Sample records for solution nmr caracterizacao

  1. Solution NMR in structural genomics. (United States)

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


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

  2. Preparation of polyurethane/montmorillonite nanocomposites by solution: characterization using low-field NMR and study of thermal stability;Preparacao de nanocompositos polimericos de poliurfetano/montmorilonita via solucao: caracterizacao por RMN de baixo campo e estudo da estabilidade termica

    Energy Technology Data Exchange (ETDEWEB)

    Silva, Marcos Anacleto da; Tavares, Maria Ines B., E-mail: mibt@ima.ufrj.b [Coordenacao de Pos-Graduacao e Pesquisa de Engenharia (NUCAT/COPPE/UFRJ), RJ (Brazil). Programa em Engenharia Quimica. Nucleo de Catalise


    Polyurethanes (PU) are important and versatile class of polymer materials, especially because of their desirable properties, such as high abrasion resistance, tear strength, excellent shock absorption, flexibility and elasticity. However, there also exist some disadvantages, for example, low thermal stability and barrier properties. To overcome the disadvantages, research on novel polyurethane/clay nanocomposites has been carried out. The investigation of the structure of polyurethane/clay nanocomposites has been mostly done by X-ray diffraction (XRD) and transmission electron microscopy (TEM). In this work, PU/clay films were prepared by solution, and the obtained nanocomposites were characterized by XRD and low-field nuclear magnetic resonance (NMR). Low field NMR measurements were able to provide important information on molecular dynamics of the polymeric nanocomposites PU/OMMT. In addition, they also confirmed the results obtained by XRD. The thermal stability was determined by thermogravimetric analysis (TGA). (author)

  3. Dilute Bicellar Solutions for Structural NMR Work (United States)

    Struppe, Jochem; Vold, Regitze R.


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

  4. Selected topics in solution-phase biomolecular NMR spectroscopy (United States)

    Kay, Lewis E.; Frydman, Lucio


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

  5. Characterization of polyurethane/organophilic montmorillonite nanocomposites by low field NMR; Caracterizacao de nanocompositos de poliuretano/montmorilonita organofilica por RMN de baixo campo

    Energy Technology Data Exchange (ETDEWEB)

    Silva, Marcos Anacleto da [Universidade Federal do Rio de Janeiro (UFRJ), RJ (Brazil). Laboratorio de Nanocompositos Polimericos; Tavares, Maria I.B.; Nascimento, Suelen A.M.; Rodrigues, Elton J. da R [Universidade Federal do Rio de Janeiro (NUCAT/PEQ/COPPE/UFRJ), RJ (Brazil). Laboratorio de Nanocompositos Polimericos


    Polyurethanes are important and versatile materials, mainly due to some of their properties, such as high resistance to abrasion and tearing, excellent absorption of mechanical shocks and good flexibility and elasticity. However, they have some drawbacks as well, such as low thermal stability and barrier properties. To overcome these disadvantages, various studies have been conducted involving organophilic polyurethane/montmorillonite nanocomposites. The investigation of the structure of polyurethane/clay nanocomposites has mainly been done by X-ray diffraction (XRD) and transmission electron microscopy (TEM). In this work, PU/clay nanocomposite films obtained by solution intercalation were studied. The nanocomposites were characterized by XRD and low-field nuclear magnetic resonance (LF-NMR). The LF-NMR measurements, with determination of the spin-lattice relaxation time of the hydrogen nucleus, supplied important information about the molecular dynamics of these nanocomposites. The X-ray diffraction measurements validated the results found by NMR. The thermal stability of the material was also determined by thermogravimetric analysis (TGA) under an inert atmosphere. A slight improvement in this stability was observed in the nanocomposite in comparison with polyurethane (author)

  6. Computational Protocols for Prediction of Solute NMR Relative Chemical Shifts

    DEFF Research Database (Denmark)

    Eriksen, Janus Juul; Olsen, Jógvan Magnus Haugaard; Aidas, Kestutis


    In this study, we have applied two different spanning protocols for obtaining the molecular conformations of L-tryptophan in aqueous solution, namely a molecular dynamics simulation and a molecular mechanics conformational search with subsequent geometry re-optimization of the stable conformers...... using a quantum mechanically based method. These spanning protocols represent standard ways of obtaining a set of conformations on which NMR calculations may be performed. The results stemming from the solute–solvent configurations extracted from the MD simulation at 300 K are found to be inferior...... to the results stemming from the conformations extracted from the MM conformational search in terms of replicating an experimental reference as well as in achieving the correct sequence of the NMR relative chemical shifts of L-tryptophan in aqueous solution. We find this to be due to missing conformations...

  7. Mono terpenes characterization by {sup 1} H and {sup 13} C-1 NMR; Caracterizacao de monoterpenos por RMN - {sup 1} H e de {sup 13} C-1

    Energy Technology Data Exchange (ETDEWEB)

    Araujo, Martha T. de [Universidade Federal Fluminense, Niteroi, RJ (Brazil). Dept. de Fisico-Quimica; Silveira, Carmen L.P. [Universidade Federal Fluminense, Niteroi, RJ (Brazil). Dept. de Quimica Organica; Mcchesney, James D. [Mississippi Univ., University, MS (United States). Research Inst. of Pharmaceutical Sciences


    Artemisinine, a new lactone sesquiterpene containing one peroxide binding, is the main anti malarial agent obtained from the Artemisia annua L. Viewing to obtain a simple synthetic route for artemisinic acid preparation, which is the key intermediary for total synthesis of this type of anti malarial agent, R-carvone has been chosen as starting material. The S-carvone was used as model for reaction optimization and preparation of derivatives to be used for NMR studies. The main objective of this work is the signalling of the {sup 13} C and {sup 1} H NMR spectra, using the 2 D-COSY and 2 D-Hector spectra 4 refs., 3 figs., 1 tab

  8. Characterization of nonderivatized plant cell walls using high-resolution solution-state NMR spectroscopy (United States)

    Daniel J. Yelle; John Ralph; Charles R. Frihart


    A recently described plant cell wall dissolution system has been modified to use perdeuterated solvents to allow direct in-NMR-tube dissolution and high-resolution solution-state NMR of the whole cell wall without derivatization. Finely ground cell wall material dissolves in a solvent system containing dimethylsulfoxide-d6 and 1-methylimidazole-d6 in a ratio of 4:1 (v/...

  9. Backbone Assignment of the MALT1 Paracaspase by Solution NMR.

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    Sofia Unnerståle

    Full Text Available Mucosa-associated lymphoid tissue lymphoma translocation protein 1 (MALT1 is a unique paracaspase protein whose protease activity mediates oncogenic NF-κB signalling in activated B cell-like diffuse large B cell lymphomas (ABC-DLBCLs. ABC-DLBCLs are aggressive lymphomas with high resistance to current chemotherapies. Low survival rate among patients emphasizes the urgent need for alternative treatment options. The characterization of the MALT1 will be an essential tool for developing new target-directed drugs against MALT1 dependent disorders. As the first step in the atomic-level NMR studies of the system, here we report, the (15N/(13C/(1H backbone assignment of the apo form of the MALT1 paracaspase region together with the third immunoglobulin-like (Ig3 domain, 44 kDa, by high resolution NMR. In addition, the non-uniform sampling (NUS based targeted acquisition procedure is evaluated as a mean of decreasing acquisition and analysis time for larger proteins.

  10. Fractioning of sodium polyphosphate and characterization by {sup 31}P NMR: a experience to physical-chemistry lessons; Fracionamento de polifosfato de sodio e caracterizacao por RMN de 31P: um experimento para aulas de Fisico-Quimica

    Energy Technology Data Exchange (ETDEWEB)

    Lima, Emilia Celma de Oliveira; Alcantara, Glaucia Braz Alcantara; Damasceno, Fernando Cruvinel, E-mail: elima@quimica.ufg.b [Universidade Federal de Goias (UFG), Goiania, GO (Brazil). Inst. de Quimica; Moita Neto, Jose Machado [Universidade Federal do Piaui (UFPI), Teresina, PI (Brazil). Dept. de Quimica; Galembeck, Fernando [Universidade Estadual de Campinas (UNICAMP), SP (Brazil). Inst. de Quimica


    This text describes an experiment on fractional precipitation of a polymer together with determination of average degree of polymerization by NMR. Commercial sodium polyphosphate was fractionated by precipitation from aqueous solution by adding increasing amounts of acetone. The polydisperse salt and nine fractions obtained from it were analyzed by {sup 31}P nuclear magnetic resonance and the degree of polymerization of the salts and of the fractions were calculated. Long-chain sodium polyphosphate was also synthesized and analyzed. This experiment was tested in a PChem lab course but it can be used also to illustrate topics of inorganic polymers and analytical chemistry. (author)

  11. QENS and NMR studies of 3-picoline-water solutions

    CERN Document Server

    Almasy, L; Bokor, M; Cser, L; Tompa, K; Zanotti, J M; Jancso, G


    Quasi-elastic neutron scattering measurements were performed on aqueous solutions of 3-picoline (3-methylpyridine) at room temperature. H-D substitution on both the solute and the water was used to separate the dynamics of the two species. The analysis of the translational diffusive motion at different concentrations shows that at high picoline content the diffusion coefficient of water decreases strongly and becomes similar to that of the solute, indicating strong coupling between the motions of the solute and the solvent. Activation energies characteristic of the dynamic behavior of the methyl group were determined from sup 1 H spin-lattice relaxation rate measurements for H sub 2 O and D sub 2 O solutions of 3-picoline above 310 K. (orig.)

  12. Micro-scale NMR Experiments for Monitoring the Optimization of Membrane Protein Solutions for Structural Biology. (United States)

    Horst, Reto; Wüthrich, Kurt


    Reconstitution of integral membrane proteins (IMP) in aqueous solutions of detergent micelles has been extensively used in structural biology, using either X-ray crystallography or NMR in solution. Further progress could be achieved by establishing a rational basis for the selection of detergent and buffer conditions, since the stringent bottleneck that slows down the structural biology of IMPs is the preparation of diffracting crystals or concentrated solutions of stable isotope labeled IMPs. Here, we describe procedures to monitor the quality of aqueous solutions of [2H, 15N]-labeled IMPs reconstituted in detergent micelles. This approach has been developed for studies of β-barrel IMPs, where it was successfully applied for numerous NMR structure determinations, and it has also been adapted for use with α-helical IMPs, in particular GPCRs, in guiding crystallization trials and optimizing samples for NMR studies (Horst et al., 2013). 2D [15N, 1H]-correlation maps are used as "fingerprints" to assess the foldedness of the IMP in solution. For promising samples, these "inexpensive" data are then supplemented with measurements of the translational and rotational diffusion coefficients, which give information on the shape and size of the IMP/detergent mixed micelles. Using microcoil equipment for these NMR experiments enables data collection with only micrograms of protein and detergent. This makes serial screens of variable solution conditions viable, enabling the optimization of parameters such as the detergent concentration, sample temperature, pH and the composition of the buffer.

  13. A solid state and solution NMR study of the tautomerism in hydroxyquinoline carboxylic acids. (United States)

    Gudat, Dietrich; Nycz, Jacek E; Polanski, Jaroslaw


    Some hydroxyquinoline carboxylic acids and their conjugate acids and bases were characterized by 13C and 15N NMR spectroscopy in solution and in the solid state. Differences in 13C and, in particular, 15N chemical shift patterns allow to distinguish between individual tautomers and confirm the presence of zwitterionic species in the solid state. Solution NMR spectra in dimethyl sulfoxide (DMSO) show effects resulting as a consequence of dynamic exchange and suggest the presence of an equilibrium mixture of hydroxyquinoline carboxylic acid and zwitterionic hydroxyquinolinium carboxylate tautomers.

  14. Characterization of Halogen Bonded Adducts in Solution by Advanced NMR Techniques

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    Gianluca Ciancaleoni


    Full Text Available In the last 20 years, a huge volume of experimental work into halogen bonding (XB has been produced. Most of the systems have been characterized by solid state X-ray crystallography, whereas in solution the only routine technique is titration (by using 1H and 19F nuclear magnetic resonance (NMR, infrared (IR, ultraviolet–visible (UV–Vis or Raman spectroscopies, depending on the nature of the system, with the aim of characterizing the strength of the XB interaction. Unfortunately, titration techniques have many intrinsic limitations and they should be coupled with other, more sophisticated techniques to provide an accurate and detailed description of the geometry and stoichiometry of the XB adduct in solution. This review will show how crucial information about XB adducts can be obtained by advanced NMR techniques, nuclear Overhauser effect-based spectroscopies (NOESY, ROESY, HOESY… and diffusion NMR techniques (PGSE or DOSY.

  15. Study of multi-site chemical exchange in solution state by NMR: 1D ...

    Indian Academy of Sciences (India)

    This work demonstrates a simple 1D NMR approach employing multiply selective excitation to study multi-site exchange processes in solution, applying it to systems that exhibit three-site exchange. This approach involves simultaneous excitation of all - or a chosen subset of - the exchanging sites by using an appropriately ...

  16. High-resolution solution-state NMR of unfractionated plant cell walls (United States)

    John Ralph; Fachuang Lu; Hoon Kim; Dino Ress; Daniel J. Yelle; Kenneth E. Hammel; Sally A. Ralph; Bernadette Nanayakkara; Armin Wagner; Takuya Akiyama; Paul F. Schatz; Shawn D. Mansfield; Noritsugu Terashima; Wout Boerjan; Bjorn Sundberg; Mattias Hedenstrom


    Detailed structural studies on the plant cell wall have traditionally been difficult. NMR is one of the preeminent structural tools, but obtaining high-resolution solution-state spectra has typically required fractionation and isolation of components of interest. With recent methods for dissolution of, admittedly, finely divided plant cell wall material, the wall can...

  17. New class of aggregates in aqueous solution: an NMR, thermodynamic, and dynamic light scattering study. (United States)

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


    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.

  18. Solution NMR Structures of Oxidized and Reduced Ehrlichia chaffeensis thioredoxin: NMR-Invisible Structure Owing to Backbone Dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Buchko, Garry W.; Hewitt, Stephen N.; Van Voorhis, Wesley C.; Myler, Peter J.


    Thioredoxins (Trxs) are small ubiquitous proteins that participate in a diverse variety of redox reactions via the reversible oxidation of two cysteine thiol groups in a structurally conserved active site, CGPC. Here, we describe the NMR solution structures of a Trx from Ehrlichia chaffeensis (Ec-Trx, ECH_0218), the etiological agent responsible for human monocytic ehrlichiosis, in both the oxidized and reduced states. The overall topology of the calculated structures is similar in both redox states and similar to other Trx structures, a five-strand, mixed -sheet (1:3:2:4:5) surrounded by four -helices. Unlike other Trxs studied by NMR in both redox states, the 1H-15N HSQC spectra of reduced Ec-Trx was missing eight amide cross peaks relative to the spectra of oxidized Ec-Trx. These missing amides correspond to residues C32-E39 in the active site containing helix (2) and S72-I75 in a loop near the active site and suggest a substantial change in the backbone dynamics associated with the formation of an intramolecular C32-C35 disulfide bond.

  19. Apparatus for preparing a solution of a hyperpolarized noble gas for NMR and MRI analysis (United States)

    Pines, Alexander [Berkeley, CA; Budinger, Thomas [Berkeley, CA; Navon, Gil [Ramat Gan, IL; Song, Yi-Qiao [Berkeley, CA; Appelt, Stephan [Waiblingen, DE; Bifone, Angelo [Rome, IT; Taylor, Rebecca [Berkeley, CA; Goodson, Boyd [Berkeley, CA; Seydoux, Roberto [Berkeley, CA; Room, Toomas [Albany, CA; Pietrass, Tanja [Socorro, NM


    The present invention relates generally to nuclear magnetic resonance (NMR) techniques for both spectroscopy and imaging. More particularly, the present invention relates to methods in which hyperpolarized noble gases (e.g., Xe and He) are used to enhance and improve NMR and MRI. Additionally, the hyperpolarized gas solutions of the invention are useful both in vitro and in vivo to study the dynamics or structure of a system. When used with biological systems, either in vivo or in vitro, it is within the scope of the invention to target the hyperpolarized gas and deliver it to specific regions within the system.

  20. NMR characterization of membrane protein–detergent micelle solutions using microcoil equipment (United States)

    Stanczak, Pawel; Horst, Reto; Serrano, Pedro; Wüthrich, Kurt


    Using microcoil NMR technology, the uniformly 2H,15N-labeled integral membrane protein OmpX and the phosphocholine derivative detergent Fos-10 (n-decylphosphocholine), we investigated solutions of mixed protein–detergent micelles to determine the influence of the detergent concentration on the NMR spectra of the protein. In a first step, we identified key parameters that influence the composition of the micelle solutions, which resulted in a new protocol for the preparation of well-defined concentrated protein solutions. This led to the observation that high-quality 2D [15N,1H]-TROSY spectra of OmpX reconstituted in mixed micelles with Fos-10 were obtained only in a limited range of detergent concentrations. Outside of this range from about 90 mM to 180 mM, we observed a significant decrease of the average peak intensity. Relaxation-optimized NMR measurements of the rotational and translational diffusion coefficients of the OmpX/Fos-10 mixed micelles, Dr and Dt, respectively, then showed that the stoichiometry and the effective hydrodynamic radius of the protein-containing micelles are not significantly affected by high Fos-10 concentrations, and that the deterioration of NMR spectra is due to the increased viscosity at high detergent concentrations. The paper thus provides a basis for refined guidelines on the preparation of integral membrane proteins for structural studies. PMID:19950959

  1. Solution NMR Studies of Mycobacterium tuberculosis Proteins for Antibiotic Target Discovery

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    Do-Hee Kim


    Full Text Available Tuberculosis is an infectious disease caused by Mycobacterium tuberculosis, which triggers severe pulmonary diseases. Recently, multidrug/extensively drug-resistant tuberculosis strains have emerged and continue to threaten global health. Because of the development of drug-resistant tuberculosis, there is an urgent need for novel antibiotics to treat these drug-resistant bacteria. In light of the clinical importance of M. tuberculosis, 2067 structures of M. tuberculsosis proteins have been determined. Among them, 52 structures have been solved and studied using solution nuclear magnetic resonance (NMR. The functional details based on structural analysis of M. tuberculosis using NMR can provide essential biochemical data for the development of novel antibiotic drugs. In this review, we introduce diverse structural and biochemical studies on M. tuberculosis proteins determined using NMR spectroscopy.

  2. Complexation of enalapril maleate with {beta}-cyclodextrin: NMR spectroscopic study in solution

    Energy Technology Data Exchange (ETDEWEB)

    Ali, Syed Mashhood; Maheshwari, Arti; Asmat, Fahmeena [Aligarh Muslim University, Aligarh (India). Dept. of Chemistry]. E-mail:; Koketsu, Mamoru [Gifu University, Gifu (Japan). Div. of Instrumental Analysis


    A detailed NMR ({sup 1}H , COSY, ROESY) spectroscopic study of complexation of enalapril maleate with {beta}-cyclodextrin was carried out. The {sup 1}H NMR spectrum of enalapril maleate confirmed the existence of cis-trans equilibrium in solution, possibly due to hindered rotation along the amide bond. The cis-trans ratio remained almost the same in the presence of {beta}-cyclodextrin but in one case it was found significantly different which suggests a catalytic role of {beta}-cyclodextrin in the isomerization. {sup 1}H NMR titration studies confirmed the formation of an enalapril-{beta}-cyclodextrin inclusion complex as evidenced by chemical shift variations in the proton resonances of both the host and the guest. The stoichiometry of the complex was determined to be 2:1 (guest: host). The mode of penetration of the guest into the {beta}-cyclodextrin cavity as well as the structure of the complex were established using ROESY spectroscopy. (author)

  3. Solution structure determination of oligoureas using methylene spin state selective NMR at 13C natural abundance. (United States)

    Guichard, Gilles; Violette, Aude; Chassaing, Gérard; Miclet, Emeric


    Ability of N,N'-linked oligoureas containing proteinogenic side chains to adopt a stable helix conformation in solution has been described recently. NMR as well as circular dichroism (CD) spectroscopies were employed to gain insight into their specific fold. It is herein proposed to extend the structural information available on these peptidomimetics by an advantageous use of a methylene spin state selective NMR experiment. Homodecoupling provided by the pulse scheme made it possible to readily measure conformation-dependent (3)J(HH) constants that are difficult if not impossible to obtain with standard NMR experiments. Adding those couplings to the NMR restraints improved the quality of the structure calculations significantly, as judged by a ca 30% decrease of the root mean square deviation (RMSD) obtained over an ensemble of 20 structures. Moreover, accurate determination of individual (1)J(CH) couplings within each methylene group revealed uniform values throughout the oligourea sequence, with (1)J(CH) systematically slightly larger for the pro-S hydrogen than for the pro-R. As shown in this study, the methylene spin state selective NMR experiment displays a good intrinsic sensitivity and could therefore provide valuable structural information at (13)C natural abundance for peptidomimetic molecules and foldamers bearing diastereotopic methylene protons. Copyright (c) 2008 John Wiley & Sons, Ltd.

  4. Effects of radiation damping for biomolecular NMR experiments in solution: a hemisphere concept for water suppression. (United States)

    Ishima, Rieko


    Abundant solvent nuclear spins, such as water protons in aqueous solution, cause radiation damping in NMR experiments. It is important to know how the effect of radiation damping appears in high-resolution protein NMR because macromolecular studies always require very high magnetic field strengths with a highly sensitive NMR probe that can easily cause radiation damping. Here, we show the behavior of water magnetization after a pulsed-field gradient (PFG) using nutation experiments at 900 MHz with a cryogenic probe: when water magnetization is located in the upper hemisphere (having +Z component, parallel to the external magnetic field), dephasing of the magnetization by a PFG effectively suppresses residual water magnetization in the transverse plane. In contrast, when magnetization is located in the lower hemisphere (having -Z component), the small residual transverse component remaining after a PFG is still sufficient to induce radiation damping. Based on this observation, we designed 1 H- 15 N HSQC experiments in which water magnetization is maintained in the upper hemisphere, but not necessarily along Z, and compared them with the conventional experiments, in which water magnetization is inverted during the t 1 period. The result demonstrates moderate gain of signal-to-noise ratio, 0-28%. Designing the experiments such that water magnetization is maintained in the upper hemisphere allows shorter pulses to be used compared to the complete water flip-back and, thereby, is useful as a building block of protein NMR pulse programs in solution.

  5. Recent Advances in Characterization of Lignin Polymer by Solution-State Nuclear Magnetic Resonance (NMR Methodology

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    Run-Cang Sun


    Full Text Available The demand for efficient utilization of biomass induces a detailed analysis of the fundamental chemical structures of biomass, especially the complex structures of lignin polymers, which have long been recognized for their negative impact on biorefinery. Traditionally, it has been attempted to reveal the complicated and heterogeneous structure of lignin by a series of chemical analyses, such as thioacidolysis (TA, nitrobenzene oxidation (NBO, and derivatization followed by reductive cleavage (DFRC. Recent advances in nuclear magnetic resonance (NMR technology undoubtedly have made solution-state NMR become the most widely used technique in structural characterization of lignin due to its versatility in illustrating structural features and structural transformations of lignin polymers. As one of the most promising diagnostic tools, NMR provides unambiguous evidence for specific structures as well as quantitative structural information. The recent advances in two-dimensional solution-state NMR techniques for structural analysis of lignin in isolated and whole cell wall states (in situ, as well as their applications are reviewed.

  6. Ionic Liquid-Solute Interactions Studied by 2D NOE NMR Spectroscopy. (United States)

    Khatun, Sufia; Castner, Edward W


    Intermolecular interactions between a Ru(2+)(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 {(1)H-(19)F} HOESY and {(1)H-(1)H} 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 Ru(2+)(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 Ru(2+)(bpy)3 solute interacts with both the polar head and the nonpolar tail groups of the 1-butyl-1-methylpyrrolidinium cation but only with the nonpolar tail groups of the 1-decyl-1-methylpyrrolidinium cation.

  7. Direct NMR Monitoring of Phase Separation Behavior of Highly Supersaturated Nifedipine Solution Stabilized with Hypromellose Derivatives. (United States)

    Ueda, Keisuke; Higashi, Kenjirou; Moribe, Kunikazu


    We investigated the phase separation behavior and maintenance mechanism of the supersaturated state of poorly water-soluble nifedipine (NIF) in hypromellose (HPMC) derivative solutions. Highly supersaturated NIF formed NIF-rich nanodroplets through phase separation from aqueous solution containing HPMC derivative. Dissolvable NIF concentration in the bulk water phase was limited by the phase separation of NIF from the aqueous solution. HPMC derivatives stabilized the NIF-rich nanodroplets and maintained the NIF supersaturation with phase-separated NIF for several hours. The size of the NIF-rich phase was different depending on the HPMC derivatives dissolved in aqueous solution, although the droplet size had no correlation with the time for which NIF supersaturation was maintained without NIF crystallization. HPMC acetate and HPMC acetate succinate (HPMC-AS) effectively maintained the NIF supersaturation containing phase-separated NIF compared with HPMC. Furthermore, HPMC-AS stabilized NIF supersaturation more effectively in acidic conditions. Solution 1 H NMR measurements of NIF-supersaturated solution revealed that HPMC derivatives distributed into the NIF-rich phase during the phase separation of NIF from the aqueous solution. The hydrophobicity of HPMC derivative strongly affected its distribution into the NIF-rich phase. Moreover, the distribution of HPMC-AS into the NIF-rich phase was promoted at lower pH due to the lower aqueous solubility of HPMC-AS. The distribution of a large amount of HPMC derivatives into NIF-rich phase induced the strong inhibition of NIF crystallization from the NIF-rich phase. Polymer distribution into the drug-rich phase directly monitored by solution NMR technique can be a useful index for the stabilization efficiency of drug-supersaturated solution containing a drug-rich phase.

  8. A solid-state NMR method for solution of zeolite crystal structures. (United States)

    Brouwer, Darren H; Darton, Richard J; Morris, Russell E; Levitt, Malcolm H


    Since zeolites are notoriously difficult to prepare as large single crystals, structure determination usually relies on powder X-ray diffraction (XRD). However, structure solution (i.e., deriving an initial structural model) directly from powder XRD data is often very difficult due to the diffraction phase problem and the high degree of overlap between the individual reflections, particularly for materials with the structural complexity of most zeolites. Here, we report a method for structure determination of zeolite crystal structures that combines powder XRD and nuclear magnetic resonance (NMR) spectroscopy in which the crucial step of structure solution is achieved using solid-state (29)Si double-quantum dipolar recoupling NMR, which probes the distance-dependent dipolar interactions between naturally abundant (29)Si nuclei in the zeolite framework. For two purely siliceous zeolite blind test samples, we demonstrate that the NMR data can be combined with the unit cell parameters and space group to solve structural models that refine successfully against the powder XRD data.

  9. Solution oxygen-17 NMR application for observing a peroxidized cysteine residue in oxidized human SOD1 (United States)

    Fujiwara, Noriko; Yoshihara, Daisaku; Sakiyama, Haruhiko; Eguchi, Hironobu; Suzuki, Keiichiro


    NMR active nuclei, 1H, 13C and 15N, are usually used for determination of protein structure. However, solution 17O-NMR application to proteins is extremely limited although oxygen is an essential element in biomolecules. Proteins are oxidized through cysteine residues by two types of oxidation. One is reversible oxidation such as disulphide bonding (Cys-S-S-Cys) and the other is irreversible oxidation to cysteine sulfinic acid (Cys-SO 2H) and cysteine sulfonic acid (Cys-SO 3H). Copper,Zinc-superoxide dismutase (SOD1) is a key enzyme in the protection of cells from the superoxide anion radical. The SH group at Cys 111 residue in human SOD1 is selectively oxidized to -SO 2H and -SO 3H with atmospheric oxygen, and this oxidized human SOD1 is also suggested to play an important role in the pathophysiology of various neurodegenerative diseases, probably mainly via protein aggregation. Therefore, information on the structural and the dynamics of the oxidized cysteine residue would be crucial for the understanding of protein aggregation mechanism. Although the -SO 3H group on proteins cannot be directly detected by conventional NMR techniques, we successfully performed the site-specific 17O-labeling of Cys 111 in SOD1 using ^{17}it {O}2 gas and the 17O-NMR analysis for the first time. We observed clear 17O signal derived from a protein molecule and show that 17O-NMR is a sensitive probe for studying the structure and dynamics of the 17O-labeled protein molecule. This novel and unique strategy can have great impact on many research fields in biology and chemistry.

  10. Solution NMR studies of amphibian antimicrobial peptides: linking structure to function? (United States)

    Haney, Evan F; Hunter, Howard N; Matsuzaki, Katsumi; Vogel, Hans J


    The high-resolution three-dimensional structure of an antimicrobial peptide has implications for the mechanism of its antimicrobial activity, as the conformation of the peptide provides insights into the intermolecular interactions that govern the binding to its biological target. For many cationic antimicrobial peptides the negatively charged membranes surrounding the bacterial cell appear to be a main target. In contrast to what has been found for other classes of antimicrobial peptides, solution NMR studies have revealed that in spite of the wide diversity in the amino acid sequences of amphibian antimicrobial peptides (AAMPs), they all adopt amphipathic alpha-helical structures in the presence of membrane-mimetic micelles, bicelles or organic solvent mixtures. In some cases the amphipathic AAMP structures are directly membrane-perturbing (e.g. magainin, aurein and the rana-box peptides), in other instances the peptide spontaneously passes through the membrane and acts on intracellular targets (e.g. buforin). Armed with a high-resolution structure, it is possible to relate the peptide structure to other relevant biophysical and biological data to elucidate a mechanism of action. While many linear AAMPs have significant antimicrobial activity of their own, mixtures of peptides sometimes have vastly improved antibiotic effects. Thus, synergy among antimicrobial peptides is an avenue of research that has recently attracted considerable attention. While synergistic relationships between AAMPs are well described, it is becoming increasingly evident that analyzing the intermolecular interactions between these peptides will be essential for understanding the increased antimicrobial effect. NMR structure determination of hybrid peptides composed of known antimicrobial peptides can shed light on these intricate synergistic relationships. In this work, we present the first NMR solution structure of a hybrid peptide composed of magainin 2 and PGLa bound to SDS and DPC

  11. High-resolution /sup 1/H NMR study of the solution structure of delta-hemolysin

    Energy Technology Data Exchange (ETDEWEB)

    Tappin, M.J.; Pastore, A.; Norton, R.S.; Freer, J.H.; Campbell, I.D.


    The 26-residue toxin from Staphylococcus aureus delta-hemolysin, is thought to act by traversing the plasma membrane. The structure of this peptide, in methanol solution, has been investigated by using high-resolution NMR in combination with molecular dynamics calculations. The /sup 1/H NMR spectrum has been completely assigned, and it is shown that residues 2-20 form a relatively stable helix while the residues at the C-terminal end appear to be more flexible. The structures were calculated only from nuclear Overhauser effect data and standard bond lengths. It is shown that the results are consistent with /sup 3/J/sub NH-..cap alpha..CH/ coupling constants and amide hydrogen exchange rates.

  12. (19)F labelled glycosaminoglycan probes for solution NMR and non-linear (CARS) microscopy. (United States)

    Lima, Marcelo A; Cavalheiro, Renan P; M Viana, Gustavo; Meneghetti, Maria C Z; Rudd, Timothy R; Skidmore, Mark A; Powell, Andrew K; Yates, Edwin A


    Studying polysaccharide-protein interactions under physiological conditions by conventional techniques is challenging. Ideally, macromolecules could be followed by both in vitro spectroscopy experiments as well as in tissues using microscopy, to enable a proper comparison of results over these different scales but, often, this is not feasible. The cell surface and extracellular matrix polysaccharides, glycosaminoglycans (GAGs) lack groups that can be detected selectively in the biological milieu. The introduction of (19)F labels into GAG polysaccharides is explored and the interaction of a labelled GAG with the heparin-binding protein, antithrombin, employing (19)F NMR spectroscopy is followed. Furthermore, the ability of (19)F labelled GAGs to be imaged using CARS microscopy is demonstrated. (19)F labelled GAGs enable both (19)F NMR protein-GAG binding studies in solution at the molecular level and non-linear microscopy at a microscopic scale to be conducted on the same material, essentially free of background signals.

  13. Solution NMR studies of cell-penetrating peptides in model membrane systems. (United States)

    Mäler, Lena


    Cell-penetrating peptides (CPPs) are a class of short, often cationic peptides that have the capability to translocate across cellular membranes, and although the translocation most likely involves several pathways, they interact directly with membranes, as well as with model bilayers. Most CPPs attain a three-dimensional structure when interacting with bilayers, while they are more or less unstructured in aqueous solution. To understand the relationship between structure and the effect that CPPs have on membranes it is of great importance to investigate CPPs at atomic resolution in a suitable membrane model. Moreover, the location in bilayers is likely to be correlated with the translocation mechanism. Solution-state NMR offers a unique possibility to investigate structure, dynamics and location of proteins and peptides in bilayers. This review focuses on solution NMR as a tool for investigating CPP-lipid interactions. Structural propensities and cell-penetrating capabilities can be derived from a combination of CPP solution structures and studies of the effect that the peptides have on bilayers and the localization in a bilayer. Copyright © 2012 Elsevier B.V. All rights reserved.

  14. Optimizing nanodiscs and bicelles for solution NMR studies of two β-barrel membrane proteins

    Energy Technology Data Exchange (ETDEWEB)

    Kucharska, Iga [University of Virginia, Center for Membrane Biology and Department of Molecular Physiology and Biological Physics (United States); Edrington, Thomas C. [Monsanto Company (United States); Liang, Binyong; Tamm, Lukas K., E-mail: [University of Virginia, Center for Membrane Biology and Department of Molecular Physiology and Biological Physics (United States)


    Solution NMR spectroscopy has become a robust method to determine structures and explore the dynamics of integral membrane proteins. The vast majority of previous studies on membrane proteins by solution NMR have been conducted in lipid micelles. Contrary to the lipids that form a lipid bilayer in biological membranes, micellar lipids typically contain only a single hydrocarbon chain or two chains that are too short to form a bilayer. Therefore, there is a need to explore alternative more bilayer-like media to mimic the natural environment of membrane proteins. Lipid bicelles and lipid nanodiscs have emerged as two alternative membrane mimetics that are compatible with solution NMR spectroscopy. Here, we have conducted a comprehensive comparison of the physical and spectroscopic behavior of two outer membrane proteins from Pseudomonas aeruginosa, OprG and OprH, in lipid micelles, bicelles, and nanodiscs of five different sizes. Bicelles stabilized with a fraction of negatively charged lipids yielded spectra of almost comparable quality as in the best micellar solutions and the secondary structures were found to be almost indistinguishable in the two environments. Of the five nanodiscs tested, nanodiscs assembled from MSP1D1ΔH5 performed the best with both proteins in terms of sample stability and spectral resolution. Even in these optimal nanodiscs some broad signals from the membrane embedded barrel were severely overlapped with sharp signals from the flexible loops making their assignments difficult. A mutant OprH that had two of the flexible loops truncated yielded very promising spectra for further structural and dynamical analysis in MSP1D1ΔH5 nanodiscs.

  15. Bis(pentamethylcyclopentadienyl)ytterbium: An investigation of weak interactions in solution using multinuclear NMR spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Schwartz, David Joel [Univ. of California, Berkeley, CA (United States)


    NMR spectroscopy is ideal for studying weak interactions (formation enthalpy ≤20 kcal/mol) in solution. The metallocene bis(pentamethylcyclopentadienyl)ytterbium, Cp*2Yb, is ideal for this purpose. cis-P2PtH2complexes (P = phosphine) were used to produce slow-exchange Cp*2YbL adducts for NMR study. Reversible formation of (P2PtH)2 complexes from cis-P2PtH2 complexes were also studied, followed by interactions of Cp*2Yb with phosphines, R3PX complexes. A NMR study was done on the interactions of Cp*2Yb with H2, CH4, Xe, CO, silanes, stannanes, C6H6, and toluene.

  16. Complexation of enalapril maleate with beta-cyclodextrin: NMR spectroscopic study in solution

    Directory of Open Access Journals (Sweden)

    Syed Mashhood Ali


    Full Text Available A detailed NMR (¹H , COSY, ROESY spectroscopic study of complexation of enalapril maleate with beta-cyclodextrin was carried out. The ¹H NMR spectrum of enalapril maleate confirmed the existence of cis-trans equilibrium in solution, possibly due to hindered rotation along the amide bond. The cis-trans ratio remained almost the same in the presence of beta-cyclodextrin but in one case it was found significantly different which suggests a catalytic role of beta-cyclodextrin in the isomerization. ¹H NMR titration studies confirmed the formation of an enalapril-beta-cyclodextrin inclusion complex as evidenced by chemical shift variations in the proton resonances of both the host and the guest. The stoichiometry of the complex was determined to be 2:1 (guest: host. The mode of penetration of the guest into the beta-cyclodextrin cavity as well as the structure of the complex were established using ROESY spectroscopy.

  17. {sup 1}H NMR investigation of self-association of vanillin in aqueous solution

    Energy Technology Data Exchange (ETDEWEB)

    Bogdan, Mircea; Floare, Calin G; PIrnau, Adrian, E-mail: mircea.bogdan@itim-cj.r [National Institute for Research and Development of Isotopic and Molecular Technologies, 65-103 Donath, 400293 Cluj-Napoca (Romania)


    A self-association of vanillin have been studied by {sup 1}H NMR spectroscopy using the analysis of proton chemical shifts changes in aqueous solution as a function of concentration. The experimental results have been analysed using indefinite non-cooperative and cooperative models of molecular self-association, enabling the determination of equilibrium constants, parameters of cooperativity and the limiting values of vanillin proton chemical shifts in the complex. It was found that the dimer formation creates energetically favourable conditions for subsequent molecular association.

  18. Sequence-specific sup 1 H NMR assignments and solution structure of bovine pancreatic polypeptide

    Energy Technology Data Exchange (ETDEWEB)

    Xiang Li; Dobson, C.M. (Univ. of Oxford (United Kingdom)); Sutcliffe, M.J. (Leicester Univ. (United Kingdom)); Schwartz, T.W. (Lab. for Molecular Endocrinology, Copenhagen (Denmark))


    Sequence-specific {sup 1}H NMR assignments for the 36 residue bovine pancreatic polypeptide (bPP) have been completed. The secondary and tertiary structure of bPP in solution has been determined from experimental NMR data. It is shown that bPP has a very well-defined C-terminal {alpha}-helix involving residues 15-32. Although regular secondary structure cannot be clearly defined in the N-terminal region, residues 15-32. Although regular secondary structure cannot be clearly defined in the N-terminal region, residues 4-8 maintain a rather ordered conformation in solution. This is attributed primarily to the hydrophobic interaction between this region and the C-terminal helix. The two segments of the structure are joined by a turn which is poorly defined. The four end residues both at the N-terminus and the C-terminus are highly disordered in solution. The overall fold of the bPP molecule is very closely similar to that found in the crystal structure of avian pancreatic polypeptide (aPP). The RMS deviation for backbone atoms of residues 4-8 and 15-32 between the bPP mean structure and the aPP crystal structure is 0.65 {angstrom}, although there is only 39% identity of the residues. Furthermore, the average conformations of some (mostly from the {alpha}-helix) side chains of bPP in solution are closely similar to those of aPP in the crystal structure. A large number of side chains of bPP, however, show significant conformational averaging in solution.

  19. Obtaining and ferrite nanofiber characterization through wiring in blowing solution; Obtencao e caracterizacao de nanofibras de ferrita atraves da fiacao por sopro em solucao

    Energy Technology Data Exchange (ETDEWEB)

    Santos, M.A.; Menezes, R.R.; Mota, M.F.; Severo, L.L., E-mail: [Universidade Federal de Campina Grande (UFCG), PB (Brazil)


    Recent surveys show a new method of obtaining nanofibers, spinning blow solution (SBS). In SBS technique, the advantage is given at low cost because the electrical forces used in electrospinning are replaced by aerodynamic forces. Possessing unique properties, the nanofibers have a high potential for applications in nanosensors, nanofiltration, among others. Thus, this work aims to produce and characterize nanofiber ferrite through the SBS technique. For execution of work, a solution was prepared from the alcohol solvents and DMF (dimethylformamide), with addition of iron-III nitrate, nickel and zinc, and hydrochloric acid to stabilize the solution. Spinning was performed at a rate of 7.2 ml / h, 50 psi pressure and room temperature, the sample obtained was characterized. The results showed the efficacy technique where obtaining ferrite nanofibers with an average diameter of approximately 400nm was possible.(author)

  20. Application of 29Si NMR spectroscopy to study of alkaline aqueous and alcoholic tetraoctylammonium (TOA) silicate solutions (United States)

    Goudarzi, Nasser; Arab Chamjangali, M.; Bagherian, G.


    29Si NMR spectroscopy is a powerful tool for studying the silicate species existing in aqueous and non-aqueous solutions. In the present work, 29Si NMR spectroscopy is used to characterize the species present in alkaline alcoholic solutions of silicates. Tetraoctylammonium (TOA) hydroxide is used as a template. The effects of polymerization/depolymerization of silicate anions on alkaline alcoholic solutions are investigated using different alcohols (methanol, 1-propanol, 1,3-propane-diol, and glycerin) by 29Si NMR spectroscopy. The esterification of monomeric silicate, Si(OH) 4, in the presence of different alcohols is also studied. Esterification of Si(OH) 4 depends on the alkyl chain as well as the number of hydroxyl groups present in the alcohol.

  1. Investigating the Mechanisms of Amylolysis of Starch Granules by Solution-State NMR (United States)


    Starch is a prominent component of the human diet and is hydrolyzed by α-amylase post-ingestion. Probing the mechanism of this process has proven challenging, due to the intrinsic heterogeneity of individual starch granules. By means of solution-state NMR, we demonstrate that flexible polysaccharide chains protruding from the solvent-exposed surfaces of waxy rice starch granules are highly mobile and that during hydrothermal treatment, when the granules swell, the number of flexible residues on the exposed surfaces increases by a factor of 15. Moreover, we show that these flexible chains are the primary substrates for α-amylase, being cleaved in the initial stages of hydrolysis. These findings allow us to conclude that the quantity of flexible α-glucan chains protruding from the granule surface will greatly influence the rate of energy acquisition from digestion of starch. PMID:25815624

  2. NMR Water Self-Diffusion and Relaxation Studies on Sodium Polyacrylate Solutions and Gels in Physiologic Ionic Solutions. (United States)

    Bai, Ruiliang; Basser, Peter J; Briber, Robert M; Horkay, Ferenc


    Water self-diffusion coefficients and longitudinal relaxation rates in sodium polyacrylate solutions and gels were measured by NMR, as a function of polymer content and structure in a physiological concentration range of monovalent and divalent cations, Ca(2+) and Na(+). Several physical models describing the self-diffusion of the solvent were applied and compared. A free-volume model was found to be in good agreement with the experimental results over a wide range of polymer concentrations. The longitudinal relaxation rate exhibited linear dependence on polymer concentration below a critical concentration and showed non-linear behavior at higher concentrations. Both the water self-diffusion and relaxation were less influenced by the polymer in the gel state than in the uncrosslinked polymer solutions. The effect of Na(+) on the mobility of water molecules was practically undetectable. By contrast, addition of Ca(2+) strongly increased the longitudinal relaxation rate while its effect on the self-diffusion coefficient was much less pronounced.

  3. NMR Water Self–Diffusion and Relaxation Studies on Sodium Polyacrylate Solutions and Gels in Physiologic Ionic Solutions (United States)

    Bai, Ruiliang; Basser, Peter J.; Briber, Robert M.; Horkay, Ferenc


    Water self-diffusion coefficients and longitudinal relaxation rates in sodium polyacrylate solutions and gels were measured by NMR, as a function of polymer content and structure in a physiological concentration range of monovalent and divalent cations, Ca2+ and Na+. Several physical models describing the self-diffusion of the solvent were applied and compared. A free-volume model was found to be in good agreement with the experimental results over a wide range of polymer concentrations. The longitudinal relaxation rate exhibited linear dependence on polymer concentration below a critical concentration and showed non-linear behavior at higher concentrations. Both the water self-diffusion and relaxation were less influenced by the polymer in the gel state than in the uncrosslinked polymer solutions. The effect of Na+ on the mobility of water molecules was practically undetectable. By contrast, addition of Ca2+ strongly increased the longitudinal relaxation rate while its effect on the self-diffusion coefficient was much less pronounced. PMID:24409001

  4. NMR studies of the equilibria and reaction rates in aqueous solutions of formaldehyde. (United States)

    Rivlin, Michal; Eliav, Uzi; Navon, Gil


    Formaldehyde has an important role in the chemical industry and in biological sciences. In dilute aqueous solutions of formaldehyde only traces of the molecular formaldehyde are present and the predominant species are methylene glycol and in lower concentrations, dimethylene glycol. The chemical equilibria and reaction rates of the hydration of formaldehyde in H2O and D2O solutions at low concentrations were studied by (1)H and (13)C NMR at various conditions of pH (1.8-7.8) and temperature (278-333 K). These measurements became possible by direct detection of formaldehyde (13)C and (1)H peaks. The equilibrium and rate constants of the dimerization reaction of methylene glycol were also measured. The rate constants for both the hydration and the dimerization reactions were measured by a new version of the conventional selective inversion transfer method. This study, together with previous published work, completes the description of dynamics and equilibria of all the processes occurring in dilute aqueous formaldehyde solutions.

  5. Forms and lability of phosphorus in algae and aquatic macrophytes characterized by solution 31P NMR coupled with enzymatic hydrolysis (United States)

    Increased information on forms and lability of phosphorus (P) in aquatic macrophytes and algae is crucial for better understanding of P biogeochemical cycling in eutrophic lakes. In this work, solution 31P nuclear magnetic resonance (NMR) spectroscopy coupled with enzymatic hydrolysis (EH) was used ...

  6. A solution-state NMR approach to elucidating pMDI-wood bonding mechanisms in loblolly pine (United States)

    Daniel Joseph Yelle


    Solution-state NMR spectroscopy is a powerful tool for unambiguously determining the existence or absence of covalent chemical bonds between wood components and adhesives. Finely ground wood cell wall material dissolves in a solvent system containing DMSO-d6 and NMI-d6, keeping wood component polymers intact and in a near-...

  7. Synthesis of poly(D,L-lactide-co-glycolide) copolymers and its chemical characterization by NMR and FTIR; Sintese e caracterizacao quimica por RMN e FTIR do copolimero poli(D,L-lactideo-co-glicolideo)

    Energy Technology Data Exchange (ETDEWEB)



    Poly(D,L-lactide-co-glycolide) copolymer is of great interest for medical applications. This interest is justified by the fact that it is bioreabsorbable, biocompatible and non-toxic, while its degradation kinetics can be modified by the copolymerization ratio of the monomers. In this study, copolymers were synthesized at 175 deg C by opening the rings of the cyclic dimers of the D,L-lactide and glycolide monomers in the presence of stannous octoate initiator and lauryl alcohol co-initiator. The efficient application of a vacuum to the reaction medium, coupled with adequate stirring, is fundamental for the success of the synthesis. The following analysis techniques were used to characterize the synthesized copolymers: Nuclear Magnetic Resonance Spectroscopy (NMR) and Fourier Transform Infrared Spectroscopy (FTIR). The chemical composition and the ratio of the monomers in the synthesized copolymer were determined. (author)

  8. Application of phosphorus-31 and aluminum-27 NMR spectroscopic techniques to study aqueous and methanolic solutions of tetraphenylammonium aluminophosphate (United States)

    Goudarzi, Nasser; Amin, Amir H.


    In this work, aluminum-27 and phosphorus-31 NMR spectroscopic techniques were used to investigate and characterize the distribution of aluminophosphate (AlPO) species soluble in the aqueous and methanolic solutions of tetraphenylammonium (TPhA) chloride. The reaction between hexaaquaaluminum cations, [A1(H2O)6]3+, and different phosphate ligands such as H3PO4, H2PO4-, and the acidic dimers H6P2O8 and H5P2O8- resulted in the formation of the soluble AlPO cations. The effective aluminum-27 and phosphorous-31 NMR spectroscopies can be employed to characterize the species present in a solution. Assignment of the peaks present in the aluminum-27 NMR spectra to the aluminate species or aluminate connectivities was done to acquire information about different AlPO complexes. Some resonance lines were observed in the phosphorus-31 {1H} NMR spectra, indicating the existence of different complexes in the AlPO solutions. Some peaks were observed in the methanolic solutions of AlPO at the chemical shifts of -0.41, -6.4, -7.5, -7.9, -13.1, -13.9, -16.6, -18.1, and -20.6 ppm. Four additional peaks were also observed in the phosphorus-31 {1H} NMR spectra of the methanolic solutions of AlPO, whose intensities changed with changes in the methanol:water volume ratio; they were observed in methanol but not in aqueous AlPO.

  9. The PP-fold solution structure of human polypeptide YY and human PYY3-36 as determined by NMR

    DEFF Research Database (Denmark)

    Nygaard, Rie; Nielbo, Steen; Schwartz, Thue W


    revealed a highly ordered, back-folded structure for human PYY in aqueous solution similar to the classical PP-fold structure of pancreatic polypeptide. The NMR analysis of PYY3-36 also showed a folded structure resembling a PP-fold, which however was characterized by far fewer long distance NOEs than......PYY3-36 is a biopharmaceutical antiobesity agent under development as well as an endogenous satiety hormone, which is generated by dipeptidyl peptidase-IV digestion of polypetide YY (PYY), and in contrast to the parent hormone, PYY is highly selective for the Y2 versus the Y1 receptor. NMR analysis...

  10. Effects of Anesthetic Membrane Solutes on Orientational Order in Lecithin Bilayer Membranes: a Deuterium NMR Study. (United States)

    Phonphok, Nason

    The interaction of eight n-alkanols and three volatile anesthetics with bilayers of dimyristoylphosphatidylcholine (DMPC) has been studied by deuterium nuclear magnetic resonance (^2H NMR). At comparable temperatures and concentrations of solute in the bilayer, order parameters measured at the 1-methylene segment of the n-alkanols, and average order parameters for the whole alkyl chain, show a maximum for n-dodecanol. This maximum in orientational ordering also occurs for n-dodecanol at the much lower levels of solute concentration which produce anesthesia. For both n-dodecanol and n-tetradecanol, orientational ordering shows a maximum at the C-4 to C-7 methylene segments, with labels at both ends of the n-alkanol exhibiting reduced order. Unlike the longer chain n-alkanols, ordering in n-butanol decreases from the hydroxyl group end to the methyl group end of the molecule. The quadrupole splittings observed in DMPC-water systems containing perdeuterated ether, chloroform and n-hexane show that these volatile anesthetics are also ordered in the bilayer in the L _{alpha} phase. The temperature dependence of the quadrupole splitting ^2H_2O in DMPC bilayers at low hydration indicates that both the n-alkanols and volatile anesthetics do not affect water structure in the L_alpha phase, but they do so below the main phase transition. Orientational ordering at nine inequivalent sites in the headgroup region of DMPC, as well as the acyl chains, has also been measured. Every anesthetic produces a disordering at the beta-methylene of the choline, the 3-methylene segment and the 1-R site (except chloroform) of the glycerol backbone. Molecular and conformational ordering at the interfacial region of DMPC in the L _alpha phase have been examined by analysing ^2H-NMR data from multiple sites in the most rigid region of the DMPC molecule. It was found that these anesthetics change the conformation at the glycerol moiety of DMPC without changing the molecular order parameter rm S

  11. Forms and Lability of Phosphorus in Algae and Aquatic Macrophytes Characterized by Solution 31P NMR Coupled with Enzymatic Hydrolysis (United States)

    Feng, Weiying; Zhu, Yuanrong; Wu, Fengchang; He, Zhongqi; Zhang, Chen; Giesy, John P.


    Solution Phosphorus-31 nuclear magnetic resonance (31P NMR) spectroscopy coupled with enzymatic hydrolysis (EH) with commercially available phosphatases was used to characterize phosphorus (P) compounds in extracts of the dominant aquatic macrophytes and algae in a eutrophic lake. Total extractable organic P (Po) concentrations ranged from 504 to 1643 mg kg−1 and 2318 to 8395 mg kg−1 for aquatic macrophytes and algae, respectively. Using 31P NMR spectroscopy, 11 Po species were detected in the mono- and diester region. Additionally, orthophosphate, pyrophosphate and phosphonates were also detected. Using EH, phytate-like P was identified as the prevalent class of enzyme-labile Po, followed by labile monoester- and diester-P. Comparison of the NMR and EH data indicated that the distribution pattern of major P forms in the samples determined by the two methods was similar (r = 0.712, p eutrophic lakes. PMID:27849040

  12. Designing amphotropic smectic liquid crystals based on phosphonium salts for partial ordering of solutes as monitored by NMR spectroscopy. (United States)

    Shahkhatuni, Astghik A; Ma, Kefeng; Weiss, Richard G


    The ordering parameters of selected solutes from NMR spectroscopic measurements have been assessed in the thermotropic and amphotropic smectic liquid-crystalline phases of a wide structural range of phosphonium salts with three equivalent long n-alkyl chains, one shorter chain, and various anions. The nature of the added liquids that convert the salts to amphotropic phasesalcohols and other small organic moleculesand their concentrations have been determined. These factors are correlated with the NMR-derived parameters in order to understand how the phases can be optimized to maximize information about the solutes. The various salts cover a range of liquid crystallinity from -40 to 100 degrees C. The phosphonium salts are easily aligned in the strong magnetic fields of the spectrometers. In several of the systems, a coexistence of isotropic and anisotropic phases is observed over a wide range of temperatures. The order parameters of the amphotropic liquid-crystalline phases vary from high to very low values, and some of the systems provide good spectral resolution for the solute molecules. Also, structural and orientational parameters of a model molecule, (13)C-enriched acetonitrile, have been calculated in various systems in order to evaluate more precisely the applicability of the host systems for determining solute structures by NMR. The results, in toto, indicate that several of the phosphonium salts are very promising as hosts to determine solute structures.

  13. NMR solution structure of a Chymotrypsin inhibitor from the Taiwan cobra Naja naja atra. (United States)

    Lin, Yi-Jan; Ikeya, Teppei; Güntert, Peter; Chang, Long-Sen


    The Taiwan cobra (Naja naja atra) chymotrypsin inhibitor (NACI) consists of 57 amino acids and is related to other Kunitz-type inhibitors such as bovine pancreatic trypsin inhibitor (BPTI) and Bungarus fasciatus fraction IX (BF9), another chymotrypsin inhibitor. Here we present the solution structure of NACI. We determined the NMR structure of NACI with a root-mean-square deviation of 0.37 Å for the backbone atoms and 0.73 Å for the heavy atoms on the basis of 1,075 upper distance limits derived from NOE peaks measured in its NOESY spectra. To investigate the structural characteristics of NACI, we compared the three-dimensional structure of NACI with BPTI and BF9. The structure of the NACI protein comprises one 310-helix, one α-helix and one double-stranded antiparallel β-sheet, which is comparable with the secondary structures in BPTI and BF9. The RMSD value between the mean structures is 1.09 Å between NACI and BPTI and 1.27 Å between NACI and BF9. In addition to similar secondary and tertiary structure, NACI might possess similar types of protein conformational fluctuations as reported in BPTI, such as Cys14-Cys38 disulfide bond isomerization, based on line broadening of resonances from residues which are mainly confined to a region around the Cys14-Cys38 disulfide bond.

  14. Thermodynamic Study on the Protonation Reactions of Glyphosate in Aqueous Solution: Potentiometry, Calorimetry and NMR spectroscopy. (United States)

    Liu, Bijun; Dong, Lan; Yu, Qianhong; Li, Xingliang; Wu, Fengchang; Tan, Zhaoyi; Luo, Shunzhong


    Glyphosate [N-(phosphonomethyl)glycine] has been described as the ideal herbicide because of its unique properties. There is some conflicting information concerning the structures and conformations involved in the protonation process of glyphosate. Protonation may influence the chemical and physical properties of glyphosate, modifying its structure and the chemical processes in which it is involved. To better understand the species in solution associated with changes in pH, thermodynamic study (potentiometry, calorimetry and NMR spectroscopy) about the protonation pathway of glyphosate is performed. Experimental results confirmed that the order of successive protonation sites of totally deprotonated glyphosate is phosphonate oxygen, amino nitrogen, and finally carboxylate oxygen. This trend is in agreement with the most recent theoretical work in the literature on the subject (J. Phys. Chem. A 2015, 119, 5241-5249). The result is important because it confirms that the protonated site of glyphosate in pH range 7-8, is not on the amino but on the phosphonate group instead. This corrected information can improve the understanding of the glyphosate chemical and biochemical action.

  15. Conformational disorder in phosphopeptides: solution studies by CD and NMR techniques

    Directory of Open Access Journals (Sweden)

    Leone Marilisa


    Full Text Available In the last few years intrinsically disordered proteins (IDPs have received great attention from the scientific community as they participate in several important biological processes and diseases. The intrinsic disorder and flexibility of IDPs grant them a number of advantages with respect to ordered proteins, such as conformational plasticity to bind several targets, a large interaction surface, involvement in high specificity/low affinity interactions, enhanced binding kinetics. It is assumed that post-translational modifications such as phosphorylation can stimulate structural rearrangement in IDPs and facilitate their binding to partners. To better understand at a structural level the multifaceted mechanisms that govern molecular recognition processes involving IDPs, we designed, synthesized by solid phase methods, and structurally characterized unstructured peptides. These molecules contain a putative disordered module, flanked at either the N- or C-terminal ends by a different phosphorylated amino acid (serine or threonine to mimick the effects of phosphorylation. The absence of an ordered state in the designed peptides was proved experimentally by CD and NMR conformational studies that were carried out under different solution conditions

  16. {sup 13}C solution NMR spectra of poly(ether)urethanes. Technical memorandum

    Energy Technology Data Exchange (ETDEWEB)

    Hiltz, J.A


    The {sup 13}C solution nuclear magnetic resonance (NMR) spectra of the 15 poly(ether)urethanes are presented. The poly(urethane)s were prepared using one of two diisocyanates, either methylene diphenyl diisocyanate (MDI) or hexamethylene diisocyanate (HDI), one of five poly(ether glycol)s, poly(tetramethylene ether glycol) of molecular weight 650, 1000, or 1400, or poly(ethylene glycol) of molecular weight 600 or 1000, and one of three chain extenders, 1,4-butanediol, 2,2-dimethyl-1,3-propanediol, or diethylene glycol. These polymers were prepared as part of a modelling study to determine if Group Contribution Theory and Group Interaction Modelling could be used to predict dynamic mechanical properties of poly(ether)urethanes on the basis of the structural fragments in the polymers. The chemical shifts of the unique carbons in each of the poly(urethane)s are assigned. They can be used to unambiguously identify the diisocyanate/diol/poly(ether glycol) used to prepare the various polyurethanes. For some compounds the spectra show resonances for terminal hydroxyl substituted carbons. These could provide a method, under the right experimental conditions, to compare molecular weights of batches of the same polymer. (author)

  17. Direct observation and characterization of DMPC/DHPC aggregates under conditions relevant for biological solution NMR. (United States)

    van Dam, Lorens; Karlsson, Göran; Edwards, Katarina


    We have used cryo-transmission electron microscopy (cryo-TEM) for inspection of aggregates formed by dimyristoylphosphatidylcholine (DMPC) and dihexanoylphosphatidylcholine (DHPC) in aqueous solution at total phospholipid concentrations cL DHPC ratios q < or = 4.0. In combination with ocular inspections, we are able to sketch out this part of phase-diagram at T = 14-80 degrees C. The temperature and the ratio q are the dominating variables for changing sample morphology, while cL to a lesser extent affects the aggregate structure. At q = 0.5, small, possibly disc-shaped, aggregates with a diameter of approximately 6 nm are formed. At higher q-values, distorted discoidal micelles that tend to short cylindrical micelles are observed. The more well-shaped discs have a diameter of around 20 nm. Upon increasing q or the temperature, long slightly flattened cylindrical micelles that eventually branch are formed. A holey lamellar phase finally appears upon further elevation of q or temperature. The implications for biological NMR work are two. First, discs prepared as membrane mimics are frequently much smaller than predicted by current "ideal bicelle" models. Second, the q approximately 3 preparations used for aligning water-soluble biomolecules in magnetic fields consist of perforated lamellar sheets. Furthermore, the discovered sequence of morphological transitions may have important implications for the development of bicelle-based membrane protein crystallization methods.

  18. Measurement of Solution Viscosity via Diffusion-Ordered NMR Spectroscopy (DOSY) (United States)

    Li, Weibin; Kagan, Gerald; Hopson, Russell; Williard, Paul G.


    Increasingly, the undergraduate chemistry curriculum includes nuclear magnetic resonance (NMR) spectroscopy. Advanced NMR techniques are often taught including two-dimensional gradient-based experiments. An investigation of intermolecular forces including viscosity, by a variety of methods, is often integrated in the undergraduate physical and…

  19. Characteristics and degradation of carbon and phosphorus from aquatic macrophytes in lakes: Insights from solid-state {sup 13}C NMR and solution {sup 31}P NMR spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Shasha [College of Water Sciences, Beijing Normal University, Beijing 100875 (China); State Key Laboratory of Environment Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012 (China); Zhu, Yuanrong, E-mail: [State Key Laboratory of Environment Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012 (China); Meng, Wei, E-mail: [State Key Laboratory of Environment Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012 (China); He, Zhongqi [USDA-ARS Southern Regional Research Center, 1100 Robert E Lee Blvd, New Orleans, LA 70124 (United States); Feng, Weiying [College of Water Sciences, Beijing Normal University, Beijing 100875 (China); State Key Laboratory of Environment Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012 (China); Zhang, Chen [State Key Laboratory of Environment Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012 (China); Giesy, John P. [State Key Laboratory of Environment Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012 (China); Department of Biomedical and Veterinary Biosciences and Toxicology Centre, University of Saskatchewan, Saskatoon, Saskatchewan (Canada)


    Water extractable organic matter (WEOM) derived from macrophytes plays an important role in biogeochemical cycling of nutrients, including carbon (C), nitrogen (N) and phosphorus (P) in lakes. However, reports of their composition and degradation in natural waters are scarce. Therefore, compositions and degradation of WEOM derived from six aquatic macrophytes species of Tai Lake, China, were investigated by use of solid-state {sup 13}C NMR and solution {sup 31}P NMR spectroscopy. Carbohydrates were the predominant constituents of WEOM fractions, followed by carboxylic acid. Orthophosphate (ortho-P) was the dominant form of P (78.7% of total dissolved P) in the water extracts, followed by monoester P (mono-P) (20.6%) and little diester P (0.65%). The proportion of mono-P in total P species increased with the percentage of O-alkyl and O–C–O increasing in the WEOM, which is likely due to degradation and dissolution of biological membranes and RNA from aquatic plants. Whereas the proportion of mono-P decreased with alkyl-C, NCH/OCH{sub 3} and COO/N–C=O increasing, which may be owing to the insoluble compounds including C functional groups of alkyl-C, NCH/OCH{sub 3} and COO/N–C=O, such as aliphatic biopolymers, lignin and peptides. Based on the results of this study and information in the literature about water column and sediment, we propose that WEOM, dominated by polysaccharides, are the most labile and bioavailable component in debris of macrophytes. Additionally, these WEOMs would also be a potential source for bioavailable organic P (e.g., RNA, DNA and phytate) for lakes. - Highlights: • WEOM derived from aquatic macrophytes was characterized. • C and P in WEOM were characterized by solid {sup 13}C NMR and solution {sup 31}P NMR. • Degradation and transformation of macrophyte-derived C and P were investigated. • Macrophyte-derived WEOM are important source for bioavailable nutrients in lakes.

  20. Three-dimensional solution structure of alpha-conotoxin MII by NMR spectroscopy: effects of solution environment on helicity. (United States)

    Hill, J M; Oomen, C J; Miranda, L P; Bingham, J P; Alewood, P F; Craik, D J


    alpha-Conotoxin MII, a 16-residue polypeptide from the venom of the piscivorous cone snail Conus magus, is a potent and highly specific blocker of mammalian neuronal nicotinic acetylcholine receptors composed of alpha3 beta2 subunits. The role of this receptor type in the modulation of neurotransmitter release and its relevance to the problems of addiction and psychosis emphasize the importance of a structural understanding of the mode of interaction of MII with the alpha3 beta2 interface. Here we describe the three-dimensional solution structure of MII determined using 2D 1H NMR spectroscopy. Structural restraints consisting of 376 interproton distances inferred from NOEs and 12 dihedral restraints derived from spin-spin coupling constants were used as input for simulated annealing calculations and energy minimization in the program X-PLOR. The final set of 20 structures is exceptionally well-defined with mean pairwise rms differences over the whole molecule of 0.07 A for the backbone atoms and 0.34 A for all heavy atoms. MII adopts a compact structure incorporating a central segment of alpha-helix and beta-turns at the N- and C-termini. The molecule is stabilized by two disulfide bonds, which provide cross-links between the N-terminus and both the middle and C-terminus of the structure. The susceptibility of the structure to conformational change was examined using several different solvent conditions. While the global fold of MII remains the same, the structure is stabilized in a more hydrophobic environment provided by the addition of acetonitrile or trifluoroethanol to the aqueous solution. The distribution of amino acid side chains in MII creates distinct hydrophobic and polar patches on its surface that may be important for the specific interaction with the alpha3beta2 neuronal nAChR. A comparison of the structure of MII with other neuronal-specific alpha-conotoxins provides insights into their mode of interaction with these receptors.

  1. Structural analysis of flavonoids in solution through DFT 1H NMR chemical shift calculations: Epigallocatechin, Kaempferol and Quercetin (United States)

    De Souza, Leonardo A.; Tavares, Wagner M. G.; Lopes, Ana Paula M.; Soeiro, Malucia M.; De Almeida, Wagner B.


    In this work, we showed that comparison between experimental and theoretical 1H NMR chemical shift patterns, calculated using Density Functional Theory (DFT), can be used for the prediction of molecular structure of flavonoids in solution, what is experimentally accessible for gas phase (electron diffraction methods) and solid samples (X-ray diffraction). The best match between B3LYP/6-31G(d,p)-PCM 1H NMR calculations for B ring rotated structures and experimental spectra can provide information on the conformation adopted by polyphenols in solution (usually DMSO-d6, acetone-d6 as solvents), which may differ from solid state and gas phase observed structures, and also DFT optimized geometry in the vacuum.

  2. Indirect use of deuterium in solution NMR studies of protein structure and hydrogen bonding. (United States)

    Tugarinov, Vitali


    A description of the utility of deuteration in protein NMR is provided with an emphasis on quantitative evaluation of the effects of deuteration on a number of NMR parameters of proteins: (1) chemical shifts, (2) scalar coupling constants, (3) relaxation properties (R1 and R2 rates) of nuclei directly attached to one or more deuterons as well as protons of methyl groups in a highly deuterated environment, (4) scalar relaxation of 15N and 13C nuclei in 15N-D and 13C-D spin systems as a measure of hydrogen bonding strength, and (5) NOE-based applications of deuteration in NMR studies of protein structure. The discussion is restricted to the 'indirect' use of deuterium in the sense that the description of NMR parameters and properties of the nuclei affected by nearby deuterons (15N, 13C, 1H) is provided rather than those of deuterium itself. Copyright © 2013 Elsevier B.V. All rights reserved.

  3. Delineating pMDI model reactions with loblolly pine via solution-state NMR spectroscopy. Part 2, Non-catalyzed reactions with the wood cell wall (United States)

    Daniel J. Yelle; John Ralph; Charles R. Frihart


    Solution-state NMR provides a powerful tool to observe the presence or absence of covalent bonds between wood and adhesives. Finely ground wood can be dissolved in an NMR compatible solvent system containing dimethylsulfoxide-d6 and N-methylimidazole-d6, in which the wood polymers remain largely intact. High-resolution...

  4. Effects of a type I antifreeze protein (AFP) on the melting of frozen AFP and AFP+solute aqueous solutions studied by NMR microimaging experiment. (United States)

    Ba, Yong; Mao, Yougang; Galdino, Luiz; Günsen, Zorigoo


    The effects of a type I AFP on the bulk melting of frozen AFP solutions and frozen AFP+solute solutions were studied through an NMR microimaging experiment. The solutes studied include sodium chloride and glucose and the amino acids alanine, threonine, arginine, and aspartic acid. We found that the AFP is able to induce the bulk melting of the frozen AFP solutions at temperatures lower than 0 °C and can also keep the ice melted at higher temperatures in the AFP+solute solutions than those in the corresponding solute solutions. The latter shows that the ice phases were in super-heated states in the frozen AFP+solute solutions. We have tried to understand the first experimental phenomenon via the recent theoretical prediction that type I AFP can induce the local melting of ice upon adsorption to ice surfaces. The latter experimental phenomenon was explained with the hypothesis that the adsorption of AFP to ice surfaces introduces a less hydrophilic water-AFP-ice interfacial region, which repels the ionic/hydrophilic solutes. Thus, this interfacial region formed an intermediate chemical potential layer between the water phase and the ice phase, which prevented the transfer of water from the ice phase to the water phase. We have also attempted to understand the significance of the observed melting phenomena to the survival of organisms that express AFPs over cold winters.

  5. Determination of the Three-dimensional Structure of Gynoside A in Solution using NMR and Molecular Modeling

    Directory of Open Access Journals (Sweden)

    Wen-Cai Ye


    Full Text Available The three-dimensional structure of Gynoside A, an ocotillone-type triterpenoid glycoside isolated from Gynostemma pentaphyllum, was determined in pyridine-d5 and DMSO-d6 solution through constrained molecular modeling using constraints derived from proton NMR spectra. The calculation yielded well-defined global minima. Except for some quantitative details the overall structure of Gynoside A in pyridine-d5 shared many common features with that in DMSO-d6. The structure in pyridine-d5 had lower energies than that in DMSO-d6 solution.

  6. Dynamics of water solutions of natural polysaccharides by fast field cycling nmr relaxometry (United States)

    Prusova, Alena; Conte, Pellegrino; Kucerik, Jiri; de Pasquale, Claudio; Alonzo, Giuseppe


    second hydration shell contains water molecules, also recognized as partly-bound (PBW), which are not directly interacting with the hyaluronan chains but with BW. Finally, water molecules, which dynamics is resembling that of the pure and undisturbed water, are indicated either as a bulk water or free water (FW). As hyaluronan concentration is increased the third FW hydration shell is lost and all water molecules are affected by the presence of hyaluronan molecules. This work showed the great potential of FFC-NMR relaxometry in revealing water nature in polysaccharide solutions and the possibility for future applications on complex biological systems. Acknowledgements A.P. gratefully acknowledges a bilateral Erasmus project between Brno University of Technology and University of Palermo which provided grant sustainment for working in Italy. Ministry of Education of the Czech Republic, project MSM 0021630501 is also acknwledged. This work was partially funded by Ce.R.T.A. s.c.r.l. (Centri Regionali per le Tecnologie Alimentari; Italy). Authors kindly acknowledge Dr. Vladimír Velebný (CPN company, Dolní Dobrouč, Czech Republic) for providing of hyaluronan sample.

  7. Determination of Water Content in THF Based on Chemical Shift Differences in Solution NMR

    Energy Technology Data Exchange (ETDEWEB)

    Jun, Jae Kyung; Park, Hey Rhee; Lee, Yunhee; Choi, Myung Gil; Chang, Suk-Kyu; Ahn, Sangdoo [Chung-Ang University, Seoul (Korea, Republic of)


    In this study, H NMR chemical shift differences were used as a probe for water content in organic solvents. Changes in chemical shift differences reflecting the competition for hydrogen bondings between fluoride ions and water were linearly proportional to water content within certain ranges. Comparison between the results obtained using the developed sensor and Karl Fischer showed that this method could be useful to understand water sensing mechanisms of dye and that the probes were sensitive to water content in organic solvents. NMR spectroscopy is one of the most powerful and versatile analytical techniques for the analysis of molecular structures and properties. Chemical shifts can be regarded as the most important information that can be obtained from NMR in regard to molecular structures. Changes in chemical and/or physical environments affecting electronic distributions result in alterations in the chemical shifts of the nuclei involved.

  8. Proton-Exchange-Induced Configuration Rearrangement in a Poly(ionic liquid) Solution: A NMR Study. (United States)

    Zhu, Haijin; Yang, Hengrui; Li, Jiaye; Barlow, Kristine J; Kong, Lingxue; Mecerreyes, David; MacFarlane, Douglas R; Forsyth, Maria


    Polymeric ionic liquids have emerged recently as a promising alternative to traditional polymers as the polymer electrolyte membrane materials of choice because of their strongly decoupled dynamics between the polymer backbone and the counterions. Knowledge of proton exchange and transport mechanism in such materials is critical to the design and development of new poly(ionic liquid) materials with improved electrochemical properties. Our NMR results show that the proton exchange between the labile proton of the diethylmethylammonium (NH122) cation and H2O molecules is accompanied by a concerted configuration rearrangement of the ammonium. Through a combination of PFG-NMR and proton relaxation (line width) analysis, we demonstrate that at lower temperatures the labile proton diffuses along with the NH122 ammonium cation as an integral unit, whereas at higher temperatures the NH/H2O proton exchange sets in gradually, and the PFG-NMR measured diffusion coefficient is a population-averaged value between the two exchanging sites.

  9. Spin-state-selective methods in solution- and solid-state biomolecular 13C NMR. (United States)

    Felli, Isabella C; Pierattelli, Roberta


    Spin-state-selective methods to achieve homonuclear decoupling in the direct acquisition dimension of (13)C detected NMR experiments have been one of the key contributors to converting (13)C detected NMR experiments into really useful tools for studying biomolecules. We discuss here in detail the various methods that have been proposed, summarize the large array of new experiments that have been developed and present applications to different kinds of proteins in different aggregation states. Copyright © 2014 Elsevier B.V. All rights reserved.

  10. Characteristics and degradation of carbon and phosphorus from aquatic macrophytes in lakes: Insights from solid-state (13)C NMR and solution (31)P NMR spectroscopy. (United States)

    Liu, Shasha; Zhu, Yuanrong; Meng, Wei; He, Zhongqi; Feng, Weiying; Zhang, Chen; Giesy, John P


    Water extractable organic matter (WEOM) derived from macrophytes plays an important role in biogeochemical cycling of nutrients, including carbon (C), nitrogen (N) and phosphorus (P) in lakes. However, reports of their composition and degradation in natural waters are scarce. Therefore, compositions and degradation of WEOM derived from six aquatic macrophytes species of Tai Lake, China, were investigated by use of solid-state (13)C NMR and solution (31)P NMR spectroscopy. Carbohydrates were the predominant constituents of WEOM fractions, followed by carboxylic acid. Orthophosphate (ortho-P) was the dominant form of P (78.7% of total dissolved P) in the water extracts, followed by monoester P (mono-P) (20.6%) and little diester P (0.65%). The proportion of mono-P in total P species increased with the percentage of O-alkyl and O-C-O increasing in the WEOM, which is likely due to degradation and dissolution of biological membranes and RNA from aquatic plants. Whereas the proportion of mono-P decreased with alkyl-C, NCH/OCH3 and COO/N-C=O increasing, which may be owing to the insoluble compounds including C functional groups of alkyl-C, NCH/OCH3 and COO/N-C=O, such as aliphatic biopolymers, lignin and peptides. Based on the results of this study and information in the literature about water column and sediment, we propose that WEOM, dominated by polysaccharides, are the most labile and bioavailable component in debris of macrophytes. Additionally, these WEOMs would also be a potential source for bioavailable organic P (e.g., RNA, DNA and phytate) for lakes. Copyright © 2015 Elsevier B.V. All rights reserved.

  11. Optimized co-solute paramagnetic relaxation enhancement for the rapid NMR analysis of a highly fibrillogenic peptide

    Energy Technology Data Exchange (ETDEWEB)

    Oktaviani, Nur Alia [University of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute (Netherlands); Risør, Michael W. [University of Aarhus, Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry (Denmark); Lee, Young-Ho [Osaka University, Institute for Protein Research (Japan); Megens, Rik P. [University of Groningen, Stratingh Institute for Chemistry (Netherlands); Jong, Djurre H. de; Otten, Renee; Scheek, Ruud M. [University of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute (Netherlands); Enghild, Jan J. [University of Aarhus, Interdisciplinary Nanoscience Center (iNANO) and Department of Molecular Biology and Genetics (Denmark); Nielsen, Niels Chr. [University of Aarhus, Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry (Denmark); Ikegami, Takahisa [Yokohama City University, Graduate School of Medical Life Science (Japan); Mulder, Frans A. A., E-mail: [University of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute (Netherlands)


    Co-solute paramagnetic relaxation enhancement (PRE) is an attractive way to speed up data acquisition in NMR spectroscopy by shortening the T{sub 1} relaxation time of the nucleus of interest and thus the necessary recycle delay. Here, we present the rationale to utilize high-spin iron(III) as the optimal transition metal for this purpose and characterize the properties of its neutral chelate form Fe(DO3A) as a suitable PRE agent. Fe(DO3A) effectively reduces the T{sub 1} values across the entire sequence of the intrinsically disordered protein α-synuclein with negligible impact on line width. The agent is better suited than currently used alternatives, shows no specific interaction with the polypeptide chain and, due to its high relaxivity, is effective at low concentrations and in ‘proton-less’ NMR experiments. By using Fe(DO3A) we were able to complete the backbone resonance assignment of a highly fibrillogenic peptide from α{sub 1}-antitrypsin by acquiring the necessary suite of multidimensional NMR datasets in 3 h.

  12. The MAS NMR study of solid solutions based on the YAG crystal

    Directory of Open Access Journals (Sweden)

    Padlyak Bohdan V.


    Full Text Available An 27Al magic angle spinning (MAS nuclear magnetic resonance (NMR study of nominally pure and Cr-doped yttrium-aluminum garnet (Y3Al5O12 and Y3Al5O12:Cr crystals is reported. It has been shown that the doping by Cr of the Y3Al5O12 crystals leads to the variation of the occupation by Al atoms both octahedrally and tetrahedrally coordinated sites of the garnet lattice.

  13. αB-Crystallin. A Hybrid Solid-State/Solution-State NMR Investigation Reveals Structural Aspects of the Heterogeneous Oligomer

    Energy Technology Data Exchange (ETDEWEB)

    Jehle, Stefan [Freie Univ., Berlin (Germany); Leibniz Inst. for Molecular Pharmacology, Berlin (Germany); van Rossum, Barth [Leibniz Inst. for Molecular Pharmacology, Berlin (Germany); Stout, Joseph R. [Univ. of Washington, Seattle, WA (United States); Noguchi, Satoshi M. [Univ. of Washington, Seattle, WA (United States); Falber, Katja [Leibniz Inst. for Molecular Pharmacology, Berlin (Germany); Rehbein, Kristina [Leibniz Inst. for Molecular Pharmacology, Berlin (Germany); Oschkinat, Hartmut [Freie Univ., Berlin (Germany); Leibniz Inst. for Molecular Pharmacology, Berlin (Germany); Klevit, Rachel E. [Univ. of Washington, Seattle, WA (United States); Rajagopal, Ponni [Univ. of Washington, Seattle, WA (United States)


    Atomic-level structural information on αB-Crystallin (αB), a prominent member of the small heat-shock protein family, has been a challenge to obtain due its polydisperse oligomeric nature. We show that magic-angle spinning solid-state NMR can be used to obtain high-resolution information on an ~580-kDa human αB assembled from 175-residue 20-kDa subunits. An ~100-residue α-crystallin domain is common to all small heat-shock proteins, and solution-state NMR was performed on two different α- crystallin domain constructs isolated from αB. In vitro, the chaperone-like activities of full-length αB and the isolated α-crystallin domain are identical. Chemical shifts of the backbone and Cβ resonances have been obtained for residues 64–162 (α-crystallin domain plus part of the C-terminus) in αB and the isolated α-crystallin domain by solid-state and solution-state NMR, respectively. Both sets of data strongly predict six β-strands in the α-crystallin domain. A majority of residues in the α-crystallin domain have similar chemical shifts in both solid-state and solution-state, indicating similar structures for the domain in its isolated and oligomeric forms. Sites of intersubunit interaction are identified from chemical shift differences that cluster to specific regions of the α-crystallin domain. Multiple signals are observed for the resonances of M68 in the oligomer, identifying the region containing this residue as existing in heterogeneous environments within αB. Evidence for a novel dimerization motif in the human α-crystallin domain is obtained by a comparison of (i) solid-state and solution-state chemical shift data and (ii) 1H–15N heteronuclear single quantum coherence spectra as a function of pH. The isolated α-crystallin domain undergoes a dimer–monomer transition over the pH range 7.5–6.8. This steep pHdependent switch may be important for αB to function optimally (e.g., to preserve the filament integrity

  14. Potentiometric, UV and 1H NMR study on the interaction of Cu2+ with ampicillin and amoxicillin in aqueous solution. (United States)

    Cardiano, Paola; Crea, Francesco; Foti, Claudia; Giuffrè, Ottavia; Sammartano, Silvio


    A potentiometric, UV and 1H NMR study on Cu2+-ampicillin [(2S,5R,6R)-6-([(2R)-2-amino-2-phenylacetyl]amino)-3,3-dimethyl-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylic acid] and -amoxicillin [(2S,5R,6R)-6-{[(2R)-2-amino-2-(4-hydroxyphenyl)-acetyl]amino}-3,3-dimethyl-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane-24-carboxylic acid] systems in NaCl aqueous solution at I=0.15molL-1 and t=25°C is reported. On the basis of potentiometric results two speciation models were proposed for each system. It was found that spectrophotometric and 1H NMR measurements are essential for selecting the most reliable speciation models. They included ML, MLOH and ML(OH)2 species in both systems and, only for Cu2+-ampicillin, also MLH species. The stability constants obtained by UV and 1H NMR titrations were comparable to the ones calculated by potentiometry. The sequestering ability of the ligands under study towards Cu2+ by pL0.5 empiric parameter (ligand concentration required to sequester 50% of the metal cation present in traces) at several pH values was calculated as well. For ampicillin and amoxicillin, pL0.5=7.19 and 6.67, respectively, at physiological pH, I=0.15molL-1 and t=25°C were obtained. Copyright © 2017 Elsevier B.V. All rights reserved.

  15. Proton NMR assignments and regular backbone structure of bovine pancreatic ribonuclease A in aqueous solution

    Energy Technology Data Exchange (ETDEWEB)

    Robertson, A.D. (Stanford Univ. Medical School, CA (USA)); Purisima, E.O. (National Research Council of Canada, Montreal, Quebec (Canada) Cornell Univ., Ithaca, NY (USA)); Eastman, M.A.; Scheraga, H.A. (Cornell Univ., Ithaca, NY (USA))


    Proton NMR assignments have been made for 121 of the 124 residues of bovine pancreatic ribonuclease A (RNase A). During the first stage of assignment, COSY and relayed COSY data were used to identify 40 amino acid spin systems belonging to alanine, valine, threonine, isoleucine, and serine residues. Approximately 60 other NH-{alpha}CH-{beta}CH systems were also identified but not assigned to specific amino acid type. NOESY data then were used to connect sequentially neighboring spin systems; approximately 475 of the possible 700 resonances in RNase A were assigned in this way. The authors' assignments agree with those for 20 residues assigned previously. NOESY correlations were used to identify regular backbone structure elements in RNase A, which are very similar to those observed in X-ray crystallographic studies.

  16. NMR solution structure of the peptide fragment 1-30, derived from unprocessed mouse Doppel protein, in DHPC micelles. (United States)

    Papadopoulos, Evangelos; Oglecka, Kamila; Mäler, Lena; Jarvet, Jüri; Wright, Peter E; Dyson, H Jane; Gräslund, Astrid


    The downstream prion-like Doppel (Dpl) protein is a homologue related to the prion protein (PrP). Dpl is expressed in the brains of mice that do not express PrP, and Dpl is known to be toxic to neurons. One mode of toxicity has been suggested to involve direct membrane interactions. PrP under certain conditions of cell trafficking retains an uncleaved signal peptide, which may also hold for the much less studied Dpl. For a peptide with a sequence derived from the N-terminal part (1-30) of mouse Dpl (mDpl(1-30)) CD spectroscopy shows about 40% alpha-helical structure in DHPC and SDS micelles. In aqueous solution it is mostly a random coil. The three-dimensional solution structure was determined by NMR for mDpl(1-30) associated with DHPC micelles. 2D 1H NMR spectra of the peptide in q = 0.25 DMPC/DHPC bicelles only showed signals from the unstructured termini, indicating that the structured part of the peptide resides within the lipid bilayer. Together with 2H2O exchange data in the DHPC micelle solvent, these results show an alpha-helix protected from solvent exchange between residues 7 and 19, and suggest that the alpha-helical segment can adopt a transmembrane localization also in a membrane. Leakage studies with entrapped calcein in large unilamellar phospholipid vesicles showed that the peptide is almost as membrane perturbing as melittin, known to form pores in membranes. The results suggest a possible channel formation mechanism for the unprocessed Dpl protein, which may be related to toxicity through direct cell membrane interaction and damage.

  17. Solution NMR analysis of the interaction between the actinoporin sticholysin I and DHPC micelles--correlation with backbone dynamics. (United States)

    López-Castilla, Aracelys; Pazos, Fabiola; Schreier, Shirley; Pires, José Ricardo


    Sticholysin I (StI), an actinoporin expressed as a water-soluble protein by the sea anemone Stichodactyla helianthus, binds to natural and model membranes, forming oligomeric pores. It is proposed that the first event of a multistep pore formation mechanism consists of the monomeric protein attachment to the lipid bilayer. To date there is no high-resolution structure of the actinoporin pore or other membrane-bound form available. Here we evaluated StI:micelle complexes of variable lipid composition to look for a suitable model for NMR studies. Micelles of pure or mixed lysophospholipids and of dihexanoyl phosphatidylcholine (DHPC) were examined. The StI:DHPC micelle was found to be the best system, yielding a stable sample and good quality spectra. A comprehensive chemical shift perturbation analysis was performed to map the StI membrane recognition site in the presence of DHPC micelles. The region mapped (residues F(51), R(52), S(53) in loop 3; F(107), D(108), Y(109), W(111), Y(112), W(115) in loop 7; Q(129), Y(132), D(134), M(135), Y(136), Y(137), G(138) in helix-α2) is in agreement with previously reported data, but additional residues were found to interact, especially residues V(81), A(82), T(83), G(84) in loop 5, and A(85), A(87) in strand-β5. Backbone dynamics measurements of StI free in solution and bound to micelles highlighted the relevance of protein flexibility for membrane binding and suggested that a conformer selection process may take place during protein-membrane interaction. We conclude that the StI:DHPC micelles system is a suitable model for further characterization of an actinoporin membrane-bound form by solution NMR. © 2013 Wiley Periodicals, Inc.

  18. Solution NMR structure and inhibitory effect against amyloid-β fibrillation of Humanin containing a D-isomerized serine residue

    Energy Technology Data Exchange (ETDEWEB)

    Alsanousi, Nesreen [Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871 (Japan); Sugiki, Toshihiko, E-mail: [Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871 (Japan); Furuita, Kyoko; So, Masatomo; Lee, Young-Ho; Fujiwara, Toshimichi [Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871 (Japan); Kojima, Chojiro, E-mail: [Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871 (Japan); Graduate School of Engineering, Yokohama National University, Tokiwadai 79-5, Hodogaya-ku, Yokohama 240-8501 (Japan)


    Humanin comprising 24 amino acid residues is a bioactive peptide that has been isolated from the brain tissue of patients with Alzheimer's disease. Humanin reportedly suppressed aging-related death of various cells due to amyloid fibrils and oxidative stress. There are reports that the cytoprotective activity of Humanin was remarkably enhanced by optical isomerization of the Ser14 residue from L to D form, but details of the molecular mechanism remained unclear. Here we demonstrated that Humanin D-Ser14 exhibited potent inhibitory activity against fibrillation of amyloid-β and remarkably higher binding affinity for amyloid-β than that of the Humanin wild-type and S14G mutant. In addition, we determined the solution structure of Humanin D-Ser14 by nuclear magnetic resonance (NMR) and showed that D-isomerization of the Ser14 residue enables drastic conformational rearrangement of Humanin. Furthermore, we identified an amyloid-β-binding site on Humanin D-Ser14 at atomic resolution by NMR. These biophysical and high-resolution structural analyses clearly revealed structure–function relationships of Humanin and explained the driving force of the drastic conformational change and molecular basis of the potent anti-amyloid-β fibrillation activity of Humanin caused by D-isomerization of the Ser14 residue. This is the first study to show correlations between the functional activity, tertiary structure, and partner recognition mode of Humanin and may lead to elucidation of the molecular mechanisms of the cytoprotective activity of Humanin. - Highlights: • Humanin D-Ser14 showed the strongest inhibitory activity against Aβ40 fibrillation. • NMR structure of Humanin D-Ser14 was determined in alcohol/water mixture solution. • Humanin D-Ser14 directly bound Aβ40 stronger than Humanin wild-type and Humanin S14G. • Aβ40 and zinc ion binding sites of Humanin D-Ser14 were identified. • Structure around Ser14 of Humanin is critical for Aβ40 binding and

  19. Simultaneous use of solution NMR and X-ray data in REFMAC5 for joint refinement/detection of structural differences

    Energy Technology Data Exchange (ETDEWEB)

    Rinaldelli, Mauro; Ravera, Enrico; Calderone, Vito; Parigi, Giacomo [University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino (Finland) (Italy); University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino (Finland) (Italy); Murshudov, Garib N., E-mail: [MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH (United Kingdom); Luchinat, Claudio, E-mail: [University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino (Finland) (Italy); University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino (Finland) (Italy)


    Paramagnetic NMR data (pseudocontact shifts and self-orientation residual dipolar couplings) and diamagnetic residual dipolar couplings can now be used in the program REFMAC5 from CCP4 as structural restraints together with X-ray crystallographic data. These NMR restraints can reveal differences between solid state and solution conformations of molecules or, in their absence, can be used together with X-ray crystallographic data for structural refinement. The program REFMAC5 from CCP4 was modified to allow the simultaneous use of X-ray crystallographic data and paramagnetic NMR data (pseudocontact shifts and self-orientation residual dipolar couplings) and/or diamagnetic residual dipolar couplings. Incorporation of these long-range NMR restraints in REFMAC5 can reveal differences between solid-state and solution conformations of molecules or, in their absence, can be used together with X-ray crystallographic data for structural refinement. Since NMR and X-ray data are complementary, when a single structure is consistent with both sets of data and still maintains reasonably ‘ideal’ geometries, the reliability of the derived atomic model is expected to increase. The program was tested on five different proteins: the catalytic domain of matrix metalloproteinase 1, GB3, ubiquitin, free calmodulin and calmodulin complexed with a peptide. In some cases the joint refinement produced a single model consistent with both sets of observations, while in other cases it indicated, outside the experimental uncertainty, the presence of different protein conformations in solution and in the solid state.

  20. From proton nuclear magnetic resonance spectra to pH. Assessment of {sup 1}H NMR pH indicator compound set for deuterium oxide solutions

    Energy Technology Data Exchange (ETDEWEB)

    Tynkkynen, Tuulia, E-mail: [Laboratory of Chemistry, Department of Biosciences, University of Kuopio, PO Box 1627, 70211 Kuopio (Finland); Tiainen, Mika; Soininen, Pasi; Laatikainen, Reino [Laboratory of Chemistry, Department of Biosciences, University of Kuopio, PO Box 1627, 70211 Kuopio (Finland)


    In this study, a protocol for pH determination from D{sub 2}O samples using {sup 1}H NMR pH indicator compounds was developed and assessed by exploring the pH-dependency of 13 compounds giving pH-dependent {sup 1}H NMR signals. The indicators cover the pH range from pH* 0 to 7.2. Equations to transform the indicator chemical shifts to pH estimates are given here for acetic acid, formic acid, chloroacetic acid, dichloroacetic acid, creatine, creatinine, glycine, histidine, 1,2,4-triazole, and TSP (2,2,3,3-tetradeutero-3-(trimethylsilyl)-propionic acid). To characterize the method in presence of typical solutes, the effects of common metabolites, albumin and ionic strength were also evaluated. For the ionic strengths, the effects were also modelled. The experiments showed that the use of pH sensitive {sup 1}H NMR chemical shifts allows the pH determination of typical metabolite solutions with accuracy of 0.01-0.05 pH units. Also, when the ionic strength is known with accuracy better than 0.1 mol dm{sup -3} and the solute concentrations are low, pH{sub nmr}{sup *} (the NMR estimate of pH) can be assumed to be within 0.05 pH units from potentiometrically determined pH.

  1. Scaling exponent and dispersity of polymers in solution by diffusion NMR. (United States)

    Williamson, Nathan H; Röding, Magnus; Miklavcic, Stanley J; Nydén, Magnus


    Molecular mass distribution measurements by pulsed gradient spin echo nuclear magnetic resonance (PGSE NMR) spectroscopy currently require prior knowledge of scaling parameters to convert from polymer self-diffusion coefficient to molecular mass. Reversing the problem, we utilize the scaling relation as prior knowledge to uncover the scaling exponent from within the PGSE data. Thus, the scaling exponent-a measure of polymer conformation and solvent quality-and the dispersity (Mw/Mn) are obtainable from one simple PGSE experiment. The method utilizes constraints and parametric distribution models in a two-step fitting routine involving first the mass-weighted signal and second the number-weighted signal. The method is developed using lognormal and gamma distribution models and tested on experimental PGSE attenuation of the terminal methylene signal and on the sum of all methylene signals of polyethylene glycol in D2O. Scaling exponent and dispersity estimates agree with known values in the majority of instances, leading to the potential application of the method to polymers for which characterization is not possible with alternative techniques. Copyright © 2017 Elsevier Inc. All rights reserved.

  2. Solution NMR of MPS-1 reveals a random coil cytosolic domain structure.

    Directory of Open Access Journals (Sweden)

    Pan Li

    Full Text Available Caenorhabditis elegans MPS1 is a single transmembrane helical auxiliary subunit that co-localizes with the voltage-gated potassium channel KVS1 in the nematode nervous system. MPS-1 shares high homology with KCNE (potassium voltage-gated channel subfamily E member auxiliary subunits, and its cytosolic domain was reported to have a serine/threonine kinase activity that modulates KVS1 channel function via phosphorylation. In this study, NMR spectroscopy indicated that the full length and truncated MPS-1 cytosolic domain (134-256 in the presence or absence of n-dodecylphosphocholine detergent micelles adopted a highly flexible random coil secondary structure. In contrast, protein kinases usually adopt a stable folded conformation in order to implement substrate recognition and phosphoryl transfer. The highly flexible random coil secondary structure suggests that MPS-1 in the free state is unstructured but may require a substrate or binding partner to adopt stable structure required for serine/threonine kinase activity.

  3. Solute NMR study of a bimesogenic liquid crystal with two nematic phases (United States)

    Dong, R. Y.; Kohlmeier, A.; Tamba, M. G.; Mehl, G. H.; Burnell, E. E.


    Recent interest in bimesogenic liquid crystals showing two nematic phases has led us to investigate the nematic mean-field interactions in these nematic phases by using rigid solutes as probes. The nematic potential that is modelled by two independent Maier-Saupe terms is successful in fitting the observed dipolar couplings (molecular order parameters) of para-, meta- and ortho-dichlorobenzene solutes in both nematic phases of 39 wt.% 4-n-pentyl-4'-cyanobiphenyl (5CB) in α,ω-bis (4-4'-cyanobiphenyl) nonane (CBC9CB) to better than the 5% level. The derived liquid-crystal potential parameters G1 and G2 for each solute in the N and Nx phases are discussed.

  4. NMR relaxation studies in solution of transition metal complexes, Pt. 7. Protonation of the vanadyl ion in aqueous solution

    Energy Technology Data Exchange (ETDEWEB)

    Nagypal, I.; Fabian, I. (Kossuth Lajos Tudomanyegyetem, Debrecen (Hungary). Szervetlen es Analitikai Kemiai Tanszek); Connick, R.E. (California Univ., Berkeley (USA). Dept. of Chemistry)


    The protonation of the vanadyl ion in aqueous solution has been detected and the equilibrium constant for the reaction has been determined spectrophotometrically at 298 K, in 6 M(Na,H)ClO/sub 4/. The transverse relaxation of water protons in acidic solutions of vanadyl ion has been studied at 2.5 and 100 MHz frequencies. A model is given to interpret the relaxation measurements, which takes into account the presence of two paramagnetic sites and the coupling between them through the proton exchange reactions. The contradictory statements concerning the relaxation behaviour of the system have been reinterpreted and reconciled by the use of the present model. An electric circuit description of the coupled chemical exchange and paramagnetic relaxation processes is introduced and proved to be equivalent with that of the descriptions based on the BLOCH equations and on formal kinetic considerations. The interrelation of the proton exchange rate constants and the paramagnetic relaxation times are calculated and illustrated on a nomogram.

  5. NMR spectroscopy of inclusion complex of D-(-)-chloramphenicol with beta-cyclodextrin in aqueous solution. (United States)

    Ali, Syed Mashhood; Asmat, Fahmeena; Maheshwari, Arti


    (1)HNMR spectroscopic study in D(2)O of mixtures of D-(-)-chloramphenicol (guest), present in two tautomeric forms in solution, and beta-cyclodextrin (host) revealed the formation of 1:1 inclusion complex in which aromatic ring of the guest is tightly held by the host cavity. There seems no discrimination between the aromatic rings of two tautomers by the host.

  6. Caffeine and Sugars Interact in Aqueous Solutions: A Simulation and NMR Study (United States)

    Tavagnacco, Letizia; Engström, Olof; Schnupf, Udo; Saboungi, Marie-Louise; Himmel, Michael; Widmalm, Göran; Cesàro, Attilio; Brady, John W.


    Molecular dynamics simulations were carried out on several systems of caffeine interacting with simple sugars. These included a single caffeine molecule in a 3 molal solution of α-D-glucopyranose, at a caffeine concentration of 0.083 molal; a single caffeine in a 3 molal solution of β-D-glucopyranose, and a single caffeine molecule in a 1.08 molal solution of sucrose (table sugar). Parallel Nuclear Magnetic Resonance titration experiments were carried out on the same solutions under similar conditions. Consistent with previous thermodynamic experiments, the sugars were found to have an affinity for the caffeine molecules in both the simulations and experiments, and that the binding in these complexes occurs by face-to-face stacking of the hydrophobic triad of protons of the pyranose rings against the caffeine face, rather than by hydrogen bonding. For the disaccharide, the binding occurs via stacking of the glucose ring against the caffeine, with a lesser affinity for the fructose observed. These findings are consistent with the association being driven by hydrophobic hydration, and are similar to the previously observed binding of glucose rings to various other planar molecules, including indole, serotonin, and phenol. PMID:22897449

  7. Solution NMR structure of Alr2454 from Nostoc sp. PCC 7120, the first structural representative of Pfam domain family PF11267


    Aramini, James M.; Petrey, Donald; Lee, Dong Yup; Janjua, Haleema; Xiao, Rong; Acton, Thomas B.; Everett, John K.; Montelione, Gaetano T.


    Protein domain family PF11267 (DUF3067) is a family of proteins of unknown function found in both bacteria and eukaryotes. Here we present the solution NMR structure of the 102-residue Alr2454 protein from Nostoc sp. PCC 7120, which constitutes the first structural representative from this conserved protein domain family. The structure of Nostoc sp. Alr2454 adopts a novel protein fold.

  8. Solution NMR structure of Alr2454 from Nostoc sp. PCC 7120, the first structural representative of Pfam domain family PF11267. (United States)

    Aramini, James M; Petrey, Donald; Lee, Dong Yup; Janjua, Haleema; Xiao, Rong; Acton, Thomas B; Everett, John K; Montelione, Gaetano T


    Protein domain family PF11267 (DUF3067) is a family of proteins of unknown function found in both bacteria and eukaryotes. Here we present the solution NMR structure of the 102-residue Alr2454 protein from Nostoc sp. PCC 7120, which constitutes the first structural representative from this conserved protein domain family. The structure of Nostoc sp. Alr2454 adopts a novel protein fold.

  9. Delineating pMDI model reactions with loblolly pine via solution-state NMR spectroscopy. Part 1, Catalyzed reactions with wood models and wood polymers (United States)

    Daniel J. Yelle; John Ralph; Charles R. Frihart


    To better understand adhesive interactions with wood, reactions between model compounds of wood and a model compound of polymeric methylene diphenyl diisocyanate (pMDI) were characterized by solution-state NMR spectroscopy. For comparison, finely ground loblolly pine sapwood, milled-wood lignin and holocellulose from the same wood were isolated and derivatized with...

  10. Solution NMR structure of the V27A drug resistant mutant of influenza A M2 channel

    Energy Technology Data Exchange (ETDEWEB)

    Pielak, Rafal M. [Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115 (United States); Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA 02115 (United States); Chou, James J., E-mail: [Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115 (United States)


    Research highlights: {yields} This paper reports the structure of the V27A drug resistant mutant of the M2 channel of influenza A virus. {yields} High quality NMR data allowed a better-defined structure for the C-terminal region of the M2 channel. {yields} Using the structure, we propose a proton transfer pathway during M2 proton conduction. {yields} Structural comparison between the wildtype, V27A and S31N variants allowed an in-depth analysis of possible modes of drug resistance. {yields} Distinct feature of the V27A channel pore also provides an explanation for its faster rate of proton conduction. -- Abstract: The M2 protein of influenza A virus forms a proton-selective channel that is required for viral replication. It is the target of the anti-influenza drugs, amantadine and rimantadine. Widespread drug resistant mutants, however, has greatly compromised the effectiveness of these drugs. Here, we report the solution NMR structure of the highly pathogenic, drug resistant mutant V27A. The structure reveals subtle structural differences from wildtype that maybe linked to drug resistance. The V27A mutation significantly decreases hydrophobic packing between the N-terminal ends of the transmembrane helices, which explains the looser, more dynamic tetrameric assembly. The weakened channel assembly can resist drug binding either by destabilizing the rimantadine-binding pocket at Asp44, in the case of the allosteric inhibition model, or by reducing hydrophobic contacts with amantadine in the pore, in the case of the pore-blocking model. Moreover, the V27A structure shows a substantially increased channel opening at the N-terminal end, which may explain the faster proton conduction observed for this mutant. Furthermore, due to the high quality NMR data recorded for the V27A mutant, we were able to determine the structured region connecting the channel domain to the C-terminal amphipathic helices that was not determined in the wildtype structure. The new structural

  11. An industrial design solution for integrating NMR magnetic field sensors into an MRI scanner. (United States)

    Kennedy, Michael; Lee, Yoojin; Nagy, Zoltan


    Neuroimaging research relies on the skills of increasingly multidisciplinary individuals and often requires the installation and use of additional home-built or third-party equipment. The purpose of the present work was the safe, ergonomic, durable, and aesthetically pleasing installation of magnetic field monitoring equipment into a scanner, while keeping the setup compatible with standard operating procedures. An extensive set of steps was required to design a 3D printed solution to install a magnetic field camera into the eight-channel head coil of a 3T MRI scanner. First, the outer surface of the plastic coil housing was recreated into a 3D model, and the installation of the magnetic field sensors around this 3D model was performed in a virtual environment. The 3D printed solution was then assembled and tested for safety, reproducible performance, and image quality. The 3D printed solution holds the probes in stable positions and guides the necessary cables in an organized fashion and away from the volunteer. Assembly is easy and the solution is ergonomic, durable, and safe. We did not find excessive heating in the 3D printed parts, nor in the electronics, that they help to incorporate. The material used interferes minimally with transmit B1+ field. The design met all of the boundary conditions for a durable, safe, cost-effective, attractive, and functional installation. This work will provide the basis for installing the magnetic field sensors into other available head coils, and for designing the experimental setup for projects with varying experimental requirements. Magn Reson Med, 2017. © 2017 International Society for Magnetic Resonance in Medicine. © 2017 International Society for Magnetic Resonance in Medicine.

  12. Identification of the Docking Site for CD3 on the T Cell Receptor β Chain by Solution NMR* (United States)

    He, Yanan; Rangarajan, Sneha; Kerzic, Melissa; Luo, Ming; Chen, Yihong; Wang, Qian; Yin, Yiyuan; Workman, Creg J.; Vignali, Kate M.; Vignali, Dario A. A.; Mariuzza, Roy A.; Orban, John


    The T cell receptor (TCR)-CD3 complex is composed of a genetically diverse αβ TCR heterodimer associated noncovalently with the invariant CD3 dimers CD3ϵγ, CD3ϵδ, and CD3ζζ. The TCR mediates peptide-MHC recognition, whereas the CD3 molecules transduce activation signals to the T cell. Although much is known about downstream T cell signaling pathways, the mechanism whereby TCR engagement by peptide-MHC initiates signaling is poorly understood. A key to solving this problem is defining the spatial organization of the TCR-CD3 complex and the interactions between its subunits. We have applied solution NMR methods to identify the docking site for CD3 on the β chain of a human autoimmune TCR. We demonstrate a low affinity but highly specific interaction between the extracellular domains of CD3 and the TCR constant β (Cβ) domain that requires both CD3ϵγ and CD3ϵδ subunits. The mainly hydrophilic docking site, comprising 9–11 solvent-accessible Cβ residues, is relatively small (∼400 Å2), consistent with the weak interaction between TCR and CD3 extracellular domains, and devoid of glycosylation sites. The docking site is centered on the αA and αB helices of Cβ, which are located at the base of the TCR. This positions CD3ϵγ and CD3ϵδ between the TCR and the T cell membrane, permitting us to distinguish among several possible models of TCR-CD3 association. We further correlate structural results from NMR with mutational data on TCR-CD3 interactions from cell-based assays. PMID:26109064

  13. Identification of the Docking Site for CD3 on the T Cell Receptor β Chain by Solution NMR. (United States)

    He, Yanan; Rangarajan, Sneha; Kerzic, Melissa; Luo, Ming; Chen, Yihong; Wang, Qian; Yin, Yiyuan; Workman, Creg J; Vignali, Kate M; Vignali, Dario A A; Mariuzza, Roy A; Orban, John


    The T cell receptor (TCR)-CD3 complex is composed of a genetically diverse αβ TCR heterodimer associated noncovalently with the invariant CD3 dimers CD3ϵγ, CD3ϵδ, and CD3ζζ. The TCR mediates peptide-MHC recognition, whereas the CD3 molecules transduce activation signals to the T cell. Although much is known about downstream T cell signaling pathways, the mechanism whereby TCR engagement by peptide-MHC initiates signaling is poorly understood. A key to solving this problem is defining the spatial organization of the TCR-CD3 complex and the interactions between its subunits. We have applied solution NMR methods to identify the docking site for CD3 on the β chain of a human autoimmune TCR. We demonstrate a low affinity but highly specific interaction between the extracellular domains of CD3 and the TCR constant β (Cβ) domain that requires both CD3ϵγ and CD3ϵδ subunits. The mainly hydrophilic docking site, comprising 9-11 solvent-accessible Cβ residues, is relatively small (∼400 Å(2)), consistent with the weak interaction between TCR and CD3 extracellular domains, and devoid of glycosylation sites. The docking site is centered on the αA and αB helices of Cβ, which are located at the base of the TCR. This positions CD3ϵγ and CD3ϵδ between the TCR and the T cell membrane, permitting us to distinguish among several possible models of TCR-CD3 association. We further correlate structural results from NMR with mutational data on TCR-CD3 interactions from cell-based assays. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

  14. NMR solution structure and membrane interaction of the N-terminal sequence (1-30) of the bovine prion protein. (United States)

    Biverståhl, Henrik; Andersson, August; Gräslund, Astrid; Mäler, Lena


    The structure and membrane interaction of the N-terminal sequence (1-30) of the bovine prion protein (bPrPp) has been investigated by NMR spectroscopy in phospholipid membrane mimetic systems. CD spectroscopy revealed that the peptide adopts a largely alpha-helical structure in zwitterionic bicelles as well as in DHPC micelles but has a less degree of alpha-helix structure in partly charged bicelles. The solution structure of bPrPp was determined in DHPC micelles, and an alpha-helix was found between residues Ser8 and Ile21. The residues within the helical region show slow amide hydrogen exchange. Translational diffusion measurements in zwitterionic q = 0.5 bicelles show that the peptide does not induce aggregation of the bicelles. Increased quadrupolar splittings were observed in the outer part of the (2)H spectrum of DMPC in q = 3.5 bicelles, indicating that the peptide induces a certain degree of order in the bilayer. The amide hydrogen exchange and the (2)H NMR results are consistent with a slight positive hydrophobic mismatch and that bPrPp forms a stable helix that inserts in a transmembrane location in the bilayer. The structure of bPrPp and its position in the membrane may be relevant for the understanding of how the N-terminal (1-30) part of the bovine PrP functions as a cell-penetrating peptide. These findings may lead to a better understanding of how the prion protein accumulates at the membrane surface and also how the conversion into the scrapie form is carried out.

  15. Solution NMR structure of the HLTF HIRAN domain: a conserved module in SWI2/SNF2 DNA damage tolerance proteins

    Energy Technology Data Exchange (ETDEWEB)

    Korzhnev, Dmitry M. [University of Connecticut Health, Department of Molecular Biology and Biophysics (United States); Neculai, Dante [Zhejiang University, School of Medicine (China); Dhe-Paganon, Sirano [Dana-Farber Cancer Institute, Department of Cancer Biology (United States); Arrowsmith, Cheryl H. [University of Toronto, Structural Genomics Consortium (Canada); Bezsonova, Irina, E-mail: [University of Connecticut Health, Department of Molecular Biology and Biophysics (United States)


    HLTF is a SWI2/SNF2-family ATP-dependent chromatin remodeling enzyme that acts in the error-free branch of DNA damage tolerance (DDT), a cellular mechanism that enables replication of damaged DNA while leaving damage repair for a later time. Human HLTF and a closely related protein SHPRH, as well as their yeast homologue Rad5, are multi-functional enzymes that share E3 ubiquitin-ligase activity required for activation of the error-free DDT. HLTF and Rad5 also function as ATP-dependent dsDNA translocases and possess replication fork reversal activities. Thus, they can convert Y-shaped replication forks into X-shaped Holliday junction structures that allow error-free replication over DNA lesions. The fork reversal activity of HLTF is dependent on 3′-ssDNA-end binding activity of its N-terminal HIRAN domain. Here we present the solution NMR structure of the human HLTF HIRAN domain, an OB-like fold module found in organisms from bacteria (as a stand-alone domain) to plants, fungi and metazoan (in combination with SWI2/SNF2 helicase-like domain). The obtained structure of free HLTF HIRAN is similar to recently reported structures of its DNA bound form, while the NMR analysis also reveals that the DNA binding site of the free domain exhibits conformational heterogeneity. Sequence comparison of N-terminal regions of HLTF, SHPRH and Rad5 aided by knowledge of the HLTF HIRAN structure suggests that the SHPRH N-terminus also includes an uncharacterized structured module, exhibiting weak sequence similarity with HIRAN regions of HLTF and Rad5, and potentially playing a similar functional role.

  16. A model for monomer and micellar concentrations in surfactant solutions: application to conductivity, NMR, diffusion, and surface tension data. (United States)

    Al-Soufi, Wajih; Piñeiro, Lucas; Novo, Mercedes


    An empirical model for the concentrations of monomeric and micellized surfactants in solution is presented as a consistent approach for the quantitative analysis of data obtained with different experimental techniques from surfactant solutions. The concentration model provides an objective definition of the critical micelle concentration (cmc) and yields precise and well defined values of derived physical parameters. The use of a general concentration model eliminates subjective graphical procedures, reduces methodological differences, and thus allows one to compare directly the results of different techniques or to perform global fits. The application and validity of the model are demonstrated with electrical conductivity, surface tension, NMR chemical shift, and self-diffusion coefficient data for the surfactants SDS, CTAB, DTAB, and LAS. In all cases, the derived models yield excellent fits of the data. It is also shown that there is no need to assume the existence of different premicellar species in order to explain the chemical shifts and self-diffusion coefficients of SDS as claimed recently by some authors. Copyright © 2011 Elsevier Inc. All rights reserved.

  17. ' q-Titration' of long-chain and short-chain lipids differentiates between structured and mobile residues of membrane proteins studied in bicelles by solution NMR spectroscopy (United States)

    Son, Woo Sung; Park, Sang Ho; Nothnagel, Henry J.; Lu, George J.; Wang, Yan; Zhang, Hua; Cook, Gabriel A.; Howell, Stanley C.; Opella, Stanley J.


    ' q-Titration' refers to the systematic comparison of signal intensities in solution NMR spectra of uniformly 15N labeled membrane proteins solubilized in micelles and isotropic bicelles as a function of the molar ratios ( q) of the long-chain lipids (typically DMPC) to short-chain lipids (typically DHPC). In general, as q increases, the protein resonances broaden and correspondingly have reduced intensities due to the overall slowing of protein reorientation. Since the protein backbone signals do not broaden uniformly, the differences in line widths (and intensities) enable the narrower (more intense) signals associated with mobile residues to be differentiated from the broader (less intense) signals associated with "structured" residues. For membrane proteins with between one and seven trans-membrane helices in isotropic bicelles, we have been able to find a value of q between 0.1 and 1.0 where only signals from mobile residues are observed in the spectra. The signals from the structured residues are broadened so much that they cannot be observed under standard solution NMR conditions. This q value corresponds to the ratio of DMPC:DHPC where the signals from the structured residues are "titrated out" of the spectrum. This q value is unique for each protein. In magnetically aligned bilayers ( q > 2.5) no signals are observed in solution NMR spectra of membrane proteins because the polypeptides are "immobilized" by their interactions with the phospholipid bilayers on the relevant NMR timescale (˜10 5 Hz). No signals are observed from proteins in liposomes (only long-chain lipids) either. We show that it is feasible to obtain complementary solution NMR and solid-state NMR spectra of the same membrane protein, where signals from the mobile residues are present in the solution NMR spectra, and signals from the structured residues are present in the solid-state NMR spectra. With assigned backbone amide resonances, these data are sufficient to describe major features

  18. Solution NMR structural study of a mixed aggregate of N-lithium triphenylphosphazene and lithium bromide. (United States)

    Fernández, Ignacio; Davidson, Matthew G; Price, Richard D; Ortiz, Fernando López


    The toluene solution structure of an N-lithio(triphenyl)phosphazene (Ph(3)PNLi) mixed aggregate with lithium bromide (LiBr), 5, has been elucidated for the first time based on multinuclear magnetic resonance measurements ((1)H, (6)Li, (7)Li, (13)C and (31)P). The structure consist of two dimers [Li(mu-Z)](2) (Z= Br, NPR(3)) linked through LiX (X= N, Br) bridges. This arrangement is a cubane-like structure analogous to that found in the solid-state.

  19. Quality assessment in in vivo NMR spectroscopy: III. Clinical test objects: design, construction, and solutions

    DEFF Research Database (Denmark)

    Leach, M.O.; Collins, D.J.; Keevil, S


    Based on the requirements of test protocols developed to evaluate clinical MRS single slice and volume localisation sequences, two clinical test objects, STO1 and STO2 have been developed. The properties of a range of potential construction materials have been assessed, demonstrating that the water....../Perspex interface produced minimum susceptibility effects. The design of the objects has been evaluated in trials on different magnetic resonance instruments, with size and loading being adjusted to allow use on currently available equipment. Appropriate test solutions for 31P and 1H measurements have been...

  20. Transport properties investigation of aqueous protic ionic liquid solutions through conductivity, viscosity, and NMR self-diffusion measurements. (United States)

    Anouti, Mérièm; Jacquemin, Johan; Porion, Patrice


    We present a study on the transport properties through conductivity (σ), viscosity (η), and self-diffusion coefficient (D) measurements of two pure protic ionic liquids--pyrrolidinium hydrogen sulfate, [Pyrr][HSO(4)], and pyrrolidinium trifluoroacetate, [Pyrr][CF(3)COO]--and their mixtures with water over the whole composition range at 298.15 K and atmospheric pressure. Based on these experimental results, transport mobilities of ions have been then investigated in each case through the Stokes-Einstein equation. From this, the proton conduction in these PILs follows a combination of Grotthuss and vehicle-type mechanisms, which depends also on the water composition in solution. In each case, the displacement of the NMR peak attributed to the labile proton on the pyrrolidinium cation with the PILs concentration in aqueous solution indicates that this proton is located between the cation and the anion for a water weight fraction lower than 8%. In other words, for such compositions, it appears that this labile proton is not solvated by water molecules. However, for higher water content, the labile protons are in solution as H(3)O(+). This water weight fraction appears to be the solvation limit of the H(+) ions by water molecules in these two PILs solutions. However, [Pyrr][HSO(4)] and [Pyrr][CF(3)COO] PILs present opposed comportment in aqueous solution. In the case of [Pyrr][CF(3)COO], η, σ, D, and the attractive potential, E(pot), between ions indicate clearly that the diffusion of each ion is similar. In other words, these ions are tightly bound together as ion pairs, reflecting in fact the importance of the hydrophobicity of the trifluoroacetate anion, whereas, in the case of the [Pyrr][HSO(4)], the strong H-bond between the HSO(4)(-) anion and water promotes a drastic change in the viscosity of the aqueous solution, as well as on the conductivity which is up to 187 mS·cm(-1) for water weight fraction close to 60% at 298 K.

  1. The solution conformation of sialyl-alpha (2----6)-lactose studied by modern NMR techniques and Monte Carlo simulations. (United States)

    Poppe, L; Stuike-Prill, R; Meyer, B; van Halbeek, H


    We present a comprehensive strategy for detailed characterization of the solution conformations of oligosaccharides by NMR spectroscopy and force-field calculations. Our experimental strategy generates a number of interglycosidic spatial constraints that is sufficiently large to allow us to determine glycosidic linkage conformations with a precision heretofore unachievable. In addition to the commonly used [1H,1H] NOE contacts between aliphatic protons, our constraints are: (a) homonuclear NOEs of hydroxyl protons in H2O to other protons in the oligosaccharide, (b) heteronuclear [1H,13C] NOEs, (c) isotope effects of O1H/O2H hydroxyl groups on 13C chemical shifts, and (d) long-range heteronuclear scalar couplings across glycosidic bonds. We have used this approach to study the trisaccharide sialyl-alpha (2----6)-lactose in aqueous solution. The experimentally determined geometrical constraints were compared to results obtained from force-field calculations based on Metropolis Monte Carlo simulations. The molecule was found to exist in 2 families of conformers. The preferred conformations of the alpha (2----6)-linkage of the trisaccharide are best described by an equilibrium of 2 conformers with phi angles at -60 degrees or 180 degrees and of the 3 staggered rotamers of the omega angle with a predominant gt conformer. Three intramolecular hydrogen bonds, involving the hydroxyl protons on C8 and C7 of the sialic acid residue and on C3 of the reducing-end glucose residue, contribute significantly to the conformational stability of the trisaccharide in aqueous solution.

  2. Sequence dependence of base-pair stacking in right-handed DNA in solution: proton nuclear Overhauser effect NMR measurements. (United States)

    Patel, D J; Kozlowski, S A; Bhatt, R


    Single-crystal x-ray studies of d(C-G-C-G-A-A-T-T-C-G-C-G) exhibit base-pair propeller twisting [Dickerson, R. E. & Drew, H. R. (1981) J. Mol. Biol. 149, 761-786] that results in close contacts between adjacent purines in the minor groove in pyrimidine (3'-5')-purine steps and in the major groove in purine (3'-5')-pyrimidine steps [Calladine, C. R. (1982) J. Mol. Biol. 161, 343-362]. These observations require an approximately 3.4 A separation between the minor groove edges of adenosines on adjacent base pairs for the dA-dA step but predict a smaller separation for the dT-dA step and a larger separation for the dA-dT step in a D(A-T-T-A).d(T-A-A-T) fragment. We have confirmed these predictions from steady-state nuclear Overhauser effect measurements between assigned minor groove adenosine H-2 protons on adjacent base pairs in the proton NMR spectrum of the d(C1-G2-A3-T4-T5-A6-T6-A5-A4-T3-C2-G1) self-complementary dodecanucleotide duplex (henceforth called the Pribnow 12-mer) in solution. The measured cross-relaxation rates (product of steady-state nuclear Overhauser effect and selective spin- lattice relaxation rates) translate to interproton separations between adjacent adenosine H-2 protons of 4.22 A in the (dA3-dT4).(dA4-dT3) step, of 3.56 A in the (dT4-dT5).dA5-dA4) step, and of 3.17 A in the (dT5-dA6).(dT6-dA5) step for the Pribnow 12-mer duplex with an isotropic rotational correlation time of 9 ns at 5 degrees C. These proton NMR results show that the sequence-dependent base-pair stacking resulting from base-pair propeller twisting of defined handedness for right-handed DNA in the solid state is maintained in aqueous solution.

  3. Assessment of preparation methods for organic phosphorus analysis in phosphorus-polluted Fe/Al-rich Haihe river sediments using solution 31P-NMR.

    Directory of Open Access Journals (Sweden)

    Wenqiang Zhang

    Full Text Available Fe/Al-rich river sediments that were highly polluted with phosphorus (P were used in tests to determine the optimum preparation techniques for measuring organic P (Po using solution (31P nuclear magnetic resonance spectroscopy ((31P-NMR. The optimum pre-treatment, extraction time, sediment to solution ratio and sodium hydroxide-ethylenediaminetetraacetic acid (NaOH-EDTA extractant solution composition were determined. The total P and Po recovery rates were higher from freeze- and air-dried samples than from fresh samples. An extraction time of 16 h was adequate for extracting Po, and a shorter or longer extraction time led to lower recoveries of total P and Po, or led to the degradation of Po. An ideal P recovery rate and good-quality NMR spectra were obtained at a sediment:solution ratio of 1:10, showing that this ratio is ideal for extracting Po. An extractant solution of 0.25 M NaOH and 50 mM EDTA was found to be more appropriate than either NaOH on its own, or a more concentrated NaOH-EDTA mixture for (31P-NMR analysis, as this combination minimized interference from paramagnetic ions and was appropriate for the detected range of Po concentrations. The most appropriate preparation method for Po analysis, therefore, was to extract the freeze-dried and ground sediment sample with a 0.25 M NaOH and 50 mM EDTA solution at a sediment:solution ratio of 1:10, for 16 h, by shaking. As lyophilization of the NaOH-EDTA extracts proved to be an optimal pre-concentration method for Po analysis in the river sediment, the extract was lyophilized as soon as possible, and analyzed by (31P-NMR.

  4. NMR solution structure of the N-terminal domain of hERG and its interaction with the S4-S5 linker

    Energy Technology Data Exchange (ETDEWEB)

    Li, Qingxin; Gayen, Shovanlal; Chen, Angela Shuyi; Huang, Qiwei; Raida, Manfred [Experimental Therapeutics Center, The Agency for Science, Technology and Research, 31 Biopolis Way Nanos, 03-01, Singapore 138669 (Singapore); Kang, CongBao, E-mail: [Experimental Therapeutics Center, The Agency for Science, Technology and Research, 31 Biopolis Way Nanos, 03-01, Singapore 138669 (Singapore)


    Research highlights: {yields} The N-terminal domain (NTD, eag domain) containing 135 residues of hERG was expressed and purified from E. coli cells. {yields} Solution structure of NTD was determined with NMR spectroscopy. {yields} The alpha-helical region (residues 13-23) was demonstrated to possess the characteristics of an amphipathic helix. {yields} NMR titration confirmed the interaction between NTD and the peptide from the S4-S5 linker. -- Abstract: The human Ether-a-go-go Related Gene (hERG) potassium channel mediates the rapid delayed rectifier current (IKr) in the cardiac action potential. Mutations in the 135 amino acid residue N-terminal domain (NTD) cause channel dysfunction or mis-translocation. To study the structure of NTD, it was overexpressed and purified from Escherichia coli cells using affinity purification and gel filtration chromatography. The purified protein behaved as a monomer under purification conditions. Far- and near-UV, circular dichroism (CD) and solution nuclear magnetic resonance (NMR) studies showed that the purified protein was well-folded. The solution structure of NTD was obtained and the N-terminal residues 13-23 forming an amphipathic helix which may be important for the protein-protein or protein-membrane interactions. NMR titration experiment also demonstrated that residues from 88 to 94 in NTD are important for the molecular interaction with the peptide derived from the S4-S5 linker.

  5. Investigation into the structural composition of hydroalcoholic solutions as basis for the development of multiple suppression pulse sequences for NMR measurement of alcoholic beverages. (United States)

    Monakhova, Yulia B; Mushtakova, Svetlana P; Kuballa, Thomas; Lachenmeier, Dirk W


    An eight-fold suppression pulse sequence was recently developed to improve sensitivity in (1) H NMR measurements of alcoholic beverages [Magn. Res. Chem. 2011 (49): 734-739]. To ensure that only one combined hydroxyl peak from water and ethanol appears in the spectrum, adjustment to a certain range of ethanol concentrations was required. To explain this observation, the structure of water-ethanol solutions was studied. Hydroalcoholic solutions showed extreme behavior at 25% vol, 46% vol, and 83% vol ethanol according to (1) H NMR experiments. Near-infrared spectroscopy confirmed the occurrence of four significant compounds ('individual' ethanol and water structures as well as two water-ethanol complexes of defined composition - 1 : 1 and 1 : 3). The successful multiple suppression can be achieved for every kind of alcoholic beverage with different alcoholic strengths, when the final ethanol concentration is adjusted to a range between 25% vol and 46% vol (e.g. using dilution or pure ethanol addition). In this optimum region, an individual ethanol peak was not detected, because the 'individual' water structure and the 1 : 1 ethanol-water complex predominate. The nature of molecular association in ethanol-water solutions is essential to elucidate NMR method development for measurement of alcoholic beverages. The presented approach can be used to optimize other NMR suppression protocols for binary water-organic solvent mixtures, where hydrogen bonding plays a dominant role. Copyright © 2014 John Wiley & Sons, Ltd.

  6. Solid-state and solution /sup 13/C NMR in the conformational analysis of methadone-hydrochloride and related narcotic analgesics

    Energy Technology Data Exchange (ETDEWEB)

    Sumner, S.C.J.


    Solid state and solution /sup 13/C NMR have been used to study the conformations of the racemic mixtures and single enantiomers of methadone hydrochloride, alpha and beta methadol hydrochloride, and alpha and beta acetylmethadol hydrochloride. The NMR spectra acquired for the compounds as solids, and in polar and nonpolar solvents are compared, in order to determine the conformation of the molecules in solution. To determine the reliability of assigning solution conformations by comparing solution and solid state chemical shift data, three bond coupling constants measured in solution are compared with those calculated from X-ray data. The conformations of the racemic mixture and plus enantiomer of methadone hydrochloride have been shown to be very similar in the solid state, where minor differences in conformation can be seen by comparing NMR spectra obtained for the solids. Also shown is that the molecules of methadone hydrochloride have conformations in polar and in nonpolar solvents which are very similar to the conformation of the molecules in the solid state.

  7. NMR relaxation studies in solutions of transition metal complexes. Pt. 6

    Energy Technology Data Exchange (ETDEWEB)

    Fabian, I.; Nagypal, I.


    The equilibria in aqueous solution of the VO/sup 2 +/-glycine system has been studied by pH-metry in very high ligand excess, to avoid the hydrolysis of vanadyl ions. It is stated that the VO/sub 2/G/sub 2/(OH)/sub 2/ is not the only binuclear (polynuclear) complex in the system; the composition of the other polynuclear complexes, however, cannot be stated unambiguously because of their very low concentrations. The rate constants of the proton exchange between the bulk water and the different complexes have been determined by measuring the T/sub 2/ relaxation time of the water protons. In contrast to the oxalate, and some other vanadyl complexes, the rate constant decreases by the decrease of the number of water molecules remaining in the first coordination sphere of the vanadyl ion. The exceedingly high proton exchange rate constant for the VOG/sub 2/(OH)/sup -/ mixed hydroxo complex is interpreted as being due to the direct proton exchange between the bulk water and the coordinated OH group.

  8. An 17O NMR Study of Hydrolyzed Nb(V) in Weakly Acidic and Basic Aqueous Solution. (United States)

    Klemperer, Walter G; Marek, Keith A


    Time-dependent 17O NMR spectra of basified decaniobate (Nb10O286-) solutions displayed intense resonances assigned to the well-known protonated hexaniobate anion (Nb6O198-) and two other species identified as heptaniobate (Nb7O229-) and protonated tetracosaniobate (Nb24O7224-) anions. The decaniobate ion showed no sign of protonation from pH 6 - 10, in contrast with the hexaniobate ion which was protonated at doubly-bridging oxygen sites at pH 10-13. Most (> 90%) of the heptaniobate formed 1 h after basification was transformed into other species after 3 weeks. Tetracosaniobate was formed reversibly from decaniobate, but only when KOH, NaOH and [(CH3)4N]OH were employed; none was observed after basification with [(n-C4H9)4N]OH. Moreover, far more tetracosaniobate was formed from KOH than from [(CH3)4N]OH. This effect was attributed to a tetracosaniobate cation binding site that binds K+ more readily than (CH3)4N+ but is too small to accommodate (n-C4H9)4N+.

  9. Lanthanide binding and IgG affinity construct: Potential applications in solution NMR, MRI, and luminescence microscopy (United States)

    Barb, Adam W; Ho, Tienhuei Grace; Flanagan-Steet, Heather; Prestegard, James H


    Paramagnetic lanthanide ions when bound to proteins offer great potential for structural investigations that utilize solution nuclear magnetic resonance spectroscopy, magnetic resonance imaging, or optical microscopy. However, many proteins do not have native metal ion binding sites and engineering a chimeric protein to bind an ion while retaining affinity for a protein of interest represents a significant challenge. Here we report the characterization of an immunoglobulin G-binding protein redesigned to include a lanthanide binding motif in place of a loop between two helices (Z-L2LBT). It was shown to bind Tb3+ with 130 nM affinity. Ions such as Dy3+, Yb3+, and Ce3+ produce paramagnetic effects on NMR spectra and the utility of these effects is illustrated by their use in determining a structural model of the metal-complexed Z-L2LBT protein and a preliminary characterization of the dynamic distribution of IgG Fc glycan positions. Furthermore, this designed protein is demonstrated to be a novel IgG-binding reagent for magnetic resonance imaging (Z-L2LBT:Gd3+ complex) and luminescence microscopy (Z-L2LBT: Tb3+ complex). PMID:22851279

  10. The structures of the active center in dark-adapted bacteriorhodopsin by solution-state NMR spectroscopy (United States)

    Patzelt, Heiko; Simon, Bernd; terLaak, Antonius; Kessler, Brigitte; Kühne, Ronald; Schmieder, Peter; Oesterhelt, Dieter; Oschkinat, Hartmut


    The two forms of bacteriorhodopsin present in the dark-adapted state, containing either all-trans or 13-cis,15-syn retinal, were examined by using solution state NMR, and their structures were determined. Comparison of the all-trans and the 13-cis,15-syn forms shows a shift in position of about 0.25 Å within the pocket of the protein. Comparing this to the 13-cis,15-anti chromophore of the catalytic cycle M-intermediate structure, the 13-cis,15-syn form demonstrates a less pronounced up-tilt of the retinal C12—C14 region, while leaving W182 and T178 essentially unchanged. The N—H dipole of the Schiff base orients toward the extracellular side in both forms, however, it reorients toward the intracellular side in the 13-cis,15-anti configuration to form the catalytic M-intermediate. Thus, the change of the N—H dipole is considered primarily responsible for energy storage, conformation changes of the protein, and the deprotonation of the Schiff base. The structural similarity of the all-trans and 13-cis,15-syn forms is taken as strong evidence for the ion dipole dragging model by which proton (hydroxide ion) translocation follows the change of the dipole. PMID:12119389

  11. NMR spectra and potentiometry studies of aluminum(III) binding with coenzyme NAD+ in acidic aqueous solutions. (United States)

    Yang, Xiaodi; Bi, Shuping; Yang, Xiaoliang; Yang, Li; Hu, Jun; Liu, Jian; Yang, Zhengbiao


    Complexation and conformational studies of coenzyme NAD+ with aluminum were conducted in acidic aqueous solutions (pH 2-5) by means of potentiometry as well as multinuclear (1H, 13C, 31P, 27Al) and two-dimensional (1H, 1H-NOESY) NMR spectroscopy. These led to the following results: (1) Al could coordinate with NAD+ through the following binding sites: N7' of adenine and pyrophosphate free oxygen (O(A)1, O(N)1,O(A)2) to form various mononuclear 1:1 (AlLH23+, AlLH2+) and 2:1 (AlL2-) species, and dinuclear 2:2 (Al2L22+) species. (2) The conformations of NAD+ and Al-NAD+ depended on the solvents and different species in the complexes. The results suggest the occurrence of an Al-linked complexation, which causes structural changes at the primary recognition sites and secondary conformational alterations for coenzymes. This finding will help us to understand role of Al in biological enzyme reaction systems.

  12. Quantitative Characterization of Configurational Space Sampled by HIV-1 Nucleocapsid Using Solution NMR, X-ray Scattering and Protein Engineering. (United States)

    Deshmukh, Lalit; Schwieters, Charles D; Grishaev, Alexander; Clore, G Marius


    Nucleic-acid-related events in the HIV-1 replication cycle are mediated by nucleocapsid, a small protein comprising two zinc knuckles connected by a short flexible linker and flanked by disordered termini. Combining experimental NMR residual dipolar couplings, solution X-ray scattering and protein engineering with ensemble simulated annealing, we obtain a quantitative description of the configurational space sampled by the two zinc knuckles, the linker and disordered termini in the absence of nucleic acids. We first compute the conformational ensemble (with an optimal size of three members) of an engineered nucleocapsid construct lacking the N- and C-termini that satisfies the experimental restraints, and then validate this ensemble, as well as characterize the disordered termini, using the experimental data from the full-length nucleocapsid construct. The experimental and computational strategy is generally applicable to multidomain proteins. Differential flexibility within the linker results in asymmetric motion of the zinc knuckles which may explain their functionally distinct roles despite high sequence identity. One of the configurations (populated at a level of ≈40 %) closely resembles that observed in various ligand-bound forms, providing evidence for conformational selection and a mechanistic link between protein dynamics and function. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  13. NMR-based homology model for the solution structure of the C-terminal globular domain of EMILIN1

    Energy Technology Data Exchange (ETDEWEB)

    Verdone, Giuliana [Istituto Biochimico Italiano ' G. Lorenzini' (Italy); Corazza, Alessandra [Universita di Udine, Dipartimento di Scienze e Tecnologie Biomediche - MATI Centre of Excellence (Italy); Colebrooke, Simon A. [University of Oxford, Department of Biochemistry (United Kingdom); Cicero, Daniel; Eliseo, Tommaso [Universita di Tor Vergata, Dipartimento di Chimica (Italy); Boyd, Jonathan [University of Oxford, Department of Biochemistry (United Kingdom); Doliana, Roberto [Centro di Riferimento Oncologico di Aviano, Divisione di Oncologia Sperimentale 2 (Italy); Fogolari, Federico; Viglino, Paolo; Colombatti, Alfonso [Universita di Udine, Dipartimento di Scienze e Tecnologie Biomediche - MATI Centre of Excellence (Italy); Campbell, Iain D. [University of Oxford, Department of Biochemistry (United Kingdom); Esposito, Gennaro [Universita di Udine, Dipartimento di Scienze e Tecnologie Biomediche - MATI Centre of Excellence (Italy)], E-mail:


    EMILIN1 is a glycoprotein of elastic tissues that has been recently linked to the pathogenesis of hypertension. The protein is formed by different independently folded structural domains whose role has been partially elucidated. In this paper the solution structure, inferred from NMR-based homology modelling of the C-terminal trimeric globular C1q domain (gC1q) of EMILIN1, is reported. The high molecular weight and the homotrimeric structure of the protein required the combined use of highly deuterated {sup 15}N, {sup 13}C-labelled samples and TROSY experiments. Starting from a homology model, the protein structure was refined using heteronuclear residual dipolar couplings, chemical shift patterns, NOEs and H-exchange data. Analysis of the gC1q domain structure of EMILIN1 shows that each protomer of the trimer adopts a nine-stranded {beta} sandwich folding topology which is related to the conformation observed for other proteins of the family. Distinguishing features, however, include a missing edge-strand and an unstructured 19-residue loop. Although the current data do not allow this loop to be precisely defined, the available evidence is consistent with a flexible segment that protrudes from each subunit of the globular trimeric assembly and plays a key role in inter-molecular interactions between the EMILIN1 gC1q homotrimer and its integrin receptor {alpha}4{beta}1.

  14. Determination of solution structures of proteins up to 40 kDa using CS-Rosetta with sparse NMR data from deuterated samples. (United States)

    Lange, Oliver F; Rossi, Paolo; Sgourakis, Nikolaos G; Song, Yifan; Lee, Hsiau-Wei; Aramini, James M; Ertekin, Asli; Xiao, Rong; Acton, Thomas B; Montelione, Gaetano T; Baker, David


    We have developed an approach for determining NMR structures of proteins over 20 kDa that utilizes sparse distance restraints obtained using transverse relaxation optimized spectroscopy experiments on perdeuterated samples to guide RASREC Rosetta NMR structure calculations. The method was tested on 11 proteins ranging from 15 to 40 kDa, seven of which were previously unsolved. The RASREC Rosetta models were in good agreement with models obtained using traditional NMR methods with larger restraint sets. In five cases X-ray structures were determined or were available, allowing comparison of the accuracy of the Rosetta models and conventional NMR models. In all five cases, the Rosetta models were more similar to the X-ray structures over both the backbone and side-chain conformations than the "best effort" structures determined by conventional methods. The incorporation of sparse distance restraints into RASREC Rosetta allows routine determination of high-quality solution NMR structures for proteins up to 40 kDa, and should be broadly useful in structural biology.

  15. Structure and Membrane Interactions of the Antibiotic Peptide Dermadistinctin K by Multidimensional Solution and Oriented 15N and 31P Solid-State NMR Spectroscopy


    Verly, Rodrigo M.; Moraes, Cléria Mendonça; Resende, Jarbas M.; Aisenbrey, Christopher; Bemquerer, Marcelo Porto; Piló-Veloso, Dorila; Valente, Ana Paula; Almeida, Fábio C.L.; Bechinger, Burkhard


    DD K, a peptide first isolated from the skin secretion of the Phyllomedusa distincta frog, has been prepared by solid-phase chemical peptide synthesis and its conformation was studied in trifluoroethanol/water as well as in the presence of sodium dodecyl sulfate and dodecylphosphocholine micelles or small unilamellar vesicles. Multidimensional solution NMR spectroscopy indicates an α-helical conformation in membrane environments starting at residue 7 and extending to the C-terminal carboxyami...

  16. Homogeneity characterization of ethylene-co-vinyl acetate copolymer (EVA) and hydrophobic silica nanocomposite by low field NMR; Caracterizacao da homogeneidade de nanocomposito do copolimero etileno acetato de vinila (EVA) e silica hidrofobica atraves de ressonancia magnetica nuclear de baixo campo

    Energy Technology Data Exchange (ETDEWEB)

    Stael, Giovanni Chaves [Observatorio Nacional, Rio de Janeiro, RJ (Brazil). Dept. de Geofisica (DGE)]. E-mail:; Tavares, Maria I.B. [Universidade Federal do Rio de Janeiro, RJ (Brazil). Inst. de Macromoleculas]. E-mail:


    This project proposes the characterization of a polymeric matrix composite material using nanometric scale hydrophobic silica as charge element, with the ethylene-vinyl acetate (EVA), by using the spin-lattice relaxation time measurement applying the low field NMR.

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

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


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

  18. Confirming the 3D Solution Structure of a Short Double-Stranded DNA Sequence Using NMR Spectroscopy (United States)

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


    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…

  19. Using solid13C NMR coupled with solution31P NMR spectroscopy to investigate molecular species and lability of organic carbon and phosphorus from aquatic plants in Tai Lake, China. (United States)

    Liu, Shasha; Zhu, Yuanrong; Wu, Fengchang; Meng, Wei; Wang, Hao; He, Zhongqi; Guo, Wenjing; Song, Fanhao; Giesy, John P


    Forms and labilities of plant-derived organic matters (OMs) including carbon (C) and phosphorus (P) were fundamental for understanding their release, degradation and environmental behaviour in lake ecosystems. Thus, solid 13 C and solution 31 P nuclear magnetic resonance (NMR) spectroscopy were used to characterize biomass of six aquatic plants in Tai Lake, China. The results showed that carbohydrates (61.2% of the total C) were predominant C functional group in the solid 13 C NMR spectra of plant biomass, which may indicate high lability and bioavailability of aquatic plants-derived organic matter in lakes. There was 72.6-103.7% of the total P in aquatic plant biomass extracted by NaOH-EDTA extracts. Solution 31 P NMR analysis of these NaOH-EDTA extracts further identified several molecular species of P including orthophosphate (50.1%), orthophosphate monoesters (46.8%), DNA (1.6%) and pyrophosphate (1.4%). Orthophosphate monoesters included β-glycerophosphate (17.7%), hydrolysis products of RNA (11.7%), α-glycerophosphate (9.2%) and other unknown monoesters (2.1%). Additionally, phytate, the major form of organic P in many lake sediments, was detected in floating plant water poppy. These inorganic P (e.g. orthophosphate and pyrophosphate) and organic P (e.g. diester and its degradation products) identified in plant biomass were all labile and bioavailable P, which would play an important role in recycling of P in lakes. These results increased knowledge of chemical composition and bioavailability of OMs derived from aquatic plants in lakes.

  20. On the molecular basis of the recognition of angiotensin II (AII) : NMR structure of AII in solution compared with the X-ray structure of AII bound to the mAb Fab131

    National Research Council Canada - National Science Library

    Tzakos, A.G; Bonvin, A.M.J.J; Troganis, A; Cordopatis, P; Amzel, M.L; Gerothanassis, I.P; van Nuland, N.A.J


    The high-resolution 3D structure of the octapeptide hormone angiotensin II (AII) in aqueous solution has been obtained by simulated annealing calculations, using high-resolution NMR-derived restraints...

  1. Solution conformation and dynamics of a tetrasaccharide related to the Lewis{sup X} antigen deduced by NMR relaxation measurements

    Energy Technology Data Exchange (ETDEWEB)

    Poveda, Ana [Universidad Autonoma de Madrid, Servicio Interdepartamental de Investigacion (Spain); Asensio, Juan Luis; Martin-Pastor, Manuel; Jimenez-Barbero, Jesus [Instituto de Quimica Organica, CSIC, Grupo de Carbohidratos (Spain)


    {sup 1}H-NMR cross-relaxation rates and nonselective longitudinal relaxation times have been obtained at two magnetic fields (7.0 and 11.8 T) and at a variety of temperatures for the branched tetrasaccharide methyl 3-O-{alpha}-N-acetyl-galactosaminyl-{beta}-galactopyranosyl-(1{sup {yields}}4)[3-O-{alpha}-fucosyl] -glucopyranoside (1), an inhibitor of astrocyte growth. In addition, {sup 13}C-NMR relaxation data have also been recorded at both fields. The {sup 1}H-NMR relaxation data have been interpreted using different motional models to obtain proton-proton correlation times. The results indicate that the GalNAc and Fuc rings display more extensive local motion than the two inner Glc and Gal moieties, since those present significantly shorter local correlation times. The{sup 13}C-NMR relaxation parameters have been interpreted in terms of the Lipari-Szabo model-free approach. Thus, order parameters and internal motion correlation times have been deduced. As obtained for the{sup 1}H-NMR relaxation data, the two outer residues possess smaller order parameters than the two inner rings. Internal correlation times are in the order of 100 ps. The hydroxymethyl groups have also different behaviour,with the exocyclic carbon on the glucopyranoside unit showing the highestS{sup 2}. Molecular dynamics simulations using a solvated system have also been performed and internal motion correlation functions have been deduced from these calculations. Order parameters and interproton distances have been compared to those inferred from the NMR measurements. The obtained results are in fair agreement with the experimental data.

  2. NMR structure of biosynthetic engineered human insulin monomer B31(Lys)-B32(Arg) in water/acetonitrile solution. Comparison with the solution structure of native human insulin monomer. (United States)

    Bocian, Wojciech; Borowicz, Piotr; Mikołajczyk, Jerzy; Sitkowski, Jerzy; Tarnowska, Anna; Bednarek, Elzbieta; Głabski, Tadeusz; Tejchman-Małecka, Bozena; Bogiel, Monika; Kozerski, Lech


    A solution NMR-derived structure of a new long -acting, B31(Lys)-B32(Arg) (LysArg), engineered human insulin monomer, in H(2)O/CD(3)CN, 65/35 vol %, pH 3.6, is presented and compared with the available X-ray structure of a monomer that forms part of a hexamer (Smith, et al., Acta Crystallogr D 2003, 59, 474) and with NMR structure of human insulin in the same solvent (Bocian, et al., J Biomol NMR 2008, 40, 55-64). Detailed analysis using PFGSE NMR (Pulsed Field Gradient Spin Echo NMR) in dilution experiments and CSI analysis prove that the structure is monomeric in the concentration range 0.1-3 mM. The presence of long-range interstrand NOEs in a studied structure, relevant to the distances found in the crystal structure of the monomer, provides the evidence for conservation of the tertiary structure. Therefore the results suggest that this solvent system is a suitable medium for studying the native conformation of the protein, especially in situations (as found for insulins) in which extensive aggregation renders structure elucidations in water difficult or impossible. Starting from the structures calculated by the program CYANA, two different molecular dynamics (MD) simulated annealing refinement protocols were applied, either using the program AMBER in vacuum (AMBER_VC), or including a generalized Born solvent model (AMBER_GB). Here we present another independent evidence to the one presented recently by us (Bocian et al., J Biomol NMR 2008, 40, 55-64), that in water/acetonitrile solvent detailed structural and dynamic information can be obtained for important proteins that are naturally present as oligomers under native conditions. (c) 2008 Wiley Periodicals, Inc.

  3. Structure and membrane interactions of the antibiotic peptide dermadistinctin K by multidimensional solution and oriented 15N and 31P solid-state NMR spectroscopy. (United States)

    Verly, Rodrigo M; de Moraes, Cléria Mendonça; Resende, Jarbas M; Aisenbrey, Christopher; Bemquerer, Marcelo Porto; Piló-Veloso, Dorila; Valente, Ana Paula; Almeida, Fábio C L; Bechinger, Burkhard


    DD K, a peptide first isolated from the skin secretion of the Phyllomedusa distincta frog, has been prepared by solid-phase chemical peptide synthesis and its conformation was studied in trifluoroethanol/water as well as in the presence of sodium dodecyl sulfate and dodecylphosphocholine micelles or small unilamellar vesicles. Multidimensional solution NMR spectroscopy indicates an alpha-helical conformation in membrane environments starting at residue 7 and extending to the C-terminal carboxyamide. Furthermore, DD K has been labeled with (15)N at a single alanine position that is located within the helical core region of the sequence. When reconstituted into oriented phosphatidylcholine membranes the resulting (15)N solid-state NMR spectrum shows a well-defined helix alignment parallel to the membrane surface in excellent agreement with the amphipathic character of DD K. Proton-decoupled (31)P solid-state NMR spectroscopy indicates that the peptide creates a high level of disorder at the level of the phospholipid headgroup suggesting that DD K partitions into the bilayer where it severely disrupts membrane packing.

  4. Phthalimides: Supramolecular Interactions in Crystals, Hypersensitive Solution 1H-NMR Dynamics and Energy Transfer to Europium(III and Terbium(III States

    Directory of Open Access Journals (Sweden)

    David J. Williams


    Full Text Available Detailed crystal structures and 1H-NMR characteristics of some alkylaminephthalimides, including dendritic polyphthalimides, are reported. These investigations were undertaken in order to obtain a better understanding of the relationship between solid-state supramolecular interactions, their persistence in solution and associated dynamics of magnetically hypersensitive phthalimide aromatic AA'BB'-AA'XX' proton NMR resonances. Some alkylamine phthalimides feature folded molecular geometries, which we attribute to n-π interactions among proximal amine-phthalimide sites; those alkylamine-phthalimides that have no possibility for such interactions feature fully extended phthalimide functionalities. Accordingly, alkylamine phthalimide compounds with folded solid-state geometries feature solvent and temperature dependent hypersensitive AA'BB'-AA'XX' 1H-NMR line profiles, which we attribute to the n-π interactions. Luminescence of Eu3+(5D0 and Tb3+(5D4 states show well defined metal ion environments in their complexes with dendritic phthalimides, as well as relatively weak phthalimide-lanthanide(III interactions.

  5. 1D and 2D NMR Spectroscopy of Bonding Interactions within Stable and Phase-Separating Organic Electrolyte-Cellulose Solutions. (United States)

    Clough, Matthew T; Farès, Christophe; Rinaldi, Roberto


    Organic electrolyte solutions (i.e. mixtures containing an ionic liquid and a polar, molecular co-solvent) are highly versatile solvents for cellulose. However, the underlying solvent-solvent and solvent-solute interactions are not yet fully understood. Herein, mixtures of the ionic liquid 1-ethyl-3-methylimidazolium acetate, the co-solvent 1,3-dimethyl-2-imidazolidinone, and cellulose are investigated using 1D and 2D NMR spectroscopy. The use of a triply-13 C-labelled ionic liquid enhances the signal-to-noise ratio for 13 C NMR spectroscopy, enabling changes in bonding interactions to be accurately pinpointed. Current observations reveal an additional degree of complexity regarding the distinct roles of cation, anion, and co-solvent toward maintaining cellulose solubility and phase stability. Unexpectedly, the interactions between the dialkylimidazolium ring C2 -H substituent and cellulose become more pronounced at high temperatures, counteracted by a net weakening of acetate-cellulose interactions. Moreover, for mixtures that exhibit critical solution behavior, phase separation is accompanied by the apparent recombination of cation-anion pairs. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

    Energy Technology Data Exchange (ETDEWEB)

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


    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, appears to maintain a conformation similar to that of residues 1-45 in the X-ray structure of intact porcine adenylate kinase, 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% ..cap 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, possible due to disorder, it can be fit by using methods developed on well-characterized globular proteins. The CD spectrum is best fit by assuming the presence of at most 13% ..cap 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 conformation changes in the backbone of the peptide are detected by NMR, with smaller alterations in the overall secondary structure as assess by CD.

  7. Solution NMR Structure of Yeast Succinate Dehydrogenase Flavinylation Factor Sdh5 Reveals a Putative Sdh1 Binding Site


    Eletsky, Alexander; Jeong, Mi-Young; Kim, Hyung; Lee, Hsiau-Wei; Xiao, Rong; Pagliarini, David J.; Prestegard, James H.; Winge, Dennis R.; Montelione, Gaetano T.; Szyperski, Thomas


    The yeast mitochondrial protein Sdh5 is required for the covalent attachment of flavin adenine dinucleotide (FAD) to protein Sdh1, a subunit of the hetero-tetrameric enzyme succinate dehydrogenase (SDH). The NMR structure of Sdh5 represents the first eukaryotic structure of the Pfam family PF03937 and reveals a conserved surface region, which likely represents a putative Sdh1-Sdh5 interaction interface. Point mutations in this region result in the loss of covalent flavinylation of Sdh1. Moreo...

  8. Solution structure of the 45-residue ATP-binding peptide of adenylate kinase as determined by 2-D NMR, FTIR, and CD spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

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


    In the X-ray structure of adenylate kinase residues 1-45 exist as 47% ..cap alpha..-helix, 29% ..beta..-structure (strands and turns) and 24% coil. The solution structure of a synthetic peptide corresponding to residues 1-45, which constitutes the MgATP binding site was studied by 3 independent spectroscopic methods. Globularity of the peptide was shown by its broad NMR resonances which narrow upon denaturation, and by its ability to bind MgATP with similar affinity and conformation as the intact enzyme does. COSY and NOESY NMR methods at 250 and 500 MHz reveal proximities among NH, C..cap alpha.., and C..beta.. protons indicative of >20% ..cap alpha..-helix, and >20% ..beta..-structure. Correlation of regions of secondary structure with the primary sequence by 2D NMR indicates at least one ..cap alpha..-helix (res. 23 to 29) and two ..beta..-strands (res. 12 to 15 and 34 to 38). The broad amide I band in the deconvoluted FTIR spectrum could be fit as the sum of 4 peaks due to specific secondary structures, yielding less than or equal to=45% ..cap alpha..-helix, less than or equal to=40% ..beta..-structure and greater than or equal to=15% coil. The CD spectrum, from 185-250 nm, interpreted with a 3-parameter basis set, yielded 20 +/- 5% ..cap alpha..=helix, and less than or equal to=20% ..beta..-structure. The solution structure of peptide 1-45 thus approximates that of residues 1-45 in the crystal.

  9. Formations of hydroxyapatite and inositol hexakisphosphate in poultry litter during the composting period: sequential fractionation, P K-edge XANES and solution (31)P NMR investigations. (United States)

    Hashimoto, Yohey; Takamoto, Akira; Kikkawa, Ren; Murakami, Keiichi; Yamaguchi, Noriko


    Little is known about how the solubility and chemical speciation of phosphorus (P) in poultry litters are altered during the composting period. This study investigated the quantitative and qualitative changes in organic P (Po) and inorganic P (Pi) compositions in poultry litters during the seven-day composting period using sequential extraction in combination with P K-edge X-ray absorption near-edge structure (XANES) and solution (31)P nuclear magnetic resonance (NMR) spectroscopy. The result of sequential extraction illustrated that the significant decrease of H2O-P by 55% in poultry litters occurred concomitantly with the increase of HCl-Pi and HCl-Po during the composting period (p poultry litter samples showed three distinct peaks indicative of hydroxyapatite. Phosphorus K-edge XANES confirmed the increase of hydroxyapatite during the composting period, corresponding to the increase of HCl-Pi determined by the sequential extraction. The NaOH-EDTA extraction for solution (31)P NMR revealed that myo-inositol hexakisphosphate (IHP) constituted about 80% of phosphate monoesters and was increased from 16 to 28% in the poultry litter during the composting period. The combined applications of chemical extraction and molecular-spectroscopic techniques determined that water-soluble P in poultry litter was transformed into less soluble phases, primarily hydroxyapatite and IHP, during the composting period.

  10. Investigation of relative metabolic changes in the organs and plasma of rats exposed to X-ray radiation using HR-MAS (1)H NMR and solution (1)H NMR. (United States)

    Jang, Won Gyo; Park, Ju Yeon; Lee, Jueun; Bang, Eunjung; Kim, So Ra; Lee, Eun Kyeong; Yun, Hyun Jin; Kang, Chang-Mo; Hwang, Geum-Sook


    Excess exposure to ionizing radiation generates reactive oxygen species and increases the cellular inflammatory response by modifying various metabolic pathways. However, an investigation of metabolic perturbations and organ-specific responses based on the amount of radiation during the acute phase has not been conducted. In this study, high-resolution magic-angle-spinning (HR-MAS) NMR and solution NMR-based metabolic profiling were used to investigate dose-dependent metabolic changes in multiple organs and tissues--including the jejunum, spleen, liver, and plasma--of rats exposed to X-ray radiation. The organs, tissues, and blood samples were obtained 24, 48, and 72 h after exposure to low-dose (2 Gy) and high-dose (6 Gy) X-ray radiation and subjected to metabolite profiling and multivariate analyses. The results showed the time course of the metabolic responses, and many significant changes were detected in the high-dose compared with the low-dose group. Metabolites with antioxidant properties showed acute responses in the jejunum and spleen after radiation exposure. The levels of metabolites related to lipid and protein metabolism were decreased in the jejunum. In addition, amino acid levels increased consistently at all post-irradiation time points as a consequence of activated protein breakdown. Consistent with these changes, plasma levels of tricarboxylic acid cycle intermediate metabolites decreased. The liver did not appear to undergo remarkable metabolic changes after radiation exposure. These results may provide insight into the major metabolic perturbations and mechanisms of the biological systems in response to pathophysiological damage caused by X-ray radiation. Copyright © 2016 John Wiley & Sons, Ltd.

  11. Interactions between cyclodextrins and TM{sup III} chelates of polyazamacrocycles as studied by NMR in aqueous solution

    Energy Technology Data Exchange (ETDEWEB)

    Zitha-Bovens, E.; Bekkum, H. van; Peters, J.A. [Delft Univ. of Technology (Netherlands). Lab. of Organic Chemistry and Catalysis; Geraldes, C.F.G.C. [Coimbra Univ. (Portugal). Dept. of Biochemistry and Center of Neurosciences


    The interactions between {alpha}-, {beta}, and {gamma}-CD and the Tm{sup III} chelates of the macrocyclic polyaminopolycarboxylates DOTA and NOTA were studied with the use of {sup 1}H- and {sup 13}C-NMR shift and relaxation rate measurements. Interactions were only observed between Tm(DOTA){sup -} and {gamma}-CD. The structure and the stability of the concerning supramolecular structures was elucidated by fitting of the NMR titration curves to a theoretical model. It appears that an inclusion compound is formed, where the hydrophobic macrocyclic part of the chelate sits in the {gamma}-CD cavity. This inclusion compound binds a second Tm(DOTA){sup -} molecule at the outside lower rim of the CD cone. The binding occurs probably via hydrogen bonds between non-chelated carboxylate oxygen atoms of the concerning Tm(DOTA){sup -} and CH{sub 2}OH groups of the {gamma}-CD molecule, which are in a favorable position due to opening of the {gamma}-CD cone angle as a result of the inclusion of the first {gamma}-CD. (orig.)

  12. Fitting of the beat pattern observed in NMR free-induction decay signals of concentrated carbohydrate-water solutions. (United States)

    Derbyshire, W; Van Den Bosch, M; Van Dusschoten, D; MacNaughtan, W; Farhat, I A; Hemminga, M A; Mitchell, J R


    A series of mathematical functions has been used to fit the proton free-induction decays (FIDs) of concentrated carbohydrate-water samples. For the solid protons, these functions included a sinc function, as well as the Fourier transforms of single and multiple Pake functions multiplied by a Gaussian broadening. The NMR signal from the mobile protons is described by an exponential function. It is found that in most cases the sinc function gives a satisfactory result and provides valuable information about the second moment M(2) and the ratio of solid to mobile protons (f(s) / f(m)). A good indication for using the sinc function is the presence of a beat in the FID. For high temperatures this approach breaks down, and a biexponential fit is more appropriate. If a clear dipolar splitting is observable in the NMR spectra, the Pake function (or a multiple Pake fit) should be used. In this case information about M(2) and f(s) / f(m) can also be obtained.

  13. Towards structural investigations on isotope labelled native bacteriorhodopsin in detergent micelles by solution-state NMR spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Patzelt, Heiko [Max-Planck-Institut fuer Biochemie, Am Klopferspitz (Germany); Ulrich, Anne S. [European Molecular Biology Laboratory (Germany); Egbringhoff, Hermann [Max-Planck-Institut fuer Biochemie, Am Klopferspitz (Germany); Duex, Petra; Ashurst, Jennifer; Simon, Bernd; Oschkinat, Hartmut [European Molecular Biology Laboratory (Germany); Oesterhelt, Dieter [Max-Planck-Institut fuer Biochemie, Am Klopferspitz (Germany)


    {sup 1}H NMR signals of the retinal moiety in detergent-solubilized bacteriorhodopsin are assigned, enabling the interpretation of NOEs within the chromophore. To achieve this, a number of differently labelled samples were prepared to test the applicability of the various assignment and distance measurement strategies. In measurements with and without light,{sup 1}H and {sup 13}C chemical shifts of the retinal in the native protein were partially assigned for both the dark- and the light-adapted states. Additionally, samples with residue-specific{sup 1}H amino acids and/or retinal in an otherwise deuterated protein were prepared to measure the distances between either two kinds of amino acids or between individual amino acids and the retinal moiety. With the observation of NOE within the bound retinal and between retinal and its neighbouring aminoacids, an important step towards the elucidation of distance constraints in the binding pocket of the proton pump is made.

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

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


    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

  15. Development of quantitative NMR method with internal standard for the standard solutions of paralytic shellfish toxins and characterisation of gonyautoxin-5 and gonyautoxin-6. (United States)

    Watanabe, Ryuichi; Suzuki, Toshiyuki; Oshima, Yasukatsu


    The chemical analysis of paralytic shellfish toxins (PSTs) requires standard solutions with accurate concentration. The mouse toxicity in each toxin is also essential knowledge for the introduction of chemical analysis as an alternative method to mouse bioassay (MBA) in routine monitoring of shellfish. In this study, we developed the quantitative analysis of PSTs by nuclear magnetic resonance (NMR), using tert-butanol as an internal standard. Only proton signals with longitudinal relaxation time (T(1)) of less than 2.5 s, including the internal standard, were used for quantitation of toxins. Our method showed good precision (results are useful to convert the amount of GTX5 and GTX6 into the mouse toxicity, especially in the areas where the dinoflagellate Gymnodinium catenatum predominantly produces both toxins. Copyright 2010 Elsevier Ltd. All rights reserved.

  16. Structure and reactivity of thiazolium azo dyes: UV-visible, resonance Raman, NMR, and computational studies of the reaction mechanism in alkaline solution. (United States)

    Abbott, Laurence C; Batchelor, Stephen N; Moore, John N


    UV-visible absorption, resonance Raman, and (1)H NMR spectroscopy, allied with density functional theory (DFT) calculations, have been used to study the structure, bonding, and alkaline hydrolysis mechanism of the cationic thiazloium azo dye, 2-[2-[4-(diethylamino)phenyl]diazenyl]-3-methyl-thiazolium (1a), along with a series of six related dyes with different 4-dialkylamino groups and/or other phenyl ring substituents (2a-c, 3a-c) and the related isothiazolium azo dye, 5-[2-[4-(dimethylamino)phenyl]diazenyl]-2-methyl-isothiazolium (4). These diazahemicyanine dyes are calculated to have a similar low-energy structure that is cis, trans at the (iso)thiazolium-azo group, and for which the calculated Raman spectra provide a good match with the experimental data; the calculations on these structures are used to assign and discuss the transitions giving rise to the experimental spectra, and to consider the bonding and its variation between the dyes. UV-visible, Raman, and NMR spectra recorded from minutes to several weeks after raising the pH of an aqueous solution of 1a to ca. 11.5 show that the dominant initial step in the reaction is loss of diethylamine to produce a quinonimine (ca. hours), with subsequent reactions occurring on longer time scales (ca. days to weeks); kinetic analyses give a rate constant of 2.6 × 10(-2) dm(3) mol(-1) s(-1) for reaction of 1a with OH(-). UV-visible spectra recorded on raising the pH of the other dyes in solution show similar changes that are attributed to the same general reaction mechanism, but with different rate constants for which the dependence on structure is discussed.

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

    Energy Technology Data Exchange (ETDEWEB)

    Carr, M.D.; Birdsall, B.; Jimenez-Barbero, J.; Polshakov, V.I.; McCormick, J.E.; Feeney, J.; Frenkiel, T.A.; Bauer, C.J. (National Inst. for Medical Research, London (England)); Roberts, G.C.K. (Univ. of Leicester (England))


    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.

  18. The NMR solution structure and function of RPA3313: a putative ribosomal transport protein from Rhodopseudomonas palustris. (United States)

    Catazaro, Jonathan; Lowe, Austin J; Cerny, Ronald L; Powers, Robert


    Protein function elucidation often relies heavily on amino acid sequence analysis and other bioinformatics approaches. The reliance is extended to structure homology modeling for ligand docking and protein-protein interaction mapping. However, sequence analysis of RPA3313 exposes a large, unannotated class of hypothetical proteins mostly from the Rhizobiales order. In the absence of sequence and structure information, further functional elucidation of this class of proteins has been significantly hindered. A high quality NMR structure of RPA3313 reveals that the protein forms a novel split ββαβ fold with a conserved ligand binding pocket between the first β-strand and the N-terminus of the α-helix. Conserved residue analysis and protein-protein interaction prediction analyses reveal multiple protein binding sites and conserved functional residues. Results of a mass spectrometry proteomic analysis strongly point toward interaction with the ribosome and its subunits. The combined structural and proteomic analyses suggest that RPA3313 by itself or in a larger complex may assist in the transportation of substrates to or from the ribosome for further processing. Proteins 2016; 85:93-102. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  19. Solution NMR structures reveal a distinct architecture and provide first structures for protein domain family PF04536. (United States)

    Eletsky, Alexander; Acton, Thomas B; Xiao, Rong; Everett, John K; Montelione, Gaetano T; Szyperski, Thomas


    The protein family (Pfam) PF04536 is a broadly conserved domain family of unknown function (DUF477), with more than 1,350 members in prokaryotic and eukaryotic proteins. High-quality NMR structures of the N-terminal domain comprising residues 41-180 of the 684-residue protein CG2496 from Corynebacterium glutamicum and the N-terminal domain comprising residues 35-182 of the 435-residue protein PG0361 from Porphyromonas gingivalis both exhibit an α/β fold comprised of a four-stranded β-sheet, three α-helices packed against one side of the sheet, and a fourth α-helix attached to the other side. In spite of low sequence similarity (18%) assessed by structure-based sequence alignment, the two structures are globally quite similar. However, moderate structural differences are observed for the relative orientation of two of the four helices. Comparison with known protein structures reveals that the α/β architecture of CG2496(41-180) and PG0361(35-182) has previously not been characterized. Moreover, calculation of surface charge potential and identification of surface clefts indicate that the two domains very likely have different functions.

  20. Sources of and Solutions to Problems in the Refinement of Protein NMR Structures against Torsion Angle Potentials of Mean Force (United States)

    Kuszewski, John; Clore, G. Marius


    It is often the case that a substantial number of torsion angles (both backbone and sidechain) in structures of proteins and nucleic acids determined by NMR are found in physically unlikely and energetically unfavorable conformations. We have previously proposed a database-derived potential of mean force comprising one-, two-, three-, and four-dimensional potential surfaces which describe the likelihood of various torsion angle combinations to bias conformational sampling during simulated annealing refinement toward those regions that are populated in very high resolution (≤1.75 Å) crystal structures. We now note a shortcoming of our original implementation of this approach: namely, the forces it places on atoms are very rough. When the density of experimental restraints is low, this roughness can both hinder convergence to commonly populated regions of torsion angle space and reduce overall conformational sampling. In this paper we describe a modification that completely eliminates these problems by replacing the original potential surfaces by a sum of multidimensional Gaussian functions. Structures refined with the new Gaussian implementation now simultaneously enjoy excellent global sampling and excellent local choices of torsion angles.

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

    Energy Technology Data Exchange (ETDEWEB)

    Kächele, Martin [Chemisches und Veterinäruntersuchungsamt (CVUA) Karlsruhe, Weissenburger Strasse 3, D-76187 Karlsruhe (Germany); Hochschule Mannheim, Paul-Wittsack-Strasse 10, D-68163 Mannheim (Germany); Monakhova, Yulia B. [Chemisches und Veterinäruntersuchungsamt (CVUA) Karlsruhe, Weissenburger Strasse 3, D-76187 Karlsruhe (Germany); Bruker Biospin GmbH, Silbersteifen, 76287 Rheinstetten (Germany); Department of Chemistry, Saratov State University, Astrakhanskaya Street 83, 410012 Saratov (Russian Federation); Kuballa, Thomas [Chemisches und Veterinäruntersuchungsamt (CVUA) Karlsruhe, Weissenburger Strasse 3, D-76187 Karlsruhe (Germany); Lachenmeier, Dirk W., E-mail: [Chemisches und Veterinäruntersuchungsamt (CVUA) Karlsruhe, Weissenburger Strasse 3, D-76187 Karlsruhe (Germany); Ministry of Rural Affairs and Consumer Protection, Kernerplatz 10, 70182 Stuttgart (Germany)


    Highlights: • Acrolein in hydroalcoholic solution degrades to 1,3,3-propanetriol and 3-hydroxypropionaldehyde. • Hydroquinone (0.2%) at pH 3.0 stabilizes acrolein solutions. • Quantitative HS-SPME/GC–MS determination of acrolein in alcoholic beverages was developed (LOD 14 μg L⁻¹. • 6 of 117 samples had acrolein levels above the WHO threshold (1500 μg L⁻¹). Abstract: Acrolein (propenal) is found in many foods and beverages and may pose a health hazard due to its cytotoxicity. Considerable knowledge gaps regarding human exposure to acrolein exist, and there is a lack of reliable analytical methods. Hydroalcoholic dilutions prepared for calibration purposes from pure acrolein show considerable degradation of the compound and nuclear magnetic resonance (NMR) spectroscopy showed that 1,3,3-propanetriol and 3-hydroxypropionaldehyde are formed. The degradation can be prevented by addition of hydroquinone as stabilizer to the calibration solutions, which then show linear concentration-response behaviour required for quantitative analysis. The stabilized calibration solutions were used for quantitative headspace solid-phase microextraction/gas chromatography–mass spectrometry (HS-SPME/GC–MS) determination of acrolein in alcoholic beverages with a detection limit of 14 μg L⁻¹. Of 117 tested alcoholic beverages, 64 were tested positive with the highest incidence in grape marc spirits and whiskey (100%, mean 252 μg L⁻¹), followed by fruit spirits (86%, mean 591 μg/L⁻¹), tequila (86%, mean 404 μg L⁻¹), Asian spirits (43%, mean 54 μg L⁻¹) and wine (9%, mean 0.7 μg L⁻¹). Acrolein could not be detected in beer, vodka, absinthe and bottled water. Six of the fruit and grape marc spirits had acrolein levels above the World Health Organization (WHO) provisional tolerable concentration of 1.5 mg L⁻¹.

  2. On the molecular basis of the recognition of angiotensin II (AII) : NMR structure of AII in solution compared with the X-ray structure of AII bound to the mAb Fab131

    NARCIS (Netherlands)

    Tzakos, A.G.; Bonvin, A.M.J.J.; Troganis, A.; Cordopatis, P.; Amzel, M.L.; Gerothanassis, I.P.; van Nuland, N.A.J.


    The high-resolution 3D structure of the octapeptide hormone angiotensin II (AII) in aqueous solution has been obtained by simulated annealing calculations, using high-resolution NMR-derived restraints. After final refinement in explicit water, a family of 13 structures was obtained with a backbone

  3. Solution NMR Structure of Hypothetical Protein CV_2116 Encoded by a Viral Prophage Element in Chromobacterium violaceum

    Directory of Open Access Journals (Sweden)

    Yunhuang Yang


    Full Text Available CV_2116 is a small hypothetical protein of 82 amino acids from the Gram-negative coccobacillus Chromobacterium violaceum. A PSI-BLAST search using the CV_2116 sequence as a query identified only one hit (E = 2e−07 corresponding to a hypothetical protein OR16_04617 from Cupriavidus basilensis OR16, which failed to provide insight into the function of CV_2116. The CV_2116 gene was cloned into the p15TvLic expression plasmid, transformed into E. coli, and 13C- and 15N-labeled NMR samples of CV_2116 were overexpressed in E. coli and purified for structure determination using NMR spectroscopy. The resulting high-quality solution NMR structure of CV_2116 revealed a novel α + β fold containing two anti-parallel β -sheets in the N-terminal two-thirds of the protein and one α-helix in the C-terminal third of the protein. CV_2116 does not belong to any known protein sequence family and a Dali search indicated that no similar structures exist in the protein data bank. Although no function of CV_2116 could be derived from either sequence or structural similarity searches, the neighboring genes of CV_2116 encode various proteins annotated as similar to bacteriophage tail assembly proteins. Interestingly, C. violaceum exhibits an extensive network of bacteriophage tail-like structures that likely result from lateral gene transfer by incorporation of viral DNA into its genome (prophages due to bacteriophage infection. Indeed, C. violaceum has been shown to contain four prophage elements and CV_2116 resides in the fourth of these elements. Analysis of the putative operon in which CV_2116 resides indicates that CV_2116 might be a component of the bacteriophage tail-like assembly that occurs in C. violaceum.

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

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


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

  5. Solution NMR characterization of magnetic/electronic properties of azide and cyanide-inhibited substrate complexes of human heme oxygenase: implications for steric ligand tilt. (United States)

    Peng, Dungeng; Ogura, Hiroshi; Ma, Li-Hua; Evans, John P; de Montellano, Paul R Ortiz; La Mar, Gerd N


    Solution 2D (1)H NMR was carried out on the azide-ligated substrate complex of human heme oxygenase, hHO, to provide information on the active site molecular structure, chromophore electronic/magnetic properties, and the distal H-bond network linked to the exogenous ligand by catalytically relevant oriented water molecules. While 2D NMR exhibited very similar patterns of two-dimensional nuclear Overhauser spectroscopy cross peaks of residues with substrate and among residues as the previously characterized cyanide complex, significant, broadly distributed chemical shift differences were observed for both labile and non-labile protons. The anisotropy and orientation of the paramagnetic susceptibility tensor, χ, were determined for both the azide and cyanide complexes. The most significant difference observed is the tilt of the major magnetic axes from the heme normal, which is only half as large for the azide than cyanide ligand, with each ligand tilted toward the catalytically cleaved α-meso position. The difference in chemical shifts is quantitatively correlated with differences in dipolar shifts in the respective complexes for all but the distal helix. The necessity of considering dipolar shifts, and hence determination of the orientation/anisotropy of χ, in comparing chemical shifts involving paramagnetic complexes, is emphasized. The analysis shows that the H-bond network cannot detect significant differences in H-bond acceptor properties of cyanide versus azide ligands. Lastly, significant retardation of distal helix labile proton exchange upon replacing cyanide with azide indicates that the dynamic stability of the distal helix is increased upon decreasing the steric interaction of the ligand with the distal helix. Copyright © 2013. Published by Elsevier Inc.

  6. Solution 1H, 15N NMR spectroscopic characterization of substrate-bound, cyanide-inhibited human heme oxygenase: water occupation of the distal cavity. (United States)

    Li, Yiming; Syvitski, Ray T; Auclair, Karine; Ortiz de Montellano, Paul; La Mar, Gerd N


    A solution NMR spectroscopic study of the cyanide-inhibited, substrate-bound complex of uniformly (15)N-labeled human heme oxygenase, hHO, has led to characterization of the active site with respect to the nature and identity of strong hydrogen bonds and the occupation of ordered water molecules within both the hydrogen bonding network and an aromatic cluster on the distal side. [(1)H-(15)N]-HSQC spectra confirm the functionalities of several key donors in particularly robust H-bonds, and [(1)H-(15)N]HSQC-NOESY spectra lead to the identification of three additional robust H-bonds, as well as the detection of two more relatively strong H-bonds whose identities could not be established. The 3D NMR experiments provided only a modest, but important, extension of assignments because of the loss of key TOCSY cross-peaks due to the line broadening from a dynamic heterogeneity in the active site. Steady-state NOEs upon saturating the water signal locate nine ordered water molecules in the immediate vicinity of the H-bond donors, six of which are readily identified in the crystal structure. The additional three are positioned in available spaces to account for the observed NOEs. (15)N-filtered steady-state NOEs upon saturating the water resonances and (15)N-filtered NOESY spectra demonstrate significant negative NOEs between water molecules and the protons of five aromatic rings. Many of the NOEs can be rationalized by water molecules located in the crystal structure, but strong water NOEs, particularly to the rings of Phe47 and Trp96, demand the presence of at least an additional two immobilized water molecules near these rings. The H-bond network appears to function to order water molecules to provide stabilization for the hydroperoxy intermediate and to serve as a conduit to the active site for the nine protons required per HO turnover.

  7. A Study of Solvation-Shell Symmetry in Electrolyte Solutions Using Quadrupolar NMR Relaxation of the Nuclei of Monoatomic Ions (United States)

    Chizhik; Podkorytov; Kaikkonen; Mikhailov


    The spin-lattice relaxation rates of 7Li, 23Na, 27Al, 71Ga, and 139La nuclei in electrolyte solutions have been investigated as functions of the isotopic composition of the solvent. The results show that quadrupolar relaxation of the nuclei of monoatomic ions is extremely sensitive to the symmetry of the solvation shells. The data are compared to the results for the 2H and 17O nuclei of the solvent molecules and the 14N nucleus of the nitrate anion. A semiquantitative description of the observed effects is given.

  8. Solution NMR study of environmental effects on substrate seating in human heme oxygenase: influence of polypeptide truncation, substrate modification and axial ligand. (United States)

    Zhu, Wenfeng; Li, Yiming; Wang, Jinling; Ortiz de Montellano, Paul R; La Mar, Gerd N


    Solution proton NMR has been used here to show that, as either the high-spin ferric, protohemin (PH) substrate complex at neutral pH, or the low-spin ferric, cyanide-inhibited PH substrate complex, the active site electronic and molecular structure of the 233- and 265-residue recombinant constructs of human heme oxygenase-1, hHO, are essentially indistinguishable. It is shown, moreover, that the equilibrium PH orientational isomerism about the alpha,gamma-meso axis is 1:1 in the water-ligated, resting-state complex, but changes to a 4:1 equilibrium ratio as the cyanide-inhibited complex, with the minor species in solution corresponding to the only one found in crystals. The introduction of significant PH orientational preference in the cyanide over the aquo complex is rationalized by the crystallographic observation for the same H2O and CN ligated complexes of rat heme oxygenase (rHO), where the steric tilt of the Fe-CN unit resulted in a approximately 1 A transition of PH into the hydrophobic interior, and stronger interaction of the vinyls with the HO matrix [M. Sugishima, H. Sakamoto, M. Noguchi, K. Fukugama, Biochemistry 42 (2003) 9898-9905]. 1H NMR spectra of the cyanide-inhibited PH complex are the most used, and most useful, for determining the distribution of orientational isomerism for PH in complexes of HO. Hence, it is imperative that the time-course of the spectra after sample preparation be considered in order to reach conclusions that relate isomeric seating of the heme with variable isomeric biliverdin products. The natural orientational isomerism of PH leads to spectral congestion that has prompted the use of a synthetic, twofold symmetric substrate, 2,4-dimethyldeuterohemin, DMDH. While the hyperfine shift pattern for non-ligated residues are very similar and are consistent with largely conserved molecular structure with the alternate substrates, the steric tilt of the Fe-CN vector towards the protein interior, as determined by the orientation of

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

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


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

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

    Directory of Open Access Journals (Sweden)

    Michael G. Siskos


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

  11. Label-free quantitative 1H NMR spectroscopy to study low-affinity ligand–protein interactions in solution: A contribution to the mechanism of polyphenol-mediated astringency (United States)

    Delius, Judith; Frank, Oliver


    Nuclear magnetic resonance (NMR) spectroscopy is well-established in assessing the binding affinity between low molecular weight ligands and proteins. However, conventional NMR-based binding assays are often limited to small proteins of high purity and may require elaborate isotopic labeling of one of the potential binding partners. As protein–polyphenol complexation is assumed to be a key event in polyphenol-mediated oral astringency, here we introduce a label-free, ligand-focused 1H NMR titration assay to estimate binding affinities and characterize soluble complex formation between proteins and low molecular weight polyphenols. The method makes use of the effects of NMR line broadening due to protein–ligand interactions and quantitation of the non-bound ligand at varying protein concentrations by quantitative 1H NMR spectroscopy (qHNMR) using electronic reference to access in vivo concentration (ERETIC 2). This technique is applied to assess the interaction kinetics of selected astringent tasting polyphenols and purified mucin, a major lubricating glycoprotein of human saliva, as well as human whole saliva. The protein affinity values (BC50) obtained are subsequently correlated with the intrinsic mouth-puckering, astringent oral sensation imparted by these compounds. The quantitative NMR method is further exploited to study the effect of carboxymethyl cellulose, a candidate “anti-astringent” protein binding antagonist, on the polyphenol–protein interaction. Consequently, the NMR approach presented here proves to be a versatile tool to study the interactions between proteins and low-affinity ligands in solution and may find promising applications in the discovery of bioactives. PMID:28886151

  12. Study and characterization of crystalline hydrate/polymorph forms of 5,11-dihydro-11-ethyl-5-methyl-8-(2-(1-oxido-4-quinolinyl)ethyl-6H-dipyrido(3,2-B:2',3'-E)(1,4)diazepin-6-one by solid-state NMR and solution NMR. (United States)

    Gonnella, N C; Smoliga, John A; Campbell, Scot; Busacca, Carl A; Cerreta, Michael; Varsolona, Richard; Norwood, Daniel L


    A novel inhibitor of reverse transcriptase was studied by solid-state NMR. Three phases of the compound were examined which included the dihydrate and two anhydrous polymorphs (Form I and Form III). By correlating (1)H and (13)C solution NMR with the solid-state (13)C NMR CP/MAS and CPPI spectral editing experiments, comparative (13)C assignments were made for each phase. Polymorphs of Form I and Form III and the dihydrate were easily distinguished based upon chemical shift patterns of the carbon resonances. The (1)H spin-lattice relaxation times were also measured for each phase which provided information on the mobility and relative crystallinity. The (13)C ssNMR spectrum of Form I showed the presence of a minor component identified as the dihydrate. Weight/percent quantitation of major and minor components in Form I was obtained from integrated intensities of a 50:50 mixture containing weighed amounts of Form I and the pure dihydrate. Comparison of the ssNMR and X-ray powder diffraction techniques is discussed. Copyright 2009 Elsevier B.V. All rights reserved.

  13. Solution 1H NMR characterization of substrate-free C. diphtheriae heme oxygenase: pertinence for determining magnetic axes in paramagnetic substrate complexes. (United States)

    Du, Zhenming; Unno, Masaki; Matsui, Toshitaka; Ikeda-Saito, Masao; La Mar, Gerd N


    Proton 2D NMR was used to confirm in solution a highly conserved portion of the molecular structure upon substrate loss for the heme oxygenase from the pathogenic bacterium Corynebacterium diphtheriae, HmuO. The chemical shifts for the conserved portion of the structure are assessed as references for the dipolar shifts needed to determine the orientation of the paramagnetic susceptibility tensor, chi, in paramagnetic substrate complexes of HmuO. It is shown that the chemical shifts for the structurally conserved portion of substrate-free HmuO serve as excellent references for residues with only small to moderate sized dipolar shifts in the cyanide-inhibited substrate complex of HmuO, yielding an orientation of chi that is essentially the same as conventionally obtained from large dipolar shifts based on empirical estimates of the diamagnetic reference. The implications of these diamagnetic chemical shifts for characterizing the hydrogen bonding in the physiologically relevant, resting-state, high-spin aquo complex are discussed. The pattern of labile proton exchange in the distal H-bond network of substrate-free HmuO allowed comparison of changes in dynamic stability of tertiary contacts in the substrate-free and substrate-bound HmuO and with the same complexes of human heme oxygenase. Copyright 2010 Elsevier Inc. All rights reserved.

  14. Solution 1H NMR characterization of substrate-free C. diphtheriae heme oxygenase; pertinence for determining magnetic axes in paramagnetic substrate complexes (United States)

    Du, Zhenming; Unno, Masaki; Matsui, Toshitaka; Ikeda-Saito, Masao; La Mar, Gerd N.


    Proton 2D NMR was used to confirm in solution a highly conserved portion of the molecular structure upon substrate loss for the heme oxygenase from the pathogenic bacterium Corynebacterium diphtheriae, HmuO. The chemical shifts for the conserved portion of the structure are assessed as references for the dipolar shifts needed to determine the orientation of the paramagnetic susceptibility tensor, χ, in paramagnetic substrate complexes of HmuO. It is shown that the chemical shifts for the structurally conserved portion of substrate-free HmuO serve as excellent references for residues with only small to moderate sized dipolar shifts in the cyanide-inhibited substrate complex of HmuO, yielding an orientation of χ that is essentially the same as conventionally obtained from large dipolar shifts based on empirical estimates of the diamagnetic reference. The implications of these diamagnetic chemical shifts for characterizing the hydrogen bonding in the physiologically relevant, resting-state, high-spin aquo complex are discussed. The pattern of labile proton exchange in the distal H-bond network of substrate-free HmuO allowed comparison of changes in dynamic stability of tertiary contacts in the substrate-free and substrate-bound HmuO and with the same complexes of human heme oxygenase. PMID:20655112

  15. Solution NMR structure of the iron-sulfur cluster assembly protein U (IscU) with zinc bound at the active site. (United States)

    Ramelot, Theresa A; Cort, John R; Goldsmith-Fischman, Sharon; Kornhaber, Gregory J; Xiao, Rong; Shastry, Ritu; Acton, Thomas B; Honig, Barry; Montelione, Gaetano T; Kennedy, Michael A


    IscU is a highly conserved protein that serves as the scaffold for IscS-mediated assembly of iron-sulfur ([Fe-S]) clusters. We report the NMR solution structure of monomeric Haemophilus influenzae IscU with zinc bound at the [Fe-S] cluster assembly site. The compact core of the globular structure has an alpha-beta sandwich architecture with a three-stranded antiparallel beta-sheet and four alpha-helices. A nascent helix is located N-terminal to the core structure. The zinc is ligated by three cysteine residues and one histidine residue that are located in and near conformationally dynamic loops at one end of the IscU structure. Removal of the zinc metal by chelation results in widespread loss of structure in the apo form. The zinc-bound IscU may be a good model for iron-loaded IscU and may demonstrate structural features found in the [Fe-S] cluster bound form. Structural and functional similarities, genomic context in operons containing other homologous genes, and distributions of conserved surface residues support the hypothesis that IscU protein domains are homologous (i.e. derived from a common ancestor) with the SufE/YgdK family of [Fe-S] cluster assembly proteins.

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

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


    Acrolein (propenal) is found in many foods and beverages and may pose a health hazard due to its cytotoxicity. Considerable knowledge gaps regarding human exposure to acrolein exist, and there is a lack of reliable analytical methods. Hydroalcoholic dilutions prepared for calibration purposes from pure acrolein show considerable degradation of the compound and nuclear magnetic resonance (NMR) spectroscopy showed that 1,3,3-propanetriol and 3-hydroxypropionaldehyde are formed. The degradation can be prevented by addition of hydroquinone as stabilizer to the calibration solutions, which then show linear concentration-response behaviour required for quantitative analysis. The stabilized calibration solutions were used for quantitative headspace solid-phase microextraction/gas chromatography-mass spectrometry (HS-SPME/GC-MS) determination of acrolein in alcoholic beverages with a detection limit of 14 μg L(-1). Of 117 tested alcoholic beverages, 64 were tested positive with the highest incidence in grape marc spirits and whiskey (100%, mean 252 μg L(-1)), followed by fruit spirits (86%, mean 591 μg/L(-1)), tequila (86%, mean 404 μg L(-1)), Asian spirits (43%, mean 54 μg L(-1)) and wine (9%, mean 0.7 μg L(-1)). Acrolein could not be detected in beer, vodka, absinthe and bottled water. Six of the fruit and grape marc spirits had acrolein levels above the World Health Organization (WHO) provisional tolerable concentration of 1.5 mg L(-1). Copyright © 2014 Elsevier B.V. All rights reserved.

  17. Solution NMR Structure and Backbone Dynamics of the Partially Disordered Arabidopsis thaliana Phloem Protein 16-1, A Putative mRNA Transporter. (United States)

    Sashi, Pulikallu; Singarapu, Kiran Kumar; Bhuyan, Abani K


    Although RNA-binding proteins in plant phloem are believed to carry out long-distance systemic transport of RNA in the phloem conduit, the structure of none of them is known. The Arabidopsis thaliana phloem protein 16-1 (AtPP16-1) is such a putative mRNA transporter whose structure and backbone dynamics have been studied at pH 4.1, 25oC, by high-resolution NMR spectroscopy. Results obtained using basic optical spectroscopic tools show that the protein is unstable with little secondary structure near the physiological pH of the phloem sap. Fluorescence-monitored titrations reveal that AtPP16-1 binds not only A. thaliana RNA (Kdiss ~ 67 nM) but also sheared DNA and model dodecamer DNA, albeit the affinity for DNA is ~15-fold less. In the solution structure of the protein secondary structural elements are formed of residues 3-9 (β1), 56-62 (β2), 133-135 (β3), and 96-110 (αα-helix). Most of the rest of the chain segments is disordered. The N-terminal disordered regions (residues 10-55) form a small lobe, which conjoins the rest of the molecule via a deep and large irregular cleft that could have functional implications. The average order parameter extracted by model-free analysis of 15N relaxation and {1H}-15N heteronuclear NOE data is 0.66, suggesting less restricted backbone motion. The average conformational entropy of the backbone NH vectors is -0.31 cal mol-1 K-1. These results also suggest structural disorder in AtPP16-1.

  18. Structural and thermodynamic insight into the process of "weak" dimerization of the ErbB4 transmembrane domain by solution NMR. (United States)

    Bocharov, Eduard V; Mineev, Konstantin S; Goncharuk, Marina V; Arseniev, Alexander S


    Specific helix-helix interactions between the single-span transmembrane domains of receptor tyrosine kinases are believed to be important for their lateral dimerization and signal transduction. Establishing structure-function relationships requires precise structural-dynamic information about this class of biologically significant bitopic membrane proteins. ErbB4 is a ubiquitously expressed member of the HER/ErbB family of growth factor receptor tyrosine kinases that is essential for the normal development of various adult and fetal human tissues and plays a role in the pathobiology of the organism. The dimerization of the ErbB4 transmembrane domain in membrane-mimicking lipid bicelles was investigated by solution NMR. In a bicellar DMPC/DHPC environment, the ErbB4 membrane-spanning α-helices (651-678)(2) form a right-handed parallel dimer through the N-terminal double GG4-like motif A(655)GxxGG(660) in a fashion that is believed to permit proper kinase domain activation. During helix association, the dimer subunits undergo a structural adjustment (slight bending) with the formation of a network of inter-monomeric polar contacts. The quantitative analysis of the observed monomer-dimer equilibrium provides insights into the kinetics and thermodynamics of the folding process of the helical transmembrane domain in the model environment that may be directly relevant to the process that occurs in biological membranes. The lipid bicelles occupied by a single ErbB4 transmembrane domain behave as a true ("ideal") solvent for the peptide, while multiply occupied bicelles are more similar to the ordered lipid microdomains of cellular membranes and appear to provide substantial entropic enhancement of the weak helix-helix interactions, which may be critical for membrane protein activity. Copyright © 2012 Elsevier B.V. All rights reserved.

  19. Annual reports on NMR spectroscopy

    CERN Document Server

    Webb, Graham A; McCarthy, M J


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

  20. Kinetic study of polymerization of N-vinylcaprolactam by {sup 1}H NMR and determination of Lower Critical Solution Temperature (LCST); Estudo cinetico da polimerizacao da N-vinilcaprolactama (NVCL) por RMN {sup 1}H e determinacao da temperatura critica inferior de solubilizacao (LCST)

    Energy Technology Data Exchange (ETDEWEB)

    Baboni, Simone F.M.G.; Santos, Amilton M.; Barboza, Jayne C.S. [Faculdade de Engenharia Quimica de Lorena (FAENQUIL), SP (Brazil). Dept. de Engenharia Quimica. Lab. de Quimica Fina]. E-mail:


    Poly(N-vinylcaprolactam) (PNVCL) is a polymer possessing a lower critical solution temperature (LCST) in aqueous solutions. Temperature-sensitive polymers with terminal carboxy groups were synthesized by free radical polymerization. The polymers have been prepared in 1,4-dioxane solvent and characterized by {sup 1}H NMR. The kinetic of polymerization was studied by {sup 1}H NMR spectroscopy. The LCST was determined by measures of transmittance versus temperature by UV-vis spectroscopy. (author)

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

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


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


    NARCIS (Netherlands)



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

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

    DEFF Research Database (Denmark)

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


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

  4. The secondary structure of the toxin ATX Ia from Anemonia sulcata in aqueous solution determined on the basis of complete sequence-specific 1H-NMR assignments. (United States)

    Widmer, H; Wagner, G; Schweitz, H; Lazdunski, M; Wüthrich, K


    The toxin preparations ATX I, ATX Ia and ATX Ib from Anemonia sulcata were investigated by proton nuclear magnetic resonance (NMR). High-resolution phase-sensitive two-dimensional NMR experiments were used to monitor the separation by high-performance liquid chromatography of the two isoproteins ATX Ia and ATX Ib. For ATX Ia complete sequence-specific resonance assignments were obtained and the secondary structure was determined. To obtain the NMR assignments we used a variant of the sequential assignment technique which relied extensively on cross-peak fine-structure analysis in phase-sensitive spectra, using spectrum simulations based on density matrix calculations with the program SPHINX. These procedures, which resulted in extensive amino acid spin system identifications prior to the sequential assignments, should be generally applicable for small proteins with relatively narrow 1H-NMR lines. The secondary structure of ATX I includes a beta sheet consisting of four strands. No evidence was found for the presence of regular helical segments. The four beta strands are connected by two extended loops and a tight turn, for which further characterization has to await the complete determination of the three-dimensional structure.

  5. Influence of water-insoluble nonionic copolymer E(6)P(39)E(6) on the microstructure and self-aggregation dynamics of aqueous SDS solution-NMR and SANS investigations. (United States)

    Prameela, G K S; Phani Kumar, B V N; Aswal, V K; Mandal, Asit Baran


    The influence of water-insoluble nonionic triblock copolymer PEO-PPO-PEO [poly(ethylene oxide)-poly(propylene oxide)-poly(ethylene oxide)] i.e., E6P39E6 with molecular weight 2800, on the microstructure and self-aggregation dynamics of anionic surfactant sodium dodecylsulfate (SDS) in aqueous solution (D2O) were investigated using high resolution nuclear magnetic resonance (NMR) and small-angle neutron scattering (SANS) measurements. Variable concentration and temperature proton ((1)H), carbon ((13)C) NMR chemical shifts, (1)H self-diffusion coefficients, (1)H spin-lattice and spin-spin relaxation rates data indicate that the higher hydrophobic nature of copolymer significantly influenced aggregation characteristics of SDS. The salient features of the NMR investigations include (i) the onset of mixed micelles at lower SDS concentrations (SDS free micelles at higher SDS concentrations (~30 mM), (ii) disintegration of copolymer-SDS mixed aggregate at moderate SDS concentrations (~10 mM) and still binding of a copolymer with SDS and (iii) preferential localization of the copolymer occurred at the SDS micelle surface. SANS investigations indicate prolate ellipsoidal shaped mixed aggregates with an increase in SDS aggregation number, while a contrasting behavior in the copolymer aggregation is observed. The aggregation features of SDS and the copolymer, the sizes of mixed aggregates and the degree of counterion dissociation (α) extracted from SANS data analysis corroborate reasonably well with those of (1)H NMR self-diffusion and sodium ((23)Na) spin-lattice relaxation data.

  6. An unambiguous structural elucidation of a 1,3-beta-D-glucan obtained from liquid-cultured Grifola frondosa by solution NMR experiments. (United States)

    Tada, Rui; Adachi, Yoshiyuki; Ishibashi, Ken-ichi; Ohno, Naohito


    Grifolan LE (GRN-LE), a purified beta-D-glucan, which is obtained from liquid-cultured Grifola frondosa, exhibits various biological activities, including antitumor effects. Significant progress has been made in the study of these effects. However, an unambiguous structural characterization of GRN-LE using NMR spectroscopy has not been carried out as yet. It is well accepted that the biological effects of a beta-glucan depend on its primary structure, conformation, and molecular weight. In the present study, we unambiguously elucidate the primary structure of GRN-LE using NMR spectroscopy. The data presented here reveal that GRN-LE comprises a 1,3-beta-D-glucan backbone with a single 1,6-beta-D-glucosyl side branching unit on every third residue.

  7. Determination of the three-dimensional solution structure of the histidine-containing phosphocarrier protein HPr from Escherichia coli using multidimensional NMR spectroscopy

    NARCIS (Netherlands)

    Nuland, Nico A.J. van; Grötzinger, Joachim; Dijkstra, Klaas; Scheek, Ruud M.; Robillard, George T.


    We recorded several types of heteronuclear three-dimensional (3D) NMR spectra on 15N-enriched and 13C/15N-enriched histidine-containing phosphocarrier protein, HPr, to extend the backbone assignments to the side-chain 1H, 15N and 13C resonances. From both 3D heteronuclear 1H-NOE 1H-13C and 1H-NOE

  8. NMR Studies of Peroxidases. (United States)

    Veitch, Nigel Charles

    Available from UMI in association with The British Library. Requires signed TDF. Peroxidases are a haem-containing group of enzymes with a wide diversity of function within biological systems. While a common characteristic is the ability to catalyse the conversion of hydrogen peroxide to water, it is the accompanying processes of hormone synthesis and degradation which have generated such a high level of interest. However, information at the molecular level is limited to a single well-resolved crystal structure, that of yeast cytochrome c peroxidase. This thesis presents a strategy for the investigation of peroxidase structure and function based on proton nuclear magnetic resonance spectroscopy, a technique which has the ability to address aspects of both protein structure and protein dynamics in solution. The application of one- and two-dimensional NMR techniques has been developed in the context of plant peroxidases, notably the isoenzyme HRP-C derived from the horseradish root. Characterisation of the proton NMR spectra of HRP -C in resting and ligated states provided new information enabling the structure of the binding site for aromatic donor molecules, such as indole-3-propionic, ferulic and benzhydroxamic acids, to be resolved. In order to overcome difficulties encountered with a protein of the complexity of peroxidase, additional information was obtained from chemical shift parameters and the use of peroxidase variants produced by site-directed mutagenesis. A comparative study using NMR spectroscopy was undertaken for wild-type recombinant HRP-C expressed in Escherichia coli, and two protein variants with substitutions made to residues located on the distal side of the haem pocket, Phe41 to Val and Arg38 to Lys. NMR analyses of a plant peroxidase from barley grains and the fungal peroxidase from Coprinus cinereus were also successful using methods conceived with HRP-C. Examination of three specifically constructed recombinant protein variants of C. cinereus

  9. Development of Two-Dimensional NMR

    Indian Academy of Sciences (India)

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

  10. Cobalt segregation in the LiNi 1-yCo yO 2 solid solution: A preliminary 7Li NMR study (United States)

    Menetrier, M.; Rougier, A.; Delmas, C.


    LiNi 1-yCo yO 2 materials exhibit a layered structure built from alternate sheets of (Ni,Co)O 6 and of LiO 6 octahedra sharing edges. They are particularly interesting as positive electrode in rechargeable lithium batteries. Single-pulse 7Li NMR spectra allow to distinguish between the Li + ions with only cobalt as their first 3d neighbors and those with at least one Ni 3+ (LS t 26e 1). The small amount of excess Ni 2+ ions (t 26e 2) known to be present in the materials with small y causes an alteration of the spectra. Li + ions with only cobalt as their first cationic neighbors are detected even for small cobalt contents, which shows the existence of a cobalt segregation while X-rays show that no phase separation occurs.

  11. Applications de la résonance magnétique nucléaire (RMN en milieux poreux Dispositif de diagraphie à RMN de résolution centimétrique Nuclear Magnetic Resonance (Nmr Applications in Porous Media an Nmr Logging Apparatus with Centimeter Resolution

    Directory of Open Access Journals (Sweden)

    Locatelli M.


    Full Text Available Après un bref rappel sur le concept des mesures de RMN, nous décrivons un dispositif de mesure de la porosité en puits présentant une résolution verticale centimétrique. Des tests effectués avec un dispositif de laboratoire en confirment les potentialités, en particulier au niveau de la vitesse de déplacement qui peut atteindre 1800 pieds/heure. After a brief review of the concept of NMR measurements, we describe an apparatus, with resolution on a scale of centimeters, for measuring well porosity. Laboratory tests confirm the potential of this apparatus, especially its speed, which can attain 1800 feet/hour.

  12. Structures and dynamics of lanthanide(III) complexes of sugar-based DTPA-bis(amides) in aqueous solution: A multinuclear NMR study

    Energy Technology Data Exchange (ETDEWEB)

    Lammers, H.; Laren, W. van; Bekkum, H. van [Delft Univ. of Technology (Netherlands)] [and others


    The structure and dynamics of the lanthanide(III) complexes of DTPA-BGLUCA{sup 3-} (DTPA-bis(glucamide)), DTPA-BENGALAA{sup 3-} (DTPA-bis(ethylenegalactamine-amide)), DTPA-BEA{sup 3-} (DTPA-bis(ethanolamide)), and DTPA-BPDA{sup 3-} (DTPA-bis(propanediolamide)) in water have been investigated. These complexes are of relevance as potential MRI contrast agents. {sup 13}C relaxation times of the Nd(III) complexes show octadentate binding of the organic ligand via the three amines, the three carboxylates, and the two amide oxygens. {sup 17}O NMR measurements indicate that the coordination sphere is completed by one water ligand. Eight diastereomeric pairs of isomers are observed for the DTPA-bis(sugaramides). Data sets obtained from variable-temperature and -pressure {sup 17}O NMR at 9.4T and variable-temperature {sup 1}H nuclear magnetic relaxation dispersion (NMRD) on the Gd(III) complexes were fitted simultaneously to give insight into the parameters governing the water {sup 1}H relaxivity. The water exchange rates, k{sub ex}{sup 298}, on [Gd(DTPA-BPDA)(H{sub 2}O)], [Gd(DTPA-BGLUCA)(H{sub 2}O)] and [Gd(DTPA-BENGALAA)-(H{sub 2}O)] are 3.6 {+-} 0.3, 3.8 {+-} 0.2, and 2.2 {+-} 0.1 x 10{sup 5} s{sup -1}, and the activation volumes are +6.7, +6.8, and +5.6 cm{sup 3} mol{sup -1} ({+-}0.2 cm{sup 3} mol{sup -1}), respectively, indicating a strongly dissociatively activated mechanism. The sugar moieties have no significant influence on the coordination of the Gd(III) ion and on the parameters governing the relaxivity, apart from the expected increase in the rotational correlation time. The relaxivity under the usual MRI conditions is limited by the water exchange rate and the electronic relaxation. The data obtained are used to explain the relaxivity of conjugates of polysaccharides and Gd(DTPA). 71 refs., 6 figs., 7 tabs.

  13. Secondary structure in solution of two anti-HIV-1 hammerhead ribozymes as investigated by two-dimensional 1H 500 MHz NMR spectroscopy in water (United States)

    Sarma, R. H.; Sarma, M. H.; Rein, R.; Shibata, M.; Setlik, R. S.; Ornstein, R. L.; Kazim, A. L.; Cairo, A.; Tomasi, T. B.


    Two hammerhead chimeric RNA/DNA ribozymes (HRz) were synthesized in pure form. Both were 30 nucleotides long, and the sequences were such that they could be targeted to cleave the HIV-1 gag RNA. Named HRz-W and HRz-M, the former had its invariable core region conserved, the latter had a uridine in the invariable region replaced by a guanine. Their secodary structures were determined by 2D NOESY 1H 500 MHz NMR spectroscopy in 90% water and 10% D2(0), following the imino protons. The data show that both HRz-M and HRz-W form identical secondary structures with stem regions consisting of continuous stacks of AT and GT pairs. An energy minimized computer model of this stem region is provided. The results suggest that the loss of catalytic activity that is known to result when an invariant core residue is replaced is not related to the secondary structure of the ribozymes in the absence of substrate.

  14. Interaction between reduced glutathione and PEO-PPO-PEO copolymers in aqueous solutions: studied by 1H NMR and spin-lattice relaxation. (United States)

    Jia, Lianwei; Guo, Chen; Yang, Liangrong; Xiang, Junfeng; Tang, Yalin; Liu, Huizhou


    In order to investigate the effect of PEO-PPO-PEO copolymers on the glutathione (GSH)/glutathione-S-transferase (GST) detoxification system, interaction between the copolymers and GSH is studied by NMR measurements. Selective rotating-frame nuclear Overhauser effect (ROE) experiment confirms that glutamyl (Glu) α-H of GSH has spatial contact with EO methylene protons. Spin-lattice relaxation times of GSH Glu α-H show a decrease when PEO-PPO-PEO copolymers are added, and the decrease is greater with copolymers possessing more EO units. Other protons of GSH show little change in the presence of the copolymers. The addition of GSH promotes the dehydration of PEO-PPO-PEO copolymers. This results from the breaking of hydrogen bonds between water and the polymers and the forming of hydrogen bonds between Glu α-carboxylate protons and oxygen atoms of EO units. The dissociation constant between GSH and P85 copolymer is determined by spin-lattice relaxation measurements, which shows the binding is of low affinity and the two molecules are in fast dissociation kinetics. This study suggests that GSH transporting or utilizing systems may be affected by treatment of PEO-PPO-PEO copolymers. © 2011 American Chemical Society

  15. An economical method for production of (2H, (13CH3-threonine for solution NMR studies of large protein complexes: application to the 670 kDa proteasome.

    Directory of Open Access Journals (Sweden)

    Algirdas Velyvis

    Full Text Available NMR studies of very high molecular weight protein complexes have been greatly facilitated through the development of labeling strategies whereby (13CH(3 methyl groups are introduced into highly deuterated proteins. Robust and cost-effective labeling methods are well established for all methyl containing amino acids with the exception of Thr. Here we describe an inexpensive biosynthetic strategy for the production of L-[α-(2H; β-(2H;γ-(13C]-Thr that can then be directly added during protein expression to produce highly deuterated proteins with Thr methyl group probes of structure and dynamics. These reporters are particularly valuable, because unlike other methyl containing amino acids, Thr residues are localized predominantly to the surfaces of proteins, have unique hydrogen bonding capabilities, have a higher propensity to be found at protein nucleic acid interfaces and can play important roles in signaling pathways through phosphorylation. The utility of the labeling methodology is demonstrated with an application to the 670 kDa proteasome core particle, where high quality Thr (13C,(1H correlation spectra are obtained that could not be generated from samples prepared with commercially available U-[(13C,(1H]-Thr.

  16. On the molecular basis of the recognition of angiotensin II (AII). NMR structure of AII in solution compared with the X-ray structure of AII bound to the mAb Fab131. (United States)

    Tzakos, Andreas G; Bonvin, Alexandre M J J; Troganis, Anasstasios; Cordopatis, Paul; Amzel, Mario L; Gerothanassis, Ioannis P; van Nuland, Nico A J


    The high-resolution 3D structure of the octapeptide hormone angiotensin II (AII) in aqueous solution has been obtained by simulated annealing calculations, using high-resolution NMR-derived restraints. After final refinement in explicit water, a family of 13 structures was obtained with a backbone RMSD of 0.73 +/- 0.23 A. AII adopts a fairly compact folded structure, with its C-terminus and N-terminus approaching to within approximately 7.2 A of each other. The side chains of Arg2, Tyr4, Ile5 and His6 are oriented on one side of a plane defined by the peptide backbone, and the Val3 and Pro7 are pointing in opposite directions. The stabilization of the folded conformation can be explained by the stacking of the Val3 side chain with the Pro7 ring and by a hydrophobic cluster formed by the Tyr4, Ile5 and His6 side chains. Comparison between the NMR-derived structure of AII in aqueous solution and the refined crystal structure of the complex of AII with a high-affinity mAb (Fab131) [Garcia, K.C., Ronco, P.M., Verroust, P.J., Brunger, A.T., Amzel, L.M. (1992) Science257, 502-507] provides important quantitative information on two common structural features: (a) a U-shaped structure of the Tyr4-Ile5-His6-Pro7 sequence, which is the most immunogenic epitope of the peptide, with the Asp1 side chain oriented towards the interior of the turn approaching the C-terminus; (b) an Asx-turn-like motif with the side chain aspartate carboxyl group hydrogen-bonded to the main chain NH group of Arg2. It can be concluded that small rearrangements of the epitope 4-7 in the solution structure of AII are required by a mean value of 0.76 +/- 0.03 A for structure alignment and approximately 1.27 +/- 0.02 A for sequence alignment with the X-ray structure of AII bound to the mAb Fab131. These data are interpreted in terms of a biological "nucleus" conformation of the hormone in solution, which requires a limited number of structural rearrangements for receptor-antigen recognition and binding.

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

    NARCIS (Netherlands)

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


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

  18. The NMR side-chain assignments and solution structure of enzyme IIBcellobiose of the phosphoenolpyruvate-dependent phosphotransferase system of Escherichia coli

    NARCIS (Netherlands)

    AB, Eiso; Schuurman-Wolters, Gea; Reizer, Jonathan; Saier, Milton H.; Dijkstra, Klaas; Scheek, Ruud M.; Robillard, George T.

    The assignment of the side-chain Nh IR resonances and the determination of the three-dimensional solution structure of the C10S mutant of enzyme IIBcellobiose (IIBcel) of the phosphoenolpyruvate-dependent phosphotransferase system of Escherichia coli are presented. The side-chain resonances were

  19. NMR of lignins (United States)

    John Ralph; Larry L. Landucci


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


    Directory of Open Access Journals (Sweden)

    Maria de Hoyos Guajardo, Ph.D. Candidate, M.Sc., B.Eng.


    Full Text Available The theory that is presented below aims to conceptualise how a group of undergraduate students tackle non-routine mathematical problems during a problem-solving course. The aim of the course is to allow students to experience mathematics as a creative process and to reflect on their own experience. During the course, students are required to produce a written ‘rubric’ of their work, i.e., to document their thoughts as they occur as well as their emotionsduring the process. These ‘rubrics’ were used as the main source of data.Students’ problem-solving processes can be explained as a three-stage process that has been called ‘solutioning’. This process is presented in the six sections below. The first three refer to a common area of concern that can be called‘generating knowledge’. In this way, generating knowledge also includes issues related to ‘key ideas’ and ‘gaining understanding’. The third and the fourth sections refer to ‘generating’ and ‘validating a solution’, respectively. Finally, once solutions are generated and validated, students usually try to improve them further before presenting them as final results. Thus, the last section deals with‘improving a solution’. Although not all students go through all of the stages, it may be said that ‘solutioning’ considers students’ main concerns as they tackle non-routine mathematical problems.

  1. 77Se NMR chemical shifts of 9-(arylselanyl)triptycenes: new standard for planar structures of ArSeR and applications to determine the structures in solutions. (United States)

    Nakamoto, Takashi; Hayashi, Satoko; Nakanishi, Waro


    A set of new delta(Se) parameters is proposed as a standard for the planar (pl) orientational effect of p-YC(6)H(4) (Ar) in ArSeR, employing 9-(arylselanyl)triptycenes (1: p-YC(6)H(4)SeTpc). The Se-C(R) bond in ArSeR is placed on the Ar plane in pl and it is perpendicular to the plane in pd. Large upfield shifts are observed for Y = NMe(2), OMe, and Me (-22 to -6 ppm) and large downfield shifts for Y = COOEt, CN, and NO(2) (19-37 ppm), relative to Y = H, with small upfield and moderate downfield shifts by Y of halogens (-1 ppm for Y = F and 4 ppm for Y = Cl and Br). This must be the result of the p(Se)-pi(C(6)H(4))-p(Y) conjugation in 1 (pl). While the character of delta(Se) in 1 (pl) is very similar to that in 9-(arylselanyl)anthracenes (2 (pl)), it is very different from that of 1-(arylselanyl)anthraquinones (3 (pd)). Sets of delta(Se) of 1 and 2 must serve as the standard for pl and that of 3 does for pd in solutions. Structures of various ArSeR in solutions are determined from the viewpoint of the orientational effect based on the standard delta(Se) of 1-3. While the structure of 2-methyl-1-(arylselanyl)naphthalenes is concluded to be all pl in solutions, those of 8-chloro- and 8-bromo-1-(arylselanyl)naphthalenes are all pd, except for Y = COOEt, CN, and NO(2): The equilibrium between pd and pl contributes to those with Y = COOEt, CN, and NO(2). The structure of 1-(arylselanyl)naphthalenes changes depending on Y. The structures of ArSeMe and ArSeCOPh are shown to be pl and pd, respectively, in solutions. Those of ArSePh and ArSeAr seem to change depending on Y. delta(Se) of 1-3 are demonstrated to serve as the standard to determine the structures in solutions. The rules of thumb derived from the characters in delta(Se) for 1-3 are very useful to determine the structures of ArSeR in solutions, in addition to the analysis based on the plots.

  2. Frontiers of NMR in Molecular Biology

    Energy Technology Data Exchange (ETDEWEB)



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

  3. Characterization of cylinder liners produced with hypereutectic Al-Si alloys and investigation of corrosion behaviour in synthetic automotive condensed solution; Caracterizacao de camisas de cilindro em ligas Al-Si hipereuteticas e investigacao do comportamento de corrosao em meio de condensado sintetico automotivo

    Energy Technology Data Exchange (ETDEWEB)

    Santos, Hamilta de Oliveira


    In the present study four hypereutectic Al-Si alloys, three produced by spray forming and one by casting, were characterized for microhardness, roughness, microstructure, texture and corrosion resistance in a synthetic automotive condensed solution (SACS). Two of the spray formed alloys tested were obtained from cylinder liners and the other was laboratory made. Spray forming involves alloy atomization and droplets deposition on a substrate, previous to the solidification of all of the droplets. This process favours the production of materials with a fine microstructure free of macrosegregation that is related to improved hot workability. The microstructure characterization of the four alloys revealed the presence of porosities in the laboratory made alloy. All the three alloys produced by spray forming showed a homogeneous distribution of primary precipitates. The microstructure of one of the alloys showed eutectic microstructure, indicating that this alloy was fabricated by casting. In the cylinder liners, the surface roughness was measured and the microhardness of all the alloys was also evaluated. Furthermore, the laboratory made alloy was hot and cold rolled. Texture determinations were carried out to investigate the correlation between the alloy type and their fabrication process. The texture investigation indicated that the fine distribution of primary silicon phase in the alloy hindered the development of texture typical of aluminium alloys deformation, even after severe mechanical work, such as those used in the conversion of pre-formed in cylinder liners. The surface roughness results indicated typical characteristics of the surface finishing used, honing or chemical etching. The microhardness results were dependent on the fabrication process used, with higher microhardness associated to the eutectic alloy comparatively to the spray formed ones. All hypereutectic alloys were tested for corrosion resistance using electrochemical impedance spectroscopy in

  4. (S)Pinning down protein interactions by NMR

    DEFF Research Database (Denmark)

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


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

  5. Comparison of mono- and di-saccharides release in aqueous solutions by raw or fried dice of onion (Allium Cepa L.) bulbs using quantitative nuclear magnetic resonance (qNMR). (United States)

    Tardieu, Audrey; Guerez, Alice; Phana, Sidarin; de Man, Walter; This, Hervé


    Although onion bulb tissues, either raw or thermally processed, are widely used as culinary ingredients in homes, in restaurants, and in the food industry, especially for sauces, little is known about the chemical constituents released from such systems. To get a straightforward and fast analysis of sugars released from onion dice soaked in model aqueous solutions, quantitative nuclear magnetic resonance (qNMR) spectroscopy was applied, and the effect of a preliminary thermal processing in oil was investigated. Soaking of raw or fried onion bulb dice at room temperature was followed for 11 d as a model of long-term storage. For the Armstrong cultivar, the extracted dry matter (in milligrams per gram of fresh weight) as well as the content in 3 sugars (glucose, fructose, and sucrose) increased up to a maximum after about 48 h of soaking. Frying induces no measurable new water-soluble compounds. However, extraction kinetics are different (about 3 times faster with frying). Using additional microscopic studies, a possible extraction mechanism is proposed: compounds from sap-including sugars-would diffuse through conductive tissue channels.

  6. Description of the behavior of dichloroalkanes-containing solutions with three [bXmpy][BF4] isomers, using the experimental information of thermodynamic properties, 1H NMR spectral and the COSMO-RS-methodology. (United States)

    Fernández, Luis; Ortega, Juan; Palomar, José; Toledo, Francisco; Marrero, Elena


    This work studies the binaries of 1-butyl-X-methylpyridinium tetrafluoroborate [bXmpy][BF4] (X = 2, 3, and 4) with four 1,ω-dichloroalkanes, ω = 1-4, using the results obtained for the mixing properties h(E) and v(E) at two temperatures. The three isomers of the ionic liquid (IL) are weakly miscible with the 1,ω-dichloroalkanes when ω ≥ 5 and moderately soluble for ω = 4. The v(E)s of all the binaries present contractive effects, v(E) 0. The experimental data are correlated with a suitable equation. The study is completed with (1)H NMR measurements of both the pure compounds and some of the solutions, which showed minor diamagnetic shifts with increasing IL compositions, related to the anisotropy of the pyridine ring. The variation in h(E) with ω for a same IL, due to an increase in the contact surfaces, is related to the reduction in polarity which, in turn, depends on the smaller chemical shifts of the pure dihalide compounds. The COSMO-RS method determines the energetic effects of the mixing process and predicts an exothermic contribution for the electrostatic Misfit-interaction which is quantitatively very similar for the three IL isomers. The differences proposed by the model are mainly reflected in the van der Waals interactions, which are exothermic and clearly influenced by the position of the methylene group in the IL. The contribution made by hydrogen bonds is negligible.

  7. Non-covalent interactions of 1-{sup 13}C-acenaphthenone with dissolved fulvic acid in a methanol/water solution as determined from {sup 13}C NMR T{sub 1} relaxation data

    Energy Technology Data Exchange (ETDEWEB)

    Nanny, M.A.; Bortiatynski, J.M.; Hatcher, P.G. [Pennsylvania State Univ., University Park, PA (United States)


    The solubility of hydrophobic pollutants in the environment, in addition to their biodegradation, bioavailability, abiotic fate, and transport, is strongly influenced by non-covalent interactions with dissolved natural organic matter. Employing the combination of {sup 13}C-labeling techniques and {sup 13}C-NMR spectroscopy methods, non-covalent interactions between 1-{sup 13}C-acenaphthenone ({sup 13}C-labeled in the carbonyl position) and fulvic acid in a methanol/aqueous solvent system were examined by observing changes in the T{sub 1} relaxation Lime of the labeled carbon. Three non-covalent interactions were inferred from this data: a weak sorption interaction between acenaphthenone and the fulvic acid, an interaction causing enhanced molecular motion of acenaphthenone by fulvic acid, and an interaction between just the solvent and acenaphthenone. Those interactions were determined to be a function of the concentration of both acenaphthenone and fulvic acid, the identity of the fulvic acid cation (i.e., H{sup +} or Na{sup +}), and the solution pH.

  8. NMR logging apparatus (United States)

    Walsh, David O; Turner, Peter


    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.

  9. Solution NMR spectroscopy of food polysaccharides (United States)

    Many polysaccharides are allowed for direct food use, where they serve a number of useful functions. In addition to possibly being a source of calories, a food polysaccharide may be a dietary fiber, bulking agent, crystallization inhibitor, thickener, encapsulant, gelling agent, foam and emulsion s...

  10. Evaluation of poly(methyl methacrylate)/poly(vinylpyrrolidone)/poly(ethylene oxide) blends by solution and solid state NMR; Avaliacao da mistura fisica de poli(metacrilato de metila)/polivinilpirrolidona/poli(oxido de etileno) por ressonancia magnetica nuclear em solucao e solido

    Energy Technology Data Exchange (ETDEWEB)

    Diniz, Teresinha M.F.F. [Instituto Nacional da Propriedade Industrial (INPI), Rio de Janeiro, RJ (Brazil)]. E-mail:; Tavares, Maria Ines B. [Universidade Federal, Rio de Janeiro, RJ (Brazil). Inst. de Macromoleculas]. E-mail:


    Ternary blends formed by poly(methyl methacrylate) (PMMA)/poly(vinyl pyrrolidone) (PVP)/poly(ethylene oxide) (PEO) have been investigated applying solution and solid state nuclear magnetic resonance. From solution NMR it can be seen that no change in the chemical shift of the microstructure detected in the carbonyl and C quaternary carbons of PMMA was found. However a small change in the form of those signals was observed. This change was attributed to the plasticization effect. The solid state techniques showed that both PEO and PVP acts as a plasticizer in different ways, which depends on these proportions that derives from different dynamical behavior. (author)

  11. Isotope effects in (195)Pt NMR spectroscopy: unique (35/37)Cl- and (16/18)O-resolved "fingerprints" for all [PtCl6-n(OH)n](2-) (n = 1-5) anions in an alkaline solution and the implications of the trans influence. (United States)

    Engelbrecht, Leon; Murray, Pieter; Koch, Klaus R


    A detailed analysis of the intrinsic (1)Δ(195)Pt((37/35)Cl) and (1)Δ(195)Pt((18/16)O) isotope 128.8 MHz (195)Pt NMR profiles of the series of kinetically inert [PtCl6-n(OH)n](2-) (n = 1-5) anions generated in strongly alkaline aqueous solutions shows that each (195)Pt NMR resonance of the [Pt(35/37)Cl6-n((16/18)OH)n](2-) (n = 1-5) anions is resolved only into [(6 - n) + 1 for n = 1-5] (35/37)Cl isotopologues at 293 K. Evidently, the greater trans influence of the hydroxido ligand in the order OH(-) > Cl(-) > H2O in [PtCl6-n(OH)n](2-) (n = 1-5) complexes results in somewhat longer Pt-Cl bond displacements trans to the hydroxido ligands, resulting in the absence of isotopomer effects in the [PtCl6-n(OH)n](2-) (n = 1-5) anions in contrast to that observed in the corresponding [PtCl6-n(H2O)n]((2-n)-) (n = 1-5) complexes. In suitably (18)O-enriched sodium hydroxide solutions, additional intrinsic (1)Δ(195)Pt((18/16)O) isotope effects are remarkably well-resolved into unique isotopologue- and isotopomer-based (195)Pt NMR profiles, ascribable to the higher trans influence of the OH(-) ligand. The consequent significantly shorter Pt-OH bonds in these anions emphasize (16/18)O isotopomer effects in the (195)Pt NMR peaks of [Pt(35/37)Cl6-n((16/18)OH)n](2-) (n = 1-5) for magnetically nonequivalent (16/18)OH isotopomers statistically possible in some isotopologues. These (195)Pt NMR profiles constitute unique NMR "fingerprints", useful for the unambiguous assignment of the series of [PtCl6-n(OH)n](2-) anions including their possible cis/trans/fac/mer stereoisomers in such solutions, without a need for accurate chemical shift measurements.

  12. 2D-NMR (HSQC) difference spectra between specifically 13C-enriched and unenriched protolignin of Ginkgo biloba obtained in the solution state of whole cell wall material (United States)

    Noritsugu Terashima; Takuya Akiyama; Sally Ralph; Dmitry Evtuguin; Carlos Neto Pascoal; Jim Parkas; Magnus Paulsson; Ulla Westermark; John Ralph


    In the structural analysis of lignins by 13C-NMR, signal overlap limits definitive assignment and accurate intensity measurement. Selective labeling by 13C-enrichment of a specific carbon in lignin enhances its signal intensity in the spectrum. Further enhancement of the specifically labeled carbons can be realized via...

  13. NMR, water and plants

    NARCIS (Netherlands)

    As, van H.


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

  14. Single-sided NMR

    CERN Document Server

    Casanova, Federico; Blümich, Bernhard


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

  15. NMR for chemists and biologists

    CERN Document Server

    Carbajo, Rodrigo J


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

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

    African Journals Online (AJOL)

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

  17. Magic Angle Spinning NMR Metabolomics

    Energy Technology Data Exchange (ETDEWEB)

    Zhi Hu, Jian


    Nuclear Magnetic Resonance (NMR) spectroscopy is a non-destructive, quantitative, reproducible, untargeted and unbiased method that requires no or minimal sample preparation, and is one of the leading analytical tools for metabonomics research [1-3]. The easy quantification and the no need of prior knowledge about compounds present in a sample associated with NMR are advantageous over other techniques [1,4]. 1H NMR is especially attractive because protons are present in virtually all metabolites and its NMR sensitivity is high, enabling the simultaneous identification and monitoring of a wide range of low molecular weight metabolites.

  18. Solution 1H NMR investigation of the active site molecular and electronic structures of substrate-bound, cyanide-inhibited HmuO, a bacterial heme oxygenase from Corynebacterium diphtheriae. (United States)

    Li, Yiming; Syvitski, Ray T; Chu, Grace C; Ikeda-Saito, Masao; Mar, Gerd N La


    The molecular structure and dynamic properties of the active site environment of HmuO, a heme oxygenase (HO) from the pathogenic bacterium Corynebacterium diphtheriae, have been investigated by (1)H NMR spectroscopy using the human HO (hHO) complex as a homology model. It is demonstrated that not only the spatial contacts among residues and between residues and heme, but the magnetic axes that can be related to the direction and magnitude of the steric tilt of the FeCN unit are strongly conserved in the two HO complexes. The results indicate that very similar contributions of steric blockage of several meso positions and steric tilt of the attacking ligand are operative. A distal H-bond network that involves numerous very strong H-bonds and immobilized water molecules is identified in HmuO that is analogous to that previously identified in hHO (Li, Y., Syvitski, R. T., Auclair, K., Wilks, A., Ortiz de Montellano, P. R., and La Mar, G. N. (2002) J. Biol. Chem. 277, 33018-33031). The NMR results are completely consistent with the very recent crystal structure of the HmuO.substrate complex. The H-bond network/ordered water molecules are proposed to orient the distal water molecule near the catalytically key Asp(136) (Asp(140) in hHO) that stabilizes the hydroperoxy intermediate. The dynamic stability of this H-bond network in HmuO is significantly greater than in hHO and may account for the slower catalytic rate in bacterial HO compared with mammalian HO.

  19. NMR of a Phospholipid: Modules for Advanced Laboratory Courses (United States)

    Gaede, Holly C.; Stark, Ruth E.


    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.

  20. NMR in pulsed magnetic field

    KAUST Repository

    Abou-Hamad, Edy


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

  1. NMR as a tool in the investigation of fundamental problems in ordered liquids

    NARCIS (Netherlands)

    Burnell, E.E.; de Lange, C.A.


    An overview is presented of modern NMR techniques and a variety of experimental and theoretical tools employed in the study of solutes dissolved in liquid crystals. The NMR techniques involve multiple quantum and spectral subtraction methods. In addition, various experimental and theoretical tools

  2. NMR studies of dynamic biomolecular conformational ensembles. (United States)

    Torchia, Dennis A


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

  3. Principles of high resolution NMR in solids

    CERN Document Server

    Mehring, Michael


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

  4. Fundamentals of Protein NMR Spectroscopy

    CERN Document Server

    Rule, Gordon S


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

  5. Applications of unilateral NMR in nondestructive testing


    Sharma, Shatrughan


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

  6. Novel recombinant insulin analogue with flexible C-terminus in B chain. NMR structure of biosynthetic engineered A22G-B31K-B32R human insulin monomer in water/acetonitrile solution. (United States)

    Borowicz, Piotr; Bocian, Wojciech; Sitkowski, Jerzy; Bednarek, Elżbieta; Mikiewicz-Syguła, Diana; Błażej-Sosnowska, Sylwia; Bogiel, Monika; Rusek, Dorota; Kurzynoga, Dariusz; Kozerski, Lech


    A tertiary structure of recombinant A22(G)-B31(K)-B32(R)-human insulin monomer (insulin GKR) has been characterized by (1)H, (13)C NMR at natural isotopic abundance using NOESY, TOCSY, (1)H/(13)C-GHSQC, and (1)H/(13)C-GHSQC-TOCSY spectra. Translational diffusion studies indicate the monomer structure in water/acetonitrile (65/35vol.%). CSI analysis confirms existence of secondary structure motifs present in human insulin standard (HIS). Both techniques allow to establish that in this solvent recombinant insulin GKR exists as a monomer. Starting from structures calculated by the program CYANA, two different refinement protocols used molecular dynamics simulated annealing with the program AMBER; in vacuum (AMBER_VC), and including a generalized Born solvent model (AMBER_GB). From these calculations an ensemble of 20 structures of lowest energy was chosen which represents the tertiary structure of studied insulin. Here we present novel insulin with added A22(G) amino acid which interacts with β-turn environment resulting in high flexibility of B chain C-terminus. Copyright © 2011 Elsevier B.V. All rights reserved.

  7. NMR-based screening of membrane protein ligands

    NARCIS (Netherlands)

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


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

  8. NMR structural studies of protein-small molecule interactions

    NARCIS (Netherlands)

    Shah, Dipen M.


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

  9. NMR Probe for Electrons in Semiconductor Mesoscopic Structures

    Indian Academy of Sciences (India)


    Nov 14, 2009 ... Strongly correlated electron systems: Overview. Problem: How to detect the electronic state in nanoscale structures. Two examples where the usual methods don't work. Solution: We showed NMR techniques can be very useful in such circumstances. Outline ...

  10. NMR Studies of Polymer Nanocomposites

    National Research Council Canada - National Science Library

    Greenbaum, Steve


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

  11. β-NMR sample optimization

    CERN Document Server

    Zakoucka, Eva


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

  12. MVAPACK: a complete data handling package for NMR metabolomics. (United States)

    Worley, Bradley; Powers, Robert


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

  13. Development of Two-Dimensional NMR

    Indian Academy of Sciences (India)

    IAS Admin

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

  14. Optical pumping and xenon NMR

    Energy Technology Data Exchange (ETDEWEB)

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


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

  15. Optical pumping and xenon NMR

    Energy Technology Data Exchange (ETDEWEB)

    Raftery, M.D.


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

  16. NMR Diffusion Measurements as a Simple Method to Examine Solvent-Solvent and Solvent-Solute Interactions in Mixtures of the Ionic Liquid [Bmim][N(SO2 CF3 )2 ] and Acetonitrile. (United States)

    Keaveney, Sinead T; Schaffarczyk McHale, Karin S; Stranger, James W; Ganbold, Batchimeg; Price, William S; Harper, Jason B


    The self-diffusion coefficients of each component in mixtures of 1-butyl-3-methylimidazolium bis(trifluoromethanesulfonyl)imide ([Bmim][N(SO2 CF3 )2 ]) and acetonitrile were determined. The results suggest that the hydrodynamic boundary conditions change from "stick" to "slip" as the solvent composition transitions from "ionic liquid dissolved in acetonitrile" (χIL acetonitrile dissolved in ionic liquid" (χIL >0.4). At higher χIL , the acetonitrile species are affected by "cage" and "jump" events, as the acetonitrile molecules reside nearer to the charged centre on the ions than in the "non-polar" regions. The self-diffusion coefficients of hexan-1-amine, dipropylamine, 1-hexanol and dipropylether in mixtures of [Bmim][N(SO2 CF3 )2 ] and acetonitrile were determined. In general, the nitrogen-containing solutes were found to diffuse slower than the oxygen-containing solutes; this indicates that there are greater ionic liquid-N interactions than ionic liquid-O interactions. This work demonstrates that the self-diffusion coefficients of species can provide valuable information about solvent-solvent and solvent-solute interactions in mixtures containing an ionic liquid. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  17. RNA structure determination by solid-state NMR spectroscopy. (United States)

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


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

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

    Directory of Open Access Journals (Sweden)

    SUN Li-juan


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

  19. Effective rotational correlation times of proteins from NMR relaxation interference (United States)

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


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

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

    Energy Technology Data Exchange (ETDEWEB)

    Matwiyoff, N.A.


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

  1. NMR in natural products: understanding conformation, configuration and receptor interactions. (United States)

    Carlomagno, Teresa


    Covering: up to 2011. Natural products are of tremendous importance in both traditional and modern medicine. For medicinal chemistry natural products represent a challenge, as their chemical synthesis and modification are complex processes, which require many, often stereo-selective, synthetic steps. A prerequisite for the design of analogs of natural products, with more accessible synthetic routes, is the availability of their bioactive conformation. Nuclear Magnetic Resonance (NMR) spectroscopy and X-ray crystallography are the two techniques of choice to investigate the structure of natural products. In this review, I describe the most recent advances in NMR to study the conformation of natural products either free in solution or bound to their cellular receptors. In chapter 2, I focus on the use of residual dipolar couplings (RDC). On the basis of a few examples, I discuss the benefit of complementing classical NMR parameters, such as NOEs and scalar couplings, with dipolar couplings to simultaneously determine both the conformation and the relative configuration of natural products in solution. Chapter 3 is dedicated to the study of the structure of natural products in complex with their cellular receptors and is further divided in two sections. In the first section, I describe two solution-state NMR methodologies to investigate the binding mode of low-affinity ligands to macromolecular receptors. The first approach, INPHARMA (Interligand Noes for PHArmacophore Mapping), is based on the observation of interligand NOEs between two small molecules binding competitively to a common receptor. INPHARMA reveals the relative binding mode of the two ligands, thus allowing ligand superimposition. The second approach is based on paramagnetic relaxation enhancement (PRE) of ligand resonances in the presence of a receptor containing a paramagnetic center. In the second section, I focus on solid-state NMR spectroscopy as a tool to access the bioactive conformation of

  2. Flow NMR of complex systems

    Energy Technology Data Exchange (ETDEWEB)

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


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

  3. Determination of the solution-bound conformation of an amino acid binding protein by NMR paramagnetic relaxation enhancement: use of a single flexible paramagnetic probe with improved estimation of its sampling space. (United States)

    Bermejo, Guillermo A; Strub, Marie-Paule; Ho, Chien; Tjandra, Nico


    We demonstrate the feasibility of elucidating the bound ("closed") conformation of a periplasmic binding protein, the glutamine-binding protein (GlnBP), in solution, using paramagnetic relaxation enhancements (PREs) arising from a single paramagnetic group. GlnBP consists of two globular domains connected by a hinge. Using the ligand-free ("open") conformation as a starting point, conjoined rigid-body/torsion-angle simulated annealing calculations were performed using backbone (1)H(N)-PREs as a major source of distance information. Paramagnetic probe flexibility was accounted for via a multiple-conformer representation. A conventional approach where the entire PRE data set is enforced at once during simulated annealing yielded poor results due to inappropriate conformational sampling of the probe. On the other hand, significant improvements in coordinate accuracy were obtained by estimating the probe sampling space prior to structure calculation. Such sampling is achieved by refining the ensemble of probe conformers with intradomain PREs only, keeping the protein backbone fixed in the open form. Subsequently, while constraining the probe to the previously found conformations, the domains are allowed to move relative to each other under the influence of the non-intradomain PREs, giving the hinge region torsional degrees of freedom. Thus, by partitioning the protocol into "probe sampling" and "backbone sampling" stages, structures significantly closer to the X-ray structure of ligand-bound GlnBP were obtained.

  4. Multiple-quantum NMR in solids

    Energy Technology Data Exchange (ETDEWEB)

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


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

  5. NMR and dynamics of biopolymers

    Energy Technology Data Exchange (ETDEWEB)

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


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

  6. Characterization of the grafting copolymer EPDM-SAN; Caracterizacao do copolimero de enxertia EPDM-SAN

    Energy Technology Data Exchange (ETDEWEB)

    Turchette, Renato; Felisberti, Maria Isabel [Universidade Estadual de Campinas, SP (Brazil). Inst. de Quimica]. E-mail:


    This work aims the characterization of the grafting copolymer EPDM-SAN. This copolymer presents a fraction of free SAN chains, which was extracted by solubilization in chloroform followed of precipitation of the grafting copolymer EPDM-g-SAN in acetone. The EPDM-SAN and EPDM-g-SAN were characterized by {sup 13}C NMR, DSC, TGA and SEM. EPDM-SAN contain 23 wt% of free SAN and 77 wt% of EPDM-g-SAN. Both materials are heterogeneous and the thermal and thermo-oxidative degradation are independent of the composition. (author)

  7. NMR Studies of Protein Structure and Dynamics (United States)

    Li, Xiang

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

  8. Push-through Direction Injectin NMR Automation (United States)

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

  9. Structure and Dynamic Properties of Membrane Proteins using NMR

    DEFF Research Database (Denmark)

    Rösner, Heike; Kragelund, Birthe


    conformational changes. Their structural and functional decoding is challenging and has imposed demanding experimental development. Solution nuclear magnetic resonance (NMR) spectroscopy is one of the techniques providing the capacity to make a significant difference in the deciphering of the membrane protein...... structure-function paradigm. The method has evolved dramatically during the last decade resulting in a plethora of new experiments leading to a significant increase in the scientific repertoire for studying membrane proteins. Besides solving the three-dimensional structures using state-of-the-art approaches......-populated states, this review seeks to introduce the vast possibilities solution NMR can offer to the study of membrane protein structure-function analyses with special focus on applicability. © 2012 American Physiological Society. Compr Physiol 2:1491-1539, 2012....

  10. Biomolecular NMR: Past and future. (United States)

    Markley, John L; Westler, William Milo


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

  11. Deuterium Exchange Kinetics by NMR. (United States)

    Roper, G. C.


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

  12. High resolution NMR theory and chemical applications

    CERN Document Server

    Becker, Edwin D


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

  13. Time domain NMR applied to food products

    NARCIS (Netherlands)

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


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

  14. (17)O NMR and Raman Spectroscopies of Green Tea Infusion with Nanomaterial to Investigate Their Properties. (United States)

    Zhou, Changyan; Zhang, Huiping; Yan, Ying; Zhang, Xinya


    (17)O NMR and Raman spectrograms of green tea infusions with nanomaterial were investigated. Different green tea infusions were prepared by steeping tea powder with different concentrations of nanomaterial aqueous solution. The tea infusions were tested with (17)O NMR and Raman spectroscopies. The (17)O NMR results showed that line width increased to 90 in the tea infusions after nanomaterial was added as a result of the effects of the self-association of Ca(2+) and tea polyphenol. The results of Raman spectroscopy showed that, in tea infusions, the enhancement of C─C and C─O stretching vibrations suggest an increase in the number of effective components in water.

  15. Variable-temperature ¹H-NMR studies on two C-glycosylflavones. (United States)

    Frank, Julia H; Powder-George, Yomica L; Ramsewak, Russel S; Reynolds, William F


    Two known C-glycosylflavones, swertisin and embinoidin, were isolated from the leaves of Anthurium aripoense, and characterized by room temperature 1D and 2D NMR experiments. At this temperature, the ¹H- and ¹³C-NMR spectra of these C-glycosylflavones revealed doubling of signals, which suggested the presence of two rotamers in solution. Variable-temperature (VT) ¹H-NMR studies supported this hypothesis. The T-ROESY data, in addition to the theoretical (MM2) calculations utilizing the Chem3D Pro software, confirmed the hypothesis that the two rotamers interchange via rotation about the C-glycosidic bond.

  16. Authenticity study of Phyllanthus species by NMR and FT-IR techniques coupled with chemometric methods

    Energy Technology Data Exchange (ETDEWEB)

    Santos, Maiara S.; Pereira-Filho, Edenir R.; Ferreira, Antonio G. [Universidade Federal de Sao Carlos (UFSCAR), SP (Brazil). Dept. de Quimica; Boffo, Elisangela F. [Universidade Federal da Bahia (UFBA), Salvador, BA (Brazil). Inst. de Quimica; Figueira, Glyn M., E-mail: [Universidade Estadual de Campinas (UNICAMP), Campinas, SP (Brazil). Centro Pluridisciplinar de Pesquisas Quimicas, Biologicas e Agricolas


    The importance of medicinal plants and their use in industrial applications is increasing worldwide, especially in Brazil. Phyllanthus species, popularly known as 'quebra-pedras' in Brazil, are used in folk medicine for treating urinary infections and renal calculus. This paper reports an authenticity study, based on herbal drugs from Phyllanthus species, involving commercial and authentic samples using spectroscopic techniques: FT-IR, {sup 1}H HR-MAS NMR and {sup 1}H NMR in solution, combined with chemometric analysis. The spectroscopic techniques evaluated, coupled with chemometric methods, have great potential in the investigation of complex matrices. Furthermore, several metabolites were identified by the NMR techniques. (author)

  17. Characterization of Chemical Weapons Convention Schedule 3 Compounds by Quantitative 13C NMR Spectroscopy (United States)


    Smith, E.G. Quantitative Silicon-29 NMR Investigations of Highly Concentrated High-Ratio Sodium Silicate Solutions. Magn. Reson. Chem. 1993, 31, 743-747...Michon, L.; Siri, 0.; Hanquet, B.; Martin, D. Qualitative and Quantitative Functional Determination in Bitumen Acidic Fractions by 29Si NME...Spectroscopy. Correlations with Bitumen Aging. Energy Fuels 1996, 10, 1142-1146. 18. Kerven, G.L.; Larsen, P.L.; Bell, L.C.; Edwards, D.G. Quantitative 27Al NMR

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

    African Journals Online (AJOL)

    Preferred Customer

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

  19. Synthesis and characterization of new ionic liquids; Sintese e caracterizacao de novos liquidos ionicos

    Energy Technology Data Exchange (ETDEWEB)

    Oliveira, L.M.C. de; Mattedi, S.; Boaventura, J.S., E-mail: [Universidade Federal da Bahia (UFBA), Salvador, BA (Brazil). Escola Politecnica. Programa de Pos-Graduacao em Engenharia Quimica; Iglesias, M. [Universidade Federal da Bahia (UFBA), Salvador, BA (Brazil). Escola Politecnica. Programa de Pos-Graduacao em Engenharia Quimica; Universidad de Santiago de Compostela (Spain). Escuela Tecnica Superior de Ingenieria. Dept. de Ingenieria Quimica


    In recent years, ionic liquids have been highlighted for its potential in various industrial applications. Among them, the salts of Broensted has a promising profile for the low toxicity, low cost and simple synthesis. This paper presents the synthesis and characterization of new salts of Bronsted with branched (lactate) or large chain anions (oleate) for future use as additives promoters of proton conductivity in fuel cells of ethanol. Experimental data were measured for density, sound velocity and conductivity of pure ionic liquids and mixtures. The density decreases linearly with increasing temperature, and sound velocity shows a similar trend, but not linear. The conductivity increases according to the Arrhenius model with activation energy less than 10 J/mol. Tests NMR, FTIR and TGA confirm ionic structure and thermal stability up to 165 deg C. (author)

  20. Polymers under mechanical stress- an NMR investigation

    Energy Technology Data Exchange (ETDEWEB)

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


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

  1. Ligand-target interactions: what can we learn from NMR? (United States)

    Carlomagno, Teresa


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

  2. Pulsed zero field NMR of solids and liquid crystals

    Energy Technology Data Exchange (ETDEWEB)

    Thayer, A.M.


    This work describes the development and applications to solids and liquid crystals of zero field nuclear magnetic resonance (NMR) experiments with pulsed dc magnetic fields. Zero field NMR experiments are one approach for obtaining high resolution spectra of amorphous and polycrystalline materials which normally (in high field) display broad featureless spectra. The behavior of the spin system can be coherently manipulated and probed in zero field with dc magnetic field pulses which are employed in a similar manner to radiofrequency pulses in high field NMR experiments. Nematic phases of liquid crystalline systems are studied in order to observe the effects of the removal of an applied magnetic field on sample alignment and molecular order parameters. In nematic phases with positive and negative magnetic susceptibility anisotropies, a comparison between the forms of the spin interactions in high and low fields is made. High resolution zero field NMR spectra of unaligned smectic samples are also obtained and reflect the symmetry of the liquid crystalline environment. These experiments are a sensitive measure of the motionally induced asymmetry in biaxial phases. Homonuclear and heteronuclear solute spin systems are compared in the nematic and smectic phases. Nonaxially symmetric dipolar couplings are reported for several systems. The effects of residual fields in the presence of a non-zero asymmetry parameter are discussed theoretically and presented experimentally. Computer programs for simulations of these and other experimental results are also reported. 179 refs., 75 figs.

  3. Solid-state NMR of the Yersinia pestis outer membrane protein Ail in lipid bilayer nanodiscs sedimented by ultracentrifugation

    Energy Technology Data Exchange (ETDEWEB)

    Ding, Yi; Fujimoto, L. Miya; Yao, Yong; Marassi, Francesca M., E-mail: [Sanford-Burnham Medical Research Institute (United States)


    Solid-state NMR studies of sedimented soluble proteins has been developed recently as an attractive approach for overcoming the size limitations of solution NMR spectroscopy while bypassing the need for sample crystallization or precipitation (Bertini et al. Proc Natl Acad Sci USA 108(26):10396–10399, 2011). Inspired by the potential benefits of this method, we have investigated the ability to sediment lipid bilayer nanodiscs reconstituted with a membrane protein. In this study, we show that nanodiscs containing the outer membrane protein Ail from Yersinia pestis can be sedimented for solid-state NMR structural studies, without the need for precipitation or lyophilization. Optimized preparations of Ail in phospholipid nanodiscs support both the structure and the fibronectin binding activity of the protein. The same sample can be used for solution NMR, solid-state NMR and activity assays, facilitating structure–activity correlation experiments across a wide range of timescales.

  4. Stereochemistry of 16a-Hydroxyfriedelin and 3-Oxo-16-methylfriedel-16-ene Established by 2D NMR Spectroscopy

    Directory of Open Access Journals (Sweden)

    Vagner Fernandes Knupp


    Full Text Available Friedelin (1, 3b-friedelinol (2, 28-hydroxyfriedelin (3, 16a-hydroxyfriedelin (4, 30-hydroxyfriedelin (5 and 16a,28-dihydroxyfriedelin (6 were isolated through fractionation of the hexane extract obtained from branches of Salacia elliptica. After a week in CDCl3 solution, 16a-hydroxyfriedelin (4 reacted turning into 3-oxo-16-methylfriedel-16-ene (7. This is the first report of a dehydration followed by a Nametkin rearrangement of a pentacyclic triterpene in CDCl3 solution occurring in the NMR tube. These seven pentacyclic triterpenes was identified through NMR spectroscopy and the stereochemistry of compound 4 and 7 was established by 2D NMR (NOESY spectroscopy and mass spectrometry (GC-MS. It is also the first time that all the 13C-NMR and 2D NMR spectral data are reported for compounds 4 and 7.

  5. PVT Degradation Studies: NMR Analysis

    Energy Technology Data Exchange (ETDEWEB)

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


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

  6. Sorption isotherm measurements by NMR. (United States)

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


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

  7. NMR hyperpolarization techniques for biomedicine. (United States)

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


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

  8. Résonance magnétique nucléaire 1H basse résolution. Le meilleur outil pour une détermination précise de la teneur en hydrogène des produits pétroliers Low Resolution 1h Nmr. The Ultimate Tool for Accurate Determination of Hydrogen Content in Petroleum Products

    Directory of Open Access Journals (Sweden)

    Gautier S.


    Full Text Available Un spectromètre RMN basse résolution à impulsions a été utilisé pour déterminer la teneur totale en hydrogène d'une large gamme de fractions pétrolières. On a constaté une excellente cohérence avec la teneur théorique en hydrogène de plusieurs composés purs; la répétabilité de la méthode est de 0,03%. La validation de cette méthode a été effectuée sur une vaste gamme de produits pétroliers comprenant notamment : distillats moyens de distillation directe, de craquage, d'hydrotraitement ou d'hydrocraquage, gazoles sous vide, bruts lourds, résidus atmosphériques de distillation directe ou d'hydrotraitement, soit au total 121 échantillons. Cette méthode s'est avérée la plus précise pour le calcul de la consommation d'hydrogène sur unités d'hydrotraitement, pour un domaine allant de 0,1 à 2,5 % pds. A low resolution pulsed NMR spectrometer has been used to determine total hydrogen content for a wide range of petroleum cuts. Excellent agreement has been found with the theoritical amount of hydrogen on pure compounds and the repeatability of the method is 0. 03%. The validation of the method has been done on a very large range of petroleum products, including straight run, cracked, hydrotreated and hydrocracked mid-distillates, vacuum gasoils, heavy crudes, straight run and hydrotreated atmospheric residues, representing 121 samples and a hydrogen consumption range during processing from 0,1 to 2. 5 wt.

  9. A multinuclear static NMR study of geopolymerisation

    Energy Technology Data Exchange (ETDEWEB)

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


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

  10. Probing acid-amide intermolecular hydrogen bonding by NMR spectroscopy and DFT calculations (United States)

    Chaudhari, Sachin Rama; Suryaprakash, N.


    Benzene carboxylic acids and benzamide act as their self-complement in molecular recognition to form inter-molecular hydrogen bonded dimers between amide and carboxylic acid groups, which have been investigated by 1H, 13C and 15N NMR spectroscopy. Extensive NMR studies using diffusion ordered spectroscopy (DOSY), variable temperature 1D, 2D NMR, established the formation of heterodimers of benzamide with benzoic acid, salicylic acid and phenyl acetic acid in deuterated chloroform solution. Association constants for the complex formation in the solution state have been determined. The results are ascertained by X-ray diffraction in the solid state. Intermolecular interactions in solution and in solid state were found to be similar. The structural parameters obtained by X-ray diffraction studies are compared with those obtained by DFT calculations.

  11. Structure determination of helical filaments by solid-state NMR spectroscopy (United States)

    Ahmed, Mumdooh; Spehr, Johannes; König, Renate; Lünsdorf, Heinrich; Rand, Ulfert; Lührs, Thorsten; Ritter, Christiane


    The controlled formation of filamentous protein complexes plays a crucial role in many biological systems and represents an emerging paradigm in signal transduction. The mitochondrial antiviral signaling protein (MAVS) is a central signal transduction hub in innate immunity that is activated by a receptor-induced conversion into helical superstructures (filaments) assembled from its globular caspase activation and recruitment domain. Solid-state NMR (ssNMR) spectroscopy has become one of the most powerful techniques for atomic resolution structures of protein fibrils. However, for helical filaments, the determination of the correct symmetry parameters has remained a significant hurdle for any structural technique and could thus far not be precisely derived from ssNMR data. Here, we solved the atomic resolution structure of helical MAVSCARD filaments exclusively from ssNMR data. We present a generally applicable approach that systematically explores the helical symmetry space by efficient modeling of the helical structure restrained by interprotomer ssNMR distance restraints. Together with classical automated NMR structure calculation, this allowed us to faithfully determine the symmetry that defines the entire assembly. To validate our structure, we probed the protomer arrangement by solvent paramagnetic resonance enhancement, analysis of chemical shift differences relative to the solution NMR structure of the monomer, and mutagenesis. We provide detailed information on the atomic contacts that determine filament stability and describe mechanistic details on the formation of signaling-competent MAVS filaments from inactive monomers. PMID:26733681

  12. Structural analysis of teicoplanin A2 by 2d NMR (United States)

    Heald, Sarah L.; Mueller, Luciano; Jeffs, Peter W.

    The analysis of the intact glycopeptide antibiotic, teicoplanin A 2, by two-dimensional proton NMR is described. Delayed-correlation spectroscopy (COSY), double-quantum coherence experiments (DACE), and nuclear Overhauser spectroscopy (NOESY) are utilized to confirm the primary structure. Distance constraints derived from NOESY data integrated with computer-assisted molecular modeling and force-field energy minimization yields a proposed three-dimensional solution-state conformation. Included are NMR methods developed for improved accuracy of distance measurements from 2D NOE experiments obtained on samples dissolved in DMSO- d6/water. The effects of different pulse sequences for water suppression on the 2D NOE spectral results are compared. Clear indication that teicoplanin exists in two unequally populated conformations which are in slow exchange is revealed by the presence of cross peaks attributable to conformational interchange in the NOESY spectra.

  13. NMR structure of the HIV-1 reverse transcriptase thumb subdomain

    Energy Technology Data Exchange (ETDEWEB)

    Sharaf, Naima G. [University of Pittsburgh, School of Medicine, Department of Structural Biology and Pittsburgh Center for HIV Protein Interactions (United States); Brereton, Andrew E. [Oregon State University, Department of Biochemistry and Biophysics, 2011 Ag & Life Sciences Bldg (United States); Byeon, In-Ja L. [University of Pittsburgh, School of Medicine, Department of Structural Biology and Pittsburgh Center for HIV Protein Interactions (United States); Andrew Karplus, P. [Oregon State University, Department of Biochemistry and Biophysics, 2011 Ag & Life Sciences Bldg (United States); Gronenborn, Angela M., E-mail: [University of Pittsburgh, School of Medicine, Department of Structural Biology and Pittsburgh Center for HIV Protein Interactions (United States)


    The solution NMR structure of the isolated thumb subdomain of HIV-1 reverse transcriptase (RT) has been determined. A detailed comparison of the current structure with dozens of the highest resolution crystal structures of this domain in the context of the full-length enzyme reveals that the overall structures are very similar, with only two regions exhibiting local conformational differences. The C-terminal capping pattern of the αH helix is subtly different, and the loop connecting the αI and αJ helices in the p51 chain of the full-length p51/p66 heterodimeric RT differs from our NMR structure due to unique packing interactions in mature RT. Overall, our data show that the thumb subdomain folds independently and essentially the same in isolation as in its natural structural context.

  14. NMR-based approach to the analysis of radiopharmaceuticals: radiochemical purity, specific activity, and radioactive concentration values by proton and tritium NMR spectroscopy. (United States)

    Schenk, David J; Dormer, Peter G; Hesk, David; Pollack, Scott R; Lavey, Carolee Flader


    Compounds containing tritium are widely used across the drug discovery and development landscape. These materials are widely utilized because they can be efficiently synthesized and produced at high specific activity. Results from internally calibrated (3)H and (1)H nuclear magnetic resonance (NMR) spectroscopy suggests that at least in some cases, this calibrated approach could supplement or potentially replace radio-high-performance liquid chromatography for radiochemical purity, dilution and scintillation counting for the measurement of radioactivity per volume, and liquid chromatography/mass spectrometry analysis for the determination of specific activity. In summary, the NMR-derived values agreed with those from the standard approaches to within 1% to 9% for solution count and specific activity. Additionally, the NMR-derived values for radiochemical purity deviated by less than 5%. A benefit of this method is that these values may be calculated at the same time that (3)H NMR analysis provides the location and distribution of tritium atoms within the molecule. Presented and discussed here is the application of this method, advantages and disadvantages of the approach, and a rationale for utilizing internally calibrated (1)H and (3)H NMR spectroscopy for specific activity, radioactive concentration, and radiochemical purity whenever acquiring (3)H NMR for tritium location. Copyright © 2015 John Wiley & Sons, Ltd.

  15. Systematic comparison of crystal and NMR protein structures deposited in the protein data bank. (United States)

    Sikic, Kresimir; Tomic, Sanja; Carugo, Oliviero


    Nearly all the macromolecular three-dimensional structures deposited in Protein Data Bank were determined by either crystallographic (X-ray) or Nuclear Magnetic Resonance (NMR) spectroscopic methods. This paper reports a systematic comparison of the crystallographic and NMR results deposited in the files of the Protein Data Bank, in order to find out to which extent these information can be aggregated in bioinformatics. A non-redundant data set containing 109 NMR - X-ray structure pairs of nearly identical proteins was derived from the Protein Data Bank. A series of comparisons were performed by focusing the attention towards both global features and local details. It was observed that: (1) the RMDS values between NMR and crystal structures range from about 1.5 Å to about 2.5 Å; (2) the correlation between conformational deviations and residue type reveals that hydrophobic amino acids are more similar in crystal and NMR structures than hydrophilic amino acids; (3) the correlation between solvent accessibility of the residues and their conformational variability in solid state and in solution is relatively modest (correlation coefficient = 0.462); (4) beta strands on average match better between NMR and crystal structures than helices and loops; (5) conformational differences between loops are independent of crystal packing interactions in the solid state; (6) very seldom, side chains buried in the protein interior are observed to adopt different orientations in the solid state and in solution.

  16. Dynamic pulsed-field-gradient NMR

    CERN Document Server

    Sørland, Geir Humborstad


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

  17. The future of NMR-based metabolomics. (United States)

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


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

  18. An Inversion Recovery NMR Kinetics Experiment


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


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

  19. Applications of NMR in Dairy Research

    Directory of Open Access Journals (Sweden)

    Anthony D. Maher


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

  20. observed by high pressure NMR and NQR

    Indian Academy of Sciences (India)

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

  1. Spin-Exchange Pumped NMR Gyros

    CERN Document Server

    Walker, Thad G


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

  2. NMR spectroscopy using liquid crystal solvents

    CERN Document Server

    Emsley, JW


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

  3. NMR-Based Metabolomics of Oral Biofluids. (United States)

    Schirra, Horst Joachim; Ford, Pauline J


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

  4. Access to NMR Spectroscopy for Two-Year College Students: The NMR Site at Trinity University (United States)

    Mills, Nancy S.; Shanklin, Michael


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

  5. NMR studies of oriented molecules

    Energy Technology Data Exchange (ETDEWEB)

    Sinton, S.W.


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

  6. Persistent Self-Association of Solute Molecules in Solution. (United States)

    Tang, Weiwei; Mo, Huaping; Zhang, Mingtao; Parkin, Sean; Gong, Junbo; Wang, Jingkang; Li, Tonglei


    The structural evolvement of a solute determines the crystallization outcome. The self-association mechanism leading to nucleation, however, remains poorly understood. Our current study explored the solution chemistry of a model compound, tolfenamic acid (TFA), in three different solvents mainly by solution NMR. It was found that hydrogen-bonded pairs of solute-solute or solute-solvent stack with each through forming a much weaker π-π interaction as the concentration increases. Depending on the solvent, configurations of the solution species may be retained in the resultant crystal structure or undergo rearrangement. Yet, the π-π stacking is always retained in the crystal regardless of the solvent used for the crystallization. The finding suggests that nucleation not only involves the primary intermolecular interaction (hydrogen bonding) but also engages the secondary forces in the self-assembly process.

  7. The dynamic duo: combining NMR and small angle scattering in structural biology. (United States)

    Hennig, Janosch; Sattler, Michael


    Structural biology provides essential information for elucidating molecular mechanisms that underlie biological function. Advances in hardware, sample preparation, experimental methods, and computational approaches now enable structural analysis of protein complexes with increasing complexity that more closely represent biologically entities in the cellular environment. Integrated multidisciplinary approaches are required to overcome limitations of individual methods and take advantage of complementary aspects provided by different structural biology techniques. Although X-ray crystallography remains the method of choice for structural analysis of large complexes, crystallization of flexible systems is often difficult and does typically not provide insights into conformational dynamics present in solution. Nuclear magnetic resonance spectroscopy (NMR) is well-suited to study dynamics at picosecond to second time scales, and to map binding interfaces even of large systems at residue resolution but suffers from poor sensitivity with increasing molecular weight. Small angle scattering (SAS) methods provide low resolution information in solution and can characterize dynamics and conformational equilibria complementary to crystallography and NMR. The combination of NMR, crystallography, and SAS is, thus, very useful for analysis of the structure and conformational dynamics of (large) protein complexes in solution. In high molecular weight systems, where NMR data are often sparse, SAS provides additional structural information and can differentiate between NMR-derived models. Scattering data can also validate the solution conformation of a crystal structure and indicate the presence of conformational equilibria. Here, we review current state-of-the-art approaches for combining NMR, crystallography, and SAS data to characterize protein complexes in solution. © 2014 The Protein Society.

  8. Wine analysis to check quality and authenticity by fully-automated 1H-NMR

    Directory of Open Access Journals (Sweden)

    Spraul Manfred


    Full Text Available Fully-automated high resolution 1H-NMR spectroscopy offers unique screening capabilities for food quality and safety by combining non-targeted and targeted screening in one analysis (15–20 min from acquisition to report. The advantage of high resolution 1H-NMR is its absolute reproducibility and transferability from laboratory to laboratory, which is not equaled by any other method currently used in food analysis. NMR reproducibility allows statistical investigations e.g. for detection of variety, geographical origin and adulterations, where smallest changes of many ingredients at the same time must be recorded. Reproducibility and transferability of the solutions shown are user-, instrument- and laboratory-independent. Sample prepara- tion, measurement and processing are based on strict standard operation procedures which are substantial for this fully automated solution. The non-targeted approach to the data allows detecting even unknown deviations, if they are visible in the 1H-NMR spectra of e.g. fruit juice, wine or honey. The same data acquired in high-throughput mode are also subjected to quantification of multiple compounds. This 1H-NMR methodology will shortly be introduced, then results on wine will be presented and the advantages of the solutions shown. The method has been proven on juice, honey and wine, where so far unknown frauds could be detected, while at the same time generating targeted parameters are obtained.

  9. Parsimony and goodness-of-fit in multi-dimensional NMR inversion (United States)

    Babak, Petro; Kryuchkov, Sergey; Kantzas, Apostolos


    Multi-dimensional nuclear magnetic resonance (NMR) experiments are often used for study of molecular structure and dynamics of matter in core analysis and reservoir evaluation. Industrial applications of multi-dimensional NMR involve a high-dimensional measurement dataset with complicated correlation structure and require rapid and stable inversion algorithms from the time domain to the relaxation rate and/or diffusion domains. In practice, applying existing inverse algorithms with a large number of parameter values leads to an infinite number of solutions with a reasonable fit to the NMR data. The interpretation of such variability of multiple solutions and selection of the most appropriate solution could be a very complex problem. In most cases the characteristics of materials have sparse signatures, and investigators would like to distinguish the most significant relaxation and diffusion values of the materials. To produce an easy to interpret and unique NMR distribution with the finite number of the principal parameter values, we introduce a new method for NMR inversion. The method is constructed based on the trade-off between the conventional goodness-of-fit approach to multivariate data and the principle of parsimony guaranteeing inversion with the least number of parameter values. We suggest performing the inversion of NMR data using the forward stepwise regression selection algorithm. To account for the trade-off between goodness-of-fit and parsimony, the objective function is selected based on Akaike Information Criterion (AIC). The performance of the developed multi-dimensional NMR inversion method and its comparison with conventional methods are illustrated using real data for samples with bitumen, water and clay.

  10. Surface characterization of titanium based dental implants; Caracterizacao de implantes odontologicos a base de titanio

    Energy Technology Data Exchange (ETDEWEB)

    Castilho, Guilherme Augusto Alcaraz


    Dental implantology uses metallic devices made of commercially pure titanium in order to replace lost teeth. Titanium presents favorable characteristics as bio material and modern implants are capable of integrate, witch is the union between bone and implant without fibrous tissue development. Three of the major Brazilian implant manufacturers were chosen to join the study. A foreign manufacturer participated as standard. The manufacturers had three specimens of each implant with two different surface finishing, as machined and porous, submitted to analysis. Surface chemical composition and implant morphology were analyzed by X-ray photoelectron spectroscopy (XP S), scanning electron microscopy (SEM) and microprobe. Implant surface is mainly composed of titanium, oxygen and carbon. Few contaminants commonly present on implant surface were found on samples. Superficial oxide layer is basically composed of titanium dioxide (TiO{sub 2}), another oxides as Ti O and Ti{sub 2}O{sub 3} were also found in small amount. Carbon on implant surface was attributed to manufacturing process. Nitrogen, Phosphorous and Silicon appeared in smaller concentration on surface. There was no surface discrepancy among foreign and Brazilian made implants. SEM images were made on different magnification, 35 X to 3500 X, and showed similarity among as machined implants. Porous surface finishing implants presented distinct morphology. This result was attributed to differences on manufacturing process. Implant bioactivity was accessed through immersion on simulated body solution (SBF) in order to verify formation of an hydroxyapatite (HA) layer on surface. Samples were divided on three groups according to immersion time: G1 (7 days), G2 (14 days), G3 (21 days), and deep in SBF solution at 37 deg C. After being removed from solution, XPS analyses were made and then implants have been submitted to microprobe analysis. XPS showed some components of SBF solution on sample surface but microprobe

  11. An Inversion Recovery NMR Kinetics Experiment (United States)

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


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

  12. A Guided Inquiry Approach to NMR Spectroscopy (United States)

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


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

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

    African Journals Online (AJOL)

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

  14. An Integrated Laboratory Project in NMR Spectroscopy. (United States)

    Hudson, Reggie L.; Pendley, Bradford D.


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

  15. Using Cloud Storage for NMR Data Distribution (United States)

    Soulsby, David


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

  16. Proton NMR relaxation in hydrous melts

    Energy Technology Data Exchange (ETDEWEB)

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


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

  17. Two-Dimensional NMR Evidence for Cleavage of Lignin and Xylan Substituents in Wheat Straw Through Hydrothermal Pretreatment and Enzymatic Hydrolysis (United States)

    Daniel J. Yelle; Prasad Kaparaju; Christopher G. Hunt; Kolby Hirth; Hoon Kim; John Ralph; Claus Felby


    Solution-state two-dimensional (2D) nuclear magnetic resonance (NMR) spectroscopy of plant cell walls is a powerful tool for characterizing changes in cell wall chemistry during the hydrothermal pretreatment process of wheat straw for second-generation bioethanol production. One-bond 13C-1H NMR correlation spectroscopy, via...

  18. Field-cycling NMR with high-resolution detection under magic-angle spinning : determination of field-window for nuclear hyperpolarization in a photosynthetic reaction center.

    NARCIS (Netherlands)

    Grasing, D.; Bielytskyi, P.; Cespedes-Camacho, I.F.; Alia, A.; Marquardsen, A.A.T.; Engelke, F.; Matysik,; J.,


    Several parameters in NMR depend on the magnetic field strength. Field-cycling NMR is an elegant way to explore the field dependence of these properties. The technique is well developed for solution state and in relaxometry. Here, a shuttle system with magic-angle spinning (MAS) detection is

  19. The role of carbon-13 NMR spectroscopy in the determination of the physical association of xylan and cellulose in the gel of Tingui

    Energy Technology Data Exchange (ETDEWEB)

    Gorin, P.A.J.; Teixeira, A.Z.A.; Iacomini, M. [Parana Univ., Curitiba, PR (Brazil). Dept. de Bioquimica


    This paper describes the analysis procedure used for characterization of the constituents from a hydrogel of tingui (Magonia pubescens), involving solid state as well as the usual solution {sup 13} C NMR spectroscopy. NMR spectra were presented and analysed, and so, some considerations were also done 7 refs., 3 figs.

  20. Billion-Fold Enhancement in Sensitivity of Nuclear Magnetic Resonance Spectroscopy for Magnesium Ions in Solution

    CERN Document Server

    Gottberg, Alexander; Kowalska, Magdalena; Bissell, Mark L; Arcisauskaite, Vaida; Blaum, Klaus; Helmke, Alexander; Johnston, Karl; Kreim, Kim; Larsen, Flemming H; Neugart, Rainer; Neyens, Gerda; Garcia Ruiz, Ronald F; Szunyogh, Daniel; Thulstrup, Peter W; Yordanov, Deyan T; Hemmingsen, Lars


    β-nuclear magnetic resonance (NMR) spectroscopy is highly sensitive compared to conventional NMR spectroscopy, and may be applied for several elements across the periodic table. β-NMR has previously been successfully applied in the fields of nuclear and solid-state physics. In this work, β-NMR is applied, for the first time, to record an NMR spectrum for a species in solution. 31Mg β-NMR spectra are measured for as few as 107 magnesium ions in ionic liquid (EMIM-Ac) within minutes, as a prototypical test case. Resonances are observed at 3882.9 and 3887.2 kHz in an external field of 0.3 T. The key achievement of the current work is to demonstrate that β-NMR is applicable for the analysis of species in solution, and thus represents a novel spectroscopic technique for use in general chemistry and potentially in biochemistry.

  1. Carbon-13 NMR spectroscopy of biological systems

    CERN Document Server

    Beckmann, Nicolau


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

  2. Challenges and perspectives in quantitative NMR. (United States)

    Giraudeau, Patrick


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

  3. NMR and MRI apparatus and method

    Energy Technology Data Exchange (ETDEWEB)

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


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

  4. NMR-based milk metabolomics

    DEFF Research Database (Denmark)

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


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

  5. NMR studies of sedimentary tetrapyrroles

    Energy Technology Data Exchange (ETDEWEB)

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

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

  6. NMR-based metabolomics applications

    DEFF Research Database (Denmark)

    Iaccarino, Nunzia

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

  7. Preprocessing of NMR metabolomics data. (United States)

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


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

  8. 15N NMR chemical shifts in papaverine decomposition products (United States)

    Czyrski, Andrzej; Girreser, Ulrich; Hermann, Tadeusz


    Papaverine can be easily oxidized to papaverinol, papaveraldine and 2,3,9,10-tetramethoxy-12-oxo-12H-indolo[2,1-a]isoquinolinium chloride. On addition of alkali solution the latter compound forms 2-(2-carboxy-4,5-dimethoxyphenyl)-6,7-dimethoxyisoquinolinium inner salt. Together with these structures the interesting 13-(3,4-dimethoxyphenyl)-2,3,8,9-tetramethoxy-6a-12a-diazadibenzo[a,g]fluorenylium chloride is discussed, which is formed in the Gadamer-Schulemann reaction of papaverine as a side product. This letter reports the 15N NMR spectra of the above mentioned compounds.

  9. Conformational analysis of protein structures derived from NMR data. (United States)

    MacArthur, M W; Thornton, J M


    A study is presented of the conformational characteristics of NMR-derived protein structures in the Protein Data Bank compared to X-ray structures. Both ensemble and energy-minimized average structures are analyzed. We have addressed the problem using the methods developed for crystal structures by examining the distribution of phi, psi, and chi angles as indicators of global conformational irregularity. All these features in NMR structures occur to varying degrees in multiple conformational states. Some measures of local geometry are very tightly constrained by the methods used to generate the structure, e.g., proline phi angles, alpha-helix phi,psi angles, omega angles, and C alpha chirality. The more lightly restrained torsion angles do show increased clustering as the number of overall experimental observations increases. phi, psi, and chi 1 angle conformational heterogeneity is strongly correlated with accessibility but shows additional differences which reflect the differing number of observations possible in NMR for the various side chains (e.g., many for Trp, few for Ser). In general, we find that the core is defined to a notional resolution of 2.0 to 2.3 A. Of real interest is the behavior of surface residues and in particular the side chains where multiple rotameric states in different structures can vary from 10% to 88%. Later generation structures show a much tighter definition which correlates with increasing use of J-coupling information, stereospecific assignments, and heteronuclear techniques. A suite of programs is being developed to address the special needs of NMR-derived structures which will take into account the existence of increased mobility in solution.

  10. Inverse problem for in vivo NMR spatial localization

    Energy Technology Data Exchange (ETDEWEB)

    Hasenfeld, A.C.


    The basic physical problem of NMR spatial localization is considered. To study diseased sites, one must solve the problem of adequately localizing the NMR signal. We formulate this as an inverse problem. As the NMR Bloch equations determine the motion of nuclear spins in applied magnetic fields, a theoretical study is undertaken to answer the question of how to design magnetic field configurations to achieve these localized excited spin populations. Because of physical constraints in the production of the relevant radiofrequency fields, the problem factors into a temporal one and a spatial one. We formulate the temporal problem as a nonlinear transformation, called the Bloch Transform, from the rf input to the magnetization response. In trying to invert this transformation, both linear (for the Fourier Transform) and nonlinear (for the Bloch Transform) modes of radiofrequency excitation are constructed. The spatial problem is essentially a statics problem for the Maxwell equations of electromagnetism, as the wavelengths of the radiation considered are on the order of ten meters, and so propagation effects are negligible. In the general case, analytic solutions are unavailable, and so the methods of computer simulation are used to map the rf field spatial profiles. Numerical experiments are also performed to verify the theoretical analysis, and experimental confirmation of the theory is carried out on the 0.5 Tesla IBM/Oxford Imaging Spectrometer at the LBL NMR Medical Imaging Facility. While no explicit inverse is constructed to ''solve'' this problem, the combined theoretical/numerical analysis is validated experimentally, justifying the approximations made. 56 refs., 31 figs.

  11. Theoretical and experimental NMR studies on muscimol from fly agaric mushroom (Amanita muscaria) (United States)

    Kupka, Teobald; Wieczorek, Piotr P.


    In this article we report results of combined theoretical and experimental NMR studies on muscimol, the bioactive alkaloid from fly agaric mushroom (Amanita muscaria). The assignment of 1H and 13C NMR spectra of muscimol in DMSO-d6 was supported by additional two-dimensional heteronuclear correlated spectra (2D NMR) and gauge independent atomic orbital (GIAO) NMR calculations using density functional theory (DFT). The effect of solvent in theoretical calculations was included via polarized continuum model (PCM) and the hybrid three-parameter B3LYP density functional in combination with 6-311++G(3df,2pd) basis set enabled calculation of reliable structures of non-ionized (neutral) molecule and its NH and zwitterionic forms in the gas phase, chloroform, DMSO and water. GIAO NMR calculations, using equilibrium and rovibrationally averaged geometry, at B3LYP/6-31G* and B3LYP/aug-cc-pVTZ-J levels of theory provided muscimol nuclear magnetic shieldings. The theoretical proton and carbon chemical shifts were critically compared with experimental NMR spectra measured in DMSO. Our results provide useful information on its structure in solution. We believe that such data could improve the understanding of basic features of muscimol at atomistic level and provide another tool in studies related to GABA analogs.

  12. Production and NMR signal optimization of hyperpolarized 13C-labeled amino acids (United States)

    Parish, Christopher; Niedbalski, Peter; Ferguson, Sarah; Kiswandhi, Andhika; Lumata, Lloyd

    Amino acids are targeted nutrients for consumption by cancers to sustain their rapid growth and proliferation. 13C-enriched amino acids are important metabolic tracers for cancer diagnostics using nuclear magnetic resonance (NMR) spectroscopy. Despite this diagnostic potential, 13C NMR of amino acids however is hampered by the inherently low NMR sensitivity of the 13C nuclei. In this work, we have employed a physics technique known as dynamic nuclear polarization (DNP) to enhance the NMR signals of 13C-enriched amino acids. DNP works by transferring the high polarization of electrons to the nuclear spins via microwave irradiation at low temperature and high magnetic field. Using a fast dissolution method in which the frozen polarized samples are dissolved rapidly with superheated water, injectable solutions of 13C-amino acids with highly enhanced NMR signals (by at least 5,000-fold) were produced at room temperature. Factors that affect the NMR signal enhancement levels such as the choice of free radical polarizing agents and sample preparation will be discussed along with the thermal mixing physics model of DNP. The authors would like to acknowledge the support by US Dept of Defense Award No. W81XWH-14-1-0048 and Robert A. Welch Foundation Grant No. AT-1877.

  13. Chiral liquid chromatography-circular dichroism-NMR for estimating separation conditions of chiral HPLC without authentic samples. (United States)

    Tokunaga, Takashi; Okamoto, Masahiko; Tanaka, Kozo; Tode, Chisato; Sugiura, Makiko


    Chiral separation by high performance liquid chromatography (Chiral HPLC) is one of the most powerful methods for estimating optical and chemical purity of chiral compounds. However, it has a weakness in that much time and effort are required to prepare authentic samples. A novel chiral liquid chromatography-circular dichroism-NMR (LC-CD-NMR) technique, on the other hand, requires only crude chiral compounds that include enantiomers as minor impurities. In this study, chiral LC-CD-NMR was constructed by connecting a conventional LC-NMR system with a CD detector. A pyridylalanine derivative mixture was prepared to mimic technical grade material in an early phase of development. By chiral LC-CD-NMR, the enantiomer peak is identified by an opposite sign of the CD Cotton effect curve and an identical (1)H NMR spectrum to that of the main component. Using NMR as a detector, this method is superior in ability to discriminate enantiomers from other isomers indistinguishable by MS. Furthermore, this method is also applicable for selecting the best separation conditions of chiral HPLC. The degrees of separation (Rs) between the main component and its enantiomer in several chiral columns were compared. Even with modern chromatographic methods, establishing the best chiral HPLC conditions in an early phase of development is difficult: chiral LC-CD-NMR is a suitable solution.

  14. The effect of cadmium ions on 2,3-bisphosphoglycerate in erythrocytes studied with 31P NMR. (United States)

    Arkowitz, R; Hoehn-Berlage, M; Gersonde, K


    The interaction of cadmium ions with human red blood cell (RBC) 2,3-bisphosphoglycerate (DPG) wasa studied by 31P NMR. 31P NMR spectra and 31P T1 and 31P T2 relaxation times give evidence for cadmium-2,3-bisphosphoglycerate complexation in aqueous solution. 31P NMR spectra indicate the occurrence of a similar complexation in RBC cryolysates. The lag phase (constant polyphosphate level) prior to DPG hydrolysis in incubated red blood cells is lengthened in the presence of cadmium.

  15. Structure and Dynamics Studies of Cytolytic Peptides in Lipid Bilayers using NMR Spectroscopy

    DEFF Research Database (Denmark)

    Hansen, Sara Krogh


    different and cytolytic peptides were investigated in this work. The peptides were SPF-5506-A4 from Trichoderma sp, Conolysin-Mt1 from Conus mustelinus, and Alamethicin from Trichoderma viride. The studies employed solution and solid-state NMR spectroscopy in combination with different biophysical methods...

  16. The U.S. Dairy Forage Research Center (USDFRC) condensed tannin NMR database (United States)

    This perspective describes a solution-state NMR database for flavan-3-ol monomers and condensed tannin dimers through tetramers obtained from the literature to 2015, containing data searchable by structure, molecular formula, degrees of polymerization, 1H and 13C chemical shifts of the condensed tan...

  17. Analysis of ethanol-soluble extractives in southern pine wood by low-field proton NMR (United States)

    Thomas L. Eberhardt; Thomas Elder; Nicole Labbe


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

  18. solvent effect on 14n nmr shielding of glycine, serine, leucine

    African Journals Online (AJOL)


    of 10 solvents with a wide range of dielectric constants on 4 amino acids. NMR shielding values. (ppm), isotropic and anisotropic effects, energy interaction between solute and solvent, and the effect of hydrogen bond on shielding are described. Direct and indirect solvent effects on shielding are also calculated.

  19. Synthesis and characterization of metallic nuclear fuels; Sintese e caracterizacao de combustiveis nucleares metalicos

    Energy Technology Data Exchange (ETDEWEB)

    Longen, F.R., E-mail: [Universidade Tecnologica Federal do Parana (UTFPR), Medianeira, PR (Brazil); Barco, R.; Paesano Junior, A. [Universidade Estadual de Maringa (UEM), PR (Brazil); Pagano Junior, L. [Centro Tecnologico da Marinha (CETEM), Sao Paulo, SP (Brazil)


    U-Zr-Mo and U-Zr-Gd ternary alloys, potentially useful as metallic nuclear fuel, were prepared at different concentrations by arc-melting and characterized by X-ray diffraction. Those alloys containing molybdenum were submitted to thermal annealing in inert atmosphere, followed by quenching in water. These samples were measured before and after the thermal treatment. The diffractometric results evidenced that the as-cast alloys solidified mostly with a body centered cubic structure (γphase) and that for the uranium richest samples a second phase formed, with an orthorhombic structure (α phase). For the U-Zr-Gd alloys the X-ray diffractometry revealed the retention of a hexagonal structure (δ phase) and gadolinium traces in the poorest uranium samples. The U{sub 57}(Zr{sub 92}Gd{sub 8}){sub 43} sample resulted monophasic becoming, according to literature, the first time that a solid solution combining uranium and gadolinium is identified. (author)

  20. Perspectives for sensitivity enhancement in proton-detected solid-state NMR of highly deuterated proteins by preserving water magnetization

    Energy Technology Data Exchange (ETDEWEB)

    Chevelkov, Veniamin, E-mail:; Xiang, ShengQi; Giller, Karin; Becker, Stefan; Lange, Adam [Max-Planck-Institut für biophysikalische Chemie (MPI-bpc) (Germany); Reif, Bernd [Technische Universität München (TUM), Munich Center for Integrated Protein Science (CIPS-M), Department Chemie (Germany)


    In this work, we show how the water flip-back approach that is widely employed in solution-state NMR can be adapted to proton-detected MAS solid-state NMR of highly deuterated proteins. The scheme allows to enhance the sensitivity of the experiment by decreasing the recovery time of the proton longitudinal magnetization. The method relies on polarization transfer from non-saturated water to the protein during the inter-scan delay.

  1. Scalar operators in solid-state NMR

    Energy Technology Data Exchange (ETDEWEB)

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


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

  2. Graphical programming for broadband pulse NMR spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

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


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

  3. Graphical programming for pulse automated NMR experiments

    Energy Technology Data Exchange (ETDEWEB)

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


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

  4. NMR reaction monitoring in flow synthesis

    Directory of Open Access Journals (Sweden)

    M. Victoria Gomez


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

  5. Oriented solid-state NMR spectrosocpy

    DEFF Research Database (Denmark)

    Bertelsen, Kresten

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

  6. Rheology of Blood by NMR (United States)

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


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

  7. NMR Study of Organic Counterion Binding to Perfluorinated Micellar Structures (United States)

    Bossev, Dobrin; Matsumoto, Mustuo; Nakahara, Masaru


    In this study we have applied our previously developed NMR method to study the adsorption of tetramethylammonium (TMA^+) and tetraethylammonium (TEA^+) counterions to micelles formed by perfluorooctylsulfonate (FOS^-) surfactant in water at 30 C. These two counterions induce formation of threadlike surfactant structures that result in well pronounced viscoelastic properties of the solution. To selectively probe the degree of counterion binding we have used ^1H and ^19F NMR chemical shifts and self-diffusion coefficients that are sensitive to the Stern and diffuse double layers, respectively. The competitive adsorption of TMA^+ and TEA^+ was examined as a function of the TMA^+/TEA^+ ratio at a constant FOS^- concentration of 100 mM. The two counterions were found to form Stern layer around the FOS^- micelles with comparable packing; about one counterion per two micellized FOS molecules. When mixed at intermediate proportions, however, the TEA^+ counterion shows preferential binding; the concentration of TEA^+ in the Stern layer is found to be twice higher than that of TMA^+ at equal total respective concentrations in the solution. These results are discussed in terms of counterion size and hydrophobicity and presented in parallel with those that involved the smaller and more hydrophilic lithium counterion.

  8. Bayesian Peak Picking for NMR Spectra

    Directory of Open Access Journals (Sweden)

    Yichen Cheng


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

  9. NMR analysis of compositional heterogeneity in polysaccharides (United States)

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

  10. Relaxation time estimation in surface NMR

    Energy Technology Data Exchange (ETDEWEB)

    Grunewald, Elliot D.; Walsh, David O.


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

  11. Bayesian Peak Picking for NMR Spectra

    KAUST Repository

    Cheng, Yichen


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

  12. Enhancement of NMR and MRI in the presence of hyperpolarized noble gases (United States)

    Pines, Alexander; Budinger, Thomas; Navon, Gil; Song, Yi-Qiao; Appelt, Stephan; Bifone, Angelo; Taylor, Rebecca; Goodson, Boyd; Seydoux, Roberto; Room, Toomas; Pietrass, Tanja


    The present invention relates generally to nuclear magnetic resonance (NMR) techniques for both spectroscopy and imaging. More particularly, the present invention relates to methods in which hyperpolarized noble gases (e.g., Xe and He) are used to enhance and improve NMR and MRI. Additionally, the hyperpolarized gas solutions of the invention are useful both in vitro and in vivo to study the dynamics or structure of a system. When used with biological systems, either in vivo or in vitro, it is within the scope of the invention to target the hyperpolarized gas and deliver it to specific regions within the system.

  13. Dynamic Processes in Prochiral Solvating Agents (pro-CSAs Studied by NMR Spectroscopy

    Directory of Open Access Journals (Sweden)

    Jan Labuta


    Full Text Available Several dynamic processes, including tautomerism and macrocyclic inversion, in 1H-NMR prochiral solvating agents (pro-CSAs are investigated. Various features of pro-CSA, including modes of interaction for complex formation, stoichiometry, binding strength and temperature effects were compared for three representative pro-CSA molecules. Structural effects of conjugated tetrapyrrole pro-CSA on the mechanism of enantiomeric excess determination are also discussed. Detailed analysis of species (complexes and dynamic processes occurring in solution and their 1H-NMR spectral manifestations at various temperatures is presented.

  14. Characterization of the inclusion complex ropivacaine: {beta}-cyclodextrin; Caracterizacao do complexo de inclusso ropivacaina: {beta}-ciclodextrina

    Energy Technology Data Exchange (ETDEWEB)

    Fraceto, Leonardo Fernandes [Universidade Estadual Paulista Julio de Mesquita Filho, Sorocaba, SP (Brazil). Dept. de Engenharia Ambiental]. E-mail:; Goncalves, Marcos Moises [Universidade de Sorocaba, SP (Brazil); Moraes, Carolina Morales; Araujo, Daniele Ribeiro de; Zanella, Luciana; Paula, Eneida de [Universidade Estadual de Campinas (UNICAMP), Campinas, SP (Brazil). Inst. de Biologia. Dept. de Bioquimica; Pertinhez, Thelma de Aguiar [Universidade de Parma (Italy). Dept. de Medicina Experimental


    Ropivacaine (RVC) is a widely used local anesthetic. The complexation of RVC with {beta}-cyclodextrin ({beta}-CD) is of great interest for the development of more efficient local anesthetic formulations. The present work focuses on the characterization of the RVC:{beta}-CD complex by nuclear magnetic resonance (NMR). The stoichiometry of the complex is 1:2 RVC:{beta}-CD. DOSY-NMR shows that the association constant is 55.5 M{sup -1}. Longitudinal relaxation time results show that RVC changes its mobility in the presence of {beta}-CD. This study is focused on the physicochemical characterization of inclusion complexes that are potentials options for pain treatment. (author)

  15. The eNMR platform for structural biology

    NARCIS (Netherlands)

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


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

  16. NMR studies of multiphase flows II

    Energy Technology Data Exchange (ETDEWEB)

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


    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.

  17. Physiological monitoring during nmr measurements of animals (United States)

    Schmidt, Paul G.; Smith, E. Norbert

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

  18. NMRbox: A Resource for Biomolecular NMR Computation. (United States)

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


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

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

    National Research Council Canada - National Science Library

    Yang Liu; Zhaoxia Liu; Huaxin Yang; Lan He


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

  20. Supramolecular Amino Acid Based Hydrogels: Probing the Contribution of Additive Molecules using NMR Spectroscopy (United States)

    Ramalhete, Susana M.; Nartowski, Karol P.; Sarathchandra, Nichola; Foster, Jamie S.; Round, Andrew N.; Angulo, Jesús


    Abstract Supramolecular hydrogels are composed of self‐assembled solid networks that restrict the flow of water. l‐Phenylalanine is the smallest molecule reported to date to form gel networks in water, and it is of particular interest due to its crystalline gel state. Single and multi‐component hydrogels of l‐phenylalanine are used herein as model materials to develop an NMR‐based analytical approach to gain insight into the mechanisms of supramolecular gelation. Structure and composition of the gel fibres were probed using PXRD, solid‐state NMR experiments and microscopic techniques. Solution‐state NMR studies probed the properties of free gelator molecules in an equilibrium with bound molecules. The dynamics of exchange at the gel/solution interfaces was investigated further using high‐resolution magic angle spinning (HR‐MAS) and saturation transfer difference (STD) NMR experiments. This approach allowed the identification of which additive molecules contributed in modifying the material properties. PMID:28401991

  1. Present and future of NMR for RNA-protein complexes: a perspective of integrated structural biology. (United States)

    Carlomagno, Teresa


    Nucleic acids are gaining enormous importance as key molecules in almost all biological processes. Most nucleic acids do not act in isolation but are generally associated with proteins to form high-molecular-weight nucleoprotein complexes. In this perspective article I focus on the structural studies of supra-molecular ribonucleoprotein (RNP) assemblies in solution by a combination of state-of-the-art TROSY-based NMR experiments and other structural biology techniques. I discuss ways how to combine sparse NMR data with low-resolution structural information from small-angle scattering, fluorescence and electron paramagnetic resonance spectroscopy to obtain the structure of large RNP particles by an integrated structural biology approach. In the last section I give a perspective for the study of RNP complexes by solid-state NMR. Copyright © 2013 The Author. Published by Elsevier Inc. All rights reserved.

  2. Identification of phosphorylethanolamine in 31P-NMR spectra of human peripheral blood lymphocytes. (United States)

    Petersen, A; Hørder, M; Jacobsen, J P


    The 31P-NMR spectrum of intact human peripheral blood lymphocytes contains a large unidentified peak in the phosphomonoester region. The pH dependency of the 31P-NMR chemical shift of this peak in perchloric acid extracts of peripheral blood lymphocytes was recorded. It was compared to the pH dependency of the chemical shift of phosphorylethanolamine, phosphorylcholine, and ribose 5-phosphate in model solutions. An excellent agreement was found between the behavior of phosphorylethanolamine and the unidentified peak. To further substantiate this assignment phosphorylethanolamine was added to extracts and the pH titrations were repeated. The added phosphorylethanolamine gave exactly the same chemical shift as the unidentified peak and no difference was observed with pH titrations. The concentration of phosphorylethanolamine in human peripheral blood lymphocytes was estimated by 31P NMR to be 2.4 mumol/10(9) cells (range 0.9-4.3/10(9) cells, n = 4).

  3. Use of NMR and NMR Prediction Software to Identify Components in Red Bull Energy Drinks (United States)

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


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

  4. NMR Spectra through the Eyes of a Student: Eye Tracking Applied to NMR Items (United States)

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


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

  5. Performance of the WeNMR CS-Rosetta3 web server in CASD-NMR. (United States)

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


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

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

    NARCIS (Netherlands)

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


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

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

    DEFF Research Database (Denmark)

    Li, Xiaozhou; Tapmeyer, Lukas; Bolte, Michael


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

  8. Dynamics and interactions of ibuprofen in cyclodextrin nanosponges by solid-state NMR spectroscopy

    Directory of Open Access Journals (Sweden)

    Monica Ferro


    Full Text Available Two different formulations of cyclodextrin nanosponges (CDNS, obtained by polycondensation of β-cyclodextrin with ethylenediaminetetraacetic acid dianhydride (EDTAn, were treated with aqueous solutions of ibuprofen sodium salt (IbuNa affording hydrogels that, after lyophilisation, gave two solid CDNS-drug formulations. 1H fast MAS NMR and 13C CP-MAS NMR spectra showed that IbuNa was converted in situ into its acidic and dimeric form (IbuH after freeze-drying. 13C CP-MAS NMR spectra also indicated that the structure of the nanosponge did not undergo changes upon drug loading compared to the unloaded system. However, the 13C NMR spectra collected under variable contact time cross-polarization (VCT-CP conditions showed that the polymeric scaffold CDNS changed significantly its dynamic regime on passing from the empty CDNS to the drug-loaded CDNS, thus showing that the drug encapsulation can be seen as the formation of a real supramolecular aggregate rather than a conglomerate of two solid components. Finally, the structural features obtained from the different solid-state NMR approaches reported matched the information from powder X-ray diffraction profiles.

  9. Analysis of Functional Dynamics of Modular Multidomain Proteins by SAXS and NMR. (United States)

    Thompson, Matthew K; Ehlinger, Aaron C; Chazin, Walter J


    Multiprotein machines drive virtually all primary cellular processes. Modular multidomain proteins are widely distributed within these dynamic complexes because they provide the flexibility needed to remodel structure as well as rapidly assemble and disassemble components of the machinery. Understanding the functional dynamics of modular multidomain proteins is a major challenge confronting structural biology today because their structure is not fixed in time. Small-angle X-ray scattering (SAXS) and nuclear magnetic resonance (NMR) spectroscopy have proven particularly useful for the analysis of the structural dynamics of modular multidomain proteins because they provide highly complementary information for characterizing the architectural landscape accessible to these proteins. SAXS provides a global snapshot of all architectural space sampled by a molecule in solution. Furthermore, SAXS is sensitive to conformational changes, organization and oligomeric states of protein assemblies, and the existence of flexibility between globular domains in multiprotein complexes. The power of NMR to characterize dynamics provides uniquely complementary information to the global snapshot of the architectural ensemble provided by SAXS because it can directly measure domain motion. In particular, NMR parameters can be used to define the diffusion of domains within modular multidomain proteins, connecting the amplitude of interdomain motion to the architectural ensemble derived from SAXS. Our laboratory has been studying the roles of modular multidomain proteins involved in human DNA replication using SAXS and NMR. Here, we present the procedure for acquiring and analyzing SAXS and NMR data, using DNA primase and replication protein A as examples. © 2017 Elsevier Inc. All rights reserved.

  10. Use of Charged Nanoparticles in NMR-Based Metabolomics for Spectral Simplification and Improved Metabolite Identification. (United States)

    Zhang, Bo; Xie, Mouzhe; Bruschweiler-Li, Lei; Bingol, Kerem; Brüschweiler, Rafael


    Metabolomics aims at a complete characterization of all metabolites in biological samples in terms of both their identities and concentrations. Because changes of metabolites and their concentrations are a direct reflection of cellular activity, it allows for a better understanding of cellular processes and function to be obtained. Although NMR spectroscopy is routinely applied to complex biological mixtures without purification, overlapping NMR peaks often pose a challenge for the comprehensive and accurate identification of the underlying metabolites. To address this problem, we present a novel nanoparticle-based strategy that differentiates between metabolites based on their electric charge. By adding electrically charged silica nanoparticles to the solution NMR sample, metabolites of opposite charge bind to the nanoparticles and their NMR signals are weakened or entirely suppressed due to peak broadening caused by the slow rotational tumbling of the nanometer-sized nanoparticles. Comparison of the edited with the original spectrum significantly facilitates analysis and reduces ambiguities in the identification of metabolites. This method makes NMR directly sensitive to the detection of molecular charges at constant pH, as demonstrated here both for model mixtures and human urine. The simplicity of the approach should make it useful for a wide range of metabolomics applications.

  11. NMR characterization of hydrate and aldehyde forms of imidazole-2-carboxaldehyde and derivatives. (United States)

    Lázaro Martínez, Juan Manuel; Romasanta, Pablo Nicolás; Chattah, Ana Karina; Buldain, Graciela Yolanda


    The existence and stability of the aldehyde-hydrate form of imidazole-2-carboxaldehyde (4) were studied using FTIR together with solution- and solid-state NMR experiments. The results allowed us to conclude that the hydrate form was stable and precipitated at pH = 8.0 and that the aldehyde form was isolated at pH = 6.5 and 9.5. Moreover, the presence of the aldehyde-hydrate form was studied through NMR experiments in D(2)O at both alkaline and acidic pH. In addition, the tautomeric forms of the 2-substituted imidazole compounds were also analyzed to investigate the influence of the hybridization on the carbon adjacent to the imidazole ring, by (13)C NMR in DMSO-d(6), acetone-d(6), and CDCl(3). The presence of the syn- and anti-isomers of oxime 8 obtained from 4 were characterized by solid-state NMR and variable-temperature NMR experiments in acetone-d(6).

  12. NMR methodologies in the analysis of blueberries. (United States)

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


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

  13. Structural Investigation in Solution of a series of five-Coordinate Bisphosphinoaryl Ruthenium(II) Complexes

    NARCIS (Netherlands)

    Koten, G. van; Dani, P.; Kink, G. van


    The structure of the ruthenium(II) complexes [RuCl{C6H2(CH2PPh2)2-2,6-R-4}(PPh3)] [R = H (1), Ph (2) or Br (3)] was investigated in solution using two-dimensional NMR techniques (1H-1H-, 13C-1H- and 31P-1H-correlation NMR spectroscopy and 1H NOESY). The 1H and 13C NMR spectra of the complexes 1-3

  14. Synthesis and characterization of polyanhydride derived from castor oil; Sintese e caracterizacao de polianidrido derivado do oleo de mamona

    Energy Technology Data Exchange (ETDEWEB)

    Borges, Fernando de M.; Reis, Roberta Yonara Nascimento; Nobre, Francisco X.; Matos, Jose M.E., E-mail: [Universidade Federal do Piaui (UFPI), Teresina, PI (Brazil)


    Polyanhydrides are biopolymers already used as drug carriers, that allow the controlled release of the drug in vivo. Currently, these polymers are produced from a polyol, such as ethyleneglycol. In this work we synthesized a polyanhydride from castor oil, from the derivatization of oil via alcoholysis reaction. The oil was then converted to a monoglyceride (MG) by alcoholysis reaction at 140 °C. The MG reacted with phthalic anhydride (PA) at 100 °C, forming the polymer P1. The polymer was characterized by FT-IR, {sup 1}H and {sup 13}C NMR. These techniques allowed confirmation of the polymer formation. (author)

  15. Exploring translocation of proteins on DNA by NMR

    Energy Technology Data Exchange (ETDEWEB)

    Marius Clore, G., E-mail: [National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Laboratory of Chemical Physics (United States)


    While an extensive body of knowledge has accumulated on the structures of transcription factors, DNA and their complexes from both NMR and crystallography, much less is known at a molecular level regarding the mechanisms whereby transcription factors locate their specific DNA target site within an overwhelming sea of non-specific DNA sites. Indirect kinetic data suggested that three processes are involved in the search procedure: jumping by dissociation of the protein from the DNA followed by re-association at another site, direct transfer from one DNA molecule or segment to another, and one-dimensional sliding. In this brief perspective I summarize recent NMR developments from our laboratory that have permitted direct characterization of the species and molecular mechanisms involved in the target search process, including the detection of highly transient sparsely-populated states. The main tool in these studies involves the application of paramagnetic relaxation enhancement, supplemented by z-exchange spectroscopy, lineshape analysis and residual dipolar couplings. These studies led to the first direct demonstration of rotation-coupled sliding of a protein along the DNA and the direct transfer of a protein from one DNA molecule to another without dissociating into free solution.

  16. Flow NMR of polymers in external fields

    Energy Technology Data Exchange (ETDEWEB)

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


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

  17. Characterization by NMR of ozonized methyl linoleate

    Energy Technology Data Exchange (ETDEWEB)

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


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

  18. NMR metabolomics of renal cancer: an overview. (United States)

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


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

  19. Isolation and characterization of soluble sulfated polysaccharide from the red seaweed Glucaric cornea; Isolamento e caracterizacao do polissacarideo sulfatado soluvel extraido da alga vermelha Gracilaria cornea

    Energy Technology Data Exchange (ETDEWEB)

    Melo, Marcia R.S.; Freitas, Ana L.P. [Ceara Univ., Fortaleza, CE (Brazil). Dept. de Bioquimica e Biologia Molecular]. E-mail:; Feitosa, Judith P.A.; Paula, Regina C.M. de [Ceara Univ., Fortaleza, CE (Brazil). Dept. de Quimica Organica e Inorganica]. E-mail:


    The composition, structure and rheological properties of soluble sulphated polysaccharide Glucaric cornea from Brazilian red seaweeds were investigated. The main components of polysaccharide were 3,6-anhydrogalactose (24.7%) and galactose (64.6%). In addition, minor components as 6-O-methyl-galactose (8.5%), glucose (1.5%), xylose (0.7%) and sulfated groups (4.8%) were detected. Comparison between sulphates content determined by Ft-IR spectroscopy and micro elemental analysis was made. Data from {sup 13}C NMR and FT-IR provided evidence of sulphation in C-4 and C-6 of galactose. No gelation with 1.5, 2.0 and 3.0 % (w/v) aqueous solution was observed, even cooled up to 4 deg C. GPC indicated two majors polysaccharide fractions of M{sub pk} 7.4 x 10{sup 4} and 1.8 x 10{sup 4} g/mol and a minor fraction of M{sub pk} 2.1 x 10{sup 6} g/mol. (author)

  20. The eNMR platform for structural biology


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


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

  1. New Designs for NMR Core Scanning (United States)

    Bluemich, B.; Anferova, S.; Talnishnikh, E.; Arnold, J.; Clauser, C.


    Within the last ten years, mobile magnetic resonance has moved from the oil field to many new areas of application. While the focus of mobile NMR in the past was on single-sided or inside-out NMR, the advent of tube-shaped Halbach magnets has introduced the conventional outside-in NMR concept to mobile NMR where the object is inside a magnet. Our Halbach magnet is constructed from small magnet blocks at light weight and low cost with a magnetic field sufficiently homogeneous. To automatize NMR measurements, the Halbach magnet is mounted on a sliding table to scan long core sections without human interaction. In homogeneous magnetic fields, the longitudinal relaxation time T1 and even the transverse relaxation time T2 are proportional to the pore diameters of rocks. Hence, the T1 and T2 signals map the pore-size distribution of the studied rock cores. For fully saturated samples the integral of the distribution curve is proportional to porosity. The porosity values from NMR measurements with the Halbach magnet are used to estimate permability. The Halbach magnet can be used for certain sample geometries in combination with exchangeable radio frequency (rf) coils with different diameters from 24 mm up to 80 mm. To measure standard Ocean Drilling Program (ODP)/Integrated Ocean Drilling Program (IODP) cores, which have a standard diameter of 60 mm and are split lengthwise after recovery, we use a surface figure-8 rf coil with an inner diameter of 60 mm. Besides 1D T2 measurements, we perform relaxation-relaxation correlation experiments, where T1 and T2 are measured in parallel. In this way, the influence of diffusion on the shape of the T2 distribution function is probed. A gradient coil system was designed to perform Pulsed Field Gradients (PFG) experiments. As the gradient coils restrict the axial access to the magnet, only cylindrical core plugs with 20 mm in diameter can be analysed by PFG NMR methods. The homogeneity of the magnetic field in the sensitive volume

  2. Untangle soil-water-mucilage interactions: 1H NMR Relaxometry is lifting the veil (United States)

    Brax, Mathilde; Buchmann, Christian; Schaumann, Gabriele Ellen


    Mucilage is mainly produced at the root tips and has a high water holding capacity derived from highly hydrophilic gel-forming substances. The objective of the MUCILAGE project is to understand the mechanistic role of mucilage for the regulation of water supply for plants. Our subproject investigates the chemical and physical properties of mucilage as pure gel and mixed with soil. 1H-NMR Relaxometry and PFG NMR represent non-intrusive powerful methods for soil scientific research by allowing quantification of the water distribution as well as monitoring of the water mobility in soil pores and gel phases.Relaxation of gel water differs from the one of pure water due to additional interactions with the gel matrix. Mucilage in soil leads to a hierarchical pore structure, consisting of the polymeric biohydrogel network surrounded by the surface of soil particles. The two types of relaxation rates 1/T1 and 1/T2 measured with 1H-NMR relaxometry refer to different relaxation mechanisms of water, while PFG-NMR measures the water self-diffusion coefficient. The objective of our study is to distinguish in situ water in gel from pore water in a simplified soil system, and to determine how the "gel effect" affects both relaxation rates and the water self-diffusion coefficient in porous systems. We demonstrate how the mucilage concentration and the soil solution alter the properties of water in the respective gel phases and pore systems in model soils. To distinguish gel-inherent processes from classical processes, we investigated the variations of the water mobility in pure chia mucilage under different conditions by using 1H-NMR relaxometry and PFG NMR. Using model soils, the signals coming from pore water and gel water were differentiated. We combined the equations describing 1H-NMR relaxation in porous systems and our experimental results, to explain how the presence of gel in soil affects 1H-NMR relaxation. Out of this knowledge we propose a method, which determines in

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


    Yang Liu; Zhaoxia Liu; Huaxin Yang; Lan He


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

  4. Examination of amber and related materials by NMR spectroscopy. (United States)

    Lambert, Joseph B; Santiago-Blay, Jorge A; Wu, Yuyang; Levy, Allison J


    Examination of the solid-state (13)C and solution (1)H NMR spectra of fossilized resins (ambers) has generated five groupings of materials based on spectral characteristics. The worldwide Group A is associated with the botanical family of the Araucariaceae. The worldwide Group B is associated with the Dipterocarpaceae. Baltic amber or succinite (Group C) is related to Group A but with a disputed conifer source. Amber from Latin America, the Caribbean, and Africa is associated with the Fabaceae, the genus Hymenaea in particular. The minor Group E contains the rare fossil polystyrene. The spectra of jet indicate that it is a coal-like material with a rank between lignite and sub-bituminous coal. Copyright © 2014 John Wiley & Sons, Ltd.


    African Journals Online (AJOL)

    Preferred Customer

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

  6. nmrML: a community supported open data standard for the description, storage, and exchange of NMR data. (United States)

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


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

  7. Hyperpolarized NMR Probes for Biological Assays

    Directory of Open Access Journals (Sweden)

    Sebastian Meier


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

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

    African Journals Online (AJOL)



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

  9. Developments in Solid-State NMR

    Indian Academy of Sciences (India)

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

  10. Bench-top NMR-food

    NARCIS (Netherlands)

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


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

  11. NMR Analysis of Some Pentacycloundecanedione Derivatives

    African Journals Online (AJOL)


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

  12. Quantification of complex mixtures by NMR

    NARCIS (Netherlands)

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


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

  13. Structures of Biomolecules by NMR Spectroscopy

    Indian Academy of Sciences (India)

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

  14. Solid-state NMR for bacterial biofilms (United States)

    Reichhardt, Courtney; Cegelski, Lynette


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

  15. NMR and mushrooms : imaging post harvest senescence

    NARCIS (Netherlands)

    Donker, H.C.W.


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

  16. NMR characterization of polymers: Review and update (United States)

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

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

    African Journals Online (AJOL)

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

  18. NMR Analysis of Some Pentacycloundecanedione Derivatives

    African Journals Online (AJOL)


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


    African Journals Online (AJOL)

    Preferred Customer

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

  20. Quantitative NMR of quadrupolar nucleus as a novel analytical method: hydrolysis behaviour analysis of aluminum ion. (United States)

    Maki, Hideshi; Sakata, Genki; Mizuhata, Minoru


    In this study, quantitative nuclear magnetic resonance (qNMR) spectroscopy of quadrupolar nuclei has been established. The complicated hydrolysis behavior of the Al(3+) ion, which causes fish poisoning and inhibits the growth of plants in environmental water, was clarified by (27)Al qNMR spectroscopy. Highly accurate simultaneous multicomponent quantitative analysis of various hydrolyzed forms of the Al ion was achieved in a non-destructive manner. The calibration curve of the external standard aqueous Al(NO3)3 solution showed excellent linearity over a very wide concentration range from 1 × 10(-4) to 1 mol L(-1) (an increase in concentration of 10 000 times), with a simple experimental and analytical procedure. Furthermore, the weaknesses of the conventional Ferron assay and the advantages of (27)Al qNMR spectroscopy were considered. The quantitative determination error for the free [Al(H2O)6](3+) ion and the trinuclear complex, which has a high complexation rate, is higher in the Ferron assay than in the (27)Al qNMR technique. The concentrations of four Al species were directly determined by (27)Al qNMR, namely, free [Al(H2O)6](3+), the trinuclear complex, Al(OH)4(-), and tridecameric hydrolyzed Al, which has a Keggin structure. The concentration of the tridecamer rapidly increased until 100 min after NaOH addition, and showed a local maximum after 1 week. In addition, the concentration of colloidal Al hydroxide, which cannot be detected by NMR spectroscopy, was determined by numerical analysis. This species was generated in the initial stage of reaction, and then the tridecamer formed very slowly.

  1. Motions and entropies in proteins as seen in NMR relaxation experiments and molecular dynamics simulations. (United States)

    Allnér, Olof; Foloppe, Nicolas; Nilsson, Lennart


    Molecular dynamics simulations of E. coli glutaredoxin1 in water have been performed to relate the dynamical parameters and entropy obtained in NMR relaxation experiments, with results extracted from simulated trajectory data. NMR relaxation is the most widely used experimental method to obtain data on dynamics of proteins, but it is limited to relatively short timescales and to motions of backbone amides or in some cases (13)C-H vectors. By relating the experimental data to the all-atom picture obtained in molecular dynamics simulations, valuable insights on the interpretation of the experiment can be gained. We have estimated the internal dynamics and their timescales by calculating the generalized order parameters (O) for different time windows. We then calculate the quasiharmonic entropy (S) and compare it to the entropy calculated from the NMR-derived generalized order parameter of the amide vectors. Special emphasis is put on characterizing dynamics that are not expressed through the motions of the amide group. The NMR and MD methods suffer from complementary limitations, with NMR being restricted to local vectors and dynamics on a timescale determined by the rotational diffusion of the solute, while in simulations, it may be difficult to obtain sufficient sampling to ensure convergence of the results. We also evaluate the amount of sampling obtained with molecular dynamics simulations and how it is affected by the length of individual simulations, by clustering of the sampled conformations. We find that two structural turns act as hinges, allowing the α helix between them to undergo large, long timescale motions that cannot be detected in the time window of the NMR dipolar relaxation experiments. We also show that the entropy obtained from the amide vector does not account for correlated motions of adjacent residues. Finally, we show that the sampling in a total of 100 ns molecular dynamics simulation can be increased by around 50%, by dividing the

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

    Energy Technology Data Exchange (ETDEWEB)

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


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

  3. Production and characterization of poly(styrene-co-methylmethacrylate);Producao e caracterizacao de poliestireno-co-metacrilato de metila

    Energy Technology Data Exchange (ETDEWEB)

    Augustinho, Tiago R.; Coan, Thais; Abarca, Silvia A.C.; Testoni, Alex A.S.; Baumgarten, Bruno P.; Machado, Ricardo A.F., E-mail: [Universidade Federal de Santa Catarina (UFSC), Florianopolis (Brazil). Dept. de Engenharia Quimica e Alimentos


    Polystyrene (PS) is a polymer used in diverse industrial segments. It is easy to process and has a low cost when compared to other materials. However, PS has low mechanical resistance, which limits its application in some areas. Thus, a methodology that is sufficiently used is the synthesis of a copolymer, formed of two or more monomers to get products that have characteristics that are not possible to obtain with only one monomer. In this work, the styrene and methyl methacrylate monomers had been carried through reactions of copolymerization by means of polymerization in suspension using (MMA) with styrene in a bigger percentage. MMA was selected for being a monomer that results in a polymeric configuration more resistant than the PS. The copolymerization was proven to occur by infra-red spectroscopy (IR) and Nuclear Magnetic Resonance (NMR). Different analyses were performed using different initiators, weight molar and conversion studies. (author)

  4. 1H NMR Analysis of Cerebrospinal Fluid from Alzheimer’s Disease Patients: An Example of a Possible Misinterpretation Due to Non-Adjustment of pH

    Directory of Open Access Journals (Sweden)

    Thomas Cruz


    Full Text Available Two publications from the same research group reporting on the detection of new possible biomarkers for the early diagnosis of Alzheimer’s disease (AD, based on the analysis of cerebrospinal fluid samples (CSF with 1H Nuclear Magnetic Resonance (NMR, are at the origin of the present study. The authors observed significant differences in 1H NMR spectra of CSF from AD patients and healthy controls and, thus, proposed some NMR signals (without attribution as possible biomarkers. However, this work was carried out in non-standardized pH conditions. Our study aims at warning about a possible misinterpretation that can arise from 1H NMR analyses of CSF samples if pH adjustment is not done before NMR analysis. Indeed, CSF pH increases rapidly after removal and is subject to changes over conservation time. We first identify the NMR signals described by the authors as biomarkers. We then focus on the chemical shift variations of their NMR signals as a function of pH in both standard solutions and CSF samples. Finally, a principal component analysis of 1H NMR data demonstrates that the same CSF samples recorded at pH 8.1 and 10.0 are statistically differentiated.

  5. Petrophysical properties of greensand as predicted from NMR measurements

    DEFF Research Database (Denmark)

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


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

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

    Indian Academy of Sciences (India)


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

  7. OPENCORE NMR: open-source core modules for implementing an integrated FPGA-based NMR spectrometer. (United States)

    Takeda, Kazuyuki


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

  8. Applications of NMR diffusion methods with emphasis on ion pairing in inorganic chemistry: a mini-review. (United States)

    Pregosin, Paul S


    This mini-review provides a brief overview of the use of NMR diffusion methods in connection with estimating molecular weights in solution, recognizing hydrogen bonding and encapsulation processes and, primarily, identifying and estimating the varying degrees of ion pairing. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

  9. Automatic Assignment of Methyl-NMR Spectra of Supramolecular Machines Using Graph Theory. (United States)

    Pritišanac, Iva; Degiacomi, Matteo T; Alderson, T Reid; Carneiro, Marta G; Ab, Eiso; Siegal, Gregg; Baldwin, Andrew J


    Methyl groups are powerful probes for the analysis of structure, dynamics and function of supramolecular assemblies, using both solution- and solid-state NMR. Widespread application of the methodology has been limited due to the challenges associated with assigning spectral resonances to specific locations within a biomolecule. Here, we present Methyl Assignment by Graph Matching (MAGMA), for the automatic assignment of methyl resonances. A graph matching protocol examines all possibilities for each resonance in order to determine an exact assignment that includes a complete description of any ambiguity. MAGMA gives 100% accuracy in confident assignments when tested against both synthetic data, and 9 cross-validated examples using both solution- and solid-state NMR data. We show that this remarkable accuracy enables a user to distinguish between alternative protein structures. In a drug discovery application on HSP90, we show the method can rapidly and efficiently distinguish between possible ligand binding modes. By providing an exact and robust solution to methyl resonance assignment, MAGMA can facilitate significantly accelerated studies of supramolecular machines using methyl-based NMR spectroscopy.

  10. speaq 2.0: A complete workflow for high-throughput 1D NMR spectra processing and quantification. (United States)

    Beirnaert, Charlie; Meysman, Pieter; Vu, Trung Nghia; Hermans, Nina; Apers, Sandra; Pieters, Luc; Covaci, Adrian; Laukens, Kris


    Nuclear Magnetic Resonance (NMR) spectroscopy is, together with liquid chromatography-mass spectrometry (LC-MS), the most established platform to perform metabolomics. In contrast to LC-MS however, NMR data is predominantly being processed with commercial software. Meanwhile its data processing remains tedious and dependent on user interventions. As a follow-up to speaq, a previously released workflow for NMR spectral alignment and quantitation, we present speaq 2.0. This completely revised framework to automatically analyze 1D NMR spectra uses wavelets to efficiently summarize the raw spectra with minimal information loss or user interaction. The tool offers a fast and easy workflow that starts with the common approach of peak-picking, followed by grouping, thus avoiding the binning step. This yields a matrix consisting of features, samples and peak values that can be conveniently processed either by using included multivariate statistical functions or by using many other recently developed methods for NMR data analysis. speaq 2.0 facilitates robust and high-throughput metabolomics based on 1D NMR but is also compatible with other NMR frameworks or complementary LC-MS workflows. The methods are benchmarked using a simulated dataset and two publicly available datasets. speaq 2.0 is distributed through the existing speaq R package to provide a complete solution for NMR data processing. The package and the code for the presented case studies are freely available on CRAN ( and GitHub (

  11. Membrane protein-lipid interactions in mixed micelles studied by NMR spectroscopy with the use of paramagnetic reagents. (United States)

    Hilty, Christian; Wider, Gerhard; Fernández, César; Wüthrich, Kurt


    For solution NMR studies of the structure and function of membrane proteins, these macromolecules have to be reconstituted and solubilized in detergent micelles. Detailed characterization of the mixed detergent/protein micelles is then of key importance to validate the results from such studies, and to evaluate how faithfully the natural environment of the protein in the biological membrane is mimicked by the micelle. In this paper, a selection of paramagnetic probes with different physicochemical properties are used to characterize the 60 kDa mixed micelles consisting of about 90 molecules of the detergent dihexanoylphosphatidylcholine (DHPC) and one molecule of the Escherichia coli outer-membrane protein X (OmpX), which had previously been extensively studied by solution NMR techniques. The observation of highly selective relaxation effects on the NMR spectra of OmpX and DHPC from a water-soluble relaxation agent and from nitroxide spin labels attached to lipophilic molecules, confirmed data obtained previously with more complex NMR studies of the diamagnetic OmpX/DHPC system, and yielded additional novel insights into the protein-detergent interactions in the mixed micelles. The application of paramagnetic probes to the well-characterized OmpX/DHPC system indicates that such probes should be widely applicable as an efficient support of NMR studies of the topology of mixed membrane protein-detergent micelles.


    Energy Technology Data Exchange (ETDEWEB)

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


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

  13. Solid state NMR of biopolymers and synthetic polymers

    Energy Technology Data Exchange (ETDEWEB)

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


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

  14. A Method for Systematic Assessment of Intrinsically Disordered Protein Regions by NMR

    Directory of Open Access Journals (Sweden)

    Natsuko Goda


    Full Text Available Intrinsically disordered proteins (IDPs that lack stable conformations and are highly flexible have attracted the attention of biologists. Therefore, the development of a systematic method to identify polypeptide regions that are unstructured in solution is important. We have designed an “indirect/reflected” detection system for evaluating the physicochemical properties of IDPs using nuclear magnetic resonance (NMR. This approach employs a “chimeric membrane protein”-based method using the thermostable membrane protein PH0471. This protein contains two domains, a transmembrane helical region and a C-terminal OB (oligonucleotide/oligosaccharide binding-fold domain (named NfeDC domain, connected by a flexible linker. NMR signals of the OB-fold domain of detergent-solubilized PH0471 are observed because of the flexibility of the linker region. In this study, the linker region was substituted with target IDPs. Fifty-three candidates were selected using the prediction tool POODLE and 35 expression vectors were constructed. Subsequently, we obtained 15N-labeled chimeric PH0471 proteins with 25 IDPs as linkers. The NMR spectra allowed us to classify IDPs into three categories: flexible, moderately flexible, and inflexible. The inflexible IDPs contain membrane-associating or aggregation-prone sequences. This is the first attempt to use an indirect/reflected NMR method to evaluate IDPs and can verify the predictions derived from our computational tools.

  15. Study of polymer film formation and their characterization using NMR, XRD and DSC

    Energy Technology Data Exchange (ETDEWEB)

    Ghoshal, Sushanta


    Film formation and their characterization of three eco-friendly polymers, namely gelatin, starch and poly(vinyl alcohol) (PVOH) were studied using nuclear magnetic resonance (NMR), wide-angle X-ray diffractometry (XRD) and differential scanning calorimetry (DSC) techniques. Polymer solutions were prepared using water as a solvent followed by casting. The drying process of the cast sample was monitored at room temperature with a single-sided NMR scanner until complete solidification occurred. Depth-dependent NMR profiles with microscopic resolution were acquired at different stages of sample drying. Each profile point was accumulated from the echo decay. Spin-spin relaxation times (T{sub 2}) were measured from the echo decays at different layers and were correlated with the drying process during film formation. Additionally, spin-lattice relaxation times (T{sub 1}) were determined. Depending on the polymer studied and the initial concentration of each polymer, different types of molecular dynamics were observed at different heights during evaporation of the solvent. The study indicates that each polymer shows a spatial heterogeneity in the molecular dynamics during drying. In the advanced stage of drying process, the microscopic arrangement of the polymer chains during their solidification is influenced by this dynamic heterogeneity and determines the final structure of the film. XRD of the film in its final state confirmed the structural heterogeneity identified by the NMR.

  16. Magic angle spinning NMR structure determination of proteins from pseudocontact shifts. (United States)

    Li, Jianping; Pilla, Kala Bharath; Li, Qingfeng; Zhang, Zhengfeng; Su, Xuncheng; Huber, Thomas; Yang, Jun


    Magic angle spinning solid-state NMR is a unique technique to study atomic-resolution structure of biomacromolecules which resist crystallization or are too large to study by solution NMR techniques. However, difficulties in obtaining sufficient number of long-range distance restraints using dipolar coupling based spectra hamper the process of structure determination of proteins in solid-state NMR. In this study it is shown that high-resolution structure of proteins in solid phase can be determined without the use of traditional dipolar-dipolar coupling based distance restraints by combining the measurements of pseudocontact shifts (PCSs) with Rosetta calculations. The PCSs were generated by chelating exogenous paramagnetic metal ions to a tag 4-mercaptomethyl-dipicolinic acid, which is covalently attached to different residue sites in a 56-residue immunoglobulin-binding domain of protein G (GB1). The long-range structural restraints with metal-nucleus distance of up to ∼20 Å are quantitatively extracted from experimentally observed PCSs, and these are in good agreement with the distances back-calculated using an X-ray structure model. Moreover, we demonstrate that using several paramagnetic ions with varied paramagnetic susceptibilities as well as the introduction of paramagnetic labels at different sites can dramatically increase the number of long-range restraints and cover different regions of the protein. The structure generated from solid-state NMR PCSs restraints combined with Rosetta calculations has 0.7 Å root-mean-square deviation relative to X-ray structure.

  17. NMR shielding calculations across the periodic table: diamagnetic uranium compounds. 2. Ligand and metal NMR. (United States)

    Schreckenbach, Georg


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

  18. Solid-state NMR basic principles and practice

    CERN Document Server

    Apperley, David C; Hodgkinson, Paul


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

  19. Multiecho scheme advances surface NMR for aquifer characterization (United States)

    Grunewald, Elliot; Walsh, David


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

  20. NMR-based diffusion lattice imaging. (United States)

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


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

  1. NMR-based diffusion lattice imaging (United States)

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


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

  2. Strange kinetics, porous media, and NMR

    Energy Technology Data Exchange (ETDEWEB)

    Kimmich, Rainer


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

  3. Structure of high-resolution NMR spectra

    CERN Document Server

    Corio, PL


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

  4. NMR characteristics of rat mammary tumors

    Energy Technology Data Exchange (ETDEWEB)

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


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

  5. Quantitative calibration of radiofrequency NMR Stark effects. (United States)

    Tarasek, Matthew R; Kempf, James G


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

  6. 3D Reconstruction of NMR Images

    Directory of Open Access Journals (Sweden)

    Peter Izak


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

  7. Structural characterization of Heusler compounds using NMR

    Energy Technology Data Exchange (ETDEWEB)

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


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

  8. Multispectral dual isotope and NMR image analysis

    Energy Technology Data Exchange (ETDEWEB)

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


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

  9. Protein NMR structures refined without NOE data. (United States)

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


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

  10. Guiding automated NMR structure determination using a global optimization metric, the NMR DP score. (United States)

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


    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.

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

    Energy Technology Data Exchange (ETDEWEB)

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


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

  12. Viscosity Solution


    Camilli, Fabio; Prados, Emmanuel


    International audience; Viscosity solution is a notion of weak solution for a class of partial differential equations of Hamilton-Jacobi type. The range of applications of the notions of viscosity solution and Hamilton-Jacobi equations is enormous, including common class of partial differential equations such as evolutive problems and problems with boundary conditions, equations arising in optimal control theory, differential games, second-order equations arising in stochastic optimal control...

  13. NMR spectroscopy of experimentally shocked single crystal quartz: A reexamination of the NMR shock barometer (United States)

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


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

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

    Energy Technology Data Exchange (ETDEWEB)

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


    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.

  15. Xenon NMR: Chemical Shifts of a General Anesthetic in Common Solvents, Proteins, and Membranes (United States)

    Miller, Keith W.; Reo, Nicholas V.; Schoot Uiterkamp, Antonius J. M.; Stengle, Diane P.; Stengle, Thomas R.; Williamson, Kenneth L.


    The rare gas xenon contains two NMR-sensitive isotopes in high natural abundance. The nuclide 129Xe has a spin of {textstyle1/2}; 131Xe is quadrupolar with a spin of {textstyle3/2}. The complementary NMR characteristics of these nuclei provide a unique opportunity for probing their environment. The method is widely applicable because xenon interacts with a useful range of condensed phases including pure liquids, protein solutions, and suspensions of lipid and biological membranes. Although xenon is chemically inert, it does interact with living systems; it is an effective general anesthetic. We have found that the range of chemical shifts of 129Xe dissolved in common solvents is ca. 200 ppm, which is 30 times larger than that found for 13C in methane dissolved in various solvents. Resonances were also observed for 131Xe in some systems; they were broader and exhibited much greater relaxation rates than did 129Xe. The use of 129Xe NMR as a probe of biological systems was investigated. Spectra were obtained from solutions of myoglobin, from suspensions of various lipid bilayers, and from suspensions of the membranes of erythrocytes and of the acetylcholine receptor-rich membranes of Torpedo californica. These systems exhibited a smaller range of chemical shifts. In most cases there was evidence of a fast exchange of xenon between the aqueous and organic environments, but the exchange was slow in suspensions of dimyristoyl lecithin vesicles.

  16. Multinuclear NMR and crystallographic studies of triorganotin valproates and their in vitro antifungal activities (United States)

    de Morais, Bárbara P.; de Lima, Geraldo M.; Pinheiro, Carlos B.; San Gil, Rosane A. S.; Takahashi, Jacqueline A.; Menezes, Daniele C.; Ardisson, José D.


    The reactions of triorganotin chlorides and sodium valproate, Na(OVp), yielded three triorganotin valproates [{SnMe3(OVp)}n] (1), [{SnBu3(OVp)}n] (2) and [SnPh3(OVp)] (3). All complexes have been authenticated in terms of infrared, 1H and 13C NMR, and solution- and solid-state 119Sn NMR, 119Sn Mössbauer and X-ray crystallography. The 119Sn NMR experiments provided important informations concerning the structures of (1)-(3) in solution and in the solid state. The X-ray experiments revealed the double-polymeric chain of complex (1), in which the geometry at the Sn(IV) is trigonal bipyramidal with intermolecular valproate bridges. The structure of complex (3) was re-determined and the new data show the tin cation at the centre of a distorted trigonal bipyramid, and not coordinated by four electron donating groups. The biological activity of all derivatives has been screened in terms of IC50 (μmol L-1) against C. albicans (ATCC 18804), C. tropicalis (ATCC 750), C. glabrata (ATCC 90030), C. parapsilosis (ATCC 22019), C. lusitaniae (CBS 6936) and C. dubliniensis (clinical isolate 28). Complex (3) exhibited the best biocide activity.

  17. Osmotic dehydration of organic kiwifruit pre-treated by pulsed electric fields and monitored by NMR. (United States)

    Traffano-Schiffo, Maria Victoria; Laghi, Luca; Castro-Giraldez, Marta; Tylewicz, Urszula; Rocculi, Pietro; Ragni, Luigi; Dalla Rosa, Marco; Fito, Pedro J


    Osmotic dehydration (OD) is a widely used preservation technique that consists in the reduction in food water activity by the immersion of the biological tissue in hypertonic solutions. The aim of this work was to analyze the effect of pulsed electric fields (PEF) in mass transfer as a pre-treatment of the OD using NMR. In this sense, PEF pre-treatments were done using three different voltages (100, 250 and 400V/cm) and 60 number of pulse. The OD of kiwifruit was carried out in 61.5% of sucrose solution at 25°C, for a contact period from 0 to 120min. The water distribution into the cellular tissue was studied by NMR relaxometry. In conclusion, NMR is an excellent technique for quantifying water molecules according to their interactions in the fruit tissue, obtaining the adsorbed water and opening the possibility to apply the BET model to fit the adsorbed isotherm over the whole range of water activity. Copyright © 2017 Elsevier Ltd. All rights reserved.

  18. Analytical approaches toward successful human cell metabolome studies by NMR spectroscopy. (United States)

    Duarte, Iola F; Marques, Joana; Ladeirinha, Ana F; Rocha, Cláudia; Lamego, Inês; Calheiros, Rita; Silva, Tânia M; Marques, M Paula M; Melo, Joana B; Carreira, Isabel M; Gil, Ana M


    The aim of this work was to investigate the effects of cell handling and storage on cell integrity and (1)H high resolution magic angle spinning (HRMAS) NMR spectra. Three different cell types have been considered (lung tumoral, amniocytes, and MG-63 osteosarcoma cells) in order for sample-dependent effects to be identified. Cell integrity of fresh cells and cells frozen in cryopreservative solution was approximately 70-80%, with the former showing higher membrane degradation, probably enzymatic, as indicated by increased phosphocholine (PC) and/or glycerophosphocholine (GPC). Unprotected freezing (either gradual or snap-freezing) was found to lyse cells completely, similar to mechanical cell lysis. Besides enhanced metabolites visibility, lysed cells showed a different lipid profile compared to intact cells, with increased choline, PC, and GPC and decreased phosphatidylcholine (PTC). Cell lysis has, therefore, a significant effect on cell lipid composition, making handling reproducibility an important issue in lipid analysis. Sample spinning was found to disrupt 5-25% of cells, depending on cell type, and HRMAS was shown to be preferable to solution-state NMR of suspensions or supernatant, giving enhanced information on lipids and comparable resolution for smaller metabolites. Relaxation- and diffusion-edited NMR experiments gave limited information on intact cells, compared to lysed cells. The (1)H HRMAS spectra of the three cell types are compared and discussed.

  19. Redox-dependent conformational changes in eukaryotic cytochromes revealed by paramagnetic NMR spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Volkov, Alexander N.; Vanwetswinkel, Sophie; Van de Water, Karen; Nuland, Nico A. J. van, E-mail: [Vrije Universiteit Brussel, Jean Jeener NMR Centre, Structural Biology Brussels (Belgium)


    Cytochrome c (Cc) is a soluble electron carrier protein, transferring reducing equivalents between Cc reductase and Cc oxidase in eukaryotes. In this work, we assessed the structural differences between reduced and oxidized Cc in solution by paramagnetic NMR spectroscopy. First, we have obtained nearly-complete backbone NMR resonance assignments for iso-1-yeast Cc and horse Cc in both oxidation states. These were further used to derive pseudocontact shifts (PCSs) arising from the paramagnetic haem group. Then, an extensive dataset comprising over 450 measured PCSs and high-resolution X-ray and solution NMR structures of both proteins were used to define the anisotropic magnetic susceptibility tensor, {Delta}{chi}. For most nuclei, the PCSs back-calculated from the {Delta}{chi} tensor are in excellent agreement with the experimental PCS values. However, several contiguous stretches-clustered around G41, N52, and A81-exhibit large deviations both in yeast and horse Cc. This behaviour is indicative of redox-dependent structural changes, the extent of which is likely conserved in the protein family. We propose that the observed discrepancies arise from the changes in protein dynamics and discuss possible functional implications.

  20. Conformation of eight-membered benzoannulated lactams by combined NMR and DFT studies. (United States)

    Witosińska, Agnieszka; Musielak, Bogdan; Serda, Paweł; Owińska, Maria; Rys, Barbara


    The title compounds were synthesized, and their structure and conformational behavior in solution (NMR and DFT), in the gas phase (DFT), and, for some of them, in the solid state (X-ray) were investigated. The variable-temperature NMR spectra were employed to determine the conformational equilibria and the activation energy of the conformational changes of the eight-membered ring. The coalescence effects are assigned to racemization of the chiral ground-state conformation with a ring inversion barrier in the range of 38-100 kJ mol(-1) depending on the relative setting of the two strong conformational constraints: benzoannulation and the amide function. The second conformational process, interconversion between two different conformers, in the molecules of benzo[c]azocin-3-one, benzo[d]azocin-2-one, and benzo[d]azocin-4-one was observed. The natures of the conformers observed in solution were elucidated by analysis of experimental and calculated NMR data. The present results are discussed in conjunction with previous experimental and theoretical data on (Z,Z)-cyclooctadienes and their benzo analogues.

  1. A portable Halbach magnet that can be opened and closed without force: The NMR-CUFF (United States)

    Windt, Carel W.; Soltner, Helmut; Dusschoten, Dagmar van; Blümler, Peter


    Portable equipment for nuclear magnetic resonance (NMR) is becoming increasingly attractive for use in a variety of applications. One of the main scientific challenges in making NMR portable is the design of light-weight magnets that possess a strong and homogeneous field. Existing NMR magnets can provide such magnetic fields, but only for small samples or in small regions, or are rather heavy. Here we show a simple yet elegant concept for a Halbach-type permanent magnet ring, which can be opened and closed with minimal mechanical force. An analytical solution for an ideal Halbach magnet shows that the magnetic forces cancel if the structure is opened at an angle of 35.3° relative to its poles. A first prototype weighed only 3.1 kg, and provided a flux density of 0.57 T with a homogeneity better than 200 ppm over a spherical volume of 5 mm in diameter without shimming. The force needed to close it was found to be about 20 N. As a demonstration, intact plants were imaged and water (xylem) flow measured. Magnets of this type (NMR-CUFF = Cut-open, Uniform, Force Free) are ideal for portable use and are eminently suited to investigate small or slender objects that are part of a larger or immobile whole, such as branches on a tree, growing fruit on a plant, or non-metallic tubing in industrial installations. This new concept in permanent-magnet design enables the construction of openable, yet strong and homogeneous magnets, which aside from use in NMR or MRI could also be of interest for applications in accelerators, motors, or magnetic bearings.

  2. PFG NMR and Bayesian analysis to characterise non-Newtonian fluids (United States)

    Blythe, Thomas W.; Sederman, Andrew J.; Stitt, E. Hugh; York, Andrew P. E.; Gladden, Lynn F.


    Many industrial flow processes are sensitive to changes in the rheological behaviour of process fluids, and there therefore exists a need for methods that provide online, or inline, rheological characterisation necessary for process control and optimisation over timescales of minutes or less. Nuclear magnetic resonance (NMR) offers a non-invasive technique for this application, without limitation on optical opacity. We present a Bayesian analysis approach using pulsed field gradient (PFG) NMR to enable estimation of the rheological parameters of Herschel-Bulkley fluids in a pipe flow geometry, characterised by a flow behaviour index n , yield stress τ0 , and consistency factor k , by analysis of the signal in q -space. This approach eliminates the need for velocity image acquisition and expensive gradient hardware. We investigate the robustness of the proposed Bayesian NMR approach to noisy data and reduced sampling using simulated NMR data and show that even with a signal-to-noise ratio (SNR) of 100, only 16 points are required to be sampled to provide rheological parameters accurate to within 2% of the ground truth. Experimental validation is provided through an experimental case study on Carbopol 940 solutions (model Herschel-Bulkley fluids) using PFG NMR at a 1H resonance frequency of 85.2 MHz; for SNR > 1000, only 8 points are required to be sampled. This corresponds to a total acquisition time of Carbopol 940 we observe a change in rheological characteristics, probably due to shear history-dependent behaviour and the different geometries used. This behaviour highlights the need for online, or inline, rheological characterisation in industrial process applications.

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

    Energy Technology Data Exchange (ETDEWEB)

    Bingol, Kerem; Brüschweiler, Rafael


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

  4. Fast automated protein NMR data collection and assignment by ADAPT-NMR on Bruker spectrometers (United States)

    Lee, Woonghee; Hu, Kaifeng; Tonelli, Marco; Bahrami, Arash; Neuhardt, Elizabeth; Glass, Karen C.; Markley, John L.


    ADAPT-NMR (Assignment-directed Data collection Algorithm utilizing a Probabilistic Toolkit in NMR) supports automated NMR data collection and backbone and side chain assignment for [U-13C, U-15N]-labeled proteins. Given the sequence of the protein and data for the orthogonal 2D 1H-15N and 1H-13C planes, the algorithm automatically directs the collection of tilted plane data from a variety of triple-resonance experiments so as to follow an efficient pathway toward the probabilistic assignment of 1H, 13C, and 15N signals to specific atoms in the covalent structure of the protein. Data collection and assignment calculations continue until the addition of new data no longer improves the assignment score. ADAPT-NMR was first implemented on Varian (Agilent) spectrometers [A. Bahrami, M. Tonelli, S.C. Sahu, K.K. Singarapu, H.R. Eghbalnia, J.L. Markley, PLoS One 7 (2012) e33173]. Because of broader interest in the approach, we present here a version of ADAPT-NMR for Bruker spectrometers. We have developed two AU console programs (ADAPT_ORTHO_run and ADAPT_NMR_run) that run under TOPSPIN Versions 3.0 and higher. To illustrate the performance of the algorithm on a Bruker spectrometer, we tested one protein, chlorella ubiquitin (76 amino acid residues), that had been used with the Varian version: the Bruker and Varian versions achieved the same level of assignment completeness (98% in 20 h). As a more rigorous evaluation of the Bruker version, we tested a larger protein, BRPF1 bromodomain (114 amino acid residues), which yielded an automated assignment completeness of 86% in 55 h. Both experiments were carried out on a 500 MHz Bruker AVANCE III spectrometer equipped with a z-gradient 5 mm TCI probe. ADAPT-NMR is available at in the form of pulse programs, the two AU programs, and instructions for installation and use.

  5. Variable-Temperature 1H-NMR Studies on Two C-Glycosylflavones

    Directory of Open Access Journals (Sweden)

    William F. Reynolds


    Full Text Available Two known C-glycosylflavones, swertisin and embinoidin, were isolated from the leaves of Anthurium aripoense, and characterized by room temperature 1D and 2D NMR experiments. At this temperature, the 1H- and 13C-NMR spectra of these C-glycosylflavones revealed doubling of signals, which suggested the presence of two rotamers in solution. Variable-temperature (VT 1H-NMR studies supported this hypothesis. The T-ROESY data, in addition to the theoretical (MM2 calculations utilizing the Chem3D Pro software, confirmed the hypothesis that the two rotamers interchange via rotation about the C-glycosidic bond.

  6. NMR in metabolomics and natural products research: two sides of the same coin. (United States)

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


    identify BSMs that are unstable to chemical isolation. We then show how the statistical method of covariance can be used to enhance the resolution of 2D NMR spectra and facilitate the semi-automated identification of individual components in a complex mixture. Comparative studies can be used with two or more samples, such as active vs inactive, diseased vs healthy, treated vs untreated, wild type vs mutant, and so on. We present two overall approaches to comparative studies: a simple but powerful method for comparing two 2D NMR spectra and a full statistical approach using multiple samples. The major bottleneck in all of these techniques is the rapid and reliable identification of unknown BSMs; the solution will require all the traditional approaches of both natural products chemistry and metabolomics as well as improved analytical methods, databases, and statistical tools.


    Directory of Open Access Journals (Sweden)

    Sutopo Hadi


    Full Text Available he synthesis of two stable platinum(IV complexes containing methoxo ligand, [Pt(CH32(OCH3(OHpy2] (1 and fac-[Pt(CH32(OCH3(H2O3] (2, has been successfully performed. Complex 1 was prepared by oxidative addition reaction of cis-[Pt(CH32py2] with dry methanol, and a subsequent reaction of 1 with 70 % HClO4 in water produced the platinum complex 2. The stability of complex 2 in acidic aqueous solution was investigated and monitored with 1H and 195Pt NMR. The platinum complex 2 was found to be quite stable toward hydrolysis and no -hydride elimination was observed. Keywords: Methoxoplatinum(IV, NMR, complex stability, hydrolysis

  8. Structural comparison of 1{beta}-Methylcarbapenem, Carbapenem and Penem: NMR studies and theoretical calculations

    Energy Technology Data Exchange (ETDEWEB)

    Sunagawa, M.; Sasaki, A.; Igarashi, J.-E.; Nishimura, T. [Research Center, Sumitomo Pharmaceuticals Co., Ltd., 3-1-98 Kasugadenaka, Konohanaku, Osaka (Japan)


    Structural comparisons of meropenem (1), desmethyl meropenem (2) and the penem analogue (3) which contain the same side chains at both C-2 and C-6 were performed using {sup 1}H NMR measurements together with 3-21G* level of ab initio MO and molecular mechanics calculations. The ab initio MO calculations reproduced the skeletons of these strained {beta}-lactam rings in good agreement with the crystallographic data. {sup 1}H NMR measurements in aqueous solution together with molecular modeling studies indicated that there were conformational differences of the C-2 and C-6 side chains in this series of compounds. These observations suggested that the conformational differences could affect their biological activities. (Copyright (c) 1998 Elsevier Science B.V., Amsterdam. All rights reserved.)

  9. /sup 13/C NMR studies of the molecular flexibility of antidepressants

    Energy Technology Data Exchange (ETDEWEB)

    Munro, S.L.; Andrews, P.R.; Craik, D.J.; Gale, D.J.


    The solution dynamics of a series of clinically potent antidepressants have been investigated by measuring /sup 13/C NMR relaxation parameters. Correlation times and internal motional rates were calculated from spin-lattice relaxation times and nuclear Overhauser effects for the protonated carbons in mianserin, imipramine-like antidepressants, and amitriptyline-like antidepressants. These data were interpreted in terms of overall molecular tumbling, internal rotations, and inherent flexibility of these structures. Of particular interest was the conformational variability of the tricyclic nucleus of the tricyclic antidepressants, where the data indicated a fivefold difference in mobility of the dimethylene bridge of imipramine-like antidepressants relative to amitriptyline-like compounds. The implications of such a difference in internal motions is discussed in relation to previous NMR studies and to the reported differences in pharmacological activity of these antidepressants.

  10. High-resolution NMR of hydrogen in organic solids by DNP enhanced natural abundance deuterium spectroscopy. (United States)

    Rossini, Aaron J; Schlagnitweit, Judith; Lesage, Anne; Emsley, Lyndon


    We demonstrate that high field (9.4 T) dynamic nuclear polarization (DNP) at cryogenic (∼100 K) sample temperatures enables the rapid acquisition of natural abundance (1)H-(2)H cross-polarization magic angle spinning (CPMAS) solid-state NMR spectra of organic solids. Spectra were obtained by impregnating substrates with a solution of the stable DNP polarizing agent TEKPol in tetrachloroethane. Tetrachloroethane is a non-solvent for the solids, and the unmodified substrates are then polarized through spin diffusion. High quality natural abundance (2)H CPMAS spectra of histidine hydrochloride monohydrate, glycylglycine and theophylline were acquired in less than 2h, providing direct access to hydrogen chemical shifts and quadrupolar couplings. The spectral resolution of the (2)H solid-state NMR spectra is comparable to that of (1)H spectra obtained with state of the art homonuclear decoupling techniques. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

  11. Solution structure of human prolactin

    DEFF Research Database (Denmark)

    Teilum, Kaare; Hoch, Jeffrey C; Goffin, Vincent


    We report the solution structure of human prolactin determined by NMR spectroscopy. Our result is a significant improvement over a previous structure in terms of number and distribution of distance restraints, regularity of secondary structure, and potential energy. More significantly, the struct......We report the solution structure of human prolactin determined by NMR spectroscopy. Our result is a significant improvement over a previous structure in terms of number and distribution of distance restraints, regularity of secondary structure, and potential energy. More significantly......, the structure is sufficiently different that it leads to different conclusions regarding the mechanism of receptor activation and initiation of signal transduction. Here, we compare the structure of unbound prolactin to structures of both the homologue ovine placental lactogen and growth hormone. The structures...... of unbound and receptor bound prolactin/placental lactogen are similar and no noteworthy structural changes occur upon receptor binding. The observation of enhanced binding at the second receptor site when the first site is occupied has been widely interpreted to indicate conformational change induced...

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

    Directory of Open Access Journals (Sweden)

    Yang Liu


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

  13. Direct Comparison of 19F qNMR and 1H qNMR by Characterizing Atorvastatin Calcium Content (United States)

    Liu, Yang; Liu, Zhaoxia; Yang, Huaxin


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

  14. Mathematical Development and Computational Analysis of Harmonic Phase-Magnetic Resonance Imaging (HARP-MRI) Based on Bloch Nuclear Magnetic Resonance (NMR) Diffusion Model for Myocardial Motion. (United States)

    Dada, Michael O; Jayeoba, Babatunde; Awojoyogbe, Bamidele O; Uno, Uno E; Awe, Oluseyi E


    Harmonic Phase-Magnetic Resonance Imaging (HARP-MRI) is a tagged image analysis method that can measure myocardial motion and strain in near real-time and is considered a potential candidate to make magnetic resonance tagging clinically viable. However, analytical expressions of radially tagged transverse magnetization in polar coordinates (which is required to appropriately describe the shape of the heart) have not been explored because the physics required to directly connect myocardial deformation of tagged Nuclear Magnetic Resonance (NMR) transverse magnetization in polar geometry and the appropriate harmonic phase parameters are not yet available. The analytical solution of Bloch NMR diffusion equation in spherical geometry with appropriate spherical wave tagging function is important for proper analysis and monitoring of heart systolic and diastolic deformation with relevant boundary conditions. In this study, we applied Harmonic Phase MRI method to compute the difference between tagged and untagged NMR transverse magnetization based on the Bloch NMR diffusion equation and obtained radial wave tagging function for analysis of myocardial motion. The analytical solution of the Bloch NMR equations and the computational simulation of myocardial motion as developed in this study are intended to significantly improve healthcare for accurate diagnosis, prognosis and treatment of cardiovascular related deceases at the lowest cost because MRI scan is still one of the most expensive anywhere. The analysis is fundamental and significant because all Magnetic Resonance Imaging techniques are based on the Bloch NMR flow equations.

  15. Direct 13C NMR Detection in HPLC Hyphenation Mode

    DEFF Research Database (Denmark)

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


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

  16. NMR conformational properties of an Anthrax Lethal Factor domain studied by multiple amino acid-selective labeling

    Energy Technology Data Exchange (ETDEWEB)

    Vourtsis, Dionysios J.; Chasapis, Christos T.; Pairas, George [Department of Pharmacy, University of Patras, GR-26504 Patras (Greece); Bentrop, Detlef [Institute of Physiology II, University of Freiburg, D-79104 Freiburg (Germany); Spyroulias, Georgios A., E-mail: [Department of Pharmacy, University of Patras, GR-26504 Patras (Greece)


    Highlights: • A polypeptide, N-ALF{sub 233}, was overexpressed in E. coli and successfully isolated. • We produced {sup 2}H/{sup 15}N/{sup 13}C labeled protein samples. • Amino acid selective approaches were applied. • We acquired several heteronuclear NMR spectra, to complete the backbone assignment. • Prediction of the secondary structure was performed. - Abstract: NMR-based structural biology urgently needs cost- and time-effective methods to assist both in the process of acquiring high-resolution NMR spectra and their subsequent analysis. Especially for bigger proteins (>20 kDa) selective labeling is a frequently used means of sequence-specific assignment. In this work we present the successful overexpression of a polypeptide of 233 residues, corresponding to the structured part of the N-terminal domain of Anthrax Lethal Factor, using Escherichia coli expression system. The polypeptide was subsequently isolated in pure, soluble form and analyzed structurally by solution NMR spectroscopy. Due to the non-satisfying quality and resolution of the spectra of this 27 kDa protein, an almost complete backbone assignment became feasible only by the combination of uniform and novel amino acid-selective labeling schemes. Moreover, amino acid-type selective triple-resonance NMR experiments proved to be very helpful.

  17. Toward a structure determination method for biomineral-associated protein using combined solid- state NMR and computational structure prediction. (United States)

    Masica, David L; Ash, Jason T; Ndao, Moise; Drobny, Gary P; Gray, Jeffrey J


    Protein-biomineral interactions are paramount to materials production in biology, including the mineral phase of hard tissue. Unfortunately, the structure of biomineral-associated proteins cannot be determined by X-ray crystallography or solution nuclear magnetic resonance (NMR). Here we report a method for determining the structure of biomineral-associated proteins. The method combines solid-state NMR (ssNMR) and ssNMR-biased computational structure prediction. In addition, the algorithm is able to identify lattice geometries most compatible with ssNMR constraints, representing a quantitative, novel method for investigating crystal-face binding specificity. We use this method to determine most of the structure of human salivary statherin interacting with the mineral phase of tooth enamel. Computation and experiment converge on an ensemble of related structures and identify preferential binding at three crystal surfaces. The work represents a significant advance toward determining structure of biomineral-adsorbed protein using experimentally biased structure prediction. This method is generally applicable to proteins that can be chemically synthesized. Copyright © 2010 Elsevier Ltd. All rights reserved.

  18. Automated Control of the Organic and Inorganic Composition of Aloe vera Extracts Using (1)H NMR Spectroscopy. (United States)

    Monakhova, Yulia B; Randel, Gabriele; Diehl, Bernd W K


    Recent classification of Aloe vera whole-leaf extract by the International Agency for Research and Cancer as a possible carcinogen to humans as well as the continuous adulteration of A. vera's authentic material have generated renewed interest in controlling A. vera. The existing NMR spectroscopic method for the analysis of A. vera, which is based on a routine developed at Spectral Service, was extended. Apart from aloverose, glucose, malic acid, lactic acid, citric acid, whole-leaf material (WLM), acetic acid, fumaric acid, sodium benzoate, and potassium sorbate, the quantification of Mg(2+), Ca(2+), and fructose is possible with the addition of a Cs-EDTA solution to sample. The proposed methodology was automated, which includes phasing, baseline-correction, deconvolution (based on the Lorentzian function), integration, quantification, and reporting. The NMR method was applied to 41 A. vera preparations in the form of liquid A. vera juice and solid A. vera powder. The advantages of the new NMR methodology over the previous method were discussed. Correlation between the new and standard NMR methodologies was significant for aloverose, glucose, malic acid, lactic acid, citric acid, and WLM (P < 0.0001, R(2) = 0.99). NMR was found to be suitable for the automated simultaneous quantitative determination of 13 parameters in A. vera.

  19. Structural fidelity and NMR relaxation analysis in a prototype RNA hairpin. (United States)

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


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

  20. Solution preparation

    Energy Technology Data Exchange (ETDEWEB)

    Seitz, M.G.


    Reviewed in this statement are methods of preparing solutions to be used in laboratory experiments to examine technical issues related to the safe disposal of nuclear waste from power generation. Each approach currently used to prepare solutions has advantages and any one approach may be preferred over the others in particular situations, depending upon the goals of the experimental program. These advantages are highlighted herein for three approaches to solution preparation that are currently used most in studies of nuclear waste disposal. Discussion of the disadvantages of each approach is presented to help a user select a preparation method for his particular studies. Also presented in this statement are general observations regarding solution preparation. These observations are used as examples of the types of concerns that need to be addressed regarding solution preparation. As shown by these examples, prior to experimentation or chemical analyses, laboratory techniques based on scientific knowledge of solutions can be applied to solutions, often resulting in great improvement in the usefulness of results.

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

    DEFF Research Database (Denmark)

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


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

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

    Energy Technology Data Exchange (ETDEWEB)

    Hirasaki, George J.; Mohanty, Kishore K.


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

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


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


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

  4. Application of quantitative 19F and 1H NMR for reaction monitoring and in situ yield determinations for an early stage pharmaceutical candidate. (United States)

    Do, Nga M; Olivier, Mark A; Salisbury, John J; Wager, Carrie B


    Quantitative NMR spectrometry (qNMR) is an attractive, viable alternative to traditional chromatographic techniques. It is a fast, easy, accurate, and nondestructive technique which allows an analyst to gain quantitative information about a component mixture without the necessity of authentic reference materials, as is the case with most other analytical techniques. This is ideal for the synthesis of active pharmaceutical ingredients (API) that are in the early stages of development where authentic standards of the analytes may not be available. In this paper, the application of (19)F and (1)H qNMR for reaction monitoring and in situ potency determinations will be discussed for an early stage pharmaceutical candidate with several analytical challenges. These challenges include low UV absorption, low ionization, thermal instability, and lack of authentic reference standards. Quantitative NMR provided quick, fit-for-purpose solutions for process development where conventional separation techniques were limited.

  5. Metal glasses in microscopic scale: NMR studies

    Energy Technology Data Exchange (ETDEWEB)

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


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

  6. Touch NMR: An NMR Data Processing Application for the iPad (United States)

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


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

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

    Energy Technology Data Exchange (ETDEWEB)

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


    Protein dynamics plays important roles in many biological events, such as ligand binding and enzyme reactions. NMR is mostly used for investigating such protein dynamics in a site-specific manner. Recently, NMR has been actively applied to large proteins and intrinsically disordered proteins, which are attractive research targets. However, signal overlap, which is often observed for such proteins, hampers accurate analysis of NMR data. In this study, we have developed a new methodology called relaxation dispersion difference that can extract conformational exchange parameters from overlapped NMR signals measured using relaxation dispersion spectroscopy. In relaxation dispersion measurements, the signal intensities of fluctuating residues vary according to the Carr-Purcell-Meiboon-Gill pulsing interval, whereas those of non-fluctuating residues are constant. Therefore, subtraction of each relaxation dispersion spectrum from that with the highest signal intensities, measured at the shortest pulsing interval, leaves only the signals of the fluctuating residues. This is the principle of the relaxation dispersion difference method. This new method enabled us to extract exchange parameters from overlapped signals of heme oxygenase-1, which is a relatively large protein. The results indicate that the structural flexibility of a kink in the heme-binding site is important for efficient heme binding. Relaxation dispersion difference requires neither selectively labeled samples nor modification of pulse programs; thus it will have wide applications in protein dynamics analysis.

  8. 31 P-NMR, 77 Se-NMR and mass spectral studies on some ...

    African Journals Online (AJOL)

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

  9. NMR structural studies of oligosaccharides and other natural products


    Kjærulff, Louise; Gotfredsen, Charlotte Held


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

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

    Energy Technology Data Exchange (ETDEWEB)

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


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

  11. Evaluation of fast 2D NMR for metabolomics. (United States)

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


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

  12. Synthesis and characterization of hydroxyapatite-doped silver nanoparticles; Sintese e caracterizacao de hidroxiapatita dopada com nanoparticulas de prata

    Energy Technology Data Exchange (ETDEWEB)

    Andrade, Flavio Augusto Cavadas da Silva; Rollo, Joao Manuel Domingos de Almeida, E-mail: [Universidade de Sao Paulo (EESC/FMRP/IQSC/USP), Sao Carlos, SP (Brazil). Programa de Pos-Graduacao Interunidades Bioengenharia; Rigo, Eliana Cristina da Silva; Vercik, Andres; Vercik, Luci Cristina de Oliveira; Valencia, German Ayala; Ferreira, Leticcia Gaviao [Universidade de Sao Paulo (USP), Pirassununga, SP (Brazil). Faculdade de Zootecnia e Engenharia de Alimentos. Departamento de Ciencias Basicas


    Hydroxyapatite-doped silver nanoparticles was obtained by immersing the powder in increasing dilutions of a solution containing AGNPS which were synthesized in different times and were characterized by UV-vis spectroscopy. The X-ray diffraction (XRD)studies demonstrate no change in the major phase of HA. Scanning Electron Microscopy (SEM) revealed morphological characteristics of powders after doping and the presence of silver was confirmed by energy dispersive X-ray (EDAX) analysis.The antibacterial effect of the doped powders was evaluated using strain of Staphylococcus aureus by disc-diffusion test. The zone of inhibition was found to vary with the amount of silver nanoparticle in the doped powder even for low concentrations of AgNPs. These results indicate that the method of immersion hydroxyapatite in solutions containing AgNPs is promising to obtain bioactive materials with low cytotoxicity and antibacterial effects. (author)

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


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


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

  14. Utilizing a Water-Soluble Cryptophane with Fast Xenon Exchange Rates for Picomolar Sensitivity NMR Measurements (United States)

    Bai, Yubin; Hill, P. Aru; Dmochowski, Ivan J.


    Hyperpolarized 129Xe chemical exchange saturation transfer (129Xe Hyper-CEST) NMR is a powerful technique for the ultrasensitive, indirect detection of Xe host molecules (e.g., cryptophane-A). Irradiation at the appropriate Xe-cryptophane resonant radio frequency results in relaxation of the bound hyperpolarized 129Xe and rapid accumulation of depolarized 129Xe in bulk solution. The cryptophane effectively ‘catalyzes’ this process by providing a unique molecular environment for spin depolarization to occur, while allowing xenon exchange with the bulk solution during the hyperpolarized lifetime (T1 ≈ 1 min). Following this scheme, a triacetic acid cryptophane-A derivative (TAAC) was indirectly detected at 1.4 picomolar concentration at 320 K in aqueous solution, which is the record for a single-unit xenon host. To investigate this sensitivity enhancement, the xenon binding kinetics of TAAC in water was studied by NMR exchange lifetime measurement. At 297 K, kon ≈ 1.5 × 106 M−1s−1 and koff = 45 s−1, which represent the fastest Xe association and dissociation rates measured for a high-affinity, water-soluble xenon host molecule near rt. NMR linewidth measurements provided similar exchange rates at rt, which we assign to solvent-Xe exchange in TAAC. At 320 K, koff was estimated to be 1.1 × 103 s−1. In Hyper-CEST NMR experiments, the rate of 129Xe depolarization achieved by 14 pM TAAC in the presence of RF pulses was calculated to be 0.17 µM·s−1. On a per cryptophane basis, this equates to 1.2 × 104 129Xe atoms s−1 (or 4.6 × 104 Xe atoms s−1, all Xe isotopes), which is more than an order of magnitude faster than koff, the directly measurable Xe-TAAC exchange rate. This compels us to consider multiple Xe exchange processes for cryptophane-mediated bulk 129Xe depolarization, which provide at least 107-fold sensitivity enhancements over directly detected hyperpolarized 129Xe NMR signals. PMID:23106513

  15. Assessment of Bone Microstructural Changes by NMR (United States)

    Ni, Qingwen; Wang, Xiaodu


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

  16. NMR-based diffusion pore imaging. (United States)

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


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

  17. NMR assessment on bone simulated under microgravity (United States)

    Ni, Q.; Qin, Y.

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

  18. Dynamic nuclear-polarization studies of paramagnetic species in solution

    Energy Technology Data Exchange (ETDEWEB)

    Glad, W.E.


    Dynamic Nuclear Polarization (DNP) was used to measure the electron spin lattice relaxation times, T/sub 1/, of transition metal ions in aqueous solution. Saturation which is induced in the electron spin system is transferred to the solvent proton spins by dipole-dipole interactions. The change in the polarization of the proton spins is much larger than it is in the electron spins. The change in proton polarization is easily measured by proton Nuclear Magnetic Resonance (NMR). In one experimental arrangement the sample solution was continuously flowed through a microwave cavity to the NMR coil. The NMR was observed with a continuous wave NMR spectrometer. In a second arrangement the whole sample tube was moved from within the microwave cavity to the NMR coil in less than 40 ms by a blast of compressed air. The NMR was then observed with a pulse-Fourier-transform spectrometer. With the second arrangement a mean-square microwave magnetic field at the sample of more than 10 G/sup 2/ is obtainable with 14 W of microwave power. Measurements of DNP at 9 GHz were made on aqueous solutions of VO/sup 2 +/, Mn/sup 2 +/, Cr(CN)/sub 6//sup 3 -/, Cu/sup 2 +/ and Cu(ethylenediamine)/sub 2/(H/sub 2/0)/sub 2//sup 2 +/ ions from 3 to 60/sup 0/C. It was also possible to observe DNP on resolved proton resonances from mixed water-acetonitrile solutions of VO/sup 2 +/ and Cr(CN)/sub 6//sup 3 -/ ions.

  19. Transformation of meta-stable calcium silicate hydrates to tobermorite: reaction kinetics and molecular structure from XRD and NMR spectroscopy

    Directory of Open Access Journals (Sweden)

    Carroll Susan A


    Full Text Available Abstract Understanding the integrity of well-bore systems that are lined with Portland-based cements is critical to the successful storage of sequestered CO2 in gas and oil reservoirs. As a first step, we investigate reaction rates and mechanistic pathways for cement mineral growth in the absence of CO2 by coupling water chemistry with XRD and NMR spectroscopic data. We find that semi-crystalline calcium (alumino-silicate hydrate (Al-CSH forms as a precursor solid to the cement mineral tobermorite. Rate constants for tobermorite growth were found to be k = 0.6 (± 0.1 × 10-5 s-1 for a solution:solid of 10:1 and 1.6 (± 0.8 × 10-4 s-1 for a solution:solid of 5:1 (batch mode; T = 150°C. This data indicates that reaction rates for tobermorite growth are faster when the solution volume is reduced by half, suggesting that rates are dependent on solution saturation and that the Gibbs free energy is the reaction driver. However, calculated solution saturation indexes for Al-CSH and tobermorite differ by less than one log unit, which is within the measured uncertainty. Based on this data, we consider both heterogeneous nucleation as the thermodynamic driver and internal restructuring as possible mechanistic pathways for growth. We also use NMR spectroscopy to characterize the site symmetry and bonding environment of Al and Si in a reacted tobermorite sample. We find two [4]Al coordination structures at δiso = 59.9 ppm and 66.3 ppm with quadrupolar product parameters (PQ of 0.21 MHz and 0.10 MHz (± 0.08 from 27Al 3Q-MAS NMR and speculate on the Al occupancy of framework sites by probing the protonation environment of Al metal centers using 27Al{1H}CP-MAS NMR.

  20. Effects of NMR spectral resolution on protein structure calculation.

    Directory of Open Access Journals (Sweden)

    Suhas Tikole

    Full Text Available Adequate digital resolution and signal sensitivity are two critical factors for protein structure determinations by solution NMR spectroscopy. The prime objective for obtaining high digital resolution is to resolve peak overlap, especially in NOESY spectra with thousands of signals where the signal analysis needs to be performed on a large scale. Achieving maximum digital resolution is usually limited by the practically available measurement time. We developed a method utilizing non-uniform sampling for balancing digital resolution and signal sensitivity, and performed a large-scale analysis of the effect of the digital resolution on the accuracy of the resulting protein structures. Structure calculations were performed as a function of digital resolution for about 400 proteins with molecular sizes ranging between 5 and 33 kDa. The structural accuracy was assessed by atomic coordinate RMSD values from the reference structures of the proteins. In addition, we monitored also the number of assigned NOESY cross peaks, the average signal sensitivity, and the chemical shift spectral overlap. We show that high resolution is equally important for proteins of every molecular size. The chemical shift spectral overlap depends strongly on the corresponding spectral digital resolution. Thus, knowing the extent of overlap can be a predictor of the resulting structural accuracy. Our results show that for every molecular size a minimal digital resolution, corresponding to the natural linewidth, needs to be achieved for obtaining the highest accuracy possible for the given protein size using state-of-the-art automated NOESY assignment and structure calculation methods.

  1. Intramolecular hydrogen-bonding studies by NMR spectroscopy

    CERN Document Server

    Cantalapiedra, N A


    o-methoxybenzamide and N-methyl-o-methylbenzamide, using the pseudo-contact shifts calculated from the sup 1 H and sup 1 sup 3 C NMR spectra. The main conformation present in solution for o-fluorobenzamide was the one held by an intramolecular N-H...F hydrogen bond. Ab-initio calculations (at the RHF/6-31G* level) have provided additional data for the geometry of the individual molecules. A conformational equilibrium study of some nipecotic acid derivatives (3-substituted piperidines: CO sub 2 H, CO sub 2 Et, CONH sub 2 , CONHMe, CONEt sub 2) and cis-1,3-disubstituted cyclohexane derivatives (NHCOMe/CO sub 2 Me, NHCOMe/CONHMe, NH sub 2 /CO sub 2 H) has been undertaken in a variety of solvents, in order to predict the intramolecular hydrogen-bonding energies involved in the systems. The conformer populations were obtained by direct integration of proton peaks corresponding to the equatorial and axial conformations at low temperature (-80 deg), and by geometrically dependent coupling constants ( sup 3 J sub H s...

  2. Experimental and theoretical NMR study of selected oxocarboxylic acid oximes. (United States)

    Malek, Kamilla; Vala, Martin; Kozłowski, Henryk; Proniewicz, Leonard M


    1H and 13C NMR spectra of the oxocarboxylic acid oximes 2-hydroxyiminopropanoic acid (1), 2-(4-methylthiazol-2-yl)-2-(hydroxyimino)acetic acid (2) and 2-cyano-2-(hydroxyimino)acetic acid (3) were measured in DMSO-d6, D2O and acetone-d6 solutions. The data indicate the presence of hydrogen bonding in 1 and 2 and a strong electron-withdrawing effect due to the cyano group in 3. The effect of intra- and intermolecular hydrogen bonding on the hydrogen and carbon chemical shifts in these molecules was studied theoretically. Total energy calculations of the stability of various hydrogen-bonded species, in addition to equilibrium parameters and chemical shifts, were calculated using ab initio methods (RHF, MP2) and density functional theory (B3LYP), implemented in the Gaussian 98 software package. The gauge-including atomic orbital (GIAO) method was used to predict magnetic shielding constants. Chemical shift calculations for the most stable species agree fairly well with the observed data, especially for the hydroxyl protons. Substituents adjacent to the alpha-carbon show some influence of the oximic and carboxyl groups on the 13C chemical shifts, as expected for groups with different polar and anisotropic character. Copyright 2003 John Wiley & Sons, Ltd.

  3. Wave Solutions

    CERN Document Server

    Christov, Ivan C


    In classical continuum physics, a wave is a mechanical disturbance. Whether the disturbance is stationary or traveling and whether it is caused by the motion of atoms and molecules or the vibration of a lattice structure, a wave can be understood as a specific type of solution of an appropriate mathematical equation modeling the underlying physics. Typical models consist of partial differential equations that exhibit certain general properties, e.g., hyperbolicity. This, in turn, leads to the possibility of wave solutions. Various analytical techniques (integral transforms, complex variables, reduction to ordinary differential equations, etc.) are available to find wave solutions of linear partial differential equations. Furthermore, linear hyperbolic equations with higher-order derivatives provide the mathematical underpinning of the phenomenon of dispersion, i.e., the dependence of a wave's phase speed on its wavenumber. For systems of nonlinear first-order hyperbolic equations, there also exists a general ...

  4. NMR-Metabolic Methodology in the Study of GM Foods (United States)

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

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

    African Journals Online (AJOL)

    Preferred Customer

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

  6. Facing and Overcoming Sensitivity Challenges in Biomolecular NMR Spectroscopy

    DEFF Research Database (Denmark)

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


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

  7. Advanced solid-state NMR spectroscopy of natural organic matter. (United States)

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


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

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

    Energy Technology Data Exchange (ETDEWEB)

    George J. Hirasaki; Kishore K. Mohanty


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

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

    Indian Academy of Sciences (India)

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

  10. Probe for high resolution NMR with sample reorientation (United States)

    Pines, A.; Samoson, A.


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

  11. Bringing NMR and IR Spectroscopy to High Schools (United States)

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


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

  12. Quantification of (1)H NMR Spectra from Human Plasma. (United States)

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


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

  13. Rapid prediction of multi-dimensional NMR data sets

    NARCIS (Netherlands)

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


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

  14. Solution Prototype

    DEFF Research Database (Denmark)

    Efeoglu, Arkin; Møller, Charles; Serie, Michel


    This paper outlines an artifact building and evaluation proposal. Design Science Research (DSR) studies usually consider encapsulated artifact that have relationships with other artifacts. The solution prototype as a composed artifact demands for a more comprehensive consideration in its systematic...... environment. The solution prototype that is composed from blending product and service prototype has particular impacts on the dualism of DSR’s “Build” and “Evaluate”. Since the mix between product and service prototyping can be varied, there is a demand for a more agile and iterative framework. Van de Ven...

  15. Monitoring drug self-aggregation and potential for promiscuity in off-target in vitro pharmacology screens by a practical NMR strategy. (United States)

    LaPlante, Steven R; Aubry, Norman; Bolger, Gordon; Bonneau, Pierre; Carson, Rebekah; Coulombe, René; Sturino, Claudio; Beaulieu, Pierre L


    A simple NMR assay was applied to monitor the tendency of compounds to self-aggregate in aqueous media. The observation of unusual spectral trends as a function of compound concentration appears to be signatory of the formation of self-assemblies. (1)H NMR resonances of aggregating compounds were sensitive to the presence of a range of molecular assemblies in solution including large molecular-size entities, smaller multimers, and mixtures of assembled species. The direct observation of aggregates via unusual NMR spectra also correlated with promiscuous behavior of molecules in off-target in vitro pharmacology assays. This empirical assay can have utility for predicting compound promiscuity and should complement predictive methods that principally rely on the computing of descriptors such as lipophilicity (cLogP) and topological surface area (TPSA). This assay should serve as a practical tool for medicinal chemists to monitor compound attributes in aqueous solution and various pharmacologically relevant media, as demonstrated herein.

  16. Development and implementation of the NMR-spectrometer on the basis of the National Instruments technologies (United States)

    Narakidze, N. D.; Shaykhutdinov, D. V.; Shirokov, K. M.; Gorbatenko, N. I.; Yanvarev, S. G.


    The quality of lubricating oil in mechanical engineering, technology of creation of units, in particular in equipment of transmission gears, is a factor which considerably defines reliability and safety of the whole propulsion system or the greased constructive components. There are many soluble oil additives such as, for example, different additives for extreme compression conditions or additives against wear. Additives are used with mineral oils, products from mineral oils or synthetic oils for lubricant action or chemical properties improvement. The most exact way of definition of the chemical composition of a substance at the moment is the method of nuclear magnetic resonance (NMR). In the first section of this article, a brief and very simplified review of the NMR basic principles using classical physics is provided. The second section is focused on the description of the hardware solutions and the architecture of the NMR spectrometers. The software developments (LabVIEW programs) of the data-acquisition and signal processing techniques are presented in the third section. At the end, results of measurements are provided.

  17. Investigation of Melts of Polybutylcarbosilane Dendrimers by 1H NMR Spectroscopy. (United States)

    Matveev, Vladimir V; Markelov, Denis A; Dvinskikh, Sergey V; Shishkin, Andrei N; Tyutyukin, Konstantin V; Penkova, Anastasia V; Tatarinova, Elena A; Ignat'eva, Galina M; Milenin, Sergey A


    Melts of polybutylcarbosilane (PBC) dendrimers from third (G3) up to sixth (G6) generations are investigated by 1H NMR spectroscopy in a wide temperature range up to 493 K. At room temperature, NMR spectra of G3-G5 dendrimers exhibit resolved, solution-like spectra ("liquid" phase). In contrast, the spectrum of the G6 dendrimer is characterized by a single unresolved broad line at whole temperature range, which supports the presence of an anomalous phase state of G6 at temperatures higher than glass transition temperature. For the first time, an unexpected transition of G5 dendrimer from a molecular liquid state to an anomalous state/phase upon temperature increase has been detected using NMR data. Specifically, an additional wide background line appears in the G5 spectrum above 473 K, and this line corresponds to a G5 state characterized by restricted molecular mobility, i.e., a state similar to the "anomalous" phase of G6 melt. The fraction of the G5 dendrimers in "anomalous" phase at 493 K is approximately 40%. Analysis of the spectral shapes suggests that changes in the G5 dendrimers are reversible with temperature.

  18. Comprehensive multiphase NMR spectroscopy of intact ¹³C-labeled seeds. (United States)

    Lam, Leayen; Soong, Ronald; Sutrisno, Andre; de Visser, Ries; Simpson, Myrna J; Wheeler, Heather L; Campbell, Malcolm; Maas, Werner E; Fey, Michael; Gorissen, Antonie; Hutchins, Howard; Andrew, Brian; Struppe, Jochem; Krishnamurthy, Sridevi; Kumar, Rajeev; Monette, Martine; Stronks, Henry J; Hume, Alan; Simpson, André J


    Seeds are complex entities composed of liquids, gels, and solids. NMR spectroscopy is a powerful tool for studying molecular structure but has evolved into two fields, solution and solid state. Comprehensive multiphase (CMP) NMR spectroscopy is capable of liquid-, gel-, and solid-state experiments for studying intact samples where all organic components are studied and differentiated in situ. Herein, intact (13)C-labeled seeds were studied by a variety of 1D/2D (1)H/(13)C experiments. In the mobile phase, an assortment of metabolites in a single (13)C-labeled wheat seed were identified; the gel phase was dominated by triacylglycerides; the semisolid phase was composed largely of carbohydrate biopolymers, and the solid phase was greatly influenced by starchy endosperm signals. Subsequently, the seeds were compared and relative similarities and differences between seed types discussed. This study represents the first application of CMP-NMR to food chemistry and demonstrates its general utility and feasibility for studying intact heterogeneous samples.

  19. Amino acid analysis of spider dragline silk using ¹H NMR. (United States)

    Shi, Xiangyan; Holland, Gregory P; Yarger, Jeffery L


    The amino acid composition of Nephila clavipes dragline silk fiber was determined by conducting ¹H nuclear magnetic resonance (NMR) spectroscopy experiments on acid-hydrolyzed material. N. clavipes dragline silk was found to consist of 43.0±0.6% Gly, 29.3±0.2% Ala, 9.1±0.1% Glx, 4.0±0.1% Leu, 3.3±0.1% Tyr, 3.4±0.2% Ser, 2.7±0.1% Pro, 2.1±0.1% Arg, 1.07±0.05% Asx, 0.96±0.05% Val, 0.48±0.03% Thr, 0.35±0.03% Phe, and 0.28±0.03% Ile. Compared with standard chromatography-based amino acid analysis (AAA), the chemical resolution of NMR allows for an amino acid solution to be characterized without separation and is shown to provide considerably higher precision. This allows for more accurate statistics on the variability of amino acids in spider dragline silk. In general, this ¹H NMR AAA technique is applicable to a large range of proteins and peptides for precise composition characterization, especially when the precise content of a minor component is critical and relatively large amounts of sample are available (microgram to milligram quantities). Published by Elsevier Inc.

  20. Electrophoretic NMR studies of electrical transport in fluid-filled porous systems. (United States)

    Holz, M; Heil, S R; Schwab, I A


    An NMR technique is described which allows the observation of ionic charge carriers moving in the electric field within a porous system saturated with electrolyte solution. This method, which was recently developed in our laboratory, gives experimental access to the study of electric transport in disordered media on a microscopic level and offers new potential for morphology studies. We performed 1H NMR PFG self-diffusion measurements on ions combined with ionic drift velocity measurements by electrophoretic NMR (ENMR), each as a function of observation time Delta. In this way we obtained time-dependent self-diffusion coefficients D(+/-) (Delta) and time-dependent electric mobilities mu(+/-) (Delta) of polyatomic cations and anions in porous media. The porous media used were gels and glass bead packs. From the behaviour of D(+/-) (Delta) and mu(+/-) (Delta) at long observation times the tortuosities T(p) (D(+/-)) and T(p) (mu(+/-)) are derived, allowing a direct experimental check of the validity of the Einstein relation (D(+/-) is proportional to mu(+/-)) in a disordered medium. The tortuosities obtained via the diffusivity of ions are compared with those obtained via the diffusivity of water molecules. We also make a first attempt to derive the specific surface S/V(p) from the time-dependence of the ionic mobility at short observation times and discuss possible advantages of those measurements in morphology studies of porous media.

  1. Symmetry Breaking in NMR Spectroscopy: The Elucidation of Hidden Molecular Rearrangement Processes

    Directory of Open Access Journals (Sweden)

    Michael J. McGlinchey


    Full Text Available Variable-temperature NMR spectroscopy is probably the most convenient and sensitive technique to monitor changes in molecular structure in solution. Rearrangements that are rapid on the NMR time-scale exhibit simplified spectra, whereby non-equivalent nuclear environments yield time-averaged resonances. At lower temperatures, when the rate of exchange is sufficiently reduced, these degeneracies are split and the underlying “static” molecular symmetry, as seen by X-ray crystallography, becomes apparent. Frequently, however, such rearrangement processes are hidden, even when they become slow on the NMR time-scale, because the molecular point group remains unchanged. Judicious symmetry breaking, such as by substitution of a molecular fragment by a similar, but not identical moiety, or by the incorporation of potentially diastereotopic (chemically non-equivalent nuclei, allows the elucidation of the kinetics and energetics of such processes. Examples are chosen that include a wide range of rotations, migrations and other rearrangements in organic, inorganic and organometallic chemistry.

  2. Sensitivity and resolution enhancement in solid-state NMR spectroscopy of bicelles (United States)

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


    Magnetically aligned bicelles are becoming attractive model membranes to investigate the structure, dynamics, geometry, and interaction of membrane-associated peptides and proteins using solution- and solid-state NMR experiments. Recent studies have shown that bicelles are more suitable than mechanically aligned bilayers for multidimensional solid-state NMR experiments. In this work, we describe experimental aspects of the natural abundance 13C and 14N NMR spectroscopy of DMPC/DHPC bicelles. In particular, approaches to enhance the sensitivity and resolution and to quantify radio-frequency heating effects are presented. Sensitivity of 13C detection using single pulse excitation, conventional cross-polarization (CP), ramp-CP, and NOE techniques are compared. Our results suggest that the proton decoupling efficiency of the FLOPSY pulse sequence is better than that of continuous wave decoupling, TPPM, SPINAL, and WALTZ sequences. A simple method of monitoring the water proton chemical shift is demonstrated for the measurement of sample temperature and calibration of the radio-frequency-induced heating in the sample. The possibility of using 14N experiments on bicelles is also discussed.

  3. Accounting for conformational variability in protein-ligand docking with NMR-guided rescoring. (United States)

    Skjærven, Lars; Codutti, Luca; Angelini, Andrea; Grimaldi, Manuela; Latek, Dorota; Monecke, Peter; Dreyer, Matthias K; Carlomagno, Teresa


    A key component to success in structure-based drug design is reliable information on protein-ligand interactions. Recent development in NMR techniques has accelerated this process by overcoming some of the limitations of X-ray crystallography and computational protein-ligand docking. In this work we present a new scoring protocol based on NMR-derived interligand INPHARMA NOEs to guide the selection of computationally generated docking modes. We demonstrate the performance in a range of scenarios, encompassing traditionally difficult cases such as docking to homology models and ligand dependent domain rearrangements. Ambiguities associated with sparse experimental information are lifted by searching a consensus solution based on simultaneously fitting multiple ligand pairs. This study provides a previously unexplored integration between molecular modeling and experimental data, in which interligand NOEs represent the key element in the rescoring algorithm. The presented protocol should be widely applicable for protein-ligand docking also in a different context from drug design and highlights the important role of NMR-based approaches to describe intermolecular ligand-receptor interactions.

  4. PINE-SPARKY.2 for automated NMR-based protein structure research. (United States)

    Lee, Woonghee; Markley, John L


    NMR (nuclear magnetic resonance) spectroscopy, along with X-ray crystallography and Cryo-EM, is one of the three major tools that enable the determination of atomic-level structural models of biological macromolecules. Of these, NMR has the unique ability to follow important processes in solution, including conformational changes, internal dynamics and protein-ligand interactions. As a means for facilitating the handling and analysis of spectra involved in these types of NMR studies, we have developed PINE-SPARKY.2, a software package that integrates and automates discrete tasks that previously required interaction with separate software packages. The graphical user interface of PINE-SPARKY.2 simplifies chemical shift assignment and verification, automated detection of secondary structural elements, predictions of flexibility and hydrophobic cores, and calculation of three-dimensional structural models. PINE-SPARKY.2 is available in the latest version of NMRFAM-SPARKY from the National Magnetic Resonance Facility at Madison (, the NMRbox Project (, and to subscribers to the SBGrid ( For a detailed description of the program, see or Supplementary data are available at Bioinformatics online.

  5. Objective Definition of Monofloral and Polyfloral Honeys Based on NMR Metabolomic Profiling. (United States)

    Schievano, Elisabetta; Finotello, Claudia; Uddin, Jalal; Mammi, Stefano; Piana, Lucia


    In this paper, a remarkably precise, simple, and objective definition of monofloral and polyfloral honey based on NMR metabolomics is proposed. The spectra of organic extracts of 983 samples of 16 botanical origins were used to derive one-versus-all OPLS-DA classification models. The predictive components of the statistical models reveal not only the principal but also the secondary floral origins present in a sample of honey, a novel feature with respect to the methods present in the literature that are able to confirm the authenticity of monofloral honeys but not to characterize a mixture of honey types. This result descends from the peculiar features of the chloroform spectra that show diagnostic resonances for almost each botanical origin, making these NMR spectra suitable fingerprints. The reliability of the method was tested with an additional 120 samples, and the class assignments were compared with those obtained by traditional analysis. The two approaches are in excellent agreement in identifying the floral species present in honeys and in the botanical classification. Therefore, this NMR method may prove to be a valid solution to the huge limitations of traditional classification, which is very demanding and complex.

  6. Quantitative analysis of dimethyl titanocene by iodometric titration, gas chromatography and NMR. (United States)

    Vailaya, A; Wang, T; Chen, Y; Huffman, M


    In this study we report the use of an automated iodometric titration method and a novel gas chromatography (GC) method for the quantitative analysis of dimethyl titanocene (DMT), a key raw material in drug synthesis. Both approaches are based on the reaction of DMT in toluene or tetrahydrofuran solutions with iodine. In the case of iodometric titration, excess iodine is titrated with a standardized aqueous sodium thiosulfate solution to a potentiometric end-point for the determination of DMT concentration. Alternatively, GC is employed to measure the concentration of iodomethane, a product of the reaction between DMT and iodine, in order to determine the concentration of DMT in the solution. Excellent agreement between iodometric titration, GC and NMR results using several DMT samples confirms the accuracy of the two methods and strongly supports the use of either method as a replacement to the expensive NMR for quantitative DMT analysis. The relatively few sources of error associated with the two methods, their ubiquitous nature and ease of application in routine analysis make them the analytical methods of choice, among all. Both methods have been validated according to ICH requirements. The use of iodometric titration method for DMT analysis is demonstrated with a couple of applications.

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

    CERN Multimedia

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

  8. Orientational Glasses: NMR and Electric Susceptibility Studies

    Directory of Open Access Journals (Sweden)

    Neil Sullivan


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

  9. NMR studies of polysaccharides from brown seaweeds

    Energy Technology Data Exchange (ETDEWEB)

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


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

  10. Two-Dimensional NMR Lineshape Analysis (United States)

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


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

  11. Long Lived NMR Signal in Bone

    CERN Document Server

    Zhang, Boyang; Khitrin, Anatoly; Jerschow, Alexej


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

  12. NMR Metabolomics Analysis of Parkinson's Disease (United States)

    Lei, Shulei; Powers, Robert


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

  13. Synthesis, characterization and thermal behavior of rare earth amido sulfonates; Sintese, caracterizacao e comportamento termico de amidossulfonatos de terras raras

    Energy Technology Data Exchange (ETDEWEB)

    Luiz, Jose Marques; Nunes, Ronaldo Spezia, E-mail: [Universidade Estadual Paulista Julio Mesquita Filho (UNESP), Guaratingueta, SP (Brazil). Faculdade de Engenharia. Departamento de Fisica e Quimica; Matos, Jivaldo do Rosario [Universidade de Sao Paulo (USP), SP (Brazil). Instituto de Quimica


    Hydrated compounds prepared in aqueous solution by reaction between amidosulfonic acid [H{sub 3}NSO{sub 3}] and suspensions of rare earth hydroxycarbonates [Ln{sub 2}(OH){sub x}(CO{sub 3}){sub y}.zH{sub 2}O] were characterized by elemental analysis (% Ln, % N and % H), infrared spectroscopy (FTIR) and thermogravimetry (TG). The compounds presented the stoichiometry Ln(NH{sub 2}SO{sub 3}){sub 3}.xH{sub 2}O (where x = 1, 5, 2.0 or 3.0). The IR spectra showed absorptions characteristic of H{sub 2}O molecules and NH{sub 2}SO{sub 3} groups. Degree of hydration, thermal decomposition steps and formation of stable intermediates of the type [Ln{sub 2}(SO{sub 4}){sub 3}] and (Ln{sub 2}O{sub 2}SO{sub 4}), besides formation of their oxides, was determined by thermogravimetry. (author)

  14. Characterization of AA7050 aluminium alloy processed by ECAP; Caracterizacao da liga de aluminio AA7050 processada por ECAP

    Energy Technology Data Exchange (ETDEWEB)

    Cardoso, K.R.; Guido, V. [Universidade do Vale do Paraiba (UNIVAP), Sao Jose dos Campos, SP (Brazil). Inst. de Pesquisa e Desenvolvimento; Travessa, D.N. [Empresa Brasileira de Aeronautica (EMBRAER), Sao Jose dos Campos, SP (Brazil); Jorge Junior, A.M. [Universidade Federal de Sao Carlos (DEMa/UFSCar), SP (Brazil). Dept. de Engenharia de Materiais


    The commercial AA7050 aluminium alloy in the solution heat treated condition (W) was processed by ECAP through route A. Two pressing temperatures (room and 150 deg C and velocities (5 and 30mm/min) were used, as well as different number of passes. The effect of such variables on the microstructure evolution was evaluated using optical and transmission electron microscopy with EDX microanalysis, and xray diffraction. It was found that the microstructure has been refined by ECAP, as a result of subgrains formed within deformation bands. ECAP at 150 deg C resulted in intense precipitation of plate like {eta} phase, which evolves to equiaxial morphology as the number of passes increases. (author)

  15. A flow-through, elevated-temperature and -pressure NMR apparatus for in-situ CO2 sequestration studies. (United States)

    Sesti, Erika L; Cui, Jinlei; Hayes, Sophia E; Conradi, Mark S


    We report an apparatus for in-situ nuclear magnetic resonance (NMR) studies of chemical reactions of dissolved 13CO2 with minerals (rock or powder) under continuous flow. The operating range of the apparatus is 18-150°C and 1-140bar. A flow pump is used to circulate a CO2-water solution, with a heated mixing vessel where CO2 gas equilibrates with a water solution. The NMR probe is built around a strong zirconia ceramic vessel, with o-ring sealed connections; the mineral is contained inside. The horizontal orientation of the zirconia vessels allows use of a radio frequency (rf) solenoid for improved spin sensitivity. Copyright © 2017 Elsevier Inc. All rights reserved.

  16. NMR identification of the terminal groups of the telomers of tetrafluoroethylene with tetrahydrofuran (United States)

    Kim, I. P.; Kunitsa, A. A.; Chernyak, A. V.


    1H, 13C, and 19F high-resolution NMR spectra with heteronuclear spin-spin decoupling and without it were recorded for identification of the terminal groups of oligomers obtained by radical polymerization of tetrafluroethylene (TFE) in tetrahydrofuran (THF) solutions. The analysis of the spectra and their comparison with the quantum-chemically calculated spectra of possible polymerization products led to the conclusion that the terminal groups of oligomers are the α radical of THF and the hydrogen atom. The structure of oligomers found in this study opens up an opportunity of synthesizing from them polymers consisting of a flexible main chain with substituents in the form of rigid perfluorinated rods.

  17. NMR-based localization of ions involved in salting out of hen egg white lysozyme. (United States)

    Poznański, Jarosław


    NaCl-induced aggregation of hen egg white lysozyme (HEWL) was monitored by NMR spectroscopy. Small, but significant, changes induced by salt addition in TOCSY spectra were attributed to the effect of local reorganization of protein backbone upon ion binding. Salt-induced variations in HN and H alpha chemical shifts were mapped on the HEWL 3D structure which allowed the construction of a scheme of the spatial localization of potential ion binding sites. It was found that in a 0.5 M NaCl solution six chloride anions and at least one sodium cation are bound to preferred sites on the HEWL surface.

  18. Synthesis of a new quaternary phosphonium salt: NMR study of the conformational structure and dynamics. (United States)

    Aganova, Oksana V; Galiullina, Leysan F; Aganov, Albert V; Shtyrlin, Nikita V; Pugachev, Mikhail V; Strel'nik, Alexey D; Koshkin, Sergey A; Shtyrlin, Yurii G; Klochkov, Vladimir V


    A novel phosphonium salt based on pyridoxine was synthesized. Conformational analysis of the compound in solution was performed using dynamic NMR experiments and calculations. The obtained results revealed some differences in the conformational transitions and the energy parameters of the conformational exchange of the studied compound in comparison to previously reported data for other phosphorus-containing pyridoxine derivatives. It was shown that increasing the substituent at the C-11 carbon leads to greater differences in the populations of stable states and the corresponding equilibrium energies. Copyright © 2015 John Wiley & Sons, Ltd. Copyright © 2015 John Wiley & Sons, Ltd.

  19. Protein Loop Closure Using Orientational Restraints from NMR Data (United States)

    Tripathy, Chittaranjan; Zeng, Jianyang; Zhou, Pei; Donald, Bruce Randall

    Protein loops often play important roles in biological functions such as binding, recognition, catalytic activities and allosteric regulation. Modeling loops that are biophysically sensible is crucial to determining the functional specificity of a protein. A variety of algorithms ranging from robotics-inspired inverse kinematics methods to fragmentbased homology modeling techniques have been developed to predict protein loops. However, determining the 3D structures of loops using global orientational restraints on internuclear vectors, such as those obtained from residual dipolar coupling (RDC) data in solution Nuclear Magnetic Resonance (NMR) spectroscopy, has not been well studied. In this paper, we present a novel algorithm that determines the protein loop conformations using a minimal amount of RDC data. Our algorithm exploits the interplay between the sphero-conics derived from RDCs and the protein kinematics, and formulates the loop structure determination problem as a system of low-degree polynomial equations that can be solved exactly and in closed form. The roots of these polynomial equations, which encode the candidate conformations, are searched systematically, using efficient and provable pruning strategies that triage the vast majority of conformations, to enumerate or prune all possible loop conformations consistent with the data. Our algorithm guarantees completeness by ensuring that a possible loop conformation consistent with the data is never missed. This data-driven algorithm provides a way to assess the structural quality from experimental data with minimal modeling assumptions. We applied our algorithm to compute the loops of human ubiquitin, the FF Domain 2 of human transcription elongation factor CA150 (FF2), the DNA damage inducible protein I (DinI) and the third IgG-binding domain of Protein G (GB3) from experimental RDC data. A comparison of our results versus those obtained by using traditional structure determination protocols on the

  20. NMR structures reveal how oxidation inactivates thrombomodulin. (United States)

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


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

  1. Podcast solutions

    CERN Document Server

    Geoghegan, Michael W


    Podcasting is the art of recording radio show style audio tracks, then distributing them to listeners on the Web via podcasting software such as iPodder. From downloading podcasts to producing a track for fun or profit, ""Podcast Solutions"" covers the entire world of podcasting with insight, humor, and the unmatched wisdom of experience.

  2. Recent advances in computational predictions of NMR parameters for the structure elucidation of carbohydrates: methods and limitations. (United States)

    Toukach, Filip V; Ananikov, Valentine P


    All living systems are comprised of four fundamental classes of macromolecules--nucleic acids, proteins, lipids, and carbohydrates (glycans). Glycans play a unique role of joining three principal hierarchical levels of the living world: (1) the molecular level (pathogenic agents and vaccine recognition by the immune system, metabolic pathways involving saccharides that provide cells with energy, and energy accumulation via photosynthesis); (2) the nanoscale level (cell membrane mechanics, structural support of biomolecules, and the glycosylation of macromolecules); (3) the microscale and macroscale levels (polymeric materials, such as cellulose, starch, glycogen, and biomass). NMR spectroscopy is the most powerful research approach for getting insight into the solution structure and function of carbohydrates at all hierarchical levels, from monosaccharides to oligo- and polysaccharides. Recent progress in computational procedures has opened up novel opportunities to reveal the structural information available in the NMR spectra of saccharides and to advance our understanding of the corresponding biochemical processes. The ability to predict the molecular geometry and NMR parameters is crucial for the elucidation of carbohydrate structures. In the present paper, we review the major NMR spectrum simulation techniques with regard to chemical shifts, coupling constants, relaxation rates and nuclear Overhauser effect prediction applied to the three levels of glycomics. Outstanding development in the related fields of genomics and proteomics has clearly shown that it is the advancement of research tools (automated spectrum analysis, structure elucidation, synthesis, sequencing and amplification) that drives the large challenges in modern science. Combining NMR spectroscopy and the computational analysis of structural information encoded in the NMR spectra reveals a way to the automated elucidation of the structure of carbohydrates.

  3. Dynamic membrane interactions of antibacterial and antifungal biomolecules, and amyloid peptides, revealed by solid-state NMR spectroscopy. (United States)

    Naito, Akira; Matsumori, Nobuaki; Ramamoorthy, Ayyalusamy


    A variety of biomolecules acting on the cell membrane folds into a biologically active structure in the membrane environment. It is, therefore, important to determine the structures and dynamics of such biomolecules in a membrane environment. While several biophysical techniques are used to obtain low-resolution information, solid-state NMR spectroscopy is one of the most powerful means for determining the structure and dynamics of membrane bound biomolecules such as antibacterial biomolecules and amyloidogenic proteins; unlike X-ray crystallography and solution NMR spectroscopy, applications of solid-state NMR spectroscopy are not limited by non-crystalline, non-soluble nature or molecular size of membrane-associated biomolecules. This review article focuses on the applications of solid-state NMR techniques to study a few selected antibacterial and amyloid peptides. Solid-state NMR studies revealing the membrane inserted bent α-helical structure associated with the hemolytic activity of bee venom melittin and the chemical shift oscillation analysis used to determine the transmembrane structure (with α-helix and 310-helix in the N- and C-termini, respectively) of antibiotic peptide alamethicin are discussed in detail. Oligomerization of an amyloidogenic islet amyloid polypeptide (IAPP, or also known as amylin) resulting from its aggregation in a membrane environment, molecular interactions of the antifungal natural product amphotericin B with ergosterol in lipid bilayers, and the mechanism of lipid raft formation by sphingomyelin studied using solid state NMR methods are also discussed in this review article. This article is part of a Special Issue entitled "Biophysical Exploration of Dynamical Ordering of Biomolecular Systems" edited by Dr. Koichi Kato. Copyright © 2017 Elsevier B.V. All rights reserved.

  4. ImatraNMR: Novel software for batch integration and analysis of quantitative NMR spectra (United States)

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


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

  5. SIMPSON: A general simulation program for solid-state NMR spectroscopy (United States)

    Bak, Mads; Rasmussen, Jimmy T.; Nielsen, Niels Chr.


    A computer program for fast and accurate numerical simulation of solid-state NMR experiments is described. The program is designed to emulate a NMR spectrometer by letting the user specify high-level NMR concepts such as spin systems, nuclear spin interactions, RF irradiation, free precession, phase cycling, coherence-order filtering, and implicit/explicit acquisition. These elements are implemented using the Tel scripting language to ensure a minimum of programming overhead and direct interpretation without the need for compilation, while maintaining the flexibility of a full-featured programming language. Basicly, there are no intrinsic limitations to the number of spins, types of interactions, sample conditions (static or spinning, powders, uniaxially oriented molecules, single crystals, or solutions), and the complexity or number of spectral dimensions for the pulse sequence. The applicability ranges from simple ID experiments to advanced multiple-pulse and multiple-dimensional experiments, series of simulations, parameter scans, complex data manipulation/visualization, and iterative fitting of simulated to experimental spectra. A major effort has been devoted to optimizing the computation speed using state-of-the-art algorithms for the time-consuming parts of the calculations implemented in the core of the program using the C programming language. Modification and maintenance of the program are facilitated by releasing the program as open source software (General Public License) currently at The general features of the program are demonstrated by numerical simulations of various aspects for REDOR, rotational resonance, DRAMA, DRAWS, HORROR, C7, TEDOR, POST-C7, CW decoupling, TPPM, F-SLG, SLF, SEMA-CP, PISEMA, RFDR, QCPMG-MAS, and MQ-MAS experiments.

  6. Detailed NMR investigation of cyclodextrin-perfluorinated surfactant interactions in aqueous media

    Energy Technology Data Exchange (ETDEWEB)

    Weiss-Errico, Mary Jo; O’Shea, Kevin E., E-mail:


    Highlights: • Perfluorochemicals (PFCs) are strongly encapsulated by cyclodextrins (CDs). • Competition studies confirm strong CD:PFC host-guest interactions. • {sup 19}F NMR Spectroscopy demonstrates association constants up to 10{sup 5} M{sup −1}. • Position of CD along PFC chain is elucidated from NMR results. • CD:PFC complex is not disturbed under a variety of water quality conditions. - Abstract: Perfluorochemicals (PFCs) are contaminants of serious concern because of their toxicological properties, widespread presence in drinking water sources, and incredible stability in the environment. To assess the potential application of α-, β-, and γ-cyclodextrins for PFC remediation, we investigated their complexation with linear fluorinated carboxylic acids, sulfonates, and a sulfonamide with carbon backbones ranging from C4-C9. {sup 19}F Nuclear Magnetic Resonance (NMR) spectroscopy studies demonstrated β-CD formed the strongest complexes with these PFCs. The polar head group had a modest influence, but for PFCs with backbones longer than six carbons, strong association constants are observed for 1:1 (K{sub 1:1} ∼ 10{sup 5} M{sup −1}) and 2:1 (K{sub 2:1} ∼ 10{sup 3} M{sup −1}) β-CD:PFC complexes. Excess β-CD can be used to complex 99.5% of the longer chain PFCs. Competition studies with adamantane-carboxylic acid and phenol confirmed the nature and persistence of the β-CD:PFC complex. Detailed analyses of the individual NMR chemical shifts and Job plots indicate the favored positions of the β-CD along the PFC chain. Solution pH, ionic strength, and the presence of humic acid have modest influence on the β-CD:PFC complexes. The strong encapsulation of PFCs by β-CD under a variety of water quality conditions demonstrates the tremendous potential of CD-based materials for the environmental remediation of PFCs.

  7. A slim-line NMR logging tool to measure moisture in soils (United States)

    Sucre, Oscar; Andreas, Pohlmeier; Bernhard, Blümich


    The transport of water in soils is a physical phenomenon of importance in soil science and climatology. This work reports progress in the development of slim-line NMR logging tool ('the sensor') to characterize soil moisture, developed within the DFG-funded interdisciplinary collaborative project TR32. To demonstrate the capability of the NMR technique to follow the drying process of water in soils, several moisture measurements were performed with the sensor on two different types of model soils (sand FH31 and a mix of sand FH31/ silt W3) during an one-step outflow experiment. The soils were packed in columns approximately one meter high. The sensor could be raised and lowered inside a plastic tube (2 mm thick) in the soil column similar to a wire-line logging tool. Working at a frequency of 12 MHz, the sensitive volume lies 6 mm away from the outer sensor surface, measuring the NMR signal of proton spins lying 4 mm inside the soil. Using the direct proportionality between the amplitude of the NMR signal and the water content, partial saturation profiles before, during and after outflow can be obtained. By comparing the data to numerical solutions by means of HYDRUS 1D, we the hydraulic parameters Ks, α, n and l of the Mualem - Van Genuchten model can be assessed for the model soils under study. Furthermore, technical advances to make this tool sturdier for outdoor field measurements and to increase the signal sensitivity are discussed. They include a reduction of the echo time by damping the magneto-acoustic oscillations and the use of the gradiometer coils to make the sensor less sensitive to far-field noise. The performance of the sensor with different coils and under different shielding principles is evaluated to find the optimum design and operating conditions. First field measurements of the sensor from the Selhausen test site are presented.

  8. Magic Angle Spinning NMR Structure Determination of Proteins from Pseudocontact Shifts

    KAUST Repository

    Li, Jianping


    Magic angle spinning solid-state NMR is a unique technique to study atomic-resolution structure of biomacromolecules which resist crystallization or are too large to study by solution NMR techniques. However, difficulties in obtaining sufficient number of long-range distance restraints using dipolar coupling based spectra hamper the process of structure determination of proteins in solid-state NMR. In this study it is shown that high-resolution structure of proteins in solid phase can be determined without the use of traditional dipolar-dipolar coupling based distance restraints by combining the measurements of pseudocontact shifts (PCSs) with Rosetta calculations. The PCSs were generated by chelating exogenous paramagnetic metal ions to a tag 4-mercaptomethyl-dipicolinic acid, which is covalently attached to different residue sites in a 56-residue immunoglobulin-binding domain of protein G (GB1). The long-range structural restraints with metal-nucleus distance of up to ∼20 Å are quantitatively extracted from experimentally observed PCSs, and these are in good agreement with the distances back-calculated using an X-ray structure model. Moreover, we demonstrate that using several paramagnetic ions with varied paramagnetic susceptibilities as well as the introduction of paramagnetic labels at different sites can dramatically increase the number of long-range restraints and cover different regions of the protein. The structure generated from solid-state NMR PCSs restraints combined with Rosetta calculations has 0.7 Å root-mean-square deviation relative to X-ray structure. © 2013 American Chemical Society.

  9. NMR analysis of ion pair formation between timolol and sorbic acid in ophthalmic preparations. (United States)

    Higashiyama, Masayo; Inada, Katsuhiro; Ohtori, Akira; Kakehi, Kazuaki


    Ion pair formation between timolol and sorbic acid was investigated using NMR spectroscopy in order to clarify their interactions within ophthalmic preparation. (13)C and (1)H NMR spectra of timolol, sorbic acid, and a mixture of the two were obtained, and the signal changes induced by pairing were observed. The carbon signals of the butylaminopropanol moiety of timolol were markedly shifted in the mixture, as were the carboxyl and conjugated carbons assigned to sorbic acid. The localizations of the changes in each molecule revealed the binding sites. The profiles of butylaminopropanol carbon chemical shifts plotted against a molar ratio of sorbate were synchronized, which suggested a single type of interaction with sorbic acid. The Job plot showed a typical pattern with a single-maximum at a mole function of 0.5, indicating the presence of a 1:1 complex of timolol and sorbic acid. The stability constants (K) of the timolol-sorbate and timolol-maleate pairs were 1.9x10(1) and 2.2x10(2)M(-1), respectively. The higher K value of the timolol-maleate interaction suggested that it was dominant to the timolol-sorbate interaction when maleate and sorbate coexisted within a timolol solution. Here, we demonstrated evidence of an interaction between timolol and sorbic acid using simple NMR measurements, which suggested the existence of ion pair formation derived from charge neutralization. Our analysis using NMR spectroscopy should advance the understanding and optimization of formulations that are based on ion pair.

  10. Solid-state 51V MAS NMR spectroscopy determines component concentration and crystal phase in co-crystallised mixtures of vanadium complexes

    DEFF Research Database (Denmark)

    Nielsen, Ulla Gro; Hazell, Alan Charles; Skibsted, Jørgen Bengaard


    resonances are sensitive to intermolecular interactions specific to each crystal phase. The solid-state V-51 MAS NMR spectroscopic data show that the different phases do not co-precipitate but the concentration of the solute (which can be either 1 or 2) can vary. Thus co-crystallised mixtures of 1 and 2 can...

  11. Conformational preferences of natural and C3-modified epothilones in aqueous solution. (United States)

    Erdélyi, Máté; Pfeiffer, Bernhard; Hauenstein, Kurt; Fohrer, Jörg; Gertsch, Jürg; Altmann, Karl-Heinz; Carlomagno, Teresa


    The conformational properties of the microtubule-stabilizing agent epothilone A ( 1a) and its 3-deoxy and 3-deoxy-2,3-didehydro derivatives 2 and 3 have been investigated in aqueous solution by a combination of NMR spectroscopic methods, Monte Carlo conformational searches, and NAMFIS calculations. The tubulin-bound conformation of epothilone A ( 1a), as previously proposed on the basis of solution NMR data, was found to represent a significant fraction of the ensemble of conformations present for the free ligands in aqueous solution.

  12. Characterization of poly pyrrole/montmorillonite electro polymerised onto Pt; Caracterizacao de filmes PPy/montmorilonita eletropolimerizados sobre Pt

    Energy Technology Data Exchange (ETDEWEB)

    Castagno, K.R.L., E-mail: [Instituto Federal Sul-rio-grandense (IFSul), RS (Brazil). Dept. de Quimica; Azambuja, D.S.; Dalmoro, V.; Mauller, R.S. [Universidade Federal do Rio Grande do Sul (UFRGS), Pelotas, RS (Brazil). Inst. de Quimica


    In this study films of polypyrrole/montmorillonite (PPy/MT) were electropolymerized on platinum in order to evaluate the performance of this technique in the preparation of nanocomposite materials and to determine the thermal properties and conductivity of the composites. The films were synthesized from a solution containing pyrrole, dodecylbenzene sulfonate, acid and two types of clays: montmorillonite-Na + (MT-Na) and montmorillonite-30B (MT-M). The characterization of the films we have used FT-IR, TEM, XRD, TGA, DSC and resistivity measurement by the four-point van der Pauw method. The study showed that the adopted method of exfoliation and the electropolymerization method used, allows obtaining nanocomposite materials. Analyses of FT-IR, TEM and XRD show that the clays are exfoliated in the polymer matrix. Thermal analysis of the films indicates that the addition of clay reflects an enhancement in the thermal properties of the matrix of PPy, but decreases the conductivity of the same. (author)

  13. NMR data visualization, processing, and analysis on mobile devices. (United States)

    Cobas, Carlos; Iglesias, Isaac; Seoane, Felipe


    Touch-screen computers are emerging as a popular platform for many applications, including those in chemistry and analytical sciences. In this work, we present our implementation of a new NMR 'app' designed for hand-held and portable touch-controlled devices, such as smartphones and tablets. It features a flexible architecture formed by a powerful NMR processing and analysis kernel and an intuitive user interface that makes full use of the smart devices haptic capabilities. Routine 1D and 2D NMR spectra acquired in most NMR instruments can be processed in a fully unattended way. More advanced experiments such as non-uniform sampled NMR spectra are also supported through a very efficient parallelized Modified Iterative Soft Thresholding algorithm. Specific technical development features as well as the overall feasibility of using NMR software apps will also be discussed. All aspects considered the functionalities of the app allowing it to work as a stand-alone tool or as a 'companion' to more advanced desktop applications such as Mnova NMR. Copyright © 2015 John Wiley & Sons, Ltd.

  14. Determination of surface relaxivity from NMR diffusion measurements. (United States)

    Slijkerman, W F; Hofman, J P


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

  15. Can NMR solve some significant challenges in metabolomics? (United States)

    Nagana Gowda, G. A.; Raftery, Daniel


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

  16. PIC microcontroller based external fast analog to digital converter to acquire wide-lined solid NMR spectra by BRUKER DRX and Avance-I spectrometers. (United States)

    Koczor, Bálint; Rohonczy, János


    Concerning many former liquid or hybrid liquid/solid NMR consoles, the built in Analog-to-Digital Converters (ADCs) are incapable of digitizing the fids at sampling rates in the MHz range. Regarding both strong anisotropic interactions in the solid state and wide chemical shift dispersion nuclei in solution phase such as (195)Pt, (119)Sn, (207)Pb etc., the spectrum range of interest might be in the MHz range. As determining the informative tensor components of anisotropic NMR interactions requires nonlinear fitting over the whole spectrum including the asymptotic baseline, it is prohibited by low sampling rates of the ADCs. Wide spectrum width is also useful in solution NMR, since windowing of wide chemical shift ranges is avoidable. We built an external analog to digital converter with 10 MHz maximal sampling rate, which can work simultaneously with the built in ADC of the spectrometer. The ADC was tested on both Bruker DRX and Avance-I NMR consoles. In addition to the analog channels it only requires three external digital lines of the NMR console. The ADC sends data to PC via USB. The whole process is controlled by software written in JAVA which is implemented under TopSpin. Copyright © 2015 Elsevier Inc. All rights reserved.

  17. Dissolution of lignin in green urea aqueous solution (United States)

    Wang, Jingyu; Li, Ying; Qiu, Xueqing; Liu, Di; Yang, Dongjie; Liu, Weifeng; Qian, Yong


    The dissolution problem is the main obstacle for the value-added modification and depolymerization of industrial lignin. Here, a green urea aqueous solution for complete dissolution of various lignin is presented and the dissolution mechanism is analyzed by AFM, DLS and NMR. The results show that the molecular interaction of lignin decreases from 32.3 mN/m in pure water to 11.3 mN/m in urea aqueous solution. The immobility of 1H NMR spectra and the shift of 17O NMR spectra of urea in different lignin/urea solutions indicate that the oxygen of carbonyl in urea and the hydrogen of hydroxyl in lignin form new hydrogen bonds and break the original hydrogen bonds among lignin molecules. The shift of 1H NMR spectra of lignin and the decrease of interactions in model compound polystyrene indicate that urea also breaks the π-π interactions between aromatic rings of lignin. Lignin dissolved in urea aqueous has good antioxidant activity and it can scavenge at least 63% free radicals in 16 min.

  18. Insights into the mechanism for gold catalysis: behaviour of gold(I) amide complexes in solution. (United States)

    Bobin, Mariusz; Day, Iain J; Roe, Stephen M; Viseux, Eddy M E


    We report the synthesis and activity of new mononuclear and dinuclear gold amide complexes 1-7. The dinuclear complexes 6b and 7 were characterised by single crystal X-ray analysis. We also report solution NMR and freezing point depression experiments to rationalise their behaviour in solution and question the de-ligation process invoked in gold catalysis.

  19. Solid-state 73Ge NMR spectroscopy of simple organogermanes. (United States)

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


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

  20. Nanoscale NMR and NQR with Nitrogen Vacancy Centers (United States)

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


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