies of the structure, dynamics, and function of membrane proteins (MPs) have long been considered one of the main applications of solid-state NMR (SSNMR). Advances in instrumentation, and the plethora of new SSNMR methodologies developed over the past decade have resulted in a number of high-resolution structures and structural models of both bitopic and polytopic α-helical MPs. The necessity to retain lipids in the sample, the high proportion of one type of secondary structure, differential dynamics, and the possibility of local disorder in the loop regions all create challenges for structure determination. In this Perspective article we describe our recent efforts directed at determining the structure and functional dynamics of Anabaena Sensory Rhodopsin, a heptahelical transmembrane (7TM) protein. We review some of the established and emerging methods which can be utilized for SSNMR-based structure determination, with a particular focus on those used for ASR, a bacterial protein which shares its 7TM architecture with G-protein coupled receptors.

  4. Application of k- and q-space encoding NMR techniques on granular media in a 3D model fluidized bed reactor

    NASA Astrophysics Data System (ADS)

    Harms, Silke; Stapf, Siegfried; Blümich, Bernhard

    2006-02-01

    A combination of PFG-NMR imaging and velocity encoding methods was applied to investigate the dynamic behavior of a bed of poppy seeds subjected to air flow, representing a model setup for fluidized bed reactors. The particle motion is described both from a statistical point of view, by determining propagators and dispersion coefficients representing an average over the whole bed volume, as well as combined with spatial resolution by generating velocity maps. Velocity images of different horizontal slices in the bed confirm the notion of a toroidal particle flow pattern inside the shallow granular bed. Despite the need of considerable averaging due to the random motion of the relatively few particles in the bed, quantitative velocity images and statistical information about the random particle motion can be obtained from monitoring the fluid component in the seeds by conventional spin-echo techniques.

  5. Analytical Applications of NMR: Summer Symposium on Analytical Chemistry.

    ERIC Educational Resources Information Center

    Borman, Stuart A.

    1982-01-01

    Highlights a symposium on analytical applications of nuclear magnetic resonance spectroscopy (NMR), discussing pulse Fourier transformation technique, two-dimensional NMR, solid state NMR, and multinuclear NMR. Includes description of ORACLE, an NMR data processing system at Syracuse University using real-time color graphics, and algorithms for…

  6. Class modeling analysis of heparin 1H NMR spectral data using the soft independent modeling of class analogy and unequal class modeling techniques.

    PubMed

    Zang, Qingda; Keire, David A; Wood, Richard D; Buhse, Lucinda F; Moore, Christine M V; Nasr, Moheb; Al-Hakim, Ali; Trehy, Michael L; Welsh, William J

    2011-02-01

    To differentiate heparin samples with varying amounts of dermatan sulfate (DS) impurities and oversulfated chondroitin sulfate (OSCS) contaminants, proton NMR spectral data for heparin sodium active pharmaceutical ingredient samples from different manufacturers were analyzed using multivariate chemometric techniques. A total of 168 samples were divided into three groups: (a) Heparin, [DS] ≤ 1.0% and [OSCS] = 0%; (b) DS, [DS] > 1.0% and [OSCS] = 0%; (c) OSCS, [OSCS] > 0% with any content of DS. The chemometric models were constructed and validated using two well-established methods: soft independent modeling of class analogy (SIMCA) and unequal class modeling (UNEQ). While SIMCA modeling was conducted using the entire set of variables extracted from the NMR spectral data, UNEQ modeling was combined with variable reduction using stepwise linear discriminant analysis to comply with the requirement that the number of samples per class exceed the number of variables in the model by at least 3-fold. Comparison of the results from these two modeling approaches revealed that UNEQ had greater sensitivity (fewer false positives) while SIMCA had greater specificity (fewer false negatives). For Heparin, DS, and OSCS, respectively, the sensitivity was 78% (56/72), 74% (37/50), and 85% (39/46) from SIMCA modeling and 88% (63/72), 90% (45/50), and 91% (42/46) from UNEQ modeling. Importantly, the specificity of both the SIMCA and UNEQ models was 100% (46/46) for Heparin with respect to OSCS; no OSCS-containing sample was misclassified as Heparin. The specificity of the SIMCA model (45/50, or 90%) was superior to that of the UNEQ model (27/50, or 54%) for Heparin with respect to DS samples. However, the overall prediction ability of the UNEQ model (85%) was notably better than that of the SIMCA model (76%) for the Heparin vs DS vs OSCS classes. The models were challenged with blends of heparin spiked with nonsulfated, partially sulfated, or fully oversulfated chondroitin sulfate

  7. Complete assignments of (1)H and (13)C NMR data for two 3beta,8beta-epoxymexicanolides from the fruit of a Chinese mangrove Xylocarpus granatum.

    PubMed

    Wu, Jun; Xiao, Zhihui; Song, Yang; Zhang, Si; Xiao, Qiang; Ma, Cha; Ding, Haixin; Li, Qingxin

    2006-01-01

    Three 3beta,8beta-epoxymexicanolides, including xyloccensin K, 6-acetoxycedrodorin and a new one named xyloccensin W, were isolated from the fruit of a Chinese mangrove Xylocarpus granatum. Their structures were determined by spectroscopic analyses. The first complete assignment of (1)H and (13)C NMR data for xyloccensin W was achieved by means of 2D NMR techniques, including (1)H-(1)H COSY, HSQC, HMBC and NOESY spectra. In addition, the confusion of (1)H and (13)C NMR data previously reported for xyloccensin K was clarified.

  8. 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.''

  9. Recent progress in NMR/MRI in petroleum applications

    NASA Astrophysics Data System (ADS)

    Song, Yi-Qiao

    2007-03-01

    NMR has become an important technique for characterization of porous materials. In particular, its importance in petroleum exploration has been enhanced by the recent progress in NMR well-logging techniques and instruments. Such advanced techniques are increasing being accepted as a valuable service especially in deep-sea exploration. This paper will outline the recent progress of MR techniques at Schlumberger-Doll Research. Well-logging - The second generation NMR well-logging tool and the 2D NMR methods (D-T2, etc) enable measurements at several depths from the well bore allowing a one-dimensional profiling of the fluid. Such data have allowed quantification of fluid invasion during drilling, obtaining the properties of native fluids and identifying oil/gas zones. MRI- Rocks from oil reservoirs are heterogeneous (e.g. large range of pore sizes and porosity variation) due to the complex geological and geochemical histories. The spatial pattern of the heterogeneity has not been well studied. We have developed several NMR techniques to quantify pore length scale previously. In order to predict flow over a large length scale, it is necessary to determine spatial heterogeneity and pore connectivity over the relevant size. We have performed MRI on a series of carbonate rocks and found interesting patterns of the heterogeneity characteristics. Mathematics - It is well known that the Laplace inversion is non-unique and the resulting spectrum can be strongly dependent on the prior constraints, specific algorithm and noise. However, the different spectra can all be solutions consistent with data. It would be useful to have a robust criterion -- independent of algorithms -- to determine the properties of the resulting spectrum. Several methods will be described to examine the statistics of the solutions, uncertainty of the spectrum and its integrals and resolution.

  10. DYNA2D96. Explicit 2-D Hydrodynamic FEM Program

    SciTech Connect

    Whirley, R.G.

    1992-04-01

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

  11. Complete 1H and 13C NMR assignments of two phytosterols from roots of Piper nigrum.

    PubMed

    Wei, Kun; Li, Wei; Koike, Kazuo; Pei, Yuping; Chen, Yingjie; Nikaido, Tamotsu

    2004-03-01

    Using modern NMR techniques, including DQF-COSY, NOESY, HETCOR and HMBC, the full assignments of all 1H and 13C chemical shifts were made for stigmastane-3,6-dione and stigmast-4-ene-3,6-dione, isolated from the roots of Piper nigrum (Piperaceae). Their stereochemistry was resolved by a combination of 2D NOESY data and analysis of coupling constants. The two compounds were isolated from the genus Piper for the first time.

  12. Quick re-introduction of selective scalar interactions in a pure-shift NMR spectrum.

    PubMed

    Lokesh, N; Chaudhari, Sachin Rama; Suryaprakash, N

    2014-12-21

    A new 1D NMR experiment cited as 'Quick G-SERF', which re-introduces selective proton-proton scalar interactions in a pure shift spectrum during real time data acquisition, is reported. The method provides information on multiple proton-proton couplings from a single experiment, analogous to the 2D G-SERF technique, while significantly shortening the experimental time by 1-2 orders of magnitude due to reduced dimension and enhanced sensitivity.

  13. 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

  14. Residue-Specific Structural Kinetics of Proteins through the Union of Isotope Labeling, Mid-IR Pulse Shaping, and Coherent 2D IR Spectroscopy

    PubMed Central

    Middleton, Chris T.; Woys, Ann Marie; Mukherjee, Sudipta S.; Zanni, Martin T.

    2010-01-01

    We describe a methodology for studying protein kinetics using a rapid-scan technology for collecting 2D IR spectra. In conjunction with isotope labeling, 2D IR spectroscopy is able to probe the secondary structure and environment of individual residues in polypeptides and proteins. It is particularly useful for membrane and aggregate proteins. Our rapid-scan technology relies on a mid-IR pulse shaper that computer generates the pulse shapes, much like in an NMR spectrometer. With this device, data collection is faster, easier, and more accurate. We describe our 2D IR spectrometer, as well as protocols for 13C=18O isotope labeling, and then illustrate the technique with an application to the aggregation of the human islet amyloid polypeptide form type 2 diabetes. PMID:20472067

  15. 2D Four-Channel Perfect Reconstruction Filter Bank Realized with the 2D Lattice Filter Structure

    NASA Astrophysics Data System (ADS)

    Sezen, S.; Ertüzün, A.

    2006-12-01

    A novel orthogonal 2D lattice structure is incorporated into the design of a nonseparable 2D four-channel perfect reconstruction filter bank. The proposed filter bank is obtained by using the polyphase decomposition technique which requires the design of an orthogonal 2D lattice filter. Due to constraint of perfect reconstruction, each stage of this lattice filter bank is simply parameterized by two coefficients. The perfect reconstruction property is satisfied regardless of the actual values of these parameters and of the number of the lattice stages. It is also shown that a separable 2D four-channel perfect reconstruction lattice filter bank can be constructed from the 1D lattice filter and that this is a special case of the proposed 2D lattice filter bank under certain conditions. The perfect reconstruction property of the proposed 2D lattice filter approach is verified by computer simulations.

  16. Two-dimensional MAS NMR correlation protocols involving double-quantum filtering of quadrupolar spin-pairs.

    PubMed

    Edén, Mattias

    2010-05-01

    Three two-dimensional (2D) NMR homonuclear correlation techniques invoking double-quantum (2Q) filtration of the central transitions of half-integer spins are evaluated numerically and experimentally. They correlate directly detected single-quantum (1Q) coherences in the t(2) domain with either of 1Q, two-spin 2Q or single-spin multiple-quantum coherence-evolutions in the indirect (t(1)) dimension. We employ experimental (23)Na and (27)Al NMR on sodium sulfite and the natural mineral sillimanite (SiAl(2)O(5)), in conjunction with simulated 2D spectra from pairs of dipolar-recoupled spins-3/2 and 5/2 at different external magnetic fields, to compare the correlation strategies from the viewpoints of 2D spectral resolution, signal sensitivity, implementational aspects and their relative merits for establishing internuclear proximities and quadrupolar tensor orientations. PMID:20202872

  17. Two-dimensional MAS NMR correlation protocols involving double-quantum filtering of quadrupolar spin-pairs

    NASA Astrophysics Data System (ADS)

    Edén, Mattias

    2010-05-01

    Three two-dimensional (2D) NMR homonuclear correlation techniques invoking double-quantum (2Q) filtration of the central transitions of half-integer spins are evaluated numerically and experimentally. They correlate directly detected single-quantum (1Q) coherences in the t2 domain with either of 1Q, two-spin 2Q or single-spin multiple-quantum coherence-evolutions in the indirect (t1) dimension. We employ experimental 23Na and 27Al NMR on sodium sulfite and the natural mineral sillimanite (SiAl2O5), in conjunction with simulated 2D spectra from pairs of dipolar-recoupled spins-3/2 and 5/2 at different external magnetic fields, to compare the correlation strategies from the viewpoints of 2D spectral resolution, signal sensitivity, implementational aspects and their relative merits for establishing internuclear proximities and quadrupolar tensor orientations.

  18. 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.

  19. NMR in metabolomics and natural products research: two sides of the same coin.

    PubMed

    Robinette, Steven L; Brüschweiler, Rafael; Schroeder, Frank C; Edison, Arthur S

    2012-02-21

    Small molecules are central to biology, mediating critical phenomena such as metabolism, signal transduction, mating attraction, and chemical defense. The traditional categories that define small molecules, such as metabolite, secondary metabolite, pheromone, hormone, and so forth, often overlap, and a single compound can appear under more than one functional heading. Therefore, we favor a unifying term, biogenic small molecules (BSMs), to describe any small molecule from a biological source. In a similar vein, two major fields of chemical research,natural products chemistry and metabolomics, have as their goal the identification of BSMs, either as a purified active compound (natural products chemistry) or as a biomarker of a particular biological state (metabolomics). Natural products chemistry has a long tradition of sophisticated techniques that allow identification of complex BSMs, but it often fails when dealing with complex mixtures. Metabolomics thrives with mixtures and uses the power of statistical analysis to isolate the proverbial "needle from a haystack", but it is often limited in the identification of active BSMs. We argue that the two fields of natural products chemistry and metabolomics have largely overlapping objectives: the identification of structures and functions of BSMs, which in nature almost inevitably occur as complex mixtures. Nuclear magnetic resonance (NMR) spectroscopy is a central analytical technique common to most areas of BSM research. In this Account, we highlight several different NMR approaches to mixture analysis that illustrate the commonalities between traditional natural products chemistry and metabolomics. The primary focus here is two-dimensional (2D) NMR; because of space limitations, we do not discuss several other important techniques, including hyphenated methods that combine NMR with mass spectrometry and chromatography. We first describe the simplest approach of analyzing 2D NMR spectra of unfractionated mixtures to

  20. 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

  1. 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.

  2. Use of diffusion-ordered NMR spectroscopy and HPLC-UV-SPE-NMR to identify undeclared synthetic drugs in medicines illegally sold as phytotherapies.

    PubMed

    Silva, Lorena M A; Filho, Elenilson G A; Thomasi, Sérgio S; Silva, Bianca F; Ferreira, Antonio G; Venâncio, Tiago

    2013-09-01

    The informal (and/or illegal) e-commerce of pharmaceutical formulations causes problems that governmental health agencies find hard to control, one of which concerns formulas sold as natural products. The purpose of this work was to explore the advantages and limitations of DOSY and HPLC-UV-SPE-NMR. These techniques were used to identify the components of a formula illegally marketed in Brazil as an herbal medicine possessing anti-inflammatory and analgesic properties. DOSY was able to detect the major components present at higher concentrations. Complete characterization was achieved using HPLC-UV-SPE-NMR, and 1D and 2D NMR analyses enabled the identification of known synthetic drugs. These were ranitidine and a mixture of orphenadrine citrate, piroxicam, and dexamethasone, which are co-formulated in a remedy called Rheumazim that is used to relieve severe pain, but it is prohibited in Brazil because of a lack of sufficient pharmacokinetic and pharmacodynamic information. PMID:23818305

  3. Use of diffusion-ordered NMR spectroscopy and HPLC-UV-SPE-NMR to identify undeclared synthetic drugs in medicines illegally sold as phytotherapies.

    PubMed

    Silva, Lorena M A; Filho, Elenilson G A; Thomasi, Sérgio S; Silva, Bianca F; Ferreira, Antonio G; Venâncio, Tiago

    2013-09-01

    The informal (and/or illegal) e-commerce of pharmaceutical formulations causes problems that governmental health agencies find hard to control, one of which concerns formulas sold as natural products. The purpose of this work was to explore the advantages and limitations of DOSY and HPLC-UV-SPE-NMR. These techniques were used to identify the components of a formula illegally marketed in Brazil as an herbal medicine possessing anti-inflammatory and analgesic properties. DOSY was able to detect the major components present at higher concentrations. Complete characterization was achieved using HPLC-UV-SPE-NMR, and 1D and 2D NMR analyses enabled the identification of known synthetic drugs. These were ranitidine and a mixture of orphenadrine citrate, piroxicam, and dexamethasone, which are co-formulated in a remedy called Rheumazim that is used to relieve severe pain, but it is prohibited in Brazil because of a lack of sufficient pharmacokinetic and pharmacodynamic information.

  4. 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

  5. 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.

  6. Advanced NMR characterization of zeolite catalysts

    NASA Astrophysics Data System (ADS)

    Welsh, L. B.

    1985-04-01

    The program discussed in this report is a two-year two-phase joint UOP-University of Illinois study of the application of improved high resolution solid state nuclear magnetic resonance (NMR) techniques to the characterization of zeolite catalysts. During the first phase of this program very pure, and in some cases isotopically enriched faujasites will be prepared and studied by magic angle sample spinning NMR (MASS NMR) and variable engine sample spinning NMR (VASS NMR) on 500 and 360 MHz (proton frequency) NMR spectrometers. The NMR techniques that will be emphasized are the measurement and analysis of the (17)O NMR properties, (27)Al NMR intensity quantitation, and (27)Al and (29)Si NMR relaxation rates. During the second phase of this program these NMR techniques will be used to study the effects of impurity concentration, dealumination treatments and cation exchange on the NMR properties of faujasites. The initial emphasis of this program during Phase I is on the preparation and measurement of the NMR properties of (17)O enriched Na-Y faujasties.

  7. 19F NMR study on the complex of fluorinated vitamin D derivatives with vitamin D receptor: elucidation of the conformation of vitamin D ligands accommodated in the receptor.

    PubMed

    Morizono, Daisuke

    2011-12-28

    Nuclear receptors mediate allosteric communications where ligand binding initiates a cascade of signal transduction. The interaction of vitamin D with vitamin D receptor (VDR) was investigated by (19)F NMR spectroscopy of the complexes of three fluorinated vitamin D derivatives with the full-length rat VDR-LBD. In the (19)F NMR spectra of the VDR-ligand complexes, the A-ring of 4,4-difluoro-1,25(OH)2D3 was revealed to adopt β-conformation in the VDR in solution, and the spectra were shown to be dependent on the dissociation constant. While the complex of 4,4-difluoro-1,25(OH)2D3 with VDR exhibited a clear distinguishable (19)F NMR spectrum, those of (19)F-1,25(OH)2D3 stereoisomers, which have 10-fold higher VDR affinity than 4,4-difluoro-1,25(OH)2D3, did not. The solid-phase NMR technique was useful for (19)F-1,25(OH)2D3 stereoisomers. The fluorinated vitamin D derivatives showed marked changes in the chemical shift (Δ4-19.7 ppm) upon VDR-complex formation, and the ab initio MO method suggested that van der Waals interactions play a major role in the complex formation.

  8. 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.

  9. Spectroscopic characterization of the 1-substituted 3,3-diphenyl-4-(2'-hydroxyphenyl)azetidin-2-ones: Application of 13C NMR, 1H- 13C COSY NMR and mass spectroscopy

    NASA Astrophysics Data System (ADS)

    Singh, Girija S.; Pheko, Tshepo

    2008-08-01

    The article deals with spectroscopic characterization of azetidin-2-ones. The presence of substituents like hydroxyl, fluoro, methoxy and benzhydryl, etc., on the azetidin-2-one ring significantly affects the IR absorption and 13C NMR frequencies of the carbonyl group present in these compounds. The presence of an ester carbonyl group or too many methine protons in the molecule has been observed to limit the scope of IR and 1H NMR spectroscopy in unambiguous assignment of the structure. The application of 13C NMR, 2D NMR ( 1H- 13C COSY) and mass spectroscopy in characterization of complex azetidin-2-ones is discussed. An application of the latter two techniques is described in deciding unequivocally between an azetidin-2-one ring and chroman-2-one ring structure for the product obtained by treatment of the 1-substituted 3,3-diphenyl-4-[2'-( O-diphenylacyl)hydroxyphenyl]-2-azetidinones with ethanolic sodium hydroxide at room temperature.

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

    PubMed

    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 T(2)-D domain. The decomposition is advantageous for better interpretation of the complex correlation maps as well as for the quantification of extracted T(2)-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 T(2)-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 x 10(-12) m(2) s(-1) and T(2)=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), T(2)=10 ms and D=3 x 10(-13) m(2) s(-1), T(2)=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

  11. 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

  12. Assessment of short and long-term effects of imidacloprid on the burrowing behaviour of two earthworm species (Aporrectodea caliginosa and Lumbricus terrestris) by using 2D and 3D post-exposure techniques.

    PubMed

    Dittbrenner, Nils; Moser, Isabelle; Triebskorn, Rita; Capowiez, Yvan

    2011-09-01

    Adverse effects of agrochemicals on earthworms' burrowing behaviour can have crucial impacts on the entire ecosystem. In the present study, we have therefore assessed short- and long-term effects on burrowing behaviour in the earthworm species Aporrectodea caliginosa and Lumbricus terrestris after exposure to a range of imidacloprid concentrations (0.2-4 mg kg(-1) dry weight (DW)) for different exposure times (1, 7, 14 d). 2D-terraria were used for the examination of post-exposure short-term effects (24-96 h), while post-exposure long-term effects were assessed by means of X-ray burrow reconstruction in three dimensional soil cores (6 weeks). For the latter each core was incubated with two specimens of L. terrestris and four of A. calignosa. Short-term effects on the burrowing behaviour (2D) of A. caliginosa were already detected at the lowest test concentration (0.2 mg kg(-1) DW), whereas such effects in L. terrestris were not observed until exposure to concentrations 10 times higher (2 mg kg(-1) DW). For both species tested in the 2D-terraria, "total burrow length after 24 h" and "maximal burrow depth after 24 h" were the most sensitive endpoints. 3D reconstructions of the burrow systems made by both earthworm species in the repacked soil cores revealed a significant linear decrease in burrow volume with increasing imidacloprid concentration. Since many of the observed effects occurred at imidacloprid concentrations relevant to natural conditions and since reduced activities of earthworms in soils can have crucial impacts on the ecosystem level, our results are of environmental concern. PMID:21632088

  13. Review of advances in coupling electrochemistry and liquid state NMR.

    PubMed

    Bussy, Ugo; Boujtita, Mohammed

    2015-05-01

    The coupling of electrochemistry and NMR spectroscopy (EC-NMR) may present an interesting approach in the environmental oxidative degradation or metabolism studies. This review presents experimental advances in the field of EC-NMR and highlights the main advantages and drawbacks of in situ and on line of NMR spectroelectrochemistry. The analysis of NMR spectra recorded in situ or on line EC-NMR permits to elucidate the reaction pathway of the electrochemical oxidation reactions and could constitute a fast way for monitoring unstable species as for instance quinone and quinone imine structures without using any coupling agents. The use of 1D and 2D NMR coupled with electrochemistry may leads to the elucidation of the major species produced from the electrochemical oxidation process. The present review gives an overview about the development of the electrochemical cells which can operate on line or in situ with NMR measurements. Future developments and potential applications of EC-NMR are also discussed.

  14. 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.

  15. Isolation and identification of two novel attractant compounds from Chinese cockroach (Eupolyphaga sinensis Walker) by combination of HSCCC, NMR and CD techniques.

    PubMed

    Jiang, Wei; Wu, Xiaodan; Wu, Bin

    2013-01-01

    High-speed counter-current chromatography (HSCCC) with a two-phase solvent system composed of n-hextane-ethyl acetate-methanol-water (1.5:1:1.5:1, v/v/v/v) was applied to the isolation and purification of attractants from Chinese cockroach, Eupolyphaga sinensis Walker. Two new attractants with attractant activity towards the male insects were obtained from the extract sample in a one-step separation. Their purities were determined by HPLC. Subsequent MS, NMR and CD analyses have led to the characterization of (R)-3-ethyl-6,8-dihydroxy-7-methyl-3,4-dihydroisochromen-1-one (1) and (R)-6,8-dihydroxy-3,7-dimethyl-3,4-dihydroisochromen-1-one (2), two novel isocumarin type attractants. Based on these results, it is concluded that HSCCC is a viable separation method option for purifying insect attractants, while effectively maintaining the attracting activity of the isolates. This is the first attempt to apply counter-current chromatography technique to separate attractants from Chinese cockroach.

  16. 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

  17. Xylocarpins A and B, two new mexicanolides from the seeds of a Chinese mangrove Xylocarpus granatum: NMR investigation in mixture.

    PubMed

    Li, Minyi; Wu, Jun; Zhang, Si; Xiao, Qiang; Li, Qingxin

    2007-08-01

    Xylocarpins A and B, two new mexicanolides with a tiglate group at C-3, have been identified in the mixture using NMR spectroscopy. Both compounds were isolated in the mixture from the seeds of a Chinese mangrove Xylocarpus granatum. The first complete assignments of 1H and 13C NMR data for these mexicanolides were achieved by means of 2D NMR techniques, including 1H-1H COSY, HSQC, HMBC and NOESY spectra. In order to separate xylocarpins A (1) and B (2) by chemical method, the mixture of two compounds was reduced with sodium borohydride in anhydrous methanol. However, the reduction led to the opening of the delta-lactone ring in xylocarpin B and afforded compound 3 as the main product. The complete NMR assignments of compound 3 were also achieved by means of the above 2D NMR techniques. Moreover, xylocarpin A was easily transformed into xylocarpin B during our normal liquid column chromatography. From this point of view, xylocarpin A was deemed to be the genuine natural product and xylocarpin B might be an artifact.

  18. Unparticle example in 2D.

    PubMed

    Georgi, Howard; Kats, Yevgeny

    2008-09-26

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

  19. Protein structure determination with paramagnetic solid-state NMR spectroscopy.

    PubMed

    Sengupta, Ishita; Nadaud, Philippe S; Jaroniec, Christopher P

    2013-09-17

    +)-tagged GB1 mutants to rapidly determine the global protein fold in a de novo fashion. Remarkably, these studies required quantitative measurements of only approximately four or five backbone amide (15)N longitudinal paramagnetic relaxation enhancements per residue, in the complete absence of the usual internuclear distance restraints. Importantly, this paramagnetic solid-state NMR methodology is general and can be directly applied to larger proteins and protein complexes for which a significant fraction of the signals can be assigned in standard 2D and 3D MAS NMR chemical shift correlation spectra.

  20. 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.

  1. The acquisition of multidimensional NMR spectra within a single scan

    PubMed Central

    Frydman, Lucio; Scherf, Tali; Lupulescu, Adonis

    2002-01-01

    A scheme enabling the complete sampling of multidimensional NMR domains within a single continuous acquisition is introduced and exemplified. Provided that an analyte's signal is sufficiently strong, the acquisition time of multidimensional NMR experiments can thus be shortened by orders of magnitude. This could enable the characterization of transient events such as proteins folding, 2D NMR experiments on samples being chromatographed, bring the duration of higher dimensional experiments (e.g., 4D NMR) into the lifetime of most proteins under physiological conditions, and facilitate the incorporation of spectroscopic 2D sequences into in vivo imaging investigations. The protocol is compatible with existing multidimensional pulse sequences and can be implemented by using conventional hardware; its performance is exemplified here with a variety of homonuclear 2D NMR acquisitions. PMID:12461169

  2. HAM2D: 2D Shearing Box Model

    NASA Astrophysics Data System (ADS)

    Gammie, Charles F.; Guan, Xiaoyue

    2012-10-01

    HAM solves non-relativistic hyperbolic partial differential equations in conservative form using high-resolution shock-capturing techniques. This version of HAM has been configured to solve the magnetohydrodynamic equations of motion in axisymmetry to evolve a shearing box model.

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

    PubMed

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

    2011-08-16

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

  5. The antibacterial activity of some sulfonamides and sulfonyl hydrazones, and 2D-QSAR study of a series of sulfonyl hydrazones

    NASA Astrophysics Data System (ADS)

    Aslan, H. Güzin; Özcan, Servet; Karacan, Nurcan

    2012-12-01

    Benzenesulfonicacid-1-methylhydrazide (1) and its four aromatic sulfonyl hydrazone derivatives (1a-1d), N-(3-amino-2-hydroxypropyl)benzene sulfonamide (2) and N-(2-hydroxyethyl)benzenesulfonamide (3) were synthesized and their structures were determined by IR, 1H NMR, 13C NMR, and LCMS techniques. Antibacterial activities of new synthesized compounds were evaluated against various bacteria strains by microdilution and disk diffusion methods. The experimental results show that presence of OH group on sulfonamides reduces the antimicrobial activity, and antimicrobial activities of the sulfonyl hydrazones (1a-1d) are smaller than that of the parent sulfonamide (1), except Candida albicans. In addition, 2D-QSAR analysis was performed on 28 aromatic sulfonyl hydrazones as antimicrobial agents against Escherichia coli and Staphylococcus aureus. In the QSAR models, the most important descriptor is total point-charge component of the molecular dipole for E. coli, and partial negative surface area (PNSA-1) for S. aureus.

  6. 'Brukin2D': a 2D visualization and comparison tool for LC-MS data

    PubMed Central

    Tsagkrasoulis, Dimosthenis; Zerefos, Panagiotis; Loudos, George; Vlahou, Antonia; Baumann, Marc; Kossida, Sophia

    2009-01-01

    Background Liquid Chromatography-Mass Spectrometry (LC-MS) is a commonly used technique to resolve complex protein mixtures. Visualization of large data sets produced from LC-MS, namely the chromatogram and the mass spectra that correspond to its compounds is the focus of this work. Results The in-house developed 'Brukin2D' software, built in Matlab 7.4, which is presented here, uses the compound data that are exported from the Bruker 'DataAnalysis' program, and depicts the mean mass spectra of all the chromatogram compounds from one LC-MS run, in one 2D contour/density plot. Two contour plots from different chromatograph runs can then be viewed in the same window and automatically compared, in order to find their similarities and differences. The results of the comparison can be examined through detailed mass quantification tables, while chromatogram compound statistics are also calculated during the procedure. Conclusion 'Brukin2D' provides a user-friendly platform for quick, easy and integrated view of complex LC-MS data. The software is available at . PMID:19534737

  7. Dynamic Nuclear Polarization (DNP) solid-state NMR spectroscopy, a new approach to study humic material?

    NASA Astrophysics Data System (ADS)

    Knicker, Heike; Lange, Sascha; van Rossum, Barth; Oschkinat, Hartmut

    2016-04-01

    Compared to solution NMR spectroscopy, solid-state NMR spectra suffer from broad resonance lines and low resolution. This could be overcome by the use of 2-dimenstional solid-state NMR pulse sequences. Until recently, this approach has been unfeasible as a routine tool in soil chemistry, mainly because of the low NMR sensitivity of the respective samples. A possibility to circumvent those sensitivity problems represents high-field Dynamic Nuclear Polarization (DNP) solid-state NMR spectroscopy (Barnes et al., 2008), allowing considerable signal enhancements (Akbey et al., 2010). This is achieved by a microwave-driven transfer of polarization from a paramagnetic center to nuclear spins. Application of DNP to MAS spectra of biological systems (frozen solutions) showed enhancements of the factor 40 to 50 (Hall et al., 1997). Enhancements of this magnitude, thus may enable the use of at least some of the 2D solid-state NMR techniques that are presently already applied for pure proteins but are difficult to apply to soil peptides in their complex matrix. After adjusting the required acquisition parameters to the system "soil organic matter", lower but still promising enhancement factors were achieved. Additional optimization was performed and allowed the acquisition of 2D 13C and 15N solid-state NMR spectra of humified 13C and 15N enriched plant residues. Within the present contribution, the first solid-state DNP NMR spectra of humic material are presented. Those data demonstrate the great potential of this approach which certainly opens new doors for a better understanding of biochemical processes in soils, sediments and water. Akbey, Ü., Franks, W.T., Linden, A., Lange, S., Griffin, R.G., van Rossum, B.-J., Oschkinat, H., 2010. Dynamic nuclear polarization of deuterated proteins. Angewandte Chemie International Edition 49, 7803-7806. Barnes, A.B., De Paëpe, G., van der Wel, P.C.A., Hu, K.N., Joo, C.G., Bajaj, V.S., Mak-Jurkauskas, M.L., Sirigiri, J.R., Herzfeld, J

  8. 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.

  9. 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…

  10. Solid-State NMR Characterization of Mixed Phosphonic Acid Ligand Binding and Organization on Silica Nanoparticles.

    PubMed

    Davidowski, Stephen K; Holland, Gregory P

    2016-04-01

    As ligand functionalization of nanomaterials becomes more complex, methods to characterize the organization of multiple ligands on surfaces is required. In an effort to further the understanding of ligand-surface interactions, a combination of multinuclear ((1)H, (29)Si, (31)P) and multidimensional solid-state nuclear magnetic resonance (NMR) techniques was utilized to characterize the phosphonic acid functionalization of fumed silica nanoparticles using methylphosphonic acid (MPA) and phenylphosphonic acid (PPA). (1)H → (29)Si cross-polarization (CP)-magic angle spinning (MAS) solid-state NMR was used to selectively detect silicon atoms near hydrogen atoms (primarily surface species); these results indicate that geminal silanols are preferentially depleted during the functionalization with phosphonic acids. (1)H → (31)P CP-MAS solid-state NMR measurements on the functionalized silica nanoparticles show three distinct resonances shifted upfield (lower ppm) and broadened compared to the resonances of the crystalline ligands. Quantitative (31)P MAS solid-state NMR measurements indicate that ligands favor a monodentate binding mode. When fumed silica nanoparticles were functionalized with an equal molar ratio of MPA and PPA, the MPA bound the nanoparticle surface preferentially. Cross-peaks apparent in the 2D (1)H exchange spectroscopy (EXSY) NMR measurements of the multiligand sample at short mixing times indicate that the MPA and PPA are spatially close (≤5 Å) on the surface of the nanostructure. Furthermore, (1)H-(1)H double quantum-single quantum (DQ-SQ) back-to-back (BABA) 2D NMR spectra further confirmed that MPA and PPA are strongly dipolar coupled with observation of DQ intermolecular contacts between the ligands. DQ experimental buildup curves and simulations indicate that the average distance between MPA and PPA is no further than 4.2 ± 0.2 Å. PMID:26914738

  11. Monitoring mechanistic details in the synthesis of pyrimidines via real-time, ultrafast multidimensional NMR spectroscopy

    PubMed Central

    Pardo, Zulay D.; Olsen, Greg; Fernández-Valle, María Encarnación; Frydman, Lucio; Martínez-Álvarez, Roberto; Herrera, Antonio

    2016-01-01

    Recent years have witnessed unprecedented advances in the development of fast multidimensional NMR acquisition techniques. This progress could open valuable new opportunities for the elucidation of chemical and biochemical processes. This study demonstrates one such capability, with the first real-time 2D dynamic analysis of a complex organic reaction relying on unlabeled substrates. Implementing such measurements required the development of new ultrafast 2D methods, capable of monitoring multiple spectral regions of interest as the reaction progressed. The alternate application of these acquisitions in an interleaved, excitation-optimized fashion, allowed us to extract new structural and dynamic insight concerning the reaction between aliphatic ketones and triflic anhydride in the presence of nitriles to yield alkylpyrimidines. Up to 2500 2D NMR data sets were thus collected over the course of this nearly 100 min long reaction, in an approach resembling that used in functional magnetic resonance imaging. With the aid of these new frequency-selective low-gradient-strength experiments, supplemented by chemical shift calculations of the spectral coordinates observed in the 2D heteronuclear correlations, previously postulated intermediates involved in the alkylpyrimidine formation process could be confirmed, and hitherto undetected ones were revealed. The potential and limitations of the resulting methods are discussed. PMID:22283498

  12. Identification of major and minor constituents of Harpagophytum procumbens (Devil's claw) using HPLC-SPE-NMR and HPLC-ESIMS/APCIMS.

    PubMed

    Clarkson, Cailean; Staerk, Dan; Hansen, Steen Honoré; Smith, Peter J; Jaroszewski, Jerzy W

    2006-09-01

    The HPLC-SPE-NMR technique, supported by HPLC-MS measurements, was used to determine structures of major as well as some minor constituents of ethanol and petroleum ether extracts of Harpagophytum procumbens (Devil's claw) roots. This method was also shown to be applicable for rapid and precise on-line identification of secondary metabolites present in commercial herbal products of H. procumbens. A total of 15 compounds (1-14 and 17) were identified from the ethanol and petroleum ether extracts, including a novel Diels-Alder dimer 14. Optimization of the HPLC-SPE-NMR experiments included quantitative (1)H NMR measurements, determination of trapping and elution efficiency, effect of multiple trapping of analytes, use of various deuterated solvents for SPE cartridge elution, and effect of post-column dilution ratio of eluent with water. Linear accumulation of apolar and relatively polar analytes was demonstrated for at least 8-10 repeated trappings, resulting in greatly improved signal-to-noise ratios in NMR spectra and reduced acquisition times. Thus, the HPLC-SPE-NMR technique provides an efficient means of identification of multiple components of crude extracts. By allowing on-line generation of high-quality 2D NMR data without traditional purification of extract components, the HPLC-SPE-NMR methodology represents a paradigm shift in natural products research with respect to structure elucidation. PMID:16989520

  13. NMR studies of isotopically labeled RNA

    SciTech Connect

    Pardi, A.

    1994-12-01

    In summary, the ability to generate NMR quantities of {sup 15}N and {sup 13}C-labeled RNAs has led to the development of heteronuclear multi-dimensional NMR techniques for simplifying the resonance assignment and structure determination of RNAs. These methods for synthesizing isotopically labeled RNAs are only several years old, and thus there are still relatively few applications of heteronuclear multi-dimensional NMR techniques to RNA. However, given the critical role that RNAs play in cellular function, one can expect to see an increasing number of NMR structural studies of biologically active RNAs.

  14. 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

  15. HCN, A Triple-Resonance NMR Technique for Selective Observation of Histidine and Tryptophan Side Chains in 13C/ 15N-Labeled Proteins

    NASA Astrophysics Data System (ADS)

    Sudmeier, James L.; Ash, Elissa L.; Günther, Ulrich L.; Luo, Xuelian; Bullock, Peter A.; Bachovchin, William W.

    1996-12-01

    HCN, a new 3D NMR technique for stepwise coherence transfer from1H to13C to15N and reverse through direct spin couplings1JCHand1JCN, is presented as a method for detection and assignment of histidine and tryptophan side-chain1H,13C, and15N resonances in uniformly13C/15N-labeled proteins. Product-operator calculations of cross-peak volumes vs adjustable delay τ3were employed for determination of optimal τ3. For the phosphatidylinositol 3-kinase (PI3K SH3 domain, MW = 9.6 kD) at pH 6, H(C)N, the1H/15N projection, produced observable cross peaks within 20 min. and was completely selective for the single tryptophan and single histidine. The 3D HCN experiment yielded well-defined cross peaks in 20 h for the13C/15N-labeled origin-specific DNA binding domain from simian virus 40 T-antigen (T-ag-OBD131-259, MW = 15.4 kD) at pH 5.5. Resonances from all six histidines in T-ag-OBD were observed, and 11 of the 121H and13C chemical shifts and 10 of the 1215N chemical shifts were determined. The13C dimension proved essential in assignment of the multiply overlapping1H and15N resonances. From the spectra recorded at a single pH, three of the imidazoles were essentially neutral and the other three were partially protonated (22-37%). HCN yielded strong cross peaks after 18 h on a 2.0 mMsample of phenylmethanesulfonyl fluoride (PMSF)-inhibited α-lytic protease (MW = 19.8 kD) at pH 4.4. No spectra have been obtained, however, of native or boronic acid-inhibited α-lytic protease after 18 h at various temperatures ranging from 5 to 55°C, probably due to efficient relaxation of active-site imidazole1H and/or15N nuclei.

  16. Live cell NMR.

    PubMed

    Freedberg, Darón I; Selenko, Philipp

    2014-01-01

    Ever since scientists realized that cells are the basic building blocks of all life, they have been developing tools to look inside them to reveal the architectures and mechanisms that define their biological functions. Whereas "looking into cells" is typically said in reference to optical microscopy, high-resolution in-cell and on-cell nuclear magnetic resonance (NMR) spectroscopy is a powerful method that offers exciting new possibilities for structural and functional studies in and on live cells. In contrast to conventional imaging techniques, in- and on-cell NMR methods do not provide spatial information on cellular biomolecules. Instead, they enable atomic-resolution insights into the native cell states of proteins, nucleic acids, glycans, and lipids. Here we review recent advances and developments in both fields and discuss emerging concepts that have been delineated with these methods.

  17. 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

  18. Structure analysis and spectroscopic characterization of 2-Fluoro-3-Methylpyridine-5-Boronic Acid with experimental (FT-IR, Raman, NMR and XRD) techniques and quantum chemical calculations

    NASA Astrophysics Data System (ADS)

    Alver, Özgür; Dikmen, Gökhan

    2016-03-01

    Possible stable conformers, geometrical molecular structures, vibrational properties as well as band assignments, nuclear magnetic shielding tensors of 2-Fluoro-3-Methylpyridine-5-Boronic Acid (2F3MP5BA) were studied experimentally and theoretically using FT-IR, Raman, (CP/MAS) NMR and XRD spectroscopic methods. FT-IR and Raman spectra were evaluated in the region of 3500-400 cm-1, and 3200-400 cm-1, respectively. The optimized geometric structures, vibrational wavenumbers and nuclear magnetic shielding tensors were examined using Becke-3-Lee-Yang-Parr (B3LYP) hybrid density functional theory method with 6-311++G(d, p) basis set. 1H, 13C NMR chemical shifts were calculated using the gauge invariant atomic orbital (GIAO) method. 1H, 13C, APT and HETCOR NMR experiments of title molecule were carried out in DMSO solution. 13C CP/MAS NMR measurement was done with 4 mm zirconium rotor and glycine was used as an external standard. Single crystal of 2F3MP5BA was also prepared for XRD measurements. Assignments of vibrational wavenumbers were also strengthened by calculating the total energy distribution (TED) values using scaled quantum mechanical (SQM) method.

  19. Synthesis and solid-state NMR characterization of cubic mesoporous silica SBA-1 functionalized with sulfonic acid groups.

    PubMed

    Tsai, Hui-Hsu Gavin; Chiu, Po-Jui; Jheng, Guang-Liang; Ting, Chun-Chiang; Pan, Yu-Chi; Kao, Hsien-Ming

    2011-07-01

    Well-ordered cubic mesoporous silicas SBA-1 functionalized with sulfonic acid groups have been synthesized through in situ oxidation of mercaptopropyl groups with H(2)O(2) via co-condensation of tetraethoxysilane (TEOS) and 3-mercaptopropyltrimethoxysilane (MPTMS) templated by cetyltriethylammonium bromide (CTEABr) under strong acidic conditions. Various synthesis parameters such as the amounts of H(2)O(2) and MPTMS on the structural ordering of the resultant materials were systematically investigated. The materials thus obtained were characterized by a variety of techniques including powder X-ray diffraction (XRD), multinuclear solid-state Nuclear Magnetic Resonance (NMR) spectroscopy, (29)Si{(1)H} 2D HETCOR (heteronuclear correlation) NMR spectroscopy, thermogravimetric analysis (TGA), and nitrogen sorption measurements. By using (13)C CPMAS NMR technique, the status of the incorporated thiol groups and their transformation to sulfonic acid groups can be monitored and, as an extension, to define the optimum conditions to be used for the oxidation reaction to be quantitative. In particular, (29)Si{(1)H} 2D HETCOR NMR revealed that the protons in sulfonic acid groups are in close proximity to the silanol Q(3) species, but not close enough to form a hydrogen bond.

  20. 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

  1. 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

  2. Imaging in 2D media

    NASA Astrophysics Data System (ADS)

    Medvedev, S. N.

    2015-10-01

    Stacking by CDP technique is inapplicable for processing of data from bottom seismic stations or acoustic sonobuoys. In addition, big amount of unknown velocity and structural parameters of the real layered medium do not allow these parameters to be defined by standard processing methods. Local sloped stacking is proposed for simultaneous obtaining the stacked tracks, travel time curve of a chosen wave, and the first derivative of this travel time curve. The additionally defined parameters are second derivative of this travel time curve and integrated average of squared travel time curve. These data are sufficient to reduce the amount of unknown parameters (down to one-two for each boundary) when layer-by-layer top-to-bottom processing. As a result, the stable estimates of velocity parameters of the layered (isotropic or anisotropic) medium can be obtained and stacked tracks obtained by local sloped staking can be transformed into boundaries in the time and depth sections.

  3. 2-D and 3-D Visualization of the Freshwater/Saltwater Mixing Front, and Zones of Preferential Groundwater Flow in the Karst Biscayne Coastal Aquifer using Electromagnetic Induction Techniques, Miami, Southeastern Florida.

    NASA Astrophysics Data System (ADS)

    Stalker, J. C.; Glaccum, R.

    2005-05-01

    The Biscayne aquifer is unconfined, composed primarily of Karst limestone, and underlies all of Miami-Dade County and much of Biscayne Bay in southeastern Florida. It is the sole source of drinking water for the 3 million inhabitants of the city of Miami and Miami-Dade County, as well as portions of Broward and Monroe Counties. Saltwater intrusion is a prominent problem for all coastal aquifers including the Biscayne aquifer. Simple and quick detection of the three-dimensional saltwater/freshwater interface has been problematic without the use of extensive sounding surveys or multiple well sampling. We are developing a technique combining rapid EM-31 surface surveys with EM-31 vertical soundings to model the depth to the saltwater/freshwater front at two sites located within a half mile of Biscayne Bay. The EM-31 has a maximum signal penetration of about 25ft allowing for accurate near shore surveys. Depths to the saltwater have ranged from over 25 ft inland to less than 2-3 ft near the Bay and saltwater mangroves. Changes in conductivity along survey lines of equal elevation that are equidistant from the Bay may indicate zones of preferential flow due to conduit networks or the presence of backfill, both of which exacerbate saltwater intrusion. All surveys show a rapid change from fresh to brackish water as you move toward the Bay indicating a shallow and abrupt mixing zone. Using a simple depth-modeling program, a wire frame contour map of the mixing zone can be constructed. This technique has proven to be a quick, inexpensive method for first-order hydrogeological and spatial analysis of the saltwater/freshwater interface. In an allied study we are using down-hole electromagnetic induction techniques with an EM-39 tool on existing wells, analyzing fluctuations in conductivity within the saltwater zone to look for zones of high permeability in the aquifer. Conductivity fluctuates within the mixing zone from brackish values to values equivalent to Biscayne Bay

  4. 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.

  5. Characterization and quantification of N-(3-aminopropyl)-N-dodecyl-1,3-propanediamine biocide by NMR, HPLC/MS and titration techniques.

    PubMed

    Mondin, Andrea; Bogialli, Sara; Venzo, Alfonso; Favaro, Gabriella; Badocco, Denis; Pastore, Paolo

    2014-01-01

    The present paper reports the determination of the tri-amine N-(3-aminopropyl)-N-dodecyl-1,3-propanediamine (TA) present in a raw material called LONZABAC used to formulate various, widely used commercial biocides. The active principle, TA, is present in LONZABAC together with other molecules at lower concentration levels. Three independent analytical approaches, namely solution NMR spectroscopy, liquid chromatography coupled to high resolution mass spectrometry (LC/HRMS) and acid-base titration in mixed solvent, were used to overcome the problem of the non-availability of the active principle as high purity standard. NMR analysis of raw material, using a suitable internal standard, evidenced in all analyzed lots the presence of the active principle, the N-dodecyl-1,3-propanediamine (DA) and the n-dodecylamine (MA) and the absence of non-organic, NMR-inactive species. NMR peak integration led to a rough composition of the MA:DA:TA as 1:9:90. The LC/HRMS analysis allowed the accurate determination of DA and MA and confirmed in all samples the presence of the TA, which was estimated by difference: MA=1.4±0.3%, DA=11.1±0.7%, TA=87.5±1.3%. The obtained results were used to setup an easy, rapid and cheap acid-base titration method able to furnish a sufficiently accurate evaluation of the active principle both in the raw material and in diluted commercial products. For the raw material the results were: TA+MA=91.1±0.8% and DA-MA=8.9±0.8%, statistically coherent with LC/MS ones. The LC/MS approach demonstrated also its great potentialities to recognize trace of the biocide components both in environmental samples and in the formulated commercial products.

  6. Finite temperature corrections in 2d integrable models

    NASA Astrophysics Data System (ADS)

    Caselle, M.; Hasenbusch, M.

    2002-09-01

    We study the finite size corrections for the magnetization and the internal energy of the 2d Ising model in a magnetic field by using transfer matrix techniques. We compare these corrections with the functional form recently proposed by Delfino and LeClair-Mussardo for the finite temperature behaviour of one-point functions in integrable 2d quantum field theories. We find a perfect agreement between theoretical expectations and numerical results. Assuming the proposed functional form as an input in our analysis we obtain a relevant improvement in the precision of the continuum limit estimates of both quantities.

  7. NMR study of magnetism and superparamagnetism

    NASA Astrophysics Data System (ADS)

    Yuan, Shaojie

    The research described in this dissertation is concerned with two different types of magnetic materials. Both types of systems involve competing interactions between transition metal ions. New approaches involving magnetic resonance in the large hyperfine fields at nuclear sites have been developed. The interactions responsible for the properties that have been investigated in the materials studied are geometric frustration in an insulator and ferromagnetic and antiferromagnetic interactions in a metal alloy. Further details are given below. The extended kagome frustrated system YBaCo4O7 has 2D kagome and triangular lattices of Co ions stacked along the c-axis. Antiferromagnetic (AF) ordering accompanied by a structural transition has been reported in the literature. From a zero field (ZF) NMR single crystal rotation experiment, we have obtained the Co spin configurations for both the kagome and triangular layers. A 'spin-flop' configuration between the spins on the kagome layer and the spins on the triangular layer is indicated by our results. Our NMR findings are compared with neutron scattering results for this intriguing frustrated AF spin system. The non-stoichiometric oxygenated sister compound YBaCo4O7.1 has application potential for oxygen storage. While, its' magnetic properties are quite different from those of the stoichiometric compound, in spite of their similar structures of alternating kagome and triangular Co layers. Various techniques, including ZF NMR have been used to investigate the spin dynamics and spin configuration in a single crystal of YBaCo4O7.1. A magnetic transition at 80 K is observed, which is interpreted as the freezing out of spins in the triangular layers. At low temperatures (below 50 K), the spin dynamics persists and a fraction of spins in the kagome layers form a viscous spin liquid. Below 10 K, a glass-like spin structure forms and a large distribution of spin correlation times are suggested by nuclear spin lattice relaxation

  8. 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.

  9. Simplification of the 1H NMR spectra of enantiomers dissolved in chiral liquid crystals, combining variable angle sample spinning and selective refocusing experiments.

    PubMed

    Beguin, Laetitia; Courtieu, Jacques; Ziani, Latifa; Merlet, Denis

    2006-12-01

    This work presents a technique to simplify overcrowded proton spectra in chiral liquid crystal solvents using rotation of the sample near the magic angle, VASS, combined with homonuclear selective refocusing 2D NMR experiments, SERF. This methodology provides a powerful tool to visualise enantiomers out of unresolved proton spectra. A modified SERF sequence is presented where the resulting 2D spectrum can be phased to increase the resolution. Accurate enantiomeric excesses are determined that are not possible to measure on static samples. Two examples are presented.

  10. High-resolution NMR characterization of low abundance oligomers of amyloid-β without purification

    NASA Astrophysics Data System (ADS)

    Kotler, Samuel A.; Brender, Jeffrey R.; Vivekanandan, Subramanian; Suzuki, Yuta; Yamamoto, Kazutoshi; Monette, Martine; Krishnamoorthy, Janarthanan; Walsh, Patrick; Cauble, Meagan; Holl, Mark M. Banaszak; Marsh, E. Neil. G.; Ramamoorthy, Ayyalusamy

    2015-07-01

    Alzheimer’s disease is characterized by the misfolding and self-assembly of the amyloidogenic protein amyloid-β (Aβ). The aggregation of Aβ leads to diverse oligomeric states, each of which may be potential targets for intervention. Obtaining insight into Aβ oligomers at the atomic level has been a major challenge to most techniques. Here, we use magic angle spinning recoupling 1H-1H NMR experiments to overcome many of these limitations. Using 1H-1H dipolar couplings as a NMR spectral filter to remove both high and low molecular weight species, we provide atomic-level characterization of a non-fibrillar aggregation product of the Aβ1-40 peptide using non-frozen samples without isotopic labeling. Importantly, this spectral filter allows the detection of the specific oligomer signal without a separate purification procedure. In comparison to other solid-state NMR techniques, the experiment is extraordinarily selective and sensitive. A resolved 2D spectra could be acquired of a small population of oligomers (6 micrograms, 7% of the total) amongst a much larger population of monomers and fibers (93% of the total). By coupling real-time 1H-1H NMR experiments with other biophysical measurements, we show that a stable, primarily disordered Aβ1-40 oligomer 5-15 nm in diameter can form and coexist in parallel with the well-known cross-β-sheet fibrils.

  11. High-resolution NMR characterization of low abundance oligomers of amyloid-β without purification

    PubMed Central

    Kotler, Samuel A.; Brender, Jeffrey R.; Vivekanandan, Subramanian; Suzuki, Yuta; Yamamoto, Kazutoshi; Monette, Martine; Krishnamoorthy, Janarthanan; Walsh, Patrick; Cauble, Meagan; Holl, Mark M. Banaszak; Marsh, E. Neil. G.; Ramamoorthy, Ayyalusamy

    2015-01-01

    Alzheimer’s disease is characterized by the misfolding and self-assembly of the amyloidogenic protein amyloid-β (Aβ). The aggregation of Aβ leads to diverse oligomeric states, each of which may be potential targets for intervention. Obtaining insight into Aβ oligomers at the atomic level has been a major challenge to most techniques. Here, we use magic angle spinning recoupling 1H-1H NMR experiments to overcome many of these limitations. Using 1H-1H dipolar couplings as a NMR spectral filter to remove both high and low molecular weight species, we provide atomic-level characterization of a non-fibrillar aggregation product of the Aβ1-40 peptide using non-frozen samples without isotopic labeling. Importantly, this spectral filter allows the detection of the specific oligomer signal without a separate purification procedure. In comparison to other solid-state NMR techniques, the experiment is extraordinarily selective and sensitive. A resolved 2D spectra could be acquired of a small population of oligomers (6 micrograms, 7% of the total) amongst a much larger population of monomers and fibers (93% of the total). By coupling real-time 1H-1H NMR experiments with other biophysical measurements, we show that a stable, primarily disordered Aβ1-40 oligomer 5–15 nm in diameter can form and coexist in parallel with the well-known cross-β-sheet fibrils. PMID:26138908

  12. High-resolution NMR characterization of low abundance oligomers of amyloid-β without purification.

    PubMed

    Kotler, Samuel A; Brender, Jeffrey R; Vivekanandan, Subramanian; Suzuki, Yuta; Yamamoto, Kazutoshi; Monette, Martine; Krishnamoorthy, Janarthanan; Walsh, Patrick; Cauble, Meagan; Holl, Mark M Banaszak; Marsh, E Neil G; Ramamoorthy, Ayyalusamy

    2015-07-03

    Alzheimer's disease is characterized by the misfolding and self-assembly of the amyloidogenic protein amyloid-β (Aβ). The aggregation of Aβ leads to diverse oligomeric states, each of which may be potential targets for intervention. Obtaining insight into Aβ oligomers at the atomic level has been a major challenge to most techniques. Here, we use magic angle spinning recoupling (1)H-(1)H NMR experiments to overcome many of these limitations. Using (1)H-(1)H dipolar couplings as a NMR spectral filter to remove both high and low molecular weight species, we provide atomic-level characterization of a non-fibrillar aggregation product of the Aβ1-40 peptide using non-frozen samples without isotopic labeling. Importantly, this spectral filter allows the detection of the specific oligomer signal without a separate purification procedure. In comparison to other solid-state NMR techniques, the experiment is extraordinarily selective and sensitive. A resolved 2D spectra could be acquired of a small population of oligomers (6 micrograms, 7% of the total) amongst a much larger population of monomers and fibers (93% of the total). By coupling real-time (1)H-(1)H NMR experiments with other biophysical measurements, we show that a stable, primarily disordered Aβ1-40 oligomer 5-15 nm in diameter can form and coexist in parallel with the well-known cross-β-sheet fibrils.

  13. Ultrafast 2D-IR spectroelectrochemistry of flavin mononucleotide

    NASA Astrophysics Data System (ADS)

    El Khoury, Youssef; Van Wilderen, Luuk J. G. W.; Bredenbeck, Jens

    2015-06-01

    We demonstrate the coupling of ultrafast two-dimensional infrared (2D-IR) spectroscopy to electrochemistry in solution and apply it to flavin mononucleotide, an important cofactor of redox proteins. For this purpose, we designed a spectroelectrochemical cell optimized for 2D-IR measurements in reflection and measured the time-dependent 2D-IR spectra of the oxidized and reduced forms of flavin mononucleotide. The data show anharmonic coupling and vibrational energy transfer between different vibrational modes in the two redox species. Such information is inaccessible with redox-controlled steady-state FTIR spectroscopy. The wide range of applications offered by 2D-IR spectroscopy, such as sub-picosecond structure determination, IR band assignment via energy transfer, disentangling reaction mixtures through band connectivity in the 2D spectra, and the measurement of solvation dynamics and chemical exchange can now be explored under controlled redox potential. The development of this technique furthermore opens new horizons for studying the dynamics of redox proteins.

  14. Ultrafast 2D-IR spectroelectrochemistry of flavin mononucleotide.

    PubMed

    El Khoury, Youssef; Van Wilderen, Luuk J G W; Bredenbeck, Jens

    2015-06-01

    We demonstrate the coupling of ultrafast two-dimensional infrared (2D-IR) spectroscopy to electrochemistry in solution and apply it to flavin mononucleotide, an important cofactor of redox proteins. For this purpose, we designed a spectroelectrochemical cell optimized for 2D-IR measurements in reflection and measured the time-dependent 2D-IR spectra of the oxidized and reduced forms of flavin mononucleotide. The data show anharmonic coupling and vibrational energy transfer between different vibrational modes in the two redox species. Such information is inaccessible with redox-controlled steady-state FTIR spectroscopy. The wide range of applications offered by 2D-IR spectroscopy, such as sub-picosecond structure determination, IR band assignment via energy transfer, disentangling reaction mixtures through band connectivity in the 2D spectra, and the measurement of solvation dynamics and chemical exchange can now be explored under controlled redox potential. The development of this technique furthermore opens new horizons for studying the dynamics of redox proteins.

  15. 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.

  16. 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.

  17. 2D materials: to graphene and beyond.

    PubMed

    Mas-Ballesté, Rubén; Gómez-Navarro, Cristina; Gómez-Herrero, Julio; Zamora, Félix

    2011-01-01

    This review is an attempt to illustrate the different alternatives in the field of 2D materials. Graphene seems to be just the tip of the iceberg and we show how the discovery of alternative 2D materials is starting to show the rest of this iceberg. The review comprises the current state-of-the-art of the vast literature in concepts and methods already known for isolation and characterization of graphene, and rationalizes the quite disperse literature in other 2D materials such as metal oxides, hydroxides and chalcogenides, and metal-organic frameworks.

  18. Proteomic Profiling of Macrophages by 2D Electrophoresis

    PubMed Central

    Bouvet, Marion; Turkieh, Annie; Acosta-Martin, Adelina E.; Chwastyniak, Maggy; Beseme, Olivia; Amouyel, Philippe; Pinet, Florence

    2014-01-01

    The goal of the two-dimensional (2D) electrophoresis protocol described here is to show how to analyse the phenotype of human cultured macrophages. The key role of macrophages has been shown in various pathological disorders such as inflammatory, immunological, and infectious diseases. In this protocol, we use primary cultures of human monocyte-derived macrophages that can be differentiated into the M1 (pro-inflammatory) or the M2 (anti-inflammatory) phenotype. This in vitro model is reliable for studying the biological activities of M1 and M2 macrophages and also for a proteomic approach. Proteomic techniques are useful for comparing the phenotype and behaviour of M1 and M2 macrophages during host pathogenicity. 2D gel electrophoresis is a powerful proteomic technique for mapping large numbers of proteins or polypeptides simultaneously. We describe the protocol of 2D electrophoresis using fluorescent dyes, named 2D Differential Gel Electrophoresis (DIGE). The M1 and M2 macrophages proteins are labelled with cyanine dyes before separation by isoelectric focusing, according to their isoelectric point in the first dimension, and their molecular mass, in the second dimension. Separated protein or polypeptidic spots are then used to detect differences in protein or polypeptide expression levels. The proteomic approaches described here allows the investigation of the macrophage protein changes associated with various disorders like host pathogenicity or microbial toxins. PMID:25408153

  19. Enhanced detectability of small objects in correlated clutter using an improved 2-D adaptive lattice algorithm.

    PubMed

    Ffrench, P A; Zeidler, J H; Ku, W H

    1997-01-01

    Two-dimensional (2-D) adaptive filtering is a technique that can be applied to many image processing applications. This paper will focus on the development of an improved 2-D adaptive lattice algorithm (2-D AL) and its application to the removal of correlated clutter to enhance the detectability of small objects in images. The two improvements proposed here are increased flexibility in the calculation of the reflection coefficients and a 2-D method to update the correlations used in the 2-D AL algorithm. The 2-D AL algorithm is shown to predict correlated clutter in image data and the resulting filter is compared with an ideal Wiener-Hopf filter. The results of the clutter removal will be compared to previously published ones for a 2-D least mean square (LMS) algorithm. 2-D AL is better able to predict spatially varying clutter than the 2-D LMS algorithm, since it converges faster to new image properties. Examples of these improvements are shown for a spatially varying 2-D sinusoid in white noise and simulated clouds. The 2-D LMS and 2-D AL algorithms are also shown to enhance a mammogram image for the detection of small microcalcifications and stellate lesions.

  20. Automatic MRI 2D brain segmentation using graph searching technique.

    PubMed

    Pedoia, Valentina; Binaghi, Elisabetta

    2013-09-01

    Accurate and efficient segmentation of the whole brain in magnetic resonance (MR) images is a key task in many neuroscience and medical studies either because the whole brain is the final anatomical structure of interest or because the automatic extraction facilitates further analysis. The problem of segmenting brain MRI images has been extensively addressed by many researchers. Despite the relevant achievements obtained, automated segmentation of brain MRI imagery is still a challenging problem whose solution has to cope with critical aspects such as anatomical variability and pathological deformation. In the present paper, we describe and experimentally evaluate a method for segmenting brain from MRI images basing on two-dimensional graph searching principles for border detection. The segmentation of the whole brain over the entire volume is accomplished slice by slice, automatically detecting frames including eyes. The method is fully automatic and easily reproducible by computing the internal main parameters directly from the image data. The segmentation procedure is conceived as a tool of general applicability, although design requirements are especially commensurate with the accuracy required in clinical tasks such as surgical planning and post-surgical assessment. Several experiments were performed to assess the performance of the algorithm on a varied set of MRI images obtaining good results in terms of accuracy and stability. PMID:23757180

  1. New class of aggregates in aqueous solution: an NMR, thermodynamic, and dynamic light scattering study.

    PubMed

    Sanna, Cecilia; La Mesa, Camillo; Mannina, Luisa; Stano, Pasquale; Viel, Stéphane; Segre, Annalaura

    2006-07-01

    We investigated the aggregation properties of two classes of aromatic and hydrophobic compounds, namely chloroacetamides and ethyl 3-phenyl-2-nitropropionates, in moderately concentrated aqueous solution (millimolar range). The identification of all species present in solution under specific experimental conditions was performed by 1D and 2D NMR, pulsed gradient spin-echo NMR, and dynamic light scattering techniques. Some physical-chemical properties (viscosity, surface tension, and colligative properties) of the aqueous solutions were also determined. Both classes of compounds behave quite similarly: in solution, three distinct species, namely a monomeric species, small and mobile aggregates, and large and stiff aggregates, are observed. The results give insight into a new class of aggregates, held together by pi-pi interactions, which show an unusual associative behavior in water.

  2. 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

  3. 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.

  4. 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.

  5. 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.

  6. 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

  7. 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.

  8. 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

  9. 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

  10. Glitter in a 2D monolayer.

    PubMed

    Yang, Li-Ming; Dornfeld, Matthew; Frauenheim, Thomas; Ganz, Eric

    2015-10-21

    We predict a highly stable and robust atomically thin gold monolayer with a hexagonal close packed lattice stabilized by metallic bonding with contributions from strong relativistic effects and aurophilic interactions. We have shown that the framework of the Au monolayer can survive 10 ps MD annealing simulations up to 1400 K. The framework is also able to survive large motions out of the plane. Due to the smaller number of bonds per atom in the 2D layer compared to the 3D bulk we observe significantly enhanced energy per bond (0.94 vs. 0.52 eV per bond). This is similar to the increase in bond strength going from 3D diamond to 2D graphene. It is a non-magnetic metal, and was found to be the global minima in the 2D space. Phonon dispersion calculations demonstrate high kinetic stability with no negative modes. This 2D gold monolayer corresponds to the top monolayer of the bulk Au(111) face-centered cubic lattice. The close-packed lattice maximizes the aurophilic interactions. We find that the electrons are completely delocalized in the plane and behave as 2D nearly free electron gas. We hope that the present work can inspire the experimental fabrication of novel free standing 2D metal systems.

  11. 2d index and surface operators

    NASA Astrophysics Data System (ADS)

    Gadde, Abhijit; Gukov, Sergei

    2014-03-01

    In this paper we compute the superconformal index of 2d (2, 2) supersymmetric gauge theories. The 2d superconformal index, a.k.a. flavored elliptic genus, is computed by a unitary matrix integral much like the matrix integral that computes the 4d superconformal index. We compute the 2d index explicitly for a number of examples. In the case of abelian gauge theories we see that the index is invariant under flop transition and under CY-LG correspondence. The index also provides a powerful check of the Seiberg-type duality for non-abelian gauge theories discovered by Hori and Tong. In the later half of the paper, we study half-BPS surface operators in = 2 super-conformal gauge theories. They are engineered by coupling the 2d (2, 2) supersymmetric gauge theory living on the support of the surface operator to the 4d = 2 theory, so that different realizations of the same surface operator with a given Levi type are related by a 2d analogue of the Seiberg duality. The index of this coupled system is computed by using the tools developed in the first half of the paper. The superconformal index in the presence of surface defect is expected to be invariant under generalized S-duality. We demonstrate that it is indeed the case. In doing so the Seiberg-type duality of the 2d theory plays an important role.

  12. NMR Studies of Protein Structure and Dynamics

    NASA Astrophysics Data System (ADS)

    Li, Xiang

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

  13. 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

  14. Application of Spectroscopic Techniques (FT-IR, 13C NMR) to the analysis of humic substances in volcanic soils along an environmental gradient (Tenerife, Canary Islands, Spain)

    NASA Astrophysics Data System (ADS)

    Rodriguez Rodriguez, Antonio; María Armas Herrera, Cecilia; González Pérez, José Antonio; González-Vila, Francisco Javier; Arbelo Rodríguez, Carmen Dolores; Mora Hernández, Juan Luis; Polvillo Polo, Oliva

    2010-05-01

    Andosols and andic soils are considered as efficient C-sinks in terms of C sequestration. These soils are usually developed from volcanic materials, and are characterized by a predominance of short-range ordered minerals like allophanes, imogolite and other Fe and Al oxyhydroxides. Such materials occur commonly associated with organic compounds, thus generating highly stable organo-mineral complexes and leading to the accumulation of a high amount of organic carbon. Spectroscopic methods like FT-IR and 13C NMR are suitable for the analysis of the chemical structure of soil humic substances, and allow identifying distinct functional groups and protein, lipids, lignin, carbohydrate-derived fragments. In this work we study the structural features of four soils developed on Pleistocene basaltic lavae in Tenerife (Canary Island, Spain), distributed along an altitudinal climatic gradient. The soil sequence comprises soils with different degree of geochemical evolution and andic character, including a mineral ‘Hypersalic Solonchak' (Tabaibal de Rasca), a slightly vitric ‘Luvic Phaeozem' (Los Frailes), a degraded and shallow ‘Endoleptic, fulvic, silandic Andosol' (Siete Lomas), and a well-developed and deep ‘Fulvic, silandic, Andosol' (Ravelo). Samples of the raw soil and humic and fulvic acids isolated from the surface horizons were analyzed. The results show a low content of organic carbon in the mineral soil, the inherited humin predominating, and a very high content of humic and fulvic acids in Andosols. The FT-IR and 13C NMR spectra of the raw soil samples show a low resolution, related to interferences from mineral complexes signals, particularly in soils with lower organic carbon content. 13C NMR shows a predominance of O-alkyl carbon (derived of carbohydrates) in andic soils, whereas O-alkyl and aromatic fractions are most evident in the mineral soil. The humic acids spectra are characterized by a dominance of alkyl and aromatic fractions with a high degree

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

    PubMed Central

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

    2011-01-01

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

  16. Modeling chemical interaction profiles: I. Spectral data-activity relationship and structure-activity relationship models for inhibitors and non-inhibitors of cytochrome P450 CYP3A4 and CYP2D6 isozymes.

    PubMed

    McPhail, Brooks; Tie, Yunfeng; Hong, Huixiao; Pearce, Bruce A; Schnackenberg, Laura K; Ge, Weigong; Valerio, Luis G; Fuscoe, James C; Tong, Weida; Buzatu, Dan A; Wilkes, Jon G; Fowler, Bruce A; Demchuk, Eugene; Beger, Richard D

    2012-03-15

    An interagency collaboration was established to model chemical interactions that may cause adverse health effects when an exposure to a mixture of chemicals occurs. Many of these chemicals--drugs, pesticides, and environmental pollutants--interact at the level of metabolic biotransformations mediated by cytochrome P450 (CYP) enzymes. In the present work, spectral data-activity relationship (SDAR) and structure-activity relationship (SAR) approaches were used to develop machine-learning classifiers of inhibitors and non-inhibitors of the CYP3A4 and CYP2D6 isozymes. The models were built upon 602 reference pharmaceutical compounds whose interactions have been deduced from clinical data, and 100 additional chemicals that were used to evaluate model performance in an external validation (EV) test. SDAR is an innovative modeling approach that relies on discriminant analysis applied to binned nuclear magnetic resonance (NMR) spectral descriptors. In the present work, both 1D ¹³C and 1D ¹⁵N-NMR spectra were used together in a novel implementation of the SDAR technique. It was found that increasing the binning size of 1D ¹³C-NMR and ¹⁵N-NMR spectra caused an increase in the tenfold cross-validation (CV) performance in terms of both the rate of correct classification and sensitivity. The results of SDAR modeling were verified using SAR. For SAR modeling, a decision forest approach involving from 6 to 17 Mold2 descriptors in a tree was used. Average rates of correct classification of SDAR and SAR models in a hundred CV tests were 60% and 61% for CYP3A4, and 62% and 70% for CYP2D6, respectively. The rates of correct classification of SDAR and SAR models in the EV test were 73% and 86% for CYP3A4, and 76% and 90% for CYP2D6, respectively. Thus, both SDAR and SAR methods demonstrated a comparable performance in modeling a large set of structurally diverse data. Based on unique NMR structural descriptors, the new SDAR modeling method complements the existing SAR

  17. Characterization of pyrogenic organic matter by 2-dimenstional HETeronucleus CORelation solid-state 13C NMR (HETCOR) spectroscopy

    NASA Astrophysics Data System (ADS)

    Knicker, Heike

    2016-04-01

    During the last years, increasing evidences are provided that the common view of charcoal as a polyaromatic network is too much simplified. Experiments with model compounds indicated that it represents a heterogeneous mixture of thermally altered biomacromolecules with N, O and likely also S substitutions as common features. If produced from a N-rich feedstock, the so called black nitrogen (BN) has to be considered as an integral part of the aromatic charcoal network. In order to study this network one-dimensional (1D) solid-state nuclear magnetic resonance (NMR) spectroscopy is often applied. However, this technique suffers from broad resonance lines and low resolution. Applying 2D techniques can help but until recently, this was unfeasible for natural organic matter (NOM) due to sensitivity problems and the high complexity of the material. On the other hand, during the last decade, the development of stronger magnetic field instruments and advanced pulse sequences has put them into reach for NOM research. Although 2D NMR spectroscopy has many different applications, all pulse sequences are based on the introduction of a preparation time during which the magnetization of a spin system is adjusted into a state appropriate to whatever properties are to be detected in the indirect dimension. Then, the spins are allowed to evolve with the given conditions and after their additional manipulation during a mixing period the modulated magnetization is detected. Assembling several 1D spectra with incrementing evolution time creates a data set which is two-dimensional in time (t1, t2). Fourier transformation of both dimensions leads to a 2D contour plot correlating the interactions detected in the indirect dimension t1 with the signals detected in the direct dimension t2. The so called solid-state heteronuclear correlation (HETCOR) NMR spectroscopy represents a 2D technique allows the determination which protons are interacting with which carbons. In the present work this

  18. ERETIC implemented in diffusion-ordered NMR as a diffusion reference.

    PubMed

    Van Lokeren, Luk; Kerssebaum, Rainer; Willem, Rudolph; Denkova, Pavletta

    2008-01-01

    The ERETIC (Electronic Reference To access In vivo Concentrations) technique generates an electronic signal in the NMR spectrometer which is detected simultaneously to the sample FID during the acquisition. The implementation of the ERETIC sequence in any 2D DOSY experimental scheme enables one to generate directly into the raw 2D DOSY spectrum a reference signal with an attenuation simulated to describe a well-defined diffusion behavior. This simulated intensity attenuation can be used to evaluate the output generated by any DOSY data treatment algorithm, in a single as well as multichannel approach and provide insight into their precision, accuracy, scope and limitations. The ERETIC sequence implemented in the standard bipolar pulsed field gradient longitudinal eddy current delay (LED) sequence is illustrated on various algorithms presented previously in the literature for the analysis of the generated ERETIC-DOSY spectra of simulated model systems representing discrete and continuous diffusion profiles in mono- and bi-Gaussian diffusion regimes.

  19. Improving VERITAS sensitivity by fitting 2D Gaussian image parameters

    NASA Astrophysics Data System (ADS)

    Christiansen, Jodi; VERITAS Collaboration

    2012-12-01

    Our goal is to improve the acceptance and angular resolution of VERITAS by implementing a camera image-fitting algorithm. Elliptical image parameters are extracted from 2D Gaussian distribution fits using a χ2 minimization instead of the standard technique based on the principle moments of an island of pixels above threshold. We optimize the analysis cuts and then characterize the improvements using simulations. We find an improvement of 20% less observing time to reach 5-sigma for weak point sources.

  20. NMR studies of multiphase flows II

    SciTech Connect

    Altobelli, S.A.; Caprihan, A.; Fukushima, E.

    1995-12-31

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

  1. Advanced NMR-based techniques for pore structure analysis of coal. Quarterly report No. 1, September 1, 1991--November 30, 1991

    SciTech Connect

    Smith, D.M.

    1991-12-31

    One of the main problems in coal utilization is the inability to properly characterize its complex pore structure. We propose to investigate the dependence of the common NMR parameters such as chemical shifts and relaxation times of several different nuclei and compounds on the pore structure of model microporous solids, carbons, and coals. In particular, we will study the interaction between several small molecules ({sup 129}Xe, {sup 3}He, {sup 2}H{sub 2}, {sup 14}N{sub 2}, {sup 14}NH{sub 3}, {sup 15}N{sub 2}, {sup 13}CH{sub 4}, {sup 13}CO{sub 2}) and the pore surfaces in coals. These molecules have been selected for their chemical and physical properties.

  2. {sup 1}H NMR spectroscopic studies establish that heparanase is a retaining glycosidase

    SciTech Connect

    Wilson, Jennifer C.; Laloo, Andrew Elohim; Singh, Sanjesh; Ferro, Vito

    2014-01-03

    Highlights: •{sup 1}H and {sup 13}C NMR chemical shifts of fondaparinux were fully assigned by 1D and 2D NMR techniques. •Hydrolysis of fondaparinux by heparanase was monitored by {sup 1}H NMR spectroscopy. •Heparanase is established to be a retaining glycosidase. -- Abstract: Heparanase is an endo-β-glucuronidase that cleaves heparan sulfate side chains of proteoglycans in basement membranes and the extracellular matrix (ECM). Heparanase is implicated in several diverse pathological processes associated with ECM degradation such as metastasis, inflammation and angiogenesis and is thus an important target for anti-cancer and anti-inflammatory drug discovery. Heparanase has been classed as belonging to the clan A glycoside hydrolase family 79 based on sequence analysis, secondary structure predictions and mutagenic analysis, and thus it has been inferred that it is a retaining glycosidase. However, there has been no direct experimental evidence to support this conclusion. Herein we describe {sup 1}H NMR spectroscopic studies of the hydrolysis of the pentasaccharide substrate fondaparinux by heparanase, and provide conclusive evidence that heparanase hydrolyses its substrate with retention of configuration and is thus established as a retaining glycosidase. Knowledge of the mechanism of hydrolysis may have implications for future design of inhibitors for this important drug target.

  3. A general Monte Carlo/simulated annealing algorithm for resonance assignment in NMR of uniformly labeled biopolymers

    PubMed Central

    Hu, Kan-Nian; Qiang, Wei; Tycko, Robert

    2011-01-01

    We describe a general computational approach to site-specific resonance assignments in multidimensional NMR studies of uniformly 15N,13C-labeled biopolymers, based on a simple Monte Carlo/simulated annealing (MCSA) algorithm contained in the program MCASSIGN2. Input to MCASSIGN2 includes lists of multidimensional signals in the NMR spectra with their possible residue-type assignments (which need not be unique), the biopolymer sequence, and a table that describes the connections that relate one signal list to another. As output, MCASSIGN2 produces a high-scoring sequential assignment of the multidimensional signals, using a score function that rewards good connections (i.e., agreement between relevant sets of chemical shifts in different signal lists) and penalizes bad connections, unassigned signals, and assignment gaps. Examination of a set of high-scoring assignments from a large number of independent runs allows one to determine whether a unique assignment exists for the entire sequence or parts thereof. We demonstrate the MCSA algorithm using two-dimensional (2D) and three-dimensional (3D) solid state NMR spectra of several model protein samples (α-spectrin SH3 domain and protein G/B1 microcrystals, HET-s218–289 fibrils), obtained with magic-angle spinning and standard polarization transfer techniques. The MCSA algorithm and MCASSIGN2 program can accommodate arbitrary combinations of NMR spectra with arbitrary dimensionality, and can therefore be applied in many areas of solid state and solution NMR. PMID:21710190

  4. Orthotropic Piezoelectricity in 2D Nanocellulose

    NASA Astrophysics Data System (ADS)

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

    2016-10-01

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

  5. Orthotropic Piezoelectricity in 2D Nanocellulose

    PubMed Central

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

    2016-01-01

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

  6. 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.

  7. 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.

  8. 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

  9. 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.

  10. NMR-Assisted Molecular Docking Methodologies.

    PubMed

    Sturlese, Mattia; Bellanda, Massimo; Moro, Stefano

    2015-08-01

    Nuclear magnetic resonance (NMR) spectroscopy and molecular docking are regularly being employed as helpful tools of drug discovery research. Molecular docking is an extremely rapid method to evaluate possible binders from a large chemical library in a fast and cheap manner. NMR techniques can directly detect a protein-ligand interaction, can determine the corresponding association constant, and can consistently identify the ligand binding cavity. Consequently, molecular docking and NMR techniques are naturally complementary techniques where the combination of the two has the potential to improve the overall efficiency of drug discovery process. In this review, we would like to summarize the state of the art of docking methods which have been recently bridged to NMR experiments to identify novel and effective therapeutic drug candidates.

  11. NMR-Assisted Molecular Docking Methodologies.

    PubMed

    Sturlese, Mattia; Bellanda, Massimo; Moro, Stefano

    2015-08-01

    Nuclear magnetic resonance (NMR) spectroscopy and molecular docking are regularly being employed as helpful tools of drug discovery research. Molecular docking is an extremely rapid method to evaluate possible binders from a large chemical library in a fast and cheap manner. NMR techniques can directly detect a protein-ligand interaction, can determine the corresponding association constant, and can consistently identify the ligand binding cavity. Consequently, molecular docking and NMR techniques are naturally complementary techniques where the combination of the two has the potential to improve the overall efficiency of drug discovery process. In this review, we would like to summarize the state of the art of docking methods which have been recently bridged to NMR experiments to identify novel and effective therapeutic drug candidates. PMID:27490497

  12. 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...

  13. Accurate coronary modeling procedure using 2D calibrated projections based on 2D centerline points on a single projection

    NASA Astrophysics Data System (ADS)

    Movassaghi, Babak; Rasche, Volker; Viergever, Max A.; Niessen, Wiro J.

    2004-05-01

    For the diagnosis of ischemic heart disease, accurate quantitative analysis of the coronary arteries is important. In coronary angiography, a number of projections is acquired from which 3D models of the coronaries can be reconstructed. A signifcant limitation of the current 3D modeling procedures is the required user interaction for defining the centerlines of the vessel structures in the 2D projections. Currently, the 3D centerlines of the coronary tree structure are calculated based on the interactively determined centerlines in two projections. For every interactively selected centerline point in a first projection the corresponding point in a second projection has to be determined interactively by the user. The correspondence is obtained based on the epipolar-geometry. In this paper a method is proposed to retrieve all the information required for the modeling procedure, by the interactive determination of the 2D centerline-points in only one projection. For every determined 2D centerline-point the corresponding 3D centerline-point is calculated by the analysis of the 1D gray value functions of the corresponding epipolarlines in space for all available 2D projections. This information is then used to build a 3D representation of the coronary arteries using coronary modeling techniques. The approach is illustrated on the analysis of calibrated phantom and calibrated coronary projection data.

  14. Multinuclear Solid-State NMR Investigation of Hexaniobate and Hexatantalate Compounds.

    PubMed

    Deblonde, Gauthier J-P; Coelho-Diogo, Cristina; Chagnes, Alexandre; Cote, Gérard; Smith, Mark E; Hanna, John V; Iuga, Dinu; Bonhomme, Christian

    2016-06-20

    This work determines the potential of solid-state NMR techniques to probe proton, alkali, and niobium environments in Lindqvist salts. Na7HNb6O19·15H2O (1), K8Nb6O19·16H2O (2), and Na8Ta6O19·24.5H2O (3) have been studied by solid-state static and magic angle spinning (MAS) NMR at high and ultrahigh magnetic field (16.4 and 19.9 T). (1)H MAS NMR was found to be a convenient and straightforward tool to discriminate between protonated and nonprotonated clusters AxH8-xM6O19·nH2O (A = alkali ion; M = Nb, Ta). (93)Nb MAS NMR studies at different fields and MAS rotation frequencies have been performed on 1. For the first time, the contributions of NbO5Oμ2H sites were clearly distinguished from those assigned to NbO6 sites in the hexaniobate cluster. The strong broadening of the resonances obtained under MAS was interpreted by combining chemical shift anisotropy (CSA) with quadrupolar effects and by using extensive fitting of the line shapes. In order to obtain the highest accuracy for all NMR parameters (CSA and quadrupolar), (93)Nb WURST QCPMG spectra in the static mode were recorded at 16.4 T for sample 1. The (93)Nb NMR spectra were interpreted in connection with the XRD data available in the literature (i.e., fractional occupancies of the NbO5Oμ2H sites). 1D (23)Na MAS and 2D (23)Na 3QMAS NMR studies of 1 revealed several distinct sodium sites. The multiplicity of the sites was again compared to structural details previously obtained by single-crystal X-ray diffraction (XRD) studies. The (23)Na MAS NMR study of 3 confirmed the presence of a much larger distribution of sodium sites in accordance with the 10 sodium sites predicted by XRD. Finally, the effect of Nb/Ta substitutions in 1 was also probed by multinuclear MAS NMR ((1)H, (23)Na, and (93)Nb).

  15. Multinuclear Solid-State NMR Investigation of Hexaniobate and Hexatantalate Compounds.

    PubMed

    Deblonde, Gauthier J-P; Coelho-Diogo, Cristina; Chagnes, Alexandre; Cote, Gérard; Smith, Mark E; Hanna, John V; Iuga, Dinu; Bonhomme, Christian

    2016-06-20

    This work determines the potential of solid-state NMR techniques to probe proton, alkali, and niobium environments in Lindqvist salts. Na7HNb6O19·15H2O (1), K8Nb6O19·16H2O (2), and Na8Ta6O19·24.5H2O (3) have been studied by solid-state static and magic angle spinning (MAS) NMR at high and ultrahigh magnetic field (16.4 and 19.9 T). (1)H MAS NMR was found to be a convenient and straightforward tool to discriminate between protonated and nonprotonated clusters AxH8-xM6O19·nH2O (A = alkali ion; M = Nb, Ta). (93)Nb MAS NMR studies at different fields and MAS rotation frequencies have been performed on 1. For the first time, the contributions of NbO5Oμ2H sites were clearly distinguished from those assigned to NbO6 sites in the hexaniobate cluster. The strong broadening of the resonances obtained under MAS was interpreted by combining chemical shift anisotropy (CSA) with quadrupolar effects and by using extensive fitting of the line shapes. In order to obtain the highest accuracy for all NMR parameters (CSA and quadrupolar), (93)Nb WURST QCPMG spectra in the static mode were recorded at 16.4 T for sample 1. The (93)Nb NMR spectra were interpreted in connection with the XRD data available in the literature (i.e., fractional occupancies of the NbO5Oμ2H sites). 1D (23)Na MAS and 2D (23)Na 3QMAS NMR studies of 1 revealed several distinct sodium sites. The multiplicity of the sites was again compared to structural details previously obtained by single-crystal X-ray diffraction (XRD) studies. The (23)Na MAS NMR study of 3 confirmed the presence of a much larger distribution of sodium sites in accordance with the 10 sodium sites predicted by XRD. Finally, the effect of Nb/Ta substitutions in 1 was also probed by multinuclear MAS NMR ((1)H, (23)Na, and (93)Nb). PMID:27245403

  16. Half-metallicity in 2D organometallic honeycomb frameworks

    NASA Astrophysics Data System (ADS)

    Sun, Hao; Li, Bin; Zhao, Jin

    2016-10-01

    Half-metallic materials with a high Curie temperature (T C) have many potential applications in spintronics. Magnetic metal free two-dimensional (2D) half-metallic materials with a honeycomb structure contain graphene-like Dirac bands with π orbitals and show excellent aspects in transport properties. In this article, by investigating a series of 2D organometallic frameworks with a honeycomb structure using first principles calculations, we study the origin of forming half-metallicity in this kind of 2D organometallic framework. Our analysis shows that charge transfer and covalent bonding are two crucial factors in the formation of half-metallicity in organometallic frameworks. (i) Sufficient charge transfer from metal atoms to the molecules is essential to form the magnetic centers. (ii) These magnetic centers need to be connected through covalent bonding, which guarantee the strong ferromagnetic (FM) coupling. As examples, the organometallic frameworks composed by (1,3,5)-benzenetricarbonitrile (TCB) molecules with noble metals (Au, Ag, Cu) show half-metallic properties with T C as high as 325 K. In these organometallic frameworks, the strong electronegative cyano-groups (CN groups) drive the charge transfer from metal atoms to the TCB molecules, forming the local magnetic centers. These magnetic centers experience strong FM coupling through the d-p covalent bonding. We propose that most of the 2D organometallic frameworks composed by molecule—CN—noble metal honeycomb structures contain similar half metallicity. This is verified by replacing TCB molecules with other organic molecules. Although the TCB-noble metal organometallic framework has not yet been synthesized, we believe the development of synthesizing techniques and facility will enable the realization of them. Our study provides new insight into the 2D half-metallic material design for the potential applications in nanotechnology.

  17. Half-metallicity in 2D organometallic honeycomb frameworks.

    PubMed

    Sun, Hao; Li, Bin; Zhao, Jin

    2016-10-26

    Half-metallic materials with a high Curie temperature (T C) have many potential applications in spintronics. Magnetic metal free two-dimensional (2D) half-metallic materials with a honeycomb structure contain graphene-like Dirac bands with π orbitals and show excellent aspects in transport properties. In this article, by investigating a series of 2D organometallic frameworks with a honeycomb structure using first principles calculations, we study the origin of forming half-metallicity in this kind of 2D organometallic framework. Our analysis shows that charge transfer and covalent bonding are two crucial factors in the formation of half-metallicity in organometallic frameworks. (i) Sufficient charge transfer from metal atoms to the molecules is essential to form the magnetic centers. (ii) These magnetic centers need to be connected through covalent bonding, which guarantee the strong ferromagnetic (FM) coupling. As examples, the organometallic frameworks composed by (1,3,5)-benzenetricarbonitrile (TCB) molecules with noble metals (Au, Ag, Cu) show half-metallic properties with T C as high as 325 K. In these organometallic frameworks, the strong electronegative cyano-groups (CN groups) drive the charge transfer from metal atoms to the TCB molecules, forming the local magnetic centers. These magnetic centers experience strong FM coupling through the d-p covalent bonding. We propose that most of the 2D organometallic frameworks composed by molecule-CN-noble metal honeycomb structures contain similar half metallicity. This is verified by replacing TCB molecules with other organic molecules. Although the TCB-noble metal organometallic framework has not yet been synthesized, we believe the development of synthesizing techniques and facility will enable the realization of them. Our study provides new insight into the 2D half-metallic material design for the potential applications in nanotechnology.

  18. Half-metallicity in 2D organometallic honeycomb frameworks.

    PubMed

    Sun, Hao; Li, Bin; Zhao, Jin

    2016-10-26

    Half-metallic materials with a high Curie temperature (T C) have many potential applications in spintronics. Magnetic metal free two-dimensional (2D) half-metallic materials with a honeycomb structure contain graphene-like Dirac bands with π orbitals and show excellent aspects in transport properties. In this article, by investigating a series of 2D organometallic frameworks with a honeycomb structure using first principles calculations, we study the origin of forming half-metallicity in this kind of 2D organometallic framework. Our analysis shows that charge transfer and covalent bonding are two crucial factors in the formation of half-metallicity in organometallic frameworks. (i) Sufficient charge transfer from metal atoms to the molecules is essential to form the magnetic centers. (ii) These magnetic centers need to be connected through covalent bonding, which guarantee the strong ferromagnetic (FM) coupling. As examples, the organometallic frameworks composed by (1,3,5)-benzenetricarbonitrile (TCB) molecules with noble metals (Au, Ag, Cu) show half-metallic properties with T C as high as 325 K. In these organometallic frameworks, the strong electronegative cyano-groups (CN groups) drive the charge transfer from metal atoms to the TCB molecules, forming the local magnetic centers. These magnetic centers experience strong FM coupling through the d-p covalent bonding. We propose that most of the 2D organometallic frameworks composed by molecule-CN-noble metal honeycomb structures contain similar half metallicity. This is verified by replacing TCB molecules with other organic molecules. Although the TCB-noble metal organometallic framework has not yet been synthesized, we believe the development of synthesizing techniques and facility will enable the realization of them. Our study provides new insight into the 2D half-metallic material design for the potential applications in nanotechnology. PMID:27541575

  19. Parallel stitching of 2D materials

    DOE PAGES

    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.

  20. Parallel Stitching of 2D Materials.

    PubMed

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

    2016-03-23

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

  1. The use of solid-state NMR techniques for the analysis of water in coal and the effect of different coal drying techniques on the structure and reactivity of coal; Quarterly report, September 1--November 30, 1993

    SciTech Connect

    Netzel, D.A.

    1993-12-31

    For the research program reported here, different methods of drying are being investigated to determine if drying can be accomplished without destroying coal reactivity toward liquefaction. In an effort to understand the mechanism of water for enhancing coal liquefaction yield, the reactions of D{sub 2}O with the molecular constituents of coal during coal liquefaction are being investigated. This study involves the use of solution-state deuterium NMR, as well as, conventional solution-state {sup 1}H and {sup 13}C NMR analyses of the coal, and the coal liquids and residue from a coal liquefaction process. These D{sub 2}O transfer reactions will be conducted on coals which have been dried by various methods and rehydrated using D{sub 2}O and by successive exchange of H{sub 2}O associated with the coals with D{sub 2}O. The drying methods include thermal, microwave, and chemical dehydration of the coal. The overall objectives of this study are to develop a nuclear magnetic resonance (NMR) method for measuring the water in coal, to measure the changes in coal structure that occur during coal drying, to determine what effect water has on retrograde/condensation reactions, to determine the mechanism by which water may impact coal reactivity toward liquefaction, and to conduct D{sub 2}O exchange studies to ascertain the role of water in coal liquefaction. The objectives for this quarterly report period were (1) to measure the volumetric swelling ratio for thermally- and microwave-dried coals and (2) to conduct preliminary experiments concerning the exchange of water in coal with deuterium oxide (D{sub 2}O).

  2. Structural investigation of aluminium doped ZnO nanoparticles by solid-state NMR spectroscopy.

    PubMed

    Avadhut, Yamini S; Weber, Johannes; Hammarberg, Elin; Feldmann, Claus; Schmedt auf der Günne, Jörn

    2012-09-01

    The electrical conductivity of aluminium doped zinc oxide (AZO, ZnO:Al) materials depends on doping induced defects and grain structure. This study aims at relating macroscopic electrical conductivity of AZO nanoparticles with their atomic structure, which is non-trivial because the derived materials are heavily disordered and heterogeneous in nature. For this purpose we synthesized AZO nanoparticles with different doping levels and narrow size distribution by a microwave assisted polyol method followed by drying and a reductive treatment with forming gas. From these particles electrically conductive, optically transparent films were obtained by spin-coating. Characterization involved energy-dispersive X-ray analysis, wet chemical analysis, X-ray diffraction, electron microscopy and dynamic light scattering, which provided a basis for a detailed structural solid-state NMR study. A multinuclear ((27)Al, (13)C, (1)H) spectroscopic investigation required a number of 1D MAS NMR and 2D MAS NMR techniques (T(1)-measurements, (27)Al-MQMAS, (27)Al-(1)H 2D-PRESTO-III heteronuclear correlation spectroscopy), which were corroborated by quantum chemical calculations with an embedded cluster method (EEIM) at the DFT level. From the combined data we conclude that only a small part of the provided Al is incorporated into the ZnO structure by substitution of Zn. The related (27)Al NMR signal undergoes a Knight shift when the material is subjected to a reductive treatment with forming gas. At higher (formal) doping levels Al forms insulating (Al, H and C containing) side-phases, which cover the surface of the ZnO:Al particles and increase the sheet resistivity of spin-coated material. Moreover, calculated (27)Al quadrupole coupling constants serve as a spectroscopic fingerprint by which previously suggested point-defects can be identified and in their great majority be ruled out. PMID:22801707

  3. High-Resolution Two-Dimensional J-Resolved NMR Spectroscopy for Biological Systems

    PubMed Central

    Huang, Yuqing; Cai, Shuhui; Zhang, Zhiyong; Chen, Zhong

    2014-01-01

    NMR spectroscopy is a principal tool in metabolomic studies and can, in theory, yield atom-level information critical for understanding biological systems. Nevertheless, NMR investigations on biological tissues generally have to contend with field inhomogeneities originating from variations in macroscopic magnetic susceptibility; these field inhomogeneities broaden spectral lines and thereby obscure metabolite signals. The congestion in one-dimensional NMR spectra of biological tissues often leads to ambiguities in metabolite identification and quantification. We propose an NMR approach based on intermolecular double-quantum coherences to recover high-resolution two-dimensional (2D) J-resolved spectra from inhomogeneous magnetic fields, such as those created by susceptibility variations in intact biological tissues. The proposed method makes it possible to acquire high-resolution 2D J-resolved spectra on intact biological samples without recourse to time-consuming shimming procedures or the use of specialized hardware, such as magic-angle-spinning probes. Separation of chemical shifts and J couplings along two distinct dimensions is achieved, which reduces spectral crowding and increases metabolite specificity. Moreover, the apparent J coupling constants observed are magnified by a factor of 3, facilitating the accurate measurement of small J couplings, which is useful in metabolic analyses. Dramatically improved spectral resolution is demonstrated in our applications of the technique on pig brain tissues. The resulting spectra contain a wealth of chemical shift and J-coupling information that is invaluable for metabolite analyses. A spatially localized experiment applied on an intact fish (Crossocheilus siamensis) reveals the promise of the proposed method in in vivo metabolite studies. Moreover, the proposed method makes few demands on spectrometer hardware and therefore constitutes a convenient and effective manner for metabonomics study of biological systems

  4. Interpretation of Magnetic Phase Anomalies over 2D Tabular Bodies

    NASA Astrophysics Data System (ADS)

    Subrahmanyam, M.

    2016-05-01

    In this study, phase angle (inverse tangent of the ratio of the horizontal to vertical gradients of magnetic anomalies) profile over two-dimensional tabular bodies has been subjected to detailed analysis for determining the source parameters. Distances between certain characteristic positions on this phase curve are related to the parameters of two-dimensional tabular magnetic sources. In this paper, I have derived the mathematical expressions for these relations. It has been demonstrated here that for locating the origin of the 2D tabular source, knowledge on the type of the model (contact, sheet, dyke, and fault) is not necessary. A procedure is evolved to determine the location, depth, width and magnetization angle of the 2D sources from the mathematical expressions. The method is tested on real field data. The effect of the overlapping bodies is also discussed with two synthetic examples. The interpretation technique is developed for contact, sheet, dike and inclined fault bodies.

  5. 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

  6. 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.

  7. Tautomeric states of the active-site histidines of phosphorylated and unphosphorylated IIIGlc, a signal-transducing protein from Escherichia coli, using two-dimensional heteronuclear NMR techniques.

    PubMed Central

    Pelton, J. G.; Torchia, D. A.; Meadow, N. D.; Roseman, S.

    1993-01-01

    IIIGlc is an 18.1-kDa signal-transducing phosphocarrier protein of the phosphoenolpyruvate:glycose phosphotransferase system from Escherichia coli. The 1H, 15N, and 13C histidine ring NMR signals of both the phosphorylated and unphosphorylated forms of IIIGlc have been assigned using two-dimensional 1H-15N and 1H-13C heteronuclear multiple-quantum coherence (HMQC) experiments and a two-dimensional 13C-13C-1H correlation spectroscopy via JCC coupling experiment. The data were acquired on uniformly 15N-labeled and uniformly 15N/13C-labeled protein samples. The experiments rely on one-bond and two-bond J couplings that allowed for assignment of the signals without the need for the analysis of through-space (nuclear Overhauser effect spectroscopy) correlations. The 15N and 13C chemical shifts were used to determine that His-75 exists predominantly in the N epsilon 2-H tautomeric state in both the phosphorylated and unphosphorylated forms of IIIGlc, and that His-90 exists primarily in the N delta 1-H state in the unphosphorylated protein. Upon phosphorylation of the N epsilon 2 nitrogen of His-90, the N delta 1 nitrogen remains protonated, resulting in the formation of a charged phospho-His-90 moiety. The 1H, 15N, and 13C signals of the phosphorylated and unphosphorylated proteins showed only minor shifts in the pH range from 6.0 to 9.0. These data indicate that the pK alpha values for both His-75 and His-90 in IIIGlc and His-75 in phospho-IIIGlc are less than 5.0, and that the pK alpha value for phospho-His-90 is greater than 10. The results are presented in relation to previously obtained structural data on IIIGlc, and implications for proposed mechanisms of phosphoryl transfer are discussed. PMID:8518729

  8. The use of solid-state NMR techniques for the analysis of water in coal and the effect of different coal drying techniques on the structure and reactivity of coal. Quarterly report, March 1, 1994--May 31, 1994

    SciTech Connect

    Netzel, D.A.

    1994-08-01

    One area for improvement in the economics of coal liquefaction is coal drying, particularly for the lower rank coals. However, there is considerable evidence to show that drying has a detrimental effect on the liquefaction behavior of coals. Regarding the liquefaction of coal, there does not appear to have been any systematic study of the methods of coal drying on coal structure and the role water plays in enhancing or lessening coal reactivity toward liquefaction. For the research program reported here, different methods of drying are being investigated to determine if drying can be accomplished without destroying coal reactivity toward liquefaction. In an effort to understand the mechanism of water for enhancing coal liquefaction yield, the reactions of D{sub 2}O with the molecular constituents of coal during coal liquefaction are being investigated. This study involves the use of solution-state deuterium NMR, as well as, conventional solution-state {sup 1}H and {sup 13}C NMR analyses of the coal, and the coal liquids and residue from a coal liquefaction process. These D{sub 2}O transfer reactions will be conducted on coals which have been dried by various methods and rehydrated using D{sub 2}O and by successive exchange of H{sub 2}O associated with the coals with D{sub 2}O. The drying methods include thermal, microwave, and chemical dehydration of the coal.

  9. Use of solid-state NMR techniques for the analysis of water in coal and the effect of different coal drying techniques on the structure and reactivity of coal. Quarterly report, September 1--November 30, 1991

    SciTech Connect

    Netzel, D.A.

    1991-12-31

    The overall objectives of this study are to develop an NMR method for measuring the water in coal, to measure the changes in coal structure that occur during coal drying, to determine what effect water has on retrograde/condensation reaction, and to determine the mechanism by which water any enhance coal reactivity toward liquefaction. Different methods of drying will be investigated to determine if drying can be accomplished without destroying coal reactivity toward liquefaction, thereby making coal drying an attractive and economical method for coal pretreatment. Coal drying methods will include thermal drying under different atmosphere and temperatures, drying with microwave radiation, and low-temperature chemical dehydration. The objectives for this quarterly report period were (1) to hire a student to help on the program, (2) to define the coals to be investigated and acquire the samples, (3) to order the necessary reagents and supplies, and (4) to conduct preliminary experiments for determining quantitatively using 2,2{prime}-dimethoxypropane and {sup 1}H NMR.

  10. Probing porous media with gas diffusion NMR.

    PubMed

    Mair, R W; Wong, G P; Hoffmann, D; Hurlimann, M D; Patz, S; Schwartz, L M; Walsworth, R L

    1999-10-18

    We show that gas diffusion nuclear magnetic resonance (GD-NMR) provides a powerful technique for probing the structure of porous media. In random packs of glass beads, using both laser-polarized and thermally polarized xenon gas, we find that GD-NMR can accurately measure the pore space surface-area-to-volume ratio, S/V rho, and the tortuosity, alpha (the latter quantity being directly related to the system's transport properties). We also show that GD-NMR provides a good measure of the tortuosity of sandstone and complex carbonate rocks. PMID:11543587

  11. Probing porous media with gas diffusion NMR

    NASA Technical Reports Server (NTRS)

    Mair, R. W.; Wong, G. P.; Hoffmann, D.; Hurlimann, M. D.; Patz, S.; Schwartz, L. M.; Walsworth, R. L.

    1999-01-01

    We show that gas diffusion nuclear magnetic resonance (GD-NMR) provides a powerful technique for probing the structure of porous media. In random packs of glass beads, using both laser-polarized and thermally polarized xenon gas, we find that GD-NMR can accurately measure the pore space surface-area-to-volume ratio, S/V rho, and the tortuosity, alpha (the latter quantity being directly related to the system's transport properties). We also show that GD-NMR provides a good measure of the tortuosity of sandstone and complex carbonate rocks.

  12. 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

  13. 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

  14. 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

  15. 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

  16. Static & Dynamic Response of 2D Solids

    SciTech Connect

    Lin, Jerry

    1996-07-15

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

  17. Explicit 2-D Hydrodynamic FEM Program

    SciTech Connect

    Lin, Jerry

    1996-08-07

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

  18. 2D photonic-crystal optomechanical nanoresonator.

    PubMed

    Makles, K; Antoni, T; Kuhn, A G; Deléglise, S; Briant, T; Cohadon, P-F; Braive, R; Beaudoin, G; Pinard, L; Michel, C; Dolique, V; Flaminio, R; Cagnoli, G; Robert-Philip, I; Heidmann, A

    2015-01-15

    We present the optical optimization of an optomechanical device based on a suspended InP membrane patterned with a 2D near-wavelength grating (NWG) based on a 2D photonic-crystal geometry. We first identify by numerical simulation a set of geometrical parameters providing a reflectivity higher than 99.8% over a 50-nm span. We then study the limitations induced by the finite value of the optical waist and lateral size of the NWG pattern using different numerical approaches. The NWG grating, pierced in a suspended InP 265-nm thick membrane, is used to form a compact microcavity involving the suspended nanomembrane as an end mirror. The resulting cavity has a waist size smaller than 10 μm and a finesse in the 200 range. It is used to probe the Brownian motion of the mechanical modes of the nanomembrane. PMID:25679837

  19. Multiple acquisition of magic angle spinning solid-state NMR experiments using one receiver: Application to microcrystalline and membrane protein preparations

    NASA Astrophysics Data System (ADS)

    Gopinath, T.; Veglia, Gianluigi

    2015-04-01

    Solid-state NMR spectroscopy of proteins is a notoriously low-throughput technique. Relatively low-sensitivity and poor resolution of protein samples require long acquisition times for multidimensional NMR experiments. To speed up data acquisition, we developed a family of experiments called Polarization Optimized Experiments (POE), in which we utilized the orphan spin operators that are discarded in classical multidimensional NMR experiments, recovering them to allow simultaneous acquisition of multiple 2D and 3D experiments, all while using conventional probes with spectrometers equipped with one receiver. POE allow the concatenation of multiple 2D or 3D pulse sequences into a single experiment, thus potentially combining all of the aforementioned advances, boosting the capability of ssNMR spectrometers at least two-fold without the addition of any hardware. In this perspective, we describe the first generation of POE, such as dual acquisition MAS (or DUMAS) methods, and then illustrate the evolution of these experiments into MEIOSIS, a method that enables the simultaneous acquisition of multiple 2D and 3D spectra. Using these new pulse schemes for the solid-state NMR investigation of biopolymers makes it possible to obtain sequential resonance assignments, as well as distance restraints, in about half the experimental time. While designed for acquisition of heteronuclei, these new experiments can be easily implemented for proton detection and coupled with other recent advancements, such as dynamic nuclear polarization (DNP), to improve signal to noise. Finally, we illustrate the application of these methods to microcrystalline protein preparations as well as single and multi-span membrane proteins reconstituted in lipid membranes.

  20. 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.

  1. 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.

  2. 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

  3. 2D Spinodal Decomposition in Forced Turbulence

    NASA Astrophysics Data System (ADS)

    Fan, Xiang; Diamond, Patrick; Chacon, Luis; Li, Hui

    2015-11-01

    Spinodal decomposition is a second order phase transition for binary fluid mixture, from one thermodynamic phase to form two coexisting phases. The governing equation for this coarsening process below critical temperature, Cahn-Hilliard Equation, is very similar to 2D MHD Equation, especially the conserved quantities have a close correspondence between each other, so theories for MHD turbulence are used to study spinodal decomposition in forced turbulence. Domain size is increased with time along with the inverse cascade, and the length scale can be arrested by a forced turbulence with direct cascade. The two competing mechanisms lead to a stabilized domain size length scale, which can be characterized by Hinze Scale. The 2D spinodal decomposition in forced turbulence is studied by both theory and simulation with ``pixie2d.'' This work focuses on the relation between Hinze scale and spectra and cascades. Similarities and differences between spinodal decomposition and MHD are investigated. Also some transport properties are studied following MHD theories. This work is supported by the Department of Energy under Award Number DE-FG02-04ER54738.

  4. 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.

  5. Multinuclear nanoliter one-dimensional and two-dimensional NMR spectroscopy with a single non-resonant microcoil.

    PubMed

    Fratila, Raluca M; Gomez, M Victoria; Sýkora, Stanislav; Velders, Aldrik H

    2014-01-01

    Nuclear magnetic resonance (NMR) spectroscopy is a powerful analytical technique, but its low sensitivity and highly sophisticated, costly, equipment severely constrain more widespread applications. Here we show that a non-resonant planar transceiver microcoil integrated in a microfluidic chip (detection volume 25 nl) can detect different nuclides in the full broad-band range of Larmor frequencies (at 9.4 T from 61 to 400 MHz). Routine one-dimensional (1D) and two-dimensional (2D), homo- and heteronuclear experiments can be carried out using the broad-band coil set-up. Noteworthy, heteronuclear 2D experiments can be performed in a straightforward manner on virtually any combination of nuclides (from classical ¹H-¹³C to more exotic combinations like ¹⁹F-³¹P) both in coupled and decoupled mode. Importantly, the concept of a non-resonant system provides magnetic field-independent NMR probes; moreover, the small-volume alleviates problems related to field inhomogeneity, making the broad-band coil an attractive option for, for example, portable and table-top NMR systems.

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

    NASA Astrophysics Data System (ADS)

    Benjamini, Dan; Basser, Peter J.

    2016-10-01

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

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

    PubMed

    Benjamini, Dan; Basser, Peter J

    2016-10-01

    Measuring multidimensional (e.g., 2D) relaxation spectra in NMR and MRI clinical applications is a holy grail of the porous media and biomedical MR communities. The main bottleneck is the inversion of Fredholm integrals of the first kind, an ill-conditioned problem requiring large amounts of data to stabilize a solution. We suggest a novel experimental design and processing framework to accelerate and improve the reconstruction of such 2D spectra that uses a priori information from the 1D projections of spectra, or marginal distributions. These 1D marginal distributions provide powerful constraints when 2D spectra are reconstructed, and their estimation requires an order of magnitude less data than a conventional 2D approach. This marginal distributions constrained optimization (MADCO) methodology is demonstrated here with a polyvinylpyrrolidone-water phantom that has 3 distinct peaks in the 2D D-T1 space. The stability, sensitivity to experimental parameters, and accuracy of this new approach are compared with conventional methods by serially subsampling the full data set. While the conventional, unconstrained approach performed poorly, the new method had proven to be highly accurate and robust, only requiring a fraction of the data. Additionally, synthetic T1-T2 data are presented to explore the effects of noise on the estimations, and the performance of the proposed method with a smooth and realistic 2D spectrum. The proposed framework is quite general and can also be used with a variety of 2D MRI experiments (D-T2,T1-T2,D-D, etc.), making these potentially feasible for preclinical and even clinical applications for the first time. PMID:27543810

  8. 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.

  9. A 2-D ECE Imaging Diagnostic for TEXTOR

    NASA Astrophysics Data System (ADS)

    Wang, J.; Deng, B. H.; Domier, C. W.; Luhmann, H. Lu, Jr.

    2002-11-01

    A true 2-D extension to the UC Davis ECE Imaging (ECEI) concept is under development for installation on the TEXTOR tokamak in 2003. This combines the use of linear arrays with multichannel conventional wideband heterodyne ECE radiometers to provide a true 2-D imaging system. This is in contrast to current 1-D ECEI systems in which 2-D images are obtained through the use of multiple plasma discharges (varying the scanned emission frequency each discharge). Here, each array element of the 20 channel mixer array measures plasma emission at 16 simultaneous frequencies to form a 16x20 image of the plasma electron temperature Te. Correlation techniques can then be applied to any pair of the 320 image elements to study both radial and poloidal characteristics of turbulent Te fluctuations. The system relies strongly on the development of low cost, wideband (2-18 GHz) IF detection electronics for use in both ECE Imaging as well as conventional heterodyne ECE radiometry. System details, with a strong focus on the wideband IF electronics development, will be presented. *Supported by U.S. DoE Contracts DE-FG03-95ER54295 and DE-FG03-99ER54531.

  10. Design Application Translates 2-D Graphics to 3-D Surfaces

    NASA Technical Reports Server (NTRS)

    2007-01-01

    Fabric Images Inc., specializing in the printing and manufacturing of fabric tension architecture for the retail, museum, and exhibit/tradeshow communities, designed software to translate 2-D graphics for 3-D surfaces prior to print production. Fabric Images' fabric-flattening design process models a 3-D surface based on computer-aided design (CAD) specifications. The surface geometry of the model is used to form a 2-D template, similar to a flattening process developed by NASA's Glenn Research Center. This template or pattern is then applied in the development of a 2-D graphic layout. Benefits of this process include 11.5 percent time savings per project, less material wasted, and the ability to improve upon graphic techniques and offer new design services. Partners include Exhibitgroup/Giltspur (end-user client: TAC Air, a division of Truman Arnold Companies Inc.), Jack Morton Worldwide (end-user client: Nickelodeon), as well as 3D Exhibits Inc., and MG Design Associates Corp.

  11. The use of solid-state NMR techniques for the analysis of water in coal and the effect of different coal drying techniques on the structure and reactivity of coal. Quarterly report, March 1--May 31, 1993

    SciTech Connect

    Netzel, D.A.

    1993-09-01

    The overall objectives of this study are to develop an NMR method for measuring the water in coal, to measure the changes in coal structure that occur during coal drying, to determine what effect water has on retrograde/condensation reactions, and to determine the mechanism by which water may impact coal reactivity toward liquefaction. Different methods of drying are being investigated to determine if drying can be accomplished without destroying coal reactivity toward liquefaction. The objectives for this quarterly report period were to (1) determine the kinetics of chemical dehydration of coals, (2) measure the volumetric, swelling ratio for initial and dried coals, and (3) determine the coal liquefaction yield for dried coals.

  12. The use of solid-state NMR techniques for the analysis of water in coal and the effect of different coal drying techniques on the structure and reactivity of coal. Quarterly report, December 1, 1993--February 28, 1994

    SciTech Connect

    Netzel, D.A.

    1994-06-01

    The overall objectives of this study are to develop a nuclear magnetic resonance (NMR) method for measuring the water in coal, to measure the changes in coal structure that occur during coal drying, to determine what effect water has on retrograde/condensation reactions, to determine the mechanism by which water may impact coal reactivity toward liquefaction, and to conduct D{sub 2}O exchange studies to ascertain the role of water in coal liquefaction. The objectives for this quarterly report period were (1) to train students in the operation of the coal liquefaction reactor, gas analysis, extraction of the coal residue and coal liquids, and to calculate the percent conversion from the coal liquefaction data; and (2) to implement the changes in the coal liquefaction experimental procedure.

  13. Monomeric and dimeric structures analysis and spectroscopic characterization of 3,5-difluorophenylboronic acid with experimental (FT-IR, FT-Raman, 1H and 13C NMR, UV) techniques and quantum chemical calculations

    NASA Astrophysics Data System (ADS)

    Karabacak, Mehmet; Kose, Etem; Atac, Ahmet; Asiri, Abdullah M.; Kurt, Mustafa

    2014-01-01

    The spectroscopic properties of 3,5-difluorophenylboronic acid (3,5-DFPBA, C6H3F2B(OH)2) were investigated by FT-IR, FT-Raman UV-Vis, 1H and 13C NMR spectroscopic techniques. FT-IR (4000-400 cm-1) and FT-Raman spectra (3500-10 cm-1) in the solid phase and 1H and 13C NMR spectra in DMSO solution were recorded. The UV spectra that dissolved in ethanol and water were recorded in the range of 200-400 nm for each solution. The structural and spectroscopic data of the molecule have been obtained for possible three conformers from DFT (B3LYP) with 6-311++G(d,p) basis set calculations. The geometry of the molecule was fully optimized, vibrational spectra were calculated and fundamental vibrations were assigned on the basis of the total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method and PQS program. Hydrogen-bonded dimer of title molecule, optimized by counterpoise correction, was also studied B3LYP at the 6-311++G(d,p) level and the effects of molecular association through O-H⋯O hydrogen bonding have been discussed. 1H and 13C NMR chemical shifts were calculated by using the gauge-invariant atomic orbital (GIAO) method. The electronic properties, such as excitation energies, oscillator strength, wavelengths, HOMO and LUMO energies, were performed by time-dependent density functional theory (TD-DFT) results complements with the experimental findings. Total and partial density of state (TDOS and PDOS) and also overlap population density of state (OPDOS) diagrams analysis were presented. The effects due to the substitutions of boric acid group and halogen were investigated. The results of the calculations were applied to simulate spectra of the title compound, which show excellent agreement with observed spectra. Besides, frontier molecular orbitals (FMO), molecular electrostatic potential (MEP), nonlinear optical properties (NLO) and thermodynamic features were performed.

  14. Attaining 2D Black Phosphorus and Investigations into Floating-Electrode Dielectric Barrier Discharge Treatment of Solutions

    NASA Astrophysics Data System (ADS)

    Smith, Joshua Benjamin

    Since the discovery and isolation of the 2D carbon allotrope, graphene, research into additional 2D materials has significantly expanded. Electrical components continue to decrease in size so there is an ever-growing need for smaller circuitry to keep up with the demand. Research with graphene and additional 2D layered materials, such as transition metal dichalcogenides, brought about a realization of many unique properties that have never been previously explored for applications in electronics, photonics, and optoelectronics. Phosphorene, a novel 2D material isolated from bulk black phosphorus, is an intrinsic p-type material with a variable band gap for a variety of applications. However, these applications are limited by the inability to isolate films of phosphorene. This work investigates some of the previously found techniques for use with graphene isolation and their adaptations to phosphorene. Isolation of phosphorene from black phosphorus was investigated by exfoliation from bulk, chemical vapor deposition, and thin film conversion. Mechanical exfoliation with a tape method, drawing method, and tape/drawing method were used to isolate few-layer black phosphorus samples from bulk material. These methods were also briefly compared to liquid exfoliation of black phosphorus. A chemical vapor deposition approach led to the discovery of a novel method for growth of amorphous red phosphorus thin films from bulk red phosphorus/black phosphorus. An in situ chemical vapor deposition type approach was developed using these thin films for growth of a variety of 2D phosphorus allotropes. Successful conversion has provided fibrous phosphorus wires and hexagons, along with violet phosphorus and eventually black phosphorus. This approach demonstrates progress towards direct growth of 2D black phosphorus onto substrates with average areas >3 microm2 and thicknesses representing samples around 4 layers. Thicker samples were also observed with average areas >100 microm2. X

  15. The use of NMR techniques for the analysis of water in coal and the effect of different coal drying techniques on the structure and reactivity of coal. Final report

    SciTech Connect

    Netzel, D.A.; Miknis, F.P.; Wallace, J.C. Jr.; Butcher, C.H.; Mitzel, J.M.; Turner, T.F.; Hurtubise, R.J.

    1995-02-01

    Western Research Institute has conducted a study of different methods of coal drying as pretreatment steps before liquefaction. The objectives of this study were to develop a combined chemical dehydration/nuclear magnetic resonance (NMR) method for measuring the moisture content of coal, to measure the changes in coal structure that occur during drying, and to determine the effects of different drying methods on liquefaction reactivity of coals. Different methods of drying were investigated to determine whether coal drying can be accomplished without reducing the reactivity of coals toward liquefaction. Drying methods included thermal, microwave, and chemical dehydration. Coals of rank lignite to high volatile bituminous were studied. Coals that were dried or partially dried thermally and with microwaves had lower liquefaction conversions than coals containing equilibrium moisture contents. However, chemically dried coals had conversions equal to or greater than the premoisturized coals. The conversion behavior is consistent with changes in the physical structure and cross linking reactions because of drying. Thermal and microwave drying appear to cause a collapse in the pore structure, thus preventing donor solvents such as tetralin from contacting reactive sites inside the coals. Chemical dehydration does not appear to collapse the pore structure. These results are supported by the solvent swelling measurements in which the swelling ratios of thermally dried and microwave-dried coals were lower than those of premoisturized coals, indicating a greater degree of cross linking in the dried coals. The swelling ratios of the chemically dried coals were greater than those of the premoisturized coals because the pore structure remaining unchanged or increased when water was removed. These results are consistent with the NMR results, which did not show significant changes in coal chemical structure.

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

    PubMed

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

    1997-01-01

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

  17. 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

  18. An introduction to biological NMR spectroscopy.

    PubMed

    Marion, Dominique

    2013-11-01

    NMR spectroscopy is a powerful tool for biologists interested in the structure, dynamics, and interactions of biological macromolecules. This review aims at presenting in an accessible manner the requirements and limitations of this technique. As an introduction, the history of NMR will highlight how the method evolved from physics to chemistry and finally to biology over several decades. We then introduce the NMR spectral parameters used in structural biology, namely the chemical shift, the J-coupling, nuclear Overhauser effects, and residual dipolar couplings. Resonance assignment, the required step for any further NMR study, bears a resemblance to jigsaw puzzle strategy. The NMR spectral parameters are then converted into angle and distances and used as input using restrained molecular dynamics to compute a bundle of structures. When interpreting a NMR-derived structure, the biologist has to judge its quality on the basis of the statistics provided. When the 3D structure is a priori known by other means, the molecular interaction with a partner can be mapped by NMR: information on the binding interface as well as on kinetic and thermodynamic constants can be gathered. NMR is suitable to monitor, over a wide range of frequencies, protein fluctuations that play a crucial role in their biological function. In the last section of this review, intrinsically disordered proteins, which have escaped the attention of classical structural biology, are discussed in the perspective of NMR, one of the rare available techniques able to describe structural ensembles. This Tutorial is part of the International Proteomics Tutorial Programme (IPTP 16 MCP).

  19. An Introduction to Biological NMR Spectroscopy*

    PubMed Central

    Marion, Dominique

    2013-01-01

    NMR spectroscopy is a powerful tool for biologists interested in the structure, dynamics, and interactions of biological macromolecules. This review aims at presenting in an accessible manner the requirements and limitations of this technique. As an introduction, the history of NMR will highlight how the method evolved from physics to chemistry and finally to biology over several decades. We then introduce the NMR spectral parameters used in structural biology, namely the chemical shift, the J-coupling, nuclear Overhauser effects, and residual dipolar couplings. Resonance assignment, the required step for any further NMR study, bears a resemblance to jigsaw puzzle strategy. The NMR spectral parameters are then converted into angle and distances and used as input using restrained molecular dynamics to compute a bundle of structures. When interpreting a NMR-derived structure, the biologist has to judge its quality on the basis of the statistics provided. When the 3D structure is a priori known by other means, the molecular interaction with a partner can be mapped by NMR: information on the binding interface as well as on kinetic and thermodynamic constants can be gathered. NMR is suitable to monitor, over a wide range of frequencies, protein fluctuations that play a crucial role in their biological function. In the last section of this review, intrinsically disordered proteins, which have escaped the attention of classical structural biology, are discussed in the perspective of NMR, one of the rare available techniques able to describe structural ensembles. This Tutorial is part of the International Proteomics Tutorial Programme (IPTP 16 MCP). PMID:23831612

  20. 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.

  1. Advanced solid-state NMR characterization of marine dissolved organic matter isolated using the coupled reverse osmosis/electrodialysis method.

    PubMed

    Mao, Jingdong; Kong, Xueqian; Schmidt-Rohr, Klaus; Pignatello, Joseph J; Perdue, E Michael

    2012-06-01

    Advanced (13)C solid-state techniques were employed to investigate the major structural characteristics of two surface-seawater dissolved organic matter (DOM) samples isolated using the novel coupled reverse osmosis/electrodialysis method. The NMR techniques included quantitative (13)C direct polarization/magic angle spinning (DP/MAS) and DP/MAS with recoupled dipolar dephasing, (13)C cross-polarization/total sideband suppression (CP/TOSS), (13)C chemical shift anisotropy filter, CH, CH(2), and CH(n) selection, two-dimensional (1)H-(13)C heteronuclear correlation NMR (2D HETCOR), 2D HETCOR combined with dipolar dephasing, and (15)N cross-polarization/magic angle spinning (CP/MAS). The two samples (Coastal and Marine DOM) were collected at the mouth of the Ogeechee River and in the Gulf Stream, respectively. The NMR results indicated that they were structurally distinct. Coastal DOM contained significantly more aromatic and carbonyl carbons whereas Marine DOM was markedly enriched in alkoxy carbon (e.g., carbohydrate-like moieties). Both samples contained significant amide N, but Coastal DOM had nitrogen bonded to aromatic carbons. Our dipolar-dephased spectra indicated that a large fraction of alkoxy carbons were not protonated. For Coastal DOM, our NMR results were consistent with the presence of the major structural units of (1) carbohydrate-like moieties, (2) lignin residues, (3) peptides or amino sugars, and (4) COO-bonded alkyls. For Marine DOM, they were (1) carbohydrate-like moieties, (2) peptides or amino sugars, and (3) COO-bonded alkyls. In addition, both samples contained significant amounts of nonpolar alkyl groups. The potential sources of the major structural units of DOM were discussed in detail. Nonprotonated O-alkyl carbon content was proposed as a possible index of humification. PMID:22553962

  2. A Primer of Fourier Transform NMR.

    ERIC Educational Resources Information Center

    Macomber, Roger S.

    1985-01-01

    Fourier transform nuclear magnetic resonance (NMR) is a new spectroscopic technique that is often omitted from undergraduate curricula because of lack of instructional materials. Therefore, information is provided to introduce students to the technique of data collection and transformation into the frequency domain. (JN)

  3. 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.

  4. 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.

  5. In-cell NMR spectroscopy.

    PubMed

    Serber, Zach; Corsini, Lorenzo; Durst, Florian; Dötsch, Volker

    2005-01-01

    The role of a protein inside a cell is determined by both its location and its conformational state. Although fluorescence techniques are widely used to determine the cellular localization of proteins in vivo, these approaches cannot provide detailed information about a protein's three-dimensional state. This gap, however, can be filled by NMR spectroscopy, which can be used to investigate both the conformation as well as the dynamics of proteins inside living cells. In this chapter we describe technical aspects of these "in-cell NMR" experiments. In particular, we show that in the case of (15)N-labeling schemes the background caused by labeling all cellular components is negligible, while (13)C-based experiments suffer from high background levels and require selective labeling schemes. A correlation between the signal-to-noise ratio of in-cell NMR experiments with the overexpression level of the protein shows that the current detection limit is 150-200 muM (intracellular concentration). We also discuss experiments that demonstrate that the intracellular viscosity is not a limiting factor since the intracellular rotational correlation time is only approximately two times longer than the correlation time in water. Furthermore, we describe applications of the technique and discuss its limitations. PMID:15808216

  6. 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.

  7. Reaction monitoring using online vs tube NMR spectroscopy: seriously different results.

    PubMed

    Foley, David A; Dunn, Anna L; Zell, Mark T

    2016-06-01

    We report findings from the qualitative evaluation of nuclear magnetic resonance (NMR) reaction monitoring techniques of how each relates to the kinetic profile of a reaction process. The study highlights key reaction rate differences observed between the various NMR reaction monitoring methods investigated: online NMR, static NMR tubes, and periodic inversion of NMR tubes. The analysis of three reaction processes reveals that rates derived from NMR analysis are highly dependent on monitoring method. These findings indicate that users must be aware of the effect of their monitoring method upon the kinetic rate data derived from NMR analysis. Copyright © 2015 John Wiley & Sons, Ltd.

  8. 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

  9. The use of solid-state NMR techniques for the analysis of water in coal and the effect of different coal drying techniques on the structure and reactivity of coal. Quarterly report, June 1--August 31, 1993

    SciTech Connect

    Netzel, D.A.

    1993-11-01

    One area for improvement in the economics of coal liquefaction is coal drying, particularly for the lower rank coals. However, there is considerable evidence to show that drying has a detrimental effect on the liquefaction behavior of coals. Regarding the liquefaction of coal, there does not appear to have been any systematic study of the methods of coal drying on coal structure and the role water plays in enhancing or lessening coal reactivity toward liquefaction. To conduct this study two coals, the North Dakota Beulah Zap lignite and the Utah Blind Canyon coals were chosen. These coals represent a low and high rank coal, respectively. In addition, the Beulah Zap lignite has a high moisture content whereas the Blind Canyon coal (hvA) bituminous has a very low moisture content. The overall objectives of this study are to develop a nuclear magnetic resonance (NMR) method for measuring the water in coal, to measure the changes in coal structure that occur during coal drying, to determine what effect water has on retrograde/condensation reactions, and to determine the mechanism by which water may impact coal reactivity toward liquefaction. Different methods of drying are being investigated to determine if drying can be accomplished without destroying coal reactivity toward liquefaction. The objectives for this quarterly report period were (1) to measure the volumetric swelling ratio for initial and chemically-dried coals and (2) to conduct preliminary experiments concerning the exchange of water in coal with deuterium oxide (D{sub 2}O).

  10. Interactive 2D to 3D stereoscopic image synthesis

    NASA Astrophysics Data System (ADS)

    Feldman, Mark H.; Lipton, Lenny

    2005-03-01

    Advances in stereoscopic display technologies, graphic card devices, and digital imaging algorithms have opened up new possibilities in synthesizing stereoscopic images. The power of today"s DirectX/OpenGL optimized graphics cards together with adapting new and creative imaging tools found in software products such as Adobe Photoshop, provide a powerful environment for converting planar drawings and photographs into stereoscopic images. The basis for such a creative process is the focus of this paper. This article presents a novel technique, which uses advanced imaging features and custom Windows-based software that utilizes the Direct X 9 API to provide the user with an interactive stereo image synthesizer. By creating an accurate and interactive world scene with moveable and flexible depth map altered textured surfaces, perspective stereoscopic cameras with both visible frustums and zero parallax planes, a user can precisely model a virtual three-dimensional representation of a real-world scene. Current versions of Adobe Photoshop provide a creative user with a rich assortment of tools needed to highlight elements of a 2D image, simulate hidden areas, and creatively shape them for a 3D scene representation. The technique described has been implemented as a Photoshop plug-in and thus allows for a seamless transition of these 2D image elements into 3D surfaces, which are subsequently rendered to create stereoscopic views.

  11. Asymmetric 2D spatial beam filtering by photonic crystals

    NASA Astrophysics Data System (ADS)

    Gailevicius, D.; Purlys, V.; Maigyte, L.; Gaizauskas, E.; Peckus, M.; Gadonas, R.; Staliunas, K.

    2016-04-01

    Spatial filtering techniques are important for improving the spatial quality of light beams. Photonic crystals (PhCs) with a selective spatial (angular) transmittance can also provide spatial filtering with the added benefit transversal symmetries, submillimeter dimensions and monolithic integration in other devices, such as micro-lasers or semiconductor lasers. Workable bandgap PhC configurations require a modulated refractive index with period lengths that are approximately less than the wavelength of radiation. This imposes technical limitations, whereby the available direct laser write (DLW) fabrication techniques are limited in resolution and refractive index depth. If, however, a deflection mechanism is chosen instead, a functional filter PhC can be produced that is operational in the visible wavelength regime. For deflection based PhCs glass is an attractive choice as it is highly stable medium. 2D and 3D PhC filter variations have already been produced on soda-lime glass. However, little is known about how to control the scattering of PhCs when approaching the smallest period values. Here we look into the internal structure of the initially symmetric geometry 2D PhCs and associating it with the resulting transmittance spectra. By varying the DLW fabrication beam parameters and scanning algorithms, we show that such PhCs contain layers that are comprised of semi-tilted structure voxels. We show the appearance of asymmetry can be compensated in order to circumvent some negative effects at the cost of potentially maximum scattering efficiency.

  12. 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.

  13. 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.

  14. 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

  15. Simulation of 2D Fields of Raindrop Size Distributions

    NASA Astrophysics Data System (ADS)

    Berne, A.; Schleiss, M.; Uijlenhoet, R.

    2008-12-01

    The raindrop size distribution (DSD hereafter) is of primary importance for quantitative applications of weather radar measurements. The radar reflectivity~Z (directly measured by radar) is related to the power backscattered by the ensemble of hydrometeors within the radar sampling volume. However, the rain rate~R (the flux of water to the surface) is the variable of interest for many applications (hydrology, weather forecasting, air traffic for example). Usually, radar reflectivity is converted into rain rate using a power law such as Z=aRb. The coefficients a and b of the Z-R relationship depend on the DSD. The variability of the DSD in space and time has to be taken into account to improve radar rain rate estimates. Therefore, the ability to generate a large number of 2D fields of DSD which are statistically homogeneous provides a very useful simulation framework that nicely complements experimental approaches based on DSD data, in order to investigate radar beam propagation through rain as well as radar retrieval techniques. The proposed approach is based on geostatistics for structural analysis and stochastic simulation. First, the DSD is assumed to follow a gamma distribution. Hence a 2D field of DSDs can be adequately described as a 2D field of a multivariate random function consisting of the three DSD parameters. Such fields are simulated by combining a Gaussian anamorphosis and a multivariate Gaussian random field simulation algorithm. Using the (cross-)variogram models fitted on data guaranties that the spatial structure of the simulated fields is consistent with the observed one. To assess its validity, the proposed method is applied to data collected during intense Mediterranean rainfall. As only time series are available, Taylor's hypothesis is assumed to convert time series in 1D range profile. Moreover, DSD fields are assumed to be isotropic so that the 1D structure can be used to simulate 2D fields. A large number of 2D fields of DSD parameters are

  16. Structural Modifications of Deoxycholic Acid to Obtain Three Known Brassinosteroid Analogues and Full NMR Spectroscopic Characterization.

    PubMed

    Herrera, Heidy; Carvajal, Rodrigo; Olea, Andrés F; Espinoza, Luis

    2016-01-01

    An improved synthesis route for obtaining known brassinosteroid analogues, i.e., methyl 2α,3α-dihydroxy-6-oxo-5α-cholan-24-oate (11), methyl 3α-hydroxy-6-oxo-7-oxa-5α-cholan-24-oate (15) and methyl 3α-hydroxy-6-oxa-7-oxo-5α-cholan-24-oate (16), from hyodeoxycholic acid (4) maintaining the native side chain is described. In the alternative procedure, the di-oxidized product 6, obtained in the oxidation of methyl hyodeoxycholate 5, was converted almost quantitatively into the target monoketone 7 by stereoselective reduction with NaBH₄, increasing the overall yield of this synthetic route to 96.8%. The complete ¹H- and (13)C-NMR assignments for all compounds synthesized in this work have been made by 1D and 2D heteronuclear correlation gs-HSQC and gs-HMBC techniques. Thus, it was possible to update the spectroscopic information of ¹H-NMR and to accomplish a complete assignment of all (13)C-NMR signals for analogues 5-16, which were previously reported only in partial form. PMID:27618889

  17. Communication: Molecular dynamics and 1H NMR of n-hexane in liquid crystals

    NASA Astrophysics Data System (ADS)

    Weber, Adrian C. J.; Burnell, E. Elliott; Meerts, W. Leo; de Lange, Cornelis A.; Dong, Ronald Y.; Muccioli, Luca; Pizzirusso, Antonio; Zannoni, Claudio

    2015-07-01

    The NMR spectrum of n-hexane orientationally ordered in the nematic liquid crystal ZLI-1132 is analysed using covariance matrix adaptation evolution strategy (CMA-ES). The spectrum contains over 150 000 transitions, with many sharp features appearing above a broad, underlying background signal that results from the plethora of overlapping transitions from the n-hexane as well as from the liquid crystal. The CMA-ES requires initial search ranges for NMR spectral parameters, notably the direct dipolar couplings. Several sets of such ranges were utilized, including three from MD simulations and others from the modified chord model that is specifically designed to predict hydrocarbon-chain dipolar couplings. In the end, only inaccurate dipolar couplings from an earlier study utilizing proton-proton double quantum 2D-NMR techniques on partially deuterated n-hexane provided the necessary estimates. The precise set of dipolar couplings obtained can now be used to investigate conformational averaging of n-hexane in a nematic environment.

  18. Communication: Molecular dynamics and {sup 1}H NMR of n-hexane in liquid crystals

    SciTech Connect

    Weber, Adrian C. J.; Burnell, E. Elliott; Meerts, W. Leo; Lange, Cornelis A. de; Dong, Ronald Y.; Muccioli, Luca Pizzirusso, Antonio Zannoni, Claudio

    2015-07-07

    The NMR spectrum of n-hexane orientationally ordered in the nematic liquid crystal ZLI-1132 is analysed using covariance matrix adaptation evolution strategy (CMA-ES). The spectrum contains over 150 000 transitions, with many sharp features appearing above a broad, underlying background signal that results from the plethora of overlapping transitions from the n-hexane as well as from the liquid crystal. The CMA-ES requires initial search ranges for NMR spectral parameters, notably the direct dipolar couplings. Several sets of such ranges were utilized, including three from MD simulations and others from the modified chord model that is specifically designed to predict hydrocarbon-chain dipolar couplings. In the end, only inaccurate dipolar couplings from an earlier study utilizing proton-proton double quantum 2D-NMR techniques on partially deuterated n-hexane provided the necessary estimates. The precise set of dipolar couplings obtained can now be used to investigate conformational averaging of n-hexane in a nematic environment.

  19. 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.

  20. Advecting Procedural Textures for 2D Flow Animation

    NASA Technical Reports Server (NTRS)

    Kao, David; Pang, Alex; Moran, Pat (Technical Monitor)

    2001-01-01

    This paper proposes the use of specially generated 3D procedural textures for visualizing steady state 2D flow fields. We use the flow field to advect and animate the texture over time. However, using standard texture advection techniques and arbitrary textures will introduce some undesirable effects such as: (a) expanding texture from a critical source point, (b) streaking pattern from the boundary of the flowfield, (c) crowding of advected textures near an attracting spiral or sink, and (d) absent or lack of textures in some regions of the flow. This paper proposes a number of strategies to solve these problems. We demonstrate how the technique works using both synthetic data and computational fluid dynamics data.

  1. NMR doesn't lie or how solid-state NMR spectroscopy contributed to a better understanding of the nature and function of soil organic matter (Philippe Duchaufour Medal Lecture)

    NASA Astrophysics Data System (ADS)

    Knicker, Heike

    2016-04-01

    for organo-mineral interactions. Since decent solid-state NMR spectra cannot be obtained from graphenic components, the successful acquisition of solid-state 13C and 15N NMR spectra of charcoals challenged the well accepted model of their chemical nature. Application of advanced 2D NMR approaches confirmed the new view of charcoal as a heterogeneous material, the composition of which depends upon the feedstock and charring condition. The respective consequences of this alternative for the understanding of C sequestration are still matter of ongoing debates. Although the sensitivity of 15N for NMR spectroscopy is 50 times lower than that of 13C, first solid-state 15N NMR spectra of soils with natural 15N abundance were already published in the 1990's. They clearly identified peptide-like structures as the main organic N form in unburnt soils. However, in spite of their high contribution to SOM, the role of peptides in soils is far from understood. Considering the new technological developments in the field of NMR spectroscopy, this technique will certainly not stop to contribute to unexpected results.

  2. Isolation and Characterization of a Novel Rebaudioside M Isomer from a Bioconversion Reaction of Rebaudioside A and NMR Comparison Studies of Rebaudioside M Isolated from Stevia rebaudiana Bertoni and Stevia rebaudiana Morita

    PubMed Central

    Prakash, Indra; Bunders, Cynthia; Devkota, Krishna P.; Charan, Romila D.; Ramirez, Catherine; Priedemann, Christopher; Markosyan, Avetik

    2014-01-01

    A minor product, rebaudioside M2 (2), from the bioconversion reaction of rebaudioside A (4) to rebaudioside D (3), was isolated and the complete structure of the novel steviol glycoside was determined. Rebaudioside M2 (2) is considered an isomer of rebaudioside M (1) and contains a relatively rare 1→6 sugar linkage. It was isolated and characterized with NMR (1H, 13C, COSY, HSQC-DEPT, HMBC, 1D-TOCSY, and NOESY) and mass spectral data. Additionally, we emphasize the importance of 1D and 2D NMR techniques when identifying complex steviol glycosides. Numerous NMR spectroscopy studies of rebaudioside M (1), rebaudioside D (3), and mixture of 1 and 3 led to the discovery that SG17 which was previously reported in literature, is a mixture of rebaudioside D (3), rebaudioside M (1), and possibly other related steviol glycosides. PMID:24970220

  3. Isolation and characterization of a novel rebaudioside M isomer from a bioconversion reaction of rebaudioside A and NMR comparison studies of rebaudioside M isolated from Stevia rebaudiana Bertoni and Stevia rebaudiana Morita.

    PubMed

    Prakash, Indra; Bunders, Cynthia; Devkota, Krishna P; Charan, Romila D; Ramirez, Catherine; Priedemann, Christopher; Markosyan, Avetik

    2014-01-01

    A minor product, rebaudioside M2 (2), from the bioconversion reaction of rebaudioside A (4) to rebaudioside D (3), was isolated and the complete structure of the novel steviol glycoside was determined. Rebaudioside M2 (2) is considered an isomer of rebaudioside M (1) and contains a relatively rare 1→6 sugar linkage. It was isolated and characterized with NMR (1H, 13C, COSY, HSQC-DEPT, HMBC, 1D-TOCSY, and NOESY) and mass spectral data. Additionally, we emphasize the importance of 1D and 2D NMR techniques when identifying complex steviol glycosides. Numerous NMR spectroscopy studies of rebaudioside M (1), rebaudioside D (3), and mixture of 1 and 3 led to the discovery that SG17 which was previously reported in literature, is a mixture of rebaudioside D (3), rebaudioside M (1), and possibly other related steviol glycosides.

  4. Application and Reliability of Solid-State NMR in Environmental Sciences

    NASA Astrophysics Data System (ADS)

    Knicker, Heike

    2010-05-01

    technique increases the sensitivity of 13C by magnetization transfer from the 1H to the 13C spin system during a contact time tc. However, one has to bear in mind that some molecular properties may obscure quantification. Thus, for carbons with large C-H internuclear distances (bigger than four bonds, i.e in graphite structures) and for C in groups with high molecular mobility (i.e. gas) the proton-dipolar interactions are weakened and the polarization transfer may be incomplete. The observed intensity can also be affected by interactions of the protons with paramagnetic compounds. To circumvent this problem, the samples are often demineralized with hydrofluoric acid. Alternatively, the Bloch decay, a technique in which the 13C is directly excited is used. Here, on the other hand, one has to consider long relaxation times which may lead to saturation effects. Nevertheless, as it will be discussed within the presentation those quantification problems can be solved for most soil samples and then solid-state NMR spectroscopy represents a powerful tool for qualitative and quantitative analysis. Special techniques, such as dipolar dephasing or the proton spin relaxation editing can be used to extract additional information about chemical properties or mobility. A more detailed examination of the cross polarization behavior can be used to analyze the interaction of organic matter and paramagnetics but also for obtaining revealing properties on a molecular level. Applications involving isotopic labeling combined with both 13C and/or 15N NMR allows to follow the fate of a specific compound i.e. in a natural matrix and- if the enrichment is high enough - the use of 2D solid-state NMR techniques. In particular with respect to environmental chemistry, this combination of isotopic labeling with the use of corresponding NMR spectroscopy shows great potential for a better understanding of the kind of interaction between pollutants and natural organic matter.

  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. 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.

  7. 2D quantum gravity from quantum entanglement.

    PubMed

    Gliozzi, F

    2011-01-21

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

  8. 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).

  9. Assigning the NMR Spectrum of Glycidol: An Advanced Organic Chemistry Exercise

    ERIC Educational Resources Information Center

    Helms, Eric; Arpaia, Nicholas; Widener, Melissa

    2007-01-01

    Various one- and two-dimensional NMR experiments have been found to be extremely useful for assigning the proton and carbon NMR spectra of glycidol. The technique provides extremely valuable information aiding in the complete assignment of the peaks.

  10. Intelligent Automated Correction of Baseplane and Systematic Noise in Two-Dimensional NMR Spectra

    NASA Astrophysics Data System (ADS)

    Levy, G. C.; Jeong, G. W.; Yu, J. Q.; Wang, K.

    A computer program useful for 2D NMR data is described that provides automatic two-dimensional baseplane correction and subsequent tl and t2 ridge suppression. The algorithm per forms combined correction of smooth baseplane distortions and sharp ridges in 2D NMR spectra through five steps: (1) identification of resonance peaks and ridges, (2) extraction of initial, putative global baseplane, (3) window filtering of the corresponding time domain, (4) construction of a 2D spectrum free of baseplane distortion, and (5) suppression of ridges, The optimal parameters for baseplane and ridge correction are automatically decided by the program, yielding a greatly improved spectrum, together with more accurate spectral information.

  11. 2D biological representations with reduced speckle obtained from two perpendicular ultrasonic arrays.

    PubMed

    Rodriguez-Hernandez, Miguel A; Gomez-Sacristan, Angel; Sempere-Payá, Víctor M

    2016-04-29

    Ultrasound diagnosis is a widely used medical tool. Among the various ultrasound techniques, ultrasonic imaging is particularly relevant. This paper presents an improvement to a two-dimensional (2D) ultrasonic system using measurements taken from perpendicular planes, where digital signal processing techniques are used to combine one-dimensional (1D) A-scans were acquired by individual transducers in arrays located in perpendicular planes. An algorithm used to combine measurements is improved based on the wavelet transform, which includes a denoising step during the 2D representation generation process. The inclusion of this new denoising stage generates higher quality 2D representations with a reduced level of speckling. The paper includes different 2D representations obtained from noisy A-scans and compares the improvements obtained by including the denoising stage.

  12. 2D biological representations with reduced speckle obtained from two perpendicular ultrasonic arrays.

    PubMed

    Rodriguez-Hernandez, Miguel A; Gomez-Sacristan, Angel; Sempere-Payá, Víctor M

    2016-04-29

    Ultrasound diagnosis is a widely used medical tool. Among the various ultrasound techniques, ultrasonic imaging is particularly relevant. This paper presents an improvement to a two-dimensional (2D) ultrasonic system using measurements taken from perpendicular planes, where digital signal processing techniques are used to combine one-dimensional (1D) A-scans were acquired by individual transducers in arrays located in perpendicular planes. An algorithm used to combine measurements is improved based on the wavelet transform, which includes a denoising step during the 2D representation generation process. The inclusion of this new denoising stage generates higher quality 2D representations with a reduced level of speckling. The paper includes different 2D representations obtained from noisy A-scans and compares the improvements obtained by including the denoising stage. PMID:27163318

  13. Magic angle spinning NMR of viruses.

    PubMed

    Quinn, Caitlin M; Lu, Manman; Suiter, Christopher L; Hou, Guangjin; Zhang, Huilan; Polenova, Tatyana

    2015-04-01

    Viruses, relatively simple pathogens, are able to replicate in many living organisms and to adapt to various environments. Conventional atomic-resolution structural biology techniques, X-ray crystallography and solution NMR spectroscopy provided abundant information on the structures of individual proteins and nucleic acids comprising viruses; however, viral assemblies are not amenable to analysis by these techniques because of their large size, insolubility, and inherent lack of long-range order. In this article, we review the recent advances in magic angle spinning NMR spectroscopy that enabled atomic-resolution analysis of structure and dynamics of large viral systems and give examples of several exciting case studies. PMID:25919197

  14. Magic Angle Spinning NMR of Viruses

    PubMed Central

    Quinn, Caitlin; Lu, Manman; Suiter, Christopher L.; Hou, Guangjin; Zhang, Huilan; Polenova, Tatyana

    2015-01-01

    Viruses, relatively simple pathogens, are able to replicate in many living organisms and to adapt to various environments. Conventional atomic-resolution structural biology techniques, X-ray crystallography and solution NMR spectroscopy provided abundant information on the structures of individual proteins and nucleic acids comprising viruses; however, viral assemblies are not amenable to analysis by these techniques because of their large size, insolubility, and inherent lack of long-range order. In this article, we review the recent advances in magic angle spinning NMR spectroscopy that enabled atomic-resolution analysis of structure and dynamics of large viral systems and give examples of several exciting case studies. PMID:25919197

  15. CYP2D6*36 gene arrangements within the cyp2d6 locus: association of CYP2D6*36 with poor metabolizer status.

    PubMed

    Gaedigk, Andrea; Bradford, L Dianne; Alander, Sarah W; Leeder, J Steven

    2006-04-01

    Unexplained cases of CYP2D6 genotype/phenotype discordance continue to be discovered. In previous studies, several African Americans with a poor metabolizer phenotype carried the reduced function CYP2D6*10 allele in combination with a nonfunctional allele. We pursued the possibility that these alleles harbor either a known sequence variation (i.e., CYP2D6*36 carrying a gene conversion in exon 9 along the CYP2D6*10-defining 100C>T single-nucleotide polymorphism) or novel sequences variation(s). Discordant cases were evaluated by long-range polymerase chain reaction (PCR) to test for gene rearrangement events, and a 6.6-kilobase pair PCR product encompassing the CYP2D6 gene was cloned and entirely sequenced. Thereafter, allele frequencies were determined in different study populations comprising whites, African Americans, and Asians. Analyses covering the CYP2D7 to 2D6 gene region established that CYP2D6*36 did not only exist as a gene duplication (CYP2D6*36x2) or in tandem with *10 (CYP2D6*36+*10), as previously reported, but also by itself. This "single" CYP2D6*36 allele was found in nine African Americans and one Asian, but was absent in the whites tested. Ultimately, the presence of CYP2D6*36 resolved genotype/phenotype discordance in three cases. We also discovered an exon 9 conversion-positive CYP2D6*4 gene in a duplication arrangement (CYP2D6*4Nx2) and a CYP2D6*4 allele lacking 100C>T (CYP2D6*4M) in two white subjects. The discovery of an allele that carries only one CYP2D6*36 gene copy provides unequivocal evidence that both CYP2D6*36 and *36x2 are associated with a poor metabolizer phenotype. Given a combined frequency of between 0.5 and 3% in African Americans and Asians, genotyping for CYP2D6*36 should improve the accuracy of genotype-based phenotype prediction in these populations.

  16. 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

  17. Developing SABRE as an analytical tool in NMR

    NASA Astrophysics Data System (ADS)

    Lloyd, Lyrelle Stacey

    Work presented in this thesis centres around the application of the new hyperpolarisation technique, SABRE, within nuclear magnetic resonance spectroscopy, focusing on optimisation of the technique to characterise small organic molecules. While pyridine was employed as a model substrate, studies on a range of molecules are investigated including substituted pyridines, quinolines, thiazoles and indoles are detailed. Initial investigations explored how the properties of the SABRE catalyst effect the extent of polarisation transfer exhibited. The most important of these properties proved to be the rate constants for loss of pyridine and hydrides as these define the contact time of pyridine with the parahydrogen derived hydride ligands in the metal template. The effect of changing the temperature, solvent or concentration of substrate or catalyst are rationalised. For instance, the catalyst ICy(a) exhibits relatively slow ligand exchange rates and increasing the temperature during hyperpolarisation increases the observed signal enhancements. These studies have revealed a second polarisation transfer template can be used with SABRE in which two substrate molecules are bound. This allows the possibility of investigation of larger substrates which might otherwise be too sterically encumbered to bind. Another significant advance relates to the first demonstration that SABRE can be used in conjunction with an automated system designed with Bruker allowing the acquisition of scan averaged, phase cycled and traditional 2D spectra. The system also allowed investigations into the effect of the polarisation transfer field and application of that knowledge to collect single-scan 13C data for characterisation. The successful acquisition of 1H NOESY, 1H-1H COSY, 1H-13C 2D and ultrafast 1H-1H COSY NMR sequences is detailed for a 10 mM concentration sample, with 1H data collected for a 1 mM sample. A range of studies which aim to demonstrate the applicability of SABRE to the

  18. NMR Measures of Heterogeneity Length

    NASA Astrophysics Data System (ADS)

    Spiess, Hans W.

    2002-03-01

    Advanced solid state NMR spectroscopy provides a wealth of information about structure and dynamics of complex systems. On a local scale, multidimensional solid state NMR has elucidated the geometry and the time scale of segmental motions at the glass transition. The higher order correlation functions which are provided by this technique led to the notion of dynamic heterogeneities, which have been characterized in detail with respect to their rate memory and length scale. In polymeric and low molar mass glass formers of different fragility, length scales in the range 2 to 4 nm are observed. In polymeric systems, incompatibility of backbone and side groups as in polyalkylmethacrylates leads to heteogeneities on the nm scale, which manifest themselves in unusual chain dynamics at the glass transition involving extended chain conformations. References: K. Schmidt-Rohr and H.W. Spiess, Multidimensional Solid-State NMR and Polymers,Academic Press, London (1994). U. Tracht, M. Wilhelm, A. Heuer, H. Feng, K. Schmidt-Rohr, H.W. Spiess, Phys. Rev. Lett. 81, 2727 (1998). S.A. Reinsberg, X.H. Qiu, M. Wilhelm, M.D. Ediger, H.W. Spiess, J.Chem.Phys. 114, 7299 (2001). S.A. Reinsberg, A. Heuer, B. Doliwa, H. Zimmermann, H.W. Spiess, J. Non-Crystal. Solids, in press (2002)

  19. Probing dipole-dipole interaction in a rubidium gas via double-quantum 2D spectroscopy.

    PubMed

    Gao, Feng; Cundiff, Steven T; Li, Hebin

    2016-07-01

    We have implemented double-quantum 2D spectroscopy on a rubidium vapor and shown that this technique provides sensitive and background-free detection of the dipole-dipole interaction. The 2D spectra include signals from both individual atoms and interatomic interactions, allowing quantitative studies of the interaction. A theoretical model based on the optical Bloch equations is used to reproduce the experimental spectrum and confirm the origin of double-quantum signals. PMID:27367074

  20. Laser fabrication of 2D and 3D metal nanoparticle structures and arrays.

    PubMed

    Kuznetsov, A I; Kiyan, R; Chichkov, B N

    2010-09-27

    A novel method for fabrication of 2D and 3D metal nanoparticle structures and arrays is proposed. This technique is based on laser-induced transfer of molten metal nanodroplets from thin metal films. Metal nanoparticles are produced by solidification of these nanodroplets. The size of the transferred nanoparticles can be controllably changed in the range from 180 nm to 1500 nm. Several examples of complex 2D and 3D microstructures generated form gold nanoparticles are demonstrated. PMID:20941016

  1. Concerted two-dimensional NMR approaches to hydrogen-1, carbon-13, and nitrogen-15 resonance assignments in proteins

    SciTech Connect

    Stockman, B.J.; Reily, M.D.; Westler, W.M.; Ulrich, E.L.; Markley, J.L. )

    1989-01-10

    When used in concert, one-bond carbon-carbon correlations, one-bond and multiple-bond proton-carbon correlations, and multiple-bond proton-nitrogen correlations, derived from two-dimensional (2D) NMR spectra of isotopically enriched proteins, provide a reliable method of assigning proton, carbon, and nitrogen resonances. In contrast to procedures that simply extend proton assignments to carbon or nitrogen resonances, this technique assigns proton, carbon, and nitrogen resonances coordinately on the basis of their integrated coupling networks. Redundant spin coupling pathways provide ways of resolving overlaps frequently encountered in homonuclear {sup 1}H 2D NMR spectra and facilitate the elucidation of complex proton spin systems. Carbon-carbon and proton-carbon couplings can be used to bridge the aromatic and aliphatic parts of proton spin systems; this avoids possible ambiguities that may result from the use of nuclear Overhauser effects to assign aromatic amino acid signals. The technique is illustrated for Anabaena 7120 flavodoxin and cytochrome c-553, both uniformly enriched with carbon-13 (26%) or nitrogen-15 (98%).

  2. 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

  3. Progress in 2D photonic crystal Fano resonance photonics

    NASA Astrophysics Data System (ADS)

    Zhou, Weidong; Zhao, Deyin; Shuai, Yi-Chen; Yang, Hongjun; Chuwongin, Santhad; Chadha, Arvinder; Seo, Jung-Hun; Wang, Ken X.; Liu, Victor; Ma, Zhenqiang; Fan, Shanhui

    2014-01-01

    In contrast to a conventional symmetric Lorentzian resonance, Fano resonance is predominantly used to describe asymmetric-shaped resonances, which arise from the constructive and destructive interference of discrete resonance states with broadband continuum states. This phenomenon and the underlying mechanisms, being common and ubiquitous in many realms of physical sciences, can be found in a wide variety of nanophotonic structures and quantum systems, such as quantum dots, photonic crystals, plasmonics, and metamaterials. The asymmetric and steep dispersion of the Fano resonance profile promises applications for a wide range of photonic devices, such as optical filters, switches, sensors, broadband reflectors, lasers, detectors, slow-light and non-linear devices, etc. With advances in nanotechnology, impressive progress has been made in the emerging field of nanophotonic structures. One of the most attractive nanophotonic structures for integrated photonics is the two-dimensional photonic crystal slab (2D PCS), which can be integrated into a wide range of photonic devices. The objective of this manuscript is to provide an in depth review of the progress made in the general area of Fano resonance photonics, focusing on the photonic devices based on 2D PCS structures. General discussions are provided on the origins and characteristics of Fano resonances in 2D PCSs. A nanomembrane transfer printing fabrication technique is also reviewed, which is critical for the heterogeneous integrated Fano resonance photonics. The majority of the remaining sections review progress made on various photonic devices and structures, such as high quality factor filters, membrane reflectors, membrane lasers, detectors and sensors, as well as structures and phenomena related to Fano resonance slow light effect, nonlinearity, and optical forces in coupled PCSs. It is expected that further advances in the field will lead to more significant advances towards 3D integrated photonics, flat

  4. 2D to 3D conversion implemented in different hardware

    NASA Astrophysics Data System (ADS)

    Ramos-Diaz, Eduardo; Gonzalez-Huitron, Victor; Ponomaryov, Volodymyr I.; Hernandez-Fragoso, Araceli

    2015-02-01

    Conversion of available 2D data for release in 3D content is a hot topic for providers and for success of the 3D applications, in general. It naturally completely relies on virtual view synthesis of a second view given by original 2D video. Disparity map (DM) estimation is a central task in 3D generation but still follows a very difficult problem for rendering novel images precisely. There exist different approaches in DM reconstruction, among them manually and semiautomatic methods that can produce high quality DMs but they demonstrate hard time consuming and are computationally expensive. In this paper, several hardware implementations of designed frameworks for an automatic 3D color video generation based on 2D real video sequence are proposed. The novel framework includes simultaneous processing of stereo pairs using the following blocks: CIE L*a*b* color space conversions, stereo matching via pyramidal scheme, color segmentation by k-means on an a*b* color plane, and adaptive post-filtering, DM estimation using stereo matching between left and right images (or neighboring frames in a video), adaptive post-filtering, and finally, the anaglyph 3D scene generation. Novel technique has been implemented on DSP TMS320DM648, Matlab's Simulink module over a PC with Windows 7, and using graphic card (NVIDIA Quadro K2000) demonstrating that the proposed approach can be applied in real-time processing mode. The time values needed, mean Similarity Structural Index Measure (SSIM) and Bad Matching Pixels (B) values for different hardware implementations (GPU, Single CPU, and DSP) are exposed in this paper.

  5. Multidimensional NMR spectroscopy in a single scan.

    PubMed

    Gal, Maayan; Frydman, Lucio

    2015-11-01

    Multidimensional NMR has become one of the most widespread spectroscopic tools available to study diverse structural and functional aspects of organic and biomolecules. A main feature of multidimensional NMR is the relatively long acquisition times that these experiments demand. For decades, scientists have been working on a variety of alternatives that would enable NMR to overcome this limitation, and deliver its data in shorter acquisition times. Counting among these methodologies is the so-called ultrafast (UF) NMR approach, which in principle allows one to collect arbitrary multidimensional correlations in a single sub-second transient. By contrast to conventional acquisitions, a main feature of UF NMR is a spatiotemporal manipulation of the spins that imprints the chemical shift and/or J-coupling evolutions being sought, into a spatial pattern. Subsequent gradient-based manipulations enable the reading out of this information and its multidimensional correlation into patterns that are identical to those afforded by conventional techniques. The current review focuses on the fundamental principles of this spatiotemporal UF NMR manipulation, and on a few of the methodological extensions that this form of spectroscopy has undergone during the years. PMID:26249041

  6. On Animating 2D Velocity Fields

    NASA Technical Reports Server (NTRS)

    Kao, David; Pang, Alex; Yan, Jerry (Technical Monitor)

    2001-01-01

    A velocity field, even one that represents a steady state flow, implies a dynamical system. Animated velocity fields is an important tool in understanding such complex phenomena. This paper looks at a number of techniques that animate velocity fields and propose two new alternatives. These are texture advection and streamline cycling. The common theme among these techniques is the use of advection on some texture to generate a realistic animation of the velocity field. Texture synthesis and selection for these methods are presented. Strengths and weaknesses of the techniques are also discussed in conjunctions with several examples.

  7. On Animating 2D Velocity Fields

    NASA Technical Reports Server (NTRS)

    Kao, David; Pang, Alex

    2000-01-01

    A velocity field. even one that represents a steady state flow implies a dynamical system. Animated velocity fields is an important tool in understanding such complex phenomena. This paper looks at a number of techniques that animate velocity fields and propose two new alternatives, These are texture advection and streamline cycling. The common theme among these techniques is the use of advection on some texture to generate a realistic animation of the velocity field. Texture synthesis and selection for these methods are presented. Strengths and weaknesses of the techniques are also discussed in conjunction with several examples.

  8. Protein structure validation and identification from unassigned residual dipolar coupling data using 2D-PDPA.

    PubMed

    Fahim, Arjang; Mukhopadhyay, Rishi; Yandle, Ryan; Prestegard, James H; Valafar, Homayoun

    2013-08-22

    More than 90% of protein structures submitted to the PDB each year are homologous to some previously characterized protein structure. The extensive resources that are required for structural characterization of proteins can be justified for the 10% of the novel structures, but not for the remaining 90%. This report presents the 2D-PDPA method, which utilizes unassigned residual dipolar coupling in order to address the economics of structure determination of routine proteins by reducing the data acquisition and processing time. 2D-PDPA has been demonstrated to successfully identify the correct structure of an array of proteins that range from 46 to 445 residues in size from a library of 619 decoy structures by using unassigned simulated RDC data. When using experimental data, 2D-PDPA successfully identified the correct NMR structures from the same library of decoy structures. In addition, the most homologous X-ray structure was also identified as the second best structural candidate. Finally, success of 2D-PDPA in identifying and evaluating the most appropriate structure from a set of computationally predicted structures in the case of a previously uncharacterized protein Pf2048.1 has been demonstrated. This protein exhibits less than 20% sequence identity to any protein with known structure and therefore presents a compelling and practical application of our proposed work.

  9. Protein structure validation and identification from unassigned residual dipolar coupling data using 2D-PDPA.

    PubMed

    Fahim, Arjang; Mukhopadhyay, Rishi; Yandle, Ryan; Prestegard, James H; Valafar, Homayoun

    2013-01-01

    More than 90% of protein structures submitted to the PDB each year are homologous to some previously characterized protein structure. The extensive resources that are required for structural characterization of proteins can be justified for the 10% of the novel structures, but not for the remaining 90%. This report presents the 2D-PDPA method, which utilizes unassigned residual dipolar coupling in order to address the economics of structure determination of routine proteins by reducing the data acquisition and processing time. 2D-PDPA has been demonstrated to successfully identify the correct structure of an array of proteins that range from 46 to 445 residues in size from a library of 619 decoy structures by using unassigned simulated RDC data. When using experimental data, 2D-PDPA successfully identified the correct NMR structures from the same library of decoy structures. In addition, the most homologous X-ray structure was also identified as the second best structural candidate. Finally, success of 2D-PDPA in identifying and evaluating the most appropriate structure from a set of computationally predicted structures in the case of a previously uncharacterized protein Pf2048.1 has been demonstrated. This protein exhibits less than 20% sequence identity to any protein with known structure and therefore presents a compelling and practical application of our proposed work. PMID:23973992

  10. Protein Structure Validation and Identification from Unassigned Residual Dipolar Coupling Data Using 2D-PDPA

    PubMed Central

    Fahim, Arjang; Mukhopadhyay, Rishi; Yandle, Ryan; Prestegard, James H.; Valafar, Homayoun

    2014-01-01

    More than 90% of protein structures submitted to the PDB each year are homologous to some previously characterized protein structure. The extensive resources that are required for structural characterization of proteins can be justified for the 10% of the novel structures, but not for the remaining 90%. This report presents the 2D-PDPA method, which utilizes unassigned residual dipolar coupling in order to address the economics of structure determination of routine proteins by reducing the data acquisition and processing time. 2D-PDPA has been demonstrated to successfully identify the correct structure of an array of proteins that range from 46 to 445 residues in size from a library of 619 decoy structures by using unassigned simulated RDC data. When using experimental data, 2D-PDPA successfully identified the correct NMR structures from the same library of decoy structures. In addition, the most homologous X-ray structure was also identified as the second best structural candidate. Finally, success of 2D-PDPA in identifying and evaluating the most appropriate structure from a set of computationally predicted structures in the case of a previously uncharacterized protein Pf2048.1 has been demonstrated. This protein exhibits less than 20% sequence identity to any protein with known structure and therefore presents a compelling and practical application of our proposed work. PMID:23973992

  11. SAR imaging via modern 2-D spectral estimation methods.

    PubMed

    DeGraaf, S R

    1998-01-01

    This paper discusses the use of modern 2D spectral estimation algorithms for synthetic aperture radar (SAR) imaging. The motivation for applying power spectrum estimation methods to SAR imaging is to improve resolution, remove sidelobe artifacts, and reduce speckle compared to what is possible with conventional Fourier transform SAR imaging techniques. This paper makes two principal contributions to the field of adaptive SAR imaging. First, it is a comprehensive comparison of 2D spectral estimation methods for SAR imaging. It provides a synopsis of the algorithms available, discusses their relative merits for SAR imaging, and illustrates their performance on simulated and collected SAR imagery. Some of the algorithms presented or their derivations are new, as are some of the insights into or analyses of the algorithms. Second, this work develops multichannel variants of four related algorithms, minimum variance method (MVM), reduced-rank MVM (RRMVM), adaptive sidelobe reduction (ASR) and space variant apodization (SVA) to estimate both reflectivity intensity and interferometric height from polarimetric displaced-aperture interferometric data. All of these interferometric variants are new. In the interferometric contest, adaptive spectral estimation can improve the height estimates through a combination of adaptive nulling and averaging. Examples illustrate that MVM, ASR, and SVA offer significant advantages over Fourier methods for estimating both scattering intensity and interferometric height, and allow empirical comparison of the accuracies of Fourier, MVM, ASR, and SVA interferometric height estimates.

  12. 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.

  13. 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

  14. 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.

  15. Pure shift NMR.

    PubMed

    Zangger, Klaus

    2015-04-01

    Although scalar-coupling provides important structural information, the resulting signal splittings significantly reduce the resolution of NMR spectra. Limited resolution is a particular problem in proton NMR experiments, resulting in part from the limited proton chemical shift range (∼10 ppm) but even more from the splittings due to scalar coupling to nearby protons. "Pure shift" NMR spectroscopy (also known as broadband homonuclear decoupling) has been developed for disentangling overlapped proton NMR spectra. The resulting spectra are considerably simplified as they consist of single lines, reminiscent of proton-decoupled C-13 spectra at natural abundance, with no multiplet structure. The different approaches to obtaining pure shift spectra are reviewed here and several applications presented. Pure shift spectra are especially useful for highly overlapped proton spectra, as found for example in reaction mixtures, natural products and biomacromolecules.

  16. Heteronuclear Multidimensional Protein NMR in a Teaching Laboratory

    ERIC Educational Resources Information Center

    Wright, Nathan T.

    2016-01-01

    Heteronuclear multidimensional NMR techniques are commonly used to study protein structure, function, and dynamics, yet they are rarely taught at the undergraduate level. Here, we describe a senior undergraduate laboratory where students collect, process, and analyze heteronuclear multidimensional NMR experiments using an unstudied Ig domain (Ig2…

  17. Functional groups identified by solid state 13C NMR spectroscopy

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Animal manure is generally high in organic matter intensity so it is well suitable for 13C nuclear magnetic resonance (NMR) analysis. Solid-state 13C NMR techniques used in characterizing organic matter and its components include, but are not limited to, cross-polarization /magic angle spinning (CP...

  18. Liquid- and solid-state high-resolution NMR methods for the investigation of aging processes of silicone breast implants.

    PubMed

    Birkefeld, Anja Britta; Bertermann, Rüdiger; Eckert, Hellmut; Pfleiderer, Bettina

    2003-01-01

    To investigate aging processes of silicone gel breast implants, which may include migration of free unreacted material from the gel and rubber to local (e.g. connective tissue capsule) or distant sites in the body, chemical alteration of the polymer and infiltration of body compounds, various approaches of multinuclear nuclear magnetic resonance (NMR) experiments (29Si, 13C, 1H) were evaluated. While 29Si, 13C, and 1H solid-state magic angle spinning (MAS) NMR techniques performed on virgin and explanted envelopes of silicone prostheses provided only limited information, high-resolution liquid-state NMR techniques of CDCl(3) extracts were highly sensitive analytical tools for the detection of aging related changes in the materials. Using 2D 1H, 1H correlation spectroscopy (COSY) and 29Si, 1H heteronuclear multiple bond coherence (HMBC) experiments with gradient selection, it was possible to detect lipids (mainly phospholipids) as well as silicone oligomer species in explanted envelopes and gels. Silicone oligomers were also found in connective tissue capsules, indicating that cyclic polysiloxanes can migrate from intact implants to adjacent and distant sites. Furthermore, lipids can permeate the implant and modify its chemical composition.

  19. High resolution NMR measurements using a 400MHz NMR with an (RE)Ba2Cu3O7-x high-temperature superconducting inner coil: Towards a compact super-high-field NMR.

    PubMed

    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 >1GHz. 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 400MHz 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 400MHz 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. PMID:26778351

  20. NMR-based dynamics of free glycosaminoglycans in solution.

    PubMed

    Pomin, Vitor H

    2014-08-01

    Glycosaminoglycans (GAGs) comprise a special class of complex carbohydrates endowed with numerous biological functions. Most of these functions are regulated by conformational arrangements or dynamical properties of GAGs in solution. Nuclear magnetic resonance (NMR) is a powerful technique used for dynamic analyses. Spin relaxation, scalar couplings, chemical shifts and nuclear Overhauser effect resonances are the commonest NMR parameters utilized in such analyses. Computational molecular dynamics are also very often employed in conjunction with, or restrained by, the NMR dataset. This report aims at describing the major NMR-based information available so far concerning the dynamical properties of free GAGs in solution.

  1. Rotational Doppler Effect and Barnett Field in Spinning NMR

    NASA Astrophysics Data System (ADS)

    Chudo, Hiroyuki; Harii, Kazuya; Matsuo, Mamoru; Ieda, Jun'ichi; Ono, Masao; Maekawa, Sadamichi; Saitoh, Eiji

    2015-04-01

    We report the observation of the rotational Doppler effect using nuclear magnetic resonance (NMR). We have developed a coil-spinning technique that enables measurements by rotating a detector and fixing a sample. We found that the rotational Doppler effect gives rise to NMR frequency shifts equal to the rotation frequency. We formulate the rotational Doppler effect and the Barnett field using a vector model for the nuclear magnetic moment. This formulation reveals that, with just the sample rotating, both effects cancel each other, thereby explaining the absence of an NMR frequency shift in conventional sample-spinning NMR measurements.

  2. 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

  3. 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

  4. 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.

  5. 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…

  6. 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)

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

    SciTech Connect

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

    1999-11-14

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

  8. The seismic analyzer: interpreting and illustrating 2D seismic data.

    PubMed

    Patel, Daniel; Giertsen, Christopher; Thurmond, John; Gjelberg, John; Gröller, M Eduard

    2008-01-01

    We present a toolbox for quickly interpreting and illustrating 2D slices of seismic volumetric reflection data. Searching for oil and gas involves creating a structural overview of seismic reflection data to identify hydrocarbon reservoirs. We improve the search of seismic structures by precalculating the horizon structures of the seismic data prior to interpretation. We improve the annotation of seismic structures by applying novel illustrative rendering algorithms tailored to seismic data, such as deformed texturing and line and texture transfer functions. The illustrative rendering results in multi-attribute and scale invariant visualizations where features are represented clearly in both highly zoomed in and zoomed out views. Thumbnail views in combination with interactive appearance control allows for a quick overview of the data before detailed interpretation takes place. These techniques help reduce the work of seismic illustrators and interpreters.

  9. Generates 2D Input for DYNA NIKE & TOPAZ

    SciTech Connect

    Hallquist, J. O.; Sanford, Larry

    1996-07-15

    MAZE is an interactive program that serves as an input and two-dimensional mesh generator for DYNA2D, NIKE2D, TOPAZ2D, and CHEMICAL TOPAZ2D. MAZE also generates a basic template for ISLAND input. MAZE has been applied to the generation of input data to study the response of two-dimensional solids and structures undergoing finite deformations under a wide variety of large deformation transient dynamic and static problems and heat transfer analyses.

  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. Position control using 2D-to-2D feature correspondences in vision guided cell micromanipulation.

    PubMed

    Zhang, Yanliang; Han, Mingli; Shee, Cheng Yap; Ang, Wei Tech

    2007-01-01

    Conventional camera calibration that utilizes the extrinsic and intrinsic parameters of the camera and the objects has certain limitations for micro-level cell operations due to the presence of hardware deviations and external disturbances during the experimental process, thereby invalidating the extrinsic parameters. This invalidation is often neglected in macro-world visual servoing and affects the visual image processing quality, causing deviation from the desired position in micro-level cell operations. To increase the success rate of vision guided biological micromanipulations, a novel algorithm monitoring the changing image pattern of the manipulators including the injection micropipette and cell holder is designed and implemented based on 2 dimensional (2D)-to 2D feature correspondences and can adjust the manipulator and perform position control simultaneously. When any deviation is found, the manipulator is retracted to the initial focusing plane before continuing the operation.

  12. Two dimensional NMR of liquids and oriented molecules

    SciTech Connect

    Gochin, M.

    1987-02-01

    Chapter 1 discusses the quantum mechanical formalism used for describing the interaction between magnetic dipoles that dictates the appearance of a spectrum. The NMR characteristics of liquids and liquid crystals are stressed. Chapter 2 reviews the theory of multiple quantum and two dimensional NMR. Properties of typical spectra and phase cycling procedures are discussed. Chapter 3 describes a specific application of heteronuclear double quantum coherence to the removal of inhomogeneous broadening in liquids. Pulse sequences have been devised which cancel out any contribution from this inhomogeneity to the final spectrum. An interpretation of various pulse sequences for the case of /sup 13/C and /sup 1/H is given, together with methods of spectral editing by removal or retention of the homo- or heteronuclear J coupling. The technique is applied to a demonstration of high resolution in both frequency and spatial dimensions with a surface coil. In Chapter 4, multiple quantum filtered 2-D spectroscopy is demonstrated as an effective means of studying randomly deuterated molecules dissolved in a nematic liquid crystal. Magnitudes of dipole coupling constants have been determined for benzene and hexane, and their signs and assignments found from high order multiple quantum spectra. For the first time, a realistic impression of the conformation of hexane can be estimated from these results. Chapter 5 is a technical description of the MDB DCHIB-DR11W parallel interface which has been set up to transfer data between the Data General Nova 820 minicomputer, interfaced to the 360 MHz spectrometer, and the Vax 11/730. It covers operation of the boards, physical specifications and installation, and programs for testing and running the interface.

  13. NMR in a Diamond Anvil Pressure Cell

    NASA Astrophysics Data System (ADS)

    Lawson, Matthew; Dioguardi, Adam; Weir, Samuel; Bush, Blaine; Dunuwille, Mihindra; Deemyad, Shanti; Curro, Nichlas

    We present recent advances in the use of diamond anvil pressure cells in nuclear magnetic resonance measurements. This technique allows access to new regions of the phase diagrams of iron pnictide and heavy fermion materials, and promises to allow NMR experiments under pressures not previously accessible.

  14. NMR characterization of polymers: Review and update

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  15. 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.

  16. Inhibition of human cytochrome P450 2D6 (CYP2D6) by methadone.

    PubMed Central

    Wu, D; Otton, S V; Sproule, B A; Busto, U; Inaba, T; Kalow, W; Sellers, E M

    1993-01-01

    1. In microsomes prepared from three human livers, methadone competitively inhibited the O-demethylation of dextromethorphan, a marker substrate for CYP2D6. The apparent Ki value of methadone ranged from 2.5 to 5 microM. 2. Two hundred and fifty-two (252) white Caucasians, including 210 unrelated healthy volunteers and 42 opiate abusers undergoing treatment with methadone were phenotyped using dextromethorphan as the marker drug. Although the frequency of poor metabolizers was similar in both groups, the extensive metabolizers among the opiate abusers tended to have higher O-demethylation metabolic ratios and to excrete less of the dose as dextromethorphan metabolites than control extensive metabolizer subjects. These data suggest inhibition of CYP2D6 by methadone in vivo as well. 3. Because methadone is widely used in the treatment of opiate abuse, inhibition of CYP2D6 activity in these patients might contribute to exaggerated response or unexpected toxicity from drugs that are substrates of this enzyme. PMID:8448065

  17. Sparse and incomplete factorial matrices to screen membrane protein 2D crystallization.

    PubMed

    Lasala, R; Coudray, N; Abdine, A; Zhang, Z; Lopez-Redondo, M; Kirshenbaum, R; Alexopoulos, J; Zolnai, Z; Stokes, D L; Ubarretxena-Belandia, I

    2015-02-01

    Electron crystallography is well suited for studying the structure of membrane proteins in their native lipid bilayer environment. This technique relies on electron cryomicroscopy of two-dimensional (2D) crystals, grown generally by reconstitution of purified membrane proteins into proteoliposomes under conditions favoring the formation of well-ordered lattices. Growing these crystals presents one of the major hurdles in the application of this technique. To identify conditions favoring crystallization a wide range of factors that can lead to a vast matrix of possible reagent combinations must be screened. However, in 2D crystallization these factors have traditionally been surveyed in a relatively limited fashion. To address this problem we carried out a detailed analysis of published 2D crystallization conditions for 12 β-barrel and 138 α-helical membrane proteins. From this analysis we identified the most successful conditions and applied them in the design of new sparse and incomplete factorial matrices to screen membrane protein 2D crystallization. Using these matrices we have run 19 crystallization screens for 16 different membrane proteins totaling over 1300 individual crystallization conditions. Six membrane proteins have yielded diffracting 2D crystals suitable for structure determination, indicating that these new matrices show promise to accelerate the success rate of membrane protein 2D crystallization.

  18. Sparse and incomplete factorial matrices to screen membrane protein 2D crystallization

    PubMed Central

    Lasala, R.; Coudray, N.; Abdine, A.; Zhang, Z.; Lopez-Redondo, M.; Kirshenbaum, R.; Alexopoulos, J.; Zolnai, Z.; Stokes, D.L.; Ubarretxena-Belandia, I.

    2014-01-01

    Electron crystallography is well suited for studying the structure of membrane proteins in their native lipid bilayer environment. This technique relies on electron cryomicroscopy of two-dimensional (2D) crystals, grown generally by reconstitution of purified membrane proteins into proteoliposomes under conditions favoring the formation of well-ordered lattices. Growing these crystals presents one of the major hurdles in the application of this technique. To identify conditions favoring crystallization a wide range of factors that can lead to a vast matrix of possible reagent combinations must be screened. However, in 2D crystallization these factors have traditionally been surveyed in a relatively limited fashion. To address this problem we carried out a detailed analysis of published 2D crystallization conditions for 12 β-barrel and 138 α-helical membrane proteins. From this analysis we identified the most successful conditions and applied them in the design of new sparse and incomplete factorial matrices to screen membrane protein 2D crystallization. Using these matrices we have run 19 crystallization screens for 16 different membrane proteins totaling over 1,300 individual crystallization conditions. Six membrane proteins have yielded diffracting 2D crystals suitable for structure determination, indicating that these new matrices show promise to accelerate the success rate of membrane protein 2D crystallization. PMID:25478971

  19. Sparse and incomplete factorial matrices to screen membrane protein 2D crystallization.

    PubMed

    Lasala, R; Coudray, N; Abdine, A; Zhang, Z; Lopez-Redondo, M; Kirshenbaum, R; Alexopoulos, J; Zolnai, Z; Stokes, D L; Ubarretxena-Belandia, I

    2015-02-01

    Electron crystallography is well suited for studying the structure of membrane proteins in their native lipid bilayer environment. This technique relies on electron cryomicroscopy of two-dimensional (2D) crystals, grown generally by reconstitution of purified membrane proteins into proteoliposomes under conditions favoring the formation of well-ordered lattices. Growing these crystals presents one of the major hurdles in the application of this technique. To identify conditions favoring crystallization a wide range of factors that can lead to a vast matrix of possible reagent combinations must be screened. However, in 2D crystallization these factors have traditionally been surveyed in a relatively limited fashion. To address this problem we carried out a detailed analysis of published 2D crystallization conditions for 12 β-barrel and 138 α-helical membrane proteins. From this analysis we identified the most successful conditions and applied them in the design of new sparse and incomplete factorial matrices to screen membrane protein 2D crystallization. Using these matrices we have run 19 crystallization screens for 16 different membrane proteins totaling over 1300 individual crystallization conditions. Six membrane proteins have yielded diffracting 2D crystals suitable for structure determination, indicating that these new matrices show promise to accelerate the success rate of membrane protein 2D crystallization. PMID:25478971

  20. DQ-DRENAR: A new NMR technique to measure site-resolved magnetic dipole-dipole interactions in multispin-1/2 systems: Theory and validation on crystalline phosphates

    NASA Astrophysics Data System (ADS)

    Ren, Jinjun; Eckert, Hellmut

    2013-04-01

    A new solid state NMR technique is described for measuring homonuclear dipole-dipole interactions in multi-spin-1/2 systems under magic-angle spinning conditions. Re-coupling is accomplished in the form of an effective double quantum (DQ) Hamiltonian created by a symmetry-based POST-C7 sequence consisting of two excitation blocks, attenuating the signal (intensity S'). For comparison, a reference signal S0 with the dipolar re-coupling absent is generated by shifting the phase of the second block by 90° relative to the first block. As in rotational echo double resonance, the homonuclear dipole-dipole coupling constant can then be extracted from a plot of the normalized difference signal (S0 - S')/S0 versus dipolar mixing time. The method is given the acronym DQ-DRENAR ("Double-Quantum-based Dipolar Re-coupling effects Nuclear Alignment Reduction"). The method is analyzed mathematically, and on the basis of detailed simulations, with respect to the order and the geometry of the spin system, the dipolar truncation phenomenon, and the influence of the chemical shift anisotropy on experimental curves. Within the range of (S0 - S')/S0 ≤0.3-0.5 such DRENAR curves can be approximated by simple parabolae, yielding effective squared dipole-dipole coupling constants summed over all the pairwise interactions present. The method has been successfully validated for 31P-31P distance determinations of numerous crystalline model compounds representing a wide range of dipolar coupling strengths.