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Sample records for nmr spectroscopy reveals

  1. NMR spectroscopy reveals the presence and association of lipids and keratin in adhesive gecko setae.

    PubMed

    Jain, Dharamdeep; Stark, Alyssa Y; Niewiarowski, Peter H; Miyoshi, Toshikazu; Dhinojwala, Ali

    2015-01-01

    Lipid and protein aggregates are one of the fundamental materials of biological systems. Examples include cell membranes, insect cuticle, vertebrate epidermis, feathers, hair and adhesive structures known as 'setae' on gecko toes. Until recently gecko setae were assumed to be composed entirely of keratin, but analysis of footprints left behind by geckos walking on surfaces revealed that setae include various kinds of lipids. However, the arrangement and molecular-level behavior of lipids and keratin in the setae is still not known. In the present study we demonstrate, for the first time, the use of Nuclear Magnetic Resonance (NMR) spectroscopy techniques to confirm the presence of lipids and investigate their association with keratin in 'pristine' sheds, or natural molts of the adhesive toe pad and non-adhesive regions of the skin. Analysis was also carried on the sheds after they were 'delipidized' to remove surface lipids. Our results show a distribution of similar lipids in both the skin and toe shed but with different dynamics at a molecular level. The present study can help us understand the gecko system both biologically and for design of synthetic adhesives, but the findings may be relevant to the characteristics of lipid-protein interactions in other biological systems. PMID:25902194

  2. Two dimensional NMR spectroscopy

    SciTech Connect

    Schram, J.; Bellama, J.M.

    1988-01-01

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

  3. The origin of molecular mobility during biomass pyrolysis as revealed by in situ (1)H NMR spectroscopy.

    PubMed

    Dufour, Anthony; Castro-Diaz, Miguel; Brosse, Nicolas; Bouroukba, Mohamed; Snape, Colin

    2012-07-01

    The thermochemical conversion of lignocellulosic biomass feedstocks offers an important potential route for the production of biofuels and value-added green chemicals. Pyrolysis is the first phenomenon involved in all biomass thermochemical processes and it controls to a major extent the product composition. The composition of pyrolysis products can be affected markedly by the extent of softening that occurs. In spite of extensive work on biomass pyrolysis, the development of fluidity during the pyrolysis of biomass has not been quantified. This paper provides the first experimental investigation of proton mobility during biomass pyrolysis by in situ (1)H NMR spectroscopy. The origin of mobility is discussed for cellulose, lignin and xylan. The effect of minerals on cellulose mobility is also investigated. Interactions between polymers in the native biomass network are revealed by in situ (1)H NMR analysis. PMID:22573541

  4. Enantiodiscrimination by NMR spectroscopy.

    PubMed

    Uccello-Barretta, Gloria; Balzano, Federica; Salvadori, Piero

    2006-01-01

    The analysis of enantiorecognition processes involves the detection of enantiomeric species as well as the study of chiral discrimination mechanisms. In both fields Nuclear Magnetic Resonance (NMR) spectroscopy plays a fundamental role, providing several tools, based on the use of suitable chiral auxiliaries, for observing distinct signals of enantiomers and for investigating the complexation phenomena involved in enantiodiscrimination processes. PMID:17100610

  5. Escherichia coli Topoisomerase IV E Subunit and an Inhibitor Binding Mode Revealed by NMR Spectroscopy.

    PubMed

    Li, Yan; Wong, Ying Lei; Ng, Fui Mee; Liu, Boping; Wong, Yun Xuan; Poh, Zhi Ying; Liu, Shuang; Then, Siew Wen; Lee, Michelle Yueqi; Ng, Hui Qi; Huang, Qiwei; Hung, Alvin W; Cherian, Joseph; Hill, Jeffrey; Keller, Thomas H; Kang, CongBao

    2016-08-19

    Bacterial topoisomerases are attractive antibacterial drug targets because of their importance in bacterial growth and low homology with other human topoisomerases. Structure-based drug design has been a proven approach of efficiently developing new antibiotics against these targets. Past studies have focused on developing lead compounds against the ATP binding pockets of both DNA gyrase and topoisomerase IV. A detailed understanding of the interactions between ligand and target in a solution state will provide valuable information for further developing drugs against topoisomerase IV targets. Here we describe a detailed characterization of a known potent inhibitor containing a 9H-pyrimido[4,5-b]indole scaffold against the N-terminal domain of the topoisomerase IV E subunit from Escherichia coli (eParE). Using a series of biophysical and biochemical experiments, it has been demonstrated that this inhibitor forms a tight complex with eParE. NMR studies revealed the exact protein residues responsible for inhibitor binding. Through comparative studies of two inhibitors of markedly varied potencies, it is hypothesized that gaining molecular interactions with residues in the α4 and residues close to the loop of β1-α2 and residues in the loop of β3-β4 might improve the inhibitor potency. PMID:27365392

  6. Revealing Aquatic Dissolved Organic Matter Composition using Direct 1H NMR Spectroscopy

    NASA Astrophysics Data System (ADS)

    Burns, D. C.; Gueguen, C.

    2009-05-01

    Dissolved organic matter (DOM) is ubiquitous in all aquatic ecosystems, and comprises a variety of chemically heterogeneous molecular structures and functional groups. DOM is often considered to be a major ligand for metals in most natural waters. However DOM reactivity is thought to be strongly dependent on its chemical structure. The purpose of this study is to evaluate the variability in molecular composition of aquatic DOM from different sources. Quantitative proton NMR spectra were obtained without any preconcentration using water suppression techniques. The reproducibility on the determination of aromatic and aliphatic proton was better than 3%. The structural information of DOM from northern rivers was compared to IHSS humic substances.

  7. Molecular degradation of ancient documents revealed by 1H HR-MAS NMR spectroscopy

    NASA Astrophysics Data System (ADS)

    Corsaro, Carmelo; Mallamace, Domenico; Łojewska, Joanna; Mallamace, Francesco; Pietronero, Luciano; Missori, Mauro

    2013-10-01

    For centuries mankind has stored its knowledge on paper, a remarkable biomaterial made of natural cellulose fibers. However, spontaneous cellulose degradation phenomena weaken and discolorate paper over time. The detailed knowledge of products arising from cellulose degradation is essential in understanding deterioration pathways and in improving durability of cultural heritage. In this study, for the first time, products of cellulose degradation were individually detected in solid paper samples by means of an extremely powerful proton HR-MAS NMR set-up, in combination to a wise use of both ancient and, as reference, artificially aged paper samples. Carboxylic acids, in addition to more complex dicarboxylic and hydroxy-carboxylic acids, were found in all samples studied. Since these products can catalyze further degradation, their knowledge is fundamental to improve conservation strategies of historical documents. Furthermore, the identification of compounds used in ancient production techniques, also suggests for artifacts dating, authentication and provenance.

  8. Nutrient-dependent Structural Changes in S. aureus Peptidoglycan Revealed by Solid-State NMR Spectroscopy

    PubMed Central

    Zhou, Xiaoxue; Cegelski, Lynette

    2012-01-01

    The bacterial cell wall is essential to cell survival and is a major target of antibiotics. The main component of the bacterial cell wall is peptidoglycan, a cage-like macromolecule that preserves cellular integrity and maintains cell shape. The insolubility and heterogeneity of peptidoglycan pose a challenge to conventional structural analyses. Here we use solid-state NMR combined with specific isotopic labeling to probe a key structural feature of the Staphylococcus aureus peptidoglycan quantitatively and nondestructively. We observed that both the cell-wall morphology and the peptidoglycan structure are functions of growth stage in S. aureus synthetic medium (SASM). Specifically, S. aureus cells at stationary phase have thicker cell walls with non-uniformly thickened septa compared to cells in exponential phase and, remarkably, 12% (±2%) of the stems in their peptidoglycan do not have pentaglycine bridges attached. Mechanistically, we determined that these observations are triggered by the depletion of glycine in the nutrient medium, which is coincident with the start of the stationary phase, and that the production of the structurally altered peptidoglycan can be prevented by the addition of excess glycine. We also demonstrated that the structural changes primarily arise within newly synthesized peptidoglycan rather than through the modification of previously synthesized peptidoglycan. Collectively, our observations emphasize the plasticity in bacterial cell-wall assembly and the possibility to manipulate peptidoglycan structure with external stimuli. PMID:22974326

  9. Molecular dynamics of neutral polymer bonding agent (NPBA) as revealed by solid-state NMR spectroscopy.

    PubMed

    Hu, Wei; Su, Yongchao; Zhou, Lei; Pang, Aimin; Cai, Rulin; Ma, Xingang; Li, Shenhui

    2013-01-01

    Neutral polymer bonding agent (NPBA) is one of the most promising polymeric materials, widely used in nitrate ester plasticized polyether (NEPE) propellant as bonding agent. The structure and dynamics of NPBA under different conditions of temperatures and sample processing are comprehensively investigated by solid state NMR (SSNMR). The results indicate that both the main chain and side chain of NPBA are quite rigid below its glass transition temperature (Tg). In contrast, above the Tg, the main chain remains relatively immobilized, while the side chains become highly flexible, which presumably weakens the interaction between bonding agent and the binder or oxidant fillers and in turn destabilizes the high modulus layer formed around the oxidant fillers. In addition, no obvious variation is found for the microstructure of NPBA upon aging treatment or soaking with acetone. These experimental results provide useful insights for understanding the structural properties of NPBA and its interaction with other constituents of solid composite propellants under different processing and working conditions. PMID:24451254

  10. Symmetrization of cationic hydrogen bridges of protonated sponges induced by solvent and counteranion interactions as revealed by NMR spectroscopy.

    PubMed

    Pietrzak, Mariusz; Wehling, Jens P; Kong, Shushu; Tolstoy, Peter M; Shenderovich, Ilya G; López, Concepción; Claramunt, Rosa María; Elguero, José; Denisov, Gleb S; Limbach, Hans-Heinrich

    2010-02-01

    The properties of the intramolecular hydrogen bonds of doubly (15)N-labeled protonated sponges of the 1,8-bis(dimethylamino)naphthalene (DMANH(+)) type have been studied as a function of the solvent, counteranion, and temperature using low-temperature NMR spectroscopy. Information about the hydrogen-bond symmetries was obtained by the analysis of the chemical shifts delta(H) and delta(N) and the scalar coupling constants J(N,N), J(N,H), J(H,N) of the (15)NH(15)N hydrogen bonds. Whereas the individual couplings J(N,H) and J(H,N) were averaged by a fast intramolecular proton tautomerism between two forms, it is shown that the sum |J(N,H)+J(H,N)| generally represents a measure of the hydrogen-bond strength in a similar way to delta(H) and J(N,N). The NMR spectroscopic parameters of DMANH(+) and of 4-nitro-DMANH(+) are independent of the anion in the case of CD(3)CN, which indicates ion-pair dissociation in this solvent. By contrast, studies using CD(2)Cl(2), [D(8)]toluene as well as the freon mixture CDF(3)/CDF(2)Cl, which is liquid down to 100 K, revealed an influence of temperature and of the counteranions. Whereas a small counteranion such as trifluoroacetate perturbed the hydrogen bond, the large noncoordinating anion tetrakis[3,5-bis(trifluoromethyl)phenyl]borate B[{C(6)H(3)(CF(3))(2)}(4)](-) (BARF(-)), which exhibits a delocalized charge, made the hydrogen bond more symmetric. Lowering the temperature led to a similar symmetrization, an effect that is discussed in terms of solvent ordering at low temperature and differential solvent order/disorder at high temperatures. By contrast, toluene molecules that are ordered around the cation led to typical high-field shifts of the hydrogen-bonded proton as well as of those bound to carbon, an effect that is absent in the case of neutral NHN chelates. PMID:20024986

  11. Two-dimensional NMR spectroscopy

    SciTech Connect

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

    1987-01-01

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

  12. Effect of internal cavities on folding rates and routes revealed by real-time pressure-jump NMR spectroscopy.

    PubMed

    Roche, Julien; Dellarole, Mariano; Caro, José A; Norberto, Douglas R; Garcia, Angel E; Garcia-Moreno, Bertrand; Roumestand, Christian; Royer, Catherine A

    2013-10-01

    The time required to fold proteins usually increases significantly under conditions of high pressure. Taking advantage of this general property of proteins, we combined P-jump experiments with NMR spectroscopy to examine in detail the folding reaction of staphylococcal nuclease (SNase) and of some of its cavity-containing variants. The nearly 100 observables that could be measured simultaneously collectively describe the kinetics of folding as a function of pressure and denaturant concentration with exquisite site-specific resolution. SNase variants with cavities in the central core of the protein exhibit a highly heterogeneous transition-state ensemble (TSE) with a smaller solvent-excluded void volume than the TSE of the parent SNase. This heterogeneous TSE experiences Hammond behavior, becoming more native-like (higher molar volume) with increasing denaturant concentration. In contrast, the TSE of the L125A variant, which has a cavity at the secondary core, is only slightly different from that of the parent SNase. Because pressure acts mainly to eliminate solvent-excluded voids, which are heterogeneously distributed throughout structures, it perturbs the protein more selectively than chemical denaturants, thereby facilitating the characterization of intermediates and the consequences of packing on folding mechanisms. Besides demonstrating how internal cavities can affect the routes and rates of folding of a protein, this study illustrates how the combination of P-jump and NMR spectroscopy can yield detailed mechanistic insight into protein folding reactions with exquisite site-specific temporal information. PMID:23987660

  13. Modern NMR Spectroscopy.

    ERIC Educational Resources Information Center

    Jelinski, Lynn W.

    1984-01-01

    Discusses direct chemical information that can be obtained from modern nuclear magnetic resonance (NMR) methods, concentrating on the types of problems that can be solved. Shows how selected methods provide information about polymers, bipolymers, biochemistry, small organic molecules, inorganic compounds, and compounds oriented in a magnetic…

  14. Two-dimensional NMR spectroscopy reveals cation-triggered backbone degradation in polysulfone-based anion exchange membranes.

    PubMed

    Arges, Christopher G; Ramani, Vijay

    2013-02-12

    Anion exchange membranes (AEMs) find widespread applications as an electrolyte and/or electrode binder in fuel cells, electrodialysis stacks, flow and metal-air batteries, and electrolyzers. AEMs exhibit poor stability in alkaline media; their degradation is induced by the hydroxide ion, a potent nucleophile. We have used 2D NMR techniques to investigate polymer backbone stability (as opposed to cation stability) of the AEM in alkaline media. We report the mechanism behind a peculiar, often-observed phenomenon, wherein a demonstrably stable polysulfone backbone degrades rapidly in alkaline solutions upon derivatization with alkaline stable fixed cation groups. Using COSY and heteronuclear multiple quantum correlation spectroscopy (2D NMR), we unequivocally demonstrate that the added cation group triggers degradation of the polymer backbone in alkaline via quaternary carbon hydrolysis and ether hydrolysis, leading to rapid failure. This finding challenges the existing perception that having a stable cation moiety is sufficient to yield a stable AEM and emphasizes the importance of the often ignored issue of backbone stability. PMID:23335629

  15. Two-dimensional NMR spectroscopy reveals cation-triggered backbone degradation in polysulfone-based anion exchange membranes

    PubMed Central

    Arges, Christopher G.; Ramani, Vijay

    2013-01-01

    Anion exchange membranes (AEMs) find widespread applications as an electrolyte and/or electrode binder in fuel cells, electrodialysis stacks, flow and metal-air batteries, and electrolyzers. AEMs exhibit poor stability in alkaline media; their degradation is induced by the hydroxide ion, a potent nucleophile. We have used 2D NMR techniques to investigate polymer backbone stability (as opposed to cation stability) of the AEM in alkaline media. We report the mechanism behind a peculiar, often-observed phenomenon, wherein a demonstrably stable polysulfone backbone degrades rapidly in alkaline solutions upon derivatization with alkaline stable fixed cation groups. Using COSY and heteronuclear multiple quantum correlation spectroscopy (2D NMR), we unequivocally demonstrate that the added cation group triggers degradation of the polymer backbone in alkaline via quaternary carbon hydrolysis and ether hydrolysis, leading to rapid failure. This finding challenges the existing perception that having a stable cation moiety is sufficient to yield a stable AEM and emphasizes the importance of the often ignored issue of backbone stability. PMID:23335629

  16. "Solvent Effects" in 1H NMR Spectroscopy.

    ERIC Educational Resources Information Center

    Cavaleiro, Jose A. S.

    1987-01-01

    Describes a simple undergraduate experiment in chemistry dealing with the "solvent effects" in nuclear magnetic resonance (NMR) spectroscopy. Stresses the importance of having students learn NMR spectroscopy as a tool in analytical chemistry. (TW)

  17. Catalytic Analysis of APOBEC3G Involving Real-Time NMR Spectroscopy Reveals Nucleic Acid Determinants for Deamination

    PubMed Central

    Kamba, Keisuke; Nagata, Takashi; Katahira, Masato

    2015-01-01

    APOBEC3G (A3G) is a single-stranded DNA-specific cytidine deaminase that preferentially converts cytidine to uridine at the third position of triplet cytosine (CCC) hotspots. A3G restricts the infectivity of viruses, such as HIV-1, by targeting CCC hotspots scattered through minus DNA strands, reverse-transcribed from genomic RNA. Previously, we developed a real-time NMR method and elucidated the origin of the 3'→5' polarity of deamination of DNA by the C-terminal domain of A3G (CD2), which is a phenomenon by which a hotspot located closer to the 5'-end is deaminated more effectively than one less close to the 5'-end, through quantitative analysis involving nonspecific binding to and sliding along DNA. In the present study we applied the real-time NMR method to analyze the catalytic activity of CD2 toward DNA oligonucleotides containing a nucleotide analog at a single or multiple positions. Analyses revealed the importance of the sugar and base moieties throughout the consecutive 5 nucleotides, the CCC hotspot being positioned at the center. It was also shown that the sugar or base moieties of the nucleotides outside this 5 nucleotide recognition sequence are also relevant as to CD2's activity. Analyses involving DNA oligonucleotides having two CCC hotspots linked by a long sequence of either deoxyribonucleotides, ribonucleotides or abasic deoxyribonucleotides suggested that the phosphate backbone is required for CD2 to slide along the DNA strand and to exert the 3'→5' polarity. Examination of the effects of different salt concentrations on the 3'→5' polarity indicated that the higher the salt concentration, the less prominent the 3'→5' polarity. This is most likely the result of alleviation of sliding due to a decrease in the affinity of CD2 with the phosphate backbone at high salt concentrations. We also investigated the reactivity of substrates containing 5-methylcytidine (5mC) or 5-hydroxymethylcytidine, and found that A3G exhibited low activity toward

  18. Acidic Properties and Structure-Activity Correlations of Solid Acid Catalysts Revealed by Solid-State NMR Spectroscopy.

    PubMed

    Zheng, Anmin; Li, Shenhui; Liu, Shang-Bin; Deng, Feng

    2016-04-19

    Solid acid materials with tunable structural and acidic properties are promising heterogeneous catalysts for manipulating and/or emulating the activity and selectivity of industrially important catalytic reactions. On the other hand, the performances of acid-catalyzed reactions are mostly dictated by the acidic features, namely, type (Brønsted vs Lewis acidity), amount, strength, and local environment of acid sites. The latter is relevant to their location (intra- vs extracrystalline), and possible confinement and Brønsted-Lewis acid synergy effects that may strongly affect the host-guest interactions, reaction mechanism, and shape selectivity of the catalytic system. This account aims to highlight some important applications of state-of-the-art solid-state NMR (SSNMR) techniques for exploring the structural and acidic properties of solid acid catalysts as well as their catalytic performances and relevant reaction pathway invoked. In addition, density functional theory (DFT) calculations may be exploited in conjunction with experimental SSNMR studies to verify the structure-activity correlations of the catalytic system at a microscopic scale. We describe in this Account the developments and applications of advanced ex situ and/or in situ SSNMR techniques, such as two-dimensional (2D) double-quantum magic-angle spinning (DQ MAS) homonuclear correlation spectroscopy for structural investigation of solid acids as well as study of their acidic properties. Moreover, the energies and electronic structures of the catalysts and detailed catalytic reaction processes, including the identification of reaction species, elucidation of reaction mechanism, and verification of structure-activity correlations, made available by DFT theoretical calculations were also discussed. Relevant discussions will focus primarily on results obtained from our laboratories in the past decade, including (i) quantitative and qualitative acidity characterization utilizing assorted probe molecules

  19. Hyperpolarized 131Xe NMR spectroscopy

    PubMed Central

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

    2011-01-01

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

  20. 1H NMR spectroscopy of serum reveals unique metabolic fingerprints associated with subtypes of surgically induced osteoarthritis in sheep.

    PubMed

    Maher, Anthony D; Coles, Chantal; White, Jason; Bateman, John F; Fuller, Emily S; Burkhardt, Dan; Little, Christopher B; Cake, Martin; Read, Richard; McDonagh, Matthew B; Rochfort, Simone Jane

    2012-08-01

    Osteoarthritis (OA) is a highly prevalent joint disease. Its slow progressive nature and the correlation between pathological changes and clinical symptoms mean that OA is often well advanced by the time of diagnosis. In the absence of any specific pharmacological treatments, there is a pressing need to develop robust biomarkers for OA. We have adopted a nuclear magnetic resonance (NMR)-based metabolomic strategy to identify molecular responses to surgically induced OA in an animal model. Sheep underwent one of three types of surgical procedure (sham (control), meniscal destabilization, MD or anterior cruciate ligament transaction, ACLT), and for every animal a serum sample was collected both pre- and postoperatively, thus, affording two types of "control" data for comparison. 1D 1H NMR spectra were acquired from each sample at 800 MHz and the digitized spectral data were analyzed using principal components analysis and partial least-squares regression discriminant analysis. Our approach, combined with the study design, allowed us to separate the metabolic responses to surgical intervention from those associated with OA. We were able to identify dimethyl sulfone (DMSO2) as being increased in MD after 4 weeks, while ACLT-induced OA exhibited increased 3-methylhistidine and decreased branched chain amino acids (BCAAs). The findings are discussed in the context of interpretation of metabolomic results in studies of human disease, and the selection of appropriate "control" data sets. PMID:22784358

  1. NMR Spectroscopy and Its Value: A Primer

    ERIC Educational Resources Information Center

    Veeraraghavan, Sudha

    2008-01-01

    Nuclear magnetic resonance (NMR) spectroscopy is widely used by chemists. Furthermore, the use of NMR spectroscopy to solve structures of macromolecules or to examine protein-ligand interactions is popular. Yet, few students entering graduate education in biological sciences have been introduced to this method or its utility. Over the last six…

  2. Modern NMR spectroscopy: a guide for chemists

    SciTech Connect

    Sanders, J.K.M.; Hunter, B.K.

    1988-01-01

    The aim of the authors of Modern NMR Spectroscopy is to bridge the communication gap between the chemist and the spectroscopist. The approach is nonmathematical, descriptive, and pictorial. To illustrate the ideas introduced in the text, the authors provide original spectra obtained specially for this purpose. Examples include spectroscopy of protons, carbon, and less receptive nuclei of interest to inorganic chemists. The authors succeed in making high-resolution NMR spectroscopy comprehensible for the average student or chemist.

  3. Phase Separation in Binary Mixtures of Bipolar and Monopolar Lipid Dispersions Revealed by 2H NMR Spectroscopy, Small Angle X-Ray Scattering, and Molecular Theory

    PubMed Central

    Brownholland, David P.; Longo, Gabriel S.; Struts, Andrey V.; Justice, Matthew J.; Szleifer, Igal; Petrache, Horia I.; Brown, Michael F.; Thompson, David H.

    2009-01-01

    Abstract Binary mixtures of C20BAS and POPC membranes were studied by solid-state 2H NMR spectroscopy and small angle x-ray scattering (SAXS) over a wide range of concentrations and at different temperatures. Three specifically deuterated C20BAS derivatives—[1′,1′,20′,20′-2H4]C20BAS, [2′,2′,19′,19′-2H4]C20BAS, and [10′,11′-2H2]C20BAS—combined with protiated 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), as well as membranes containing POPC-d31 and fully protiated bolalipid, were used in NMR experiments to obtain structural information for the mixtures. The 2H NMR spectra of [10′,11′-2H2]C20BAS/POPC membrane dispersions reveal that the bolalipid is predominantly in the transmembrane conformation at high bolalipid concentrations (100, 90, and 70 mol %). At ≤50 mol % C20BAS, smaller quadrupolar couplings appear in the spectra, indicating the presence of U-shaped conformers. The proportion of U-shaped bolalipids increases as the amount of POPC in the membrane increases; however, the transmembrane component remains the dominant bolalipid conformation in the membrane even at 45°C and 10 mol % C20BAS, where it accounts for ∼50% of the bolalipid population. The large fraction of C20BAS transmembrane conformers, regardless of the C20BAS/POPC ratio, together with the findings from molecular mean-field theory calculations, suggests the coexistence of phase-separated bolalipid-rich domains and POPC-rich domains. A single lamellar repeat distance was observed in SAXS experiments corresponding to the average repeat spacing expected for C20BAS- and POPC-rich domains. These observations are consistent with the presence of microphase-separated domains in the mixed membrane samples that arise from POPC-C20BAS hydrophobic mismatch. PMID:19917223

  4. Scalable NMR spectroscopy with semiconductor chips

    PubMed Central

    Ha, Dongwan; Paulsen, Jeffrey; Sun, Nan; Song, Yi-Qiao; Ham, Donhee

    2014-01-01

    State-of-the-art NMR spectrometers using superconducting magnets have enabled, with their ultrafine spectral resolution, the determination of the structure of large molecules such as proteins, which is one of the most profound applications of modern NMR spectroscopy. Many chemical and biotechnological applications, however, involve only small-to-medium size molecules, for which the ultrafine resolution of the bulky, expensive, and high-maintenance NMR spectrometers is not required. For these applications, there is a critical need for portable, affordable, and low-maintenance NMR spectrometers to enable in-field, on-demand, or online applications (e.g., quality control, chemical reaction monitoring) and co-use of NMR with other analytical methods (e.g., chromatography, electrophoresis). As a critical step toward NMR spectrometer miniaturization, small permanent magnets with high field homogeneity have been developed. In contrast, NMR spectrometer electronics capable of modern multidimensional spectroscopy have thus far remained bulky. Complementing the magnet miniaturization, here we integrate the NMR spectrometer electronics into 4-mm2 silicon chips. Furthermore, we perform various multidimensional NMR spectroscopies by operating these spectrometer electronics chips together with a compact permanent magnet. This combination of the spectrometer-electronics-on-a-chip with a permanent magnet represents a useful step toward miniaturization of the overall NMR spectrometer into a portable platform. PMID:25092330

  5. Scalable NMR spectroscopy with semiconductor chips.

    PubMed

    Ha, Dongwan; Paulsen, Jeffrey; Sun, Nan; Song, Yi-Qiao; Ham, Donhee

    2014-08-19

    State-of-the-art NMR spectrometers using superconducting magnets have enabled, with their ultrafine spectral resolution, the determination of the structure of large molecules such as proteins, which is one of the most profound applications of modern NMR spectroscopy. Many chemical and biotechnological applications, however, involve only small-to-medium size molecules, for which the ultrafine resolution of the bulky, expensive, and high-maintenance NMR spectrometers is not required. For these applications, there is a critical need for portable, affordable, and low-maintenance NMR spectrometers to enable in-field, on-demand, or online applications (e.g., quality control, chemical reaction monitoring) and co-use of NMR with other analytical methods (e.g., chromatography, electrophoresis). As a critical step toward NMR spectrometer miniaturization, small permanent magnets with high field homogeneity have been developed. In contrast, NMR spectrometer electronics capable of modern multidimensional spectroscopy have thus far remained bulky. Complementing the magnet miniaturization, here we integrate the NMR spectrometer electronics into 4-mm(2) silicon chips. Furthermore, we perform various multidimensional NMR spectroscopies by operating these spectrometer electronics chips together with a compact permanent magnet. This combination of the spectrometer-electronics-on-a-chip with a permanent magnet represents a useful step toward miniaturization of the overall NMR spectrometer into a portable platform. PMID:25092330

  6. A Guided Inquiry Approach to NMR Spectroscopy

    NASA Astrophysics Data System (ADS)

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

    1998-04-01

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

  7. Probing Cancer Cell Metabolism Using NMR Spectroscopy.

    PubMed

    Hollinshead, Kate E R; Williams, Debbie S; Tennant, Daniel A; Ludwig, Christian

    2016-01-01

    Altered cellular metabolism is now accepted to be at the core of many diseases including cancer. Over the past 20 years, NMR has become a core technology to study these metabolic perturbations in detail. This chapter reviews current NMR-based methods for steady-state metabolism and, in particular, the use of non-radioactive stable isotope-enriched tracers. Opportunities and challenges for each method, such as 1D (1)H NMR spectroscopy and (13)C carbon-based NMR spectroscopic methods, are discussed. Ultimately, the combination of NMR and mass spectra as orthogonal technologies are required to compensate for the drawbacks of each technique when used singly are discussed. PMID:27325263

  8. QUANTITATIVE 15N NMR SPECTROSCOPY

    EPA Science Inventory

    Line intensities in 15N NMR spectra are strongly influenced by spin-lattice and spin-spin relaxation times, relaxation mechanisms and experimental conditions. Special care has to be taken in using 15N spectra for quantitative purposes. Quantitative aspects are discussed for the 1...

  9. Interaction of a putative BH3 domain of clusterin with anti-apoptotic Bcl-2 family proteins as revealed by NMR spectroscopy

    SciTech Connect

    Lee, Dong-Hwa; Ha, Ji-Hyang; Kim, Yul; Bae, Kwang-Hee; Park, Jae-Yong; Choi, Wan Sung; Yoon, Ho Sup; Park, Sung Goo; Park, Byoung Chul; Yi, Gwan-Su; Chi, Seung-Wook

    2011-05-20

    Highlights: {yields} Identification of a conserved BH3 motif in C-terminal coiled coil region of nCLU. {yields} The nCLU BH3 domain binds to BH3 peptide-binding grooves in both Bcl-X{sub L} and Bcl-2. {yields} A conserved binding mechanism of nCLU BH3 and the other pro-apoptotic BH3 peptides with Bcl-X{sub L}. {yields} The absolutely conserved Leu323 and Asp328 of nCLU BH3 domain are critical for binding to Bcl-X{sub L.} {yields} Molecular understanding of the pro-apoptotic function of nCLU as a novel BH3-only protein. -- Abstract: Clusterin (CLU) is a multifunctional glycoprotein that is overexpressed in prostate and breast cancers. Although CLU is known to be involved in the regulation of apoptosis and cell survival, the precise molecular mechanism underlying the pro-apoptotic function of nuclear CLU (nCLU) remains unclear. In this study, we identified a conserved BH3 motif in C-terminal coiled coil (CC2) region of nCLU by sequence analysis and characterized the molecular interaction of the putative nCLU BH3 domain with anti-apoptotic Bcl-2 family proteins by nuclear magnetic resonance (NMR) spectroscopy. The chemical shift perturbation data demonstrated that the nCLU BH3 domain binds to pro-apoptotic BH3 peptide-binding grooves in both Bcl-X{sub L} and Bcl-2. A structural model of the Bcl-X{sub L}/nCLU BH3 peptide complex reveals that the binding mode is remarkably similar to those of other Bcl-X{sub L}/BH3 peptide complexes. In addition, mutational analysis confirmed that Leu323 and Asp328 of nCLU BH3 domain, absolutely conserved in the BH3 motifs of BH3-only protein family, are critical for binding to Bcl-X{sub L}. Taken altogether, our results suggest a molecular basis for the pro-apoptotic function of nCLU by elucidating the residue specific interactions of the BH3 motif in nCLU with anti-apoptotic Bcl-2 family proteins.

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

    SciTech Connect

    Matwiyoff, N.A.

    1983-01-01

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

  11. Epitope mapping by solution NMR spectroscopy.

    PubMed

    Bardelli, M; Livoti, E; Simonelli, L; Pedotti, M; Moraes, A; Valente, A P; Varani, L

    2015-06-01

    Antibodies play an ever more prominent role in basic research as well as in the biotechnology and pharmaceutical sectors. Characterizing their epitopes, that is, the region that they recognize on their target molecule, is useful for purposes ranging from molecular biology research to vaccine design and intellectual property protection. Solution NMR spectroscopy is ideally suited to the atomic level characterization of intermolecular interfaces and, as a consequence, to epitope discovery. Here, we illustrate how NMR epitope mapping can be used to rapidly and accurately determine protein antigen epitopes. The basic concept is that differences in the NMR signal of an antigen free or bound by an antibody will identify epitope residues. NMR epitope mapping provides more detailed information than mutagenesis or peptide mapping and can be much more rapid than X-ray crystallography. Advantages and drawbacks of this technique are discussed together with practical considerations. PMID:25726811

  12. Picoliter H-1 NMR Spectroscopy

    SciTech Connect

    Minard, Kevin R. ); Wind, Robert A. )

    2002-02-01

    A RF probe that fits inside the bore of a small gradient coil package is described for routine 1H-NMR microscopy measurements on small samples. The probe operates at 500 MHz and houses a 267-um-diameter solenoid transceiver. When used in three dimensional chemical shift imaging (3D-CSI) experiments, the measured signal-to-noise ratio (SNR) is shown to be within 20-30 percent of theoretical limits formulated by only considering the solenoid's resistive losses. This is illustrated using a 100-um-diameter globule of triacylglycerols ({approx}900mM) that may be an oocyte precursor in young Xenopus Laevis frogs, and water sample containing choline at a concentration often found in live cells ({approx}33mM). In chemical shift images generated using a few thousand scans, the choline methyl line is found to have an acceptable SNR in resolved from just 5 picoliters in the Xenopus globule. It is concluded that the probe's sensitivity is sufficient for performing 1H-NMR on picoliter-scale volumes in biological cells and tissues.

  13. An Introduction to Biological NMR Spectroscopy*

    PubMed Central

    Marion, Dominique

    2013-01-01

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

  14. Multidimensional NMR spectroscopy in a single scan.

    PubMed

    Gal, Maayan; Frydman, Lucio

    2015-11-01

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

  15. Tritiation methods and tritium NMR spectroscopy

    SciTech Connect

    Jaiswal, D.K.; Morimoto, H.; Salijoughian, M.; Williams, P.G.

    1991-09-01

    We have used a simple process for the production of highly tritiated water and characterized the product species by {sup 1}H and {sup 3}H NMR spectroscopy. The water is readily manipulated and used in subsequent reactions either as T{sub 2}O, CH{sub 3}COOT or CF{sub 3}COOT. Development of tritiated diimide has progressed to the point where cis-hydrogenated products at 1-20 Ci/mmole S.A. are possible. Tri-n-butyl tin tritide has been produced at >95% tritium content and well characterized by multinuclear NMR techniques. 27 refs., 3 figs.

  16. Revealing lithium-silicide phase transformations in nano-structured silicon-based lithium ion batteries via in situ NMR spectroscopy.

    PubMed

    Ogata, K; Salager, E; Kerr, C J; Fraser, A E; Ducati, C; Morris, A J; Hofmann, S; Grey, C P

    2014-01-01

    Nano-structured silicon anodes are attractive alternatives to graphitic carbons in rechargeable Li-ion batteries, owing to their extremely high capacities. Despite their advantages, numerous issues remain to be addressed, the most basic being to understand the complex kinetics and thermodynamics that control the reactions and structural rearrangements. Elucidating this necessitates real-time in situ metrologies, which are highly challenging, if the whole electrode structure is studied at an atomistic level for multiple cycles under realistic cycling conditions. Here we report that Si nanowires grown on a conducting carbon-fibre support provide a robust model battery system that can be studied by (7)Li in situ NMR spectroscopy. The method allows the (de)alloying reactions of the amorphous silicides to be followed in the 2nd cycle and beyond. In combination with density-functional theory calculations, the results provide insight into the amorphous and amorphous-to-crystalline lithium-silicide transformations, particularly those at low voltages, which are highly relevant to practical cycling strategies. PMID:24488002

  17. Metabolic responses of willow (Salix purpurea L.) leaves to mycorrhization as revealed by mass spectrometry and 1H NMR spectroscopy metabolite profiling

    PubMed Central

    Aliferis, Konstantinos A.; Chamoun, Rony; Jabaji, Suha

    2015-01-01

    The root system of most terrestrial plants form symbiotic interfaces with arbuscular mycorrhizal fungi (AMF), which are important for nutrient cycling and ecosystem sustainability. The elucidation of the undergoing changes in plants' metabolism during symbiosis is essential for understanding nutrient acquisition and for alleviation of soil stresses caused by environmental cues. Within this context, we have undertaken the task of recording the fluctuation of willow (Salix purpurea L.) leaf metabolome in response to AMF inoculation. The development of an advanced metabolomics/bioinformatics protocol employing mass spectrometry (MS) and 1H NMR analyzers combined with the in-house-built metabolite library for willow (http://willowmetabolib.research.mcgill.ca/index.html) are key components of the research. Analyses revealed that AMF inoculation of willow causes up-regulation of various biosynthetic pathways, among others, those of flavonoid, isoflavonoid, phenylpropanoid, and the chlorophyll and porphyrin pathways, which have well-established roles in plant physiology and are related to resistance against environmental stresses. The recorded fluctuation in the willow leaf metabolism is very likely to provide AMF-inoculated willows with a significant advantage compared to non-inoculated ones when they are exposed to stresses such as, high levels of soil pollutants. The discovered biomarkers of willow response to AMF inoculation and corresponding pathways could be exploited in biomarker-assisted selection of willow cultivars with superior phytoremediation capacity or genetic engineering programs. PMID:26042135

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

    ERIC Educational Resources Information Center

    Mills, Nancy S.; Shanklin, Michael

    2011-01-01

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

  19. Catalytic mechanism of α-phosphate attack in dUTPase is revealed by X-ray crystallographic snapshots of distinct intermediates, 31P-NMR spectroscopy and reaction path modelling

    PubMed Central

    Barabás, Orsolya; Németh, Veronika; Bodor, Andrea; Perczel, András; Rosta, Edina; Kele, Zoltán; Zagyva, Imre; Szabadka, Zoltán; Grolmusz, Vince I.; Wilmanns, Matthias; Vértessy, Beáta G.

    2013-01-01

    Enzymatic synthesis and hydrolysis of nucleoside phosphate compounds play a key role in various biological pathways, like signal transduction, DNA synthesis and metabolism. Although these processes have been studied extensively, numerous key issues regarding the chemical pathway and atomic movements remain open for many enzymatic reactions. Here, using the Mason–Pfizer monkey retrovirus dUTPase, we study the dUTPase-catalyzed hydrolysis of dUTP, an incorrect DNA building block, to elaborate the mechanistic details at high resolution. Combining mass spectrometry analysis of the dUTPase-catalyzed reaction carried out in and quantum mechanics/molecular mechanics (QM/MM) simulation, we show that the nucleophilic attack occurs at the α-phosphate site. Phosphorus-31 NMR spectroscopy (31P-NMR) analysis confirms the site of attack and shows the capability of dUTPase to cleave the dUTP analogue α,β-imido-dUTP, containing the imido linkage usually regarded to be non-hydrolyzable. We present numerous X-ray crystal structures of distinct dUTPase and nucleoside phosphate complexes, which report on the progress of the chemical reaction along the reaction coordinate. The presently used combination of diverse structural methods reveals details of the nucleophilic attack and identifies a novel enzyme–product complex structure. PMID:23982515

  20. Catalytic mechanism of α-phosphate attack in dUTPase is revealed by X-ray crystallographic snapshots of distinct intermediates, 31P-NMR spectroscopy and reaction path modelling.

    PubMed

    Barabás, Orsolya; Németh, Veronika; Bodor, Andrea; Perczel, András; Rosta, Edina; Kele, Zoltán; Zagyva, Imre; Szabadka, Zoltán; Grolmusz, Vince I; Wilmanns, Matthias; Vértessy, Beáta G

    2013-12-01

    Enzymatic synthesis and hydrolysis of nucleoside phosphate compounds play a key role in various biological pathways, like signal transduction, DNA synthesis and metabolism. Although these processes have been studied extensively, numerous key issues regarding the chemical pathway and atomic movements remain open for many enzymatic reactions. Here, using the Mason-Pfizer monkey retrovirus dUTPase, we study the dUTPase-catalyzed hydrolysis of dUTP, an incorrect DNA building block, to elaborate the mechanistic details at high resolution. Combining mass spectrometry analysis of the dUTPase-catalyzed reaction carried out in and quantum mechanics/molecular mechanics (QM/MM) simulation, we show that the nucleophilic attack occurs at the α-phosphate site. Phosphorus-31 NMR spectroscopy ((31)P-NMR) analysis confirms the site of attack and shows the capability of dUTPase to cleave the dUTP analogue α,β-imido-dUTP, containing the imido linkage usually regarded to be non-hydrolyzable. We present numerous X-ray crystal structures of distinct dUTPase and nucleoside phosphate complexes, which report on the progress of the chemical reaction along the reaction coordinate. The presently used combination of diverse structural methods reveals details of the nucleophilic attack and identifies a novel enzyme-product complex structure. PMID:23982515

  1. Simulation of selective pulse techniques for localized NMR spectroscopy

    NASA Astrophysics Data System (ADS)

    Garwood, Michael; Schleich, Thomas; Robin Bendall, M.

    The results of a computer simulation investigation delineating the limits of resolution, sensitivity, and accuracy of the depth- resolved suface-coil spectroscopy (DRESS), volume-selective excitation (VSE), and image-selected in vivo spectroscopy (ISIS) methods for achieving spatially localized NMR spectroscopy are presented. A computer program, which numerically solves the Bloch equations for variable input parameters, is used to simulate the spatial localization afforded by each technique. Because the numerical solution of the Bloch equations describes the behavior of the bulk magnetization with great precision, the simulations provide an objective and realistic means of evaluating the performance of the individual localization schemes and reveal nuances and limitations not discussed in the original experimental papers. The results of this computer simulation study should encourage the optimization of localization methodology for use in specific applications.

  2. Exploring RNA polymerase regulation by NMR spectroscopy

    PubMed Central

    Drögemüller, Johanna; Strauß, Martin; Schweimer, Kristian; Wöhrl, Birgitta M.; Knauer, Stefan H.; Rösch, Paul

    2015-01-01

    RNA synthesis is a central process in all organisms, with RNA polymerase (RNAP) as the key enzyme. Multisubunit RNAPs are evolutionary related and are tightly regulated by a multitude of transcription factors. Although Escherichia coli RNAP has been studied extensively, only little information is available about its dynamics and transient interactions. This information, however, are crucial for the complete understanding of transcription regulation in atomic detail. To study RNAP by NMR spectroscopy we developed a highly efficient procedure for the assembly of active RNAP from separately expressed subunits that allows specific labeling of the individual constituents. We recorded [1H,13C] correlation spectra of isoleucine, leucine, and valine methyl groups of complete RNAP and the separately labeled β’ subunit within reconstituted RNAP. We further produced all RNAP subunits individually, established experiments to determine which RNAP subunit a certain regulator binds to, and identified the β subunit to bind NusE. PMID:26043358

  3. Spatially resolved spectroscopy using tapered stripline NMR

    NASA Astrophysics Data System (ADS)

    Tijssen, Koen C. H.; Bart, Jacob; Tiggelaar, Roald M.; Janssen, J. W. G. (Hans); Kentgens, Arno P. M.; van Bentum, P. Jan M.

    2016-02-01

    Magnetic field B0 gradients are essential in modern Nuclear Magnetic Resonance spectroscopy and imaging. Although RF/B1 gradients can be used to fulfill a similar role, this is not used in common practice because of practical limitations in the design of B1 gradient coils. Here we present a new method to create B1 gradients using stripline RF coils. The conductor-width of a stripline NMR chip and the strength of its radiofrequency field are correlated, so a stripline chip can be tapered to produce any arbitrary shaped B1 field gradient. Here we show the characterization of this tapered stripline configuration and demonstrate three applications: magnetic resonance imaging on samples with nL-μL volumes, reaction monitoring of fast chemical reactions (10-2-101 s) and the compensation of B0 field gradients to obtain high-resolution spectra in inhomogeneous magnetic fields.

  4. NMR Spectroscopy and Molecular Dynamics Simulation of r(CCGCUGCGG)2 Reveal a Dynamic UU Internal Loop Found in Myotonic Dystrophy Type 1†

    PubMed Central

    Parkesh, Raman; Fountain, Matthew; Disney, Matthew D.

    2011-01-01

    The NMR structure of an RNA with a copy of the 5′CUG/3′GUC motif found in the triplet repeating disorder myotonic dystrophy type 1 (DM1) is disclosed. The lowest energy conformation of the UU pair is a single hydrogen bonded structure; however, the UU protons undergo exchange indicating structural dynamics. Molecular dynamics simulations show that the single hydrogen bonded structure is the most populated one but the UU pair interconverts between 0, 1, and 2 hydrogen bonded pairs. These studies have implications for the recognition of the DM1 RNA by small molecules and proteins. PMID:21204525

  5. Langerin-heparin interaction: two binding sites for small and large ligands as revealed by a combination of NMR spectroscopy and cross-linking mapping experiments.

    PubMed

    Muñoz-García, Juan C; Chabrol, Eric; Vivès, Romain R; Thomas, Aline; de Paz, José L; Rojo, Javier; Imberty, Anne; Fieschi, Franck; Nieto, Pedro M; Angulo, Jesús

    2015-04-01

    Langerin is a C-type lectin present on Langerhans cells that mediates capture of pathogens in a carbohydrate-dependent manner, leading to subsequent internalization and elimination in the cellular organelles called Birbeck granules. This mechanism mediated by langerin was shown to constitute a natural barrier for HIV-1 particle transmission. Besides interacting specifically with high mannose and fucosylated neutral carbohydrate structures, langerin has the ability to bind sulfated carbohydrate ligands as 6-sulfated galactosides in the Ca(2+)-dependent binding site. Very recently langerin was demonstrated to interact with sulfated glycosaminoglycans (GAGs), in a Ca(2+)-independent way, resulting in the proposal of a new binding site for GAGs. On the basis of those results, we have conducted a structural study of the interactions of small heparin (HEP)-like oligosaccharides with langerin in solution. Heparin bead cross-linking experiments, an approach specifically designed to identify HEP/heparan sulfate binding sites in proteins were first carried out and experimentally validated the previously proposed model for the interaction of langerin extracellular domain with 6 kDa HEP. High-resolution NMR studies of a set of eight synthetic HEP-like trisaccharides harboring different sulfation patterns demonstrated that all of them bound to langerin in a Ca(2+)-dependent way. The binding epitopes were determined by saturation transfer difference NMR and the bound conformations by transferred NOESY experiments. These experimental data were combined with docking and molecular dynamics and resulted in the proposal of a binding mode characterized by the coordination of calcium by the two equatorial hydroxyl groups, OH3 and OH4, at the non-reducing end. The binding also includes the carboxylate group at the adjacent iduronate residue. This epitope is shared by all eight ligands, explaining the absence of any impact on binding from differences in their substitution patterns

  6. Detailed Investigation of the Immunodominant Role of O-Antigen Stoichiometric O-Acetylation as Revealed by Chemical Synthesis, Immunochemistry, Solution Conformation and STD-NMR Spectroscopy for Shigella flexneri 3a.

    PubMed

    Boutet, Julien; Blasco, Pilar; Guerreiro, Catherine; Thouron, Françoise; Dartevelle, Sylvie; Nato, Farida; Cañada, F Javier; Ardá, Ana; Phalipon, Armelle; Jiménez-Barbero, Jesús; Mulard, Laurence A

    2016-07-25

    Shigella flexneri 3a causes bacillary dysentery. Its O-antigen has the {2)-[α-d-Glcp-(1→3)]-α-l-Rhap-(1→2)-α-l-Rhap-(1→3)-[Ac→2]-α-l-Rhap-(1→3)-[Ac→6]≈40 % -β-d-GlcpNAc-(1→} ([(E)ABAc CAc D]) repeating unit, and the non-O-acetylated equivalent defines S. flexneri X. Propyl hepta-, octa-, and decasaccharides sharing the (E')A'BAc CD(E)A sequence, and their non-O-acetylated analogues were synthesized from a fully protected BAc CD(E)A allyl glycoside. The stepwise introduction of orthogonally protected mono- and disaccharide imidate donors was followed by a two-step deprotection process. Monoclonal antibody binding to twenty-six S. flexneri types 3a and X di- to decasaccharides was studied by an inhibition enzyme-linked immunosorbent assay (ELISA) and STD-NMR spectroscopy. Epitope mapping revealed that the 2C -acetate dominated the recognition by monoclonal IgG and IgM antibodies and that the BAc CD segment was essential for binding. The glucosyl side chain contributed to a lesser extent, albeit increasingly with the chain length. Moreover, tr-NOESY analysis also showed interaction but did not reveal any meaningful conformational change upon antibody binding. PMID:27376496

  7. Hyper-mobility of water around actin filaments revealed using pulse-field gradient spin-echo {sup 1}H NMR and fluorescence spectroscopy

    SciTech Connect

    Wazawa, Tetsuichi; Sagawa, Takashi; Ogawa, Tsubasa; Morimoto, Nobuyuki; Kodama, Takao; Suzuki, Makoto

    2011-01-28

    Research highlights: {yields} Translationally hyper-mobile water has been detected around actin filaments. {yields} Translationally hyper-mobile water is formed upon polymerization of actin. {yields} Low water viscosity was found around F-actin using fluorescence anisotropy. {yields} Formation of hyper-mobile water may explain endothermic actin polymerization. -- Abstract: This paper reports that water molecules around F-actin, a polymerized form of actin, are more mobile than those around G-actin or in bulk water. A measurement using pulse-field gradient spin-echo {sup 1}H NMR showed that the self-diffusion coefficient of water in aqueous F-actin solution increased with actin concentration by {approx}5%, whereas that in G-actin solution was close to that of pure water. This indicates that an F-actin/water interaction is responsible for the high self-diffusion of water. The local viscosity around actin was also investigated by fluorescence measurements of Cy3, a fluorescent dye, conjugated to Cys 374 of actin. The steady-state fluorescence anisotropy of Cy3 attached to F-actin was 0.270, which was lower than that for G-actin, 0.334. Taking into account the fluorescence lifetimes of the Cy3 bound to actin, their rotational correlation times were estimated to be 3.8 and 9.1 ns for F- and G-actin, respectively. This indicates that Cy3 bound to F-actin rotates more freely than that bound to G-actin, and therefore the local water viscosity is lower around F-actin than around G-actin.

  8. Zwitterionic phosphorylated quinines as chiral solvating agents for NMR spectroscopy.

    PubMed

    Rudzińska-Szostak, Ewa; Górecki, Łukasz; Berlicki, Łukasz; Ślepokura, Katarzyna; Mucha, Artur

    2015-10-01

    Because of their unique 3D arrangement, naturally occurring Cinchona alkaloids and their synthetic derivatives have found wide-ranging applications in chiral recognition. Recently, we determined the enantioselective properties of C-9-phosphate mixed triesters of quinine as versatile chiral solvating agents in nuclear magnetic resonance (NMR) spectroscopy. In the current study, we introduce new zwitterionic members of this class of molecules containing a negatively charged phosphate moiety (i.e., ethyl, n-butyl and phenyl hydrogen quininyl phosphate). An efficient approach for synthesizing these compounds is elaborated, and full characterization, including conformational and autoaggregation phenomena studies, was performed. Therefore, their ability to induce NMR anisochrony of selected enantiomeric substrates (i.e., primarily N-DNB-protected amino acids and their methyl esters) was analyzed compared to uncharged diphenyl quininyl phosphate and its positively charged quaternary ammonium hydrochloride salt. In addition, (1) H and (13) C NMR experiments revealed their enantiodiscrimination potential toward novel analytes, such as secondary amines and nonprotected amino acids. PMID:26415853

  9. Interionic Interactions in Imidazolium-Based Ionic Liquids: The Role of the C2-Position Revealed by Raman Scattering and Supported by IR and NMR Spectroscopy

    NASA Astrophysics Data System (ADS)

    Noack, Kristina; Paape, Natalia; Kiefer, Johannes; Wasserscheid, Peter; Leipertz, Alfred

    2010-08-01

    Intermolecular interactions determine the state of aggregation of a substance at given temperature. Based on that, changes in intermolecular interactions can lead to microscopic reordering which may be observed macroscopically in terms of altered physicochemical properties. Especially, when chemicals are employed in technical processes, it is important to control and regulate their properties to guarantee product quality. A special group of chemical substances increasingly gaining interest in the field of chemical and process engineering are room temperature ionic liquids (RTILs). In general, RTILs are organic salts with melting points "below the boiling point of water". The variety of possible combinations of cations and anions lead to a wide range of chemical and thermo-physical properties. In fact, it is possible to tune their properties by adjusting the ratio of Coulomb and van der Waals interactions. However, because it is hardly possible to investigate a reasonable fraction of the potential cation-anion combinations, a molecular-based understanding of their properties is crucial to make a rational design possible. In this regard vibrational spectroscopy has proven to be very beneficial for structural analysis and the investigation of interionic and intermolecular interactions. Therein, especially Raman spectroscopy shows a significant advantage of being insensitive to water interference and it is widely applied in the field of ionic liquids. Among others the 1-alkyl-3-methylimidazolium [RMIM] based ILs have been employed as model ILs in structural analysis, and most vibrational studies available in literature have been carried out investigating this kind of ILs. In contrast, spectroscopic data and calculations of C2-methylated 1,2-dialkyl-3-methylimidazolium based ILs, are available to a much lesser extend. The substitution in the C2 position in those ILs disrupts the main hydrogen-bonding interaction between the cation and the anion and is expected to lead

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

    ERIC Educational Resources Information Center

    Alonso, David E.; Warren, Steven E.

    2005-01-01

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

  11. Multiplet-separated heteronuclear two-dimensional NMR spectroscopy

    NASA Astrophysics Data System (ADS)

    Levitt, Malcolm H.; Sørensen, O. W.; Ernst, R. R.

    1983-02-01

    Techniques are described for the identification and separation of peaks of different multiplicity in heteronuclear two-dimensional NMR spectroscopy. The methods are applied to the two-dimensional 13C- 1H shift correlation spectrum of menthol.

  12. Report on neptunium speciation by NMR and optical spectroscopies

    SciTech Connect

    Tait, C.D.; Palmer, P.D.; Ekberg, S.A.; Clark, D.L.

    1995-11-01

    Hydrolysis and carbonate complexation reactions were examined for NpO{sub 2}{sup 2+} and NpO{sub 2}{sup +} ions by a variety of techniques including potentiometric titration, UV-Vis-NIR and NMR spectroscopy. The equilibrium constant for the reaction 3NpO{sub 2}(CO{sub 3}){sub 3}{sup 4{minus}} + 3H{sup +} {rightleftharpoons} (NpO{sub 2}){sub 3}(CO{sub 3}){sub 6}{sup 6{minus}} + 3HCO{sub 3}{sup {minus}} was determined to be logK = 19.7 ({plus_minus} 0.8) (I = 2.5 m). {sup 17}O NMR spectroscopy of NpO{sub 2}{sup n+} ions (n = 1,2) reveals a readily observable {sup 17}O resonance for n = 2, but not for n = 1. The first hydrolysis constant for NpO{sub 2}{sup +} was studied as a function of temperature, and the functional form for the temperature-dependent equilibrium constant for the reaction written as NpO{sub 2}{sup +} + H{sub 2}O {rightleftharpoons} NpO{sub 2}OH + H{sup +} was found to be logK = 2.28 {minus} 3780/T, where T is in {degree}K. Finally, the temperature dependence of neptunium(V) carbonate complexation constants was studied. For the first carbonate complexation constant, the appropriate functional form was found to be log{beta}{sub 01} = 1.47 + 786/T.

  13. An Integrated Laboratory Project in NMR Spectroscopy.

    ERIC Educational Resources Information Center

    Hudson, Reggie L.; Pendley, Bradford D.

    1988-01-01

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

  14. Fragment-Based Drug Discovery Using NMR Spectroscopy

    PubMed Central

    Harner, Mary J.; Frank, Andreas O.; Fesik, Stephen W.

    2013-01-01

    Nuclear magnetic resonance (NMR) spectroscopy has evolved into a powerful tool for fragment-based drug discovery over the last two decades. While NMR has been traditionally used to elucidate the three-dimensional structures and dynamics of biomacromolecules and their interactions, it can also be a very valuable tool for the reliable identification of small molecules that bind to proteins and for hit-to-lead optimization. Here, we describe the use of NMR spectroscopy as a method for fragment-based drug discovery and how to most effectively utilize this approach for discovering novel therapeutics based on our experience. PMID:23686385

  15. Facing and Overcoming Sensitivity Challenges in Biomolecular NMR Spectroscopy.

    PubMed

    Ardenkjaer-Larsen, Jan-Henrik; Boebinger, Gregory S; Comment, Arnaud; Duckett, Simon; Edison, Arthur S; Engelke, Frank; Griesinger, Christian; Griffin, Robert G; Hilty, Christian; Maeda, Hidaeki; Parigi, Giacomo; Prisner, Thomas; Ravera, Enrico; van Bentum, Jan; Vega, Shimon; Webb, Andrew; Luchinat, Claudio; Schwalbe, Harald; Frydman, Lucio

    2015-08-01

    In the Spring of 2013, NMR spectroscopists convened at the Weizmann Institute in Israel to brainstorm on approaches to improve the sensitivity of NMR experiments, particularly when applied in biomolecular settings. This multi-author interdisciplinary Review presents a state-of-the-art description of the primary approaches that were considered. Topics discussed included the future of ultrahigh-field NMR systems, emerging NMR detection technologies, new approaches to nuclear hyperpolarization, and progress in sample preparation. All of these are orthogonal efforts, whose gains could multiply and thereby enhance the sensitivity of solid- and liquid-state experiments. While substantial advances have been made in all these areas, numerous challenges remain in the quest of endowing NMR spectroscopy with the sensitivity that has characterized forms of spectroscopies based on electrical or optical measurements. These challenges, and the ways by which scientists and engineers are striving to solve them, are also addressed. PMID:26136394

  16. Studies of organic paint binders by NMR spectroscopy

    NASA Astrophysics Data System (ADS)

    Spyros, A.; Anglos, D.

    2006-06-01

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

  17. In vivo two-dimensional NMR correlation spectroscopy

    NASA Astrophysics Data System (ADS)

    Kraft, Robert A.

    1999-10-01

    The poor resolution of in-vivo one- dimensional nuclear magnetic resonance spectroscopy (NMR) has limited its clinical potential. Currently, only the large singlet methyl resonances arising from N-acetyl aspartate (NAA), choline, and creatine are quantitated in a clinical setting. Other metabolites such as myo- inositol, glutamine, glutamate, lactate, and γ- amino butyric acid (GABA) are of clinical interest but quantitation is difficult due to the overlapping resonances and limited spectral resolution. To improve the spectral resolution and distinguish between overlapping resonances, a series of two- dimensional chemical shift correlation spectroscopy experiments were developed for a 1.5 Tesla clinical imaging magnet. Two-dimensional methods are attractive for in vivo spectroscopy due to their ability to unravel overlapping resonances with the second dimension, simplifying the interpretation and quantitation of low field NMR spectra. Two-dimensional experiments acquired with mix-mode line shape negate the advantages of the second dimension. For this reason, a new experiment, REVOLT, was developed to achieve absorptive mode line shape in both dimensions. Absorptive mode experiments were compared to mixed mode experiments with respect to sensitivity, resolution, and water suppression. Detailed theoretical and experimental calculations of the optimum spin lock and radio frequency power deposition were performed. Two-dimensional spectra were acquired from human bone marrow and human brain tissue. The human brain tissue spectra clearly reveal correlations among the coupled spins of NAA, glutamine, glutamate, lactate, GABA, aspartate and myo-inositol obtained from a single experiment of 23 minutes from a volume of 59 mL. (Copies available exclusively from MIT Libraries, Rm. 14-0551, Cambridge, MA 02139-4307. Ph. 617-253-5668; Fax 617-253-1690.)

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

    ERIC Educational Resources Information Center

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

    2013-01-01

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

  19. A modularized pulse programmer for NMR spectroscopy

    NASA Astrophysics Data System (ADS)

    Mao, Wenping; Bao, Qingjia; Yang, Liang; Chen, Yiqun; Liu, Chaoyang; Qiu, Jianqing; Ye, Chaohui

    2011-02-01

    A modularized pulse programmer for a NMR spectrometer is described. It consists of a networked PCI-104 single-board computer and a field programmable gate array (FPGA). The PCI-104 is dedicated to translate the pulse sequence elements from the host computer into 48-bit binary words and download these words to the FPGA, while the FPGA functions as a sequencer to execute these binary words. High-resolution NMR spectra obtained on a home-built spectrometer with four pulse programmers working concurrently demonstrate the effectiveness of the pulse programmer. Advantages of the module include (1) once designed it can be duplicated and used to construct a scalable NMR/MRI system with multiple transmitter and receiver channels, (2) it is a totally programmable system in which all specific applications are determined by software, and (3) it provides enough reserve for possible new pulse sequences.

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

    PubMed Central

    Theillet, Francois-Xavier; Smet-Nocca, Caroline; Liokatis, Stamatios; Thongwichian, Rossukon; Kosten, Jonas; Yoon, Mi-Kyung; Kriwacki, Richard W.; Landrieu, Isabelle; Lippens, Guy

    2016-01-01

    Post-translationally modified proteins make up the majority of the proteome and establish, to a large part, the impressive level of functional diversity in higher, multi-cellular organisms. Most eukaryotic post-translational protein modifications (PTMs) denote reversible, covalent additions of small chemical entities such as phosphate-, acyl-, alkyl- and glycosyl-groups onto selected subsets of modifiable amino acids. In turn, these modifications induce highly specific changes in the chemical environments of individual protein residues, which are readily detected by high-resolution NMR spectroscopy. In the following, we provide a concise compendium of NMR characteristics of the main types of eukaryotic PTMs: serine, threonine, tyrosine and histidine phosphorylation, lysine acetylation, lysine and arginine methylation, and serine, threonine O-glycosylation. We further delineate the previously uncharacterized NMR properties of lysine propionylation, butyrylation, succinylation, malonylation and crotonylation, which, altogether, define an initial reference frame for comprehensive PTM studies by high-resolution NMR spectroscopy. PMID:23011410

  1. Membrane Protein Structure and Dynamics from NMR Spectroscopy

    NASA Astrophysics Data System (ADS)

    Hong, Mei; Zhang, Yuan; Hu, Fanghao

    2012-05-01

    We review the current state of membrane protein structure determination using solid-state nuclear magnetic resonance (NMR) spectroscopy. Multidimensional magic-angle-spinning correlation NMR combined with oriented-sample experiments has made it possible to measure a full panel of structural constraints of membrane proteins directly in lipid bilayers. These constraints include torsion angles, interatomic distances, oligomeric structure, protein dynamics, ligand structure and dynamics, and protein orientation and depth of insertion in the lipid bilayer. Using solid-state NMR, researchers have studied potassium channels, proton channels, Ca2+ pumps, G protein-coupled receptors, bacterial outer membrane proteins, and viral fusion proteins to elucidate their mechanisms of action. Many of these membrane proteins have also been investigated in detergent micelles using solution NMR. Comparison of the solid-state and solution NMR structures provides important insights into the effects of the solubilizing environment on membrane protein structure and dynamics.

  2. Combining solid-state NMR spectroscopy with first-principles calculations - a guide to NMR crystallography.

    PubMed

    Ashbrook, Sharon E; McKay, David

    2016-06-01

    Recent advances in the application of first-principles calculations of NMR parameters to periodic systems have resulted in widespread interest in their use to support experimental measurement. Such calculations often play an important role in the emerging field of "NMR crystallography", where NMR spectroscopy is combined with techniques such as diffraction, to aid structure determination. Here, we discuss the current state-of-the-art for combining experiment and calculation in NMR spectroscopy, considering the basic theory behind the computational approaches and their practical application. We consider the issues associated with geometry optimisation and how the effects of temperature may be included in the calculation. The automated prediction of structural candidates and the treatment of disordered and dynamic solids are discussed. Finally, we consider the areas where further development is needed in this field and its potential future impact. PMID:27117884

  3. Quantitative structure parameters from the NMR spectroscopy of quadrupolar nuclei

    DOE PAGESBeta

    Perras, Frédéric A.

    2016-01-01

    Nuclear magnetic resonance (NMR) spectroscopy is one of the most important characterization tools in chemistry, however, 3/4 of the NMR active nuclei are underutilized due to their quadrupolar nature. This short review centers on the development of methods that use solid-state NMR of quadrupolar nuclei for obtaining quantitative structural information. Namely, techniques using dipolar recoupling as well as the resolution afforded by double-rotation are presented for the measurement of spin–spin coupling between quadrupoles, enabling the measurement of internuclear distances and connectivities. Two-dimensional

  4. Quantitative structure parameters from the NMR spectroscopy of quadrupolar nuclei

    SciTech Connect

    Perras, Frederic A.

    2015-12-15

    Here, nuclear magnetic resonance (NMR) spectroscopy is one of the most important characterization tools in chemistry, however, 3/4 of the NMR active nuclei are underutilized due to their quadrupolar nature. This short review centers on the development of methods that use solid-state NMR of quadrupolar nuclei for obtaining quantitative structural information. Namely, techniques using dipolar recoupling as well as the resolution afforded by double-rotation are presented for the measurement of spin–spin coupling between quadrupoles, enabling the measurement of internuclear distances and connectivities.

  5. New Views of Functionally Dynamic Proteins by Solution NMR Spectroscopy.

    PubMed

    Kay, Lewis E

    2016-01-29

    In the past several decades solution NMR spectroscopy has emerged as a powerful technique for the study of the structure and dynamics of proteins, providing detailed insights into biomolecular function. Herein, I provide a summary of two important areas of application, focusing on NMR studies of (i) supramolecular systems with aggregate molecular masses in the hundreds of kilodaltons and of (ii) sparsely populated and transiently formed protein states that are thermally accessible from populated ground-state conformers. The critical role of molecular dynamics in function is emphasized, highlighting the utility of the NMR technique in providing such often elusive information. PMID:26707200

  6. Analysis of experimentally shocked minerals by NMR spectroscopy

    SciTech Connect

    Cygan, R.T.; Boslough, M.B.

    1994-10-01

    The shock-loading of natural materials by an impact or explosion can result in the formation of modified and altered phases. In order to characterize the resulting material and to evaluate the extent of shock modification, the authors have used nuclear magnetic resonance (NMR) spectroscopy to examine several experimentally shocked minerals. In three related NMR studies, they have (1) examined shocked clinoptilolite, (2) performed a preliminary analysis of shocked quartz, and (3) reproduced shocked quartz results with detailed spectral deconvolutions, and extended it with NMR analysis of shocked feldspar powders.

  7. Nanoscale NMR spectroscopy and imaging of multiple nuclear species

    NASA Astrophysics Data System (ADS)

    Devience, Stephen J.; Pham, Linh M.; Lovchinsky, Igor; Sushkov, Alexander O.; Bar-Gill, Nir; Belthangady, Chinmay; Casola, Francesco; Corbett, Madeleine; Zhang, Huiliang; Lukin, Mikhail; Park, Hongkun; Yacoby, Amir; Walsworth, Ronald L.

    2015-02-01

    Nuclear magnetic resonance (NMR) spectroscopy and magnetic resonance imaging (MRI) provide non-invasive information about multiple nuclear species in bulk matter, with wide-ranging applications from basic physics and chemistry to biomedical imaging. However, the spatial resolution of conventional NMR and MRI is limited to several micrometres even at large magnetic fields (>1 T), which is inadequate for many frontier scientific applications such as single-molecule NMR spectroscopy and in vivo MRI of individual biological cells. A promising approach for nanoscale NMR and MRI exploits optical measurements of nitrogen-vacancy (NV) colour centres in diamond, which provide a combination of magnetic field sensitivity and nanoscale spatial resolution unmatched by any existing technology, while operating under ambient conditions in a robust, solid-state system. Recently, single, shallow NV centres were used to demonstrate NMR of nanoscale ensembles of proton spins, consisting of a statistical polarization equivalent to ˜100-1,000 spins in uniform samples covering the surface of a bulk diamond chip. Here, we realize nanoscale NMR spectroscopy and MRI of multiple nuclear species (1H, 19F, 31P) in non-uniform (spatially structured) samples under ambient conditions and at moderate magnetic fields (˜20 mT) using two complementary sensor modalities.

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

    SciTech Connect

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

    1987-01-01

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

  9. CHARACTERIZATION OF METABOLITES IN SMALL FISH BIOFLUIDS AND TISSUES BY NMR SPECTROSCOPY

    EPA Science Inventory

    Nuclear magnetic resonance (NMR) spectroscopy has been utilized for assessing ecotoxicity in small fish models by means of metabolomics. Two fundamental challenges of NMR-based metabolomics are the detection limit and characterization of metabolites (or NMR resonance assignments...

  10. Protein folding on the ribosome studied using NMR spectroscopy

    PubMed Central

    Waudby, Christopher A.; Launay, Hélène; Cabrita, Lisa D.; Christodoulou, John

    2013-01-01

    NMR spectroscopy is a powerful tool for the investigation of protein folding and misfolding, providing a characterization of molecular structure, dynamics and exchange processes, across a very wide range of timescales and with near atomic resolution. In recent years NMR methods have also been developed to study protein folding as it might occur within the cell, in a de novo manner, by observing the folding of nascent polypeptides in the process of emerging from the ribosome during synthesis. Despite the 2.3 MDa molecular weight of the bacterial 70S ribosome, many nascent polypeptides, and some ribosomal proteins, have sufficient local flexibility that sharp resonances may be observed in solution-state NMR spectra. In providing information on dynamic regions of the structure, NMR spectroscopy is therefore highly complementary to alternative methods such as X-ray crystallography and cryo-electron microscopy, which have successfully characterized the rigid core of the ribosome particle. However, the low working concentrations and limited sample stability associated with ribosome–nascent chain complexes means that such studies still present significant technical challenges to the NMR spectroscopist. This review will discuss the progress that has been made in this area, surveying all NMR studies that have been published to date, and with a particular focus on strategies for improving experimental sensitivity. PMID:24083462

  11. Mechanisms of amyloid formation revealed by solution NMR

    PubMed Central

    Karamanos, Theodoros K.; Kalverda, Arnout P.; Thompson, Gary S.; Radford, Sheena E.

    2015-01-01

    Amyloid fibrils are proteinaceous elongated aggregates involved in more than fifty human diseases. Recent advances in electron microscopy and solid state NMR have allowed the characterization of fibril structures to different extents of refinement. However, structural details about the mechanism of fibril formation remain relatively poorly defined. This is mainly due to the complex, heterogeneous and transient nature of the species responsible for assembly; properties that make them difficult to detect and characterize in structural detail using biophysical techniques. The ability of solution NMR spectroscopy to investigate exchange between multiple protein states, to characterize transient and low-population species, and to study high molecular weight assemblies, render NMR an invaluable technique for studies of amyloid assembly. In this article we review state-of-the-art solution NMR methods for investigations of: (a) protein dynamics that lead to the formation of aggregation-prone species; (b) amyloidogenic intrinsically disordered proteins; and (c) protein–protein interactions on pathway to fibril formation. Together, these topics highlight the power and potential of NMR to provide atomic level information about the molecular mechanisms of one of the most fascinating problems in structural biology. PMID:26282197

  12. High-resolution NMR spectroscopy under the fume hood.

    PubMed

    Küster, Simon K; Danieli, Ernesto; Blümich, Bernhard; Casanova, Federico

    2011-08-01

    This work reports the possibility to acquire high-resolution (1)H NMR spectra with a fist-sized NMR magnet directly installed under the fume hood. The small NMR sensor based on permanent magnets was used to monitor the trimerization of propionaldehyde catalyzed by indium trichloride in real time by continuously circulating the reaction mixture through the magnet bore in a closed loop with the help of a peristaltic pump. Thanks to the chemical selectivity of NMR spectroscopy the progress of the reaction can be monitored on-line by determining the concentrations of both reactant and product from the area under their respective lines in the NMR spectra as a function of time. This in situ measurement demonstrates that NMR probes can be used in chemistry laboratories, e.g. for reaction optimization, or installed at specific points of interest along industrial process lines. Therefore, it will open the door for the implementation of feedback control based on spectroscopic NMR data. PMID:21698335

  13. MULTIVARIATE CURVE RESOLUTION OF NMR SPECTROSCOPY METABONOMIC DATA

    EPA Science Inventory

    Sandia National Laboratories is working with the EPA to evaluate and develop mathematical tools for analysis of the collected NMR spectroscopy data. Initially, we have focused on the use of Multivariate Curve Resolution (MCR) also known as molecular factor analysis (MFA), a tech...

  14. Recovering Invisible Signals by Two-Field NMR Spectroscopy.

    PubMed

    Cousin, Samuel F; Kadeřávek, Pavel; Haddou, Baptiste; Charlier, Cyril; Marquardsen, Thorsten; Tyburn, Jean-Max; Bovier, Pierre-Alain; Engelke, Frank; Maas, Werner; Bodenhausen, Geoffrey; Pelupessy, Philippe; Ferrage, Fabien

    2016-08-16

    Nuclear magnetic resonance (NMR) studies have benefited tremendously from the steady increase in the strength of magnetic fields. Spectacular improvements in both sensitivity and resolution have enabled the investigation of molecular systems of rising complexity. At very high fields, this progress may be jeopardized by line broadening, which is due to chemical exchange or relaxation by chemical shift anisotropy. In this work, we introduce a two-field NMR spectrometer designed for both excitation and observation of nuclear spins in two distinct magnetic fields in a single experiment. NMR spectra of several small molecules as well as a protein were obtained, with two dimensions acquired at vastly different magnetic fields. Resonances of exchanging groups that are broadened beyond recognition at high field can be sharpened to narrow peaks in the low-field dimension. Two-field NMR spectroscopy enables the measurement of chemical shifts at optimal fields and the study of molecular systems that suffer from internal dynamics, and opens new avenues for NMR spectroscopy at very high magnetic fields. PMID:27417269

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

    PubMed

    Giraudeau, Patrick; Frydman, Lucio

    2014-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Giraudeau, Patrick; Frydman, Lucio

    2014-06-01

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

  17. Surface Binding of TOTAPOL Assists Structural Investigations of Amyloid Fibrils by Dynamic Nuclear Polarization NMR Spectroscopy.

    PubMed

    Nagaraj, Madhu; Franks, Trent W; Saeidpour, Siavash; Schubeis, Tobias; Oschkinat, Hartmut; Ritter, Christiane; van Rossum, Barth-Jan

    2016-07-15

    Dynamic nuclear polarization (DNP) NMR can enhance sensitivity but often comes at the price of a substantial loss of resolution. Two major factors affect spectral quality: low-temperature heterogeneous line broadening and paramagnetic relaxation enhancement (PRE) effects. Investigations by NMR spectroscopy, isothermal titration calorimetry (ITC), and EPR revealed a new substantial affinity of TOTAPOL to amyloid surfaces, very similar to that shown by the fluorescent dye thioflavin-T (ThT). As a consequence, DNP spectra with remarkably good resolution and still reasonable enhancement could be obtained at very low TOTAPOL concentrations, typically 400 times lower than commonly employed. These spectra yielded several long-range constraints that were difficult to obtain without DNP. Our findings open up new strategies for structural studies with DNP NMR spectroscopy on amyloids that can bind the biradical with affinity similar to that shown towards ThT. PMID:27147408

  18. Silver-109 NMR spectroscopy of inorganic solids.

    PubMed

    Penner, Glenn H; Li, Wenli

    2004-09-01

    In this study the (109)Ag NMR spectra of the following solid inorganic silver-containing compounds were investigated: AgNO(3), AgNO(2), Ag(2)SO(4), Ag(2)SO(3), AgCO(3), Ag(3)PO(4), AgCl, AgBr, AgI, AgSO(3)CH(3), silver p-toluenesulfonate, NaAg(CN)(2), KAg(CN)(2), K(3)Ag(CN)(4), Me(4)NAgCl(2), silver diethylthiocarbamate, silver lactate, silver acetate, silver citrate, and bis[(N,N(1)-di-tert-butylformamidinato)silver(I)]. The magic angle spinning (MAS) spectra of all compounds were obtained. In some cases, when protons were available, the (1)H to (109)Ag cross-polarization (CP) technique was used to enhance the signal and shorten the experimental relaxation delay. It was possible to obtain slow MAS (or CP/MAS) or nonspinning spectra for 10 samples, allowing the determination of the principal components of the (109)Ag chemical shift (CS) tensors. The isotropic chemical shifts and the CS tensors are discussed in light of the available crystal structures. The need for an accepted standard for referencing (109)Ag chemical shifts and the use of AgSO(3)CH(3) as a CP setup sample are also discussed. PMID:15332810

  19. Coherence selection in double CP MAS NMR spectroscopy

    NASA Astrophysics Data System (ADS)

    Yang, Jen-Hsien; Chou, Fang-Chieh; Tzou, Der-Lii M.

    2008-11-01

    Applications of double cross-polarization (CP) magic-angle spinning (MAS) NMR spectroscopy, via 1H/ 15N and then 15N/ 13C coherence transfers, for 13C coherence selection are demonstrated on a 15N/ 13C-labeled N-acetyl-glucosamine (GlcNAc) compound. The 15N/ 13C coherence transfer is very sensitive to the settings of the experimental parameters. To resolve explicitly these parameter dependences, we have systematically monitored the 13C{ 15N/ 1H} signal as a function of the rf field strength and the MAS frequency. The data reveal that the zero-quantum coherence transfer, with which the 13C effective rf field is larger than that of the 15N by the spinning frequency, would give better signal sensitivity. We demonstrate in one- and two-dimensional double CP experiments that spectral editing can be achieved by tailoring the experimental parameters, such as the rf field strengths and/or the MAS frequency.

  20. Mobile sensor for high resolution NMR spectroscopy and imaging

    NASA Astrophysics Data System (ADS)

    Danieli, Ernesto; Mauler, Jörg; Perlo, Juan; Blümich, Bernhard; Casanova, Federico

    2009-05-01

    In this work we describe the construction of a mobile NMR tomograph with a highly homogeneous magnetic field. Fast MRI techniques as well as NMR spectroscopy measurements were carried out. The magnet is based on a Halbach array built from identical permanent magnet blocks generating a magnetic field of 0.22 T. To shim the field inhomogeneities inherent to magnet arrays constructed from these materials, a shim strategy based on the use of movable magnet blocks is employed. With this approach a reduction of the line-width from ˜20 kHz to less than 0.1 kHz was achieved, that is by more than two orders of magnitude, in a volume of 21 cm 3. Implementing a RARE sequence, 3D images of different objects placed in this volume were obtained in short experimental times. Moreover, by reducing the sample size to 1 cm 3, sub ppm resolution is obtained in 1H NMR spectra.

  1. RNA structure determination by solid-state NMR spectroscopy

    PubMed Central

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

    2015-01-01

    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. PMID:25960310

  2. 103Rh NMR spectroscopy and its application to rhodium chemistry.

    PubMed

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

    2004-09-01

    Rhodium is used for a number of large processes that rely on homogeneous rhodium-catalyzed reactions, for instance rhodium-catalyzed hydroformylation of alkenes, carbonylation of methanol to acetic acid and hydrodesulfurization of thiophene derivatives (in crude oil). Many laboratory applications in organometallic chemistry and catalysis involve organorhodium chemistry and a wealth of rhodium coordination compounds is known. For these and other areas, 103Rh NMR spectroscopy appears to be a very useful analytical tool. In this review, most of the literature concerning 103Rh NMR spectroscopy published from 1989 up to and including 2003 has been covered. After an introduction to several experimental methods for the detection of the insensitive 103Rh nucleus, a discussion of factors affecting the transition metal chemical shift is given. Computational aspects and calculations of chemical shifts are also briefly addressed. Next, the application of 103Rh NMR in coordination and organometallic chemistry is elaborated in more detail by highlighting recent developments in measurement and interpretation of 103Rh NMR data, in relation to rhodium-assisted reactions and homogeneous catalysis. The dependence of the 103Rh chemical shift on the ligands at rhodium in the first coordination sphere, on the complex geometry, oxidation state, temperature, solvent and concentration is treated. Several classes of compounds and special cases such as chiral rhodium compounds are reviewed. Finally, a section on scalar coupling to rhodium is provided. PMID:15307053

  3. Molecular structure by two-dimensional NMR spectroscopy

    NASA Astrophysics Data System (ADS)

    Freeman, R.

    Two examples are presented of the use of two-dimensional NMR spectroscopy to solve molecular structure problems. The first is called correlation spectroscopy (COSY) and it allows us to disentangle a complex network of spin-spin couplings. By dispersing the NMR information in two frequency dimensions, it facilitates the analysis of very complex spectra of organic and biochemical molecules, normally too crowded to be tractable. The second application exploits the special properties of multiple-quantum coherence to explore the molecular framework one CC linkage at a time. The natural product panamine is used as a test example; with some supplementary evidence, the structure of this six-ringed heterocyclic molecule is elucidated from the double-quantum filtered two-dimensional spectrum.

  4. Single-sided sensor for high-resolution NMR spectroscopy

    NASA Astrophysics Data System (ADS)

    Perlo, J.; Casanova, F.; Blümich, B.

    2006-06-01

    The unavoidable spatial inhomogeneity of the static magnetic field generated by open sensors has precluded their use for high-resolution NMR spectroscopy. In fact, this application was deemed impossible because these field variations are usually orders of magnitude larger than those created by the microscopic structure of the molecules to be detected. Recently, chemical shift resolved NMR spectra were observed for the first time outside a portable single-sided magnet by implementing a method that exploits inhomogeneities in the rf field designed to reproduce variations of the static magnetic field [J. Perlo, V. Demas, F. Casanova, C.A. Meriles, J. Reimer, A. Pines, B. Blümich, High-resolution spectroscopy with a portable single-sided sensor, Science 308 (2005) 1279]. In this communication, we describe in detail the magnet system built from permanent magnets as well as the rf coil geometry used to compensate the static field variations.

  5. Ultra-wideline solid-state NMR spectroscopy.

    PubMed

    Schurko, Robert W

    2013-09-17

    large spectral breadths. We have suggested the term ultra-wideline NMR (UWNMR) spectroscopy to describe this set of methodologies. This Account describes recent developments in pulse sequences and strategies for the efficient acquisition of UWNMR spectra. After an introduction to anisotropically broadened NMR patterns, we give a brief history of methods used to acquire UWNMR spectra. We then discuss new acquisition methodologies, including the acquisition of CPMG echo trains and the application of pulses capable of broadband excitation and refocusing. Finally, we present several applications of UWNMR methods that use these broadband pulses. PMID:23745683

  6. Simultaneous 19F-1H medium resolution NMR spectroscopy for online reaction monitoring

    NASA Astrophysics Data System (ADS)

    Zientek, Nicolai; Laurain, Clément; Meyer, Klas; Kraume, Matthias; Guthausen, Gisela; Maiwald, Michael

    2014-12-01

    Medium resolution nuclear magnetic resonance (MR-NMR) spectroscopy is currently a fast developing field, which has an enormous potential to become an important analytical tool for reaction monitoring, in hyphenated techniques, and for systematic investigations of complex mixtures. The recent developments of innovative MR-NMR spectrometers are therefore remarkable due to their possible applications in quality control, education, and process monitoring. MR-NMR spectroscopy can beneficially be applied for fast, non-invasive, and volume integrating analyses under rough environmental conditions. Within this study, a simple 1/16″ fluorinated ethylene propylene (FEP) tube with an ID of 0.04″ (1.02 mm) was used as a flow cell in combination with a 5 mm glass Dewar tube inserted into a benchtop MR-NMR spectrometer with a 1H Larmor frequency of 43.32 MHz and 40.68 MHz for 19F. For the first time, quasi-simultaneous proton and fluorine NMR spectra were recorded with a series of alternating 19F and 1H single scan spectra along the reaction time coordinate of a homogeneously catalysed esterification model reaction containing fluorinated compounds. The results were compared to quantitative NMR spectra from a hyphenated 500 MHz online NMR instrument for validation. Automation of handling, pre-processing, and analysis of NMR data becomes increasingly important for process monitoring applications of online NMR spectroscopy and for its technical and practical acceptance. Thus, NMR spectra were automatically baseline corrected and phased using the minimum entropy method. Data analysis schemes were designed such that they are based on simple direct integration or first principle line fitting, with the aim that the analysis directly revealed molar concentrations from the spectra. Finally, the performance of 1/16″ FEP tube set-up with an ID of 1.02 mm was characterised regarding the limit of detection (LOQ (1H) = 0.335 mol L-1 and LOQ (19F) = 0.130 mol L-1 for trifluoroethanol in

  7. Simultaneous (19)F-(1)H medium resolution NMR spectroscopy for online reaction monitoring.

    PubMed

    Zientek, Nicolai; Laurain, Clément; Meyer, Klas; Kraume, Matthias; Guthausen, Gisela; Maiwald, Michael

    2014-10-18

    Medium resolution nuclear magnetic resonance (MR-NMR) spectroscopy is currently a fast developing field, which has an enormous potential to become an important analytical tool for reaction monitoring, in hyphenated techniques, and for systematic investigations of complex mixtures. The recent developments of innovative MR-NMR spectrometers are therefore remarkable due to their possible applications in quality control, education, and process monitoring. MR-NMR spectroscopy can beneficially be applied for fast, non-invasive, and volume integrating analyses under rough environmental conditions. Within this study, a simple 1/16″ fluorinated ethylene propylene (FEP) tube with an ID of 0.04″ (1.02mm) was used as a flow cell in combination with a 5mm glass Dewar tube inserted into a benchtop MR-NMR spectrometer with a (1)H Larmor frequency of 43.32MHz and 40.68MHz for (19)F. For the first time, quasi-simultaneous proton and fluorine NMR spectra were recorded with a series of alternating (19)F and (1)H single scan spectra along the reaction time coordinate of a homogeneously catalysed esterification model reaction containing fluorinated compounds. The results were compared to quantitative NMR spectra from a hyphenated 500MHz online NMR instrument for validation. Automation of handling, pre-processing, and analysis of NMR data becomes increasingly important for process monitoring applications of online NMR spectroscopy and for its technical and practical acceptance. Thus, NMR spectra were automatically baseline corrected and phased using the minimum entropy method. Data analysis schemes were designed such that they are based on simple direct integration or first principle line fitting, with the aim that the analysis directly revealed molar concentrations from the spectra. Finally, the performance of 1/16″ FEP tube set-up with an ID of 1.02mm was characterised regarding the limit of detection (LOQ ((1)H)=0.335molL(-1) and LOQ ((19)F)=0.130molL(-1) for trifluoroethanol

  8. NMR spectroscopy to follow reaction progress in ionic liquids.

    PubMed

    Butler, Bradley J; Thomas, Donald S; Hook, James M; Harper, Jason B

    2016-06-01

    In order to understand reaction outcomes in ionic liquids, it is crucial to be able to follow the progress of these reactions. This review highlights the advantages of NMR spectroscopy over other analytical techniques in following reaction progress in ionic liquids, particularly addressing the practical aspects of the methodology and highlighting the range of processes that can be readily followed. Copyright © 2014 John Wiley & Sons, Ltd. PMID:25287592

  9. NMR clinical imaging and spectroscopy: Its impact on nuclear medicine

    SciTech Connect

    Not Available

    1990-02-02

    This is a collection of four papers describing aspects of past and future use of nuclear magnetic resonance as a clinical diagnostic tool. The four papers are entitled (1) What Does NMR Offer that Nuclear Medicine Does Not by Jerry W. Froelich, (2) Oncological Imaging: Now, Future and Impact Jerry W. Froelich, (3) Magnetic Resonance Spectroscopy/Spectroscopic Imaging and Nuclear Medicine: Past, Present and Future by H. Cecil Charles, and (4) MR Cardiology: Now, Future and Impact by Robert J. Herfkens.

  10. NMR clinical imaging and spectroscopy: Its impact on nuclear medicine

    SciTech Connect

    Not Available

    1990-02-02

    This is a collection of four papers describing aspects of past and future use of nuclear magnetic resonance as a clinical diagnostic tool. The four papers are entitled (1) What Does NMR Offer that Nuclear Medicine Does Not? by Jerry W. Froelich, (2) Oncological Imaging: Now, Future and Impact Jerry W. Froelich, (3) Magnetic Resonance Spectroscopy/Spectroscopic Imaging and Nuclear Medicine: Past, Present and Future by H. Cecil Charles, and (4) MR Cardiology: Now, Future and Impact by Robert J. Herfkens.

  11. Characterization of protein hydration by solution NMR spectroscopy

    NASA Astrophysics Data System (ADS)

    Wand, Joshua

    A comprehensive understanding of the interactions between protein molecules and hydration water remains elusive. Solution nuclear magnetic resonance (NMR) spectroscopy has been proposed as a means to characterize these interactions but is plagued with artifacts when employed in bulk aqueous solution. Encapsulation of proteins in reverse micelles prepared in short chain alkane solvents can overcome these technical limitations. Application of this approach has revealed that the interaction of water with the surface of protein molecules is quite heterogeneous with some regions of the protein having long-lived interactions while other regions show relatively transient hydration. Results from several proteins will be presented including ubiquitin, staphylococcal nuclease, interleukin 1beta, hen egg white lysozyme (HEWL) and T4 lysozyme. Ubiquitin and interleukin 1beta are signaling proteins and interact with other proteins through formation of dry protein-protein interfaces. Interestingly, the protein surfaces of the free proteins show relatively slowed (restricted) motion at the surface, which is indicative of low residual entropy. Other regions of the protein surface have relatively high mobility water. These results are consistent with the idea that proteins have evolved to maximize the hydrophobic effect in optimization of binding with protein partners. As predicted by simulation and theory, we find that hydration of internal hydrophobic cavities of interleukin 1beta and T4 lysozyme is highly disfavored. In contrast, the hydrophilic polar cavity of HEWL is occupied by water. Initial structural correlations suggest that hydration of alpha helical structure is characterized by relatively mobile water while those of beta strands and loops are more ordered and slowed. These and other results from this set of proteins reveals that the dynamical and structural character of hydration of proteins is heterogeneous and complex. Supported by the National Science Foundation.

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

    PubMed Central

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

    2011-01-01

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

  13. 2D NMR-spectroscopic screening reveals polyketides in ladybugs.

    PubMed

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

    2011-06-14

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

  14. Complex Mixture Analysis of Organic Compounds in Yogurt by NMR Spectroscopy

    PubMed Central

    Lu, Yi; Hu, Fangyu; Miyakawa, Takuya; Tanokura, Masaru

    2016-01-01

    NMR measurements do not require separation and chemical modification of samples and therefore rapidly and directly provide non-targeted information on chemical components in complex mixtures. In this study, one-dimensional (1H, 13C, and 31P) and two-dimensional (1H-13C and 1H-31P) NMR spectroscopy were conducted to analyze yogurt without any pretreatment. 1H, 13C, and 31P NMR signals were assigned to 10 types of compounds. The signals of α/β-lactose and α/β-galactose were separately observed in the 1H NMR spectra. In addition, the signals from the acyl chains of milk fats were also successfully identified but overlapped with many other signals. Quantitative difference spectra were obtained by subtracting the diffusion ordered spectroscopy (DOSY) spectra from the quantitative 1H NMR spectra. This method allowed us to eliminate interference on the overlaps; therefore, the correct intensities of signals overlapped with those from the acyl chains of milk fat could be determined directly without separation. Moreover, the 1H-31P HMBC spectra revealed for the first time that N-acetyl-d-glucosamine-1-phosphate is contained in yogurt. PMID:27322339

  15. Complex Mixture Analysis of Organic Compounds in Yogurt by NMR Spectroscopy.

    PubMed

    Lu, Yi; Hu, Fangyu; Miyakawa, Takuya; Tanokura, Masaru

    2016-01-01

    NMR measurements do not require separation and chemical modification of samples and therefore rapidly and directly provide non-targeted information on chemical components in complex mixtures. In this study, one-dimensional (¹H, (13)C, and (31)P) and two-dimensional (¹H-(13)C and ¹H-(31)P) NMR spectroscopy were conducted to analyze yogurt without any pretreatment. ¹H, (13)C, and (31)P NMR signals were assigned to 10 types of compounds. The signals of α/β-lactose and α/β-galactose were separately observed in the ¹H NMR spectra. In addition, the signals from the acyl chains of milk fats were also successfully identified but overlapped with many other signals. Quantitative difference spectra were obtained by subtracting the diffusion ordered spectroscopy (DOSY) spectra from the quantitative ¹H NMR spectra. This method allowed us to eliminate interference on the overlaps; therefore, the correct intensities of signals overlapped with those from the acyl chains of milk fat could be determined directly without separation. Moreover, the ¹H-(31)P HMBC spectra revealed for the first time that N-acetyl-d-glucosamine-1-phosphate is contained in yogurt. PMID:27322339

  16. Advancements in waste water characterization through NMR spectroscopy: review.

    PubMed

    Alves Filho, Elenilson G; Alexandre e Silva, Lorena M; Ferreira, Antonio G

    2015-09-01

    There are numerous organic pollutants that lead to several types of ecosystem damage and threaten human health. Wastewater treatment plants are responsible for the removal of natural and anthropogenic pollutants from the sewage, and because of this function, they play an important role in the protection of human health and the environment. Nuclear magnetic resonance (NMR) has proven to be a valuable analytical tool as a result of its versatility in characterizing both overall chemical composition as well as individual species in a wide range of mixtures. In addition, NMR can provide physical information (rigidity, dynamics, etc.) as well as permit in depth quantification. Hyphenation with other techniques such as liquid chromatography, solid phase extraction and mass spectrometry creates unprecedented capabilities for the identification of novel and unknown chemical species. Thus, NMR is widely used in the study of different components of wastewater, such as complex organic matter (fulvic and humic acids), sludge and wastewater. This review article summarizes the NMR spectroscopy methods applied in studies of organic pollutants from wastewater to provide an exhaustive review of the literature as well as a guide for readers interested in this topic. PMID:25280056

  17. NMR spectroscopy of proteins encapsulated in a positively charged surfactant.

    PubMed

    Lefebvre, Brian G; Liu, Weixia; Peterson, Ronald W; Valentine, Kathleen G; Wand, A Joshua

    2005-07-01

    Traditionally, large proteins, aggregation-prone proteins, and membrane proteins have been difficult to examine by modern multinuclear and multidimensional solution NMR spectroscopy. A major limitation presented by these protein systems is that their slow molecular reorientation compromises many aspects of the more powerful solution NMR methods. Several approaches have emerged to deal with the various spectroscopic difficulties arising from slow molecular reorientation. One of these takes the approach of actively seeking to increase the effective rate of molecular reorientation by encapsulating the protein of interest within the protective shell of a reverse micelle and dissolving the resulting particle in a low viscosity fluid. Since the encapsulation is largely driven by electrostatic interactions, the preparation of samples of acidic proteins suitable for NMR spectroscopy has been problematic owing to the paucity of suitable cationic surfactants. Here, it is shown that the cationic surfactant CTAB may be used to prepare samples of encapsulated anionic proteins dissolved in low viscosity solvents. In a more subtle application, it is further shown that this surfactant can be employed to encapsulate a highly basic protein, which is completely denatured upon encapsulation using an anionic surfactant. PMID:15949753

  18. Solid-State NMR Spectroscopy of Protein Complexes

    PubMed Central

    Sun, Shangjin; Han, Yun; Paramasivam, Sivakumar; Yan, Si; Siglin, Amanda E.; Williams, John C.; Byeon, In-Ja L.; Ahn, Jinwoo; Gronenborn, Angela M.; Polenova, Tatyana

    2016-01-01

    Protein-protein interactions are vital for many biological processes. These interactions often result in the formation of protein assemblies that are large in size, insoluble and difficult to crystallize, and therefore are challenging to study by structure biology techniques, such as single crystal X-ray diffraction and solution NMR spectroscopy. Solid-state NMR (SSNMR) spectroscopy is emerging as a promising technique for studies of such protein assemblies because it is not limited by molecular size, solubility or lack of long-range order. In the past several years, we have applied magic angle spinning SSNMR based methods to study several protein complexes. In this chapter, we discuss the general solid-state NMR methodologies employed for structural and dynamics analyses of protein complexes with specific examples from our work on thioredoxin reassemblies, HIV-1 capsid protein assemblies and microtubule-associated protein assemblies. We present protocols for sample preparation and characterization, pulse sequences, SSNMR spectra collection and data analysis. PMID:22167681

  19. Perspectives on DNP-enhanced NMR spectroscopy in solutions

    NASA Astrophysics Data System (ADS)

    van Bentum, Jan; van Meerten, Bas; Sharma, Manvendra; Kentgens, Arno

    2016-03-01

    More than 60 years after the seminal work of Albert Overhauser on dynamic nuclear polarization by dynamic cross relaxation of coupled electron-nuclear spin systems, the quest for sensitivity enhancement in NMR spectroscopy is as pressing as ever. In this contribution we will review the status and perspectives for dynamic nuclear polarization in the liquid state. An appealing approach seems to be the use of supercritical solvents that may allow an extension of the Overhauser mechanism towards common high magnetic fields. A complementary approach is the use of solid state DNP on frozen solutions, followed by a rapid dissolution or in-situ melting step and NMR detection with substantially enhanced polarization levels in the liquid state. We will review recent developments in the field and discuss perspectives for the near future.

  20. Perspectives on DNP-enhanced NMR spectroscopy in solutions.

    PubMed

    van Bentum, Jan; van Meerten, Bas; Sharma, Manvendra; Kentgens, Arno

    2016-03-01

    More than 60 years after the seminal work of Albert Overhauser on dynamic nuclear polarization by dynamic cross relaxation of coupled electron-nuclear spin systems, the quest for sensitivity enhancement in NMR spectroscopy is as pressing as ever. In this contribution we will review the status and perspectives for dynamic nuclear polarization in the liquid state. An appealing approach seems to be the use of supercritical solvents that may allow an extension of the Overhauser mechanism towards common high magnetic fields. A complementary approach is the use of solid state DNP on frozen solutions, followed by a rapid dissolution or in-situ melting step and NMR detection with substantially enhanced polarization levels in the liquid state. We will review recent developments in the field and discuss perspectives for the near future. PMID:26920831

  1. Recombinant Kinase Production and Fragment Screening by NMR Spectroscopy.

    PubMed

    Han, Byeonggu; Ahn, Hee-Chul

    2016-01-01

    During the past decade fragment-based drug discovery (FBDD) has rapidly evolved and several drugs or drug candidates developed by FBDD approach are clinically in use or in clinical trials. For example, vemurafenib, a V600E mutated BRAF inhibitor, was developed by utilizing FBDD approach and approved by FDA in 2011. In FBDD, screening of fragments is the starting step for identification of hits and lead generation. Fragment screening usually relies on biophysical techniques by which the protein-bound small molecules can be detected. NMR spectroscopy has been extensively used to study the molecular interaction between the protein and the ligand, and has many advantages in fragment screening over other biophysical techniques. This chapter describes the practical aspects of fragment screening by saturation transfer difference NMR. PMID:26501900

  2. Maximum entropy signal processing in practical NMR spectroscopy

    NASA Astrophysics Data System (ADS)

    Sibisi, Sibusiso; Skilling, John; Brereton, Richard G.; Laue, Ernest D.; Staunton, James

    1984-10-01

    NMR spectroscopy is intrinsically insensitive, a frequently serious limitation especially in biochemical applications where sample size is limited and compounds may be too insoluble or unstable for data to be accumulated over long periods. Fourier transform (FT) NMR was developed by Ernst1 to speed up the accumulation of useful data, dramatically improving the quality of spectra obtained in a given observing time by recording the free induction decay (FID) data directly in time, at the cost of requiring numerical processing. Ernst also proposed that more information could be obtained from the spectrum if the FID was multiplied by a suitable apodizing function before being Fourier transformed. For example (see ref. 2), an increase in sensitivity can result from the use of a matched filter1, whereas an increase in resolution can be achieved by the use of gaussian multiplication1,3, application of sine bells4-8 or convolution difference9. These methods are now used routinely in NMR data processing. The maximum entropy method (MEM)10 is theoretically capable of achieving simultaneous enhancement in both respects11, and this has been borne out in practice in other fields where it has been applied. However, this technique requires relatively heavy computation. We describe here the first practical application of MEM to NMR, and we analyse 13C and 1H NMR spectra of 2-vinyl pyridine. Compared with conventional spectra, MEM gives considerable suppression of noise, accompanied by significant resolution enhancement. Multiplets in the 1H spectra are resolved better leading to improved visual clarity.

  3. New generation NMR bioreactor coupled with high-resolution NMR spectroscopy leads to novel discoveries in Moorella thermoaceticum metabolic profiles

    SciTech Connect

    Xue, Junfeng; Isern, Nancy G.; Ewing, R James; Liyu, Andrey V.; Sears, Jesse A.; Knapp, Harlan; Iversen, Jens; Sisk, Daniel R.; Ahring, Birgitte K.; Majors, Paul D.

    2014-06-20

    An in-situ nuclear magnetic resonance (NMR) bioreactor was developed and employed to monitor microbial metabolism under batch-growth conditions in real time. We selected Moorella thermoacetica ATCC 49707 as a test case. M. thermoacetica (formerly Clostridium thermoaceticum) is a strictly anaerobic, thermophilic, acetogenic, gram-positive bacterium with potential for industrial production of chemicals. The metabolic profiles of M. thermoacetica were characterized during growth in batch mode on xylose (a component of lignocellulosic biomass) using the new generation NMR bioreactor in combination with high-resolution, high sensitivity NMR (HR-NMR) spectroscopy. In-situ NMR measurements were performed using water-suppressed H-1 NMR spectroscopy at an NMR frequency of 500 MHz, and aliquots of the bioreactor contents were taken for 600 MHz HR-NMR spectroscopy at specific intervals to confirm metabolite identifications and expand metabolite coverage. M. thermoacetica demonstrated the metabolic potential to produce formate, ethanol and methanol from xylose, in addition to its known capability of producing acetic acid. Real-time monitoring of bioreactor conditions showed a temporary pH decrease, with a concomitant increase in formic acid during exponential growth. Fermentation experiments performed outside of the magnet showed that the strong magnetic field employed for NMR detection did not significantly affect cell metabolism. Use of the in-situ NMR bioreactor facilitated monitoring of the fermentation process in real time, enabling identification of intermediate and end-point metabolites and their correlation with pH and biomass produced during culture growth. Real-time monitoring of culture metabolism using the NMR bioreactor in combination with the HR-NMR spectroscopy will allow optimization of the metabolism of microorganisms producing valuable bioproducts.

  4. TOCCATA: a customized carbon total correlation spectroscopy NMR metabolomics database.

    PubMed

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

    2012-11-01

    A customized metabolomics NMR database, TOCCATA, is introduced, which uses (13)C chemical shift information for the reliable identification of metabolites, their spin systems, and isomeric states. TOCCATA, whose information was derived from the BMRB and HMDB databases and the literature, currently contains 463 compounds and 801 spin systems, and it can be used through a publicly accessible web server. TOCCATA allows the identification of metabolites in the submillimolar concentration range from (13)C-(13)C total correlation spectroscopy experiments of complex mixtures, which is demonstrated for an Escherichia coli cell lysate, a carbohydrate mixture, and an amino acid mixture, all of which were uniformly (13)C-labeled. PMID:23016498

  5. Discrimination of Basal Cell Carcinoma from Normal Skin Tissue Using High-Resolution Magic Angle Spinning 1H NMR Spectroscopy

    PubMed Central

    Mun, Je-Ho; Lee, Heonho; Yoon, Dahye; Kim, Byung-Soo; Kim, Moon-Bum; Kim, Shukmann

    2016-01-01

    High-resolution magic angle spinning nuclear magnetic resonance (HR-MAS NMR) spectroscopy is a useful tool for investigating the metabolism of various cancers. Basal cell carcinoma (BCC) is the most common skin cancer. However, to our knowledge, data on metabolic profiling of BCC have not been reported in the literature. The objective of the present study was to investigate the metabolic profiling of cutaneous BCC using HR-MAS 1H NMR spectroscopy. HR-MAS 1H NMR spectroscopy was used to analyze the metabolite profile and metabolite intensity of histopathologically confirmed BCC tissues and normal skin tissue (NST) samples. The metabolic intensity normalized to the total spectral intensities in BCC and NST was compared, and multivariate analysis was performed with orthogonal partial least-squares discriminant analysis (OPLS-DA). P values < 0.05 were considered statistically significant. Univariate analysis revealed 9 metabolites that showed statistically significant difference between BCC and NST. In multivariate analysis, the OPLS-DA models built with the HR-MAS NMR metabolic profiles revealed a clear separation of BCC from NST. The receiver operating characteristic curve generated from the results revealed an excellent discrimination of BCC from NST with an area under the curve (AUC) value of 0.961. The present study demonstrated that the metabolite profile and metabolite intensity differ between BCC and NST, and that HR-MAS 1H NMR spectroscopy can be a valuable tool in the diagnosis of BCC. PMID:26934749

  6. New generation NMR bioreactor coupled with high-resolution NMR spectroscopy leads to novel discoveries in Moorella thermoacetica metabolic profiles.

    PubMed

    Xue, Junfeng; Isern, Nancy G; Ewing, R James; Liyu, Andrei V; Sears, Jesse A; Knapp, Harlan; Iversen, Jens; Sisk, Daniel R; Ahring, Birgitte K; Majors, Paul D

    2014-10-01

    An in situ nuclear magnetic resonance (NMR) bioreactor was developed and employed to monitor microbial metabolism under batch growth conditions in real time. We selected Moorella thermoacetica ATCC 49707 as a test case. M. thermoacetica (formerly Clostridium thermoaceticum) is a strictly anaerobic, thermophilic, acetogenic, gram-positive bacterium with potential for industrial production of chemicals. The metabolic profiles of M. thermoacetica were characterized during growth in batch mode on xylose (a component of lignocellulosic biomass) using the new generation NMR bioreactor in combination with high-resolution NMR (HR-NMR) spectroscopy. In situ NMR measurements were performed using water-suppressed H-1 NMR spectroscopy at 500 MHz, and aliquots of the bioreactor contents were taken for 600-MHz HR-NMR spectroscopy at specific intervals to confirm metabolite identifications and expand metabolite coverage. M. thermoacetica demonstrated the metabolic potential to produce formate, ethanol, and methanol from xylose, in addition to its known capability of producing acetic acid. Real-time monitoring of bioreactor conditions showed a temporary pH decrease, with a concomitant increase in formic acid during exponential growth. Fermentation experiments performed outside of the magnet showed that the strong magnetic field employed for NMR detection did not significantly affect cell metabolism. Use of the in situ NMR bioreactor facilitated monitoring of the fermentation process, enabling identification of intermediate and endpoint metabolites and their correlation with pH and biomass produced during culture growth. Real-time monitoring of culture metabolism using the NMR bioreactor in combination with HR-NMR spectroscopy will allow optimization of the metabolism of microorganisms producing valuable bioproducts. PMID:24946863

  7. 13C NMR spectroscopy applications to brain energy metabolism

    PubMed Central

    Rodrigues, Tiago B.; Valette, Julien; Bouzier-Sore, Anne-Karine

    2013-01-01

    13C nuclear magnetic resonance (NMR) spectroscopy is the method of choice for studying brain metabolism. Indeed, the most convincing data obtained to decipher metabolic exchanges between neurons and astrocytes have been obtained using this technique, thus illustrating its power. It may be difficult for non-specialists, however, to grasp thefull implication of data presented in articles written by spectroscopists. The aim of the review is, therefore, to provide a fundamental understanding of this topic to facilitate the non-specialists in their reading of this literature. In the first part of this review, we present the metabolic fate of 13C-labeled substrates in the brain in a detailed way, including an overview of some general neurochemical principles. We also address and compare the various spectroscopic strategies that can be used to study brain metabolism. Then, we provide an overview of the 13C NMR experiments performed to analyze both intracellular and intercellular metabolic fluxes. More particularly, the role of lactate as a potential energy substrate for neurons is discussed in the light of 13C NMR data. Finally, new perspectives and applications offered by 13C hyperpolarization are described. PMID:24367329

  8. NMR Spectroscopy of Human Eye Tissues: A New Insight into Ocular Biochemistry

    PubMed Central

    Kryczka, Tomasz; Wylęgała, Edward; Dobrowolski, Dariusz; Midelfart, Anna

    2014-01-01

    Background. The human eye is a complex organ whose anatomy and functions has been described very well to date. Unfortunately, the knowledge of the biochemistry and metabolic properties of eye tissues varies. Our objective was to reveal the biochemical differences between main tissue components of human eyes. Methods. Corneas, irises, ciliary bodies, lenses, and retinas were obtained from cadaver globes 0-1/2 hours postmortem of 6 male donors (age: 44–61 years). The metabolic profile of tissues was investigated with HR MAS 1H NMR spectroscopy. Results. A total of 29 metabolites were assigned in the NMR spectra of the eye tissues. Significant differences between tissues were revealed in contents of the most distant eye-tissues, while irises and ciliary bodies showed minimal biochemical differences. ATP, acetate, choline, glutamate, lactate, myoinositol, and taurine were identified as the primary biochemical compounds responsible for differentiation of the eye tissues. Conclusions. In this study we showed for the first time the results of the analysis of the main human eye tissues with NMR spectroscopy. The biochemical contents of the selected tissues seemed to correspond to their primary anatomical and functional attributes, the way of the delivery of the nutrients, and the location of the tissues in the eye. PMID:25525621

  9. Computational Analysis of Solvent Effects in NMR Spectroscopy.

    PubMed

    Dračínský, Martin; Bouř, Petr

    2010-01-12

    Solvent modeling became a standard part of first principles computations of molecular properties. However, a universal solvent approach is particularly difficult for the nuclear magnetic resonance (NMR) shielding and spin-spin coupling constants that in part result from collective delocalized properties of the solute and the environment. In this work, bulk and specific solvent effects are discussed on experimental and theoretical model systems comprising solvated alanine zwitterion and chloroform molecules. Density functional theory computations performed on larger clusters indicate that standard dielectric continuum solvent models may not be sufficiently accurate. In some cases, more reasonable NMR parameters were obtained by approximation of the solvent with partial atomic charges. Combined cluster/continuum models yielded the most reasonable values of the spectroscopic parameters, provided that they are dynamically averaged. The roles of solvent polarizability, solvent shell structure, and bulk permeability were investigated. NMR shielding values caused by the macroscopic solvent magnetizability exhibited the slowest convergence with respect to the cluster size. For practical computations, however, inclusion of the first solvation sphere provided satisfactory corrections of the vacuum values. The simulations of chloroform chemical shifts and CH J-coupling constants were found to be very sensitive to the molecular dynamics model used to generate the cluster geometries. The results show that computationally efficient solvent modeling is possible and can reveal fine details of molecular structure, solvation, and dynamics. PMID:26614339

  10. Mapping hypoxia-induced bioenergetic rearrangements and metabolic signaling by 18O-assisted 31P NMR and 1H NMR spectroscopy.

    PubMed

    Pucar, Darko; Dzeja, Petras P; Bast, Peter; Gumina, Richard J; Drahl, Carmen; Lim, Lynette; Juranic, Nenad; Macura, Slobodan; Terzic, Andre

    2004-01-01

    Brief hypoxia or ischemia perturbs energy metabolism inducing paradoxically a stress-tolerant state, yet metabolic signals that trigger cytoprotection remain poorly understood. To evaluate bioenergetic rearrangements, control and hypoxic hearts were analyzed with 18O-assisted 31P NMR and 1H NMR spectroscopy. The 18O-induced isotope shift in the 31P NMR spectrum of CrP, betaADP and betaATP was used to quantify phosphotransfer fluxes through creatine kinase and adenylate kinase. This analysis was supplemented with determination of energetically relevant metabolites in the phosphomonoester (PME) region of 31P NMR spectra, and in both aromatic and aliphatic regions of 1H NMR spectra. In control conditions, creatine kinase was the major phosphotransfer pathway processing high-energy phosphoryls between sites of ATP consumption and ATP production. In hypoxia, creatine kinase flux was dramatically reduced with a compensatory increase in adenylate kinase flux, which supported heart energetics by regenerating and transferring beta- and gamma-phosphoryls of ATP. Activation of adenylate kinase led to a build-up of AMP, IMP and adenosine, molecules involved in cardioprotective signaling. 31P and 1H NMR spectral analysis further revealed NADH and H+ scavenging by alpha-glycerophosphate dehydrogenase (alphaGPDH) and lactate dehydrogenase contributing to maintained glycolysis under hypoxia. Hypoxia-induced accumulation of alpha-glycerophosphate and nucleoside 5'-monophosphates, through alphaGPDH and adenylate kinase reactions, respectively, was mapped within the increased PME signal in the 31P NMR spectrum. Thus, 18O-assisted 31P NMR combined with 1H NMR provide a powerful approach in capturing rearrangements in cardiac bioenergetics, and associated metabolic signaling that underlie the cardiac adaptive response to stress. PMID:14977188

  11. The application of HPLC and microprobe NMR spectroscopy in the identification of metabolites in complex biological matrices.

    PubMed

    Miao, Zhaoxia; Jin, Mengxia; Liu, Xia; Guo, Wei; Jin, Xiangju; Liu, Hongyue; Wang, Yinghong

    2015-05-01

    Nuclear magnetic resonance (NMR)-based metabolomics can be used directly to identify a variety of metabolites in biological fluids and tissues. Metabolite analysis is an important part of life science and metabolomics research. However, the identification of some metabolites using NMR spectroscopy remains a big challenge owing to low abundance or signal overlap. It is important to develop a method to measure these compounds accurately. Two-dimensional NMR spectroscopy, metabolite prediction software packages, and spike-in experiments with authentic standards are often used to solve these problems, but they are costly and time-consuming. In this study, methods were developed to identify metabolites in complex biological mixtures using both high-performance liquid chromatography (HPLC) and off-line microprobe NMR spectroscopy. With use of these methods, 83 and 73 metabolites were identified in Sprague Dawley rat urine and feces, respectively. Among them, 40 and 45 metabolites, respectively, could not be identified with traditional NMR methods. Our research revealed that the combination of HPLC and NMR techniques could significantly improve the accuracy of trace and overlapped metabolite identification, while offering an effective and convenient approach to identify potential biomarkers in complex biological systems. PMID:25814271

  12. An Oil Spill in a Tube: An Accessible Approach for Teaching Environmental NMR Spectroscopy

    ERIC Educational Resources Information Center

    Simpson, Andre´ J.; Mitchell, Perry J.; Masoom, Hussain; Mobarhan, Yalda Liaghati; Adamo, Antonio; Dicks, Andrew P.

    2015-01-01

    NMR spectroscopy has great potential as an instrumental method for environmental chemistry research and monitoring but may be underused in teaching laboratories because of its complexity and the level of expertise required in operating the instrument and interpreting data. This laboratory experiment introduces environmental NMR spectroscopy to…

  13. Multiplicative or t1 Noise in NMR Spectroscopy

    SciTech Connect

    Granwehr, Josef

    2005-01-25

    The signal in an NMR experiment is highly sensitive to fluctuations of the environment of the sample. If, for example, the static magnetic field B{sub 0}, the amplitude and phase of radio frequency (rf) pulses, or the resonant frequency of the detection circuit are not perfectly stable and reproducible, the magnetic moment of the spins is altered and becomes a noisy quantity itself. This kind of noise not only depends on the presence of a signal, it is in fact proportional to it. Since all the spins at a particular location in a sample experience the same environment at any given time, this noise primarily affects the reproducibility of an experiment, which is mainly of importance in the indirect dimensions of a multidimensional experiment, when intense lines are suppressed with a phase cycle, or for difference spectroscopy techniques. Equivalently, experiments which are known to be problematic with regard to their reproducibility, like flow experiments or experiments with a mobile target, tend to be affected stronger by multiplicative noise. In this article it is demonstrated how multiplicative noise can be identified and characterized using very simple, repetitive experiments. An error estimation approach is developed to give an intuitive, yet quantitative understanding of its properties. The consequences for multidimensional NMR experiments are outlined, implications for data analysis are shown, and strategies for the optimization of experiments are summarized.

  14. Protein Motions and Folding Investigated by NMR Spectroscopy

    NASA Astrophysics Data System (ADS)

    Palmer, Arthur

    2002-03-01

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

  15. Saturation in Deuteron Hadamard NMR Spectroscopy of Solids

    NASA Astrophysics Data System (ADS)

    Greferath, M.; Blumich, B.; Griffith, W. M.; Hoatson, G. L.

    Hadamard NMR was investigated for wide-line solid-state deuteron spectroscopy by numerical simulations and experiments on hexamethylbenzene. Similar signal-to-noise ratios were obtained at large filter bandwidths (500 kHz) by both the quadrupolar echo and the Hadamard methods, although the excitation power differs by up to four orders in magnitude. Increasing the excitation power leads to systematic, noise-like features in Hadamard spectra. In contrast to phase modulation, simulations indicate that for amplitude modulation of the pseudorandom excitation, the pulse sequence burns a saturation hole into the lineshape at the carrier frequency. Violation of the cyclicity requirement by introduction of a recycle delay between successive Hadamard scans results in a high-frequency noise contribution. Finite pulse widths are shown not to cause significant spectral distortions.

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

    PubMed

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

    2016-06-01

    We report findings from the qualitative evaluation of nuclear magnetic resonance (NMR) reaction monitoring techniques of how each relates to the kinetic profile of a reaction process. The study highlights key reaction rate differences observed between the various NMR reaction monitoring methods investigated: online NMR, static NMR tubes, and periodic inversion of NMR tubes. The analysis of three reaction processes reveals that rates derived from NMR analysis are highly dependent on monitoring method. These findings indicate that users must be aware of the effect of their monitoring method upon the kinetic rate data derived from NMR analysis. Copyright © 2015 John Wiley & Sons, Ltd. PMID:26248898

  17. Probing the Pu4 + magnetic moment in PuF4 with 19F NMR spectroscopy

    NASA Astrophysics Data System (ADS)

    Capan, Cigdem; Dempsey, Richard J.; Sinkov, Sergey; McNamara, Bruce K.; Cho, Herman

    2016-06-01

    The magnetic fields produced by Pu4 + centers have been measured by 19F NMR spectroscopy to elucidate the Pu-F electronic interactions in polycrystalline PuF4. Spectra acquired at applied fields of 2.35 and 7.05 T reveal a linear scaling of the 19F line shape. A model is presented that treats the line broadening and shifts as due to dipolar fields produced by Pu valence electrons in localized noninteracting orbitals. Alternative explanations for the observed line shape involving covalent Pu-F bonding, superexchange interactions, and electronic configurations with enhanced magnetic moments are considered.

  18. pKa determination by ¹H NMR spectroscopy - an old methodology revisited.

    PubMed

    Bezençon, Jacqueline; Wittwer, Matthias B; Cutting, Brian; Smieško, Martin; Wagner, Bjoern; Kansy, Manfred; Ernst, Beat

    2014-05-01

    pKa values of acids and protonated bases have an essential impact on organic synthesis, medicinal chemistry, and material and food sciences. In drug discovery and development, they are of utmost importance for the prediction of pharmacokinetic and pharmacodynamic properties. To date, various methods for the determination of pKa values are available, including UV-spectroscopic, potentiometric, and capillary electrophoretic techniques. An additional option is provided by nuclear magnetic resonance (NMR) spectroscopy. The underlying principle is the alteration of chemical shifts of NMR-active nuclei (e.g., (13)C and (1)H) depending on the protonation state of adjacent acidic or basic sites. When these chemical shifts are plotted against the pH, the inflection point of the resulting sigmoidal curve defines the pKa value. Although pKa determinations by (1)H NMR spectroscopy are reported for numerous cases, the potential of this approach is not yet fully evaluated. We therefore revisited this method with a diverse set of test compounds covering a broad range of pKa values (pKa 0.9-13.8) and made a comparison with four commonly used approaches. The methodology revealed excellent correlations (R(2)=0.99 and 0.97) with electropotentiometric and UV spectroscopic methods. Moreover, the comparison with in silico results (Epik and Marvin) also showed high correlations (R(2)=0.92 and 0.94), further confirming the reliability and utility of this approach. PMID:24462329

  19. Quantitative high-resolution on-line NMR spectroscopy in reaction and process monitoring.

    PubMed

    Maiwald, Michael; Fischer, Holger H; Kim, Young-Kyu; Albert, Klaus; Hasse, Hans

    2004-02-01

    On-line nuclear magnetic resonance spectroscopy (on-line NMR) is a powerful technique for reaction and process monitoring. Different set-ups for direct coupling of reaction and separation equipment with on-line NMR spectroscopy are described. NMR spectroscopy can be used to obtain both qualitative and quantitative information from complex reacting multicomponent mixtures for equilibrium or reaction kinetic studies. Commercial NMR probes can be used at pressures up to 35 MPa and temperatures up to 400 K. Applications are presented for studies of equilibria and kinetics of complex formaldehyde-containing mixtures as well as homogeneously and heterogeneously catalyzed esterification kinetics. Direct coupling of a thin-film evaporator is described as an example for the benefits of on-line NMR spectroscopy in process monitoring. PMID:14729025

  20. Investigation of Oxidative Degradation in Polymers Using (17)O NMR Spectroscopy

    SciTech Connect

    Alam, Todd M.; Celina, Mathew; Assink, Roger A.; Clough, Roger L.; Gillen, Kenneth T.; Wheeler David R.

    1999-07-20

    The thermal oxidation of pentacontane (C{sub 50}H{sub 102}), and of the homopolymer polyisoprene, has been investigated using {sup 17}O NMR spectroscopy. By performing the oxidation using {sup 17}O labeled O{sub 2} gas, it is possible to easily identify degradation products, even at relatively low concentrations. It is demonstrated that details of the degradation mechanism can be obtained from analysis of the {sup 17}O NMR spectra as a function of total oxidation. Pentacontane reveals the widest variety of reaction products, and exhibits changes in the relative product distributions with increasing O{sub 2} consumption. At low levels of oxygen incorporation, peroxides are the major oxidation product, while at later stages of degradation these species are replaced by increasing concentrations of ketones, alcohols, carboxylic acids and esters. Analyzing the product distribution can help in identification of the different free-radical decomposition pathways of hydroperoxides, including recombination, proton abstraction and chain scission, as well as secondary reactions. The {sup 17}O NMR spectra of thermally oxidized polyisoprene reveal fewer degradation functionalities, but exhibit an increased complexity in the type of observed degradation species due to structural features such as unsaturation and methyl branching. Alcohols and ethers formed from hydrogen abstraction and free radical termination.

  1. Interaction of the replication terminator protein of Bacillus subtilis with DNA probed by NMR spectroscopy

    SciTech Connect

    Hastings, Adam F.; Otting, Gottfried; Folmer, Rutger H.A.; Duggin, Iain G.; Wake, R. Gerry; Wilce, Matthew C.J.; Wilce, Jacqueline A. . E-mail: Jackie.Wilce@med.monash.edu.au

    2005-09-23

    Termination of DNA replication in Bacillus subtilis involves the polar arrest of replication forks by a specific complex formed between the dimeric 29 kDa replication terminator protein (RTP) and DNA terminator sites. We have used NMR spectroscopy to probe the changes in {sup 1}H-{sup 15}N correlation spectra of a {sup 15}N-labelled RTP.C110S mutant upon the addition of a 21 base pair symmetrical DNA binding site. Assignment of the {sup 1}H-{sup 15}N correlations was achieved using a suite of triple resonance NMR experiments with {sup 15}N,{sup 13}C,70% {sup 2}H enriched protein recorded at 800 MHz and using TROSY pulse sequences. Perturbations to {sup 1}H-{sup 15}N spectra revealed that the N-termini, {alpha}3-helices and several loops are affected by the binding interaction. An analysis of this data in light of the crystallographically determined apo- and DNA-bound forms of RTP.C110S revealed that the NMR spectral perturbations correlate more closely to protein structural changes upon complex formation rather than to interactions at the protein-DNA interface.

  2. Detection of Taurine in Biological Tissues by 33S NMR Spectroscopy

    NASA Astrophysics Data System (ADS)

    Musio, Roberta; Sciacovelli, Oronzo

    2001-12-01

    The potential of 33S NMR spectroscopy for biochemical investigations on taurine (2-aminoethanesulfonic acid) is explored. It is demonstrated that 33S NMR spectroscopy allows the selective and unequivocal identification of taurine in biological samples. 33S NMR spectra of homogenated and intact tissues are reported for the first time, together with the spectrum of a living mollusc. Emphasis is placed on the importance of choosing appropriate signal processing methods to improve the quality of the 33S NMR spectra of biological tissues.

  3. Nuclear Magnetic Resonance (NMR) Spectroscopy For Metabolic Profiling of Medicinal Plants and Their Products.

    PubMed

    Kumar, Dinesh

    2016-09-01

    NMR spectroscopy has multidisciplinary applications, including excellent impact in metabolomics. The analytical capacity of NMR spectroscopy provides information for easy qualitative and quantitative assessment of both endogenous and exogenous metabolites present in biological samples. The complexity of a particular metabolite and its contribution in a biological system are critically important for understanding the functional state that governs the organism's phenotypes. This review covers historical aspects of developments in the NMR field, its applications in chemical profiling, metabolomics, and quality control of plants and their derived medicines, foods, and other products. The bottlenecks of NMR in metabolic profiling are also discussed, keeping in view the future scope and further technological interventions. PMID:26575437

  4. Applications of Diffusion Ordered Spectroscopy (DOSY-NMR)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Diffusion-ordered NMR (DOSY-NMR) is a powerful, but under-utilized, technique for the investigation of mixtures based on translational diffusion rates. DOSY spectra allow for determination by NMR of components that may differ in molecular weight, geometry or complexation. Typical applications coul...

  5. Drug solubilization mechanism of α-glucosyl stevia by NMR spectroscopy.

    PubMed

    Zhang, Junying; Higashi, Kenjirou; Ueda, Keisuke; Kadota, Kazunori; Tozuka, Yuichi; Limwikrant, Waree; Yamamoto, Keiji; Moribe, Kunikazu

    2014-04-25

    We investigated the drug solubilization mechanism of α-glucosyl stevia (Stevia-G) which was synthesized from stevia (rebaudioside-A) by transglycosylation. (1)H and (13)C NMR peaks of Stevia-G in water were assigned by two-dimensional (2D) NMR experiments including (1)H-(1)H correlation, (1)H-(13)C heteronuclear multiple bond correlation, and (1)H-(13)C heteronuclear multiple quantum coherence spectroscopies. The (1)H and (13)C peaks clearly showed the incorporation of two glucose units into rebaudioside-A to produce Stevia-G, supported by steviol glycoside and glucosyl residue assays. The concentration-dependent chemical shifts of Stevia-G protons correlated well with a mass-action law model, indicating the self-association of Stevia-G molecules in water. The critical micelle concentration (CMC) was 12.0 mg/mL at 37°C. The aggregation number was 2 below the CMC and 12 above the CMC. Dynamic light scattering and 2D (1)H-(1)H nuclear Overhauser effect spectroscopy (NOESY) NMR experiments demonstrated that Stevia-G self-associated into micelles of a few nanometers in size with a core-shell structure, containing a kaurane diterpenoid-based hydrophobic core and a glucose-based shell. 2D (1)H-(1)H NOESY NMR measurements also revealed that a poorly water-soluble drug, naringenin, was incorporated into the hydrophobic core of the Stevia-G micelle. The Stevia-G self-assembly behavior and micellar drug inclusion capacity can achieve significant enhancement in drug solubility. PMID:24508331

  6. A detailed mechanistic investigation into the reaction of 3-methylpentanoic acid with Meldrum's acid utilizing online NMR spectroscopy.

    PubMed

    Dunn, Anna L; Codina, Anna; Foley, David A; Marquez, Brian L; Zell, Mark T

    2016-06-01

    A thorough investigation into the mechanism of the reaction of 3-methylpentanoic acid and Meldrum's acid using online NMR spectroscopy is reported. This study is an expansion of a previous analysis of this chemical transformation in the synthesis of an active pharmaceutical ingredient imagabalin. The 3-methylpentanoic acid analogue reveals similar behavior under the reaction conditions. Online NMR spectroscopy and offline characterization experiments reveal new information about the mechanism, providing conclusive spectroscopic evidence for the previously hypothesized dimer anhydride intermediate species 3-methylpentanoic anhydride as a productive intermediate. The presence of an acyl chloride intermediate species, 3-methylpentanoyl chloride, is also revealed for the first time in this synthesis. Copyright © 2015 John Wiley & Sons, Ltd. PMID:26332370

  7. NMR spectroscopy of intermetallic compounds: an experimental and theoretical approach to local atomic arrangements in binary gallides.

    PubMed

    Haarmann, Frank; Koch, Katrin; Jeglič, Peter; Pecher, Oliver; Rosner, Helge; Grin, Yuri

    2011-06-27

    The results of the investigation of MGa(2) with M = Ca, Sr, Ba and of MGa(4) with M = Na, Ca, Sr, Ba by a combined application of NMR spectroscopy and quantum mechanical calculations are comprehensively evaluated. The electric-field gradient (EFG) was identified as the most reliable measure to study intermetallic compounds, since it is accessible with high precision by quantum mechanical calculations and, for nuclear spin I>1/2, by NMR spectroscopy. The EFG values obtained by NMR spectroscopy and quantum mechanical calculations agree very well for both series of investigated compounds. A deconvolution of the calculated EFGs into their contributions reveals its sensitivity to the local environment of the atoms. The EFGs of the investigated di- and tetragallides are dominated by the population of the p(x)-, p(y)-, and p(z)-like states of the Ga atoms. A general combined approach for the investigation of disordered intermetallic compounds by application of diffraction methods, NMR spectroscopy, and quantum mechanical calculations is suggested. This scheme can also be applied to other classes of crystalline disordered inorganic materials. PMID:21590820

  8. Structural Changes Associated with Transthyretin Misfolding and Amyloid Formation Revealed by Solution and Solid-State NMR.

    PubMed

    Lim, Kwang Hun; Dasari, Anvesh K R; Hung, Ivan; Gan, Zhehong; Kelly, Jeffery W; Wemmer, David E

    2016-04-01

    Elucidation of structural changes involved in protein misfolding and amyloid formation is crucial for unraveling the molecular basis of amyloid formation. Here we report structural analyses of the amyloidogenic intermediate and amyloid aggregates of transthyretin using solution and solid-state nuclear magnetic resonance (NMR) spectroscopy. Our solution NMR results show that one of the two main β-sheet structures (CBEF β-sheet) is maintained in the aggregation-competent intermediate, while the other DAGH β-sheet is more flexible on millisecond time scales. Magic-angle-spinning solid-state NMR revealed that AB loop regions interacting with strand A in the DAGH β-sheet undergo conformational changes, leading to the destabilized DAGH β-sheet. PMID:26998642

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

    NASA Astrophysics Data System (ADS)

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

    1997-11-01

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

  10. Rapid Etiological Classification of Meningitis by NMR Spectroscopy Based on Metabolite Profiles and Host Response

    PubMed Central

    Himmelreich, Uwe; Malik, Richard; Kühn, Till; Daniel, Heide-Marie; Somorjai, Ray L.; Dolenko, Brion; Sorrell, Tania C.

    2009-01-01

    Bacterial meningitis is an acute disease with high mortality that is reduced by early treatment. Identification of the causative microorganism by culture is sensitive but slow. Large volumes of cerebrospinal fluid (CSF) are required to maximise sensitivity and establish a provisional diagnosis. We have utilised nuclear magnetic resonance (NMR) spectroscopy to rapidly characterise the biochemical profile of CSF from normal rats and animals with pneumococcal or cryptococcal meningitis. Use of a miniaturised capillary NMR system overcame limitations caused by small CSF volumes and low metabolite concentrations. The analysis of the complex NMR spectroscopic data by a supervised statistical classification strategy included major, minor and unidentified metabolites. Reproducible spectral profiles were generated within less than three minutes, and revealed differences in the relative amounts of glucose, lactate, citrate, amino acid residues, acetate and polyols in the three groups. Contributions from microbial metabolism and inflammatory cells were evident. The computerised statistical classification strategy is based on both major metabolites and minor, partially unidentified metabolites. This data analysis proved highly specific for diagnosis (100% specificity in the final validation set), provided those with visible blood contamination were excluded from analysis; 6–8% of samples were classified as indeterminate. This proof of principle study suggests that a rapid etiologic diagnosis of meningitis is possible without prior culture. The method can be fully automated and avoids delays due to processing and selective identification of specific pathogens that are inherent in DNA-based techniques. PMID:19390697

  11. Novel monosaccharide fermentation products in Caldicellulosiruptor saccharolyticus identified using NMR spectroscopy

    SciTech Connect

    Isern, Nancy G.; Xue, Junfeng; Rao, Jaya V.; Cort, John R.; Ahring, Birgitte K.

    2013-04-03

    Profiles of metabolites produced by the thermophilic obligately anaerobic cellulose-degrading Gram-positive bacterium Caldicellulosiruptor saccharolyticus DSM 8903 strain following growth on different monosaccharides (D-glucose, D-mannose, L-arabinose, D-arabinose, D-xylose, L-fucose, and D-fucose) as carbon sources revealed several unexpected fermentation products, suggesting novel metabolic capacities and unexplored metabolic pathways in this organism. Both 1H and 13C nuclear magnetic resonance (NMR) spectroscopy were used to determine intracellular and extracellular metabolite profiles. Metabolite profiles were determined from 1-D 1H NMR spectra by curve fitting against spectral libraries provided in Chenomx software. To reduce uncertainties due to unassigned, overlapping, or poorly-resolved peaks, metabolite identifications were confirmed with 2-D homonuclear and heteronuclear NMR experiments. In addition to expected metabolites such as acetate, lactate, glycerol, and ethanol, several novel fermentation products were identified: ethylene glycol (from growth on D-arabinose, though not L-arabinose), acetoin and 2,3-butanediol (from D-glucose and L-arabinose), and hydroxyacetone (from D-mannose and L-arabinose). Production of ethylene glycol from D-arabinose was particularly notable, with around 10% of the substrate carbon converted into this uncommon fermentation product. The novel products have not previously been reported to be produced by C. saccharolyticus, nor would they be easily predicted from the current genome annotation, and show new potentials for using this strain for production of bioproducts.

  12. Development of a micro flow-through cell for high field NMR spectroscopy.

    SciTech Connect

    Alam, Todd Michael; McIntyre, Sarah K.

    2011-05-01

    A highly transportable micro flow-through detection cell for nuclear magnetic resonance (NMR) spectroscopy has been designed, fabricated and tested. This flow-through cell allows for the direct coupling between liquid chromatography (LC) and gel permeation chromatography (GPC) resulting in the possibility of hyphenated LC-NMR and GPC-NMR. The advantage of the present flow cell design is that it is independent and unconnected to the detection probe electronics, is compatible with existing commercial high resolution NMR probes, and as such can be easily implemented at any NMR facility. Two different volumes were fabricated corresponding to between {approx}3.8 and 10 {micro}L detection volume. Examples of the performance of the cell on different NMR instruments, and using different NMR detection probes were demonstrated.

  13. Measurement of Solution Viscosity via Diffusion-Ordered NMR Spectroscopy (DOSY)

    ERIC Educational Resources Information Center

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

    2011-01-01

    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…

  14. Functional group analysis in coal by sup 31 P NMR spectroscopy

    SciTech Connect

    Verkade, J.G.

    1989-05-01

    The purpose of this research is to determine the labile-hydrogen functional group composition of coal and coal-derived materials by the nmr spectroscopy of their derivatives made with reagents containing the nmr-active nuclei {sup 31}P, {sup 119}Sn, or {sup 205}Tl. 7 refs.

  15. Mobility and Diffusion-Ordered Two-Dimensional NMR Spectroscopy

    NASA Astrophysics Data System (ADS)

    Morris, Kevin Freeman

    Mobility and diffusion-ordered two-dimensional nuclear magnetic resonance spectroscopy experiments have been developed for the analysis of mixtures. In the mobility -ordered experiments, the full range of positive and negative electrophoretic mobilities is displayed in one dimension and chemical shifts are displayed in the other. A concentric cylindrical tube electrophoresis chamber was designed to reduce the effective pathlength for current and to provide unidirectional flow for ions of interest. Techniques based upon the reverse precession method were also implemented to recover the signs of the mobilities and improved resolution in the mobility dimension was obtained by replacing Fourier transformation of truncated data sets with a linear prediction analysis. In the diffusion-ordered two-dimensional NMR experiments, the conventional chemical shift spectrum is resolved in one dimension and spectra of diffusion rates or molecular radii are resolved in the other. Diffusion dependent pulsed field gradient NMR data sets were inverted by means of the computer programs SPLMOD or DISCRETE, when discrete diffusion coefficients were present, and CONTIN when continuous distributions were present. Since the inversion is ill -conditioned, it was necessary to introduce additional information to limit the range of the solutions. In addition to prior knowledge of the decay kernels and non-negativity of amplitudes and damping constants, a set of rejection criteria was constructed for the discrete analysis case that took into account physical limits on diffusion coefficients, experimentally accessible values, and variations in effective decay kernels resulting from instrumental non-linearities. Examples of analyses of simulated data and experimental data for mixtures are presented as well as two-dimensional spectra generated by CONTIN for polydisperse polymer samples. Also, resolution in the diffusion dimension was increased by performing experiments on hydrophobic molecules in

  16. Probing the interaction of U(VI) with phosphonate-functionalized mesoporous silica using solid-state NMR spectroscopy

    DOE PAGESBeta

    Uribe, Eva C.; Mason, Harris E.; Shusterman, Jennifer A.; Bruchet, Anthony; Nitsche, Heino

    2016-05-30

    The fundamental interaction of U(VI) with diethylphosphatoethyl triethoxysilane functionalized SBA-15 mesoporous silica is studied by macroscopic batch experiments and solid-state NMR spectroscopy. DPTS-functionalized silica has been shown to extract U(VI) from nitric acid solutions at or above pH 3. Extraction is dependent on pH and ionic strength. Single-pulse 31P NMR on U(VI) contacted samples revealed that U(VI)only interacts with a fraction of the ligands present on the surface. At pH 4 the U(VI) extraction capacity of the material is limited to 27–37% of the theoretical capacity, based on ligand loading. We combined single pulse 31P NMR on U(VI)-contacted samples withmore » batch studies to measure a ligand-to-metal ratio of approximately 2 : 1 at pH 3 and 4. Batch studies and cross-polarization NMR measurements reveal that U(VI) binds to deprotonated phosphonate and/or silanol sites. We use 31P–31P DQ-DRENAR NMR studies to compare the average dipolar coupling between phosphorus spins for both U(VI)-complexed and non-complexed ligand environments. Furthermore, these measurements reveal that U(VI) extraction is not limited by inadequate surface distribution of ligands, but rather by low stability of the surface phosphonate complex.« less

  17. Probing the interaction of U(vi) with phosphonate-functionalized mesoporous silica using solid-state NMR spectroscopy.

    PubMed

    Uribe, Eva C; Mason, Harris E; Shusterman, Jennifer A; Bruchet, Anthony; Nitsche, Heino

    2016-06-21

    The fundamental interaction of U(vi) with diethylphosphatoethyl triethoxysilane functionalized SBA-15 mesoporous silica is studied by macroscopic batch experiments and solid-state NMR spectroscopy. DPTS-functionalized silica has been shown to extract U(vi) from nitric acid solutions at or above pH 3. Extraction is dependent on pH and ionic strength. Single-pulse (31)P NMR on U(vi) contacted samples revealed that U(vi) only interacts with a fraction of the ligands present on the surface. At pH 4 the U(vi) extraction capacity of the material is limited to 27-37% of the theoretical capacity, based on ligand loading. We combined single pulse (31)P NMR on U(vi)-contacted samples with batch studies to measure a ligand-to-metal ratio of approximately 2 : 1 at pH 3 and 4. Batch studies and cross-polarization NMR measurements reveal that U(vi) binds to deprotonated phosphonate and/or silanol sites. We use (31)P-(31)P DQ-DRENAR NMR studies to compare the average dipolar coupling between phosphorus spins for both U(vi)-complexed and non-complexed ligand environments. These measurements reveal that U(vi) extraction is not limited by inadequate surface distribution of ligands, but rather by low stability of the surface phosphonate complex. PMID:27265020

  18. Broad identification of bacterial type in urinary tract infection using (1)h NMR spectroscopy.

    PubMed

    Gupta, Ashish; Dwivedi, Mayank; Mahdi, Abbas Ali; Khetrapal, Chunni Lal; Bhandari, Mahendra

    2012-03-01

    To address the shortcomings of urine culture for the rapid identification of urinary tract infection (UTI), we applied (1)H-nuclear magnetic resonance (NMR) spectroscopy as a surrogate method for fast screening of microorganisms. Study includes 682 urine samples from suspected UTI patients, 50 healthy volunteers, and commercially available standard strains of gram negative bacilli (GNB) (Escherichia coli, Pseudomonas aeruginosa, Klebsiella pneumonia, Enterobacter, Acinetobacter, Proteus mirabilis, Citrobacter frundii) and gram positive cocci (GPC) (Enterococcus faecalis, Streptococcus group B, Staphylococcus saprophyticus). Acetate, lactate, ethanol, succinate, creatinine, trimethylamine (TMA), citrate, trimethylamin-N-oxide, glycine, urea, and hippurate were measured by (1)H NMR spectroscopy. All urine specimens were evaluated with culture method. Multivariate discriminant function analysis (DFA) reveals that acetate, lactate, succinate, and formate were able to differentiate, with high accuracy (99.5%), healthy controls from UTI patients. This statistical analysis was also able to classify GNB to GPC infected urine samples with high accuracy (96%). This technique appears to be a promising, rapid, and noninvasive approach to probing GNB and GPC infected urine specimens with its distinguishing metabolic profile. The determination of infection will be very important for rapidly and efficiently measuring the efficacy of a tailored treatment, leading to prompt and appropriate care of UTI patients. PMID:22292465

  19. β-Helical architecture of cytoskeletal bactofilin filaments revealed by solid-state NMR

    PubMed Central

    Vasa, Suresh; Lin, Lin; Shi, Chaowei; Habenstein, Birgit; Riedel, Dietmar; Kühn, Juliane; Thanbichler, Martin; Lange, Adam

    2015-01-01

    Bactofilins are a widespread class of bacterial filament-forming proteins, which serve as cytoskeletal scaffolds in various cellular pathways. They are characterized by a conserved architecture, featuring a central conserved domain (DUF583) that is flanked by variable terminal regions. Here, we present a detailed investigation of bactofilin filaments from Caulobacter crescentus by high-resolution solid-state NMR spectroscopy. De novo sequential resonance assignments were obtained for residues Ala39 to Phe137, spanning the conserved DUF583 domain. Analysis of the secondary chemical shifts shows that this core region adopts predominantly β-sheet secondary structure. Mutational studies of conserved hydrophobic residues located in the identified β-strand segments suggest that bactofilin folding and polymerization is mediated by an extensive and redundant network of hydrophobic interactions, consistent with the high intrinsic stability of bactofilin polymers. Transmission electron microscopy revealed a propensity of bactofilin to form filament bundles as well as sheet-like, 2D crystalline assemblies, which may represent the supramolecular arrangement of bactofilin in the native context. Based on the diffraction pattern of these 2D crystalline assemblies, scanning transmission electron microscopy measurements of the mass per length of BacA filaments, and the distribution of β-strand segments identified by solid-state NMR, we propose that the DUF583 domain adopts a β-helical architecture, in which 18 β-strand segments are arranged in six consecutive windings of a β-helix. PMID:25550503

  20. NMR metabolomic profiling reveals new roles of SUMOylation in DNA damage response.

    PubMed

    Cano, Kristin E; Li, Yi-Jia; Chen, Yuan

    2010-10-01

    Post-translational modifications by the Small Ubiquitin-like Modifier (SUMO) family of proteins have been established as critical events in the cellular response to a wide range of DNA damaging reagents and radiation; however, the detailed mechanism of SUMOylation in DNA damage response is not well understood. In this study, we used a nuclear magnetic resonance (NMR) spectroscopy-based metabolomics approach to examine the effect of an inhibitor of SUMO-mediated protein-protein interactions on MCF7 breast cancer cell response to radiation. Metabolomics is sensitive to changes in cellular functions and thus provides complementary information to other biological studies. The peptide inhibitor (SUMO interaction motif mimic, SIM) and a control peptide were stably expressed in MCF-7 cell line. Metabolite profiles of the cell lines before and after radiation were analyzed using solution NMR methods. Various statistical methods were used to isolate significant changes. Differences in the amounts of glutamine, aspartate, malate, alanine, glutamate and NADH between the SIM-expressing and control cells suggest a role for SUMOylation in regulating mitochondrial function. This is also further verified following the metabolism of (13)C-labeled glutamine. The inability of the cells expressing the SIM peptide to increase production of the antioxidants carnosine and glutathione after radiation damage suggests an important role of SUMOylation in regulating the levels of antioxidants that protect cells from free radicals and reactive oxygen species generated by radiation. This study reveals previously unknown roles of SUMOylation in DNA damage response. PMID:20695451

  1. Functional groups identified by solid state 13C NMR spectroscopy

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Animal manure is generally high in organic matter intensity so it is well suitable for 13C nuclear magnetic resonance (NMR) analysis. Solid-state 13C NMR techniques used in characterizing organic matter and its components include, but are not limited to, cross-polarization /magic angle spinning (CP...

  2. Dissolution DNP-NMR spectroscopy using galvinoxyl as a polarizing agent

    NASA Astrophysics Data System (ADS)

    Lumata, Lloyd L.; Merritt, Matthew E.; Malloy, Craig R.; Sherry, A. Dean; van Tol, Johan; Song, Likai; Kovacs, Zoltan

    2013-02-01

    The goal of this work was to test feasibility of using galvinoxyl (2,6-di-tert-butyl-α-(3,5-di-tert-butyl-4-oxo-2,5-cyclohexadien-1-ylidene)-p-tolyloxy) as a polarizing agent for dissolution dynamic nuclear polarization (DNP) NMR spectroscopy. We have found that galvinoxyl is reasonably soluble in ethyl acetate, chloroform, or acetone and the solutions formed good glasses when mixed together or with other solvents such as dimethyl sulfoxide. W-band electron spin resonance (ESR) measurements revealed that galvinoxyl has an ESR linewidth D intermediate between that of carbon-centered free radical trityl OX063 and the nitroxide-based 4-oxo-TEMPO, thus the DNP with galvinoxyl for nuclei with low gyromagnetic ratio γ such as 13C and 15N is expected to proceed predominantly via the thermal mixing process. The optimum radical concentration that would afford the highest 13C nuclear polarization (approximately 6% for [1-13C]ethyl acetate) at 3.35 T and 1.4 K was found to be around 40 mM. After dissolution, large liquid-state NMR enhancements were achieved for a number of 13C and 15N compounds with long spin-lattice relaxation time T1. In addition, the hydrophobic galvinoxyl free radical can be easily filtered out from the dissolution liquid when water is used as the solvent. These results indicate that galvinoxyl can be considered as an easily available free radical polarizing agent for routine dissolution DNP-NMR spectroscopy.

  3. Metabolic Characterization of Advanced Liver Fibrosis in HCV Patients as Studied by Serum 1H-NMR Spectroscopy

    PubMed Central

    Embade, Nieves; Mariño, Zoe; Diercks, Tammo; Cano, Ainara; Lens, Sabela; Cabrera, Diana; Navasa, Miquel; Falcón-Pérez, Juan M.; Caballería, Joan; Castro, Azucena; Bosch, Jaume; Mato, José M.; Millet, Oscar

    2016-01-01

    Several etiologies result in chronic liver diseases including chronic hepatitis C virus infection (HCV). Despite its high incidence and the severe economic and medical consequences, liver disease is still commonly overlooked due to the lack of efficient non-invasive diagnostic methods. While several techniques have been tested for the detection of fibrosis, the available biomarkers still present severe limitations that preclude their use in clinical diagnostics. Liver diseases have also been the subject of metabolomic analysis. Here, we demonstrate the suitability of 1H NMR spectroscopy for characterizing the metabolism of liver fibrosis induced by HCV. Serum samples from HCV patients without fibrosis or with liver cirrhosis were analyzed by NMR spectroscopy and the results were submitted to multivariate and univariate statistical analysis. PLS-DA test was able to discriminate between advanced fibrotic and non-fibrotic patients and several metabolites were found to be up or downregulated in patients with cirrhosis. The suitability of the most significantly regulated metabolites was validated by ROC analysis. Our study reveals that choline, acetoacetate and low-density lipoproteins are the most informative biomarkers for predicting cirrhosis in HCV patients. Our results demonstrate that statistical analysis of 1H-NMR spectra is able to distinguish between fibrotic and non-fibrotic patients suffering from HCV, representing a novel diagnostic application for NMR spectroscopy. PMID:27158896

  4. [Non-invasive analysis of proteins in living cells using NMR spectroscopy].

    PubMed

    Tochio, Hidehito; Murayama, Shuhei; Inomata, Kohsuke; Morimoto, Daichi; Ohno, Ayako; Shirakawa, Masahiro

    2015-01-01

    NMR spectroscopy enables structural analyses of proteins and has been widely used in the structural biology field in recent decades. NMR spectroscopy can be applied to proteins inside living cells, allowing characterization of their structures and dynamics in intracellular environments. The simplest "in-cell NMR" approach employs bacterial cells; in this approach, live Escherichia coli cells overexpressing a specific protein are subjected to NMR. The cells are grown in an NMR active isotope-enriched medium to ensure that the overexpressed proteins are labeled with the stable isotopes. Thus the obtained NMR spectra, which are derived from labeled proteins, contain atomic-level information about the structure and dynamics of the proteins. Recent progress enables us to work with higher eukaryotic cells such as HeLa and HEK293 cells, for which a number of techniques have been developed to achieve isotope labeling of the specific target protein. In this review, we describe successful use of electroporation for in-cell NMR. In addition, (19)F-NMR to characterize protein-ligand interactions in cells is presented. Because (19)F nuclei rarely exist in natural cells, when (19)F-labeled proteins are delivered into cells and (19)F-NMR signals are observed, one can safely ascertain that these signals originate from the delivered proteins and not other molecules. PMID:25759048

  5. Characterization of Al30 in commercial poly-aluminum chlorohydrate by solid-state (27)Al NMR spectroscopy.

    PubMed

    Phillips, Brian L; Vaughn, John S; Smart, Scott; Pan, Long

    2016-08-15

    Investigation of commercially produced hydrolysis salts of aluminum by solid-state (27)Al NMR spectroscopy and size-exclusion chromatography (SEC) reveals well-defined and distinct Al environments that can be related to physicochemical properties. (27)Al MAS and MQ-MAS NMR spectroscopic data show that the local structure of the solids is dominated by moieties that closely resemble the Al30 polyoxocation (Al30O8(OH)56(H2O)26(18+)), accounting for 72-85% of the total Al. These Al30-like clusters elute as several size fractions by SEC. Comparison of the SEC and NMR results indicates that the Al30-like clusters includes intact isolated clusters, moieties of larger polymers or aggregates, and possibly fragments resembling δ-Al13 Keggin clusters. The coagulation efficacy of the solids appears to correlate best with the abundance of intact Al30-like clusters and of smaller species available to promote condensation reactions. PMID:27232539

  6. Bonding in hard and elastic amorphous carbon nitride films investigated using 15N, 13C, and 1H NMR spectroscopy

    NASA Astrophysics Data System (ADS)

    Gammon, W. J.; Hoatson, G. L.; Holloway, B. C.; Vold, R. L.; Reilly, A. C.

    2003-11-01

    The nitrogen bonding in hard and elastic amorphous carbon nitride (a-CNx) films is examined with 15N, 13C, and 1H nuclear magnetic resonance (NMR) spectroscopy. Films were deposited by dc magnetron sputtering, in a pure nitrogen discharge on Si(001) substrates at 300 °C. Nanoindentation tests revealed an elastic recovery of 80%, a hardness of 5 GPa, and an elastic modulus of 47 GPa. The NMR results show that nitrogen bonding in this material is consistent with sp2 hybridized nitrogen incorporated in an aromatic carbon environment. The data also indicate that the a-CNx prepared for this study has very low hydrogen content and is hydrophilic. Specifically, analysis of 15N and 13C cross polarization magic angle spinning and 1H NMR experiments suggests that water preferentially protonates nitrogen sites.

  7. Perspectives of solution NMR spectroscopy for structural and functional studies of integral membrane proteins

    NASA Astrophysics Data System (ADS)

    Reckel, Sina; Hiller, Sebastian

    2013-04-01

    This article discusses future perspectives of solution NMR spectroscopy to study structures and functions of integral membrane proteins at atomic resolution, based on a review of recent progress in this area. Several selected examples of structure determinations, as well as functional studies of integral membrane proteins are highlighted. We expect NMR spectroscopy to make future key scientific contributions to understanding membrane protein function, in particular for large membrane protein systems with known three-dimensional structure. Such situations can benefit from the fact that functional NMR studies have substantially less limitations by molecular size than a full de novo structure determination. Therefore, the general potential for NMR spectroscopy to solve biologic key questions associated with integral membrane proteins is very promising.

  8. NMR Stark Spectroscopy: New Methods to Calibrate NMR Sensitivity to Electric Fields

    NASA Astrophysics Data System (ADS)

    Tarasek, Matthew R.

    The influence of electrostatics on NMR parameters is well accepted. Thus, NMR is a promising route to probe electrical features within molecules and materials. However, applications of NMR Stark effects (E-field induced changes in spin energy levels) have been elusive. I have developed new approaches to resolve NMR Stark effects from an applied E field. This calibrates nuclear probes whose spectral response might later be used to evaluate internal E fields that are critical to function, such as those due to local charge distributions or sample structure. I will present two novel experimental approaches for direct calibration of NMR quadrupolar Stark effects (QSEs). In the first, steady-state (few-second) excitation by an E field at twice the NMR frequency (2ω 0) is used to saturate spin magnetization. The extent of saturation vs. E-field amplitude calibrates the QSE response rate, while measurements vs sample orientation determine tensorial character. The second method instead synchronizes short (few µs) pulses of the 2ω0 E field with a multiple-pulse NMR sequence. This, “POWER” (Perturbations Observed With Enhanced Resolution) approach enables more accurate measure of small QSEs (i.e. few Hz spectral changes). A 2nd key advantage is the ability to define tensorial response without reorienting the sample, but instead varying the phase of the 2ω0 field. I will describe these experiments and my home-built NMR “Stark probe”, employed on a conventional wide-bore solid-state NMR system. Results with GaAs demonstrate each method, while extensions to a wider array of molecular and material systems may now be possible using these methods.

  9. NMR Spectroscopy for Thin Films by Magnetic Resonance Force Microscopy

    PubMed Central

    Won, Soonho; Saun, Seung-Bo; Lee, Soonchil; Lee, SangGap; Kim, Kiwoong; Han, Yunseok

    2013-01-01

    Nuclear magnetic resonance (NMR) is a fundamental research tool that is widely used in many fields. Despite its powerful applications, unfortunately the low sensitivity of conventional NMR makes it difficult to study thin film or nano-sized samples. In this work, we report the first NMR spectrum obtained from general thin films by using magnetic resonance force microscopy (MRFM). To minimize the amount of imaging information inevitably mixed into the signal when a gradient field is used, we adopted a large magnet with a flat end with a diameter of 336 μm that generates a homogeneous field on the sample plane and a field gradient in a direction perpendicular to the plane. Cyclic adiabatic inversion was used in conjunction with periodic phase inversion of the frequency shift to maximize the SNR. In this way, we obtained the 19F NMR spectrum for a 34 nm-thick CaF2 thin film. PMID:24217000

  10. Applications of high resolution /sup 3/H NMR spectroscopy

    SciTech Connect

    Williams, P.G.

    1987-10-01

    The advantages of tritium as an NMR nucleus are pointed out. Examples of its use are given, including labelled toluene, hydrogenation of ..beta..-methylstyrene, and maltose and its binding proteins. 7 refs., 2 figs. (DLC)

  11. Rapid characterization of molecular diffusion by NMR spectroscopy.

    PubMed

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

    2014-11-24

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

  12. Functional genomics by NMR spectroscopy. Phenylacetate catabolism in Escherichia coli.

    PubMed

    Ismail, Wael; El-Said Mohamed, Magdy; Wanner, Barry L; Datsenko, Kirill A; Eisenreich, Wolfgang; Rohdich, Felix; Bacher, Adelbert; Fuchs, Georg

    2003-07-01

    Aerobic metabolism of phenylalanine in most bacteria proceeds via oxidation to phenylacetate. Surprisingly, the further metabolism of phenylacetate has not been elucidated, even in well studied bacteria such as Escherichia coli. The only committed step is the conversion of phenylacetate into phenylacetyl-CoA. The paa operon of E. coli encodes 14 polypeptides involved in the catabolism of phenylacetate. We have found that E. coli K12 mutants with a deletion of the paaF, paaG, paaH, paaJ or paaZ gene are unable to grow with phenylacetate as carbon source. Incubation of a paaG mutant with [U-13C8]phenylacetate yielded ring-1,2-dihydroxy-1,2-dihydrophenylacetyl lactone as shown by NMR spectroscopy. Incubation of the paaF and paaH mutants with phenylacetate yielded delta3-dehydroadipate and 3-hydroxyadipate, respectively. The origin of the carbon atoms of these C6 compounds from the aromatic ring was shown using [ring-13C6]phenylacetate. The paaG and paaZ mutants also converted phenylacetate into ortho-hydroxyphenylacetate, which was previously identified as a dead end product of phenylacetate catabolism. These data, in conjunction with protein sequence data, suggest a novel catabolic pathway via CoA thioesters. According to this, phenylacetyl-CoA is attacked by a ring-oxygenase/reductase (PaaABCDE proteins), generating a hydroxylated and reduced derivative of phenylacetyl-CoA, which is not re-oxidized to a dihydroxylated aromatic intermediate, as in other known aromatic pathways. Rather, it is proposed that this nonaromatic intermediate CoA ester is further metabolized in a complex reaction sequence comprising enoyl-CoA isomerization/hydration, nonoxygenolytic ring opening, and dehydrogenation catalyzed by the PaaG and PaaZ proteins. The subsequent beta-oxidation-type degradation of the resulting CoA dicarboxylate via beta-ketoadipyl-CoA to succinyl-CoA and acetyl-CoA appears to be catalyzed by the PaaJ, PaaF and PaaH proteins. PMID:12846838

  13. Determination of Dihydrobenzoacridinone Structures by NMR, IR, and UV Spectroscopy and Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Kozlov, N. G.; Zhiharko, Yu. D.; Skakovsky, E. D.; Baranovsky, A. V.; Ogorodnikova, M. M.; Basalaeva, L. I.

    2016-01-01

    Condensation of 2-naphthylamine, aromatic aldehydes, and dimedone was found to produce 9,10-dihydrobenzo[a] acridin-11-one derivatives according to PMR, 13C NMR, and IR spectroscopy and mass spectrometry. Correlation spectroscopy showed that the carbonyl in the synthesized dihydrobenzoacridinone derivatives was located on C11.

  14. GFT projection NMR spectroscopy for proteins in the solid state

    PubMed Central

    Franks, W. Trent; Atreya, Hanudatta S.; Szyperski, Thomas

    2011-01-01

    Recording of four-dimensional (4D) spectra for proteins in the solid state has opened new avenues to obtain virtually complete resonance assignments and three-dimensional (3D) structures of proteins. As in solution state NMR, the sampling of three indirect dimensions leads per se to long minimal measurement time. Furthermore, artifact suppression in solid state NMR relies primarily on radio-frequency pulse phase cycling. For an n-step phase cycle, the minimal measurement times of both 3D and 4D spectra are increased n times. To tackle the associated ‘sampling problem’ and to avoid sampling limited data acquisition, solid state G-Matrix Fourier Transform (SS GFT) projection NMR is introduced to rapidly acquire 3D and 4D spectral information. Specifically, (4,3)D (HA)CANCOCX and (3,2)D (HACA)NCOCX were implemented and recorded for the 6 kDa protein GB1 within about 10% of the time required for acquiring the conventional congeners with the same maximal evolution times and spectral widths in the indirect dimensions. Spectral analysis was complemented by comparative analysis of expected spectral congestion in conventional and GFT NMR experiments, demonstrating that high spectral resolution of the GFT NMR experiments enables one to efficiently obtain nearly complete resonance assignments even for large proteins. PMID:21052779

  15. The Stoichiometry of Synthetic Alunite as a Function of Hydrothermal Aging Investigated by Solid-State NMR Spectroscopy, Powder X-ray Diffraction and Infrared Spectroscopy

    SciTech Connect

    Grube, Elisabeth; Nielsen, Ulla Gro

    2015-05-01

    The stoichiometry of a series of synthetic alunite [nominally KAl3(SO4)2(OH)6] samples prepared by hydrothermal methods as a function of reaction time (1–31 days) has been investigated by powder X-ray diffraction, Fourier transform infrared spectroscopy as well as solid-state 1H and 27Al magic angle spinning (MAS) nuclear magnetic resonance (NMR) spectroscopy. The 1H MAS NMR spectra recorded at high magnetic field (21.1 T, 900 MHz) allowed for a clear separation of the different proton environments and for quantitative determination of the aluminum vacancy concentration as a function of time. The concentration of structural defects determined from, i.e., aluminum vacancies was reduced from 4 to 1 %, as the reaction time was extended from one to 31 days based on 1H MAS NMR. This was further supported by an increase of the unit cell parameter c, which is indicative of the relative concentration of potassium defects present, from 17.261(1) to 17.324(5) Å. Solid-state 27Al MAS NMR revealed a decrease in the defect concentration as a function of time and showed the presence of 7–10 % impurities in the samples.

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

    SciTech Connect

    Krishnan, V V

    2005-04-26

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

  17. Characterization of alkyl carbon in forest soils by CPMAS 13C NMR spectroscopy and dipolar dephasing

    USGS Publications Warehouse

    Kogel-Knabner, I.; Hatcher, P.G.

    1989-01-01

    Samples obtained from forest soils at different stages of decomposition were treated sequentially with chloroform/methanol (extraction of lipids), sulfuric acid (hydrolysis), and sodium chlorite (delignification) to enrich them in refractory alkyl carbon. As revealed by NMR spectroscopy, this treatment yielded residues with high contents of alkyl carbon. In the NMR spectra of residues obtained from litter samples, resonances for carbohydrates are also present, indicating that these carbohydrates are tightly bound to the alkyl carbon structures. During decomposition in the soils this resistant carbohydrate fraction is lost almost completely. In the litter samples the alkyl carbon shows a dipolar dephasing behavior indicative of two structural components, a rigid and a more mobile component. As depth and decomposition increase, only the rigid component is observed. This fact could be due to selective degradation of the mobile component or to changes in molecular mobility during decomposition, e.g., because of an increase in cross linking or contact with the mineral matter of the soil.

  18. (1)H NMR Spectroscopy of Fecal Extracts Enables Detection of Advanced Colorectal Neoplasia.

    PubMed

    Amiot, Aurelien; Dona, Anthony C; Wijeyesekera, Anisha; Tournigand, Christophe; Baumgaertner, Isabelle; Lebaleur, Yann; Sobhani, Iradj; Holmes, Elaine

    2015-09-01

    Colorectal cancer (CRC) is a growing cause of mortality in developing countries, warranting investigation into its etiopathogenesis and earlier diagnosis. Here, we investigated the fecal metabolic phenotype of patients with advanced colorectal neoplasia and controls using (1)H-nuclear magnetic resonance (NMR) spectroscopy and multivariate modeling. The fecal microbiota composition was assessed by quantitative real-time PCR as well as Wif-1 methylation levels in stools, serum, and urine and correlated to the metabolic profile of each patient. The predictivity of the model was 0.507 (Q(2)Y), and the explained variance was 0.755 (R(2)Y). Patients with advanced colorectal neoplasia demonstrated increased fecal concentrations of four short-chain fatty acids (valerate, acetate, propionate, and butyrate) and decreased signals relating to β-glucose, glutamine, and glutamate. The predictive accuracy of the multivariate (1)H NMR model was higher than that of the guaiac-fecal occult blood test and the Wif-1 methylation test for predicting advanced colorectal neoplasia. Correlation analysis between fecal metabolites and bacterial profiles revealed strong associations between Faecalibacterium prausnitzii and Clostridium leptum species with short-chain fatty acids concentration and inverse correlation between Faecalibacterium prausnitzii and glucose. These preliminary results suggest that fecal metabonomics may potentially have a future role in a noninvasive colorectal screening program and may contribute to our understanding of the role of these dysregulated molecules in the cross-talk between the host and its bacterial microbiota. PMID:26211820

  19. Quantitating Metabolites in Protein Precipitated Serum Using NMR Spectroscopy

    PubMed Central

    2015-01-01

    Quantitative NMR-based metabolite profiling is challenged by the deleterious effects of abundant proteins in the intact blood plasma/serum, which underscores the need for alternative approaches. Protein removal by ultrafiltration using low molecular weight cutoff filters thus represents an important step. However, protein precipitation, an alternative and simple approach for protein removal, lacks detailed quantitative assessment for use in NMR based metabolomics. In this study, we have comprehensively evaluated the performance of protein precipitation using methanol, acetonitrile, perchloric acid, and trichloroacetic acid and ultrafiltration approaches using 1D and 2D NMR, based on the identification and absolute quantitation of 44 human blood metabolites, including a few identified for the first time in the NMR spectra of human serum. We also investigated the use of a “smart isotope tag,” 15N-cholamine for further resolution enhancement, which resulted in the detection of a number of additional metabolites. 1H NMR of both protein precipitated and ultrafiltered serum detected all 44 metabolites with comparable reproducibility (average CV, 3.7% for precipitation; 3.6% for filtration). However, nearly half of the quantified metabolites in ultrafiltered serum exhibited 10–74% lower concentrations; specifically, tryptophan, benzoate, and 2-oxoisocaproate showed much lower concentrations compared to protein precipitated serum. These results indicate that protein precipitation using methanol offers a reliable approach for routine NMR-based metabolomics of human blood serum/plasma and should be considered as an alternative to ultrafiltration. Importantly, protein precipitation, which is commonly used by mass spectrometry (MS), promises avenues for direct comparison and correlation of metabolite data obtained from the two analytical platforms to exploit their combined strength in the metabolomics of blood. PMID:24796490

  20. Localized double-quantum-filtered 1H NMR spectroscopy

    NASA Astrophysics Data System (ADS)

    Thomas, M. A.; Hetherington, H. P.; Meyerhoff, D. J.; Twieg, D. B.

    The image-guided in vivo spectroscopic (ISIS) pulse sequence has been combined with a double-quantum-filter scheme in order to obtain localized and water-suppressed 1H NMR spectra of J-coupled metabolites. The coherence-transfer efficiency associated with the DQ filter for AX and A 3X spin systems is described. Phantom results of carnosine, alanine, and ethanol in aqueous solution are presented. For comparison, the 1H NMR spectrum of alanine in aqueous solution with the binomial (1331, 2662) spin-echo sequence is also shown.

  1. Forensic examination of electrical tapes using high resolution magic angle spinning ¹H NMR spectroscopy.

    PubMed

    Schoenberger, Torsten; Simmross, Ulrich; Poppe, Christian

    2016-01-01

    The application of high resolution magic angle spinning (HR-MAS) (1)H NMR spectroscopy is ideally suited for the differentiation of plastics. In addition to the actual material composition, the different types of polymer architectures and tacticity provide characteristic signals in the fingerprint of the (1)H NMR spectra. The method facilitates forensic comparison, as even small amounts of insoluble but swellable plastic particles are utilized. The performance of HR-MAS NMR can be verified against other methods that were recently addressed in various articles about forensic tape comparison. In this study samples of the 90 electrical tapes already referenced by the FBI laboratory were used. The discrimination power of HR-MAS is demonstrated by the fact that more tape groups can be distinguished by NMR spectroscopy than by using the combined evaluation of several commonly used analytical techniques. An additional advantage of this robust and quick method is the very simple sample preparation. PMID:26558760

  2. High-Resolution 3D Structure Determination of Kaliotoxin by Solid-State NMR Spectroscopy

    PubMed Central

    Korukottu, Jegannath; Schneider, Robert; Vijayan, Vinesh; Lange, Adam; Pongs, Olaf; Becker, Stefan; Baldus, Marc; Zweckstetter, Markus

    2008-01-01

    High-resolution solid-state NMR spectroscopy can provide structural information of proteins that cannot be studied by X-ray crystallography or solution NMR spectroscopy. Here we demonstrate that it is possible to determine a protein structure by solid-state NMR to a resolution comparable to that by solution NMR. Using an iterative assignment and structure calculation protocol, a large number of distance restraints was extracted from 1H/1H mixing experiments recorded on a single uniformly labeled sample under magic angle spinning conditions. The calculated structure has a coordinate precision of 0.6 Å and 1.3 Å for the backbone and side chain heavy atoms, respectively, and deviates from the structure observed in solution. The approach is expected to be applicable to larger systems enabling the determination of high-resolution structures of amyloid or membrane proteins. PMID:18523586

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

    NASA Technical Reports Server (NTRS)

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

    1993-01-01

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

  4. Macromolecular NMR spectroscopy for the non-spectroscopist: beyond macromolecular solution structure determination.

    PubMed

    Bieri, Michael; Kwan, Ann H; Mobli, Mehdi; King, Glenn F; Mackay, Joel P; Gooley, Paul R

    2011-03-01

    A strength of NMR spectroscopy is its ability to monitor, on an atomic level, molecular changes and interactions. In this review, which is intended for non-spectroscopist, we describe major uses of NMR in protein science beyond solution structure determination. After first touching on how NMR can be used to quickly determine whether a mutation induces structural perturbations in a protein, we describe the unparalleled ability of NMR to monitor binding interactions over a wide range of affinities, molecular masses and solution conditions. We discuss the use of NMR to measure the dynamics of proteins at the atomic level and over a wide range of timescales. Finally, we outline new and expanding areas such as macromolecular structure determination in multicomponent systems, as well as in the solid state and in vivo. PMID:21214861

  5. NMR spectroscopy and perfusion of mammalian cells using surface microprobes.

    PubMed

    Ehrmann, Klaus; Pataky, Kristopher; Stettler, Matthieu; Wurm, Florian Maria; Brugger, Jürgen; Besse, Pierre-André; Popovic, Radivoje

    2007-03-01

    NMR spectra of mammalian cells are taken using surface microprobes that are based on microfabricated planar coils. The surface microprobe resembles a miniaturized Petri dish commonly used in biological research. The diameter of the planar coils is 1 mm. Chinese Hamster Ovaries are immobilized in a uniform layer on the microprobe surface or patterned by an ink-jet printer in the centre of the microcoil, where the rf-field of the planar microcoil is most uniform. The acquired NMR spectra show the prevalent metabolites found in mammalian cells. The volumes of the detected samples range from 25 nL to 1 nL (or 50,000 to 1800 cells). With an extended set-up that provides fluid inlets and outlets to the microprobe, the cells can be perfused within the NMR-magnet while constantly taking NMR spectra. Perfusion of the cells opens the way to increased cell viability for long acquisitions or to analysis of the cells' response to environmental change. PMID:17330170

  6. Guanidinoacetate methyltransferase (GAMT) deficiency diagnosed by proton NMR spectroscopy of body fluids.

    PubMed

    Engelke, Udo F H; Tassini, Maria; Hayek, Joseph; de Vries, Maaike; Bilos, Appie; Vivi, Antonio; Valensin, Gianni; Buoni, Sabrina; Zannolli, Raffaella; Brussel, Wim; Kremer, Berry; Salomons, Gajja S; Veendrick-Meekes, Monique J B M; Kluijtmans, Leo A J; Morava, Eva; Wevers, Ron A

    2009-06-01

    In patients with guanidinoacetate methyltransferase (GAMT) deficiency several parameters may point towards the diagnosis of GAMT deficiency. These include the low levels of creatine and creatinine in urine, the high concentration of guanidinoacetic acid (GAA) in urine and the low levels of creatine and creatinine in the cerebrospinal fluid (CSF). In this study, body fluids from 10 GAMT deficient patients were analysed using (1)H NMR spectroscopy. The urine 1D (1)H NMR spectra of all the patients showed a doublet resonance at 3.98 ppm (pH 2.50) derived from GAA present in high concentration. For this compound, a good recovery and good correlation was found between an LC-MS/MS method and (1)H NMR spectroscopy. In CSF NMR spectra of these patients, the singlet resonances of creatine and creatinine (3.05 and 3.13 ppm, respectively) were absent (normally always present in (1)H NMR spectra of CSF). Due to overlap by other resonances, the doublet of GAA could not be observed. Our data demonstrate that (1)H NMR spectroscopy of urine and CSF can be used to diagnose patients with GAMT deficiency. PMID:19288536

  7. Molecular characterization of dissolved organic matter in glacial ice: coupling natural abundance 1H NMR and fluorescence spectroscopy.

    PubMed

    Pautler, Brent G; Woods, Gwen C; Dubnick, Ashley; Simpson, André J; Sharp, Martin J; Fitzsimons, Sean J; Simpson, Myrna J

    2012-04-01

    Glaciers and ice sheets are the second largest freshwater reservoir in the global hydrologic cycle, and the onset of global climate warming has necessitated an assessment of their contributions to sea-level rise and the potential release of nutrients to nearby aquatic environments. In particular, the release of dissolved organic matter (DOM) from glacier melt could stimulate microbial activity in both glacial ecosystems and adjacent watersheds, but this would largely depend on the composition of the material released. Using fluorescence and (1)H NMR spectroscopy, we characterize DOM at its natural abundance in unaltered samples from a number of glaciers that differ in geographic location, thermal regime, and sample depth. Parallel factor analysis (PARAFAC) modeling of DOM fluorophores identifies components in the ice that are predominantly proteinaceous in character, while (1)H NMR spectroscopy reveals a mixture of small molecules that likely originate from native microbes. Spectrofluorescence also reveals a terrestrial contribution that was below the detection limits of NMR; however, (1)H nuclei from levoglucosan was identified in Arctic glacier ice samples. This study suggests that the bulk of the DOM from these glaciers is a mixture of biologically labile molecules derived from microbes. PMID:22385100

  8. DSP-based on-line NMR spectroscopy using an anti-Hebbian learning algorithm

    SciTech Connect

    Razazian, K.; Dieckman, S.L.; Raptis, A.C.; Bobis, J.P. |

    1995-07-01

    This paper describes a nuclear magnetic resonance (NMR) system that uses an adaptive algorithm to carry out real-time NMR spectroscopy. The system employs a digital signal processor (DSP) chip to regulate the transmitted and received signal together with spectral analysis of the received signal to determine free induction decay (FID). To implement such a signal-processing routine for detection of the desired signal, an adaptive line enhancer filter that uses an anti-Hebbian learning algorithm is applied to the FID spectra. The results indicate that the adaptive filter can be a reliable technique for on-line spectroscopy study.

  9. Genetic algorithm optimized triply compensated pulses in NMR spectroscopy

    NASA Astrophysics Data System (ADS)

    Manu, V. S.; Veglia, Gianluigi

    2015-11-01

    Sensitivity and resolution in NMR experiments are affected by magnetic field inhomogeneities (of both external and RF), errors in pulse calibration, and offset effects due to finite length of RF pulses. To remedy these problems, built-in compensation mechanisms for these experimental imperfections are often necessary. Here, we propose a new family of phase-modulated constant-amplitude broadband pulses with high compensation for RF inhomogeneity and heteronuclear coupling evolution. These pulses were optimized using a genetic algorithm (GA), which consists in a global optimization method inspired by Nature's evolutionary processes. The newly designed π and π / 2 pulses belong to the 'type A' (or general rotors) symmetric composite pulses. These GA-optimized pulses are relatively short compared to other general rotors and can be used for excitation and inversion, as well as refocusing pulses in spin-echo experiments. The performance of the GA-optimized pulses was assessed in Magic Angle Spinning (MAS) solid-state NMR experiments using a crystalline U-13C, 15N NAVL peptide as well as U-13C, 15N microcrystalline ubiquitin. GA optimization of NMR pulse sequences opens a window for improving current experiments and designing new robust pulse sequences.

  10. Genetic algorithm optimized triply compensated pulses in NMR spectroscopy.

    PubMed

    Manu, V S; Veglia, Gianluigi

    2015-11-01

    Sensitivity and resolution in NMR experiments are affected by magnetic field inhomogeneities (of both external and RF), errors in pulse calibration, and offset effects due to finite length of RF pulses. To remedy these problems, built-in compensation mechanisms for these experimental imperfections are often necessary. Here, we propose a new family of phase-modulated constant-amplitude broadband pulses with high compensation for RF inhomogeneity and heteronuclear coupling evolution. These pulses were optimized using a genetic algorithm (GA), which consists in a global optimization method inspired by Nature's evolutionary processes. The newly designed π and π/2 pulses belong to the 'type A' (or general rotors) symmetric composite pulses. These GA-optimized pulses are relatively short compared to other general rotors and can be used for excitation and inversion, as well as refocusing pulses in spin-echo experiments. The performance of the GA-optimized pulses was assessed in Magic Angle Spinning (MAS) solid-state NMR experiments using a crystalline U-(13)C, (15)N NAVL peptide as well as U-(13)C, (15)N microcrystalline ubiquitin. GA optimization of NMR pulse sequences opens a window for improving current experiments and designing new robust pulse sequences. PMID:26473327

  11. Discovering [superscript 13]C NMR, [superscript 1]H NMR, and IR Spectroscopy in the General Chemistry Laboratory through a Sequence of Guided-Inquiry Exercises

    ERIC Educational Resources Information Center

    Iler, H. Darrell; Justice, David; Brauer, Shari; Landis, Amanda

    2012-01-01

    This sequence of three guided-inquiry labs is designed for a second-semester general chemistry course and challenges students to discover basic theoretical principles associated with [superscript 13]C NMR, [superscript 1]H NMR, and IR spectroscopy. Students learn to identify and explain basic concepts of magnetic resonance and vibrational…

  12. Probing oxidative degradation in polymers using {sup 17}O NMR spectroscopy

    SciTech Connect

    Alam, T.M.; Click, C.A.; Assink, R.A.

    1997-09-01

    Understanding the mechanism of oxidative degradation remains an important goal in being able to predict the aging process in polymer materials. Nuclear magnetic resonance (NMR) spectroscopy has previously been utilized to investigate polymer degradation, including both proton ({sup 1}H) and carbon ({sup 13}C) studies. These previous NMR studies, as well as other spectroscopic investigations, are complicated by the almost overwhelming signal arising from the native undegraded polymer. This makes the identification and quantification of degradation species at small concentrations difficult. In this note we discuss recent investigation into the use of oxygen ({sup 17}O) NMR spectroscopy to probe the oxidative degradation process in polymers at a molecular level. Due to the low natural abundance (0.037%) and a nuclear spin of I=5/2 possessing an appreciable quadrupolar moment, the use of {sup 17}O NMR in polymer investigations has been limited. By utilizing synthetically enriched oxygen gas during the accelerated aging process, both the difficulties of low natural abundance and background interference signals are eliminated. For enriched samples {sup 17}O NMR spectra now provide a unique probe since all of the observed NMR resonances are the direct result of oxidative degradation.

  13. Theory of mirrored time domain sampling for NMR spectroscopy

    NASA Astrophysics Data System (ADS)

    Ghosh, Arindam; Wu, Yibing; He, Yunfen; Szyperski, Thomas

    2011-12-01

    A generalized theory is presented for novel mirrored hypercomplex time domain sampling (MHS) of NMR spectra. It is the salient new feature of MHS that two interferograms are acquired with different directionality of time evolution, that is, one is sampled forward from time t = 0 to the maximal evolution time tmax, while the second is sampled backward from t = 0 to - tmax. The sampling can be accomplished in a (semi) constant time or non constant-time manner. Subsequently, the two interferograms are linearly combined to yield a complex time domain signal. The manifold of MHS schemes considered here is defined by arbitrary settings of sampling phases ('primary phase shifts') and amplitudes of the two interferograms. It is shown that, for any two given primary phase shifts, the addition theorems of trigonometric functions yield the unique linear combination required to form the complex signal. In the framework of clean absorption mode (CAM) acquisition of NMR spectra being devoid of residual dispersive signal components, 'secondary phase shifts' represent time domain phase errors which are to be eliminated. In contrast, such secondary phase shifts may be introduced by experimental design in order to encode additional NMR parameters, a new class of NMR experiments proposed here. For generalization, it is further considered that secondary phase shifts may depend on primary phase shifts and/or sampling directionality. In order to compare with MHS theory, a correspondingly generalized theory is derived for widely used hypercomplex ('States') sampling (HS). With generalized theory it is shown, first, that previously introduced 'canonical' schemes, characterized by primary phases being multiples of π/4, afford maximal intensity of the desired absorptive signals in the absence of secondary phase shifts, and second, how primary phases can be adjusted to maximize the signal intensity provided that the secondary phase shifts are known. Third, it is demonstrated that theory

  14. Theory of mirrored time domain sampling for NMR spectroscopy.

    PubMed

    Ghosh, Arindam; Wu, Yibing; He, Yunfen; Szyperski, Thomas

    2011-12-01

    A generalized theory is presented for novel mirrored hypercomplex time domain sampling (MHS) of NMR spectra. It is the salient new feature of MHS that two interferograms are acquired with different directionality of time evolution, that is, one is sampled forward from time t=0 to the maximal evolution time tmax, while the second is sampled backward from t=0 to -tmax. The sampling can be accomplished in a (semi) constant time or non constant-time manner. Subsequently, the two interferograms are linearly combined to yield a complex time domain signal. The manifold of MHS schemes considered here is defined by arbitrary settings of sampling phases ('primary phase shifts') and amplitudes of the two interferograms. It is shown that, for any two given primary phase shifts, the addition theorems of trigonometric functions yield the unique linear combination required to form the complex signal. In the framework of clean absorption mode (CAM) acquisition of NMR spectra being devoid of residual dispersive signal components, 'secondary phase shifts' represent time domain phase errors which are to be eliminated. In contrast, such secondary phase shifts may be introduced by experimental design in order to encode additional NMR parameters, a new class of NMR experiments proposed here. For generalization, it is further considered that secondary phase shifts may depend on primary phase shifts and/or sampling directionality. In order to compare with MHS theory, a correspondingly generalized theory is derived for widely used hypercomplex ('States') sampling (HS). With generalized theory it is shown, first, that previously introduced 'canonical' schemes, characterized by primary phases being multiples of π/4, afford maximal intensity of the desired absorptive signals in the absence of secondary phase shifts, and second, how primary phases can be adjusted to maximize the signal intensity provided that the secondary phase shifts are known. Third, it is demonstrated that theory enables

  15. Citron and lemon under the lens of HR-MAS NMR spectroscopy.

    PubMed

    Mucci, Adele; Parenti, Francesca; Righi, Valeria; Schenetti, Luisa

    2013-12-01

    High Resolution Magic Angle Spinning (HR-MAS) is an NMR technique that can be applied to semi-solid samples. Flavedo, albedo, pulp, seeds, and oil gland content of lemon and citron were studied through HR-MAS NMR spectroscopy, which was used directly on intact tissue specimens without any physicochemical manipulation. HR-MAS NMR proved to be a very suitable technique for detecting terpenes, sugars, organic acids, aminoacids and osmolites. It is valuable in observing changes in sugars, principal organic acids (mainly citric and malic) and ethanol contents of pulp specimens and this strongly point to its use to follow fruit ripening, or commercial assessment of fruit maturity. HR-MAS NMR was also used to derive the molar percentage of fatty acid components of lipids in seeds, which can change depending on the Citrus species and varieties. Finally, this technique was employed to elucidate the metabolic profile of mold flavedo. PMID:23871074

  16. Structural studies of PCU-hydrazones: NMR spectroscopy, X-ray diffractions, and DFT calculations

    NASA Astrophysics Data System (ADS)

    Veljković, Jelena; Šekutor, Marina; Molčanov, Krešimir; Lo, Rabindranath; Ganguly, Bishwajit; Mlinarić-Majerski, Kata

    2011-06-01

    In this article we present a detailed structural investigation for the configurational isomers of PCU-hydrazones. The structural characterization of these hydrazones was performed using NMR spectroscopy, X-ray diffraction analysis and theoretical calculations. The single crystal X-ray structures of PCU-hydrazones 6B and 6C have been solved and used to conclusively confirm the characterization obtained via NMR spectra of a particular isomer. Nuclear magnetic shielding values calculated for 6A-C using DFT calculations were correlated with the experimentally determined chemical shifts. The computed results were found to be in good agreement with the observed 13C NMR values. The computed NMR results helped to ascertain the isomers of PCU-hydrazones 4A-C.

  17. Automated sample preparation station for studying self-diffusion in porous solids with NMR spectroscopy

    SciTech Connect

    Hedin, Niklas; DeMartin, Gregory J.; Reyes, Sebastian C.

    2006-03-15

    In studies of gas diffusion in porous solids with nuclear magnetic resonance (NMR) spectroscopy the sample preparation procedure becomes very important. An apparatus is presented here that pretreats the sample ex situ and accurately sets the desired pressure and temperature within the NMR tube prior to its introduction in the spectrometer. The gas manifold that supplies the NMR tube is also connected to a microbalance containing another portion of the same sample, which is kept at the same temperature as the sample in the NMR tube. This arrangement permits the simultaneous measurement of the adsorption loading on the sample, which is required for the interpretation of the NMR diffusion experiments. Furthermore, to ensure a good seal of the NMR tube, a hybrid valve design composed of titanium, a Teflon registered seat, and Kalrez registered O-rings is utilized. A computer controlled algorithm ensures the accuracy and reproducibility of all the procedures, enabling the NMR diffusion experiments to be performed at well controlled conditions of pressure, temperature, and amount of gas adsorbed on the porous sample.

  18. Characterization of proteins by in-cell NMR spectroscopy in cultured mammalian cells.

    PubMed

    Barbieri, Letizia; Luchinat, Enrico; Banci, Lucia

    2016-06-01

    In-cell NMR spectroscopy is a unique tool for characterizing biological macromolecules in their physiological environment at atomic resolution. Recent progress in NMR instruments and sample preparation methods allows functional processes, such as metal uptake, disulfide-bond formation and protein folding, to be analyzed by NMR in living, cultured human cells. This protocol describes the necessary steps to overexpress one or more proteins of interest inside human embryonic kidney 293T (HEK293T) cells, and it explains how to set up in-cell NMR experiments. The cDNA is transiently transfected as a complex with a cationic polymer (DNA:PEI (polyethylenimine)), and protein expression is carried on for 2-3 d, after which the NMR sample is prepared. (1)H and (1)H-(15)N correlation NMR experiments (for example, using band-selective optimized flip-angle short-transient heteronuclear multiple quantum coherence (SOFAST-HMQC)) can be carried out in <2 h, ensuring cell viability. Uniform (15)N labeling and amino-acid-specific (e.g., cysteine, methionine) labeling schemes are possible. The entire procedure takes 4 d from cell culture seeding to NMR data collection. PMID:27196722

  19. Structure determination of helical filaments by solid-state NMR spectroscopy

    PubMed Central

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

    2016-01-01

    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

  20. NMR difference spectroscopy with a dual saddle-coil difference probe.

    PubMed

    Macnaughtan, Megan A; Smith, Aaron P; Goldsbrough, Peter B; Santini, Robert E; Raftery, Daniel

    2004-03-01

    A new difference probe for nuclear magnetic resonance (NMR) spectroscopy is presented. The difference probe uses two saddle-shaped coils to excite and detect two samples simultaneously. The samples are held in a specially modified 3-mm NMR tube with an Ultem plastic disk to separate the samples. The probe's resonant circuit contains two crossed diodes that passively switch the relative phase of each coil during the NMR experiment. The result is a difference spectrum from the two samples. The degree of cancellation of common signals was determined to be approximately 90%, and the application of the probe to relaxation-edited difference spectroscopy for identifying protein-ligand interactions was demonstrated using glutathione and glutathione S-transferase binding protein. PMID:15214412

  1. Chiral Recognition Studies of α-(Nonafluoro-tert-butoxy)carboxylic Acids by NMR Spectroscopy.

    PubMed

    Nemes, Anikó; Csóka, Tamás; Béni, Szabolcs; Farkas, Viktor; Rábai, József; Szabó, Dénes

    2015-06-19

    Three chiral α-(nonafluoro-tert-butoxy)carboxylic acids (R)-1, (RS)-2, (R)-3 were synthesized to examine their application as chiral solvating agents with amines. As a model compound, first (S)- and/or (RS)-α-phenylethylamine was used, and their diastereomeric salts were investigated by (1)H and (19)F NMR and ECD spectroscopy. The NMR spectroscopic studies were carried out at room temperature using the slightly polar CDCl3 and apolar C6D6 as solvents in 5 mM and 54 mM concentrations. The difference of the chemical shifts (Δδ) in the diastereomeric complexes is comparable with other, well-known chiral derivatizing and solvating agents (e.g., Mosher's acid, Pirkle's alcohol). Diastereomeric salts of racemic acids (RS)-1 and (RS)-2 with biologically active amines (1R,2S)-ephedrine and (S)-dapoxetine were also investigated by (19)F NMR spectroscopy. PMID:26024423

  2. Probing acid-amide intermolecular hydrogen bonding by NMR spectroscopy and DFT calculations

    NASA Astrophysics Data System (ADS)

    Chaudhari, Sachin Rama; Suryaprakash, N.

    2012-05-01

    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.

  3. Water Behavior in Bacterial Spores by Deuterium NMR Spectroscopy

    PubMed Central

    2015-01-01

    Dormant bacterial spores are able to survive long periods of time without nutrients, withstand harsh environmental conditions, and germinate into metabolically active bacteria when conditions are favorable. Numerous factors influence this hardiness, including the spore structure and the presence of compounds to protect DNA from damage. It is known that the water content of the spore core plays a role in resistance to degradation, but the exact state of water inside the core is a subject of discussion. Two main theories present themselves: either the water in the spore core is mostly immobile and the core and its components are in a glassy state, or the core is a gel with mobile water around components which themselves have limited mobility. Using deuterium solid-state NMR experiments, we examine the nature of the water in the spore core. Our data show the presence of unbound water, bound water, and deuterated biomolecules that also contain labile deuterons. Deuterium–hydrogen exchange experiments show that most of these deuterons are inaccessible by external water. We believe that these unreachable deuterons are in a chemical bonding state that prevents exchange. Variable-temperature NMR results suggest that the spore core is more rigid than would be expected for a gel-like state. However, our rigid core interpretation may only apply to dried spores whereas a gel core may exist in aqueous suspension. Nonetheless, the gel core, if present, is inaccessible to external water. PMID:24950158

  4. Characterization of animal manure using advanced solid-state C-13 NMR spectroscopy

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Knowledge of chemical structure of animal manure is necessary for its effective utilization. However, characterization of animal manure is challenging since it is a complex mixture and partially soluble. Solid-state C-13 NMR (nuclear magnetic resonance) spectroscopy is regarded as the best tool to i...

  5. USING HIGH-RESOLUTION SOLUTION-STATE NMR SPECTROSCOPY TO INVESTIGATE PMDI REACTIONS WITH WOOD

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Solution-state NMR spectroscopy provides a powerful tool for understanding the formation of chemical bonds between wood components and adhesives. Finely ground cell wall (CW) material fully dissolves in a solvent system containing dimethylsulfoxide (DMSO-d6) and N-methyl¬imidazole (NMI-d6), keeping ...

  6. NMR imaging and spectroscopy of the mammalian central nervous system after heavy ion radiation

    SciTech Connect

    Richards, T.

    1984-09-01

    NMR imaging, NMR spectroscopic, and histopathologic techniques were used to study the proton relaxation time and related biochemical changes in the central nervous system after helium beam in vivo irradiation of the rodent brain. The spectroscopic observations reported in this dissertation were made possible by development of methods for measuring the NMR parameters of the rodent brain in vivo and in vitro. The methods include (1) depth selective spectroscopy using an optimization of rf pulse energy based on a priori knowledge of N-acetyl aspartate and lipid spectra of the normal brain, (2) phase-encoded proton spectroscopy of the living rodent using a surface coil, and (3) dual aqueous and organic tissue extraction technique for spectroscopy. Radiation induced increases were observed in lipid and p-choline peaks of the proton spectrum, in vivo. Proton NMR spectroscopy measurements on brain extracts (aqueous and organic solvents) were made to observe chemical changes that could not be seen in vivo. Radiation-induced changes were observed in lactate, GABA, glutamate, and p-choline peak areas of the aqueous fraction spectra. In the organic fraction, decreases were observed in peak area ratios of the terminal-methyl peaks, the N-methyl groups of choline, and at a peak at 2.84 ppM (phosphatidyl ethanolamine and phosphatidyl serine resonances) relative to TMS. With histology and Evans blue injections, blood-brain barrier alternations were seen as early as 4 days after irradiation. 83 references, 53 figures.

  7. Introducing High School Students to NMR Spectroscopy through Percent Composition Determination Using Low-Field Spectrometers

    ERIC Educational Resources Information Center

    Bonjour, Jessica L.; Pitzer, Joy M.; Frost, John A.

    2015-01-01

    Mole to gram conversions, density, and percent composition are fundamental concepts in first year chemistry at the high school or undergraduate level; however, students often find it difficult to engage with these concepts. We present a simple laboratory experiment utilizing portable nuclear magnetic resonance spectroscopy (NMR) to determine the…

  8. Structure Determination of Unknown Organic Liquids Using NMR and IR Spectroscopy: A General Chemistry Laboratory

    ERIC Educational Resources Information Center

    Pavel, John T.; Hyde, Erin C.; Bruch, Martha D.

    2012-01-01

    This experiment introduced general chemistry students to the basic concepts of organic structures and to the power of spectroscopic methods for structure determination. Students employed a combination of IR and NMR spectroscopy to perform de novo structure determination of unknown alcohols, without being provided with a list of possible…

  9. High-Resolution Solid-State NMR Spectroscopy: Characterization of Polymorphism in Cimetidine, a Pharmaceutical Compound

    ERIC Educational Resources Information Center

    Pacilio, Julia E.; Tokarski, John T.; Quiñones, Rosalynn; Iuliucci, Robbie J.

    2014-01-01

    High-resolution solid-state NMR (SSNMR) spectroscopy has many advantages as a tool to characterize solid-phase material that finds applications in polymer chemistry, nanotechnology, materials science, biomolecular structure determination, and others, including the pharmaceutical industry. The technology associated with achieving high resolution…

  10. NMR Spectroscopy of Aqueous Extracts of Fenugreek ( Trigonella foenum- graecum L.)

    NASA Astrophysics Data System (ADS)

    Skakovskii, E. D.; Tychinskaya, L. Yu.; Matveichuk, S. V.; Karankevich, E. G.; Agabalaeva, E. D.; Reshetnikov, V. N.

    2014-09-01

    The amino-acid and monosaccharide compositions of aqueous extracts of fenugreek herb were determined using PMR and 13C NMR spectroscopy. The content of identified extract constituents was >70 mol%, of which the dominant amino acid was 4-hydroxyisoleucine (26.5 mol%); the major carbohydrate, glucose (10.1 mol%).

  11. In situ measurement of molecular diffusion during catalytic reaction by pulsed-field gradient NMR spectroscopy

    SciTech Connect

    Hong, Y.; Kaerger, J.; Hunger, B. ); Feoktistova, N.N.; Zhdanov, S.P. )

    1992-09-01

    Pulsed-field gradient (PFG) NMR spectroscopy is applied to study the intracrystalline diffusivity of the reactant and product molecules during the conversion of cyclopropane to propene in Zeolite X. The diffusivities are found to be large enough that any influence of intracrystalline diffusion on the overall reaction in flow reactors may be excluded.

  12. Characterization of various fast pyrolysis bio-oils by NMR spectroscopy

    Technology Transfer Automated Retrieval System (TEKTRAN)

    NMR spectroscopy, including 1H, 13 C and DEPT spectra were used to characterize fast pyrolysis oil from numerous energy crops and other agricultural feedstocks. The bio-oils studied were produced from swithchgrass, alfalfa stems, corn stover, guayule (whole plant and latex extracted bagasse) and ch...

  13. Analyzing the adsorption of blood plasma components by means of fullerene-containing silica gels and NMR spectroscopy in solids

    NASA Astrophysics Data System (ADS)

    Melenevskaya, E. Yu.; Mokeev, M. V.; Nasonova, K. V.; Podosenova, N. G.; Sharonova, L. V.; Gribanov, A. V.

    2012-10-01

    The results from studying the adsorption of blood plasma components (e.g., protein, triglycerides, cholesterol, and lipoproteins of low and high density) using silica gels modified with fullerene molecules (in the form of C60 or the hydroxylated form of C60(OH) x ) and subjected to hydration (or, alternatively, dehydration) are presented. The conditions for preparing adsorbents that allow us to control the adsorption capacity of silica gel and the selectivity of adsorption toward the components of blood plasma, are revealed. The nature and strength of the interactions of the introduced components (fullerene molecules and water) with functional groups on the silica surface are studied by means of solid state NMR spectroscopy (NMR-SS). Conclusions regarding the nature of the centers that control adsorption are drawn on the basis of NMR-SS spectra in combination with direct measurements of adsorption. The interaction of the oxygen of the hydroxyl group of silica gel with fullerene, leading to the formation of electron-donor complexes of C60-H, C60-OH, or C60-OSi type, is demonstrated by the observed changes in the NMR-SS spectra of silica gels in the presence of fullerene.

  14. Characterization and quantification of microstructures of a fluorinated terpolymer by both homonuclear and heteronuclear two-dimensional NMR spectroscopy.

    PubMed

    Ok, Salim

    2015-02-01

    Fluoropolymers are usually insoluble in organic solvents. Insolubility of fluoropolymers limits basic characterization such as microstructural investigations. In the family of fluoropolymers, terpolymer of tetrafluorethylene (TFE), hexafluoropropylene (HFP), and vinylidene fluoride (VDF), named THV is one of the newest members. There are nine grades of THV available. Among the nine grades, THV-221 G is an ideal model polymer for basic characterization purposes. THV-221 G is soluble in solvents such as acetone and ethyl acetate. In the current report, both homonuclear and heteronuclear 2D NMR experiments were employed in solution on THV-221 G. The homonuclear gradient correlation spectroscopy NMR measurement revealed that THV has two adjacent TFE units in addition to TFE-HFP sequence orders. The fraction of the microstructures is quantified by the analysis of 1D solution (19)F NMR spectrum. Further, the gradient heteronuclear single quantum coherence experiment helped with the clarification of chemical environments of the units TFE, HFP, and VDF. The 1D solution (13)C NMR spectrum was helpful in clarifying sequence assignments of VDF. It is concluded that THV is a random polymer with a limited fraction of TFE-TFE and TFE-HFP sequence orders in addition to head-to-tail polymerization of VDF unit. PMID:25327292

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

    PubMed

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

    2016-10-20

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

  16. NMR spectroscopy in studies of light-induced structural changes in mammalian rhodopsin: applicability of solution (19)F NMR.

    PubMed

    Klein-Seetharaman, J; Getmanova, E V; Loewen, M C; Reeves, P J; Khorana, H G

    1999-11-23

    We report high resolution solution (19)F NMR spectra of fluorine-labeled rhodopsin mutants in detergent micelles. Single cysteine substitution mutants in the cytoplasmic face of rhodopsin were labeled by attachment of the trifluoroethylthio (TET), CF(3)-CH(2)-S, group through a disulfide linkage. TET-labeled cysteine mutants at amino acid positions 67, 140, 245, 248, 311, and 316 in rhodopsin were thus prepared. Purified mutant rhodopsins (6-10 mg), in dodecylmaltoside, were analyzed at 20 degrees C by solution (19)F NMR spectroscopy. The spectra recorded in the dark showed the following chemical shifts relative to trifluoroacetate: Cys-67, 9.8 ppm; Cys-140, 10.6 ppm; Cys-245, 9.9 ppm; Cys-248, 9.5 ppm; Cys-311, 9.9 ppm; and Cys-316, 10.0 ppm. Thus, all mutants showed chemical shifts downfield that of free TET (6.5 ppm). On illumination to form metarhodopsin II, upfield changes in chemical shift were observed for (19)F labels at positions 67 (-0.2 ppm) and 140 (-0.4 ppm) and downfield changes for positions 248 (+0.1 ppm) and 316 (+0.1 ppm) whereas little or no change was observed at positions 311 and 245. On decay of metarhodopsin II, the chemical shifts reverted largely to those originally observed in the dark. The results demonstrate the applicability of solution (19)F NMR spectroscopy to studies of the tertiary structures in the cytoplasmic face of intact rhodopsin in the dark and on light activation. PMID:10570143

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

  18. Higher Order Amyloid Fibril Structure by MAS NMR and DNP Spectroscopy

    PubMed Central

    Debelouchina, Galia T.; Bayro, Marvin J.; Fitzpatrick, Anthony W.; Ladizhansky, Vladimir; Colvin, Michael T.; Caporini, Marc A.; Jaroniec, Christopher P.; Bajaj, Vikram S.; Rosay, Melanie; MacPhee, Cait E.; Vendruscolo, Michele; Maas, Werner E.; Dobson, Christopher M.; Griffin, Robert G.

    2014-01-01

    Protein magic angle spinning (MAS) NMR spectroscopy has generated structural models of several amyloid fibril systems, thus providing valuable information regarding the forces and interactions that confer the extraordinary stability of the amyloid architecture. Despite these advances, however, obtaining atomic resolution information describing the higher levels of structural organization within the fibrils remains a significant challenge. Here, we detail MAS NMR experiments and sample labeling schemes designed specifically to probe such higher order amyloid structure and we have applied them to the fibrils formed by an eleven-residue segment of the amyloidogenic protein transthyretin (TTR(105-115)). These experiments have allowed us to define unambiguously not only the arrangement of the peptide β-strands into β-sheets but also the β-sheet interfaces within each protofilament, and in addition to identify the nature of the protofilament-to-protofilament contacts that lead to the formation of the complete fibril. Our efforts have resulted in 111 quantitative distance and torsion angle restraints (10 per residue) that describe the various levels of structure organization. The experiments benefited extensively from the use of dynamic nuclear polarization (DNP), which in some cases allowed us to shorten the data acquisition time from days to hours and to improve significantly the signal-to-noise ratios of the spectra. The β-sheet interface and protofilament interactions identified here revealed local variations in the structure that result in multiple peaks for the exposed N- and C-termini of the peptide and in inhomogeneous line-broadening for the side-chains buried within the interior of the fibrils. PMID:24304221

  19. New methods and applications in solid-state NMR spectroscopy of quadrupolar nuclei.

    PubMed

    Ashbrook, Sharon E; Sneddon, Scott

    2014-11-01

    Solid-state nuclear magnetic resonance (NMR) spectroscopy has long been established as offering unique atomic-scale and element-specific insight into the structure, disorder, and dynamics of materials. NMR spectra of quadrupolar nuclei (I > (1)/2) are often perceived as being challenging to acquire and to interpret because of the presence of anisotropic broadening arising from the interaction of the electric field gradient and the nuclear electric quadrupole moment, which broadens the spectral lines, often over several megahertz. Despite the vast amount of information contained in the spectral line shapes, the problems with sensitivity and resolution have, until very recently, limited the application of NMR spectroscopy of quadrupolar nuclei in the solid state. In this Perspective, we provide a brief overview of the quadrupolar interaction, describe some of the basic experimental approaches used for acquiring high-resolution NMR spectra, and discuss the information that these spectra can provide. We then describe some interesting recent examples to showcase some of the more exciting and challenging new applications of NMR spectra of quadrupolar nuclei in the fields of energy materials, microporous materials, Earth sciences, and biomaterials. Finally, we consider the possible directions that this highly informative technique may take in the future. PMID:25296129

  20. Solvation and crystal effects in bilirubin studied by NMR spectroscopy and density functional theory.

    PubMed

    Rohmer, Thierry; Matysik, Jörg; Mark, Franz

    2011-10-27

    The open-chain tetrapyrrole compound bilirubin was investigated in chloroform and dimethyl sulfoxide solutions by liquid-state NMR and as solid by (1)H, (13)C, and (15)N magic-angle spinning (MAS) solid-state NMR spectroscopy. Density functional theory (DFT) calculations were performed to interpret the data, using the B3LYP exchange-correlation functional to optimize geometries and to compute NMR chemical shieldings by the gauge-including atomic orbital method. The dependence of geometries and chemical shieldings on the size of the basis sets was investigated for the reference molecules tetramethylsilane, NH(3), and H(2)O, and for bilirubin as a monomer and in clusters consisting of up to six molecules. In order to assess the intrinsic errors of the B3LYP approximation in calculating NMR shieldings, complete basis set estimates were obtained for the nuclear shielding values of the reference molecules. The experimental liquid-state NMR data of bilirubin are well reproduced by a monomeric bilirubin molecule using the 6-311+G(2d,p) basis set for geometry optimization and for calculating chemical shieldings. To simulate the bilirubin crystal, a hexameric model was required. It was constructed from geometry-optimized monomers using information from the X-ray structure of bilirubin to fix the monomeric entities in space and refined by partial optimization. Combining experimental (1)H-(13)C and (1)H-(15)N NMR correlation spectroscopy and density functional theory, almost complete sets of (1)H, (13)C, and (15)N chemical shift assignments were obtained for both liquid and solid states. It is shown that monomeric bilirubin in chloroform solution is formed by 3-vinyl anti conformers, while bilirubin crystals are formed by 3-vinyl syn conformers. This conformational change leads to characteristic differences between the liquid- and solid-state NMR resonances. PMID:21846145

  1. Conformational solution studies of neuropeptide gamma using CD and NMR spectroscopy.

    PubMed

    Rodziewicz-Motowidło, Sylwia; Brzozowskl, Krzysztof; Legowska, Anna; Liwo, Adam; Silbering, Jerzy; Smoluch, Marek; Rolka, Krzysztof

    2002-05-01

    Neuropeptide gamma is one of the largest members of the tachykinin family of peptides, exhibiting strong agonistic activity towards the NK-2 tachykinin receptor. This peptide was synthesized by the solid-phase method using the Fmoc chemistry. Circular-dichroism spectroscopy (CD) investigations of this peptide were performed in phosphate buffer, in the presence of sodium dodecylsulphate (SDS) micelles and trifluoroethanol (TFE) solutions and in DMSO-d6 using the 2D NMR technique in conjunction with two different theoretical approaches. The first assumes multiconformational equilibrium of the peptide studied characterized by the values of statistical weights of low-energy conformations. These calculations were performed using three different force fields ECEPP/3, AMBER4.1 and CHARMM (implemented in the X-PLOR program). The second method incorporates interproton distance and dihedral angle constraints into the starting conformation using the Simulated Annealing algorithm (X-PLOR program). The CD experiments revealed that although the peptide studied is flexible in polar solvents, a tendency to adopt a helical structure was observed in the hydrophobic environment. The NMR data (NOE effects) indicate a helical or reverse structure in the Ile7-His12 fragment of the peptide studied in DMSO-d6 solution. The results obtained cannot be interpreted in terms of a single conformation. Most of the conformations obtained with the ECEPP/3 force field possess a high content of a helical structure. None of the conformers, obtained with the AMBER4.1 and CHARMM force fields, can be considered as the dominant one. In all conformations several beta-turns were detected and in some cases gamma-turns were also found. But in fact, it is rather difficult to select the position of the secondary element(s) present in the structure of NPgamma in solution. All conformers calculated with the X-PLOR program (with using NMR derived distance and torsion angle constraints) are stabilized by several

  2. High-resolution heteronuclear multi-dimensional NMR spectroscopy in magnetic fields with unknown spatial variations

    NASA Astrophysics Data System (ADS)

    Zhang, Zhiyong; Huang, Yuqing; Smith, Pieter E. S.; Wang, Kaiyu; Cai, Shuhui; Chen, Zhong

    2014-05-01

    Heteronuclear NMR spectroscopy is an extremely powerful tool for determining the structures of organic molecules and is of particular significance in the structural analysis of proteins. In order to leverage the method’s potential for structural investigations, obtaining high-resolution NMR spectra is essential and this is generally accomplished by using very homogeneous magnetic fields. However, there are several situations where magnetic field distortions and thus line broadening is unavoidable, for example, the samples under investigation may be inherently heterogeneous, and the magnet’s homogeneity may be poor. This line broadening can hinder resonance assignment or even render it impossible. We put forth a new class of pulse sequences for obtaining high-resolution heteronuclear spectra in magnetic fields with unknown spatial variations based on distant dipolar field modulations. This strategy’s capabilities are demonstrated with the acquisition of high-resolution 2D gHSQC and gHMBC spectra. These sequences’ performances are evaluated on the basis of their sensitivities and acquisition efficiencies. Moreover, we show that by encoding and decoding NMR observables spatially, as is done in ultrafast NMR, an extra dimension containing J-coupling information can be obtained without increasing the time necessary to acquire a heteronuclear correlation spectrum. Since the new sequences relax magnetic field homogeneity constraints imposed upon high-resolution NMR, they may be applied in portable NMR sensors and studies of heterogeneous chemical and biological materials.

  3. The Solid Solution Sr(1-x)Ba(x)Ga2: Substitutional Disorder and Chemical Bonding Visited by NMR Spectroscopy and Quantum Mechanical Calculations.

    PubMed

    Pecher, Oliver; Mausolf, Bernhard; Lamberts, Kevin; Oligschläger, Dirk; Niewieszol, Carina; Englert, Ulli; Haarmann, Frank

    2015-09-28

    Complete miscibility of the intermetallic phases (IPs) SrGa2 and BaGa2 forming the solid solution Sr(1-x)Ba(x)Ga2 is shown by means of X-ray diffraction, thermoanalytical and metallographic studies. Regarding the distances of Sr/Ba sites versus substitution degree, a model of isolated substitution centres (ISC) for up to 10% cation substitution is explored to study the influence on the Ga bonding situation. A combined application of NMR spectroscopy and quantum mechanical (QM) calculations proves the electric field gradient (EFG) to be a sensitive measure of different bonding situations. The experimental resolution is boosted by orientation-dependent NMR on magnetically aligned powder samples, revealing in first approximation two different Ga species in the ISC regimes. EFG calculations using superlattice structures within periodic boundary conditions are in fair agreement with the NMR spectroscopy data and are discussed in detail regarding their application on disordered IPs. PMID:26272697

  4. Binding of Sulfonamide Antibiotics to CTABr Micelles Characterized Using (1)H NMR Spectroscopy.

    PubMed

    Sarker, Ashish K; Cashin, Patrick J; Balakrishnan, Vimal K; Exall, Kirsten; Buncel, Erwin; Brown, R Stephen

    2016-08-01

    Interactions of nine sulfonamide antibiotics (sulfadoxine, sulfathiazole, sulfamethoxazole, sulfamerazine, sulfadiazine, sulfamethazine, sulfacetamide, sulfaguanidine, and sulfanilamide) with cetyltrimethylamonium bromide (CTABr) micelles were examined using (1)H NMR spectroscopy. Seven of the nine provided a significant change in the (1)H NMR chemical shift such that the magnitude and direction (upfield vs downfield) of the chemical shift could be used to propose a locus and orientation of the sulfonamide within the micelle structure. The magnitude of the chemical shift was used to estimate the binding constant for seven sulfonamides with CTABr micelles, providing values and an overall pattern consistent with previous studies of these sulfonamides. PMID:27391918

  5. Synthesis and Proton NMR Spectroscopy of Intra-Vesicular Gamma-Aminobutyric Acid (GABA)*

    PubMed Central

    Wang, Luke Y.-J.; Tong, Rong; Kohane, Daniel S.

    2014-01-01

    We report the synthesis of vesicles containing gamma-aminobutyric acid (GABA), and their proton nuclear magnetic resonance (1H NMR) spectra. These vesicles were constructed to more closely mimic the intracellular environment wherein GABA exists. For this study, these GABA-containing vesicles were examined under 1H NMR as a potential platform for future studies on the differences between aqueous phantoms, ex vivo brain extracts, and in vivo magnetic resonance spectroscopy results. We found that intra-vesicular GABA faithfully yielded the chemical shifts and J-coupling constants of free aqueous GABA, alongside the chemical shift signals of the vesicle wall. PMID:24109882

  6. Assessing the fate and transformation of plant residues in the terrestrial environment using HR-MAS NMR spectroscopy

    NASA Astrophysics Data System (ADS)

    Kelleher, Brian P.; Simpson, Myrna J.; Simpson, Andre J.

    2006-08-01

    Plant litter decomposition plays a fundamental role in carbon and nitrogen cycles, provides key nutrients to the soil environment and represents a potentially large positive feedback to atmospheric CO 2. However, the full details of decomposition pathways and products are unknown. Here we present the first application of HR-MAS NMR spectroscopy on 13C and 15N labeled plant materials, and apply this approach in a preliminary study to monitor the environmental degradation of the pine and wheatgrass residues over time. In HR-MAS, is it possible to acquire very high resolution NMR data of plant biomass, and apply the vast array of multidimensional experiments available in conventional solution-state NMR. High levels of isotopic enrichment combined with HR-MAS significantly enhance the detection limits, and provide a wealth of information that is unattainable by any other method. Diffusion edited HR-MAS NMR data reveal the rapid loss of carbohydrate structures, while two-dimensional (2-D) HR-MAS NMR spectra demonstrate the relatively fast loss of both hydrolysable and condensed tannin structures from all plant tissues studied. Aromatic (partially lignin) and aliphatic components (waxes, cuticles) tend to persist, along with a small fraction of carbohydrate, and become highly functionalized over time. While one-dimensional (1-D) 13C HR-MAS NMR spectra of fresh plant tissue reflect compositional differences between pine and grass, these differences become negligible after decomposition suggesting that recalcitrant carbon may be similar despite the plant source. Two-dimensional 1H- 15N HR-MAS NMR analysis of the pine residue suggests that nitrogen from specific peptides is either selectively preserved or used for the synthesis of what appears to be novel structures. The amount of relevant data generated from plant components in situ using HR-MAS NMR is highly encouraging, and demonstrates that complete assignment will yield unprecedented structural knowledge of plant cell

  7. High frequency volume coils for clinical NMR imaging and spectroscopy.

    PubMed

    Vaughan, J T; Hetherington, H P; Otu, J O; Pan, J W; Pohost, G M

    1994-08-01

    A tuned transmission line resonator has been developed in theory and in practical design for the clinical NMR volume coil application at 4.1 tesla. The distributed circuit transmission line resonator was designed for high frequency, large conductive volume applications where conventional lumped element coil designs perform less efficiently. The resonator design has made use of a resonant coaxial cavity, which could be variably tuned to the Larmor frequency of interest by tunable transmission line elements. Large head- and body-sized volumes, high efficiencies, and broad tuning ranges have been shown to be characteristic of the transmission line resonator to frequencies of 500 MHz. The B1 homogeneity of the resonator has been demonstrated to be a function of the electromagnetic properties of the load itself. By numerically solving Maxwell's equations for the fully time-dependent B1 field, coil homogeneity was predicted with finite-element models of anatomic structure, and inhomogeneities corrected for. A how-to exposition of coil design and construction has been included. Simple methods of quadrature driving and double tuning the transmission line resonator have also been presented. Human head images obtained with a tuned transmission line resonator at 175 MHz have clearly demonstrated uncompromised high field advantages of signal-to-noise and spatial resolution. PMID:7968443

  8. Broadband "Infinite-Speed" Magic-Angle Spinning NMR Spectroscopy

    SciTech Connect

    Hu, Yan-Yan; Levin, E.M; Schmidt-Rohr, Klaus

    2009-06-02

    High-resolution magic-angle spinning NMR of high-Z spin- 1/2 nuclei such as {sup 125}Te, {sup 207}Pb, {sup 119}Sn, {sup 113}Cd, and {sup 195}Pt is often hampered by large (>1000 ppm) chemical-shift anisotropies, which result in strong spinning sidebands that can obscure the centerbands of interest. In various tellurides with applications as thermoelectrics and as phase-change materials for data storage, even 22-kHz magic-angle spinning cannot resolve the center- and sidebands broadened by chemical-shift dispersion, which precludes peak identification or quantification. For sideband suppression over the necessary wide spectral range (up to 200 kHz), radio frequency pulse sequences with few, short pulses are required. We have identified Gan's two-dimensional magic-angle-turning (MAT) experiment with five 90{sup o} pulses as a promising broadband technique for obtaining spectra without sidebands. We have adapted it to broad spectra and fast magic-angle spinning by accounting for long pulses (comparable to the dwell time in t{sub 1}) and short rotation periods. Spectral distortions are small and residual sidebands negligible even for spectra with signals covering a range of 1.5 {gamma}B{sub 1}, due to a favorable disposition of the narrow ranges containing the signals of interest in the spectral plane. The method is demonstrated on various technologically interesting tellurides with spectra spanning up to 170 kHz, at 22 kHz MAS.

  9. Fundamental studies of supported bimetallic catalysts by NMR spectroscopy

    SciTech Connect

    Savargaonkar, N.

    1996-10-17

    Various hydrogenation reactions on transition metals are important commercially whereas certain hydrogenolysis reactions are useful from fundamental point of view. Understanding the hydrogen mobility and kinetics of adsorption-desorption of hydrogen is important in understanding the mechanisms of such reactions involving hydrogen. The kinetics of hydrogen chemisorption was studied by means of selective excitation NMR on silica supported Pt, Rh and Pt-Rh catalysts. The activation energy of hydrogen desorption was found to be lower on silica supported Pt catalysts as compared to Rh and Pt-Rh catalysts. It was found that the rates of hydrogen adsorption and desorption on Pt-Rh catalyst were similar to those on Rh catalyst and much higher as compared to Pt catalyst. The Ru-Ag bimetallic system is much simpler to study than the Pt-Rh system and serves as a model system to characterize more complicated systems such as the K/Ru system. Ag was found to decrease the amounts of adsorbed hydrogen and the hydrogen-to-ruthenium stoichiometry. Ag reduced the populations of states with low and intermediate binding energies of hydrogen on silica supported Ru catalyst. The rates of hydrogen adsorption and desorption were also lower on silica supported Ru-Ag catalyst as compared to Ru catalyst. This report contains introductory information, the literature review, general conclusions, and four appendices. An additional four chapters and one appendix have been processed separately for inclusion on the data base.

  10. Deuterium NMR spectroscopy of biosynthetically deuterated mammalian tissues

    SciTech Connect

    Curatolo, W.; Jungalwala, F.B.; Sears, B.; Tuck, L.; Neuringer, L.J.

    1985-07-30

    The choline-containing phospholipids of mammalian membranes have been biosynthetically deuterated by raising rats on a diet supplemented with (HOCH2CH2N(CD3)3) Cl or (HOCD2CH2N(CH3)3) Cl . Deuterium NMR spectra have been obtained from excised deuterated brain, sciatic nerve, heart, and lung, from isolated brain myelin and brain microsomes, and from aqueous dispersions of lipid extracts. Measurements of residual quadrupole splittings for excised deuterated neural tissues demonstrate that the orientational order of the choline head group is similar to that observed in model membranes. The spin-lattice relaxation time of the choline head group in deuterated neural tissue is indistinguishable from that observed in model membranes. These results support the proposal that the conformation and motional dynamics of the choline head groups of the bulk choline-containing lipids of neural tissue are similar to those in model membranes. Spectra of biosynthetically deuterated brain myelin and brain microsomes exhibit similar quadrupole splittings. Since these membranes have significantly different protein contents, these results indicate that no strong polar interactions exist between membrane proteins and the choline head groups of choline-containing membrane lipids. Spectra of intact deuterated heart and lung exhibit broad lines and a range of quadrupole splittings.

  11. Fractional deuteration applied to biomolecular solid-state NMR spectroscopy.

    PubMed

    Nand, Deepak; Cukkemane, Abhishek; Becker, Stefan; Baldus, Marc

    2012-02-01

    Solid-state Nuclear Magnetic Resonance can provide detailed insight into structural and dynamical aspects of complex biomolecules. With increasing molecular size, advanced approaches for spectral simplification and the detection of medium to long-range contacts become of critical relevance. We have analyzed the protonation pattern of a membrane-embedded ion channel that was obtained from bacterial expression using protonated precursors and D(2)O medium. We find an overall reduction of 50% in protein protonation. High levels of deuteration at H(α) and H(β) positions reduce spectral congestion in ((1)H,(13)C,(15)N) correlation experiments and generate a transfer profile in longitudinal mixing schemes that can be tuned to specific resonance frequencies. At the same time, residual protons are predominantly found at amino-acid side-chain positions enhancing the prospects for obtaining side-chain resonance assignments and for detecting medium to long-range contacts. Fractional deuteration thus provides a powerful means to aid the structural analysis of complex biomolecules by solid-state NMR. PMID:22105305

  12. Membrane Interactions of Phylloseptin-1, -2, and -3 Peptides by Oriented Solid-State NMR Spectroscopy

    PubMed Central

    Resende, Jarbas M.; Verly, Rodrigo M.; Aisenbrey, Christopher; Cesar, Amary; Bertani, Philippe; Piló-Veloso, Dorila; Bechinger, Burkhard

    2014-01-01

    Phylloseptin-1, -2, and -3 are three members of the family of linear cationic antimicrobial peptides found in tree frogs. The highly homologous peptides encompass 19 amino acids, and only differ in the amino acid composition and charge at the six most carboxy-terminal residues. Here, we investigated how such subtle changes are reflected in their membrane interactions and how these can be correlated to their biological activities. To this end, the three peptides were labeled with stable isotopes, reconstituted into oriented phospholipid bilayers, and their detailed topology determined by a combined approach using 2H and 15N solid-state NMR spectroscopy. Although phylloseptin-2 and -3 adopt perfect in-plane alignments, the tilt angle of phylloseptin-1 deviates by 8° probably to assure a more water exposed localization of the lysine-17 side chain. Furthermore, different azimuthal angles are observed, positioning the amphipathic helices of all three peptides with the charged residues well exposed to the water phase. Interestingly, our studies also reveal that two orientation-dependent 2H quadrupolar splittings from methyl-deuterated alanines and one 15N amide chemical shift are sufficient to unambiguously determine the topology of phylloseptin-1, where quadrupolar splittings close to the maximum impose the most stringent angular restraints. As a result of these studies, a strategy is proposed where the topology of a peptide structure can be determined accurately from the labeling with 15N and 2H isotopes of only a few amino acid residues. PMID:25140425

  13. An Investigation of Lanthanum Coordination Compounds by Using Solid- State 139La NMR Spectroscopy and Relativistic Density Functional Theory

    SciTech Connect

    Willans, Mathew J.; Feindel, Kirk W.; Ooms, Kristopher J.; Wasylishen, Roderick E.

    2005-12-16

    Lanthanum-139 NMR spectra of stationary samples of several solid LaIII coordination compounds have been obtained at applied magnetic fields of 11.75 and 17.60 T. The breadth and shape of the 139La NMR spectra of the central transition are dominated by the interaction between the 139La nuclear quadrupole moment and the electric field gradient (EFG) at that nucleus; however, the influence of chemical-shift anisotropy on the NMR spectra is non-negligible for the majority of the compounds investigated. Analysis of the experimental NMR spectra reveals that the 139La quadrupolar coupling constants (CQ) range from 10.0 to 35.6 MHz, the spans of the chemical-shift tensor (W) range from 50 to 260 ppm, and the isotropic chemical shifts (diso) range from -80 to 178 ppm. In general, there is a correlation between the magnitudes of CQ and W, and diso is shown to depend on the La coordination number. Magnetic shielding tensors, calculated by using relativistic zeroth-order regular approximation density functional theory (ZORA-DFT) and incorporating scalar only or scalar plus spin-orbit relativistic effects, qualitatively reproduce the experimental chemical-shift tensors. In general, the inclusion of spin-orbit coupling yields results that are in better agreement with those from the experiment. The magnetic-shielding calculations and experimentally determined Euler angles can be used to predict the orientation of the chemical-shift and EFG tensors in the molecular frame. This study demonstrates that solid state 139La NMR spectroscopy is a useful characterization method and can provide insight into the molecular structure of lanthanum coordination compounds.

  14. Site-directed mutagenesis and high-resolution NMR spectroscopy of the active site of porphobilinogen deaminase

    SciTech Connect

    Scott, A.I.; Roessner, C.A.; Stolowich, N.J.; Karuso, P.; Williams, H.J.; Grant, S.K.; Gonzalez, M.D.; Hoshino, T. )

    1988-10-18

    The active site of porphobilinogen (PBG){sup 1} deaminase from Escherichia coli has been found to contain an unusual dipyrromethane derived from four molecules of 5-aminolevulinic acid (ALA) covalently linked to Cys-242, one of the two cysteine residues conserved in E. coli and human deaminase. By use of a hemA{sup {minus}} strain of E. coli the enzyme was enriched from (5-{sup 13}C)ALA and examined by {sup 1}H-detected multiple quantum coherence spectroscopy, which revealed all of the salient features of a dipyrromethane composed of two PBG units linked heat to tail and terminating in a CH{sub 2}-S bond to a cysteine residue. Site-specific mutagenesis of Cys-99 and Cys-242, respectively, has shown that substitution of Ser for Cys-99 does not affect the enzymatic activity, whereas substitution of Ser for Cys-242 removes essentially all of the catalytic activity as measured by the conversion of the substrate PBG to uro'gen I. The NMR spectrum of the covalent complex of deaminase with the suicide inhibitor 2-bromo-(2,11-{sup 13}C{sub 2})PBG reveals that the aminomethyl terminus of the inhibitor reacts with the enzyme's cofactor at the {alpha}-free pyrrole. NMR spectroscopy of the ES{sub 2} complex confirmed a PBG-derived head-to-tail dipyrromethane attached to the {alpha}-free pyrrole position of the enzyme. A mechanistic rationale for deaminase is presented.

  15. Chromophore/DNA interactions: femto- to nanosecond spectroscopy, NMR structure, and electron transfer theory.

    PubMed

    von Feilitzsch, Till; Tuma, Jennifer; Neubauer, Heike; Verdier, Laurent; Haselsberger, Reinhard; Feick, Reiner; Gurzadyan, Gagik; Voityuk, Alexander A; Griesinger, Christian; Michel-Beyerle, Maria E

    2008-01-24

    The mechanism of photoinduced hole injection into DNA has been studied using an integrated approach that combines NMR structural analysis, time-resolved spectroscopy, and quantum-chemical calculations. A covalently linked acridinium derivative, the protonated 9-amino-6-chloro-2-methoxyacridine (X+), is replacing a thymine and separated from either guanine (G) or the easier to oxidize 7-deazaguanine (Z) by one adenine.thymine (A.T) base pair. The key features of this donor/acceptor system are the following: (i) In more than 95% of the duplexes, X+ is located in a central, coplanar position between the neighboring A.T base pairs with its long axis in parallel showing minimal twist and tilt angles (<15 degrees). The complementary adenine base is turned out into the extrahelical space. In a minority of less than 5%, X+ is found to be still attached to the duplex. X+ is most probably associated with one of the phosphates, since it is neither intercalated between more remote base pairs nor bound to sugars or grooves. This minority characterized by an excited state lifetime >10 ns gives rise to a small background signal in time-resolved measurements and contributes predominantly to steady-state fluorescence spectra. (ii) Although the intercalation mode of X+ is well defined, the NMR structure reveals that there are two conformations of X+ with respect to the arrangement of its methoxy substituent. In one conformation, the methoxy group is in the plane of the chromophore, while, in the other extraplanar conformation, the methoxy group forms an angle of 70 degrees with the acridinium ring. The fluorescence decay of 5'-ZAX and 5'-GAX tracts can be fitted to a biexponential function with similar amplitudes, reflecting the oxidation dynamics of G and Z, with the slower rate being determined by larger thermal activation energy. The attribution of biexponential electron transfer (ET) dynamics to the bimodal orientation of the methoxy group at the acridinium is supported by

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

    SciTech Connect

    Schwartz, D.J.

    1995-07-01

    NMR spectroscopy is ideal for studying weak interactions (formation enthalpy {le}20 kcal/mol) in solution. The metallocene bis(pentamethylcyclopentadienyl)ytterbium, Cp*{sub 2}Yb, is ideal for this purpose. cis-P{sub 2}PtH{sub 2}complexes (P = phosphine) were used to produce slow-exchange Cp*{sub 2}YbL adducts for NMR study. Reversible formation of (P{sub 2}PtH){sub 2} complexes from cis-P{sub 2}PtH{sub 2} complexes were also studied, followed by interactions of Cp*{sub 2}Yb with phosphines, R{sub 3}PX complexes. A NMR study was done on the interactions of Cp*{sub 2}Yb with H{sub 2}, CH{sub 4}, Xe, CO, silanes, stannanes, C{sub 6}H{sub 6}, and toluene.

  17. Target-based whole-cell screening by ¹H NMR spectroscopy.

    PubMed

    Ma, Junhe; Cao, Qing; McLeod, Sarah M; Ferguson, Keith; Gao, Ning; Breeze, Alexander L; Hu, Jun

    2015-04-13

    An NMR-based approach marries the two traditional screening technologies (phenotypic and target-based screening) to find compounds inhibiting a specific enzymatic reaction in bacterial cells. Building on a previous study in which it was demonstrated that hydrolytic decomposition of meropenem in living Escherichia coli cells carrying New Delhi metallo-β-lactamase subclass 1 (NDM-1) can be monitored in real time by NMR spectroscopy, we designed a cell-based NMR screening platform. A strong NDM-1 inhibitor was identified with cellular IC50 of 0.51 μM, which is over 300-fold more potent than captopril, a known NDM-1 inhibitor. This new screening approach has great potential to be applied to targets in other cell types, such as mammalian cells, and to targets that are only stable or functionally competent in the cellular environment. PMID:25693499

  18. Structures of larger proteins in solution: Three- and four-dimensional heteronuclear NMR spectroscopy

    SciTech Connect

    Gronenborn, A.M.; Clore, G.M.

    1994-12-01

    Complete understanding of a protein`s function and mechanism of action can only be achieved with a knowledge of its three-dimensional structure at atomic resolution. At present, there are two methods available for determining such structures. The first method, which has been established for many years, is x-ray diffraction of protein single crystals. The second method has blossomed only in the last 5 years and is based on the application of nuclear magnetic resonance (NMR) spectroscopy to proteins in solution. This review paper describes three- and four-dimensional NMR methods applied to protein structure determination and was adapted from Clore and Gronenborn. The review focuses on the underlying principals and practice of multidimensional NMR and the structural information obtained.

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

    NASA Astrophysics Data System (ADS)

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

    2016-05-01

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

  20. Metabolomic differentiation of Cannabis sativa cultivars using 1H NMR spectroscopy and principal component analysis.

    PubMed

    Choi, Young Hae; Kim, Hye Kyong; Hazekamp, Arno; Erkelens, Cornelis; Lefeber, Alfons W M; Verpoorte, Robert

    2004-06-01

    The metabolomic analysis of 12 Cannabis sativa cultivars was carried out by 1H NMR spectroscopy and multivariate analysis techniques. Principal component analysis (PCA) of the 1H NMR spectra showed a clear discrimination between those samples by principal component 1 (PC1) and principal component 3 (PC3) in cannabinoid fraction. The loading plot of PC value obtained from all 1)H NMR signals shows that Delta9-tetrahydrocannabinolic acid (THCA) and cannabidiolic acid (CBDA) are important metabolites to differentiate the cultivars from each other. The discrimination of the cultivars could also be obtained from a water extract containing carbohydrates and amino acids. The level of sucrose, glucose, asparagine, and glutamic acid are found to be major discriminating metabolites of these cultivars. This method allows an efficient differentiation between cannabis cultivars without any prepurification steps. PMID:15217272

  1. 33S NMR spectroscopy 3. Substituent effects on 33S NMR parameters in 2-substituted ethanesulfonates.

    PubMed

    Musio, Roberta; Sciacovelli, Oronzo

    2006-08-01

    33S NMR parameters (chemical shifts and linewidths) in 2-substituted sodium ethanesulfonates, XCH2CH2SO3Na (X = H, CH3, OH, SH, NH2, Cl, Br, NH3+) depend upon the electronic properties of substituents. To explain experimental results and obtain additional information on the origin of the observed substituent effect (SE), sulfur isotropic absolute shielding constants have been calculated at DFT level of theory (B3LYP/6-311++G(2d,p)) by gauge-including atomic orbitals (GIAO) method. Data have been interpreted with the aid of natural bond orbital (NBO) method and natural chemical shielding (NCS) analysis. It has been demonstrated that in the class of compounds considered the diamagnetic contribution to sulfur-shielding constant is constant and the observed upfield shift of 33S resonance induced by electron-withdrawing substituents (reverse chemical shift effect) can be related to variations of the paramagnetic contribution. Substituents with different electronic properties cause variations in the polarization of S-C and S-O bonds of the -C-SO3- moiety thus determining changes of the electron density at sulfur nucleus and consequently the expansion or contraction of 3p sulfur orbitals. Also oxygen lone-pairs and sulfur core 2p electrons can play an active role in determining the paramagnetic contribution to sulfur shielding. With regard to linewidth variations, they can be ascribed primarily to changes in the nuclear quadrupole coupling constant values. B3LYP/6-311++G(2d,p) method allows obtaining a good reproducibility of SE on the electric field gradient (EFG) at sulfur, although its values tend to be underestimated significantly. Moreover, 17O shielding constants have been calculated. PMID:16741982

  2. In situ solid-state NMR spectroscopy of electrochemical cells: batteries, supercapacitors, and fuel cells.

    PubMed

    Blanc, Frédéric; Leskes, Michal; Grey, Clare P

    2013-09-17

    Electrochemical cells, in the form of batteries (or supercapacitors) and fuel cells, are efficient devices for energy storage and conversion. These devices show considerable promise for use in portable and static devices to power electronics and various modes of transport and to produce and store electricity both locally and on the grid. For example, high power and energy density lithium-ion batteries are being developed for use in hybrid electric vehicles where they improve the efficiency of fuel use and help to reduce greenhouse gas emissions. To gain insight into the chemical reactions involving the multiple components (electrodes, electrolytes, interfaces) in the electrochemical cells and to determine how cells operate and how they fail, researchers ideally should employ techniques that allow real-time characterization of the behavior of the cells under operating conditions. This Account reviews the recent use of in situ solid-state NMR spectroscopy, a technique that probes local structure and dynamics, to study these devices. In situ NMR studies of lithium-ion batteries are performed on the entire battery, by using a coin cell design, a flat sealed plastic bag, or a cylindrical cell. The battery is placed inside the NMR coil, leads are connected to a potentiostat, and the NMR spectra are recorded as a function of state of charge. (7)Li is used for many of these experiments because of its high sensitivity, straightforward spectral interpretation, and relevance to these devices. For example, (7)Li spectroscopy was used to detect intermediates formed during electrochemical cycling such as LixC and LiySiz species in batteries with carbon and silicon anodes, respectively. It was also used to observe and quantify the formation and growth of metallic lithium microstructures, which can cause short circuits and battery failure. This approach can be utilized to identify conditions that promote dendrite formation and whether different electrolytes and additives can help

  3. HRMAS-NMR spectroscopy and multivariate analysis meat characterisation.

    PubMed

    Ritota, Mena; Casciani, Lorena; Failla, Sebastiana; Valentini, Massimiliano

    2012-12-01

    ¹H-High resolution magic angle spinning-nuclear magnetic resonance spectroscopy was employed to gain the metabolic profile of longissimus dorsi and semitendinosus muscles of four different breeds: Chianina, Holstein Friesian, Maremmana and Buffalo. Principal component analysis, partial least squares projection to latent structure - discriminant analysis and orthogonal partial least squares projection to latent structure - discriminant analysis were used to build models capable of discriminating the muscle type according to the breed. Data analysis led to an excellent classification for Buffalo and Chianina, while for Holstein Friesian the separation was lower. In the case of Maremmana the use of intelligent bucketing was necessary due to some resonances shifting allowed improvement of the discrimination ability. Finally, by using the Variable Importance in Projection values the metabolites relevant for the classification were identified. PMID:22819725

  4. Sensitivity-enhanced NMR reveals alterations in protein structure by cellular milieus.

    PubMed

    Frederick, Kendra K; Michaelis, Vladimir K; Corzilius, Björn; Ong, Ta-Chung; Jacavone, Angela C; Griffin, Robert G; Lindquist, Susan

    2015-10-22

    Biological processes occur in complex environments containing a myriad of potential interactors. Unfortunately, limitations on the sensitivity of biophysical techniques normally restrict structural investigations to purified systems, at concentrations that are orders of magnitude above endogenous levels. Dynamic nuclear polarization (DNP) can dramatically enhance the sensitivity of nuclear magnetic resonance (NMR) spectroscopy and enable structural studies in biologically complex environments. Here, we applied DNP NMR to investigate the structure of a protein containing both an environmentally sensitive folding pathway and an intrinsically disordered region, the yeast prion protein Sup35. We added an exogenously prepared isotopically labeled protein to deuterated lysates, rendering the biological environment "invisible" and enabling highly efficient polarization transfer for DNP. In this environment, structural changes occurred in a region known to influence biological activity but intrinsically disordered in purified samples. Thus, DNP makes structural studies of proteins at endogenous levels in biological contexts possible, and such contexts can influence protein structure. PMID:26456111

  5. Investigating brain metabolism at high fields using localized 13C NMR spectroscopy without 1H decoupling.

    PubMed

    Deelchand, Dinesh Kumar; Uğurbil, Kâmil; Henry, Pierre-Gilles

    2006-02-01

    Most in vivo 13C NMR spectroscopy studies in the brain have been performed using 1H decoupling during acquisition. Decoupling imposes significant constraints on the experimental setup (particularly for human studies at high magnetic field) in order to stay within safety limits for power deposition. We show here that incorporation of the 13C label from 13C-labeled glucose into brain amino acids can be monitored accurately using localized 13C NMR spectroscopy without the application of 1H decoupling. Using LCModel quantification with prior knowledge of one-bond and multiple-bond J(CH) coupling constants, the uncertainty on metabolites concentrations was only 35% to 91% higher (depending on the carbon resonance of interest) in undecoupled spectra compared to decoupled spectra in the rat brain at 9.4 Tesla. Although less sensitive, 13C NMR without decoupling dramatically reduces experimental constraints on coil setup and pulse sequence design required to keep power deposition within safety guidelines. This opens the prospect of safely measuring 13C NMR spectra in humans at varied brain locations (not only the occipital lobe) and at very high magnetic fields above 4 Tesla. PMID:16345037

  6. Characterisation of oxygen permeation into a microfluidic device for cell culture by in situ NMR spectroscopy.

    PubMed

    Yilmaz, Ali; Utz, Marcel

    2016-05-24

    A compact microfluidic device for perfusion culture of mammalian cells under in situ metabolomic observation by NMR spectroscopy is presented. The chip is made from poly(methyl methacrylate) (PMMA), and uses a poly(dimethyl siloxane) (PDMS) membrane to allow gas exchange. It is integrated with a generic micro-NMR detector developed recently by our group [J. Magn. Reson., 2016, 262, 73-80]. While PMMA is an excellent material in the context of NMR, PDMS is known to produce strong background signals. To mitigate this, the device keeps the PDMS away from the detection area. The oxygen permeation into the device is quantified using a flow chemistry approach. A solution of glucose is mixed on the chip with a solution of glucose oxidase, before flowing through the gas exchanger. The resulting concentration of gluconate is measured by (1)H NMR spectroscopy as a function of flow rate. An oxygen equilibration rate constant of 2.4 s(-1) is found for the device, which is easily sufficient to maintain normoxic conditions in a cell culture at low perfusion flow rates. PMID:27149932

  7. Differentiating and characterizing geminal silanols in silicas by (29)Si NMR spectroscopy.

    PubMed

    Murray, David K

    2010-12-01

    Single and geminal hydroxyl species in silicas have been characterized using solid-state (29)Si NMR spectroscopy. Differentiating hydroxyl types is important in understanding their roles in chemical toxicity mechanisms for inhaled crystalline silicas responsible for silicosis. (1)H-(29)Si cross polarization NMR spectroscopy has been employed to obtain (29)Si NMR chemical shift data and signal accrual and relaxation characteristics. Spectral deconvolution is used to examine relative single and geminal hydroxyl resonance areas for a series of representative silicas and silica gels. Silicon-containing materials examined include 1878a quartz, and 1879a cristobalite from the National Institute for Science and Technology, kaolin, and several widely used respirable silicas and silica gels. Geminal hydroxyls were observed in every case, with relative resonance areas accounting for 21-65% of total hydroxyl signals. Factors affecting relative areas measured as a function of contact time, relaxation, and surface area are discussed. Subsequent (29)Si and (31)P NMR studies of a silica coated with various sodium hydrogen phosphates show preferential single silanol-phosphate interaction for basic phosphates, and oligomerization products for acidic phosphates. Geminal hydroxyl resonance areas displayed significant error (4-17%) for low surface area silicas, limiting this method to studies exhibiting major changes in chemical or spectroscopic properties. PMID:20825948

  8. Structural characterization of selenosubtilisin by sup 77 Se-NMR spectroscopy

    SciTech Connect

    House, K.L.; Dunlap, R.B.; Odom, J.D.; Wu, Z.P.; Hilvert. D. Research Inst. of Scripps Clinic, La Jolla, CA )

    1991-03-15

    Selenosubtilisin is an artificial enzyme containing an active site selenocysteine residue. In this environment the selenium atom is a valuable probe of structure-function relationships and also confers novel redox and hydrolytic properties to the original protease template. The authors have used {sup 77}Se NMR spectroscopy to characterize different oxidation states of {sup 77}Se isotopically enriched selenosubtilisin. The oxidized form of the enzyme exhibits a {sup 77}Se resonance at 1,189 ppm. This is in good agreement with the {sup 77}Se chemical shifts for model seleninic acids, confirming that the prosthetic group is in the seleninic acid oxidation state. On treatment of the oxidized enzyme with three equivalents of 3-carboxy-4-nitrobenzenethiol at pH 5.0, they observe the enzyme bound selenenyl sulfide at 388.5 ppm. This work demonstrates the utility of {sup 77}Se NMR spectroscopy for examining structure-function relationships of selenium containing proteins.

  9. Analysis and aging of unsaturated polyester resins in contemporary art installations by NMR spectroscopy.

    PubMed

    Stamatakis, Georgios; Knuutinen, Ulla; Laitinen, Kai; Spyros, Apostolos

    2010-12-01

    Two original art installations constructed from unsaturated polyester resins (UPR) and four different reference UPR products (before and after UVB aging) were analyzed by high-resolution 1D and 2D nuclear magnetic resonance (NMR) spectroscopy. Breaking strain studies were also conducted for the four UPR model products before and after different aging procedures (moisture, UVB exposure, melt/freeze). NMR analysis of the chemical composition of the UPR resin extracts showed they contain several low MW organic compounds and oligomers rich in polar -OH groups that play a significant role in the degradation behavior of the composite UPR materials. Statistical analysis of the NMR compositional data showed that styrene and benzaldehyde contents can be used to differentiate between fresh and aged UPR samples. The phthalate and propylene glycol unit speciation (esterified, primary or secondary -OH) of the extracts provided evidence that UPR resin C was used in the construction of the two art installations, and direct comparison of (1)H and (13)C NMR spectra verified this compositional similarity. UPR resin C was shown by both NMR and breaking strain studies to be the reference UPR most susceptible to degradation by different aging procedures, a characteristic attributed to the lower styrene content of resin C. PMID:20922516

  10. Monitoring the Electrochemical Processes in the Lithium-Air Battery by Solid State NMR Spectroscopy.

    PubMed

    Leskes, Michal; Moore, Amy J; Goward, Gillian R; Grey, Clare P

    2013-12-27

    A multi-nuclear solid-state NMR approach is employed to investigate the lithium-air battery, to monitor the evolution of the electrochemical products formed during cycling, and to gain insight into processes affecting capacity fading. While lithium peroxide is identified by (17)O solid state NMR (ssNMR) as the predominant product in the first discharge in 1,2-dimethoxyethane (DME) based electrolytes, it reacts with the carbon cathode surface to form carbonate during the charging process. (13)C ssNMR provides evidence for carbonate formation on the surface of the carbon cathode, the carbonate being removed at high charging voltages in the first cycle, but accumulating in later cycles. Small amounts of lithium hydroxide and formate are also detected in discharged cathodes and while the hydroxide formation is reversible, the formate persists and accumulates in the cathode upon further cycling. The results indicate that the rechargeability of the battery is limited by both the electrolyte and the carbon cathode stability. The utility of ssNMR spectroscopy in directly detecting product formation and decomposition within the battery is demonstrated, a necessary step in the assessment of new electrolytes, catalysts, and cathode materials for the development of a viable lithium-oxygen battery. PMID:24489976

  11. Monitoring the Electrochemical Processes in the Lithium–Air Battery by Solid State NMR Spectroscopy

    PubMed Central

    2013-01-01

    A multi-nuclear solid-state NMR approach is employed to investigate the lithium–air battery, to monitor the evolution of the electrochemical products formed during cycling, and to gain insight into processes affecting capacity fading. While lithium peroxide is identified by 17O solid state NMR (ssNMR) as the predominant product in the first discharge in 1,2-dimethoxyethane (DME) based electrolytes, it reacts with the carbon cathode surface to form carbonate during the charging process. 13C ssNMR provides evidence for carbonate formation on the surface of the carbon cathode, the carbonate being removed at high charging voltages in the first cycle, but accumulating in later cycles. Small amounts of lithium hydroxide and formate are also detected in discharged cathodes and while the hydroxide formation is reversible, the formate persists and accumulates in the cathode upon further cycling. The results indicate that the rechargeability of the battery is limited by both the electrolyte and the carbon cathode stability. The utility of ssNMR spectroscopy in directly detecting product formation and decomposition within the battery is demonstrated, a necessary step in the assessment of new electrolytes, catalysts, and cathode materials for the development of a viable lithium–oxygen battery. PMID:24489976

  12. Solid-state proton multiple-quantum NMR spectroscopy with fast magic angle spinning

    NASA Astrophysics Data System (ADS)

    Geen, Helen; Titman, Jeremy J.; Gottwald, Johannes; Spiess, Hans W.

    1994-09-01

    The feasibility of multiple-quantum NMR spectroscopy with high resolution for protons in solids is explored. A new multiple-quantum excitation sequence suitable for use with fast magic angle spinning is described, and its performance is compared to that of both static and slow-spinning multiple-quantum methods. Modified sequences with scale the rate of development of the multiple-quantum coherences are also demonstrated, and two-dimensional double-quantum spectra of adamantane and polycarbonate are presented.

  13. Gyrotron FU CW VII for 300 MHz and 600 MHz DNP-NMR Spectroscopy

    NASA Astrophysics Data System (ADS)

    Idehara, Toshitaka; Kosuga, Kosuke; Agusu, La; Ogawa, Isamu; Takahashi, Hiroki; Smith, Mark E.; Dupree, Ray

    2010-07-01

    Gyrotron FU CW VII, one of the FU CW Series Gyrotrons, has been designed, constructed and completed operational tests successfully in the Research Center for Development of Far Infrared Region, University of Fukui (FIR FU). The gyrotron operates at around 200 GHz for the fundamental cyclotron resonances and at around 400 GHz for the second harmonics. These radiation frequencies will be applied to 300 MHz and 600 MHz DNP enhanced NMR spectroscopy.

  14. Highly resolved in vivo 1H NMR spectroscopy of the mouse brain at 9.4 T.

    PubMed

    Tkác, Ivan; Henry, Pierre-Gilles; Andersen, Peter; Keene, C Dirk; Low, Walter C; Gruetter, Rolf

    2004-09-01

    An efficient shim system and an optimized localization sequence were used to measure in vivo 1H NMR spectra from cerebral cortex, hippocampus, striatum, and cerebellum of C57BL/6 mice at 9.4 T. The combination of automatic first- and second-order shimming (FASTMAP) with strong custom-designed second-order shim coils (shim strength up to 0.04 mT/cm2) was crucial to achieve high spectral resolution (water line width of 11-14 Hz). Requirements for second-order shim strengths to compensate field inhomogeneities in the mouse brain at 9.4 T were assessed. The achieved spectral quality (resolution, S/N, water suppression, localization performance) allowed reliable quantification of 16 brain metabolites (LCModel analysis) from 5-10-microL brain volumes. Significant regional differences (up to 2-fold, P < 0.05) were found for all quantified metabolites but Asp, Glc, and Gln. In contrast, 1H NMR spectra measured from the striatum of C57BL/6, CBA, and CBA/BL6 mice revealed only small (<13%, P < 0.05) interstrain differences in Gln, Glu, Ins, Lac, NAAG, and PE. It is concluded that 1H NMR spectroscopy at 9.4 T can provide precise biochemical information from distinct regions of the mouse brain noninvasively that can be used for monitoring of disease progression and treatment as well as phenotyping in transgenic mice models. PMID:15334565

  15. 1H to 13C Energy Transfer in Solid State NMR Spectroscopy of Natural Organic Systems

    NASA Astrophysics Data System (ADS)

    Berns, Anne E.; Conte, Pellegrino

    2010-05-01

    Cross polarization (CP) magic angle spinning (MAS) 13C-NMR spectroscopy is a solid state NMR technique widely used to study chemical composition of organic materials with low or no solubility in the common deuterated solvents used to run liquid state NMR experiments. Based on the magnetization transfer from abundant nuclei (with spin of 1 -2) having a high gyromagnetic ratio (γ), such as protons, to the less abundant 13C nuclei with low γ values, 13C-CPMAS NMR spectroscopy is often applied in environmental chemistry to obtain quantitative information on the chemical composition of natural organic matter (NOM) (Conte et al., 2004), although its quantitative assessment is still matter of heavy debates. Many authors (Baldock et al., 1997; Conte et al., 1997, 2002; Dria et al., 2002; Kiem et al., 2000; Kögel-Knabner, 2000; Preston, 2001), reported that the application of appropriate instrument setup as well as the use of special pulse sequences and correct spectra elaboration may provide signal intensities that are directly proportional to the amount of nuclei creating a NMR signal. However, many other papers dealt with the quantitative unsuitability of 13C-CPMAS NMR spectroscopy. Among those, Mao et al. (2000), Smernik and Oades (2000 a,b), and Preston (2001) reported that cross-polarized NMR techniques may fail in a complete excitation of the 13C nuclei. In fact, the amount of observable carbons via 13C-CPMAS NMR spectroscopy appeared, in many cases, lower than that measured by a direct observation of the 13C nuclei. As a consequence, cross-polarized NMR techniques may provide spectra where signal distribution may not be representative of the quantitative distribution of the different natural organic matter components. Cross-polarization is obtained after application of an initial 90° x pulse on protons and a further spin lock pulse (along the y axis) having a fixed length (contact time) for both nuclei (1H and 13C) once the Hartmann-Hahn condition is matched

  16. Primary structure determination of five sialylated oligosaccharides derived from bronchial mucus glycoproteins of patients suffering from cystic fibrosis. The occurrence of the NeuAc alpha(2----3)Gal beta(1----4)[Fuc alpha(1----3)] GlcNAc beta(1----.) structural element revealed by 500-MHz 1H NMR spectroscopy.

    PubMed

    Lamblin, G; Boersma, A; Klein, A; Roussel, P; van Halbeek, H; Vliegenthart, J F

    1984-07-25

    The structure of sialylated carbohydrate units of bronchial mucins obtained from cystic fibrosis patients was investigated by 500-MHz 1H NMR spectroscopy in conjunction with sugar analysis. After subjecting the mucins to alkaline borohydride degradation, sialylated oligosaccharide-alditols were isolated by anion-exchange chromatography and fractionated by high performance liquid chromatography. Five compounds could be obtained in a rather pure state; their structures were established as the following: A-1, NeuAc alpha(2----3)Gal beta(1----4) [Fuc alpha(1----3)]GlcNAc beta(1----3)Gal-NAc-ol; A-2, NeuAc alpha(2----3)Gal beta(1----4)GlcNAc beta(1----6)-[GlcNAc beta (1----3)]GalNAc-o1; A-3, NeuAc alpha(2----3)Gal beta-(1----4)[Fuc alpha(1----3)]GlcNAc beta(1----3)Gal beta(1----3) GalNAc-o1; A-4, NeuAc alpha(2----3)Gal beta(1----4)[Fuc alpha(1----3)]Glc-NAc NAc beta(1----6)[GlcNAc beta(1----3)]GalNAc-o1; A-6,NeuAc alpha-(2----3) Gal beta(1----4)[Fuc alpha(1----3)]GlcNAc beta(1----6)[Gal beta-(1----4) GlcNAc beta(1----3)]GalNAc-o1. The simultaneous presence of sialic acid in alpha(2----3)-linkage to Gal and fucose in alpha(1----3)-linkage to GlcNAc of the same N-acetyllactosamine unit could be adequately proved by high resolution 1H NMR spectroscopy. This sequence constitutes a novel structural element for mucins. PMID:6746638

  17. Single-shot diffusion trace (1)H NMR spectroscopy.

    PubMed

    de Graaf, R A; Braun, K P; Nicolay, K

    2001-05-01

    Ignoring diffusion anisotropy can severely hamper the quantitative determination of water and metabolite diffusion in complex tissues. The measurement of the trace of the diffusion tensor provides unambiguous and rotationally invariant ADC values, but usually requires three separate experiments. A single-shot technique developed earlier, originally designed for diffusion trace MR imaging (Mori and van Zijl, Magn Reson Med 1995;33:41-52), was improved and adapted for diffusion trace MR spectroscopy. A double spin-echo pulse sequence was incorporated with four pairs of bipolar gradients with specific predetermined relative signs in each of the three orthogonal directions. The combination of gradient directions leads to cancellation of all off-diagonal tensor elements while constructively adding the diagonal elements. Furthermore, the pulse scheme provides complete compensation for cross-terms between static magnetic field gradients and the applied diffusion gradients, while simultaneously avoiding cross-terms with localization gradients. The sequence was tested at 4.7 T in vivo on rat brain for MRI and on rat skeletal muscle and brain for MRS. It is shown that the average ADC as determined from the measurement of the ADCs in the three orthogonal directions is in close agreement with the ADC obtained along the trace of the diffusion tensor in a single acquisition, for both water and metabolite diffusion. The large differences in water and metabolite diffusion coefficients as measured in the individual orthogonal directions illustrate the need for diffusion trace measurements when accurate and rotationally invariant diffusion quantitation is required. The pulse scheme presented here may be applied for such purposes in MRS and MRI studies. PMID:11323799

  18. Methodology of 1H NMR Spectroscopy of the Human Brain at Very High Magnetic Fields

    PubMed Central

    Tkáč, I.; Gruetter, R.

    2009-01-01

    An ultrashort-echo-time stimulated echo-acquisition mode (STEAM) pulse sequence with interleaved outer volume suppression and VAPOR (variable power and optimized relaxation delays) water suppression was redesigned and optimized for human applications at 4 and 7 T, taking into account the specific requirements for spectroscopy at high magnetic fields and limitations of currently available hardware. In combination with automatic shimming, automated parameter adjustments and data processing, this method provided a user-friendly tool for routine 1H nuclear magnetic resonance (NMR) spectroscopy of the human brain at very high magnetic fields. Effects of first- and second-order shimming, single-scan averaging, frequency and phase corrections, and eddy currents were described. LCModel analysis of an in vivo 1H NMR spectrum measured from the human brain at 7 T allowed reliable quantification of more than fifteen metabolites noninvasively, illustrating the potential of high-field NMR spectroscopy. Examples of spectroscopic studies performed at 4 and 7 T demonstrated the high reproducibility of acquired spectra quality. PMID:20179773

  19. INVESTIGATION INTO HOW WOOD CELL WALLS INTERACT WITH SYNTHETIC ADHESIVES USING HIGH-RESOLUTION SOLUTION-STATE NMR SPECTROSCOPY

    Technology Transfer Automated Retrieval System (TEKTRAN)

    With the continued growth of the wood adhesive industry and the need to create durable and environmentally friendly adhesive systems, it is still unclear whether covalent bonds contribute to wood adhesive bond strength. In order to investigate this question, solid-state NMR spectroscopy (NMR) has be...

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

    PubMed Central

    Polenova, Tatyana; Gupta, Rupal; Goldbourt, Amir

    2016-01-01

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

  1. NMR-spectroscopic screening of spider venom reveals sulfated nucleosides as major components for the brown recluse and related species.

    PubMed

    Schroeder, Frank C; Taggi, Andrew E; Gronquist, Matthew; Malik, Rabia U; Grant, Jacqualine B; Eisner, Thomas; Meinwald, Jerrold

    2008-09-23

    Extensive chemical analyses of spider venoms from many species have revealed complex mixtures of biologically active compounds, of which several have provided important leads for drug development. We have recently shown that NMR spectroscopy can be used advantageously for a direct structural characterization of the small-molecule content of such complex mixtures. Here, we report the application of this strategy to a larger-scale analysis of a collection of spider venoms representing >70 species, which, in combination with mass spectrometric analyses, allowed the identification of a wide range of known, and several previously undescribed, small molecules. These include polyamines, common neurotransmitters, and amino acid derivatives as well as two additional members of a recently discovered family of natural products, the sulfated nucleosides. In the case of the well studied brown recluse spider, Loxosceles reclusa, sulfated guanosine derivatives were found to comprise the major small-molecule components of the venom. PMID:18794518

  2. NMR-spectroscopic screening of spider venom reveals sulfated nucleosides as major components for the brown recluse and related species

    PubMed Central

    Schroeder, Frank C.; Taggi, Andrew E.; Gronquist, Matthew; Malik, Rabia U.; Grant, Jacqualine B.; Eisner, Thomas; Meinwald, Jerrold

    2008-01-01

    Extensive chemical analyses of spider venoms from many species have revealed complex mixtures of biologically active compounds, of which several have provided important leads for drug development. We have recently shown that NMR spectroscopy can be used advantageously for a direct structural characterization of the small-molecule content of such complex mixtures. Here, we report the application of this strategy to a larger-scale analysis of a collection of spider venoms representing >70 species, which, in combination with mass spectrometric analyses, allowed the identification of a wide range of known, and several previously undescribed, small molecules. These include polyamines, common neurotransmitters, and amino acid derivatives as well as two additional members of a recently discovered family of natural products, the sulfated nucleosides. In the case of the well studied brown recluse spider, Loxosceles reclusa, sulfated guanosine derivatives were found to comprise the major small-molecule components of the venom. PMID:18794518

  3. Characterization of bio-oil from hydrothermal liquefaction of organic waste by NMR spectroscopy and FTICR mass spectrometry.

    PubMed

    Leonardis, Irene; Chiaberge, Stefano; Fiorani, Tiziana; Spera, Silvia; Battistel, Ezio; Bosetti, Aldo; Cesti, Pietro; Reale, Samantha; De Angelis, Francesco

    2013-01-01

    Solid wastes of organic origins are potential feedstocks for the production of liquid biofuels, which could be suitable alternatives to fossil fuels for the transport and heating sectors, as well as for industrial use. By hydrothermal liquefaction, the wet biomass is partially transformed into a water-immiscible, oil-like organic matter called bio-oil. In this study, an integrated NMR spectroscopy/mass spectrometry approach has been developed for the characterization of the hydrothermal liquefaction of bio-oil at the molecular level. (1)H and (13)C NMR spectroscopy were used for the identification of functional groups and gauging the aromatic carbon content in the mixture. GC-MS analysis revealed that the volatile fraction was rich in fatty acids, as well as in amides and esters. High-resolution Fourier-transform ion cyclotron resonance mass spectrometry (FTICR-MS) has been applied in a systematic way to fully categorize the bio-oil in terms of different classes of components, according to their molecular formulas. Most importantly, for the first time, by using this technique, and for the liquefaction bio-oil characterization in particular, FT-MS data have been used to develop a methodology for the determination of the aromatic versus aliphatic carbon and nitrogen content. It is well known that, because they resist hydrogenation and represent sources of polluting species, both aromatic molecules and nitrogen-containing species raise concerns for subsequent upgrading of bio-oil into a diesel-like fuel. PMID:23139164

  4. Proton chemical shift tensors determined by 3D ultrafast MAS double-quantum NMR spectroscopy

    SciTech Connect

    Zhang, Rongchun; Mroue, Kamal H.; Ramamoorthy, Ayyalusamy

    2015-10-14

    Proton NMR spectroscopy in the solid state has recently attracted much attention owing to the significant enhancement in spectral resolution afforded by the remarkable advances in ultrafast magic angle spinning (MAS) capabilities. In particular, proton chemical shift anisotropy (CSA) has become an important tool for obtaining specific insights into inter/intra-molecular hydrogen bonding. However, even at the highest currently feasible spinning frequencies (110–120 kHz), {sup 1}H MAS NMR spectra of rigid solids still suffer from poor resolution and severe peak overlap caused by the strong {sup 1}H–{sup 1}H homonuclear dipolar couplings and narrow {sup 1}H chemical shift (CS) ranges, which render it difficult to determine the CSA of specific proton sites in the standard CSA/single-quantum (SQ) chemical shift correlation experiment. Herein, we propose a three-dimensional (3D) {sup 1}H double-quantum (DQ) chemical shift/CSA/SQ chemical shift correlation experiment to extract the CS tensors of proton sites whose signals are not well resolved along the single-quantum chemical shift dimension. As extracted from the 3D spectrum, the F1/F3 (DQ/SQ) projection provides valuable information about {sup 1}H–{sup 1}H proximities, which might also reveal the hydrogen-bonding connectivities. In addition, the F2/F3 (CSA/SQ) correlation spectrum, which is similar to the regular 2D CSA/SQ correlation experiment, yields chemical shift anisotropic line shapes at different isotropic chemical shifts. More importantly, since the F2/F1 (CSA/DQ) spectrum correlates the CSA with the DQ signal induced by two neighboring proton sites, the CSA spectrum sliced at a specific DQ chemical shift position contains the CSA information of two neighboring spins indicated by the DQ chemical shift. If these two spins have different CS tensors, both tensors can be extracted by numerical fitting. We believe that this robust and elegant single-channel proton-based 3D experiment provides useful atomistic

  5. 13C NMR spectroscopy of methane adsorbed in SAPO-11 molecular sieve

    NASA Astrophysics Data System (ADS)

    Koskela, Tuomas; Ylihautala, Mika; Vaara, Juha; Jokisaari, Jukka

    1996-10-01

    Static 13C and 13C-{ 1H} NMR spectra of carbon-13 enriched methane ( 13CH 4) adsorbed into SAPO-11 molecular sieve were recorded at variable temperatures. Moreover, the corresponding MAS NMR spectra were measured. These experiments reveal a temperature-dependent, anisotropic and asymmetric 13C nuclear shielding tensor. Ab initio model calculations of methane in the field of a positive point charge suggest that the deformation of the shielding tensor may be related to the interaction between the methane molecule and the charge-compensating protons. A comparison with existing Xe data is made.

  6. Toxin-induced conformational changes in a potassium channel revealed by solid-state NMR

    NASA Astrophysics Data System (ADS)

    Lange, Adam; Giller, Karin; Hornig, Sönke; Martin-Eauclaire, Marie-France; Pongs, Olaf; Becker, Stefan; Baldus, Marc

    2006-04-01

    The active site of potassium (K+) channels catalyses the transport of K+ ions across the plasma membrane-similar to the catalytic function of the active site of an enzyme-and is inhibited by toxins from scorpion venom. On the basis of the conserved structures of K+ pore regions and scorpion toxins, detailed structures for the K+ channel-scorpion toxin binding interface have been proposed. In these models and in previous solution-state nuclear magnetic resonance (NMR) studies using detergent-solubilized membrane proteins, scorpion toxins were docked to the extracellular entrance of the K+ channel pore assuming rigid, preformed binding sites. Using high-resolution solid-state NMR spectroscopy, here we show that high-affinity binding of the scorpion toxin kaliotoxin to a chimaeric K+ channel (KcsA-Kv1.3) is associated with significant structural rearrangements in both molecules. Our approach involves a combined analysis of chemical shifts and proton-proton distances and demonstrates that solid-state NMR is a sensitive method for analysing the structure of a membrane protein-inhibitor complex. We propose that structural flexibility of the K+ channel and the toxin represents an important determinant for the high specificity of toxin-K+ channel interactions.

  7. Identifying metabolites related to nitrogen mineralisation using 1H NMR spectroscopy

    NASA Astrophysics Data System (ADS)

    . T McDonald, Noeleen; Graham, Stewart; Watson, Catherine; Gordon, Alan; Lalor, Stan; Laughlin, Ronnie; Elliott, Chris; . P Wall, David

    2015-04-01

    Exploring new analysis techniques to enhance our knowledge of the various metabolites within our soil systems is imperative. Principally, this knowledge would allow us to link key metabolites with functional influences on critical nutrient processes, such as the nitrogen (N) mineralisation in soils. Currently there are few studies that utilize proton nuclear magnetic resonance spectroscopy (1H NMR) to characterize multiple metabolites within a soil sample. The aim of this research study was to examine the effectiveness of 1H NMR for isolating multiple metabolites that are related to the mineralizable N (MN) capacity across a range of 35 Irish grassland soils. Soils were measured for MN using the standard seven day anaerobic incubation (AI-7). Additionally, soils were also analysed for a range of physio-chemical properties [e.g. total N, total C, mineral N, texture and soil organic matter (SOM)]. Proton NMR analysis was carried on these soils by extracting with 40% methanol:water, lyophilizing and reconstituting in deuterium oxide and recording the NMR spectra on a 400MHz Bruker AVANCE III spectrometer. Once the NMR data were spectrally processed and analysed using multivariate statistical analysis, seven metabolites were identified as having significant relationships with MN (glucose, trimethylamine, glutamic acid, serine, aspartic acid, 4-aminohippuirc acid and citric acid). Following quantification, glucose was shown to explain the largest percentage variability in MN (72%). These outcomes suggest that sources of labile carbon are essential in regulating N mineralisation and the capacity of plant available N derived from SOM-N pools in these soils. Although, smaller in concentration, the amino acids; 4-aminohippuirc acid, glutamic acid and serine also significantly (P<0.05) explained 43%, 27% and 19% of the variability in MN, respectively. This novel study highlights the effectiveness of using 1H NMR as a practical approach to profile multiple metabolites in

  8. Phospho-selective mechanisms of arrestin conformations and functions revealed by unnatural amino acid incorporation and 19F-NMR

    PubMed Central

    Yang, Fan; Yu, Xiao; Liu, Chuan; Qu, Chang-Xiu; Gong, Zheng; Liu, Hong-Da; Li, Fa-Hui; Wang, Hong-Mei; He, Dong-Fang; Yi, Fan; Song, Chen; Tian, Chang-Lin; Xiao, Kun-Hong; Wang, Jiang-Yun; Sun, Jin-Peng

    2015-01-01

    Specific arrestin conformations are coupled to distinct downstream effectors, which underlie the functions of many G-protein-coupled receptors (GPCRs). Here, using unnatural amino acid incorporation and fluorine-19 nuclear magnetic resonance (19F-NMR) spectroscopy, we demonstrate that distinct receptor phospho-barcodes are translated to specific β-arrestin-1 conformations and direct selective signalling. With its phosphate-binding concave surface, β-arrestin-1 ‘reads' the message in the receptor phospho-C-tails and distinct phospho-interaction patterns are revealed by 19F-NMR. Whereas all functional phosphopeptides interact with a common phosphate binding site and induce the movements of finger and middle loops, different phospho-interaction patterns induce distinct structural states of β-arrestin-1 that are coupled to distinct arrestin functions. Only clathrin recognizes and stabilizes GRK2-specific β-arrestin-1 conformations. The identified receptor-phospho-selective mechanism for arrestin conformation and the spacing of the multiple phosphate-binding sites in the arrestin enable arrestin to recognize plethora phosphorylation states of numerous GPCRs, contributing to the functional diversity of receptors. PMID:26347956

  9. Distinguishing Phosphate Structural Defects From Inclusions in Calcite and Aragonite by NMR Spectroscopy (Invited)

    NASA Astrophysics Data System (ADS)

    Phillips, B. L.; Mason, H. E.

    2010-12-01

    Variations in the concentration of minor and trace elements are being studied extensively for potential use as proxies to infer environmental conditions at the time of mineral deposition. Such proxies rely fundamentally on a relationship between the activities in the solution and in the solid that would seem to be simple only in the case that the species substitutes into the mineral structure. Other incorporation mechanisms are possible, including inclusions (both mineral and fluid) and occlusion of surface adsorbate complexes, that might be sensitive to other factors, such as crystallization kinetics, and difficult to distinguish analytically. For example, it is known from mineral adsorption studies that surface precipitates can be nanoscopic, and might not be apparent at resolutions typical of microchemical analysis. Techniques by which a structural relationship between the substituting element and the host mineral structure are needed to provide a sound basis for geochemical proxies. NMR spectroscopy offers methods for probing such spatial relationship. We are using solid-state NMR spectroscopy to investigate phosphate incorporation in calcium carbonate minerals, including calcite speleothems and coral skeletal aragonite, at concentrations of the order 100 μg P g -1. In 31P NMR spectra of most samples, narrow peaks arising from crystalline inclusions can be resolved, including apatite in coral aragonite and an unidentified phase in calcite. All samples studied yield also a broad 31P signal, centered near chemical shifts of +3 to +4 ppm, that could be assigned to phosphate defects in the host mineral and from which the fraction of P occurring in the carbonate mineral structure can be determined. To test this assignment we applied rotational-echo double-resonance (REDOR) NMR techniques that probe the molecular-scale proximity of carbonate groups to the phosphate responsible for the broad 31P peak. This method measures dipole-dipole coupling between 31P of

  10. NMR based metabolomics reveals acute hippocampal metabolic fluctuations during cranial irradiation in murine model.

    PubMed

    Rana, Poonam; Gupta, Mamta; Khan, Ahmad Raza; Hemanth Kumar, B S; Roy, Raja; Khushu, Subash

    2014-07-01

    Cranial irradiation is widely used as a treatment modality or prophylactic treatment in cancer patients, but it is frequently related to neurocognitive impairment in cancer survivors. Though most of radiation-induced changes occur during early and late delayed phase of radiation sickness, recent reports have supported the evidence of impaired neurogenesis within 24-48 h of radiation exposure that may implicate changes in acute phase as well. Inspection of these acute changes could be considered important as they may have long lasting effect on cognitive development and functions. In the present study, (1)H NMR spectroscopy based metabolomic approach was used to obtain comprehensive information of hippocampus metabolic physiology during acute phase of radiation sickness in a mouse model for single dose 8 Gy cranial irradiation. The analysis demonstrated reduced metabolic activity in irradiated animals compared to controls, typically evident in citric acid cycle intermediates, glutamine/glutamate and ketone bodies metabolism thus providing strong indication that the hippocampus is metabolically responsive to radiation exposure. The data suggested reduced glucose utilization, altered intermediary and neurotransmitter metabolism in hippocampus tissue extract. To the best of our knowledge this is the first metabolomic study to document cranial irradiation induced acute metabolic changes using in vitro(1)H NMR spectroscopy. PMID:24787771

  11. In vivo NMR metabolic profiling of Fabrea salina reveals sequential defense mechanisms against ultraviolet radiation.

    PubMed

    Marangoni, Roberto; Paris, Debora; Melck, Dominique; Fulgentini, Lorenzo; Colombetti, Giuliano; Motta, Andrea

    2011-01-01

    Fabrea salina is a hypersaline ciliate that is known to be among the strongest ultraviolet (UV)-resistant microorganisms; however, the molecular mechanisms of this resistance are almost unknown. By means of in vivo NMR spectroscopy, we determined the metabolic profile of living F. salina cells exposed to visible light and to polychromatic UV-B + UV-A + Vis radiation for several different exposure times. We used unsupervised pattern-recognition analysis to compare these profiles and discovered some metabolites whose concentration changed specifically upon UV exposure and in a dose-dependent manner. This variation was interpreted in terms of a two-phase cell reaction involving at least two different pathways: an early response consisting of degradation processes, followed by a late response activating osmoprotection mechanisms. The first step alters the concentration of formate, acetate, and saturated fatty-acid metabolites, whereas the osmoprotection modifies the activity of betaine moieties and other functionally related metabolites. In the latter pathway, alanine, proline, and sugars suggest a possible incipient protein synthesis as defense and/or degeneration mechanisms. We conclude that NMR spectroscopy on in vivo cells is an optimal approach for investigating the effect of UV-induced stress on the whole metabolome of F. salina because it minimizes the invasiveness of the measurement. PMID:21190674

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

    PubMed

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

    2009-01-01

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

  13. NMR spectroscopy as a tool to close the gap on metabolite characterization under MIST.

    PubMed

    Caceres-Cortes, Janet; Reily, Michael D

    2010-07-01

    Withdrawals from the market due to unforeseen adverse events have triggered changes in the way therapeutics are discovered and developed. This has resulted in an emphasis on truly understanding the efficacy and toxicity profile of new chemical entities (NCE) and the contributions of their metabolites to on-target pharmacology and off-target receptor-mediated toxicology. Members of the pharmaceutical industry, scientific community and regulatory agencies have held dialogues with respect to metabolites in safety testing (MIST); and both the US FDA and International Conference on Harmonisation have issued guidances with respect to when and how to characterize metabolites for human safety testing. This review provides a brief overview of NMR spectroscopy as applied to the structure elucidation and quantification of drug metabolites within the drug discovery and development process. It covers advances in this technique, including cryogenic cooling of detection circuitry for enhanced sensitivity, hyphenated LC-NMR techniques, improved dynamic range through new solvent-suppression pulse sequences and quantitation. These applications add to the already diverse NMR toolkit and further anchor NMR as a technique that is directly applicable to meeting the requirements of MIST guidelines. PMID:21083239

  14. Survey and qualification of internal standards for quantification by 1H NMR spectroscopy.

    PubMed

    Rundlöf, Torgny; Mathiasson, Marie; Bekiroglu, Somer; Hakkarainen, Birgit; Bowden, Tim; Arvidsson, Torbjörn

    2010-09-01

    In quantitative NMR (qNMR) selection of an appropriate internal standard proves to be crucial. In this study, 25 candidate compounds considered to be potent internal standards were investigated with respect to the ability of providing unique signal chemical shifts, purity, solubility, and ease of use. The (1)H chemical shift (delta) values, assignments, multiplicities and number of protons (for each signal), appropriateness (as to be used as internal standards) in four different deuterated solvents (D(2)O, DMSO-d(6), CD(3)OD, CDCl(3)) were studied. Taking into account the properties of these 25 internal standards, the most versatile eight compounds (2,4,6-triiodophenol, 1,3,5-trichloro-2-nitrobenzene, 3,4,5-trichloropyridine, dimethyl terephthalate, 1,4-dinitrobenzene, 2,3,5-triiodobenzoic acid, maleic acid and fumaric acid) were qualified using both differential scanning calorimetry (DSC) and NMR spectroscopy employing highly pure acetanilide as the reference standard. The data from these two methods were compared as well as utilized in the quality assessment of the compounds as internal standards. Finally, the selected internal standards were tested and evaluated in a real case of quantitative NMR analysis of a paracetamol pharmaceutical product. PMID:20207092

  15. Natural abundance 17O DNP two-dimensional and surface-enhanced NMR spectroscopy

    DOE PAGESBeta

    Perras, Frédéric A.; Kobayashi, Takeshi; Pruski, Marek

    2015-06-22

    Due to its extremely low natural abundance and quadrupolar nature, the 17O nuclide is very rarely used for spectroscopic investigation of solids by NMR without isotope enrichment. Additionally, the applicability of dynamic nuclear polarization (DNP), which leads to sensitivity enhancements of 2 orders of magnitude, to 17O is wrought with challenges due to the lack of spin diffusion and low polarization transfer efficiency from 1H. Here, we demonstrate new DNP-based measurements that extend 17O solid-state NMR beyond its current capabilities. The use of the PRESTO technique instead of conventional 1H–17O cross-polarization greatly improves the sensitivity and enables the facile measurementmore » of undistorted line shapes and two-dimensional 1H–17O HETCOR NMR spectra as well as accurate internuclear distance measurements at natural abundance. This was applied for distinguishing hydrogen-bonded and lone 17O sites on the surface of silica gel; the one-dimensional spectrum of which could not be used to extract such detail. As a result, this greatly enhanced sensitivity has enabled, for the first time, the detection of surface hydroxyl sites on mesoporous silica at natural abundance, thereby extending the concept of DNP surface-enhanced NMR spectroscopy to the 17O nuclide.« less

  16. Structure-Correlation NMR Spectroscopy for Macromolecules Using Repeated Bidirectional Photoisomerization of Azobenzene.

    PubMed

    Nagashima, Toshio; Ueda, Keisuke; Nishimura, Chiaki; Yamazaki, Toshio

    2015-11-17

    Control over macromolecular structure offers bright potentials for manipulation of macromolecular functions. We here present structure-correlation NMR spectroscopy to analyze the correlation between polymorphic macromolecular structures driven by photoisomerization of azobenzene. The structural conversion of azobenzene was induced within the mixing time of a NOESY experiment using a colored light source, and the reverse structural conversion was induced during the relaxation delay using a light source of another color. The correlation spectrum between trans- and cis-azobenzene was then obtained. To maximize the efficiency of the bidirectional photoisomerization of azobenzene-containing macromolecules, we developed a novel light-irradiation NMR sample tube and method for irradiating target molecules in an NMR radio frequency (rf) coil. When this sample tube was used for photoisomerization of an azobenzene derivative at a concentration of 0.2 mM, data collection with reasonable sensitivity applicable to macromolecules was achieved. We performed isomerization of an azobenzene-cross-linked peptide within the mixing time of a NOESY experiment that produced cross-peaks between helix and random-coil forms of the peptide. Thus, these results indicate that macromolecular structure manipulation can be incorporated into an NMR pulse sequence using an azobenzene derivative and irradiation with light of two types of wavelengths, providing a new method for structural analysis of metastable states of macromolecules. PMID:26479462

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

    NASA Astrophysics Data System (ADS)

    Knicker, Heike

    2016-04-01

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

  18. Hydrogenation of Carbon Dioxide Catalyzed by Ruthenium Trimethylphosphine Complexes: A Mechanistic Investigation using High-Pressure NMR Spectroscopy

    SciTech Connect

    Getty, April D.; Tai, Chih-Cheng; Linehan, John C.; Jessop, Philip G.; Olmstead, Marilyn M.; Rheingold, Arnold

    2009-08-26

    The previously reported complex, cis-(PMe3)4RuCl(OAc) (1) acts as a catalyst for CO2 hydrogenation into formic acid in the presence of a base and an alcohol co-catalyst. NMR spectroscopy has revealed that 1 exists in solution in equilibrium with fac-(PMe3)3RuCl(h2-OAc) (2), [(PMe3)4Ru(h2-OAc)]Cl (3a), and free PMe3. Complex 2 has been isolated and characterized by elemental analysis, NMR spectroscopy, and X-ray crystallography. 2 has been tested as a CO2 hydrogenation catalyst, however, it performed poorly under the conditions of catalysis used for 1. Complex 3a can be prepared by adding certain alcohols, such as MeOH, EtOH, or o-C6H5OH, to a solution of 1 in CDCl3. The chloride ion of 3a has been exchanged for the non-coordinating anions BPh4 or B(ArF )4 (B(ArF)4 = tetrakis(3,5-bis(trifluoromethyl)phenyl)borate) to produce [(PMe3)4Ru(h2-OAc)]BPh4 (3b) and [(PMe3)4Ru(h2-OAc)]B(ArF)4 (3c). Both of these complexes have been isolated and characterized by elemental analysis, NMR spectroscopy, and in the case of 3b, X-ray crystallography. Complexes 3b and 3c perform just as well as 1 for CO2 hydrogenation to formic acid in the presence of an alcohol co-catalyst; however, 3b,c perform equally well without the added alcohol. High-pressure NMR has been used to investigate the mechanism of CO2 hydrogenation via 3a,b in the presence of base. Two of the intermediates involved have been identified as cis-(PMe3)4RuH2 (5) and cis-(PMe3)4Ru(H)O2CH (6), and the role of the base includes not only trapping of the formic acid product, but also initiation of the catalysis by aiding the conversion of 3b,c to 5.

  19. Qualitative and Quantitative Control of Carbonated Cola Beverages Using 1H NMR Spectroscopy

    PubMed Central

    2012-01-01

    1H Nuclear magnetic resonance (NMR) spectroscopy (400 MHz) was used in the context of food surveillance to develop a reliable analytical tool to differentiate brands of cola beverages and to quantify selected constituents of the soft drinks. The preparation of the samples required only degassing and addition of 0.1% of TSP in D2O for locking and referencing followed by adjustment of pH to 4.5. The NMR spectra obtained can be considered as “fingerprints” and were analyzed by principal component analysis (PCA). Clusters from colas of the same brand were observed, and significant differences between premium and discount brands were found. The quantification of caffeine, acesulfame-K, aspartame, cyclamate, benzoate, hydroxymethylfurfural (HMF), sulfite ammonia caramel (E 150D), and vanillin was simultaneously possible using external calibration curves and applying TSP as internal standard. Limits of detection for caffeine, aspartame, acesulfame-K, and benzoate were 1.7, 3.5, 0.8, and 1.0 mg/L, respectively. Hence, NMR spectroscopy combined with chemometrics is an efficient tool for simultaneous identification of soft drinks and quantification of selected constituents. PMID:22356160

  20. 51V solid-state magic angle spinning NMR spectroscopy of vanadium chloroperoxidase.

    PubMed

    Pooransingh-Margolis, Neela; Renirie, Rokus; Hasan, Zulfiqar; Wever, Ron; Vega, Alexander J; Polenova, Tatyana

    2006-04-19

    We report 51V solid-state NMR spectroscopy of the 67.5-kDa vanadium chloroperoxidase, at 14.1 T. We demonstrate that, despite the low concentration of vanadium sites in the protein (one per molecule, 1 mumol of vanadium spins in the entire sample), the spinning sideband manifold spanning the central and the satellite transitions is readily detectable. The quadrupolar and chemical shift anisotropy tensors have been determined by numerical simulations of the spinning sideband envelopes and the line shapes of the individual spinning sidebands corresponding to the central transition. The observed quadrupolar coupling constant C(Q) of 10.5 +/- 1.5 MHz and chemical shift anisotropy delta(sigma) of -520 +/- 13 ppm are sensitive reporters of the geometric and electronic structure of the vanadium center. Density functional theory calculations of the NMR spectroscopic observables for an extensive series of active site models indicate that the vanadate cofactor is most likely anionic with one axial hydroxo- group and an equatorial plane consisting of one hydroxo- and two oxo- groups. The work reported in this manuscript is the first example of 51V solid-state NMR spectroscopy applied to probe the vanadium center in a protein directly. This approach yields the detailed coordination environment of the metal unavailable from other experimental measurements and is expected to be generally applicable for studies of diamagnetic vanadium sites in metalloproteins. PMID:16608356

  1. Qualitative and quantitative control of carbonated cola beverages using ¹H NMR spectroscopy.

    PubMed

    Maes, Pauline; Monakhova, Yulia B; Kuballa, Thomas; Reusch, Helmut; Lachenmeier, Dirk W

    2012-03-21

    ¹H Nuclear magnetic resonance (NMR) spectroscopy (400 MHz) was used in the context of food surveillance to develop a reliable analytical tool to differentiate brands of cola beverages and to quantify selected constituents of the soft drinks. The preparation of the samples required only degassing and addition of 0.1% of TSP in D₂O for locking and referencing followed by adjustment of pH to 4.5. The NMR spectra obtained can be considered as "fingerprints" and were analyzed by principal component analysis (PCA). Clusters from colas of the same brand were observed, and significant differences between premium and discount brands were found. The quantification of caffeine, acesulfame-K, aspartame, cyclamate, benzoate, hydroxymethylfurfural (HMF), sulfite ammonia caramel (E 150D), and vanillin was simultaneously possible using external calibration curves and applying TSP as internal standard. Limits of detection for caffeine, aspartame, acesulfame-K, and benzoate were 1.7, 3.5, 0.8, and 1.0 mg/L, respectively. Hence, NMR spectroscopy combined with chemometrics is an efficient tool for simultaneous identification of soft drinks and quantification of selected constituents. PMID:22356160

  2. Ultrafast double-quantum NMR spectroscopy with optimized sensitivity for the analysis of mixtures.

    PubMed

    Rouger, Laetitia; Gouilleux, Boris; Pourchet-Gellez, Mariane; Dumez, Jean-Nicolas; Giraudeau, Patrick

    2016-03-01

    Ultrafast (UF) 2D NMR enables the acquisition of 2D spectra within a single-scan. This methodology has become a powerful analytical tool, used in a large array of applications. However, UF NMR spectroscopy still suffers from the need to compromise between sensitivity, spectral width and resolution. With the commonly used UF-COSY pulse sequence, resolution issues are compounded by the presence of strong auto-correlation signals, particularly in the case of samples with high dynamic ranges. The recently proposed concept of UF Double Quantum Spectroscopy (DQS) allows a better peak separation as it provides a lower spectral peak density. This paper presents the detailed investigation of this new NMR tool in an analytical chemistry context. Theoretical calculations and numerical simulations are used to characterize the modulation of peak intensities as a function of pulse-sequence parameters, and thus enable a significant enhancement of the sensitivity. The analytical comparison of UF-COSY and UF-DQS shows similar performances, however the ultrafast implementation of the DQS approach is found to have some sensitivity advantages over its conventional counterpart. The analytical performance of the pulse sequence is illustrated by the quantification of taurine in complex mixtures (homemade and commercial energy drinks). The results demonstrate the high potential of this experiment, which forms a valuable alternative to UF-COSY spectra when the latter are characterized by strong overlaps and high dynamic ranges. PMID:26865359

  3. Mapping Inhibitor Binding Modes on an Active Cysteine Protease via NMR Spectroscopy

    PubMed Central

    Lee, Gregory M.; Balouch, Eaman; Goetz, David H.; Lazic, Ana; McKerrow, James H.; Craik, Charles S.

    2013-01-01

    Cruzain is a member of the papain/cathepsin-L family of cysteine proteases, and the major cysteine protease of the protozoan Trypanosoma cruzi, the causative agent of Chagas’ disease. We report an auto-induction methodology that provides soluble-cruzain at high yields (> 30 mg per liter in minimal media). These increased yields provide sufficient quantities of active enzyme for use in NMR-based ligand mapping. Using CD and NMR spectroscopy, we also examined the solution-state structural dynamics of the enzyme in complex with a covalently bound vinyl sulfone inhibitor (K777). We report the backbone amide and side chain carbon chemical shift assignments of cruzain in complex with K777. These resonance assignments were used to identify and map residues located in the substrate binding pocket, including the catalytic Cys25 and His162. Selective 15N-Cys, 15N-His, and 13C-Met labeling was performed to quickly assess cruzain-ligand interactions for a set of eight low molecular weight compounds exhibiting micromolar binding or inhibition. Chemical shift perturbation mapping verifies that six of the eight compounds bind to cruzain at the active site. Three different binding modes were delineated for the compounds, namely covalent, non-covalent, and non-interacting. These results provide examples of how NMR spectroscopy can be used to screen compounds for fast evaluation of enzyme-inhibitor interactions in order to facilitate lead compound identification and subsequent structural studies. PMID:23181936

  4. Revealing of HII-regions in Galaxies with Panoramic Spectroscopy

    NASA Astrophysics Data System (ADS)

    Hakopian, S. A.; Balayan, S. K.

    2016-06-01

    Observations intended to investigation and revealing of nodes of processes of nuclear and starforming activity in galaxies were performed via panoramic spectroscopy. Data obtained on Mrk 1050 revealed evidence of starforming activity also outside the central engine of high surface brightness. Two small HII-regions, being likely a part of the chain, are located in the part of the spiral branch coming from the nucleus part.

  5. Determination of the biogenic secondary organic aerosol fraction in the boreal forest by NMR spectroscopy

    NASA Astrophysics Data System (ADS)

    Finessi, E.; Decesari, S.; Paglione, M.; Giulianelli, L.; Carbone, C.; Gilardoni, S.; Fuzzi, S.; Saarikoski, S.; Raatikainen, T.; Hillamo, R.; Allan, J.; Mentel, Th. F.; Tiitta, P.; Laaksonen, A.; Petäjä, T.; Kulmala, M.; Worsnop, D. R.; Facchini, M. C.

    2012-01-01

    The study investigates the sources of fine organic aerosol (OA) in the boreal forest, based on measurements including both filter sampling (PM1) and online methods and carried out during a one-month campaign held in Hyytiälä, Finland, in spring 2007. Two aerosol mass spectrometers (Q-AMS, ToF-AMS) were employed to measure on-line concentrations of major non-refractory aerosol species, while the water extracts of the filter samples were analyzed by nuclear magnetic resonance (NMR) spectroscopy for organic functional group characterization of the polar organic fraction of the aerosol. AMS and NMR spectra were processed separately by non-negative factorization algorithms, in order to apportion the main components underlying the submicrometer organic aerosol composition and depict them in terms of both mass fragmentation patterns and functional group compositions. The NMR results supported the AMS speciation of oxidized organic aerosol (OOA) into two main fractions, which could be generally labelled as more and less oxidized organics. The more oxidized component was characterized by a mass spectrum dominated by the m/z 44 peak, and in parallel by a NMR spectrum showing aromatic and aliphatic backbones highly substituted with oxygenated functional groups (carbonyls/carboxyls and hydroxyls). Such component, contributing on average 50% of the OA mass throughout the observing period, was associated with pollution outbreaks from the Central Europe. The less oxidized component was enhanced in concomitance with air masses originating from the North-to-West sector, in agreement with previous investigations conducted at this site. NMR factor analysis was able to separate two distinct components under the less oxidized fraction of OA. One of these NMR-factors was associated with the formation of terrestrial biogenic secondary organic aerosol (BSOA), based on the comparison with spectral profiles obtained from laboratory experiments of terpenes photo-oxidation. The second NMR

  6. A structural homologue of colipase in black mamba venom revealed by NMR floating disulphide bridge analysis.

    PubMed

    Boisbouvier, J; Albrand, J P; Blackledge, M; Jaquinod, M; Schweitz, H; Lazdunski, M; Marion, D

    1998-01-01

    The solution structure of mamba intestinal toxin 1 (MIT1), isolated from Dendroaspis polylepis polylepis venom, has been determined. This molecule is a cysteine-rich polypeptide exhibiting no recognised family membership. Resistance to MIT1 to classical specific endoproteases produced contradictory NMR and biochemical information concerning disulphide-bridge topology. We have used distance restraints allowing ambiguous partners between S atoms in combination with NMR-derived structural information, to correctly determine the disulphide-bridge topology. The resultant solution structure of MIT1, determined to a resolution of 0.5 A, reveals an unexpectedly similar global fold with respect to colipase, a protein involved in fatty acid digestion. Colipase exhibits an analogous resistance to endoprotease activity, indicating for the first time the possible topological origins of this biochemical property. The biochemical and structural homology permitted us to propose a mechanically related digestive function for MIT1 and provides novel information concerning snake venom protein evolution. PMID:9761684

  7. NMR structure of a fungal virulence factor reveals structural homology with mammalian saposin B

    PubMed Central

    Beck, Moriah R.; DeKoster, Gregory T.; Cistola, David P.; Goldman, William E.

    2011-01-01

    SUMMARY The fungal protein CBP (calcium binding protein) is a known virulence factor with an unknown virulence mechanism. The protein was identified based on its ability to bind calcium and its prevalence as Histoplasma capsulatum’s most abundant secreted protein. However, CBP has no sequence homology with other calcium binding proteins and contains no known calcium-binding motifs. Here, the NMR structure of CBP reveals a highly intertwined homodimer and represents the first atomic level NMR model of any fungal virulence factor. Each CBP monomer is comprised of four α-helices that adopt the saposin fold, characteristic of a protein family that binds to membranes and lipids. This structural homology suggests that CBP functions as a lipid-binding protein, potentially interacting with host glycolipids in the phagolysosome of host cells. PMID:19298372

  8. Isomers and conformers of two push pull hydrazines studied by NMR and vibrational spectroscopy and by ab initio calculations

    NASA Astrophysics Data System (ADS)

    Gróf, M.; Polovková, J.; Gatial, A.; Milata, V.; Černuchová, P.; Prónayová, N.; Matějka, P.

    2007-05-01

    The isomers and conformers of two push-pull hydrazines: 3- N, N-dimethylhydrazino-2-acetyl propenenitrile [(H 3C) 2N sbnd NH sbnd CH dbnd C(CN)(COCH 3)] (DMHAP) and 3- N, N-dimethylhydrazino-2-methylsulfonyl propenenitrile [(H 3C) 2N sbnd NH sbnd CH dbnd C(CN)(SO 2CH 3)] (DMHSP) have been studied experimentally by NMR and vibrational spectroscopy and theoretically by the ab initio calculations at MP2 level in 6-31G** basis set. The IR and Raman spectra of both compounds as a solid and solute in various solvents have been recorded. The NMR spectra were obtained in chloroform and DMSO at room temperature. Both compounds have been prepared by the same way. NMR spectra revealed that DMHAP was prepared as a pure Z-isomer whereas in the case of DMHSP a pure E-isomer was obtained. Due to the low barrier for both compounds practically free isomerisation process occurred in the solutions but in opposite directions. Whereas DMHAP exists in the solid state and in the less polar solvent as Z-isomer, in more polar solvents the appearance of next two conformers of E-isomer was observed. On the contrary DMHSP exists in the solid state and in the more polar solvent as E-isomer only but in less polar solvent the presence of Z-isomer was observed as well. Conformational possibilities of both studied compounds are given by the rotation of dimethylhydrazino group with its anti- or syn-orientation towards the olefinic double bond. Moreover, by the rotation of the acetyl group with Z- and E-orientation of carbonyl bond towards olefinic double bond can occur in DMHAP. Vibrational and NMR spectra revealed the existence of single conformer with intramolecular hydrogen bond for Z-isomer in less polar solvent and next two conformers for E-isomer of DMHAP with Z-orientation of acetyl group and anti and syn orientation of dimethylhydrazine group in more polar solvents. For E-isomer of DMHSP two conformers with anti or syn orientations of dimethylhydrazino group have been also confirmed by NMR

  9. NMR spectroscopy of hyperpolarized ^129Xe at high fields: Maintaining spin polarization after optical pumping.

    NASA Astrophysics Data System (ADS)

    Patton, Brian; Kuzma, Nicholas N.; Lisitza, Natalia V.; Happer, William

    2003-05-01

    Spin-polarized ^129Xe has become an invaluable tool in nuclear magnetic resonance research, with applications ranging from medical imaging to high-resolution spectroscopy. High-field NMR studies using hyperpolarized xenon as a spectroscopic probe benefit from the high signal-to-noise ratios and large chemical shifts typical of optically-pumped noble gases. The experimental sensitivity is ultimately determined by the absolute polarization of the xenon in the sample, which can be substantially decreased during purification and transfer. NMR of xenon at high fields (9.4 Tesla) will be discussed, and potential mechanisms of spin relaxation during the distillation, storage(N. N. Kuzma, B. Patton, K. Raman, and W. Happer, Phys. Rev. Lett. 88), 147602 (2002)., and delivery of hyperpolarized xenon will be analyzed.

  10. An instrument control and data analysis program for NMR imaging and spectroscopy

    SciTech Connect

    Roos, M.S.; Mushlin, R.A.; Veklerov, E.; Port, J.D.; Ladd, C.; Harrison, C.G.

    1988-01-01

    We describe a software environment created to support real-time instrument control and signal acquisition as well as array-processor based signal and image processing in up to five dimensions. The environment is configured for NMR imaging and in vivo spectroscopy. It is designed to provide flexible tools for implementing novel NMR experiments in the research laboratory. Data acquisition and processing operations are programmed in macros which are loaded in assembled from to minimize instruction overhead. Data arrays are dynamically allocated for efficient use of memory and can be mapped directly into disk files. The command set includes primitives for real-time control of data acquisition, scalar arithmetic, string manipulation, branching, a file system and vector operations carried out by an array processor. 6 figs.

  11. Uncovering the triggers for GPCR activation using solid-state NMR spectroscopy

    NASA Astrophysics Data System (ADS)

    Kimata, Naoki; Reeves, Philip J.; Smith, Steven O.

    2015-04-01

    G protein-coupled receptors (GPCRs) span cell membranes with seven transmembrane helices and respond to a diverse array of extracellular signals. Crystal structures of GPCRs have provided key insights into the architecture of these receptors and the role of conserved residues. However, the question of how ligand binding induces the conformational changes that are essential for activation remains largely unanswered. Since the extracellular sequences and structures of GPCRs are not conserved between receptor subfamilies, it is likely that the initial molecular triggers for activation vary depending on the specific type of ligand and receptor. In this article, we describe NMR studies on the rhodopsin subfamily of GPCRs and propose a mechanism for how retinal isomerization switches the receptor to the active conformation. These results suggest a general approach for determining the triggers for activation in other GPCR subfamilies using NMR spectroscopy.

  12. Isotope-Filtered 4D NMR Spectroscopy for Structure Determination of Humic Substances**

    PubMed Central

    Bell, Nicholle G A; Michalchuk, Adam A L; Blackburn, John W T; Graham, Margaret C; Uhrín, Dušan

    2015-01-01

    Humic substances, the main component of soil organic matter, could form an integral part of green and sustainable solutions to the soil fertility problem. However, their global-scale application is hindered from both scientific and regulatory perspectives by the lack of understanding of the molecular make-up of these chromatographically inseparable mixtures containing thousands of molecules. Here we show how multidimensional NMR spectroscopy of isotopically tagged molecules enables structure characterization of humic compounds. We illustrate this approach by identifying major substitution patterns of phenolic aromatic moieties of a peat soil fulvic acid, an operational fraction of humic substances. Our methodology represents a paradigm shift in the use of NMR active tags in structure determination of small molecules in complex mixtures. Unlike previous tagging methodologies that focused on the signals of the tags, we utilize tags to directly probe the identity of the molecules they are attached to. PMID:26036217

  13. (1)H NMR spectroscopy in the diagnosis of Pseudomonas aeruginosa-induced urinary tract infection.

    PubMed

    Gupta, Ashish; Dwivedi, Mayank; Nagana Gowda, G A; Ayyagari, Archana; Mahdi, A A; Bhandari, M; Khetrapal, C L

    2005-08-01

    The utility of (1)H NMR spectroscopy is suggested and demonstrated for the diagnosis of Pseudomonas aeruginosa in urinary tract infection (UTI). The specific property of P. aeruginosa of metabolizing nicotinic acid to 6-hydroxynicotinic acid (6-OHNA) is exploited. The quantity of 6-OHNA produced correlates well with the viable bacterial count. Other common bacteria causing UTI such as Escherichia coli, Klebsiella pneumonia, Enterobacter aerogenes, Acinetobacter baumanii, Proteus mirabilis, Citrobacter frundii, Enterococcus faecalis, Streptococcus gp B and Staphylococcus aureus do not metabolize nicotinic acid under similar conditions. The method provides a single-step documentation of P. aeruginosa qualitatively as well as quantitatively. The NMR method is demonstrated on urine samples from 30 patients with UTI caused by P. aeruginosa. PMID:15759292

  14. Determination of iodine value of lubricating oils by nuclear magnetic resonance (NMR) spectroscopy

    SciTech Connect

    Sarpal, A.S.; Kapur, G.S.; Mukherjee, S.

    1995-03-01

    A direct, quick and non-destructive method for estimating the iodine value of fats, fatty oils and their blends in mineral oils has been developed based on {sup 1}H and {sup 13}C-NMR spectroscopy. The method involves the determination of unsaturation content of the samples by {sup 1}H and {sup 13}C-NMR spectroscopic techniques. The iodine value of the sample is directly proportional to the unsaturated proton or carbon content. The value of the proportionality constant is independent of the nature of the fats and their blends in mineral oils for the limited samples studied. The iodine value determined by this method also includes the contribution from additives containing unsaturation. Saturated ingredients in the sample do not contribute to the iodine value as is the case with the standard IP-84 method. 5 refs., 3 figs., 4 tabs.

  15. N-15 NMR Spectroscopy as a Method for Comparing the Rates of Imidization of Several Diamines

    NASA Technical Reports Server (NTRS)

    Johnson, J. Christopher; Kuczmarski, Maria A.

    2006-01-01

    The relative rates of the conversion of amide-acid to imide was measured for a series or aromatic diamines that have been identified as potential replacements for 4,4'-methylene dianiline (MDA) in high-temperature polyimides and polymer composites. These rates were compared with the N-15 NMR resonances of the unreacted amines. The initial rates of imidization track with the difference in chemical shift between the amine nitrogens in MDA and those in the subject diamines. This comparison demonstrated that N-15 NMR spectroscopy is appropriate for the rapid screening of candidate diamines to determine their reactivity relative to MDA, and can serve to provide guidance to the process of creating the time-temperature profiles used in processing these materials into polymer matrix composites.

  16. Natural abundance high-resolution solid state 2 H NMR spectroscopy

    NASA Astrophysics Data System (ADS)

    Aliev, Abil E.; Harris, Kenneth D. M.; Apperley, David C.

    1994-08-01

    We report for the first time an approach for natural abundance solid state 2 H NMR spectroscopy involving magic angle sample spinning (MAS), high-power 1 H decoupling (HPPD) and 1 H- 2 H cross polarization (CP). Taking tetrakis(trimethylsilyl)silane (TTMSS), adamantane, 1-chloroadamantane, hexamethylbenzene (HMB), 2,2-dimethyl-1,3-propanediol (DMPD) and 2-hydroxymethyl-2-methyl-1,3-propanediol (HMPD) as examples, it has been shown that the combination of HPPD and MAS can be applied readily to study rotator phase solids, allowing isotropic peaks arising from chemically inequivalent 2 H nuclei to be resolved. For natural abundance samples of TTMSS and chloroadamantane, it has been shown that 2 H CP/HPPD/MAS NMR experiments, involving polarization transfer from 1 H to 2 H, may provide considerable sensitivity enhancement in comparison with single pulse experiments.

  17. Natural abundance high-resolution solid state 2 H NMR spectroscopy

    NASA Astrophysics Data System (ADS)

    Aliev, Abil E.; Harris, Kenneth D. M.; Apperley, David C.

    1994-08-01

    We report for the first time an approach for natural abundance solid state 2H NMR spectroscopy involving magic angle sample spinning (MAS), high-power 1H decoupling (HPPD) and 1H- 2H cross polarization (CP). Taking tetrakis(trimethylsilyl)silane (TTMSS), adamantane, 1-chloroadamantane, hexamethylbenzene (HMB), 2,2-dimethyl-1,3-propanediol (DMPD) and 2-hydroxymethyl-2-methyl-1,3-propanediol (HMPD) as examples, it has been shown that the combination of HPPD and MAS can be applied readily to study rotator phase solids, allowing isotropic peaks arising from chemically inequivalent 2H nuclei to be resolved. For natural abundance samples of TTMSS and chloroadamantane, it has been shown that 2H CP/HPPD/MAS NMR experiments, involving polarization transfer from 1H to 2H, may provide considerable sensitivity enhancement in comparison with single pulse experiments.

  18. Structural studies of pravastatin and simvastatin and their complexes with SDS micelles by NMR spectroscopy

    NASA Astrophysics Data System (ADS)

    Rakhmatullin, I. Z.; Galiullina, L. F.; Klochkova, E. A.; Latfullin, I. A.; Aganov, A. V.; Klochkov, V. V.

    2016-02-01

    Conformational features of pravastatin and simvastatin molecules in solution and in their complexes with sodium dodecyl sulfate micelles (SDS) were studied by 2D NOESY NMR spectroscopy. On the basis of the nuclear magnetic resonance experiments it was established that pravastatin and simvastatin can form molecular complex with SDS micelles which were considered as the model of cell membrane. In addition, interatomic distances for studied compounds were calculated based on 2D NOESY NMR experiments. It was shown that pravastatin interacts only with a surface of model membrane. However, in contrast to pravastatin, simvastatin penetrates into the inner part of SDS micelles. Observed distinctions in the mechanisms of interaction of pravastatin and simvastatin with models of cell membranes could explain the differences in their pharmacological properties.

  19. 2H-DNP-enhanced 2H–13C solid-state NMR correlation spectroscopy

    PubMed Central

    Maly, Thorsten; Andreas, Loren B.; Smith, Albert A.

    2015-01-01

    Perdeuteration of biological macromolecules for magic angle spinning solid-state NMR spectroscopy can yield high-resolution 2H–13C correlation spectra and the method is therefore of great interest for the structural biology community. Here we demonstrate that the combination of sample deuteration and dynamic nuclear polarization yields resolved 2H–13C correlation spectra with a signal enhancement of ε ≥ 700 compared to a spectrum recorded with microwaves off and otherwise identical conditions. To our knowledge, this is the first time that 2H-DNP has been employed to enhance MAS-NMR spectra of a biologically relevant system. The DNP process is studied using several polarizing agents and the technique is applied to obtain 2H–13C correlation spectra of U-[2H, 13C] proline. PMID:20458422

  20. Detoxification of organophosphorus pesticides and nerve agents through RSDL: efficacy evaluation by (31)P NMR spectroscopy.

    PubMed

    Elsinghorst, Paul W; Worek, Franz; Koller, Marianne

    2015-03-01

    Intoxication by organophosphorus compounds, especially by pesticides, poses a considerable risk to the affected individual. Countermeasures involve both medical intervention by means of antidotes as well as external decontamination to reduce the risk of dermal absorption. One of the few decontamination options available is Reactive Skin Decontamination Lotion (RSDL), which was originally developed for military use. Here, we present a (31)P NMR spectroscopy based methodology to evaluate the detoxification efficacy of RSDL with respect to a series of organophosphorus pesticides and nerve agents. Kinetic analysis of the obtained NMR data provided degradation half-lives proving that RSDL is also reasonably effective against organophosphorus pesticides. Unexpected observations of different RSDL degradation patterns are presented in view of its reported oximate-catalyzed mechanism of action. PMID:25597861

  1. Microfabricated Inserts for Magic Angle Coil Spinning (MACS) Wireless NMR Spectroscopy

    PubMed Central

    Badilita, Vlad; Fassbender, Birgit; Kratt, Kai; Wong, Alan; Bonhomme, Christian; Sakellariou, Dimitris; Korvink, Jan G.; Wallrabe, Ulrike

    2012-01-01

    This article describes the development and testing of the first automatically microfabricated probes to be used in conjunction with the magic angle coil spinning (MACS) NMR technique. NMR spectroscopy is a versatile technique for a large range of applications, but its intrinsically low sensitivity poses significant difficulties in analyzing mass- and volume-limited samples. The combination of microfabrication technology and MACS addresses several well-known NMR issues in a concerted manner for the first time: (i) reproducible wafer-scale fabrication of the first-in-kind on-chip LC microresonator for inductive coupling of the NMR signal and reliable exploitation of MACS capabilities; (ii) improving the sensitivity and the spectral resolution by simultaneous spinning the detection microcoil together with the sample at the “magic angle” of 54.74° with respect to the direction of the magnetic field (magic angle spinning – MAS), accompanied by the wireless signal transmission between the microcoil and the primary circuit of the NMR spectrometer; (iii) given the high spinning rates (tens of kHz) involved in the MAS methodology, the microfabricated inserts exhibit a clear kinematic advantage over their previously demonstrated counterparts due to the inherent capability to produce small radius cylindrical geometries, thus tremendously reducing the mechanical stress and tearing forces on the sample. In order to demonstrate the versatility of the microfabrication technology, we have designed MACS probes for various Larmor frequencies (194, 500 and 700 MHz) testing several samples such as water, Drosophila pupae, adamantane solid and LiCl at different magic angle spinning speeds. PMID:22936994

  2. Solid-state Ru-99 NMR spectroscopy: a useful tool for characterizing prototypal diamagnetic ruthenium compounds.

    PubMed

    Ooms, Kristopher J; Wasylishen, Roderick E

    2004-09-01

    The feasibility of (99)Ru NMR spectroscopy as a tool to characterize solid compounds is demonstrated. Results of the first solid-state (99)Ru NMR investigation of diamagnetic compounds are presented for Ru(NH(3))(6)Cl(2), K(4)Ru(CN)(6). xH(2)O (x = 0, 3), LaKRu(CN)(6), and Ru(3)(CO)(12). The sensitivity of the ruthenium magnetic shielding tensor to subtle changes in the local structure about the ruthenium nucleus is highlighted by comparing the (99)Ru isotropic chemical shift of Ru(NH(3))(6)Cl(2) in aqueous solutions and in the solid state. The narrow isotropic (99)Ru NMR peak observed for solid Ru(NH(3))(6)Cl(2) indicates that this compound is an ideal secondary reference sample for solid-state (99)Ru NMR studies. The isotropic (99)Ru chemical shift, (99)Ru nuclear quadrupolar coupling constant, C(Q), and quadrupolar asymmetry parameter of K(4)Ru(CN)(6). xH(2)O (x = 0, 3) are shown to be sensitive to x. For Ru(3)(CO)(12), the magnetic shielding tensors of each of the three nonequivalent Ru nuclei have spans of 1300-1400 ppm, and the (99)Ru C(Q) values are also similar, 1.36-1.85 MHz, and are surprisingly small given that (99)Ru has a moderate nuclear quadrupole moment. Information about the relative orientation of the Ru magnetic shielding and electric field gradient tensors has been determined for Ru(3)(CO)(12) from experimental (99)Ru NMR spectra as well as quantum chemical calculations. PMID:15339183

  3. Microfabricated inserts for magic angle coil spinning (MACS) wireless NMR spectroscopy.

    PubMed

    Badilita, Vlad; Fassbender, Birgit; Kratt, Kai; Wong, Alan; Bonhomme, Christian; Sakellariou, Dimitris; Korvink, Jan G; Wallrabe, Ulrike

    2012-01-01

    This article describes the development and testing of the first automatically microfabricated probes to be used in conjunction with the magic angle coil spinning (MACS) NMR technique. NMR spectroscopy is a versatile technique for a large range of applications, but its intrinsically low sensitivity poses significant difficulties in analyzing mass- and volume-limited samples. The combination of microfabrication technology and MACS addresses several well-known NMR issues in a concerted manner for the first time: (i) reproducible wafer-scale fabrication of the first-in-kind on-chip LC microresonator for inductive coupling of the NMR signal and reliable exploitation of MACS capabilities; (ii) improving the sensitivity and the spectral resolution by simultaneous spinning the detection microcoil together with the sample at the "magic angle" of 54.74° with respect to the direction of the magnetic field (magic angle spinning - MAS), accompanied by the wireless signal transmission between the microcoil and the primary circuit of the NMR spectrometer; (iii) given the high spinning rates (tens of kHz) involved in the MAS methodology, the microfabricated inserts exhibit a clear kinematic advantage over their previously demonstrated counterparts due to the inherent capability to produce small radius cylindrical geometries, thus tremendously reducing the mechanical stress and tearing forces on the sample. In order to demonstrate the versatility of the microfabrication technology, we have designed MACS probes for various Larmor frequencies (194, 500 and 700 MHz) testing several samples such as water, Drosophila pupae, adamantane solid and LiCl at different magic angle spinning speeds. PMID:22936994

  4. Revealing and Characterizing Dark Excitons through Coherent Multidimensional Spectroscopy.

    PubMed

    Tollerud, Jonathan O; Cundiff, Steven T; Davis, Jeffrey A

    2016-08-26

    Dark excitons are of fundamental importance in a broad range of contexts but are difficult to study using conventional optical spectroscopy due to their weak interaction with light. We show how coherent multidimensional spectroscopy can reveal and characterize dark states. Using this approach, we identify parity-forbidden and spatially indirect excitons in InGaAs/GaAs quantum wells and determine details regarding lifetimes, homogeneous and inhomogeneous linewidths, broadening mechanisms, and coupling strengths. The observations of coherent coupling between these states and bright excitons hint at a role for a multistep process by which excitons in the barrier can relax into the quantum wells. PMID:27610881

  5. Correlating high-resolution magic angle spinning NMR spectroscopy and gene analysis in osteoarthritic cartilage.

    PubMed

    Tufts, Lauren; Shet Vishnudas, Keerthi; Fu, Eunice; Kurhanewicz, John; Ries, Michael; Alliston, Tamara; Li, Xiaojuan

    2015-05-01

    Osteoarthritis (OA) is a common multifactorial and heterogeneous degenerative joint disease, and biochemical changes in cartilage matrix occur during the early stages of OA before morphological changes occur. Thus, it is desired to measure regional biochemical changes in the joint. High-resolution magic angle spinning (HRMAS) NMR spectroscopy is a powerful method of observing cartilaginous biochemical changes ex vivo, including the concentrations of alanine and N-acetyl, which are markers of collagen and total proteoglycan content, respectively. Previous studies have observed significant changes in chondrocyte metabolism of OA cartilage via the altered gene expression profiles of ACAN, COL2A1 and MMP13, which encode aggrecan, type II collagen and matrix metalloproteinase 13 (a protein crucial in the degradation of type II collagen), respectively. Employing HRMAS, this study aimed to elucidate potential relationships between N-acetyl and/or alanine and ACAN, COL2A1 and/or MMP13 expression profiles in OA cartilage. Thirty samples from the condyles of five subjects undergoing total knee arthroplasty to treat OA were collected. HRMAS spectra were obtained at 11.7 T for each sample. RNA was subsequently extracted to determine gene expression profiles. A significant negative correlation between N-acetyl metabolite and ACAN gene expression levels was observed; this provides further evidence of N-acetyl as a biomarker of cartilage degeneration. The alanine doublet was distinguished in the spectra of 15 of the 30 specimens of this study. Alanine can only be detected with HRMAS NMR spectroscopy when the collagen framework has been degraded such that alanine is sufficiently mobile to form a distinguished peak in the spectrum. Thus, HRMAS NMR spectroscopy may provide unique localized measurements of collagenous degeneration in OA cartilage. The identification of imaging markers that could provide a link between OA pathology and chondrocyte metabolism will facilitate the

  6. Heteronuclear dipolar couplings, total spin coherence, and bilinear rotations in NMR spectroscopy

    SciTech Connect

    Garbow, J.R.

    1983-07-01

    In Chapter 1 a variety of different introductory topics are presented. The potential complexity of the nuclear magnetic resonsnace (NMR) spectra of molecules dissolved in liquid crystal solvents serves to motivate the development of multiple quantum (MQ) spectroscopy. The basics of MQ NMR are reviewed in Chapter 2. An experimental search procedure for the optimization of MQ pulse sequences is introduced. Chapter 3 discusses the application of MQ NMR techniques to the measurement of dipolar couplings in heteronuclear spin systems. The advantages of MQ methods in such systems are developed and experimental results for partially oriented (1-/sup 13/C) benzene are presented. Several pulse sequences are introduced which employ a two-step excitation of heteronuclear MQ coherence. A new multiple pulse method, involving the simultaneous irradiation of both rare and abundant spin species, is described. The problem of the broadening of MQ transitions due to magnetic field inhomogeneity is considered in Chapter 4. The method of total spin coherence transfer echo spectroscopy (TSCTES) is presented, with experimets on partially oriented acetaldehyde serving to demonstrate this new technique. TSCTES results in MQ spectra which are sensitive to all chemical shifts and spin-spin couplings and which are free of inhomogeneous broadening. In Chapter 5 the spectroscopy of spin systems of several protons and a /sup 13/C nucleus in the isotropic phase is discussed. The usefulness of the heteronuclear bilinear rotation as a calculational tool is illustrated. Compensated bilinear ..pi.. rotations, which are relatively insensitive to timing parameter missets, are presented. A new technique for homonuclear proton decoupling, Bilinear Rotation Decoupling, is described and its success in weakly coupled systems is demonstrated.

  7. High-resolution magic-angle-spinning NMR spectroscopy of intact tissue.

    PubMed

    Giskeødegård, Guro F; Cao, Maria D; Bathen, Tone F

    2015-01-01

    High-resolution magic-angle-spinning (HR-MAS) NMR spectroscopy is a nondestructive technique that is used to obtain the metabolite profile of a tissue sample. This method requires minimal sample preparation. However, it is important to handle the sample with care and keep it frozen during preparation to minimize degradation. Here, we describe a typical protocol for HR-MAS analysis of intact tissue. We also include examples of typical pulse sequence programs and quantification methods that are used today. PMID:25677145

  8. Electromagnetic susceptibility anisotropy and its importance for paramagnetic NMR and optical spectroscopy in lanthanide coordination chemistry.

    PubMed

    Blackburn, Octavia A; Edkins, Robert M; Faulkner, Stephen; Kenwright, Alan M; Parker, David; Rogers, Nicola J; Shuvaev, Sergey

    2016-04-19

    The importance of the directional dependence of magnetic susceptibility in magnetic resonance and of electric susceptibility in the optical spectroscopy of lanthanide coordination complexes is assessed. A body of more reliable shift, relaxation and optical emission data is emerging for well-defined isostructural series of complexes, allowing detailed comparative analyses to be undertaken. Such work is highlighting the limitations of the current NMR shift and relaxation theories, as well as emphasising the absence of a compelling theoretical framework to explain optical emission phenomena. PMID:26898996

  9. Application of nmr spectroscopy to determine the thermodynamic characteristics of water bound to OX-50 nanosilica

    NASA Astrophysics Data System (ADS)

    Turov, V. V.; Gun'ko, V. M.; Gaishun, V. E.; Kosenok, Ya. A.; Golovan, A. P.

    2010-09-01

    We have used low-temperature 1H NMR spectroscopy to determine the thermodynamic characteristics of water bound to OX-50 nanosilica (SBET ≈ 50 m2/g) in different media: aqueous, air, chloroform medium, and gaseous methane. We demonstrate the difference between the hydration parameters of silica OX-50 on going from an aqueous suspension to a hydrated powder. We present the water cluster size distributions in the studied systems, calculated from the Gibbs-Thomson equation. We found that the average water cluster size in suspension is considerably larger than the cluster sizes in hydrated powders.

  10. Silica sol assisted chromatographic NMR spectroscopy for resolution of trans- and cis-isomers.

    PubMed

    Yang, Ying; Wu, Rui; Huang, Shaohua; Bai, Zhengwu

    2016-04-01

    Chromatographic NMR spectroscopy can separate the mixtures of species with significantly different molecular size, but generally fails for isomeric species. Herein, we reported the resolution of trans- and cis-isomers and their structural analogue, which are different in molecular shapes, but similar in mass, were greatly enhanced in the presence of silica sol. The mixtures of maleic acid, fumaric acid and succinic acid, and the mixtures of trans- and cis-1,2-cyclohexanedicarboxylic acids, were distinguished by virtue of their different degrees of interaction with silica sol. Moreover, we found mixed solvents could improve the spectral resolution of DOSY spectra of mixtures. PMID:26942864

  11. Silica sol assisted chromatographic NMR spectroscopy for resolution of trans- and cis-isomers

    NASA Astrophysics Data System (ADS)

    Yang, Ying; Wu, Rui; Huang, Shaohua; Bai, Zhengwu

    2016-04-01

    Chromatographic NMR spectroscopy can separate the mixtures of species with significantly different molecular size, but generally fails for isomeric species. Herein, we reported the resolution of trans- and cis-isomers and their structural analogue, which are different in molecular shapes, but similar in mass, were greatly enhanced in the presence of silica sol. The mixtures of maleic acid, fumaric acid and succinic acid, and the mixtures of trans- and cis-1,2-cyclohexanedicarboxylic acids, were distinguished by virtue of their different degrees of interaction with silica sol. Moreover, we found mixed solvents could improve the spectral resolution of DOSY spectra of mixtures.

  12. Impact of Hydrophilic Surfaces on Interfacial Water Dynamics Probed with NMR Spectroscopy

    PubMed Central

    Yoo, Hyok; Paranji, Rajan

    2011-01-01

    In suspensions of Nafion beads and of cationic gel beads, NMR spectroscopy showed two water–proton resonances, one representing intimate water layers next to the polymer surface, the other corresponding to water lying beyond. Both resonances show notably shorter spin–lattice relaxation times (T1) and smaller self-diffusion coefficients (D) indicating slower dynamics than bulk water. These findings confirm the existence of highly restricted water layers adsorbed onto hydrophilic surfaces and dynamically stable water beyond the first hydration layers. Thus, aqueous regions on the order of micrometers are dynamically different from bulk water. PMID:22003430

  13. Application of 13C NMR spectroscopy to paratope mapping for larger antigen-Fab complexes.

    PubMed

    Kim, H; Kato, K; Yamato, S; Igarashi, T; Matsunaga, C; Ohtsuka, H; Higuchi, A; Nomura, N; Noguchi, H; Arata, Y

    1994-06-13

    For the purpose of engineering the antibody combining site, mapping residues that are involved in antigen binding provide us with valuable information. By use of 13C NMR spectroscopy with selectively 13C-labeled Fv fragments, we have established a general strategy to identify the residues that are perturbed upon binding of small antigen (hapten) molecules [(1990) Biochemistry 30, 6604-6610]. In the present paper, we demonstrate that this strategy can be extended to molecular structural analyses of the complexes of an Fab fragment and a larger antigen molecule such as Pseudomonas aeruginosa exotoxin A with a molecular mass of 67 kDa. PMID:8013642

  14. Novel surfactant mixtures for NMR spectroscopy of encapsulated proteins dissolved in low-viscosity fluids

    PubMed Central

    Peterson, Ronald W.; Pometun, Maxim S.; Shi, Zhengshuang; Wand, A. Joshua

    2005-01-01

    NMR spectroscopy of encapsulated proteins dissolved in low-viscosity fluids is emerging as a tool for biophysical studies of proteins in atomic detail in a variety of otherwise inaccessible contexts. The central element of the approach is the encapsulation of the protein of interest within the aqueous core of a reverse micelle with high structural fidelity. The process of encapsulation is highly dependent upon the nature of the surfactant(s) employed. Here we describe novel mixtures of surfactants that are capable of successfully encapsulating a range of types of proteins under a variety of conditions. PMID:16199658

  15. Total assignment and structure in solution of tetrandrine by NMR spectroscopy and molecular modelling

    NASA Astrophysics Data System (ADS)

    Thevand, André; Stanculescu, Ioana; Mandravel, Cristina; Woisel, Patrice; Surpateanu, Gheorghe

    2004-07-01

    High-resolution 1- and 2D NMR spectra of tetrandrine and molecular modelling were employed to characterise its structure in solution. Complete and unambiguous assignment of all proton and carbon resonance signals is reported. Scalar couplings were determined from dihedral angles with the Karplus equation. Inter-proton distances were evaluated from NOE correlation peaks. Comparison of simulated and X-ray conformations of tetrandrine reveals only small differences.

  16. Dynamic processes and chemical composition of Lepidium sativum seeds determined by means of field-cycling NMR relaxometry and NMR spectroscopy.

    PubMed

    Rachocki, A; Latanowicz, L; Tritt-Goc, J

    2012-12-01

    Proton nuclear magnetic resonance (NMR) techniques, such as field-cycling relaxometry, wide-line NMR spectroscopy, and magic angle spinning NMR spectroscopy, were applied to study the seeds of cress, Lepidium sativum. Field-cycling NMR relaxometry was used for the first time to investigate the properties of the whole molecular system of dry cress seeds. This method not only allowed the dynamics to be studied, but was also successful in the differentiation among the solid (i.e., carbohydrates, proteins, or fats forming a solid form of lipids) and liquid-like (oil compounds) components of the seeds. The (1)H NMR relaxation dispersion of oils was interpreted as a superposition of intramolecular and intermolecular contributions. The intramolecular part was described in terms of a Lorentzian spectral density function, whereas a log-Gaussian distribution of correlation times was applied for the intermolecular dipole-dipole contribution. The models applied led to very good agreement with the experimental data and demonstrate that the contribution of the intermolecular relaxation to the overall relaxation should not be disregarded, especially at low frequencies. A power-law frequency dependence of the proton relaxation dispersion was used for the interpretation of the solid components. From the analysis of the (1)H wide-line NMR spectra of the liquid-like component of hydrated cress seeds, we can conclude that the contribution of oil protons should always be taken into account when evaluating the spin-lattice relaxation times values or measuring the moisture and oil content. The application of (1)H magic angle spinning NMR significantly improves resolution in the liquid-like spectrum of seeds and allows the determination of the chemical composition of cress seeds. PMID:23001307

  17. Probabilistic Interaction Network of Evidence Algorithm and its Application to Complete Labeling of Peak Lists from Protein NMR Spectroscopy

    PubMed Central

    Bahrami, Arash; Assadi, Amir H.; Markley, John L.; Eghbalnia, Hamid R.

    2009-01-01

    The process of assigning a finite set of tags or labels to a collection of observations, subject to side conditions, is notable for its computational complexity. This labeling paradigm is of theoretical and practical relevance to a wide range of biological applications, including the analysis of data from DNA microarrays, metabolomics experiments, and biomolecular nuclear magnetic resonance (NMR) spectroscopy. We present a novel algorithm, called Probabilistic Interaction Network of Evidence (PINE), that achieves robust, unsupervised probabilistic labeling of data. The computational core of PINE uses estimates of evidence derived from empirical distributions of previously observed data, along with consistency measures, to drive a fictitious system M with Hamiltonian H to a quasi-stationary state that produces probabilistic label assignments for relevant subsets of the data. We demonstrate the successful application of PINE to a key task in protein NMR spectroscopy: that of converting peak lists extracted from various NMR experiments into assignments associated with probabilities for their correctness. This application, called PINE-NMR, is available from a freely accessible computer server (http://pine.nmrfam.wisc.edu). The PINE-NMR server accepts as input the sequence of the protein plus user-specified combinations of data corresponding to an extensive list of NMR experiments; it provides as output a probabilistic assignment of NMR signals (chemical shifts) to sequence-specific backbone and aliphatic side chain atoms plus a probabilistic determination of the protein secondary structure. PINE-NMR can accommodate prior information about assignments or stable isotope labeling schemes. As part of the analysis, PINE-NMR identifies, verifies, and rectifies problems related to chemical shift referencing or erroneous input data. PINE-NMR achieves robust and consistent results that have been shown to be effective in subsequent steps of NMR structure determination. PMID

  18. Moving NMR

    NASA Astrophysics Data System (ADS)

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

    2008-12-01

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

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

    PubMed

    Li, Pan; Shi, Pan; Lai, Chaohua; Li, Juan; Zheng, Yuanyuan; Xiong, Ying; Zhang, Longhua; Tian, Changlin

    2014-01-01

    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. PMID:25347290

  20. Solution NMR of MPS-1 Reveals a Random Coil Cytosolic Domain Structure

    PubMed Central

    Lai, Chaohua; Li, Juan; Zheng, Yuanyuan; Xiong, Ying; Zhang, Longhua; Tian, Changlin

    2014-01-01

    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. PMID:25347290

  1. Advanced Structural Determination of Diterpene Esters Using Molecular Modeling and NMR Spectroscopy.

    PubMed

    Nothias-Scaglia, Louis-Félix; Gallard, Jean-François; Dumontet, Vincent; Roussi, Fanny; Costa, Jean; Iorga, Bogdan I; Paolini, Julien; Litaudon, Marc

    2015-10-23

    Three new jatrophane esters (1-3) were isolated from Euphorbia amygdaloides ssp. semiperfoliata, including an unprecedented macrocyclic jatrophane ester bearing a hemiketal substructure, named jatrohemiketal (3). The chemical structures of compounds 1-3 and their relative configurations were determined by spectroscopic analysis. The absolute configuration of compound 3 was determined unambiguously through an original strategy combining NMR spectroscopy and molecular modeling. Conformational search calculations were performed for the four possible diastereomers 3a-3d differing in their C-6 and C-9 stereocenters, and the lowest energy conformer was used as input structure for geometry optimization. The prediction of NMR parameters ((1)H and (13)C chemical shifts and (1)H-(1)H coupling constants) by density functional theory (DFT) calculations allowed identifying the most plausible diastereomer. Finally, the stereostructure of 3 was solved by comparison of the structural features obtained by molecular modeling for 3a-3d with NMR-derived data (the values of dihedral angles deduced from the vicinal proton-proton coupling constants ((3)JHH) and interproton distances determined by ROESY). The methodology described herein provides an efficient way to solve or confirm structural elucidation of new macrocyclic diterpene esters, in particular when no crystal structure is available. PMID:26431312

  2. Oil droplet size determination in complex flavor delivery systems by diffusion NMR spectroscopy.

    PubMed

    Fieber, Wolfgang; Hafner, Valeria; Normand, Valéry

    2011-04-15

    Droplet size distribution of flavor oils in two different solid flavor delivery systems were determined with pulsed field gradient NMR spectroscopy: yeast encapsulation system, a spray dried flavor encapsulation system based on empty yeast cells, and glassy encapsulation system, an extruded solid water soluble carbohydrate delivery system. The oil droplet sizes are limited by the yeast cell walls in the yeast encapsulation system and the size distribution is unimodal according to images from transmission electron microscopy. The droplet size determination with diffusion NMR is based on the Murday and Cotts theory of restricted diffusion of liquids in geometrical confinements. Good fits of the diffusion data could be obtained by applying a unimodal, log-normal size distribution model and average droplet sizes of about 2 μm were found that correspond approximately to the inner diameter of the yeast cells. Scanning electron microscopy images showed a multimodal droplet size distribution in the glassy extruded delivery systems. To fit the NMR data a bimodal log-normal distribution function with five independent fitting parameters was implemented that yielded consistent and robust results. The two size populations were found in the micron and sub-micron range, respectively. The method was sufficiently accurate to depict variation of droplet size distributions in glassy encapsulation systems of different formulation. PMID:21316700

  3. Methylation patterns of aquatic humic substances determined by 13C NMR spectroscopy

    USGS Publications Warehouse

    Thorn, K.A.; Steelink, C.; Wershaw, R. L.

    1987-01-01

    13C NMR spectroscopy is used to examine the hydroxyl group functionality of a series of humic and fulvic acids from different aquatic environments. Samples first are methylated with 13C-labeled diazomethane. The NMR spectra of the diazomethylated samples allow one to distinguish between methyl esters of carboxylic acids, methyl ethers of phenolic hydroxyls, and methyl ethers of phenolic hydroxyls adjacent to two substituents. Samples are then permethylated with 13C-labeled methyl iodide/NaH. 13C NMR spectra of permethylated samples show that a significant fraction of the hydroxyl groups is not methylated with diazomethane alone. In these spectra methyl ethers of carbohydrate and aliphatic hydroxyls overlap with methyl ethers of phenolic hydroxyls. Side reactions of the methyltion procedure including carbon methylation in the CH3I/NaH procedure, are also examined. Humic and fulvic acids from bog, swamp, groundwater, and lake waters showssome differences in their distribution of hydroxyl groups, mainly in the concentrations of phenolic hydroxyls, which may be attributed to their different biogeochemical origins. ?? 1987.

  4. Determination of rank and kerogen type by high resolution NMR spectroscopy

    SciTech Connect

    Dickinson, W.W.; Collen, J.D. ); Newman, R.H. )

    1990-06-01

    Nuclear magnetic resonance (NMR) spectroscopy is a nondestructive technique for measuring the chemical and structural properties of organic matter. Although used in organic geochemistry for the past 14 years, the technique has continually undergone refinement. Initially, only the aromatic and aliphatic signal areas of the carbon NMR spectrum could be measured. Carboxylic groups as well as oxygen-substituted groups on aromatic and aliphatic carbon can now be qualitatively measured. The authors have examined coal and shale samples of various ranks from the Williston and San Juan basins, USA, and the Taranaki and Great South basins, New Zealand. Kerogen type can be distinguished on a plot of aromaticity versus the methylene to methyl ratio. For type III kerogens, vitrinite reflectance correlates very well with the percent of oxygen substitution on aromatic carbon and aromaticity. These parameters are excellent indicators of rank because they reflect the decrease in oxygen content and the increase in aromatic carbon as organic matter matures. Although the initial cost of NMR equipment is high, the vast amount of chemical information on kerogen that may be obtained from a small sample and very little laboratory preparation make it a valuable tool for petroleum geochemistry.

  5. Biological effects and physical safety aspects of NMR imaging and in vivo spectroscopy

    SciTech Connect

    Tenforde, T.S.; Budinger, T.F.

    1985-08-01

    An assessment is made of the biological effects and physical hazards of static and time-varying fields associated with the NMR devices that are being used for clinical imaging and in vivo spectroscopy. A summary is given of the current state of knowledge concerning the mechanisms of interaction and the bioeffects of these fields. Additional topics that are discussed include: (1) physical effects on pacemakers and metallic implants such as aneurysm clips, (2) human health studies related to the effects of exposure to nonionizing electromagnetic radiation, and (3) extant guidelines for limiting exposure of patients and medical personnel to the fields produced by NMR devices. On the basis of information available at the present time, it is concluded that the fields associated with the current generation of NMR devices do not pose a significant health risk in themselves. However, rigorous guidelines must be followed to avoid the physical interaction of these fields with metallic implants and medical electronic devices. 476 refs., 5 figs., 2 tabs.

  6. Quality assessment and authentication of virgin olive oil by NMR spectroscopy: a critical review.

    PubMed

    Dais, Photis; Hatzakis, Emmanuel

    2013-02-26

    Nuclear Magnetic Resonance (NMR) Spectroscopy has been extensively used for the analysis of olive oil and it has been established as a valuable tool for its quality assessment and authenticity. To date, a large number of research and review articles have been published with regards to the analysis of olive oil reflecting the potential of the NMR technique in these studies. In this critical review, we cover recent results in the field and discuss deficiencies and precautions of the three NMR techniques ((1)H, (13)C, (31)P) used for the analysis of olive oil. The two methodological approaches of metabonomics, metabolic profiling and metabolic fingerprinting, and the statistical methods applied for the classification of olive oils will be discussed in critical way. Some useful information about sample preparation, the required instrumentation for an effective analysis, the experimental conditions and data processing for obtaining high quality spectra will be presented as well. Finally, a constructive criticism will be exercised on the present methodologies used for the quality control and authentication of olive oil. PMID:23410622

  7. Functional group analysis in coal and on coal surfaces by NMR spectroscopy

    SciTech Connect

    Verkade, J.G.

    1990-01-01

    An accurate knowledge of the oxygen-bearing labile hydrogen functional groups (e.g., carboxylic acids, phenols and alcohols) in coal is required for today's increasingly sophisticated coal cleaning and beneficiation processes. Phospholanes (compounds having the general structure -POCH{sub 2}CH{sub 2}O (1)) are being investigated as reagents for the tagging of liable hydrogen functional groups in coal materials with the NMR-active {sup 31}P nucleus. Of twelve such reagents investigated so far, 2 (2-chloro-1,3-dioxaphospholane, ClPOCH{sub 2}CH{sub 2}O) and 8 (2-chloro-1,3-dithiaphospholane, ClPSCH{sub 2}CH{sub 2}S) have been found to be useful in identifying and quantitating, by {sup 31}P NMR spectroscopy, labile hydrogen functional groups in an Illinois No. 6 coal condensate. Reagent 2 has also been used to quantitate moisture in pyridine extracts of Argonne Premium Coal Samples. Preliminary {sup 119}Sn NMR spectroscopic results on model compounds with the new reagent CF{sub 3}C(O)NHSnMe{sub 3} (N-trimethylstannyltrifluoroacetamide, 14) suggest that labile hydrogen functional groups in coal materials may be more precisely identified with 14 than with phospholanes. 14 refs., 2 figs., 2 tabs.

  8. 60 MHz (1)H NMR spectroscopy for the analysis of edible oils.

    PubMed

    Parker, T; Limer, E; Watson, A D; Defernez, M; Williamson, D; Kemsley, E Kate

    2014-05-01

    We report the first results from a new 60 MHz (1)H nuclear magnetic resonance (NMR) bench-top spectrometer, Pulsar, in a study simulating the adulteration of olive oil with hazelnut oil. There were qualitative differences between spectra from the two oil types. A single internal ratio of two isolated groups of peaks could detect hazelnut oil in olive oil at the level of ∼13%w/w, whereas a whole-spectrum chemometric approach brought the limit of detection down to 11.2%w/w for a set of independent test samples. The Pulsar's performance was compared to that of Fourier transform infrared (FTIR) spectroscopy. The Pulsar delivered comparable sensitivity and improved specificity, making it a superior screening tool. We also mapped NMR onto FTIR spectra using a correlation-matrix approach. Interpretation of this heat-map combined with the established annotations of the NMR spectra suggested a hitherto undocumented feature in the IR spectrum at ∼1130 cm(-1), attributable to a double-bond vibration. PMID:24850979

  9. Structure of Colloidal Quantum Dots from Dynamic Nuclear Polarization Surface Enhanced NMR Spectroscopy.

    PubMed

    Piveteau, Laura; Ong, Ta-Chung; Rossini, Aaron J; Emsley, Lyndon; Copéret, Christophe; Kovalenko, Maksym V

    2015-11-01

    Understanding the chemistry of colloidal quantum dots (QDs) is primarily hampered by the lack of analytical methods to selectively and discriminately probe the QD core, QD surface and capping ligands. Here, we present a general concept for studying a broad range of QDs such as CdSe, CdTe, InP, PbSe, PbTe, CsPbBr3, etc., capped with both organic and inorganic surface capping ligands, through dynamic nuclear polarization (DNP) surface enhanced NMR spectroscopy. DNP can enhance NMR signals by factors of 10-100, thereby reducing the measurement times by 2-4 orders of magnitude. 1D DNP enhanced spectra acquired in this way are shown to clearly distinguish QD surface atoms from those of the QD core, and environmental effects such as oxidation. Furthermore, 2D NMR correlation experiments, which were previously inconceivable for QD surfaces, are demonstrated to be readily performed with DNP and provide the bonding motifs between the QD surfaces and the capping ligands. PMID:26473384

  10. Implementation and characterization of flow injection in dissolution dynamic nuclear polarization NMR spectroscopy.

    PubMed

    Chen, Hsueh-Ying; Hilty, Christian

    2015-08-24

    The use of dissolution dynamic nuclear polarization (D-DNP) offers substantially increased signals in liquid-state NMR spectroscopy. A challenge in realizing this potential lies in the transfer of the hyperpolarized sample to the NMR detector without loss of hyperpolarization. Here, the use of a flow injection method using high-pressure liquid leads to improved performance compared to the more common gas-driven injection, by suppressing residual fluid motions during the NMR experiment while still achieving a short injection time. Apparent diffusion coefficients are determined from pulsed field gradient echo measurements, and are shown to fall below 1.5 times the value of a static sample within 0.8 s. Due to the single-scan nature of D-DNP, pulsed field gradients are often the only choice for coherence selection or encoding, but their application requires stationary fluid. Sample delivery driven by a high-pressure liquid will improve the applicability of these types of D-DNP advanced experiments. PMID:26139513

  11. Bile acids conjugation in human bile is not random: new insights from (1)H-NMR spectroscopy at 800 MHz.

    PubMed

    Nagana Gowda, G A; Shanaiah, Narasimhamurthy; Cooper, Amanda; Maluccio, Mary; Raftery, Daniel

    2009-06-01

    Bile acids constitute a group of structurally closely related molecules and represent the most abundant constituents of human bile. Investigations of bile acids have garnered increased interest owing to their recently discovered additional biological functions including their role as signaling molecules that govern glucose, fat and energy metabolism. Recent NMR methodological developments have enabled single-step analysis of several highly abundant and common glycine- and taurine- conjugated bile acids, such as glycocholic acid, glycodeoxycholic acid, glycochenodeoxycholic acid, taurocholic acid, taurodeoxycholic acid, and taurochenodeoxycholic acid. Investigation of these conjugated bile acids in human bile employing high field (800 MHz) (1)H-NMR spectroscopy reveals that the ratios between two glycine-conjugated bile acids and their taurine counterparts correlate positively (R2 = 0.83-0.97; p = 0.001 x 10(-2)-0.006 x 10(-7)) as do the ratios between a glycine-conjugated bile acid and its taurine counterpart (R2 = 0.92-0.95; p = 0.004 x 10(-3)-0.002 x 10(-10)). Using such correlations, concentration of individual bile acids in each sample could be predicted in good agreement with the experimentally determined values. These insights into the pattern of bile acid conjugation in human bile between glycine and taurine promise useful clues to the mechanism of bile acids' biosynthesis, conjugation and enterohepatic circulation, and may improve our understanding of the role of individual conjugated bile acids in health and disease. PMID:19373503

  12. DNP-Enhanced Ultrawideline Solid-State NMR Spectroscopy: Studies of Platinum in Metal-Organic Frameworks.

    PubMed

    Kobayashi, Takeshi; Perras, Frédéric A; Goh, Tian Wei; Metz, Tanner L; Huang, Wenyu; Pruski, Marek

    2016-07-01

    Ultrawideline dynamic nuclear polarization (DNP)-enhanced (195)Pt solid-state NMR (SSNMR) spectroscopy and theoretical calculations are used to determine the coordination of atomic Pt species supported within the pores of metal-organic frameworks (MOFs). The (195)Pt SSNMR spectra, with breadths reaching 10 000 ppm, were obtained by combining DNP with broadbanded cross-polarization and CPMG acquisition. Although the DNP enhancements in static samples are lower than those typically observed under magic-angle spinning conditions, the presented measurements would be very challenging using the conventional SSNMR methods. The DNP-enhanced ultrawideline NMR spectra served to separate signals from cis- and trans-coordinated atomic Pt(2+) species supported on the UiO-66-NH2 MOF. Additionally, the data revealed a dominance of kinetic effects in the formation of Pt(2+) complexes and the thermodynamic effects in their reduction to nanoparticles. A single cis-coordinated Pt(2+) complex was confirmed in MOF-253. PMID:27266444

  13. DNP-enhanced ultrawideline solid-state NMR spectroscopy: Studies of platinum in metal–organic frameworks

    DOE PAGESBeta

    Kobayashi, Takeshi; Perras, Frederic A.; Goh, Tian Wei; Metz, Tanner L.; Huang, Wenyu; Pruski, Marek

    2016-06-06

    Ultrawideline dynamic nuclear polarization (DNP)-enhanced 195Pt solid-state NMR (SSNMR) spectroscopy and theoretical calculations are used to determine the coordination of atomic Pt species supported within the pores of metal–organic frameworks (MOFs). The 195Pt SSNMR spectra, with breadths reaching 10,000 ppm, were obtained by combining DNP with broadbanded cross-polarization and CPMG acquisition. Although the DNP enhancements in static samples are lower than those typically observed under magic-angle spinning conditions, the presented measurements would be very challenging using the conventional SSNMR methods. The DNP-enhanced ultrawideline NMR spectra served to separate signals from cis- and trans-coordinated atomic Pt2+ species supported on the UiO-66-NH2more » MOF. Here, the data revealed a dominance of kinetic effects in the formation of Pt2+ complexes and the thermodynamic effects in their reduction to nanoparticles. A single cis-coordinated Pt2+ complex was confirmed in MOF-253.« less

  14. High field NMR spectroscopy and FTICR mass spectrometry: powerful discovery tools for the molecular level characterization of marine dissolved organic matter from the South Atlantic Ocean

    NASA Astrophysics Data System (ADS)

    Hertkorn, N.; Harir, M.; Koch, B. P.; Michalke, B.; Grill, P.; Schmitt-Kopplin, P.

    2012-01-01

    Non target high resolution organic structural spectroscopy of marine dissolved organic matter (DOM) isolated on 27 November 2008 by means of solid phase extraction (SPE) from four different depths in the South Atlantic Ocean off the Angola coast (3.1° E; -17.7° S; Angola basin) provided molecular level information of complex unknowns with unprecedented coverage and resolution. The sampling was intended to represent major characteristic oceanic regimes of general significance: 5 m (FISH; near surface photic zone), 48 m (FMAX; fluorescence maximum), 200 m (upper mesopelagic zone) and 5446 m (30 m above ground). 800 MHz proton (1H) nuclear magnetic resonance (NMR) 1H NMR, spectra were least affected by fast and differential transverse NMR relaxation and produced at first similar looking, rather smooth bulk NMR envelopes reflecting intrinsic averaging from massive signal overlap. Visibly resolved NMR signatures were most abundant in surface DOM but contributed at most a few percent to the total 1H NMR integral and were mainly limited to unsaturated and singly oxygenated carbon chemical environments. The relative abundance and variance of resolved signatures between samples was maximal in the aromatic region; in particular, the aromatic resolved NMR signature of the deep ocean sample at 5446 m was considerably different from that of all other samples. When scaled to equal total NMR integral, 1H NMR spectra of the four marine DOM samples revealed considerable variance in abundance for all major chemical environments across the entire range of chemical shift. Abundance of singly oxygenated CH units and acetate derivatives declined from surface to depth whereas aliphatics and carboxyl-rich alicyclic molecules (CRAM) derived molecules increased in abundance. Surface DOM contained a remarkably lesser abundance of methyl esters than all other marine DOM, likely a consequence of photodegradation from direct exposure to sunlight. All DOM showed similar overall 13C NMR

  15. Characterization of noninnocent metal complexes using solid-state NMR spectroscopy: o-dioxolene vanadium complexes.

    PubMed

    Chatterjee, Pabitra B; Goncharov-Zapata, Olga; Quinn, Laurence L; Hou, Guangjin; Hamaed, Hiyam; Schurko, Robert W; Polenova, Tatyana; Crans, Debbie C

    2011-10-17

    (51)V solid-state NMR (SSNMR) studies of a series of noninnocent vanadium(V) catechol complexes have been conducted to evaluate the possibility that (51)V NMR observables, quadrupolar and chemical shift anisotropies, and electronic structures of such compounds can be used to characterize these compounds. The vanadium(V) catechol complexes described in these studies have relatively small quadrupolar coupling constants, which cover a surprisingly small range from 3.4 to 4.2 MHz. On the other hand, isotropic (51)V NMR chemical shifts cover a wide range from -200 to 400 ppm in solution and from -219 to 530 ppm in the solid state. A linear correlation of (51)V NMR isotropic solution and solid-state chemical shifts of complexes containing noninnocent ligands is observed. These experimental results provide the information needed for the application of (51)V SSNMR spectroscopy in characterizing the electronic properties of a wide variety of vanadium-containing systems and, in particular, those containing noninnocent ligands and that have chemical shifts outside the populated range of -300 to -700 ppm. The studies presented in this report demonstrate that the small quadrupolar couplings covering a narrow range of values reflect the symmetric electronic charge distribution, which is also similar across these complexes. These quadrupolar interaction parameters alone are not sufficient to capture the rich electronic structure of these complexes. In contrast, the chemical shift anisotropy tensor elements accessible from (51)V SSNMR experiments are a highly sensitive probe of subtle differences in electronic distribution and orbital occupancy in these compounds. Quantum chemical (density functional theory) calculations of NMR parameters for [VO(hshed)(Cat)] yield a (51)V chemical shift anisotropy tensor in reasonable agreement with the experimental results, but surprisingly the calculated quadrupolar coupling constant is significantly greater than the experimental value. The

  16. Electrostatic influence on rotational mobilities of sol-gel-encapsulated solutes by NMR and EPR spectroscopies.

    PubMed

    Wheeler, Korin E; Lees, Nicholas S; Gurbiel, Ryszard J; Hatch, Shelby L; Nocek, Judith M; Hoffman, Brian M

    2004-10-20

    The rotational mobilities of small solute molecules encapsulated in tetramethyl orthosilicate (TMOS) sol-gels have been investigated by EPR spectroscopy of encapsulated nitroxide probes and by high-resolution NMR spectroscopic measurements of transferred NOE's (trNOE's), of T(1)'s, and of T(1)'s in the rotating frame (T(1)rho). The two spectroscopic methods are sensitive to motions on different time scales and hence, are nicely complementary. Suites of neutral, positively, and negatively charged nitroxide probes (EPR) and of simple diamagnetic small molecules (NMR) were selected to disclose influences of electrostatic interactions with the sol-gel walls and to probe the presence of multiple populations of molecules in distinct regions of the sol-gel pores. For neutral and negatively charged solute probes, both techniques disclose a single population with a significantly increased average rotational correlation time, which we interpret at least in part as resulting from exchange between free-volume and transiently immobilized surface populations. The electrostatic attraction between cationic probes and the negatively charged sol-gel walls causes the positively charged probes to be more effectively immobilized and/or causes a greater percentage of probes to undergo this transient immobilization. The EPR spectra directly disclose a population of cationic probes which are immobilized on the X-band EPR time scale: tau(c) greater than or approximately equal 10(-7) s. However, NMR measurements of trNOE's and of T(1)rho demonstrate that this population does exchange with the free-volume probes on the slower time scale of NMR. This approach is equally applicable to the study of solutes within other types of confined spaces, as well. PMID:15479102

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

    ERIC Educational Resources Information Center

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

    2010-01-01

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

  18. Noninvasive quantitation of phosphorus metabolites in human tissue by NMR spectroscopy

    NASA Astrophysics Data System (ADS)

    Roth, K.; Hubesch, B.; Meyerhoff, D. J.; Naruse, S.; Gober, J. R.; Lawry, T. J.; Boska, M. D.; Matson, G. B.; Weiner, M. W.

    Quantitation of metabolite concentrations by NMR spectroscopy is complicated by the need to determine the volume from which signals are detected, and by the need to obtain the relative sensitivity of detection within this volume. The use of coils with inhomogeneous B1 fields further complicates these problems. In order to quantify metabolite concentrations using 31P NMR spectroscopy, an external reference of hexamethyl phosphoroustriamide was used. Studies were performed on phantoms, using either a surface coil or a Helmholtz head coil to confirm the accuracy of both the ISIS volume selection technique and the use of an external reference. The limitations of this method are related to contamination and signal loss inherent in the ISIS technique and difficulties with integration of broad overlapping peaks. The method was applied to seven normal human subjects. The integrals for metabolite signals in normal brain and calf muscle were determined by using NMRI software. The T1 values of the signals of all phosphorus metabolites in the selected volume were measured in order to correct for saturation effects. The concentrations for PCr, P i, and ATP were 4.9, 2.0, and 2.5 m M in brain and 36.5, 5.7, and 7.3 m M in muscle. These results are in good agreement with those reported for animals, demonstrating the validity of this quantitation technique.

  19. Labeling strategy and signal broadening mechanism of Protein NMR spectroscopy in Xenopus laevis oocytes.

    PubMed

    Ye, Yansheng; Liu, Xiaoli; Chen, Yanhua; Xu, Guohua; Wu, Qiong; Zhang, Zeting; Yao, Chendie; Liu, Maili; Li, Conggang

    2015-06-01

    We used Xenopus laevis oocytes, a paradigm for a variety of biological studies, as a eukaryotic model system for in-cell protein NMR spectroscopy. The small globular protein GB1 was one of the first studied in Xenopus oocytes, but there have been few reports since then of high-resolution spectra in oocytes. The scarcity of data is at least partly due to the lack of good labeling strategies and the paucity of information on resonance broadening mechanisms. Here, we systematically evaluate isotope enrichment and labeling methods in oocytes injected with five different proteins with molecular masses of 6 to 54 kDa. (19) F labeling is more promising than (15) N, (13) C, and (2) H enrichment. We also used (19) F NMR spectroscopy to quantify the contribution of viscosity, weak interactions, and sample inhomogeneity to resonance broadening in cells. We found that the viscosity in oocytes is only about 1.2 times that of water, and that inhomogeneous broadening is a major factor in determining line width in these cells. PMID:25965532

  20. Secondary structure determination of human. beta. -endorphin by /sup 1/H NMR spectroscopy

    SciTech Connect

    Lichtarge, O.; Jardetzky, O.; Li, C.H.

    1987-09-08

    The /sup 1/H NMR spectra of human ..beta..-endorphin indicate that the peptide exists in random-coil form in aqueous solution but becomes helical in mixed solvent. Thermal denaturation NMR experiments show that in water there is no transition between 24 and 75/sup 0/C, while a slow noncooperative thermal unfolding is observed in a 60% methanol-40% water mixed solvent in the same temperature range. These findings are consistent with circular dichroism studies by other workers concluding that ..beta..-endorphin is a random coil in water but that it forms 50% ..cap alpha..-helix or more in mixed solvents. The peptide in the mixed water-methanol solvent was further studied by correlated spectroscopy (COSY) and nuclear Overhauser effect spectroscopy (NOESY) experiments. These allow a complete set of assignments to be made and establish two distinct stretches over which the solvent induces formation of ..cap alpha..-helices: the first occurs between Tyr-1 and Thr-12 and the second between Leu-14 and extending to Lys-28. There is evidence that the latter is capped by a turn occurring between Lys-28 and Glu-31. These helices form at the enkephalin receptor binding site, which is at the amino terminus, and at the morphine receptor binding site, located at the carboxyl terminus. The findings suggest that these two receptors may specifically recognize ..cap alpha..-helices.

  1. Phosphorus Speciation of Sequential Extracts of Organic Amendments using NMR Spectroscopy

    NASA Astrophysics Data System (ADS)

    Akinremi, O.

    2009-04-01

    O.O. 1Akinremi Babasola Ajiboye and Donald N. Flaten 1Department of Soil Science, University of Manitoba, Winnipeg, R3T 2NT, Canada We carried out this study in order to determine the forms of phosphorus in various organic amendments using state-of-the art spectroscopic technique. Anaerobically digested biosolids (BIO), hog (HOG), dairy (DAIRY), beef (BEEF) and poultry (POULTRY) manures were subjected to sequential extraction. The extracts were analyzed by solution 31P nuclear magnetic resonance (NMR) spectroscopy. Most of the total P analysed by inductively coupled plasma-optical emission spectroscopy (ICP-OES) in the sequential extracts of organic amendments were orthophosphate, except POULTRY, which was dominated by organic P. The labile P fraction in all the organic amendments, excluding POULTRY, was mainly orthophosphate P from readily soluble calcium and some aluminum phosphates. In the poultry litter, however, Ca phytate was the main P species controlling P solubility. Such knowledge of the differences in the chemical forms of phosphorus in organic amendments are essential for proper management of these amendments for agro-environmental purposes Key words: organic amendments, solution NMR, sequential fractionation, labile phosphorus

  2. Characterization of prednisolone in controlled porosity osmotic pump pellets using solid-state NMR spectroscopy.

    PubMed

    Sotthivirat, S; Lubach, J W; Haslam, J L; Munson, E J; Stella, V J

    2007-05-01

    The overall objective of this study was to demonstrate the influence of formulation and processing variables on the physical state of prednisolone (PDL) in formulations consisting of PDL, microcrystalline cellulose (MCC), and sulfobutylether-beta-cyclodextrin (CD). PDL was used as a model drug in controlled porosity osmotic pump pellet (CP-OPP) formulations, and was characterized using solid-state NMR spectroscopy and other complimentary analytical techniques. Dosage forms and the solid-state properties of drugs and excipients in a formulation may be influenced by the processing conditions used. Several processing parameters, such as amount of water used in wet granulation and subsequent drying conditions, were found to affect the solid-state transformation of PDL. In addition, the presence of excipients in the CP-OPP was observed to decrease the degree of PDL crystallinity, presumably by creating an inclusion complex with the CD. A hydrated form of PDL was created when PDL was ground with water alone; however, this form was not observed in formulated products. Solid-state NMR spectroscopy was shown to be a powerful technique for the analysis of drug formulations and investigations of the effects of processing conditions. PMID:17455361

  3. The Development of 460 GHz gyrotrons for 700 MHz DNP-NMR spectroscopy

    NASA Astrophysics Data System (ADS)

    Idehara, T.; Tatematsu, Y.; Yamaguchi, Y.; Khutoryan, E. M.; Kuleshov, A. N.; Ueda, K.; Matsuki, Y.; Fujiwara, T.

    2015-07-01

    Two demountable gyrotrons with internal mode converters were developded as sub-THz radiation sources for 700 MHz DNP (Dynamic Nuclear Polarization) enhanced NMR spectroscopy. Experimental study on the DNP-NMR spectroscopy will be carried out in Osaka University, Institute for Protein Research, as a collaboration with FIR UF. Both gyrotrons operate near 460 GHz and the output CW power measured at the end of transmission system made by circular waveguides is typically 20 to 30 watts. One of them named Gyrotron FU CW GVI (we are using "Gyrotron FU CW GO-1" as an official name in Osaka University) is designed to have a special function of high speed frequency modulation δ f within 100 MHz band. This will expand excitable band width of ESR and increase the number of electron spins contributing to DNP. The other gyrotron, Gyrotron FU CW GVIA ("Gyrotron FU CW GO-II") has a function of frequency tunability Δ f in the range of wider than 1.5 GHz, which is achieved in steady state by changing magnetic field intensity. This function should be used for adjusting the output frequency at the optimal value to achieve the highest enhancement factor of DNP.

  4. Determination of RNA polymerase binding surfaces of transcription factors by NMR spectroscopy

    PubMed Central

    Drögemüller, Johanna; Strauß, Martin; Schweimer, Kristian; Jurk, Marcel; Rösch, Paul; Knauer, Stefan H.

    2015-01-01

    In bacteria, RNA polymerase (RNAP), the central enzyme of transcription, is regulated by N-utilization substance (Nus) transcription factors. Several of these factors interact directly, and only transiently, with RNAP to modulate its function. As details of these interactions are largely unknown, we probed the RNAP binding surfaces of Escherichia coli (E. coli) Nus factors by nuclear magnetic resonance (NMR) spectroscopy. Perdeuterated factors with [1H,13C]-labeled methyl groups of Val, Leu, and Ile residues were titrated with protonated RNAP. After verification of this approach with the N-terminal domain (NTD) of NusG and RNAP we determined the RNAP binding site of NusE. It overlaps with the NusE interaction surface for the NusG C-terminal domain, indicating that RNAP and NusG compete for NusE and suggesting possible roles for the NusE:RNAP interaction, e.g. in antitermination and direct transcription:translation coupling. We solved the solution structure of NusA-NTD by NMR spectroscopy, identified its RNAP binding site with the same approach we used for NusG-NTD, and here present a detailed model of the NusA-NTD:RNAP:RNA complex. PMID:26560741

  5. Understanding J-Modulation during Spatial Encoding for Sensitivity-Optimized Ultrafast NMR Spectroscopy.

    PubMed

    Gouilleux, Boris; Rouger, Laetitia; Charrier, Benoît; Kuprov, Ilya; Akoka, Serge; Dumez, Jean-Nicolas; Giraudeau, Patrick

    2015-10-01

    Ultrafast (UF) NMR spectroscopy is an approach that yields 2D spectra in a single scan. This methodology has become a powerful analytical tool that is used in a large array of applications. However, UF NMR spectroscopy still suffers from an intrinsic low sensitivity, and from the need to compromise between sensitivity, spectral width, and resolution. In particular, the modulation of signal intensities by the spin-spin J-coupling interaction (J-modulation) impacts significantly on the intensities of the spectral peaks. This effect can lead to large sensitivity losses and even to missing spectral peaks, depending on the nature of the spin system. Herein, a general simulation package (Spinach) is used to describe J-modulation effects in UF experiments. The results from simulations match with experimental data and the results of product operator calculations. Several methods are proposed to optimize the sensitivity in UF COSY spectra. The potential and drawbacks of the different strategies are also discussed. These approaches provide a way to adjust the sensitivity of UF experiments for a large range of applications. PMID:26401975

  6. The isomers and conformers of some push pull enamines studied by vibrational and NMR spectroscopy and by ab initio calculations

    NASA Astrophysics Data System (ADS)

    Pigošová, J.; Gatial, A.; Milata, V.; Černuchová, P.; Prónayová, N.; Liptaj, T.; Matějka, P.

    2005-06-01

    The isomers and conformers of six push-pull enamines: 3-dimethylamino-, 3-methylamino- and 3-amino-2-acetyl propenenitrile [(H 3C) 2N-CH dbnd6 C(CN)(COCH 3), H 3C-NH-CH dbnd6 C(CN)(COCH 3) and H 2N-CH dbnd6 C(CN)(COCH 3)] and 3-dimethylamino-, 3-methylamino- and 3-amino-2-methylsulfonyl propenenitrile [(H 3C) 2N-CH dbnd6 C(CN)(SO 2CH 3), H 3C-NH-CH dbnd6 C(CN)(SO 2CH 3) and H 2N-CH dbnd6 C(CN)(SO 2CH 3)] have been studied experimentally by vibrational and NMR spectroscopy and theoretically by the ab initio calculations at MP2 level in 6-31G** basis set. The IR and Raman spectra of all compounds as a solid and solute in various solvents have been recorded in the region 4000-50 cm -1. The NMR spectra were obtained in chloroform and DMSO at room temperature. All six compounds have been prepared by the same way. NMR spectra revealed that both dimethylamino compounds were prepared as a pure E isomers whereas in the case of methylamino compounds the 3-methylamino-2-methylsulfonyl propenenitrile was prepared also as a pure E isomer but 3-methylamino-2-acetyl propenenitrile as a pure Z isomer. Also 3-amino-2-methylsulfonyl propenenitrile was obtained as a pure the E isomer, but 3-amino-2-acetyl propenenitrile as a mixture of both E and Z isomers. Confomational possibilities of studied compounds are given only by the rotation of the acetyl and methylamino groups. Vibrational spectra revealed existence of two conformers with Z and E orientation of acetyl group for 3-dimethylamino-2-acetyl propenenitrile. Two conformers with anti or syn orientation of methylamino group for 3-methylamino-2-methylsulfonyl propenenitrile have been confirmed by vibrational and NMR spectra, but only one conformer with anti orientation of methylamino group for 3-methylamino-2-acetyl propenenitrile in chloroform solution and in solid phase was found. For latter compound the additional isomer/conformer was detected in more polar solvents (acetonitrile/DMSO). These experimental findings have been

  7. Flexible Stoichiometry and Asymmetry of the PIDDosome Core Complex by Heteronuclear NMR Spectroscopy and Mass Spectrometry

    PubMed Central

    Nematollahi, Lily A.; Garza-Garcia, Acely; Bechara, Chérine; Esposito, Diego; Morgner, Nina; Robinson, Carol V.; Driscoll, Paul C.

    2015-01-01

    Homotypic death domain (DD)–DD interactions are important in the assembly of oligomeric signaling complexes such as the PIDDosome that acts as a platform for activation of caspase-2-dependent apoptotic signaling. The structure of the PIDDosome core complex exhibits an asymmetric three-layered arrangement containing five PIDD-DDs in one layer, five RAIDD-DDs in a second layer and an additional two RAIDD-DDs. We addressed complex formation between PIDD-DD and RAIDD-DD in solution using heteronuclear nuclear magnetic resonance (NMR) spectroscopy, nanoflow electrospray ionization mass spectrometry and size-exclusion chromatography with multi-angle light scattering. The DDs assemble into complexes displaying molecular masses in the range 130–158 kDa and RAIDD-DD:PIDD-DD stoichiometries of 5:5, 6:5 and 7:5. These data suggest that the crystal structure is representative of only the heaviest species in solution and that two RAIDD-DDs are loosely attached to the 5:5 core. Two-dimensional 1H,15N-NMR experiments exhibited signal loss upon complexation consistent with the formation of high-molecular-weight species. 13C-Methyl-transverse relaxation optimized spectroscopy measurements of the PIDDosome core exhibit signs of differential line broadening, cross-peak splitting and chemical shift heterogeneity that reflect the presence of non-equivalent sites at interfaces within an asymmetric complex. Experiments using a mutant RAIDD-DD that forms a monodisperse 5:5 complex with PIDD-DD show that the spectroscopic signature derives from the quasi- but non-exact equivalent environments of each DD. Since this characteristic was previously demonstrated for the complex between the DDs of CD95 and FADD, the NMR data for this system are consistent with the formation of a structure homologous to the PIDDosome core. PMID:25528640

  8. Flexible stoichiometry and asymmetry of the PIDDosome core complex by heteronuclear NMR spectroscopy and mass spectrometry.

    PubMed

    Nematollahi, Lily A; Garza-Garcia, Acely; Bechara, Chérine; Esposito, Diego; Morgner, Nina; Robinson, Carol V; Driscoll, Paul C

    2015-02-27

    Homotypic death domain (DD)-DD interactions are important in the assembly of oligomeric signaling complexes such as the PIDDosome that acts as a platform for activation of caspase-2-dependent apoptotic signaling. The structure of the PIDDosome core complex exhibits an asymmetric three-layered arrangement containing five PIDD-DDs in one layer, five RAIDD-DDs in a second layer and an additional two RAIDD-DDs. We addressed complex formation between PIDD-DD and RAIDD-DD in solution using heteronuclear nuclear magnetic resonance (NMR) spectroscopy, nanoflow electrospray ionization mass spectrometry and size-exclusion chromatography with multi-angle light scattering. The DDs assemble into complexes displaying molecular masses in the range 130-158kDa and RAIDD-DD:PIDD-DD stoichiometries of 5:5, 6:5 and 7:5. These data suggest that the crystal structure is representative of only the heaviest species in solution and that two RAIDD-DDs are loosely attached to the 5:5 core. Two-dimensional (1)H,(15)N-NMR experiments exhibited signal loss upon complexation consistent with the formation of high-molecular-weight species. (13)C-Methyl-transverse relaxation optimized spectroscopy measurements of the PIDDosome core exhibit signs of differential line broadening, cross-peak splitting and chemical shift heterogeneity that reflect the presence of non-equivalent sites at interfaces within an asymmetric complex. Experiments using a mutant RAIDD-DD that forms a monodisperse 5:5 complex with PIDD-DD show that the spectroscopic signature derives from the quasi- but non-exact equivalent environments of each DD. Since this characteristic was previously demonstrated for the complex between the DDs of CD95 and FADD, the NMR data for this system are consistent with the formation of a structure homologous to the PIDDosome core. PMID:25528640

  9. Reexamination of C-NMR13 in (TMTTF)2AsF6 : Comparison with infrared spectroscopy

    NASA Astrophysics Data System (ADS)

    Hirose, Shinji; Kawamoto, Atsushi; Matsunaga, Noriaki; Nomura, Kazushige; Yamamoto, Kaoru; Yakushi, Kyuya

    2010-05-01

    The charge order (CO) state can be observed by microprobe measurements such as nuclear magnetic resonance (NMR) and infrared spectroscopy. We used the infrared spectroscopy to examine (TMTTF)2AsF6 and confirmed the CO transition seen in previous C13 -NMR studies. However we found the degree of charge disproportionation, Δρ=0.16 , to be smaller than that obtained from the analysis of T1 in C13 -NMR and the redistribution of charge density below spin Peierls transition predicted by C13 -NMR was not observed at low temperature. We estimated the degree of spin disproportionation to be 0.11 from the analysis of the NMR shift in previous NMR studies. This small disproportionation does not require the redistribution of charge density at low temperature. The different behaviors of T1 at charge-rich and charge-poor molecular sites observed by C13 -NMR can be examined by the contribution of the commensurate antiferromagnetic fluctuation with 4kF .

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

    PubMed

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

    2014-01-01

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

  11. The contribution of solid-state NMR spectroscopy to understanding biomineralization: Atomic and molecular structure of bone

    NASA Astrophysics Data System (ADS)

    Duer, Melinda J.

    2015-04-01

    Solid-state NMR spectroscopy has had a major impact on our understanding of the structure of mineralized tissues, in particular bone. Bone exemplifies the organic-inorganic composite structure inherent in mineralized tissues. The organic component of the extracellular matrix in bone is primarily composed of ordered fibrils of collagen triple-helical molecules, in which the inorganic component, calcium phosphate particles, composed of stacks of mineral platelets, are arranged around the fibrils. This perspective argues that key factors in our current structural model of bone mineral have come about through NMR spectroscopy and have yielded the primary information on how the mineral particles interface and bind with the underlying organic matrix. The structure of collagen within the organic matrix of bone or any other structural tissue has yet to be determined, but here too, this perspective shows there has been real progress made through application of solid-state NMR spectroscopy in conjunction with other techniques. In particular, NMR spectroscopy has highlighted the fact that even within these structural proteins, there is considerable dynamics, which suggests that one should be cautious when using inherently static structural models, such as those arising from X-ray diffraction analyses, to gain insight into molecular roles. It is clear that the NMR approach is still in its infancy in this area, and that we can expect many more developments in the future, particularly in understanding the molecular mechanisms of bone diseases and ageing.

  12. No-D NMR (no-deuterium proton NMR) spectroscopy: a simple yet powerful method for analyzing reaction and reagent solutions.

    PubMed

    Hoye, Thomas R; Eklov, Brian M; Ryba, Troy D; Voloshin, Mikhail; Yao, Letitia J

    2004-03-18

    [reaction: see text] The title technique is a convenient and powerful method for directly monitoring or assaying any reaction mixture or reagent solution. Examples of some common processes (Fischer esterification, lithiation, butyllithium/THF compatibility, olefin metathesis, and a quantification assay), each interrogated in its native solvent, are presented. The spectral data are easy to acquire, and the information content makes a compelling case for routine use of No-D NMR spectroscopy. PMID:15012073

  13. Characterization of reactive intermediates by multinuclear diffusion-ordered NMR spectroscopy (DOSY).

    PubMed

    Li, Deyu; Keresztes, Ivan; Hopson, Russell; Williard, Paul G

    2009-02-17

    Nuclear magnetic resonance (NMR) is the most powerful and widely utilized technique for determining molecular structure. Although traditional NMR data analysis involves the correlation of chemical shift, coupling constant, and NOE interactions to specific structural features, a largely overlooked method introduced more than 40 years ago, pulsed gradient spin-echo (PGSE), measures diffusion coefficients of molecules in solution, thus providing their relative particle sizes. In the early 1990s, the PGSE sequence was incorporated into a two-dimensional experiment, dubbed diffusion-ordered NMR spectroscopy (DOSY), in which one dimension represents chemical shift data while the second dimension resolves species by their diffusion properties. This combination provides a powerful tool for identifying individual species in a multicomponent solution, earning the nickname "chromatography by NMR". In this Account, we describe our efforts to utilize DOSY techniques to characterize organometallic reactive intermediates in solution in order to correlate structural data to solid-state crystal structures determined by X-ray diffraction and to discover the role of aggregate formation and solvation states in reaction mechanisms. In 2000, we reported our initial efforts to employ DOSY techniques in the characterization of reactive intermediates such as organolithium aggregates. Since then, we have explored DOSY experiments with various nuclei beyond (1)H, including (6)Li, (7)Li, (11)B, (13)C, and (29)Si. Additionally, we proposed a diffusion coefficient-formula weight relationship to determine formula weight, aggregation number, and solvation state of reactive intermediates. We also introduced an internal reference system to correlate the diffusion properties of unknown reactive intermediates with known inert molecular standards, such as aromatic compounds, terminal olefins, cycloolefins, and tetraalkylsilanes. Furthermore, we utilized DOSY to interpret the role of aggregation number

  14. NMR metabolomics of human lung tumours reveals distinct metabolic signatures for adenocarcinoma and squamous cell carcinoma.

    PubMed

    Rocha, Cláudia M; Barros, António S; Goodfellow, Brian J; Carreira, Isabel M; Gomes, Ana; Sousa, Vitor; Bernardo, João; Carvalho, Lina; Gil, Ana M; Duarte, Iola F

    2015-01-01

    Lung tumour subtyping, particularly the distinction between adenocarcinoma (AdC) and squamous cell carcinoma (SqCC), is a critical diagnostic requirement. In this work, the metabolic signatures of lung carcinomas were investigated through (1)H NMR metabolomics, with a view to provide additional criteria for improved diagnosis and treatment planning. High Resolution Magic Angle Spinning Nuclear Magnetic Resonance (NMR) spectroscopy was used to analyse matched tumour and adjacent control tissues from 56 patients undergoing surgical excision of primary lung carcinomas. Multivariate modeling allowed tumour and control tissues to be discriminated with high accuracy (97% classification rate), mainly due to significant differences in the levels of 13 metabolites. Notably, the magnitude of those differences were clearly distinct for AdC and SqCC: major alterations in AdC were related to phospholipid metabolism (increased phosphocholine, glycerophosphocholine and phosphoethanolamine, together with decreased acetate) and protein catabolism (increased peptide moieties), whereas SqCC had stronger glycolytic and glutaminolytic profiles (negatively correlated variations in glucose and lactate and positively correlated increases in glutamate and alanine). Other tumour metabolic features were increased creatine, glutathione, taurine and uridine nucleotides, the first two being especially prominent in SqCC and the latter in AdC. Furthermore, multivariate analysis of AdC and SqCC profiles allowed their discrimination with a 94% classification rate, thus showing great potential for aiding lung tumours subtyping. Overall, this study has provided new, clear evidence of distinct metabolic signatures for lung AdC and SqCC, which can potentially impact on diagnosis and provide important leads for future research on novel therapeutic targets or imaging tracers. PMID:25368033

  15. High pressure NMR reveals that apomyoglobin is an equilibrium mixture from the native to the unfolded.

    PubMed

    Kitahara, Ryo; Yamada, Hiroaki; Akasaka, Kazuyuki; Wright, Peter E

    2002-07-01

    Pressure-induced reversible conformational changes of sperm whale apomyoglobin have been studied between 30 bar and 3000 bar on individual residue basis by utilizing 1H/15N hetero nuclear single-quantum coherence two-dimensional NMR spectroscopy at pH 6.0 and 35 degrees C. Apomyoglobin showed a series of pressure-dependent NMR spectra as a function of pressure, assignable to the native (N), intermediates (I), molten globule (MG) and unfolded (U) conformers. At 30 bar, the native fold (N) shows disorder only in the F helix. Between 500 bar and 1200 bar, a series of locally disordered conformers I are produced, in which local disorder occurs in the C helix, the CD loop, the G helix and part of the H helix. At 2000 bar, most cross-peaks exhibit severe line-broadening, suggesting the formation of a molten globule, but at 3000 bar all the cross-peaks reappear, showing that the molten globule turns into a well-hydrated, mobile unfolded conformation U. Since all the spectral changes were reversible with pressure, apomyoglobin is considered to exist as an equilibrium mixture of the N, I, MG and U conformers at all pressures. MG is situated at 2.4+/-(0.1) kcal/mol above N at 1 bar and the unfolding transition from the combined N-I state to MG is accompanied by a loss of partial molar volume by 75+/-(3) ml/mol. On the basis of these observations, we postulate a theorem that the partial molar volume of a protein decreases in parallel with the loss of its conformational order. PMID:12079388

  16. Magneto-optical contrast in liquid-state optically detected NMR spectroscopy.

    PubMed

    Pagliero, Daniela; Meriles, Carlos A

    2011-12-01

    We use optical Faraday rotation (OFR) to probe nuclear spins in real time at high-magnetic field in a range of diamagnetic sample fluids. Comparison of OFR-detected NMR spectra reveals a correlation between the relative signal amplitude and the fluid Verdet constant, which we interpret as a manifestation of the variable detuning between the probe beam and the sample optical transitions. The analysis of chemical-shift-resolved, optically detected spectra allows us to set constraints on the relative amplitudes of hyperfine coupling constants, both for protons at chemically distinct sites and other lower-gyromagnetic-ratio nuclei including carbon, fluorine, and phosphorous. By considering a model binary mixture we observe a complex dependence of the optical response on the relative concentration, suggesting that the present approach is sensitive to the solvent-solute dynamics in ways complementary to those known in inductive NMR. Extension of these experiments may find application in solvent suppression protocols, sensitivity-enhanced NMR of metalloproteins in solution, the investigation of solvent-solute interactions, or the characterization of molecular orbitals in diamagnetic systems. PMID:22100736

  17. Determination of neo- and D-chiro-inositol hexakisphosphate in soils by solution 31P NMR spectroscopy.

    PubMed

    Turner, Benjamin L; Cheesman, Alexander W; Godage, H Yasmin; Riley, Andrew M; Potter, Barry V L

    2012-05-01

    The inositol phosphates are an abundant but poorly understood group of organic phosphorus compounds found widely in the environment. Four stereoisomers of inositol hexakisphosphate (IP(6)) occur, although for three of these (scyllo, neo, and D-chiro) the origins, dynamics, and biological function remain unknown, due in large part to analytical limitations in their measurement in environmental samples. We synthesized authentic neo- and D-chiro-IP(6) and used them to identify signals from these compounds in three soils from the Falkland Islands. Both compounds resisted hypobromite oxidation and gave quantifiable (31)P NMR signals at δ = 6.67 ppm (equatorial phosphate groups of the 4-equatorial/2-axial conformer of neo-IP(6)) and δ = 6.48 ppm (equatorial phosphate groups of the 2-equatorial/4-axial conformer of D-chiro-IP(6)) in soil extracts. Inositol hexakisphosphate accounted for 46-54% of the soil organic phosphorus, of which the four stereoisomers constituted, on average, 55.9% (myo), 32.8% (scyllo), 6.1% (neo), and 5.2% (D-chiro). Reappraisal of the literature based on the new signal assignments revealed that neo- and D-chiro-IP(6) occur widely in both terrestrial and aquatic ecosystems. These results confirm that the inositol phosphates can constitute a considerable fraction of the organic phosphorus in soils and reveal the prevalence of neo- and D-chiro-IP(6) in the environment. The hypobromite oxidation and solution (31)P NMR spectroscopy procedure allows the simultaneous quantification of all four IP(6) stereoisomers in environmental samples and provides a platform for research into the origins and ecological significance of these enigmatic compounds. PMID:22489788

  18. Radiofrequency quadrupolar NMR stark spectroscopy: steady state response calibration and tensorial mapping.

    PubMed

    Tarasek, Matthew R; Kempf, James G

    2010-10-01

    Radiofrequency electric (E) fields oscillating at twice the usual NMR frequency (2ω(0)) can induce double-quantum transitions in quadrupolar nuclei, an NMR Stark effect. Characterization of such is of interest to aid understanding of electrostatic effects in NMR spectra. Calibration of Stark responses to an applied electric field may also be used to assess native fields within molecules and materials. We present high-field (14.1 T), room-temperature NMR experiments to calibrate the 2ω(0) Stark response in crystalline GaAs. This system presents an important test of current techniques and conditions, as historical studies at low field (500-900 mT) and low temperature (77 K) provide a basis for comparison. Our measurements of steady state response reveal the quadrupolar Stark tuning rate for (69)Ga in this material. The value, β(Q) = (11.5 ± 0.1) × 10(12) m(-1), is 3.6 times larger than the most-reliable prior result. In the process, we also uncovered a previously unobserved double-quantum steady state coherence. It appears as a completely separable dispersive signal component in quadrature-detected presaturation spectra versus offset from 2ω(0). The new component may eventually afford an independent route to calibrating β(Q). Finally, we demonstrated exceptional agreement with theory of the orientation-dependent Stark response for rotation of the sample relative to B(0) over a range of 90° and for E-field amplitudes from 30-180 V/cm. PMID:20839890

  19. In vivo 31P-NMR spectroscopy of right ventricle in pigs.

    PubMed

    Schwartz, G G; Steinman, S K; Weiner, M W; Matson, G B

    1992-06-01

    The energy metabolism of the right ventricle (RV) in vivo has been largely unexplored. The goal of this study was to develop and implement techniques for in vivo 31P nuclear magnetic resonance (NMR) spectroscopy of the RV free wall. A two-turn, crossover-design elliptical surface coil was constructed to provide high sensitivity across the thin RV wall but minimal sensitivity in the blood-filled RV cavity. In 36 open-chest, anesthetized pigs, 31P spectroscopy of the RV free wall was performed with this coil at a field strength of 2 Tesla. Spectra were obtained from 800 acquisitions in 24 min with an average signal-to-noise ratio of 13.2 for phosphocreatine (PCr). The PCr-to-ATP (PCr/ATP) ratio of porcine RV was 1.42 +/- 0.05 (mean +/- SE), uncorrected for saturation at a repetition time of 1.8 s. With the use of literature values of the time constant of longitudinal relaxation (T1) to correct for partial saturation, the RV PCr/ATP was estimated to lie between 1.7 and 2.3. Decreased RV PCr/ATP was observed during RV ischemia and pressure overload. Thus in vivo 31P spectroscopy of the RV is readily accomplished with an appropriate surface coil and can provide new information about RV energy metabolism. PMID:1621852

  20. Organic solute changes with acidification in Lake Skjervatjern as shown by 1H-NMR spectroscopy

    USGS Publications Warehouse

    Malcolm, R.L.; Hayes, T.

    1994-01-01

    1H-NMR spectroscopy has been found to be a useful tool to establish possible real differences and trends between all natural organic solute fractions (fulvic acids, humic acids, and XAD-4 acids) after acid-rain additions to the Lake Skjervatjern watershed. The proton NMR technique used in this study determined the spectral distribution of nonexchangeable protons among four peaks (aliphatic protons; aliphatic protons on carbon ?? or attached to electronegative groups; protons on carbons attached to O or N heteroatoms; and aromatic protons). Differences of 10% or more in the respective peak areas were considered to represent a real difference. After one year of acidification, fulvic acids decreased 13% (relative) in Peak 3 protons on carbon attached to N and O heteratoms and exhibited a decrease in aromatic protons between 27% and 31%. Humic acids also exhibited an 11% relative decrease in aromatic protons as a result of acidification. After one year of acidification, real changes were shown in three of the four proton assignments in XAD-4 acids. Peak 1 aliphatic protons increased by 14% (relative), Peak 3 protons on carbons attached to O and N heteroatoms decreased by 13% (relative), and aromatic protons (Peak 4) decreased by 35% (relative). Upon acidification, there was a trend in all solutes for aromatic protons to decrease and aliphatic protons to increase. The natural variation in organic solutes as shown in the Control Side B of the lake from 1990 to 1991 is perhaps a small limitation to the same data interpretations of acid rain changes at the Lake Skjervatjern site, but the proton NMR technique shows great promise as an independent scientific tool to detect and support other chemical techniques in establishing organic solute changes with different treatments (i.e., additions of acid rain).

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

    ERIC Educational Resources Information Center

    Mak, Kendrew K. W.

    2004-01-01

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

  2. Multinuclear NMR spectroscopy for differentiation of molecular configurations and solvent properties between acetone and dimethyl sulfoxide

    NASA Astrophysics Data System (ADS)

    Wen, Yuan-Chun; Kuo, Hsiao-Ching; Jia, Hsi-Wei

    2016-04-01

    The differences in molecular configuration and solvent properties between acetone and dimethyl sulfoxide (DMSO) were investigated using the developed technique of 1H, 13C, 17O, and 1H self-diffusion liquid state nuclear magnetic resonance (NMR) spectroscopy. Acetone and DMSO samples in the forms of pure solution, ionic salt-added solution were used to deduce their active sites, relative dipole moments, dielectric constants, and charge separations. The NMR results suggest that acetone is a trigonal planar molecule with a polarized carbonyl double bond, whereas DMSO is a trigonal pyramidal-like molecule with a highly polarized S-O single bond. Both molecules use their oxygen atoms as the active sites to interact other molecules. These different molecular models explain the differences their physical and chemical properties between the two molecules and explain why DMSO is classified as an aprotic but highly dipolar solvent. The results are also in agreement with data obtained using X-ray diffraction, neutron diffraction, and theoretical calculations.

  3. Authentication of beef versus horse meat using 60 MHz 1H NMR spectroscopy.

    PubMed

    Jakes, W; Gerdova, A; Defernez, M; Watson, A D; McCallum, C; Limer, E; Colquhoun, I J; Williamson, D C; Kemsley, E K

    2015-05-15

    This work reports a candidate screening protocol to distinguish beef from horse meat based upon comparison of triglyceride signatures obtained by 60 MHz (1)H NMR spectroscopy. Using a simple chloroform-based extraction, we obtained classic low-field triglyceride spectra from typically a 10 min acquisition time. Peak integration was sufficient to differentiate samples of fresh beef (76 extractions) and horse (62 extractions) using Naïve Bayes classification. Principal component analysis gave a two-dimensional "authentic" beef region (p=0.001) against which further spectra could be compared. This model was challenged using a subset of 23 freeze-thawed training samples. The outcomes indicated that storing samples by freezing does not adversely affect the analysis. Of a further collection of extractions from previously unseen samples, 90/91 beef spectra were classified as authentic, and 16/16 horse spectra as non-authentic. We conclude that 60 MHz (1)H NMR represents a feasible high-throughput approach for screening raw meat. PMID:25577043

  4. The Interaction between tRNALys3 and the Primer Activation Signal Deciphered by NMR Spectroscopy

    PubMed Central

    Brachet, Franck; Tisne, Carine

    2013-01-01

    The initiation of reverse transcription of the human immunodeficiency virus type 1 (HIV-1) requires the opening of the three-dimensional structure of the primer tRNALys3 for its annealing to the viral RNA at the primer binding site (PBS). Despite the fact that the result of this rearrangement is thermodynamically more stable, there is a high-energy barrier that requires the chaperoning activity of the viral nucleocapsid protein. In addition to the nucleotide complementarity to the PBS, several regions of tRNALys3 have been described as interacting with the viral genomic RNA. Among these sequences, a sequence of the viral genome called PAS for “primer activation signal” was proposed to interact with the T-arm of tRNALys3, this interaction stimulating the initiation of reverse transcription. In this report, we investigate the formation of this additional interaction with NMR spectroscopy, using a simple system composed of the primer tRNALys3, the 18 nucleotides of the PBS, the PAS (8 nucleotides) encompassed or not in a hairpin structure, and the nucleocapsid protein. Our NMR study provides molecular evidence of the existence of this interaction and highlights the role of the nucleocapsid protein in promoting this additional RNA-RNA annealing. This study presents the first direct observation at a single base-pair resolution of the PAS/anti-PAS association, which has been proposed to be involved in the chronological regulation of the reverse transcription. PMID:23762248

  5. XRD, TEM, IR, Raman and NMR Spectroscopy of In Situ Crystallization of Lithium Disilicate Glass

    NASA Technical Reports Server (NTRS)

    Fuss, T.; Mogus-Milankovic, A.; Ray, C. S.; Lesher, C. E.; Youngman, R.; Day, D. E.

    2006-01-01

    The structure of a Li2O-2SiO2 (LS2) glass was investigated as a function of pressure and temperature up to 6 GPa and 750 C respectively, using XRD, TEM, IR, Raman and NMR spectroscopy. Glass densified at 6 GPa has an average Si-O-Si bond angle approx.7deg lower than that found in glass processed at 4.5 GPa. At 4.5 GPa, lithium disilicate crystallizes from the glass, while at 6 GPa a new high pressure form of lithium metasilicate crystallizes. The new phase, while having lithium metasilicate crystal symmetry, contains at least 4 different Si sites. NMR results for 6 GPa sample indicate the presence of Q4 species with (Q(sup 4))Si-O-Si(Q(sup 4)) bond angles of approx.157deg. This is the first reported occurrence of Q(sup 4) species with such large bond angles in alumina free alkali silicate glass. No five- or six- coordinated Si are found.

  6. In Situ and Ex Situ Low-Field NMR Spectroscopy and MRI Endowed by SABRE Hyperpolarization**

    PubMed Central

    Barskiy, Danila A.; Kovtunov, Kirill V.; Koptyug, Igor V.; He, Ping; Groome, Kirsten A.; Best, Quinn A.; Shi, Fan; Goodson, Boyd M.; Shchepin, Roman V.; Truong, Milton L.; Coffey, Aaron M.; Waddell, Kevin W.; Chekmenev, Eduard Y.

    2015-01-01

    By using 5.75 and 47.5 mT nuclear magnetic resonance (NMR) spectroscopy, up to 105-fold sensitivity enhancement through signal amplification by reversible exchange (SABRE) was enabled, and subsecond temporal resolution was used to monitor an exchange reaction that resulted in the buildup and decay of hyperpolarized species after parahydrogen bubbling. We demonstrated the high-resolution low-field proton magnetic resonance imaging (MRI) of pyridine in a 47.5 mT magnetic field endowed by SABRE. Molecular imaging (i.e. imaging of dilute hyperpolarized substances rather than the bulk medium) was conducted in two regimes: in situ real-time MRI of the reaction mixture (in which pyridine was hyperpolarized), and ex situ MRI (in which hyperpolarization decays) of the liquid hyperpolarized product. Low-field (milli-Tesla range, e.g. 5.75 and 47.5 mT used in this study) parahydrogen-enhanced NMR and MRI, which are free from the limitations of high-field magnetic resonance (including susceptibility-induced gradients of the static magnetic field at phase interfaces), potentially enables new imaging applications as well as differentiation of hyperpolarized chemical species on demand by exploiting spin manipulations with static and alternating magnetic fields. PMID:25367202

  7. In vivo 31P-NMR spectroscopy of chronically stimulated canine skeletal muscle.

    PubMed

    Clark, B J; Acker, M A; McCully, K; Subramanian, H V; Hammond, R L; Salmons, S; Chance, B; Stephenson, L W

    1988-02-01

    Chronic stimulation converts skeletal muscle of mixed fiber type to a uniform muscle made up of type I, fatigue-resistant fibers. Here, the bioenergetic correlates of fatigue resistance in conditioned canine latissimus dorsi are assessed with in vivo phosphorus-31 nuclear magnetic resonance (31P-NMR) spectroscopy. After chronic electrical stimulation, five dogs underwent 31P-NMR spectroscopic and isometric tension measurements on conditioned and contralateral control muscle during stimulation for 200, 300, 500, and 800 ms of an 1,100-ms duty cycle. With stimulation, phosphocreatine (PCr) fell proportional to the degree of stimulation in both conditioned and control muscle but fell significantly less in conditioned muscle at all but the least intense stimulation period (200 ms). Isometric tension, expressed as a tension time index per gram muscle, was significantly greater in the conditioned muscle at the two longest stimulation periods. The overall small change in PCr and the lack of a plateau in tension observed in the conditioned muscle are similar to that seen in cardiac muscle during increased energy demand. This study indicates that the conditioned muscle's markedly enhanced resistance to fatigue is in part the result of its increased capacity for oxidative phosphorylation. PMID:3348365

  8. Conformations of banana-shaped molecules studied by 2H NMR spectroscopy in liquid crystalline solvents.

    PubMed

    Calucci, Lucia; Forte, Claudia; Csorba, Katalin Fodor; Mennucci, Benedetta; Pizzanelli, Silvia

    2007-01-11

    ClPbis11BB and Pbis11BB, two banana-shaped mesogens differing by a chlorine substituent on the central phenyl ring, show a nematic and a B2 phase, respectively. To obtain information on the structural features responsible for their different mesomorphic behavior, a study of the preferred conformations of these mesogens has been performed by NMR spectroscopy in two nematic media (Phase IV and ZLI1167), which should mimic the environment of the molecules in their own mesophases, avoiding problems of sample alignment by a magnetic field. To this aim, 2H NMR experiments have been performed on selectively deuterated isotopomers of ClPbis11BB and Pbis11BB and of two parent molecules, ClPbisB and PbisB, assumed as models in previous theoretical and experimental conformational studies. We found that only a limited number of conformations is compatible with experimental data, often very different from those inferred from theoretical calculations in vacuo, indicating a strong influence of the liquid crystalline environment on molecular conformation. No significant differences between chlorinated and non-chlorinated molecules were found, this suggesting that chlorine does not change the molecular conformational equilibrium, as previously proposed. PMID:17201428

  9. The dynamic complex of cytochrome c6 and cytochrome f studied with paramagnetic NMR spectroscopy.

    PubMed

    Díaz-Moreno, Irene; Hulsker, Rinske; Skubak, Pavol; Foerster, Johannes M; Cavazzini, Davide; Finiguerra, Michelina G; Díaz-Quintana, Antonio; Moreno-Beltrán, Blas; Rossi, Gian-Luigi; Ullmann, G Matthias; Pannu, Navraj S; De la Rosa, Miguel A; Ubbink, Marcellus

    2014-08-01

    The rapid transfer of electrons in the photosynthetic redox chain is achieved by the formation of short-lived complexes of cytochrome b6f with the electron transfer proteins plastocyanin and cytochrome c6. A balance must exist between fast intermolecular electron transfer and rapid dissociation, which requires the formation of a complex that has limited specificity. The interaction of the soluble fragment of cytochrome f and cytochrome c6 from the cyanobacterium Nostoc sp. PCC 7119 was studied using NMR spectroscopy and X-ray diffraction. The crystal structures of wild type, M58H and M58C cytochrome c6 were determined. The M58C variant is an excellent low potential mimic of the wild type protein and was used in chemical shift perturbation and paramagnetic relaxation NMR experiments to characterize the complex with cytochrome f. The interaction is highly dynamic and can be described as a pure encounter complex, with no dominant stereospecific complex. Ensemble docking calculations and Monte-Carlo simulations suggest a model in which charge-charge interactions pre-orient cytochrome c6 with its haem edge toward cytochrome f to form an ensemble of orientations with extensive contacts between the hydrophobic patches on both cytochromes, bringing the two haem groups sufficiently close to allow for rapid electron transfer. This model of complex formation allows for a gradual increase and decrease of the hydrophobic interactions during association and dissociation, thus avoiding a high transition state barrier that would slow down the dissociation process. PMID:24685428

  10. Authentication of beef versus horse meat using 60 MHz 1H NMR spectroscopy

    PubMed Central

    Jakes, W.; Gerdova, A.; Defernez, M.; Watson, A.D.; McCallum, C.; Limer, E.; Colquhoun, I.J.; Williamson, D.C.; Kemsley, E.K.

    2015-01-01

    This work reports a candidate screening protocol to distinguish beef from horse meat based upon comparison of triglyceride signatures obtained by 60 MHz 1H NMR spectroscopy. Using a simple chloroform-based extraction, we obtained classic low-field triglyceride spectra from typically a 10 min acquisition time. Peak integration was sufficient to differentiate samples of fresh beef (76 extractions) and horse (62 extractions) using Naïve Bayes classification. Principal component analysis gave a two-dimensional “authentic” beef region (p = 0.001) against which further spectra could be compared. This model was challenged using a subset of 23 freeze–thawed training samples. The outcomes indicated that storing samples by freezing does not adversely affect the analysis. Of a further collection of extractions from previously unseen samples, 90/91 beef spectra were classified as authentic, and 16/16 horse spectra as non-authentic. We conclude that 60 MHz 1H NMR represents a feasible high-throughput approach for screening raw meat. PMID:25577043

  11. Low Temperature 1H MAS NMR Spectroscopy Studies of Proton Motion in Zeolite

    SciTech Connect

    Huo, H.; Peng, L; Grey, C

    2009-01-01

    Low temperature {sup 1}H MAS NMR spectroscopy is used to study protonic motion in zeolite HZSM-5 in both samples that have been dried using procedures that are standard in the literature and samples that have been more carefully dehydrated. A significant enhancement of proton mobility is seen for the ''standard'' dehydrated HZSM-5 sample in comparison to that seen for the much drier sample. This is ascribed to a vehicle-hopping mechanism involving the residual water that is present in these zeolites. A gradual change of the framework structure is observed on cooling to approximately 213 K, as monitored via the change in {sup 1}H chemical shift values of the Broensted acid resonances and by X-ray diffraction. A more sudden change in structure is seen by differential scanning calorimetry and NMR at approximately 220?230 K, which is associated with changes in both the mobility and the modes of binding of the residual water to the Broensted acid sites and the zeolite framework.

  12. In vivo sup 31 P-NMR spectroscopy of chronically stimulated canine skeletal muscle

    SciTech Connect

    Clark, B.J. III; McCully, A.K.; Subramanian, H.V.; Hammond, R.L.; Salmons, S.; Chance, B.; Stephenson, L.W. Univ. of Pennsylvania School of Medicine, Philadelphia Univ. of Birmingham )

    1988-02-01

    Chronic stimulation converts skeletal muscle of mixed fiber type to a uniform muscle made up of type I, fatigue-resistant fibers. Here, the bioenergetic correlates of fatigue resistance in conditioned canine latissimus dorsi are assessed with in vivo phosphorus-31 nuclear magnetic resonance ({sup 31}P-NMR) spectroscopy. After chronic electrical stimulation, five dogs underwent {sup 31}P-NMR spectroscopic and isometric tension measurements on conditioned and contralateral control muscle during stimulation for 200, 300, 500, and 800 ms of an 1,100-ms duty cycle. With stimulation, phosphocreatine (PCr) fell proportional to the degree of stimulation in both conditioned and control muscle but fell significantly less in conditioned muscle at all the least intense stimulation period (200 ms). Isometric tension, expressed as a tension time index per gram muscle, was significantly greater in the conditioned muscle at the two longest stimulation periods. The overall small change in PCr and the lack of a plateau in tension observed in the conditioned muscle are similar to that seen in cardiac muscle during increased energy demand. This study indicates that the conditioned muscle's markedly enhanced resistance to fatigue is in part the result of its increased capacity for oxidative phosphorylation.

  13. An exploratory NMR nutri-metabonomic investigation reveals dimethyl sulfone as a dietary biomarker for onion intake.

    PubMed

    Winning, Hanne; Roldán-Marín, Eduvigis; Dragsted, Lars O; Viereck, Nanna; Poulsen, Morten; Sánchez-Moreno, Concepción; Cano, M Pilar; Engelsen, Søren B

    2009-11-01

    The metabolome following intake of onion by-products is evaluated. Thirty-two rats were fed a diet containing an onion by-product or one of the two derived onion by-product fractions: an ethanol extract and the residue. A 24 hour urine sample was analyzed using (1)H NMR spectroscopy in order to investigate the effects of onion intake on the rat metabolism. Application of interval extended canonical variates analysis (ECVA) proved to be able to distinguish between the metabolomic profiles from rats consuming normal feed and rats fed with an onion diet. Two dietary biomarkers for onion intake were identified as dimethyl sulfone and 3-hydroxyphenylacetic acid. The same two dietary biomarkers were subsequently revealed by interval partial least squares regression (PLS) to be perfect quantitative markers for onion intake. The best PLS calibration model yielded a root mean square error of cross-validation (RMSECV) of 0.97% (w/w) with only 1 latent variable and a squared correlation coefficient of 0.94. This indicates that urine from rats on the by-product diet, the extract diet, and the residue diet all contain the same dietary biomarkers and it is concluded that dimethyl sulfone and 3-hydroxyphenylacetic acid are dietary biomarkers for onion intake. Being able to detect specific dietary biomarkers is highly beneficial in the control of nutritionally enhanced functional foods. PMID:19838425

  14. Single-Quantum Coherence Filter for Strongly Coupled Spin Systems for Localized 1H NMR Spectroscopy

    NASA Astrophysics Data System (ADS)

    Trabesinger, Andreas H.; Mueller, D. Christoph; Boesiger, Peter

    2000-08-01

    A pulse sequence for localized in vivo1H NMR spectroscopy is presented, which selectively filters single-quantum coherence built up by strongly coupled spin systems. Uncoupled and weakly coupled spin systems do not contribute to the signal output. Analytical calculations using a product operator description of the strongly coupled AB spin system as well as in vitro tests demonstrate that the proposed filter produces a signal output for a strongly coupled AB spin system, whereas the resonances of a weakly coupled AX spin system and of uncoupled spins are widely suppressed. As a potential application, the detection of the strongly coupled AA‧BB‧ spin system of taurine at 1.5 T is discussed.

  15. Spatial structure of fibrinopeptide B in water solution with DPC micelles by NMR spectroscopy

    NASA Astrophysics Data System (ADS)

    Blokhin, Dmitriy S.; Fayzullina, Adeliya R.; Filippov, Andrei V.; Karataeva, Farida Kh.; Klochkov, Vladimir V.

    2015-12-01

    Fibrinopeptide B (GluFib) is one of the factors of thrombosis. Normal blood protein soluble, fibrinogen (fibrinopeptide A and fibrinopeptide B), is transformed into the insoluble, fibrin, which in the form of filaments adheres to the vessel wall at the site of injury, forming a grid. However, the spatial structure of this peptide has not been established till now. In this article, GluFib peptide is investigated together with dodecylphosphocholine (DPC) micelles which were used for mimicking the environment of peptide in blood vessels. The spatial structure was obtained by applying 1D and 2D 1H-1H NMR spectroscopy (TOCSY, NOESY). It was shown that the fibrinopeptide B does not have a secondary structure but we can distinguish the fragment Gly 9 - Arg 14 with a good convergence (the backbone RMSD for the Gly9 - Arg14 is 0.18 ± 0.08 Å).

  16. Low-field (1)H NMR spectroscopy for distinguishing between arabica and robusta ground roast coffees.

    PubMed

    Defernez, Marianne; Wren, Ella; Watson, Andrew D; Gunning, Yvonne; Colquhoun, Ian J; Le Gall, Gwénaëlle; Williamson, David; Kemsley, E Kate

    2017-02-01

    This work reports a new screening protocol for addressing issues of coffee authenticity using low-field (60MHz) bench-top (1)H NMR spectroscopy. Using a simple chloroform-based extraction, useful spectra were obtained from the lipophilic fraction of ground roast coffees. It was found that 16-O-methylcafestol (16-OMC, a recognized marker compound for robusta beans) gives rise to an isolated peak in the 60MHz spectrum, which can be used as an indicator of the presence of robusta beans in the sample. A total of 81 extracts from authenticated coffees and mixtures were analysed, from which the detection limit of robusta in arabica was estimated to be between 10% and 20% w/w. Using the established protocol, a surveillance exercise was conducted of 27 retail samples of ground roast coffees which were labelled as "100% arabica". None were found to contain undeclared robusta content above the estimated detection limit. PMID:27596398

  17. Coupled effect of salt and pH on proteins probed with NMR spectroscopy

    NASA Astrophysics Data System (ADS)

    Kukic, Predrag; O'Meara, Fergal; Hewage, Chandralal; Erik Nielsen, Jens

    2013-07-01

    The coupled effect of ionic strength (50-400 mM) and pH (2-8) on ionization and conformation equilibria of lysozyme was studied using NMR spectroscopy. Observed changes in pKa values of the ionizable groups were found to originate from perturbations in the geometry of hydrogen bonds rather than screening of electric fields. Moreover, at the ionic strengths used here, salt-induced local conformational changes had a dominant effect on chemical shifts measured on 1HN and 15N amide nuclei. Accurate modeling of these localized perturbations in structure-based energy calculations is a necessary prerequisite on the way to complete understanding of any salt-induced processes in proteins.

  18. Structural studies of homoisoflavonoids: NMR spectroscopy, X-ray diffraction, and theoretical calculations

    NASA Astrophysics Data System (ADS)

    Sievänen, Elina; Toušek, Jaromír; Lunerová, Kamila; Marek, Jaromír; Jankovská, Dagmar; Dvorská, Margita; Marek, Radek

    2010-08-01

    In this article we present a detailed structural investigation for five homoisoflavonoids, molecules important from the pharmacological point of view. For studying the electron distribution as well as its influence on the physicochemical properties, NMR spectroscopy, X-ray diffraction, and theoretical calculations have been used. Nuclear magnetic shieldings obtained by using DFT calculations for optimized molecular geometries are correlated with the experimentally determined chemical shifts. The theoretical data are well in agreement with the experimental values. The single crystal X-ray structures of homoisoflavonoid derivatives 1, 3, and 4 have been solved. The molecular geometries and crystal packing determined by X-ray diffraction are used for characterizing the intermolecular interactions. Electron distribution is crucial for the stability of radicals and hence the antioxidant efficiency of flavonoid structures. The hydrogen bonding governs the formation of complexes of homoisoflavonoids with biological targets.

  19. Recent applications of /sup 13/C NMR spectroscopy to biological systems

    SciTech Connect

    Matwiyoff, N.A.

    1981-01-01

    Carbon-13 nuclear magnetic resonance (NMR) spectroscopy, in conjunction with carbon-13 labelling, is a powerful new analytical technique for the study of metabolic pathways and structural components in intact organelles, cells, and tissues. The technique can provide, rapidly and non-destructively, unique information about: the architecture and dynamics of structural components; the nature of the intracellular environment; and metabolic pathways and relative fluxes of individual carbon atoms. With the aid of results recently obtained by us and those reported by a number of other laboratories, the problems and potentialities of the technique will be reviewed with emphasis on: the viscosities of intracellular fluids; the structure and dynamics of the components of membranes; and the primary and secondary metabolic pathways of carbon in microorganisms, plants, and mammalian cells in culture.

  20. Quantitative {sup 29}Si MAS NMR spectroscopy of cement and silica fume containing paramagnetic impurities

    SciTech Connect

    Hilbig, H. . E-mail: hilbig@cbm.bv.tum.de; Koehler, F.H.; Schiessl, P.

    2006-02-15

    The low natural abundance and the long spin lattice relaxation time of {sup 29}Si lead to long measurement times and/or low signal-to-noise ratios using {sup 29}Si magic angle spinning NMR spectroscopy. By contrast, samples containing paramagnetic iron ions have much shorter relaxation times, making measurements up to seven times more efficient, but at the same time making quantitative analysis unreliable. To solve the problem, the spin-lattice relaxation times of ordinary Portland cement (opc) and silica fume with and without iron content has been determined with inversion recovery experiments. The effect of varying the spectrum repetition time on the quantitative analysis is demonstrated for mixtures of opc with silica fume. For opc and silica fume with iron impurities repetition times as short as 5 s has permitted accurate quantitative analysis of the silicates present in these materials.

  1. Solid-State Ru-99 NMR Spectroscopy: A Useful Tool for Characterizing Prototypal Diamagnetic Ruthenium Compounds Compounds

    SciTech Connect

    Ooms, Kristopher J.; Wasylishen, Roderick E.

    2004-09-08

    The feasibility of 99Ru NMR spectroscopy as a tool to characterize solid compounds is demonstrated. Results of the first solid-state 99Ru NMR investigation of diamagnetic compounds are presented for Ru(NH3)6Cl2, K4Ru(CN)6 xH2O (x) 0, 3, LaKRu(CN)6, and Ru3(CO)12. The sensitivity of the ruthenium magnetic shielding tensor to subtle changes in the local structure about the ruthenium nucleus is highlighted by comparing the 99Ru isotropic chemical shift of Ru(NH3)6Cl2 in aqueous solutions and in the solid state. The narrow isotropic 99Ru NMR peak observed for solid Ru(NH3)6Cl2 indicates that this compound is an ideal secondary reference sample for solid-state 99Ru NMR studies.

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

    PubMed

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

    2016-06-01

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

  3. NMR spectroscopy with force-gradient detection on a GaAs epitaxial layer.

    PubMed

    Alexson, Dimitri A; Smith, Doran D

    2013-10-01

    We demonstrate nuclear magnetic resonance spectroscopy on 35 μm(3) of (69)Ga in a GaAs epitaxial layer in vacuum at 5K, and 5T yielding a linewidth on the order of 10 kHz. This was achieved by a force-gradient magnetic resonance detection scheme, using the interaction between the force-gradient of a Ni sphere-tipped single crystal Si cantilever and the nuclear spins to register changes in the spin state as a change in the driven cantilever's natural resonant frequency. The dichotomy between the background magnetic field (B0) homogeneity requirements imposed by NMR spectroscopy and the magnetic particle's large magnetic field gradient is resolved via sample shuttling during the NMR pulse encoding. A GaAs sample is polarized in a B0 of 5T for 3 T1. The sample is shuttled away from the magnetic particle to a region of negligible magnetic field inhomogeneity. A (π/2)x pulse rotates the polarization to the xy-plane, the magnetization is allowed to precess for 2-200 μs before a (π/2)x or (π/2)y pulse stores the remaining spin along the z-axis that represents a single point of the free induction decay (FID). The sample is shuttled back to the established tip-sample distance. An adiabatic rapid passage (ARP) sweep inverts the spins in a volume of interest, causing the cantilever's natural resonance frequency to shift an amount proportional to the spin polarization in the volume. By varying the delay between the first and second (π/2) pulses the entire FID is measured. PMID:23962899

  4. Investigation of multiaxial molecular dynamics by 2H MAS NMR spectroscopy.

    PubMed

    Kristensen, J H; Hoatson, G L; Vold, R L

    1998-11-01

    The technique of 2H MAS NMR spectroscopy is presented for the investigation of multiaxial molecular dynamics. To evaluate the effects of discrete random reorientation a Lie algebraic formalism based on the stochastic Liouville-von Neumann equation is developed. The solution to the stochastic Liouville-von Neumann equation is obtained both in the presence and absence of rf irradiation. This allows effects of molecular dynamics to be evaluated during rf pulses and extends the applicability of the formalism to arbitrary multiple pulse experiments. Theoretical methods are presented for the description of multiaxial dynamics with particular emphasis on the application of vector parameters to represent molecular rotations. Numerical time and powder integration algorithms are presented that are both efficient and easy to implement computationally. The applicability of 2H MAS NMR spectroscopy for investigating molecular dynamics is evaluated from theoretical spectra. To demonstrate the potential of the technique the dynamics of thiourea-2H4 is investigated experimentally. From a series of variable temperature MAS and quadrupole echo spectra it has been found that the dynamics can be described by composite rotation about the CS and CN bonds. Both experiments are sensitive to the fast CS rotation which is shown to be described by the Arrhenius parameters E(CS) = 46.4 +/- 2.3 kJ mol(-1) and ln(A(CS))= 32.6 +/- 0.9. The MAS experiment represents a significant improvement by simultaneously allowing the dynamics of the slow CN rotation to be fully characterized in terms of E(CN) = 56.3 +/- 3.4 kJ mol(-1) and ln(A(CN)) = 25.3 +/- 1.1. PMID:9875600

  5. Probing the calcium and sodium local environment in bones and teeth using multinuclear solid state NMR and X-ray absorption spectroscopy.

    PubMed

    Laurencin, Danielle; Wong, Alan; Chrzanowski, Wojciech; Knowles, Jonathan C; Qiu, Dong; Pickup, David M; Newport, Robert J; Gan, Zhehong; Duer, Melinda J; Smith, Mark E

    2010-02-01

    Despite the numerous studies of bone mineral, there are still many questions regarding the exact structure and composition of the mineral phase, and how the mineral crystals become organised with respect to each other and the collagen matrix. Bone mineral is commonly formulated as hydroxyapatite, albeit with numerous substitutions, and has previously been studied by (31)P and (1)H NMR, which has given considerable insight into the complexity of the mineral structure. However, to date, there has been no report of an NMR investigation of the other major component of bone mineral, calcium, nor of common minority cations like sodium. Here, direct analysis of the local environment of calcium in two biological apatites, equine bone (HB) and bovine tooth (CT), was carried out using both (43)Ca solid state NMR and Ca K-edge X-ray absorption spectroscopy, revealing important structural information about the calcium coordination shell. The (43)Ca delta(iso) in HB and CT is found to correlate with the average Ca-O bond distance measured by Ca K-edge EXAFS, and the (43)Ca NMR linewidths show that there is a greater distribution in chemical bonding around calcium in HB and CT, compared to synthetic apatites. In the case of sodium, (23)Na MAS NMR, high resolution 3Q-MAS NMR, as well as (23)Na{(31)P} REDOR and (1)H{(23)Na} R(3)-HMQC correlation experiments give the first direct evidence that some sodium is located inside the apatite phase in HB and CT, but with a greater distribution of environments compared to a synthetic sodium substituted apatite (Na-HA). PMID:20094673

  6. Aliphatic chain length by isotropic mixing (ALCHIM): determining composition of complex lipid samples by 1H NMR spectroscopy

    PubMed Central

    Yi, Ruiyang; Volden, Paul A.; Conzen, Suzanne D.

    2015-01-01

    Quantifying the amounts and types of lipids present in mixtures is important in fields as diverse as medicine, food science, and biochemistry. Nuclear magnetic resonance (NMR) spectroscopy can quantify the total amounts of saturated and unsaturated fatty acids in mixtures, but identifying the length of saturated fatty acid or the position of unsaturation by NMR is a daunting challenge. We have developed an NMR technique, aliphatic chain length by isotropic mixing, to address this problem. Using a selective total correlation spectroscopy technique to excite and transfer magnetization from a resolved resonance, we demonstrate that the time dependence of this transfer to another resolved site depends linearly on the number of aliphatic carbons separating the two sites. This technique is applied to complex natural mixtures allowing the identification and quantification of the constituent fatty acids. The method has been applied to whole adipocytes demonstrating that it will be of great use in studies of whole tissues. PMID:24831341

  7. In situ NMR spectroscopy: inulin biomass conversion in ZnCl₂ molten salt hydrate medium-SnCl₄ addition controls product distribution.

    PubMed

    Wang, Yingxiong; Pedersen, Christian Marcus; Qiao, Yan; Deng, Tiansheng; Shi, Jing; Hou, Xianglin

    2015-01-22

    The dehydration of inulin biomass to the platform chemicals, 5-hydroxymethylfurfural (5-HMF) and levulinic acid (LA), in ZnCl2 molten salt hydrate medium was investigated. The influence of the Lewis acid catalyst, SnCl4, on the product distribution was examined. An in situ(1)H NMR technique was employed to follow the reaction at the molecular level. The experimental results revealed that only 5-HMF was obtained from degradation of inulin biomass in ZnCl2 molten salt hydrate medium, while the LA was gradually becoming the main product when the reaction temperature was increased in the presence of the Lewis acid catalyst SnCl4. In situ NMR spectroscopy could monitor the reaction and give valuable insight. PMID:25439916

  8. 1H and 23Na MAS NMR spectroscopy of cationic species in CO2 selective alkaline earth metal porous silicoaluminophosphates prepared via liquid and solid state ion exchange

    NASA Astrophysics Data System (ADS)

    Arévalo-Hidalgo, Ana G.; Dugar, Sneha; Fu, Riqiang; Hernández-Maldonado, Arturo J.

    2012-07-01

    The location of extraframework cations in Sr2+ and Ba2+ ion-exchanged SAPO-34 was estimated by means of 1H and 23Na MAS NMR spectroscopy and spectral deconvolution. Incorporation of the alkaline earth metal cations onto the SAPO framework was achieved via liquid state ion exchange, coupled partial detemplation/solid-state ion exchange, and combination of both techniques. MAS NMR revealed that the level of ion exchange was limited by the presence of protons and sodium cations near hexagonal prisms (site SI), which are relatively difficult to exchange with the alkaline earth metal due to steric and charge repulsion criteria. In addition, the presence of ammonium cations in the supercages facilitated the exchange of otherwise tenacious hydrogen as corroborated by unit cell compositional data as well as enhanced CO2 adsorption at low partial pressures. The extraframework ammonium species were produced from partial detemplation of the structure-directing agent employed for the SAPO-34 synthesis, tetraethylammonium.

  9. Nontarget analysis of Murchison soluble organic matter by high-field NMR spectroscopy and FTICR mass spectrometry.

    PubMed

    Hertkorn, N; Harir, M; Schmitt-Kopplin, Ph

    2015-09-01

    High-field NMR spectra of Murchison meteorite methanolic extracts revealed primarily aliphatic extraterrestrial organic matter (EOM) with near statistical branching of commonly C(3-5) units separated by heteroatoms and aromatic units. The ratios of CCH, OCH and C(sp2)H units were 89 : 8 : 3, whereas carbon-based aliphatic chain termination was in the order methyl >  -COOH >  -CH(CH3)COOH. Aliphatic methine carbon was abundant, but its weak NMR signatures were primarily deduced from JRES (J-resolved) NMR spectra. Carbon NMR spectra were dominated by methylene and methyl carbon; strong apodization revealed methine carbon, of which about 20% was aromatic. Extrapolation provided 5-7% aromatic carbon present in Murchison soluble EOM. Compositional heterogeneity in Murchison methanolic extracts was visible in NMR and Fourier transform ion cyclotron (FTICR) mass spectra obtained from a few cubic millimeters of solid Murchison meteorite; increasing sample size enhanced uniformity of NMR spectra. Intrinsic chemical diversity and pH-dependent chemical shift variance contributed to the disparity of NMR spectra. FTICR mass spectra provided distinct clustering of CHO/CHOS and CHNO/CHNOS molecular series and confirmed the prevalence of aliphatic/alicyclic (73%) over single aromatic (21%) and polyaromatic (6%) molecular compositions, suggesting extensive aliphatic substitution of aromatic units as proposed by NMR. Murchison soluble EOM molecules feature a center with enhanced aromatic and heteroatom content, which provides rather diffuse and weak NMR signatures resulting from a huge overall chemical diversity. The periphery of Murchison EOM molecules comprises flexible branched aliphatic chains and aliphatic carboxylic acids. These project on narrow ranges of chemical shift, facilitating observation in one-dimensional and two-dimensional NMR spectra. The conformational entropy provided by these flexible surface moieties facilitates the solubility of EOM. PMID

  10. 1,3-Alternate calix[4]arene nitronyl nitroxide tetraradical and diradical: synthesis, X-ray crystallography, paramagnetic NMR spectroscopy, EPR spectroscopy, and magnetic studies

    SciTech Connect

    Rajca, Andrzej; Pink, Maren; Mukherjee, Sumit; Rajca, Suchada; Das, Kausik

    2008-04-02

    Calix[4]arenes constrained to 1,3-alternate conformation and functionalized at the upper rim with four and two nitronyl nitroxides have been synthesized, and characterized by X-ray crystallography, magnetic resonance (EPR and {sup 1}H NMR) spectroscopy, and magnetic studies. Such calix[4]arene tetraradicals and diradicals provide scaffolds for through-bond and through-space intramolecular exchange couplings.

  11. NMR and IR Spectroscopy for the Structural Characterization of Edible Fats and Oils: An Instrumental Analysis Laboratory

    ERIC Educational Resources Information Center

    Crowther, Molly W.

    2008-01-01

    This article describes an upper-level instrumental laboratory for undergraduates that explores the complementary nature of IR and NMR spectroscopy for analysis of several edible fats and oils that are structurally similar but differ in physical properties and health implications. Five different fats and oils are analyzed for average chain length,…

  12. Response to the Letter to the Editor regarding "Determination of the fatty acid profile by 1H-NMR spectroscopy."

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In expansion of previous work (G. Knothe, J.A. Kenar, Determination of the fatty acid profile by 1H-NMR spectroscopy, Eur. J. Lipid Sci. Technol. 2004, 106, 88-96), an additional approach is discussed for quantitating saturated fatty acids in the fatty acid profiles of common vegetable oils by 1H-NM...

  13. LEGO-NMR spectroscopy: a method to visualize individual subunits in large heteromeric complexes.

    PubMed

    Mund, Markus; Overbeck, Jan H; Ullmann, Janina; Sprangers, Remco

    2013-10-18

    Seeing the big picture: Asymmetric macromolecular complexes that are NMR active in only a subset of their subunits can be prepared, thus decreasing NMR spectral complexity. For the hetero heptameric LSm1-7 and LSm2-8 rings NMR spectra of the individual subunits of the complete complex are obtained, showing a conserved RNA binding site. This LEGO-NMR technique makes large asymmetric complexes accessible to detailed NMR spectroscopic studies. PMID:23946163

  14. An investigation of the sol-gel process in ionic liquid-silica gels by time resolved Raman and 1H NMR spectroscopy.

    PubMed

    Martinelli, Anna; Nordstierna, Lars

    2012-10-14

    We report, by employing time resolved Raman and nuclear magnetic resonance (NMR) spectroscopy, on the gelation process in ionogels. These are prepared from a non-aqueous sol-gel reaction in the ionic liquid 1-hexyl-3-methylimidazolium bis(trifluoromethanesulfonyl)imide (C(1)C(6)ImTFSI). Raman and NMR spectroscopies are complementarily used to decipher the chemical reactions that occur during synthesis and to clarify the state of the ionic liquid up to, and well beyond, gelation. We find that the ionic liquid concentration affects both the reaction rate and the gelation time (t(gel)). In addition, NMR and Raman data reveal inherently different roles of the cation and the anion in the gelation process. While the oscillating behavior of the TFSI Raman signature at ~740 cm(-1) is mainly an effect of solvation and chemical composition, the evolution of the relative chemical shifts (Δδ) of different hydrogen atoms on the imidazolium correlates with gelation, as does the width of the chemical shift of -OH containing groups (δ(OH)). We also observe that in the confined state the TFSI anion preferably adopts the cisoid conformation and experiences a stronger ion-ion interaction. PMID:22910853

  15. Consortium to develop the medical uses of NMR imaging, NMR spectroscopy, and positron emission tomography. Final technical report

    SciTech Connect

    Pohost, G.M.

    1998-06-01

    The goal of this work is to, perform clinically relevant studies using a new whole-body 4.1 T NMR imaging spectrometer. Initially we will develop and approach for the assessment of the severity of skeletal muscle involvement in ischemic peripheral vascular disease.

  16. Intrauterine fetal brain NMR spectroscopy: 1H and 31P studies in rats

    SciTech Connect

    Nakada, T.; Kwee, I.L.; Suzuki, N.; Houkin, K. )

    1989-11-01

    Fetal brain metabolism was investigated in utero noninvasively using multinuclear nuclear magnetic resonance spectroscopy in rats at two representative prenatal stages: early (17-18 days) and late (20-21 days) stages. Phosphorus-31 (31P) spectroscopy revealed that phosphocreatine is significantly lower in the early stage and increases to the level of early neonates by the late prenatal stage. Intracellular pH at the early stage was found to be strikingly high (7.52 +/- 0.21) and decreased to a level similar to that of neonates by the late stage (7.29 +/- 0.07). Phosphomonoester levels at both stages were similar to the values reported for early neonates. Water-suppressed proton (1H) spectroscopy demonstrated a distinctive in vivo fetal brain spectral pattern characterized by low levels of N-acetyl aspartate and high levels of taurine. High-resolution proton spectroscopy and homonuclear chemical-shift correlate spectroscopy of brain perchloric acid extracts confirmed these in vivo findings. In vitro 31P spectroscopy of acidified chloroform methanol extracts showed the characteristic membrane phospholipid profiles of fetal brain. The phosphatidylethanolamine (PE)-to-phosphatidylcholine (PC) ratio (PE/PC) did not show significant changes between the two stages at 0.40 +/- 0.11, a value similar to that of early neonates.

  17. Distinguishing Polymorphs of the Semiconducting Pigment Copper Phthalocyanine by Solid-state NMR and Raman Spectroscopy

    PubMed Central

    Shaibat, Medhat A.; Casabianca, Leah B.; Siberio-Pérez, Diana Y.; Matzger, Adam J; Ishii, Yoshitaka

    2010-01-01

    Cu(II)(phthalocyanine) (CuPc) is broadly utilized as an archetypal molecular semiconductor and is the most widely used blue printing pigment. CuPc crystallizes in six different forms; the chemical and physical properties are substantially modulated by its molecular packing among these polymorphs. Despite the growing importance of this system, spectroscopic identification of different polymorphs for CuPc has posed difficulties. This study presents the first example of spectroscopic distinction of α- and β-forms of CuPc, the most widely used polymorphs, by solid-state NMR (SSNMR) and Raman spectroscopy. 13C high-resolution SSNMR spectra of α- and β-CuPc using very-fast magic angle spinning (VFMAS) at 20 kHz show that hyperfine shifts sensitively reflect polymorphs of CuPc. The experimental results were confirmed by ab initio chemical shift calculations. 13C and 1H SSNMR relaxation times of α- and β-CuPc under VFMAS also showed marked differences, presumably because of the difference in electronic spin correlation times in the two forms. Raman spectroscopy also provided another reliable method of differentiation between the two polymorphs. PMID:20225842

  18. Membrane topology of a 14-mer model amphipathic peptide: a solid-state NMR spectroscopy study.

    PubMed

    Ouellet, Marise; Doucet, Jean-Daniel; Voyer, Normand; Auger, Michèle

    2007-06-01

    We have investigated the interaction between a synthetic amphipathic 14-mer peptide and model membranes by solid-state NMR. The 14-mer peptide is composed of leucines and phenylalanines modified by the addition of crown ethers and forms a helical amphipathic structure in solution and bound to lipid membranes. To shed light on its membrane topology, 31P, 2H, 15N solid-state NMR experiments have been performed on the 14-mer peptide in interaction with mechanically oriented bilayers of dilauroylphosphatidylcholine (DLPC), dimyristoylphosphatidylcholine (DMPC), and dipalmitoylphosphatidylcholine (DPPC). The 31P, 2H, and 15N NMR results indicate that the 14-mer peptide remains at the surface of the DLPC, DMPC, and DPPC bilayers stacked between glass plates and perturbs the lipid orientation relative to the magnetic field direction. Its membrane topology is similar in DLPC and DMPC bilayers, whereas the peptide seems to be more deeply inserted in DPPC bilayers, as revealed by the greater orientational and motional disorder of the DPPC lipid headgroup and acyl chains. 15N{31P} rotational echo double resonance experiments have also been used to measure the intermolecular dipole-dipole interaction between the 14-mer peptide and the phospholipid headgroup of DMPC multilamellar vesicles, and the results indicate that the 14-mer peptide is in contact with the polar region of the DMPC lipids. On the basis of these studies, the mechanism of membrane perturbation of the 14-mer peptide is associated to the induction of a positive curvature strain induced by the peptide lying on the bilayer surface and seems to be independent of the bilayer hydrophobic thickness. PMID:17487978

  19. State-of-the-Art Direct 13C and Indirect 1H-[13C] NMR Spectroscopy In Vivo

    PubMed Central

    de Graaf, Robin A.; Rothman, Douglas L.; Behar, Kevin L.

    2013-01-01

    Carbon-13 NMR spectroscopy in combination with 13C-labeled substrate infusion is a powerful technique to measure a large number of metabolic fluxes non-invasively in vivo. It has been used to quantify glycogen synthesis rates, establish quantitative relationships between energy metabolism and neurotransmission and evaluate the importance of different substrates. All measurements can, in principle, be performed through direct 13C NMR detection or via indirect 1H-[13C] NMR detection of the protons attached to 13C nuclei. The choice for detection scheme and pulse sequence depends on the magnetic field strength, whereas substrate selection depends on the metabolic pathways that are studied. 13C NMR spectroscopy remains a challenging technique that requires several non-standard hardware modifications, infusion of 13C-labeled substrates and sophisticated processing and metabolic modeling. Here the various aspects of direct 13C and indirect 1H-[13C] NMR are reviewed with the aim of providing a practical guide. PMID:21919099

  20. Multiple acquisition/multiple observation separated local field/chemical shift correlation solid-state magic angle spinning NMR spectroscopy.

    PubMed

    Das, Bibhuti B; Opella, Stanley J

    2014-08-01

    Multiple acquisition spectroscopy (MACSY) experiments that enable multiple free induction decays to be recorded during individual experiments are demonstrated. In particular, the experiments incorporate separated local field spectroscopy into homonuclear and heteronuclear correlation spectroscopy. The measured heteronuclear dipolar couplings are valuable in structure determination as well as in enhancing resolution by providing an additional frequency axis. In one example four different three-dimensional spectra are obtained in a single experiment, demonstrating that substantial potential saving in experimental time is available when multiple multi-dimensional spectra are required as part of solid-state NMR studies. PMID:25023566

  1. Multiple Acquisition/Multiple Observation Separated Local Field/Chemical Shift Correlation Solid-state Magic Angle Spinning NMR Spectroscopy

    PubMed Central

    Das, Bibhuti B.; Opella, Stanley J.

    2014-01-01

    Multiple acquisition spectroscopy (MACSY) experiments that enable multiple free induction decays to be recorded during individual experiments are demonstrated. In particular, the experiments incorporate separated local field spectroscopy into homonuclear and heteronuclear correlation spectroscopy. The measured heteronuclear dipolar couplings are valuable in structure determination as well as in enhancing resolution by providing an additional frequency axis. In one example four different three-dimensional spectra are obtained in a single experiment, demonstrating that substantial potential saving in experimental time is available when multiple multi-dimensional spectra are required as part of solid-state NMR studies. PMID:25023566

  2. Oscillatory Enzyme Dynamics Revealed by Two-Dimensional Infrared Spectroscopy.

    PubMed

    Pagano, Philip; Guo, Qi; Kohen, Amnon; Cheatum, Christopher M

    2016-07-01

    Enzymes move on a variety of length and time scales. While much is known about large structural fluctuations that impact binding of the substrates and release of products, little is known about faster motions of enzymes and how these motions may influence enzyme-catalyzed reactions. This Letter reports frequency fluctuations of the azide anion bound to the active site of formate dehydrogenase measured via 2D IR spectroscopy. These measurements reveal an underdamped oscillatory component to the frequency-frequency correlation function when the azide is bound to the NAD(+) ternary complex. This oscillation disappears when the reduced cofactor is added, indicating that the oscillating contributions most likely come from the charged nicotinamide ring. These oscillatory motions may be relevant to donor-acceptor distance sampling of the catalyzed hydride transfer and therefore may give future insights into the dynamic behavior involved in enzyme catalysis. PMID:27305279

  3. A strategy for co-translational folding studies of ribosome-bound nascent chain complexes using NMR spectroscopy.

    PubMed

    Cassaignau, Anaïs M E; Launay, Hélène M M; Karyadi, Maria-Evangelia; Wang, Xiaolin; Waudby, Christopher A; Deckert, Annika; Robertson, Amy L; Christodoulou, John; Cabrita, Lisa D

    2016-08-01

    During biosynthesis on the ribosome, an elongating nascent polypeptide chain can begin to fold, in a process that is central to all living systems. Detailed structural studies of co-translational protein folding are now beginning to emerge; such studies were previously limited, at least in part, by the inherently dynamic nature of emerging nascent chains, which precluded most structural techniques. NMR spectroscopy is able to provide atomic-resolution information for ribosome-nascent chain complexes (RNCs), but it requires large quantities (≥10 mg) of homogeneous, isotopically labeled RNCs. Further challenges include limited sample working concentration and stability of the RNC sample (which contribute to weak NMR signals) and resonance broadening caused by attachment to the large (2.4-MDa) ribosomal complex. Here, we present a strategy to generate isotopically labeled RNCs in Escherichia coli that are suitable for NMR studies. Uniform translational arrest of the nascent chains is achieved using a stalling motif, and isotopically labeled RNCs are produced at high yield using high-cell-density E. coli growth conditions. Homogeneous RNCs are isolated by combining metal affinity chromatography (to isolate ribosome-bound species) with sucrose density centrifugation (to recover intact 70S monosomes). Sensitivity-optimized NMR spectroscopy is then applied to the RNCs, combined with a suite of parallel NMR and biochemical analyses to cross-validate their integrity, including RNC-optimized NMR diffusion measurements to report on ribosome attachment in situ. Comparative NMR studies of RNCs with the analogous isolated proteins permit a high-resolution description of the structure and dynamics of a nascent chain during its progressive biosynthesis on the ribosome. PMID:27466710

  4. Improvements in localized proton NMR spectroscopy of human brain. Water suppression, short echo times, and 1 ml resolution

    NASA Astrophysics Data System (ADS)

    Frahm, J.; Michaelis, T.; Merboldt, K. D.; Bruhn, H.; Gyngell, M. L.; Hänicke, W.

    Considerable technical improvements are reported for localized proton NMR spectroscopy using stimulated echoes. When compared to previous results, proton NMR spectra of the human brain are now obtainable (i) with in vivo water suppression factors of ⩾1000, (ii) with only minor T2 losses and negligible distortions due to J modulation at short echo times of 10-20 ms, and (iii) from volumes of interest as small as 1-8 ml within measuring times of 1-10 min. As a consequence, the detection of cerebral metabolites is greatly facilitated. This particularly applies to the assignment of those resonances (e.g., glutamate, taurine, inositols) that suffer from strong spin-spin coupling at the field strengths commonly in use for NMR in man. Studies of regional metabolite differences, tissue heterogeneity, and focal lesions in patients benefit from the increased spatial resolution and a concomitant reduction of partial volume effects. Localized proton NMR spectroscopy was performed on young healthy volunteers. Experiments were carried out on a 2.0 T whole-body MRI/MRS system using the standard headcoil for both imaging and spectroscopy.

  5. Transport Properties of Ibuprofen Encapsulated in Cyclodextrin Nanosponge Hydrogels: A Proton HR-MAS NMR Spectroscopy Study.

    PubMed

    Ferro, Monica; Castiglione, Franca; Punta, Carlo; Melone, Lucio; Panzeri, Walter; Rossi, Barbara; Trotta, Francesco; Mele, Andrea

    2016-01-01

    The chemical cross-linking of β-cyclodextrin (β-CD) with ethylenediaminetetraacetic dianhydride (EDTA) led to branched polymers referred to as cyclodextrin nanosponges (CDNSEDTA). Two different preparations are described with 1:4 and 1:8 CD-EDTA molar ratios. The corresponding cross-linked polymers were contacted with 0.27 M aqueous solution of ibuprofen sodium salt (IP) leading to homogeneous, colorless, drug loaded hydrogels. The systems were characterized by high resolution magic angle spinning (HR-MAS) NMR spectroscopy. Pulsed field gradient spin echo (PGSE) NMR spectroscopy was used to determine the mean square displacement (MSD) of IP inside the polymeric gel at different observation times td. The data were further processed in order to study the time dependence of MSD: MSD = f(td). The proposed methodology is useful to characterize the different diffusion regimes that, in principle, the solute may experience inside the hydrogel, namely normal or anomalous diffusion. The full protocols including the polymer preparation and purification, the obtainment of drug-loaded hydrogels, the NMR sample preparation, the measurement of MSD by HR-MAS NMR spectroscopy and the final data processing to achieve the time dependence of MSD are here reported and discussed. The presented experiments represent a paradigmatic case and the data are discussed in terms of innovative approach to the characterization of the transport properties of an encapsulated guest within a polymeric host of potential application for drug delivery. PMID:27585291

  6. Identification of different oxygen species in oxide nanostructures with (17)O solid-state NMR spectroscopy.

    PubMed

    Wang, Meng; Wu, Xin-Ping; Zheng, Sujuan; Zhao, Li; Li, Lei; Shen, Li; Gao, Yuxian; Xue, Nianhua; Guo, Xuefeng; Huang, Weixin; Gan, Zhehong; Blanc, Frédéric; Yu, Zhiwu; Ke, Xiaokang; Ding, Weiping; Gong, Xue-Qing; Grey, Clare P; Peng, Luming

    2015-02-01

    Nanostructured oxides find multiple uses in a diverse range of applications including catalysis, energy storage, and environmental management, their higher surface areas, and, in some cases, electronic properties resulting in different physical properties from their bulk counterparts. Developing structure-property relations for these materials requires a determination of surface and subsurface structure. Although microscopy plays a critical role owing to the fact that the volumes sampled by such techniques may not be representative of the whole sample, complementary characterization methods are urgently required. We develop a simple nuclear magnetic resonance (NMR) strategy to detect the first few layers of a nanomaterial, demonstrating the approach with technologically relevant ceria nanoparticles. We show that the (17)O resonances arising from the first to third surface layer oxygen ions, hydroxyl sites, and oxygen species near vacancies can be distinguished from the oxygen ions in the bulk, with higher-frequency (17)O chemical shifts being observed for the lower coordinated surface sites. H2 (17)O can be used to selectively enrich surface sites, allowing only these particular active sites to be monitored in a chemical process. (17)O NMR spectra of thermally treated nanosized ceria clearly show how different oxygen species interconvert at elevated temperature. Density functional theory calculations confirm the assignments and reveal a strong dependence of chemical shift on the nature of the surface. These results open up new strategies for characterizing nanostructured oxides and their applications. PMID:26601133

  7. Screening protein – Single stranded RNA complexes by NMR spectroscopy for structure determination☆

    PubMed Central

    Foot, Jaelle N.; Feracci, Mikael; Dominguez, Cyril

    2014-01-01

    In the past few years, RNA molecules have been revealed to be at the center of numerous biological processes. Long considered as passive molecules transferring genetic information from DNA to proteins, it is now well established that RNA molecules play important regulatory roles. Associated with that, the number of identified RNA binding proteins (RBPs) has increased considerably and mutations in RNA molecules or RBP have been shown to cause various diseases, such as cancers. It is therefore crucial to understand at the molecular level how these proteins specifically recognise their RNA targets in order to design new generation drug therapies targeting protein–RNA complexes. Nuclear magnetic resonance (NMR) is a particularly well-suited technique to study such protein–RNA complexes at the atomic level and can provide valuable information for new drug discovery programs. In this article, we describe the NMR strategy that we and other laboratories use for screening optimal conditions necessary for structural studies of protein-single stranded RNA complexes, using two proteins, Sam68 and T-STAR, as examples. PMID:24096002

  8. Identification of different oxygen species in oxide nanostructures with 17O solid-state NMR spectroscopy

    PubMed Central

    Wang, Meng; Wu, Xin-Ping; Zheng, Sujuan; Zhao, Li; Li, Lei; Shen, Li; Gao, Yuxian; Xue, Nianhua; Guo, Xuefeng; Huang, Weixin; Gan, Zhehong; Blanc, Frédéric; Yu, Zhiwu; Ke, Xiaokang; Ding, Weiping; Gong, Xue-Qing; Grey, Clare P.; Peng, Luming

    2015-01-01

    Nanostructured oxides find multiple uses in a diverse range of applications including catalysis, energy storage, and environmental management, their higher surface areas, and, in some cases, electronic properties resulting in different physical properties from their bulk counterparts. Developing structure-property relations for these materials requires a determination of surface and subsurface structure. Although microscopy plays a critical role owing to the fact that the volumes sampled by such techniques may not be representative of the whole sample, complementary characterization methods are urgently required. We develop a simple nuclear magnetic resonance (NMR) strategy to detect the first few layers of a nanomaterial, demonstrating the approach with technologically relevant ceria nanoparticles. We show that the 17O resonances arising from the first to third surface layer oxygen ions, hydroxyl sites, and oxygen species near vacancies can be distinguished from the oxygen ions in the bulk, with higher-frequency 17O chemical shifts being observed for the lower coordinated surface sites. H217O can be used to selectively enrich surface sites, allowing only these particular active sites to be monitored in a chemical process. 17O NMR spectra of thermally treated nanosized ceria clearly show how different oxygen species interconvert at elevated temperature. Density functional theory calculations confirm the assignments and reveal a strong dependence of chemical shift on the nature of the surface. These results open up new strategies for characterizing nanostructured oxides and their applications. PMID:26601133

  9. Effects of high fructose and salt feeding on systematic metabonome probed via (1) H NMR spectroscopy.

    PubMed

    Yang, Yongxia; Zheng, Lingyun; Wang, Linlin; Wang, Shumei; Wang, Yaling; Han, Zhihui

    2015-04-01

    Diets rich in high fructose and salt are increasingly popular in our daily life. A combination consumption of excessive fructose and salt can induce insulin resistance (IR) and hypertension (HT), which are major public health problems around the world. However, the effects of high fructose and salt on systematic metabonome remain unknown, which is very important for revealing the molecular mechanism of IR and HT induced by this dietary pattern. The metabolic profiling in urine, plasma, and fecal extracts from high fructose and salt-fed rats was investigated by use of (1) H nuclear magnetic resonance (NMR)-based metabonomics approach in this study. Multivariate analysis of NMR data showed the effects of high fructose and salt on the global metabonome. The metabolite analysis in urine and fecal extracts showed the time-dependent metabolic changes, which displayed metabonomic progression axes from normal to IR and HT status. The changes of 2-oxoglutarate, creatine and creatinine, citrate, hippurate, trimethylamine N-oxide (TMAO), and betaine in urine, together with gut microbiota disorder in feces, were observed at the preliminary formation stage of IR and HT (fourth week). At the severe stage (eighth week), the previously mentioned metabolic changes were aggravated, and the changes of lipid and choline metabolism in plasma suggested the increased risk of cardiovascular diseases. These findings provide an overview of biochemistry consequences of high fructose and salt feeding and comprehensive insights into the progression of systematic metabonome for IR and HT induced by this dietary pattern. PMID:25641270

  10. Mechanism of host-guest complex formation and identification of intermediates through NMR titration and diffusion NMR spectroscopy.

    PubMed

    Lamm, Jan-Hendrik; Niermeier, Philipp; Mix, Andreas; Chmiel, Jasmin; Neumann, Beate; Stammler, Hans-Georg; Mitzel, Norbert W

    2014-07-21

    The formation of host-guest (H-G) complexes between 1,8-bis[(diethylgallanyl)ethynyl]anthracene (H) and the N-heterocycles pyridine and pyrimidine (G) was studied in solution using a combination of NMR titration and diffusion NMR experiments. For the latter, diffusion coefficients of potential host-guest structures in solution were compared with those of tailor-made reference compounds of similar shape (synthesized and characterized by NMR, HRMS, and in part XRD). Highly dynamic behavior was observed in both cases, but with different host-guest species and equilibria. With increasing concentrations of the pyridine guest, the equilibrium H2⇄H2κ(1)-G1⇄HG2 is observed (in the second step a host dimer coordinates one guest molecule); for pyrimidine the equilibrium H2→H1κ(2)-G1⇄HG2 is observed (the formation of a 1:1 aggregate is the second step). PMID:24925835

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

    PubMed

    García, Víctor P

    2011-05-01

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

  12. Intracellular free calcium concentration measured with /sup 19/F NMR spectroscopy in intact ferret hearts

    SciTech Connect

    Marban, E.; Kitakaze, M.; Kusuoka, H.; Porterfield, J.K.; Yue, D.T.; Chacko, V.P.

    1987-08-01

    Changes in the intracellular free Ca/sup 2 +/ concentration, (Ca/sup 2 +/)/sub i/, mediate excitation-contraction coupling in the heart and contribute to cellular injury during ischemia and reperfusion. To study these processes directly, the authors measured (Ca/sup 2 +/)/sub i/ in perfused ferret (Mustela putorius furo) hearts using /sup 19/F NMR spectroscopy to detect the 5,5'-difluoro derivative of the Ca/sup 2 +/ chelator, 1,2-bis(o-aminophenoxy)ethane-N,N,N',N'-tetraacetic acid (BAPTA). To load cells, hearts were perfused with the acetoxymethyl ester derivative of 5,5'-F/sub 2/-BAPTA. They measured /sup 19/F NMR spectra and left ventricular pressure simultaneously,at rest and during pacing at various external Ca concentrations ((Ca)/sub 0/). Although contractile force was attenuated by the Ca/sup 2 +/ buffering properties of 5,5'-F/sup 2/-BAPTA, the decrease in pressure could be overcome by raising (Ca)/sub 0/. The mean value of 104 nM for (Ca/sup 2 +/)/sub i/ at rest in the perfused heart agrees well with previous measurements in isolated ventricular muscle. During pacing at 0.6-4 Hz, time-averaged (Ca/sup 2 +/)/sub i/ increased; the effect of pacing was augmented by increasing (Ca)/sub 0/. (Ca/sup 2 +/)/sub i/ more than tripled during 10-20 min of global ischemia, and returned toward control levels upon reperfusion. This approach promises to be particularly useful in investigating the physiology of intact hearts and the pathophysiology of alterations in the coronary circulation

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

    PubMed Central

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

    2013-01-01

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

  14. Characterization of plant-derived carbon and phosphorus in lakes by sequential fractionation and NMR spectroscopy.

    PubMed

    Liu, Shasha; Zhu, Yuanrong; Wu, Fengchang; Meng, Wei; He, Zhongqi; Giesy, John P

    2016-10-01

    Although debris from aquatic macrophytes is one of the most important endogenous sources of organic matter (OM) and nutrients in lakes, its biogeochemical cycling and contribution to internal load of nutrients in eutrophic lakes are still poorly understood. In this study, sequential fractionation by H2O, 0.1M NaOH and 1.0M HCl, combined with (13)C and (31)P NMR spectroscopy, was developed and used to characterize organic carbon (C) and phosphorus (P) in six aquatic plants collected from Tai Lake (Ch: Taihu), China. Organic matter, determined by total organic carbon (TOC), was unequally distributed in H2O (21.2%), NaOH (29.9%), HCl (3.5%) and residual (45.3%) fractions. For P in debris of aquatic plants, 53.3% was extracted by H2O, 31.9% by NaOH, and 11% by HCl, with 3.8% in residual fractions. Predominant OM components extracted by H2O and NaOH were carbohydrates, proteins and aliphatic acids. Inorganic P (Pi) was the primary form of P in H2O fractions, whereas organic P (Po) was the primary form of P in NaOH fractions. The subsequent HCl fractions extracted fewer species of C and P. Some non-extractable carbohydrates, aromatics and metal phytate compounds remained in residual fractions. Based on sequential extraction and NMR analysis, it was proposed that those forms of C (54.7% of TOC) and P (96.2% of TP) in H2O, NaOH and HCl fractions are potentially released to overlying water as labile components, while those in residues are stable and likely preserved in sediments of lakes. These results will be helpful in understanding internal loading of nutrients from debris of aquatic macrophytes and their recycling in lakes. PMID:27282495

  15. Dynamic Nuclear Polarization Enhanced MAS NMR Spectroscopy for Structural Analysis of HIV-1 Protein Assemblies.

    PubMed

    Gupta, Rupal; Lu, Manman; Hou, Guangjin; Caporini, Marc A; Rosay, Melanie; Maas, Werner; Struppe, Jochem; Suiter, Christopher; Ahn, Jinwoo; Byeon, In-Ja L; Franks, W Trent; Orwick-Rydmark, Marcella; Bertarello, Andrea; Oschkinat, Hartmut; Lesage, Anne; Pintacuda, Guido; Gronenborn, Angela M; Polenova, Tatyana

    2016-01-21

    Mature infectious HIV-1 virions contain conical capsids composed of CA protein, generated by the proteolytic cleavage cascade of the Gag polyprotein, termed maturation. The mechanism of capsid core formation through the maturation process remains poorly understood. We present DNP-enhanced MAS NMR studies of tubular assemblies of CA and Gag CA-SP1 maturation intermediate and report 20-64-fold sensitivity enhancements due to DNP at 14.1 T. These sensitivity enhancements enabled direct observation of spacer peptide 1 (SP1) resonances in CA-SP1 by dipolar-based correlation experiments, unequivocally indicating that the SP1 peptide is unstructured in assembled CA-SP1 at cryogenic temperatures, corroborating our earlier results. Furthermore, the dependence of DNP enhancements and spectral resolution on magnetic field strength (9.4-18.8 T) and temperature (109-180 K) was investigated. Our results suggest that DNP-based measurements could potentially provide residue-specific dynamics information by allowing for the extraction of the temperature dependence of the anisotropic tensorial or relaxation parameters. With DNP, we were able to detect multiple well-resolved isoleucine side-chain conformers; unique intermolecular correlations across two CA molecules; and functionally relevant conformationally disordered states such as the 14-residue SP1 peptide, none of which are visible at ambient temperatures. The detection of isolated conformers and intermolecular correlations can provide crucial constraints for structure determination of these assemblies. Overall, our results establish DNP-based MAS NMR spectroscopy as an excellent tool for the characterization of HIV-1 assemblies. PMID:26709853

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

    NASA Astrophysics Data System (ADS)

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

    2013-06-01

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

  17. High-Speed Frequency Modulation of a 460-GHz Gyrotron for Enhancement of 700-MHz DNP-NMR Spectroscopy

    NASA Astrophysics Data System (ADS)

    Idehara, T.; Khutoryan, E. M.; Tatematsu, Y.; Yamaguchi, Y.; Kuleshov, A. N.; Dumbrajs, O.; Matsuki, Y.; Fujiwara, T.

    2015-09-01

    The high-speed frequency modulation of a 460-GHz Gyrotron FU CW GVI (the official name in Osaka University is Gyrotron FU CW GOI) was achieved by modulation of acceleration voltage of beam electrons. The modulation speed f m can be increased up to 10 kHz without decreasing the modulation amplitude δ f of frequency. The amplitude δ f was increased almost linearly with the modulation amplitude of acceleration voltage Δ V a. At the Δ V a = 1 kV, frequency spectrum width df was 50 MHz in the case of f m < 10 kHz. The frequency modulation was observed as both the variation of the IF frequency in the heterodyne detection system measured by a high-speed oscilloscope and the widths of frequency spectra df measured on a frequency spectrum analyzer. Both results well agree reasonably. When f m exceeds 10 kHz, the amplitude δ f is decreased gradually with increasing f m because of the degradation of the used amplifier in response for high-speed modulation. The experiment was performed successfully for both a sinusoidal wave and triangle wave modulations. We can use the high-speed frequency modulation for increasing the enhancement factor of the dynamic nuclear polarization (DNP)-enhanced nuclear magnetic resonance (NMR) spectroscopy, which is one of effective and attractive methods for the high-frequency DNP-NMR spectroscopy, for example, at 700 MHz. Because the sensitivity of NMR is inversely proportional to the frequency, high-speed frequency modulation can compensate the decreasing the enhancement factor in the high-frequency DNP-NMR spectroscopy and keep the factor at high value. In addition, the high-speed frequency modulation is useful for frequency stabilization by a PID control of an acceleration voltage by feeding back of the fluctuation of frequency. The frequency stabilization in long time is also useful for application of a DNP-NMR spectroscopy to the analysis of complicated protein molecules.

  18. Two-dimensional NMR spectroscopy strongly enhances soil organic matter composition analysis

    NASA Astrophysics Data System (ADS)

    Soucemarianadin, Laure; Erhagen, Björn; Öquist, Mats; Nilsson, Mats; Hedenström, Mattias; Schleucher, Jürgen

    2016-04-01

    Soil organic matter (SOM) is the largest terrestrial carbon pool and strongly affects soil properties. With climate change, understanding SOM processes and turnover and how they could be affected by increasing temperatures becomes critical. This is particularly key for organic soils as they represent a huge carbon pool in very sensitive ecosystems, like boreal ecosystems and peatlands. Nevertheless, characterization of SOM molecular composition, which is essential to elucidate soil carbon processes, is not easily achieved, and further advancements in that area are greatly needed. Solid-state one-dimensional (1D) 13C nuclear magnetic resonance (NMR) spectroscopy is often used to characterize its molecular composition, but only provides data on a few major functional groups, which regroup many different molecular fragments. For instance, in the carbohydrates region, signals of all monosaccharides present in many different polymers overlap. This overlap thwarts attempts to identify molecular moieties, resulting in insufficient information to characterize SOM composition. Here we show that two-dimensional (2D) liquid-state 1H-13C NMR spectra provided much richer data on the composition of boreal plant litter and organic surface soil. The 2D spectra indeed resolved overlaps observed in 1D 13C spectra and displayed signals from hundreds of identifiable molecular groups. For example, in the aromatics region, signals from individual lignin units could be recognized. It was hence possible to follow the fate of specific structural moieties in soils. We observed differences between litter and soil samples, and were able to relate them to the decomposition of identifiable moieties. Sample preparation and data acquisition were both simple and fast. Further, using multivariate data analysis, we aimed at linking the detailed chemical fingerprints of SOM to turnover rates in a soil incubation experiment. With the multivariate models, we were able to identify specific molecular

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

    SciTech Connect

    Mao, Kanmi

    2011-01-01

    The development of fast magic angle spinning (MAS) opened up an opportunity for the indirect detection of insensitive low-γ nuclei (e.g., 13C and 15N) via the sensitive high-{gamma} nuclei (e.g., 1H and 19F) in solid-state NMR, with advanced sensitivity and resolution. In this thesis, new methodology utilizing fast MAS is presented, including through-bond indirectly detected heteronuclear correlation (HETCOR) spectroscopy, which is assisted by multiple RF pulse sequences for 1H-1H homonuclear decoupling. Also presented is a simple new strategy for optimization of 1H-1H homonuclear decoupling. As applications, various classes of materials, such as catalytic nanoscale materials, biomolecules, and organic complexes, are studied by combining indirect detection and other one-dimensional (1D) and two-dimensional (2D) NMR techniques. Indirectly detected through-bond HETCOR spectroscopy utilizing refocused INEPT (INEPTR) mixing was developed under fast MAS (Chapter 2). The time performance of this approach in 1H detected 2D 1H{l_brace}13C{r_brace} spectra was significantly improved, by a factor of almost 10, compared to the traditional 13C detected experiments, as demonstrated by measuring naturally abundant organic-inorganic mesoporous hybrid materials. The through-bond scheme was demonstrated as a new analytical tool, which provides complementary structural information in solid-state systems in addition to through-space correlation. To further benefit the sensitivity of the INEPT transfer in rigid solids, the combined rotation and multiple-pulse spectroscopy (CRAMPS) was implemented for homonuclear 1H decoupling under fast MAS (Chapter 3). Several decoupling schemes (PMLG5m$\\bar{x}$, PMLG5mm$\\bar{x}$x and SAM3) were analyzed to maximize the performance of through-bond transfer based

  20. Induced Secondary Structure and Polymorphism in an Intrinsically Disordered Structural Linker of the CNS: Solid-State NMR and FTIR Spectroscopy of Myelin Basic Protein Bound to Actin

    PubMed Central

    Ahmed, Mumdooh A.M.; Bamm, Vladimir V.; Shi, Lichi; Steiner-Mosonyi, Marta; Dawson, John F.; Brown, Leonid; Harauz, George; Ladizhansky, Vladimir

    2009-01-01

    Abstract The 18.5 kDa isoform of myelin basic protein (MBP) is a peripheral membrane protein that maintains the structural integrity of the myelin sheath of the central nervous system by conjoining the cytoplasmic leaflets of oligodendrocytes and by linking the myelin membrane to the underlying cytoskeleton whose assembly it strongly promotes. It is a multifunctional, intrinsically disordered protein that behaves primarily as a structural stabilizer, but with elements of a transient or induced secondary structure that represent binding sites for calmodulin or SH3-domain-containing proteins, inter alia. In this study we used solid-state NMR (SSNMR) and Fourier transform infrared (FTIR) spectroscopy to study the conformation of 18.5 kDa MBP in association with actin microfilaments and bundles. FTIR spectroscopy of fully 13C,15N-labeled MBP complexed with unlabeled F-actin showed induced folding of both protein partners, viz., some increase in β-sheet content in actin, and increases in both α-helix and β-sheet content in MBP, albeit with considerable extended structure remaining. Solid-state NMR spectroscopy revealed that MBP in MBP-actin assemblies is structurally heterogeneous but gains ordered secondary structure elements (both α-helical and β-sheet), particularly in the terminal fragments and in a central immunodominant epitope. The overall conformational polymorphism of MBP is consistent with its in vivo roles as both a linker (membranes and cytoskeleton) and a putative signaling hub. PMID:19134474

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

    PubMed

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

    2016-02-16

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

  2. Phosphorus speciation in agro-industrial byproducts: sequential fractionation, solution (31)P NMR, and P K- and L(2,3)-edge XANES spectroscopy.

    PubMed

    Negassa, Wakene; Kruse, Jens; Michalik, Dirk; Appathurai, Narayana; Zuin, Lucia; Leinweber, Peter

    2010-03-15

    Little is known about P species in agro-industrial byproducts from developing countries, which may be either pollutants or valuable soil amendments. The present study speciated P in dry (COD) and wet (COW) coffee, sisal (SIS), barley malt (BEB) and sugar cane processing (FIC) byproducts, and filter cakes of linseed (LIC) and niger seed (NIC)with sequential fractionation, solution (31)P nuclear magnetic resonance (NMR) spectroscopy, and P K- and L(2,3)-edge X-ray absorption near-edge structure (XANES) spectroscopy. The sequential P fractionation recovered 59% to almost 100% of total P (P(t)), and more than 50% of P(t) was extracted by H(2)O and NaHCO(3) in five out of seven samples. Similarly, the NaOH + EDTA extraction for solution (31)P NMR recovered 48-94% of P(t). The (31)P NMR spectra revealed orthophosphate (6-81%), pyrophosphate (0-10%), and orthophosphate monoesters (6-94%). Orthophosphate predominated in COD, COW, SIS, and FIC, whereas BEB, UC, and NIC were rich in orthophosphate monoesters. The concentrations of P(i), and P(o) determined in the sequential and NaOH + EDTA extractions and (31)P NMR spectra were strongly and positively correlated (r = 0.88-1.00). Furthermore, the P K- and L(2,3)-edge XANES confirmed the H(2)SO(4)--P(i) detected in the sequential fractionation by unequivocal identification of Ca--P phases in a few samples. The results indicate that the combined use of all four analytical methods is crucial for comprehensive P speciation in environmental samples and the application of these byproducts to soil. PMID:20146464

  3. Self-healing capacity of nuclear glass observed by NMR spectroscopy

    PubMed Central

    Charpentier, Thibault; Martel, Laura; Mir, Anamul H.; Somers, Joseph; Jégou, Christophe; Peuget, Sylvain

    2016-01-01

    Safe management of high level nuclear waste is a worldwide significant issue for which vitrification has been selected by many countries. There exists a crucial need for improving our understanding of the ageing of the glass under irradiation. While external irradiation by ions provides a rapid simulation of damage induced by alpha decays, short lived actinide doping is more representative of the reality. Here, we report radiological NMR experiments to compare the damage in International Simplified Glass (ISG) when irradiated by these two methods. In the 0.1 mole percent 244Cm doped glass, accumulation of high alpha decay only shows small modifications of the local structure, in sharp contrast to heavy ion irradiation. These results reveal the ability of the alpha particle to partially repair the damage generated by the heavy recoil nuclei highlighting the radiation resistance of nuclear glass and the difficulty to accurately simulate its behaviour by single ion beam irradiations. PMID:27149700

  4. Self-healing capacity of nuclear glass observed by NMR spectroscopy.

    PubMed

    Charpentier, Thibault; Martel, Laura; Mir, Anamul H; Somers, Joseph; Jégou, Christophe; Peuget, Sylvain

    2016-01-01

    Safe management of high level nuclear waste is a worldwide significant issue for which vitrification has been selected by many countries. There exists a crucial need for improving our understanding of the ageing of the glass under irradiation. While external irradiation by ions provides a rapid simulation of damage induced by alpha decays, short lived actinide doping is more representative of the reality. Here, we report radiological NMR experiments to compare the damage in International Simplified Glass (ISG) when irradiated by these two methods. In the 0.1 mole percent (244)Cm doped glass, accumulation of high alpha decay only shows small modifications of the local structure, in sharp contrast to heavy ion irradiation. These results reveal the ability of the alpha particle to partially repair the damage generated by the heavy recoil nuclei highlighting the radiation resistance of nuclear glass and the difficulty to accurately simulate its behaviour by single ion beam irradiations. PMID:27149700

  5. Self-healing capacity of nuclear glass observed by NMR spectroscopy

    NASA Astrophysics Data System (ADS)

    Charpentier, Thibault; Martel, Laura; Mir, Anamul H.; Somers, Joseph; Jégou, Christophe; Peuget, Sylvain

    2016-05-01

    Safe management of high level nuclear waste is a worldwide significant issue for which vitrification has been selected by many countries. There exists a crucial need for improving our understanding of the ageing of the glass under irradiation. While external irradiation by ions provides a rapid simulation of damage induced by alpha decays, short lived actinide doping is more representative of the reality. Here, we report radiological NMR experiments to compare the damage in International Simplified Glass (ISG) when irradiated by these two methods. In the 0.1 mole percent 244Cm doped glass, accumulation of high alpha decay only shows small modifications of the local structure, in sharp contrast to heavy ion irradiation. These results reveal the ability of the alpha particle to partially repair the damage generated by the heavy recoil nuclei highlighting the radiation resistance of nuclear glass and the difficulty to accurately simulate its behaviour by single ion beam irradiations.

  6. Gender-Specific Metabolomic Profiling of Obesity in Leptin-Deficient ob/ob Mice by 1H NMR Spectroscopy

    PubMed Central

    Kim, Sang-Woo; Jung, Youngae; Bae, Hyun-Whee; Lee, Daeyoup; Park, Sung Goo; Lee, Chul-Ho; Hwang, Geum-Sook; Chi, Seung-Wook

    2013-01-01

    Despite the numerous metabolic studies on obesity, gender bias in obesity has rarely been investigated. Here, we report the metabolomic analysis of obesity by using leptin-deficient ob/ob mice based on the gender. Metabolomic analyses of urine and serum from ob/ob mice compared with those from C57BL/6J lean mice, based on the 1H NMR spectroscopy in combination with multivariate statistical analysis, revealed clear metabolic differences between obese and lean mice. We also identified 48 urine and 22 serum metabolites that were statistically significantly altered in obese mice compared to lean controls. These metabolites are involved in amino acid metabolism (leucine, alanine, ariginine, lysine, and methionine), tricarbocylic acid cycle and glucose metabolism (pyruvate, citrate, glycolate, acetoacetate, and acetone), lipid metabolism (cholesterol and carnitine), creatine metabolism (creatine and creatinine), and gut-microbiome-derived metabolism (choline, TMAO, hippurate, p-cresol, isobutyrate, 2-hydroxyisobutyrate, methylamine, and trigonelline). Notably, our metabolomic studies showed distinct gender variations. The obese male mice metabolism was specifically associated with insulin signaling, whereas the obese female mice metabolism was associated with lipid metabolism. Taken together, our study identifies the biomarker signature for obesity in ob/ob mice and provides biochemical insights into the metabolic alteration in obesity based on gender. PMID:24098417

  7. (1) H NMR spectroscopy of glioblastoma stem-like cells identifies alpha-aminoadipate as a marker of tumor aggressiveness.

    PubMed

    Rosi, Antonella; Ricci-Vitiani, Lucia; Biffoni, Mauro; Grande, Sveva; Luciani, Anna Maria; Palma, Alessandra; Runci, Daniele; Cappellari, Marianna; De Maria, Ruggero; Guidoni, Laura; Pallini, Roberto; Viti, Vincenza

    2015-03-01

    Patients suffering from glioblastoma multiforme (GBM) face a poor prognosis with median survival of about 14 months. High recurrence rate and failure of conventional treatments are attributed to the presence of GBM cells with stem-like properties (GSCs). Metabolite profiles of 42 GSC lines established from the tumor tissue of adult GBM patients were screened with (1) H NMR spectroscopy and compared with human neural progenitor cells from human adult olfactory bulb (OB-NPCs) and from the developing human brain (HNPCs). A first subset (n=12) of GSCs exhibited a dramatic accumulation of the metabolite α-aminoadipate (αAAD), product of the oxidation of α-aminoadipic semialdehyde catalyzed by the ALDH7A1 aldehyde dehydrogenase (ALDH) family in lysine catabolism. αAAD was low/not detectable in a second GSC subset (n=13) with the same neural metabolic profile as well as in a third GSC subset (n=17) characterized by intense lipid signals. Likewise, αAAD was not detected in the spectra of OB-NPCs or HNPCs. Inhibition of mitochondrial ATP synthase by oligomycin treatment revealed that the lysine degradative pathway leading to αAAD formation proceeds through saccharopine, as usually observed in developing brain. Survival curves indicated that high αAAD levels in GSCs significantly correlated with poor patient survival, similarly to prostate and non-small-cell-lung cancers, where activity of ALDH7A1 correlates with tumor aggressiveness. PMID:25581615

  8. Photodegradation of major soil microbial biomolecules is comparable to biodegradation: Insights from infrared and diffusion editing NMR spectroscopies

    NASA Astrophysics Data System (ADS)

    Spence, Adrian; Kelleher, Brian P.

    2016-03-01

    As a primary decomposition process in terrestrial biosystems, biodegradation has been extensively studied with regard to its impact on soil organic matter transformation. However, the biotransformation of soil microbial biomass (a primary source of soil organic carbon) remains poorly understood, and even less is known about the fate of microbial-derived carbon under photodegradation. Here, we combine infrared and diffusion editing NMR spectroscopies to provide molecular-level information on the photodegradation of major biochemical components in soil microbial biomass and leachates over time. Results indicate a considerable enrichment in aliphatic components, presumably polymethylenic-C [(C-H2)n] and the simultaneous loss of carbohydrate and protein structures in the biomass. An immediate conclusion is that photodegradation increased the conversion of macromolecular carbohydrates and proteins to smaller components. However, further analysis reveals that macromolecular carbohydrates and proteins may be more resistant to photodegradation than initially thought and are found in the leachates. Although attenuated, there is also evidence to suggest that some aliphatic structures persist in the leachates. Overall, the photodegradation pathway reported here is remarkably similar to that of biodegradation, suggesting that under rapidly expanding anthropogenic land disturbances, photodegradation could be an important driver of the transformation of microbial-derived organic matter in terrestrial biosystems.

  9. Conformation switching of AIM2 PYD domain revealed by NMR relaxation and MD simulation.

    PubMed

    Wang, Haobo; Yang, Lijiang; Niu, Xiaogang

    2016-04-29

    Protein absent in melanoma 2 (AIM2) is a double-strand DNA (ds DNA) sensor mainly located in cytoplasm of cell. It includes one N terminal PYD domain and one C terminal HIN domain. When the ds DNA such as DNA viruses and bacteria entered cytoplasm, the HIN domain of AIM2 will recognize and bind to DNA, and the PYD domain will bind to ASC protein which will result in the formation of AIM2 inflammasome. Three AIM2 PYD domain structures have been solved, but every structure yields a unique conformation around the α3 helix region. To understand why different AIM2 PYD structures show different conformations in this region, we use NMR relaxation techniques to study the backbone dynamics of mouse AIM2 PYD domain and perform molecular dynamics (MD) simulations on both mouse and human AIM2 PYD structures. Our results indicate that this region is highly flexible in both mouse and human AIM2 PYD domains, and the PYD domain may exist as a conformation ensemble in solution. Different environment makes the population vary among pre-existing conformational substrates of the ensemble, which may be the reason why different AIM2 PYD structures were observed under different conditions. Further docking analysis reveals that the conformation switching may be important for the autoinhibition of the AIM2 protein. PMID:27037024

  10. Insight into the dynamics of lanthanide-DTPA complexes as revealed by oxygen-17 NMR.

    PubMed

    Fusaro, Luca; Mocci, Francesca; Muller, Robert N; Luhmer, Michel

    2012-08-01

    DTPA chelates of various diamagnetic and paramagnetic lanthanide(III) metal ions, as well as the chemically similar DTPA chelate of Y(3+), were studied in aqueous solution by variable temperature (17)O NMR with the aim of characterizing their internal dynamics. As a consequence of poor chemical shift dispersion and fast quadrupole relaxation, no dynamic exchange process could be detected for the diamagnetic complexes nor for the Sm-DTPA complex. In contrast, the spectra recorded for the Eu-DTPA complex show chemical exchange due to the well-known racemization process and, at high temperature, feature signal broadening that reveals a fluxional process involving the interchange of the coordinated and noncoordinated oxygen atoms of the carboxylate groups. The spectra recorded for the Pr-DTPA complex feature coalescence events due to such a fluxional process, which is ascribable to the rotation of the carboxylate groups. The activation free energy barriers determined experimentally are remarkably lower than the calculated activation barriers recently reported for the rotation of the carboxylate groups of various Ln-DOTA complexes. Furthermore, the smallest activation free energy measured for the Pr-DTPA complex, about 45 kJ mol(-1), is significantly lower than the activation free energy characterizing the racemization process. The fluxional behavior of the carboxylate groups is, however, not expected to significantly affect the residence time of the water molecule coordinated to the metal ion. PMID:22817329

  11. Physics of ultracold Fermi gases revealed by spectroscopies

    NASA Astrophysics Data System (ADS)

    Törmä, Päivi

    2016-04-01

    This article provides a brief review of how various spectroscopies have been used to investitage many-body quantum phenomena in the context of ultracold Fermi gases. In particular, work done with RF spectroscopy, Bragg spectroscopy and lattice modulation spectroscopy is considered. The theoretical basis of these spectroscopies, namely linear response theory in the many-body quantum physics context is briefly presented. Experiments related to the BCS-BEC crossover, imbalanced Fermi gases, polarons, possible pseudogap and Fermi liquid behaviour and measuring the contact are discussed. Remaining open problems and goals in the field are sketched from the perspective how spectroscopies could contribute.

  12. Coexistence of multiple charge-density waves and superconductivity in SrPt2As2 revealed by 75As-NMR /NQR and 195Pt-NMR

    NASA Astrophysics Data System (ADS)

    Kawasaki, Shinji; Tani, Yoshihiko; Mabuchi, Tomosuke; Kudo, Kazutaka; Nishikubo, Yoshihiro; Mitsuoka, Daisuke; Nohara, Minoru; Zheng, Guo-qing

    2015-02-01

    The relationship between charge-density wave (CDW) orders and superconductivity in arsenide superconductor SrPt2As2 with Tc=5.2 K which crystallizes in the CaBe2Ge2 -type structure was studied by 75As nuclear magnetic resonance (NMR) measurements up to 520 K, and 75As nuclear quadrupole resonance (NQR) and 195Pt-NMR measurements down to 1.5 K. At high temperature, 75As-NMR spectrum and nuclear-spin-relaxation rate (1 /T1) have revealed two distinct CDW orders, one realized in the As-Pt-As layer below TCDWAs (1 )=410 K and the other in the Pt-As-Pt layer below TCDWAs (2 )=255 K . The 1 /T1 measured by 75As-NQR shows a clear Hebel-Slichter peak just below Tc and decreases exponentially well below Tc. Concomitantly, 195Pt Knight shift decreases below Tc. Our results indicate that superconductivity in SrPt2As2 is in the spin-singlet state with an s -wave gap and is robust under the two distinct CDW orders in different layers.

  13. (1)H NMR based metabolomic profiling revealed doxorubicin-induced systematic alterations in a rat model.

    PubMed

    Niu, Qian-Yun; Li, Zhen-Yu; Du, Guan-Hua; Qin, Xue-Mei

    2016-01-25

    Doxorubicin (DOX) is used as a chemotherapy drug with severe carditoxicity. In this study, an integrated echocardiography along with pathological examination and (1)H NMR analysis of multiple biological matrices (urine, serum, heart, and kidney) was employed to systemically assess the toxicity of DOX. Echocardiographic results showed that impaired left ventricular contractility and degenerative pathology lesions in DOX group, which were in consistent with pathology. The endogenous metabolites in the urine, serum, heart and kidney was identified by comparison with the data from the literature and databases. Multivariate analysis, including PCA and OPLS, revealed 8 metabolites in urine, including succinate, 2-ketoglutarate, citrate, hippurate, methylamine, benzoate, allantion, and acetate were the potential changed biomarkers. In serum, perturbed metabolites include elevation of leucine, β-glucose, O-acetyl-glycoprotein, creatine, lysine, glycerin, dimethylglycine, trimethylamine-N-oxide, myo-inositol, and N-acetyl-glycoprotein, together with level decreases of acetone, lipid, lactate, glutamate, phosphocholine, acetoacetate and pyruvate. For heart, DOX exposure caused decline of lipid, lactate, leucine, alanine, glutamate, choline, xanthine, glycerin, carnitine, and fumarate, together with elevation of glutamine, creatine, inosine, taurine and malate. Metabolic changes of kidney were mainly involved in the accumulation of α-glucose, lactate, phosphocholine, betaine, threonine, choline, taurine, glycine, urea, hypoxanthine, glutamate, and nicotinamide, coupled with reduction of asparagine, valine, methionine, tyrosine, lysine, alanine, leucine, ornithine, creatine, lipid, and acetate. In addition, alterations of urinary metabolites exhibited a time-dependent manner. Complementary evidences by multiple matrices revealed disturbed pathways concerning energy metabolism, fatty acids oxidation, amino acids and purine metabolism, choline metabolism, and gut microbiota

  14. Selective Host-Guest Interaction between Metal Ions and Metal-Organic Frameworks using Dynamic Nuclear Polarization Enhanced Solid-State NMR Spectroscopy

    SciTech Connect

    Guo, Zhiyong; Kobayashi, Takeshi; Wang, Lin-Lin; Goh, Tian Wei; Xiao, Chaoxian; Caporini, Marc A; Rosay, Melanie; Johnson, Duane D; Pruski, Marek; Huang, Wenyu

    2014-10-08

    The host–guest interaction between metal ions (Pt2+ and Cu2+) and a zirconium metal–organic framework (UiO-66-NH2) was explored using dynamic nuclear polarization-enhanced 15N{1H} CPMAS NMR spectroscopy supported by X-ray absorption spectroscopy and density functional calculations. The combined experimental results conclude that each Pt2+ coordinates with two NH2 groups from the MOF and two Cl- from the metal precursor, whereas Cu2+ do not form chemical bonds with the NH2 groups of the MOF framework. Density functional calculations reveal that Pt2+ prefers a square-planar structure with the four ligands and resides in the octahedral cage of the MOF in either cis or trans configurations.

  15. Selective Host-Guest Interaction between Metal Ions and Metal-Organic Frameworks Using Dynamic Nuclear Polarization Enhanced Solid-State NMR Spectroscopy

    SciTech Connect

    Guo, Zhiyong; Kobayashi, Takeshi; Wang, Lin-Lin; Goh, Tian Wei; Xiao, Chaoxian; Caporini, Marc A.; Rosay, Melanie; Johnson, Duane D.; Pruski, Marek; Huang, Wenyu

    2014-10-08

    The host–guest interaction between metal ions (Pt²⁺ and Cu²⁺) and a zirconium metal–organic framework (UiO-66-NH₂) was explored using dynamic nuclear polarization-enhanced ¹⁵N{¹H} CPMAS NMR spectroscopy supported by X-ray absorption spectroscopy and density functional calculations. The combined experimental results conclude that each Pt²⁺ coordinates with two NH₂ groups from the MOF and two Cl⁻ from the metal precursor, whereas Cu²⁺ do not form chemical bonds with the NH₂ groups of the MOF framework. Density functional calculations reveal that Pt²⁺ prefers a square-planar structure with the four ligands and resides in the octahedral cage of the MOF in either cis or trans configurations.

  16. Selective host-guest interaction between metal ions and metal-organic frameworks using dynamic nuclear polarization enhanced solid-state NMR spectroscopy.

    PubMed

    Guo, Zhiyong; Kobayashi, Takeshi; Wang, Lin-Lin; Goh, Tian Wei; Xiao, Chaoxian; Caporini, Marc A; Rosay, Melanie; Johnson, Duane D; Pruski, Marek; Huang, Wenyu

    2014-12-01

    The host-guest interaction between metal ions (Pt(2+) and Cu(2+) ) and a zirconium metal-organic framework (UiO-66-NH2 ) was explored using dynamic nuclear polarization-enhanced (15) N{(1) H} CPMAS NMR spectroscopy supported by X-ray absorption spectroscopy and density functional calculations. The combined experimental results conclude that each Pt(2+) coordinates with two NH2 groups from the MOF and two Cl(-) from the metal precursor, whereas Cu(2+) do not form chemical bonds with the NH2 groups of the MOF framework. Density functional calculations reveal that Pt(2+) prefers a square-planar structure with the four ligands and resides in the octahedral cage of the MOF in either cis or trans configurations. PMID:25297002

  17. Selectively Labeling the Heterologous Protein in Escherichia coli for NMR Studies: A Strategy to Speed Up NMR Spectroscopy

    NASA Astrophysics Data System (ADS)

    Almeida, F. C. L.; Amorim, G. C.; Moreau, V. H.; Sousa, V. O.; Creazola, A. T.; Américo, T. A.; Pais, A. P. N.; Leite, A.; Netto, L. E. S.; Giordano, R. J.; Valente, A. P.

    2001-01-01

    Nuclear magnetic resonance is an important tool for high-resolution structural studies of proteins. It demands high protein concentration and high purity; however, the expression of proteins at high levels often leads to protein aggregation and the protein purification step can correspond to a high percentage of the overall time in the structural determination process. In the present article we show that the step of sample optimization can be simplified by selective labeling the heterologous protein expressed in Escherichia coli by the use of rifampicin. Yeast thioredoxin and a coix transcription factor Opaque 2 leucine zipper (LZ) were used to show the effectiveness of the protocol. The 1H/15N heteronuclear correlation two-dimensional NMR spectrum (HMQC) of the selective 15N-labeled thioredoxin without any purification is remarkably similar to the spectrum of the purified protein. The method has high yields and a good 1H/15N HMQC spectrum can be obtained with 50 ml of M9 growth medium. Opaque 2 LZ, a difficult protein due to the lower expression level and high hydrophobicity, was also probed. The 15N-edited spectrum of Opaque 2 LZ showed only the resonances of the protein of heterologous expression (Opaque 2 LZ) while the 1H spectrum shows several other resonances from other proteins of the cell lysate. The demand for a fast methodology for structural determination is increasing with the advent of genome/proteome projects. Selective labeling the heterologous protein can speed up NMR structural studies as well as NMR-based drug screening. This methodology is especially effective for difficult proteins such as hydrophobic transcription factors, membrane proteins, and others.

  18. Complex mixture analysis of organic compounds in green coffee bean extract by two-dimensional NMR spectroscopy.

    PubMed

    Wei, Feifei; Furihata, Kazuo; Hu, Fangyu; Miyakawa, Takuya; Tanokura, Masaru

    2010-11-01

    A complex mixture analysis by one- and two-dimensional nuclear magnetic resonance (NMR) spectroscopy was carried out for the first time for the identification and quantification of organic compounds in green coffee bean extract (GCBE). A combination of (1)H-(1)H DQF-COSY, (1)H-(13)C HSQC, and (1)H-(13)C CT-HMBC two-dimensional sequences was used, and 16 compounds were identified. In particular, three isomers of caffeoylquinic acid were identified in the complex mixture without any separation. In addition, GCBE components were quantified by the integration of carbon signals by use of a relaxation reagent and an inverse-gated decoupling method without a nuclear Overhauser effect. This NMR methodology provides detailed information about the kinds and amounts of GCBE components, and in our study, the chemical makeup of GCBE was clarified by the NMR results. PMID:20818806

  19. Direct detection of ligand binding to Sepharose-immobilised protein using saturation transfer double difference (STDD) NMR spectroscopy

    SciTech Connect

    Haselhorst, Thomas; Muenster-Kuehnel, Anja K.; Oschlies, Melanie; Tiralongo, Joe; Gerardy-Schahn, Rita; Itzstein, Mark von . E-mail: m.vonitzstein@griffith.edu.au

    2007-08-10

    We report an easy and direct application of 'Saturation Transfer Double Difference' (STDD) NMR spectroscopy to identify ligands that bind to a Sepharose-immobilised target protein. The model protein, cytidine 5'-monophosphate sialic acid (CMP-Sia) synthetase, was expressed as a Strep-Tag II fusion protein and immobilised on Strep-Tactin Sepharose. STD NMR experiments of the protein-enriched Sepharose matrix in the presence of a binding ligand (cytidine 5'-triphosphate, CTP) and a non-binding ligand ({alpha}/{beta}-glucose) clearly show that CTP binds to the immobilised enzyme, whereas glucose has no affinity. This approach has three major advantages: (a) only low quantities of protein are required, (b) no specialised NMR technology or the application of additional data analysis by non-routine methods is required, and (c) easy multiple use of the immobilised protein is available.

  20. Investigation of Local Structures in Layered Niobates by Solid-state NMR Spectroscopy

    NASA Astrophysics Data System (ADS)

    Liu, Ting

    Research on ion-exchangeable layered niobates has attracted great attention due to their unique structures and corresponding variations in properties and applications, such as ion conductors, solid acids, and water splitting catalysts. Families of layered niobates include double-layered or triple-layered Dion-Jacobson type perovskites (ALaNb2O7, A = Cs, Rb, K, H; AM2Nb3O10, A = Rb, K, H; M = Sr, Ca), layered niobates with both edge and corner sharing of NbO6 octahedra (KNb3O8, HNb3O6, Nb 6O17 and H4Nb6O17) and many others. Lately, more developments in the layered niobates through a variety of topochemical manipulations have been achieved. The topochemical reactions include ion exchange, exfoliation, substitution, and etc. As a result, many new materials have been successfully prepared, for example, solid solutions (ALa2NbTi2O10, ACaLaNb2TiO 10 and ACa2Nb3-xTaxO10, etc.), nanosheets (HNb3O8, H4Nb6O17, HLaNb2O7, HCa2Nb3O10, etc., to intercalate with organic molecules such as tetrabutylammonium hydroxide or n-butylamines), and nanoscrolls (from H2K2Nb 6O17). While these structural modifications often induce improvements in properties, the fundamental mechanisms of improvements in properties upon the modifications, especially local structural arrangements are poorly understood, which is often limited by structural characterizations. Particularly, the characterizations of the exfoliated nanosheets can be difficult by conventional X-ray diffraction (XRD) method due to disordered structures. Alternatively, solid-state nuclear magnetic resonance (NMR) spectroscopy is a useful tool to study local structures in solids. The structural information can be extracted by examining intrinsic interactions, such as quadrupolar, chemical shielding, and dipolar interactions, which are all associated with local environments surrounding a specific nucleus, 1H or 93Nb in layered niobates. The ultimate goal of this dissertation is to understand the relationships between local structures of

  1. A solution NMR study of the interactions of oligomannosides and the anti-HIV-1 2G12 antibody reveals distinct binding modes for branched ligands.

    PubMed

    Enríquez-Navas, Pedro M; Marradi, Marco; Padro, Daniel; Angulo, Jesús; Penadés, Soledad

    2011-02-01

    The structural and affinity details of the interactions of synthetic oligomannosides, linear (di-, tri-, and tetra-) and branched (penta- and hepta-), with the broadly neutralizing anti-HIV-1 antibody 2G12 (HIV=human immunodeficiency virus) have been investigated in solution by using ligand-based NMR techniques, specifically saturation transfer difference (STD) NMR spectroscopy and transferred NOE experiments. Linear oligomannosides show similar binding modes to the antibody, with the nonreducing terminal disaccharide Manα(1→2)Man (Man=mannose) making the closest protein/ligand contacts in the bound state. In contrast, the branched pentamannoside shows two alternate binding modes, involving both ligand arms (D2- and D3-like), a dual binding description of the molecular recognition of this ligand by 2G12 in solution that differs from the single binding mode deduced from X-ray studies. On the contrary, the antibody shows an unexpected selectivity for one arm (D1-like) of the other branched ligand (heptamannoside). This result explains the previously reported lack of affinity enhancement relative to that of the D1-like tetramannoside. Single-ligand STD NMR titration experiments revealed noticeable differences in binding affinities among the linear and branched ligands in solution, with the latter showing decreased affinity. Among the analyzed series of ligands, the strongest 2G12 binders were the linear tri- and tetramannosides because both show similar affinity for the antibody. These results demonstrate that NMR spectroscopic techniques can deliver abundant structural, dynamics, and affinity information for the characterization of oligomannose-2G12 binding in solution, thus complementing, and, as in the case of the pentamannoside, extending, the structural view from X-ray crystallography. This information is of key importance for the development of multivalent synthetic gp120 high-mannose glycoconjugate mimics in the context of vaccine development. PMID:21268157

  2. Mixed micelles of Triton X-100, sodium dodecyl dioxyethylene sulfate, and synperonic l61 investigated by NOESY and diffusion ordered NMR spectroscopy.

    PubMed

    Denkova, Pavletta S; Van Lokeren, Luk; Willem, Rudolph

    2009-05-14

    Mixed micelles formed from nonionic surfactant Triton X-100 (TX100), anionic surfactant sodium dodecyl dioxyethylene sulfate (SDP2S), and triblock copolymer Synperonic L61 (SL61) were investigated by 1H NMR spectroscopy. The size and shape of the aggregates were determined by diffusion ordered NMR spectroscopy (DOSY), while 2D nuclear Overhauser enhanced spectroscopy (NOESY) NMR was used to study the mutual spatial arrangement of the surfactant molecules in the aggregated state. An average micellar hydrodynamic radius of 3.6 nm, slightly increasing upon increasing TX100 molar fraction, was found for the mixed systems without additives. Addition of SL61 to the mixed micellar systems results in a slight increase of micellar radii. In the presence of AlCl3, an increase of TX100/SDP2S micellar sizes from 4 to 10 nm was found when increasing the SDP2S molar fraction. The mixed TX100/SDP2S micelles in the presence of both AlCl3 and polymer SL61 are almost spherical, with a radius of 4.5 nm. 2D NOESY data reveal that, as the individual TX100 micelles, mixed TX100/SDP2S and TX100/SDP2S/SL61/AlCl3 micelles also have a multilayer structure, with partially overlapping internal and external layers of TX100 molecules. In these mixed micelles, the SDP2S molecules are located at the level of the external layer of TX100 molecules, whereas the SL61 polymer is partially incorporated inside of the micellar core. PMID:19385612

  3. Effect of Oxygen Concentration on Viability and Metabolism in a Fluidized-Bed Bioartificial Liver Using 31P and 13C NMR Spectroscopy

    PubMed Central

    Jeffries, Rex E.; Gamcsik, Michael P.; Keshari, Kayvan R.; Pediaditakis, Peter; Tikunov, Andrey P.; Young, Gregory B.; Lee, Haakil; Watkins, Paul B.

    2013-01-01

    Many oxygen mass-transfer modeling studies have been performed for various bioartificial liver (BAL) encapsulation types; yet, to our knowledge, there is no experimental study that directly and noninvasively measures viability and metabolism as a function of time and oxygen concentration. We report the effect of oxygen concentration on viability and metabolism in a fluidized-bed NMR-compatible BAL using in vivo 31P and 13C NMR spectroscopy, respectively, by monitoring nucleotide triphosphate (NTP) and 13C-labeled nutrient metabolites, respectively. Fluidized-bed bioreactors eliminate the potential channeling that occurs with packed-bed bioreactors and serve as an ideal experimental model for homogeneous oxygen distribution. Hepatocytes were electrostatically encapsulated in alginate (avg. diameter, 500 μm; 3.5×107 cells/mL) and perfused at 3 mL/min in a 9-cm (inner diameter) cylindrical glass NMR tube. Four oxygen treatments were tested and validated by an in-line oxygen electrode: (1) 95:5 oxygen:carbon dioxide (carbogen), (2) 75:20:5 nitrogen:oxygen:carbon dioxide, (3) 60:35:5 nitrogen:oxygen:carbon dioxide, and (4) 45:50:5 nitrogen:oxygen:carbon dioxide. With 20% oxygen, β-NTP steadily decreased until it was no longer detected at 11 h. The 35%, 50%, and 95% oxygen treatments resulted in steady β-NTP levels throughout the 28-h experimental period. For the 50% and 95% oxygen treatment, a 13C NMR time course (∼5 h) revealed 2-13C-glycine and 2-13C-glucose to be incorporated into [2-13C-glycyl]glutathione (GSH) and 2-13C-lactate, respectively, with 95% having a lower rate of lactate formation. 31P and 13C NMR spectroscopy is a noninvasive method for determining viability and metabolic rates. Modifying tissue-engineered devices to be NMR compatible is a relatively easy and inexpensive process depending on the bioreactor shape. PMID:22835003

  4. Effect of oxygen concentration on viability and metabolism in a fluidized-bed bioartificial liver using ³¹P and ¹³C NMR spectroscopy.

    PubMed

    Jeffries, Rex E; Gamcsik, Michael P; Keshari, Kayvan R; Pediaditakis, Peter; Tikunov, Andrey P; Young, Gregory B; Lee, Haakil; Watkins, Paul B; Macdonald, Jeffrey M

    2013-02-01

    Many oxygen mass-transfer modeling studies have been performed for various bioartificial liver (BAL) encapsulation types; yet, to our knowledge, there is no experimental study that directly and noninvasively measures viability and metabolism as a function of time and oxygen concentration. We report the effect of oxygen concentration on viability and metabolism in a fluidized-bed NMR-compatible BAL using in vivo ³¹P and ¹³C NMR spectroscopy, respectively, by monitoring nucleotide triphosphate (NTP) and ¹³C-labeled nutrient metabolites, respectively. Fluidized-bed bioreactors eliminate the potential channeling that occurs with packed-bed bioreactors and serve as an ideal experimental model for homogeneous oxygen distribution. Hepatocytes were electrostatically encapsulated in alginate (avg. diameter, 500 μm; 3.5×10⁷ cells/mL) and perfused at 3 mL/min in a 9-cm (inner diameter) cylindrical glass NMR tube. Four oxygen treatments were tested and validated by an in-line oxygen electrode: (1) 95:5 oxygen:carbon dioxide (carbogen), (2) 75:20:5 nitrogen:oxygen:carbon dioxide, (3) 60:35:5 nitrogen:oxygen:carbon dioxide, and (4) 45:50:5 nitrogen:oxygen:carbon dioxide. With 20% oxygen, β-NTP steadily decreased until it was no longer detected at 11 h. The 35%, 50%, and 95% oxygen treatments resulted in steady β-NTP levels throughout the 28-h experimental period. For the 50% and 95% oxygen treatment, a ¹³C NMR time course (∼5 h) revealed 2-¹³C-glycine and 2-¹³C-glucose to be incorporated into [2-¹³C-glycyl]glutathione (GSH) and 2-¹³C-lactate, respectively, with 95% having a lower rate of lactate formation. ³¹P and ¹³C NMR spectroscopy is a noninvasive method for determining viability and metabolic rates. Modifying tissue-engineered devices to be NMR compatible is a relatively easy and inexpensive process depending on the bioreactor shape. PMID:22835003

  5. ¹¹³Cd NMR experiments reveal an unusual metal cluster in the solution structure of the yeast splicing protein Bud31p.

    PubMed

    van Roon, Anne-Marie M; Yang, Ji-Chun; Mathieu, Daniel; Bermel, Wolfgang; Nagai, Kiyoshi; Neuhaus, David

    2015-04-13

    Establishing the binding topology of structural zinc ions in proteins is an essential part of their structure determination by NMR spectroscopy. Using (113)Cd NMR experiments with (113)Cd-substituted samples is a useful approach but has previously been limited mainly to very small protein domains. Here we used (113)Cd NMR spectroscopy during structure determination of Bud31p, a 157-residue yeast protein containing an unusual Zn3Cys9 cluster, demonstrating that recent hardware developments make this approach feasible for significantly larger systems. PMID:25703931

  6. 113Cd NMR Experiments Reveal an Unusual Metal Cluster in the Solution Structure of the Yeast Splicing Protein Bud31p**

    PubMed Central

    van Roon, Anne-Marie M; Yang, Ji-Chun; Mathieu, Daniel; Bermel, Wolfgang; Nagai, Kiyoshi; Neuhaus, David

    2015-01-01

    Establishing the binding topology of structural zinc ions in proteins is an essential part of their structure determination by NMR spectroscopy. Using 113Cd NMR experiments with 113Cd-substituted samples is a useful approach but has previously been limited mainly to very small protein domains. Here we used 113Cd NMR spectroscopy during structure determination of Bud31p, a 157-residue yeast protein containing an unusual Zn3Cys9 cluster, demonstrating that recent hardware developments make this approach feasible for significantly larger systems. PMID:25703931

  7. Structural investigations of borosilicate glasses containing MoO 3 by MAS NMR and Raman spectroscopies

    NASA Astrophysics Data System (ADS)

    Caurant, D.; Majérus, O.; Fadel, E.; Quintas, A.; Gervais, C.; Charpentier, T.; Neuville, D.

    2010-01-01

    High molybdenum concentration in glass compositions may lead to alkali and alkaline-earth molybdates crystallization during melt cooling that must be controlled particularly during the preparation of highly radioactive nuclear glassy waste forms. To understand the effect of molybdenum addition on the structure of a simplified nuclear glass and to know how composition changes can affect molybdates crystallization tendency, the structure of two glass series belonging to the SiO 2-B 2O 3-Na 2O-CaO-MoO 3 system was studied by 29Si, 11B, 23Na MAS NMR and Raman spectroscopies by increasing MoO 3 or B 2O 3 concentrations. Increasing MoO 3 amount induced an increase of the silicate network reticulation but no significant effect was observed on the proportion of BO4- units and on the distribution of Na + cations in glass structure. By increasing B 2O 3 concentration, a strong evolution of the distribution of Na + cations was observed that could explain the evolution of the nature of molybdate crystals (CaMoO 4 or Na 2MoO 4) formed during melt cooling.

  8. Protein fold determined by paramagnetic magic-angle spinning solid-state NMR spectroscopy

    NASA Astrophysics Data System (ADS)

    Sengupta, Ishita; Nadaud, Philippe S.; Helmus, Jonathan J.; Schwieters, Charles D.; Jaroniec, Christopher P.

    2012-05-01

    Biomacromolecules that are challenging for the usual structural techniques can be studied with atomic resolution by solid-state NMR spectroscopy. However, the paucity of distance restraints >5 Å, traditionally derived from measurements of magnetic dipole-dipole couplings between protein nuclei, is a major bottleneck that hampers such structure elucidation efforts. Here, we describe a general approach that enables the rapid determination of global protein fold in the solid phase via measurements of nuclear paramagnetic relaxation enhancements (PREs) in several analogues of the protein of interest containing covalently attached paramagnetic tags, without the use of conventional internuclear distance restraints. The method is demonstrated using six cysteine-EDTA-Cu2+ mutants of the 56-residue B1 immunoglobulin-binding domain of protein G, for which ~230 longitudinal backbone 15N PREs corresponding to distances of ~10-20 Å were obtained. The mean protein fold determined in this manner agrees with the X-ray structure with a backbone atom root-mean-square deviation of 1.8 Å.

  9. Hetergeneous tumour response to photodynamic therapy assessed by in vivo localised 31P NMR spectroscopy.

    PubMed Central

    Ceckler, T. L.; Gibson, S. L.; Kennedy, S. D.; Hill, R.; Bryant, R. G.

    1991-01-01

    Photodynamic therapy (PDT) is efficacious in the treatment of small malignant lesions when all cells in the tumour receive sufficient drug, oxygen and light to induce a photodynamic effect capable of complete cytotoxicity. In large tumours, only partial effectiveness is observed presumably because of insufficient light penetration into the tissue. The heterogeneity of the metabolic response in mammary tumours following PDT has been followed in vivo using localised phosphorus NMR spectroscopy. Alterations in nucleoside triphosphates (NTP), inorganic phosphate (Pi) and pH within localised regions of the tumour were monitored over 24-48 h following PDT irradiation of the tumour. Reduction of NTP and increases in Pi were observed at 4-6 h after PDT irradiation in all regions of treated tumours. The uppermost regions of the tumours (those nearest the skin surface and exposed to the greatest light fluence) displayed the greatest and most prolonged reduction of NTP and concomitant increase in Pi resulting in necrosis. The metabolite concentrations in tumour regions located towards the base of the tumour returned a near pre-treatment levels by 24-48 h after irradiation. The ability to follow heterogeneous metabolic responses in situ provides one means to assess the degree of metabolic inhibition which subsequently leads to tumour necrosis. Images Figure 4 PMID:1829953

  10. Unraveling complex small-molecule binding mechanisms by using simple NMR spectroscopy.

    PubMed

    Quinternet, Marc; Starck, Jean-Philippe; Delsuc, Marc-André; Kieffer, Bruno

    2012-03-26

    Heteronuclear NMR spectroscopy provides a unique way to obtain site-specific information about protein-ligand interactions. Usually, such studies rely on the availability of isotopically labeled proteins, thereby allowing both editing of the spectra and ligand signals to be filtered out. Herein, we report that the use of the methyl SOFAST correlation experiment enables the determination of site-specific equilibrium binding constants by using unlabeled proteins. By using the binding of L- and D-tryptophan to serum albumin as a test case, we determined very accurate dissociation constants for both the high- and low-affinity sites present at the protein surface. The values of site-specific dissociation constants were closer to those obtained by isothermal titration calorimetry than those obtained from ligand-observed methods, such as saturation transfer difference. The possibility of measuring ligand binding to serum albumin at physiological concentrations with unlabeled proteins may open up new perspectives in the field of drug discovery. PMID:22336999

  11. 1H NMR Spectroscopy and MVA Analysis of Diplodus sargus Eating the Exotic Pest Caulerpa cylindracea

    PubMed Central

    De Pascali, Sandra A.; Del Coco, Laura; Felline, Serena; Mollo, Ernesto; Terlizzi, Antonio; Fanizzi, Francesco P.

    2015-01-01

    The green alga Caulerpa cylindracea is a non-autochthonous and invasive species that is severely affecting the native communities in the Mediterranean Sea. Recent researches show that the native edible fish Diplodus sargus actively feeds on this alga and cellular and physiological alterations have been related to the novel alimentary habits. The complex effects of such a trophic exposure to the invasive pest are still poorly understood. Here we report on the metabolic profiles of plasma from D. sargus individuals exposed to C. cylindracea along the southern Italian coast, using 1H NMR spectroscopy and multivariate analysis (Principal Component Analysis, PCA, Orthogonal Partial Least Square, PLS, and Orthogonal Partial Least Square Discriminant Analysis, OPLS-DA). Fish were sampled in two seasonal periods from three different locations, each characterized by a different degree of algal abundance. The levels of the algal bisindole alkaloid caulerpin, which is accumulated in the fish tissues, was used as an indicator of the trophic exposure to the seaweed and related to the plasma metabolic profiles. The profiles appeared clearly influenced by the sampling period beside the content of caulerpin, while the analyses also supported a moderate alteration of lipid and choline metabolism related to the Caulerpa-based diet. PMID:26058009

  12. Probing the structural details of xylan degradation by real-time NMR spectroscopy.

    PubMed

    Petersen, Bent Ole; Lok, Finn; Meier, Sebastian

    2014-11-01

    The biodegradation of abundantly available cell wall polysaccharides has recently received much attention, not least because cell wall polysaccharides are substrates for the human gut microbiota and for environmentally sustainable processes of biomass conversion to value-added compounds. A major fraction of cereal cell wall polysaccharides consists of arabinoxylans. Arabinoxylan and its degradation products are therefore present in a variety of agro-industrial residues and products. Here, we undertook to track the structural details of wheat arabinoxylan degradation with high resolution NMR spectroscopy. More than 15 carbohydrate residues were distinguished in the substrate and more than 20 residues in partially degraded samples without any sample cleanup. The resolution of a plethora of structural motifs in situ permits the readout of persisting structures in degradation processes and in products. Reaction progress was visualized for the biodegradation of arabinoxylan by different crude microbial enzyme preparations. The direct observation of structural details in complex mixtures containing arabinoxylan fragments is significant, as such structural details reportedly modulate the health-promoting functions of arabinoxylan fragments. PMID:25129786

  13. Application of NMR Spectroscopy in the Assessment of Radiation Dose in Human Primary Cells.

    PubMed

    Kang, Chang-Mo; Seong Hyeon, Jin; Ra Kim, So; Kyeong Lee, Eun; Jin Yun, Hyun; Young Kim, Sun; Kee Chae, Young

    2015-11-01

    We employed the primary cell model system as a first step toward establishing a method to assess the influence of ionizing radiation by using a combination of common and abundant metabolites. We applied X-ray irradiation amounts of 0, 1, and 5 Gy to the cells that were harvested 24, 48, or 72 h later, and profiled metabolites by 2D-NMR spectroscopy to sort out candidate molecules that could be used to distinguish the samples under different irradiation conditions. We traced metabolites stemming from the input ¹³C-glucose, identified twelve of them from the cell extracts, and applied statistical analysis to find out that all the metabolites, including glycine, alanine, and gluatamic acid, increased upon irradiation. The combinatorial use of the selected metabolites showed promising results where the product of signal intensities of alanine and lactate could differentiate samples according to the dose of X-ray irradiation. We hope that this work can form a base for treating radiation-poisoned patients in the future. PMID:26567947

  14. Protein fold determined by paramagnetic magic-angle spinning solid-state NMR spectroscopy.

    PubMed

    Sengupta, Ishita; Nadaud, Philippe S; Helmus, Jonathan J; Schwieters, Charles D; Jaroniec, Christopher P

    2012-05-01

    Biomacromolecules that are challenging for the usual structural techniques can be studied with atomic resolution by solid-state NMR spectroscopy. However, the paucity of distance restraints >5 Å, traditionally derived from measurements of magnetic dipole-dipole couplings between protein nuclei, is a major bottleneck that hampers such structure elucidation efforts. Here, we describe a general approach that enables the rapid determination of global protein fold in the solid phase via measurements of nuclear paramagnetic relaxation enhancements (PREs) in several analogues of the protein of interest containing covalently attached paramagnetic tags, without the use of conventional internuclear distance restraints. The method is demonstrated using six cysteine-EDTA-Cu(2+) mutants of the 56-residue B1 immunoglobulin-binding domain of protein G, for which ~230 longitudinal backbone (15)N PREs corresponding to distances of ~10-20 Å were obtained. The mean protein fold determined in this manner agrees with the X-ray structure with a backbone atom root-mean-square deviation of 1.8 Å. PMID:22522262

  15. On the role of NMR spectroscopy for characterization of antimicrobial peptides

    PubMed Central

    Porcelli, Fernando; Ramamoorthy, Ayyalusamy; Barany, George; Veglia, Gianluigi

    2016-01-01

    Summary Antimicrobial peptides (AMPs) provide a primordial source of immunity, conferring upon eukaryotic cells resistance against bacteria, protozoa, and viruses. Despite a few examples of anionic peptides, AMPs are usually relatively short positively charged polypeptides, consisting of a dozen to about a hundred amino acids, and exhibiting amphipathic character. Despite significant differences in their primary and secondary structures, all AMPs discovered to date share the ability to interact with cellular membranes, thereby affecting bilayer stability, disrupting membrane organization, and/or forming well-defined pores. AMPs selectively target infectious agents without being susceptible to any of the common pathways by which these acquire resistance, thereby making AMPs prime candidates to provide therapeutic alternatives to conventional drugs. However, the mechanisms of AMP actions are still a matter of intense debate. The structure-function paradigm suggests that a better understanding of how AMPs elicit their biological functions could result from atomic resolution studies of peptide-lipid interactions. In contrast, more strict thermodynamic views preclude any roles for three-dimensional structures. Indeed, the design of selective AMPs based soley on structural parameters has been challenging. In this chapter, we will focus on selected AMPs for which studies on the corresponding AMP-lipid interactions have helped reach an understanding of how AMP effects are mediated. We will emphasize the roles of both liquid- and solid-state NMR spectroscopy for elucidating the mechanisms of action of AMPs. PMID:23975777

  16. 1H NMR Spectroscopy and MVA Analysis of Diplodus sargus Eating the Exotic Pest Caulerpa cylindracea.

    PubMed

    De Pascali, Sandra A; Del Coco, Laura; Felline, Serena; Mollo, Ernesto; Terlizzi, Antonio; Fanizzi, Francesco P

    2015-06-01

    The green alga Caulerpa cylindracea is a non-autochthonous and invasive species that is severely affecting the native communities in the Mediterranean Sea. Recent researches show that the native edible fish Diplodus sargus actively feeds on this alga and cellular and physiological alterations have been related to the novel alimentary habits. The complex effects of such a trophic exposure to the invasive pest are still poorly understood. Here we report on the metabolic profiles of plasma from D. sargus individuals exposed to C. cylindracea along the southern Italian coast, using 1H NMR spectroscopy and multivariate analysis (Principal Component Analysis, PCA, Orthogonal Partial Least Square, PLS, and Orthogonal Partial Least Square Discriminant Analysis, OPLS-DA). Fish were sampled in two seasonal periods from three different locations, each characterized by a different degree of algal abundance. The levels of the algal bisindole alkaloid caulerpin, which is accumulated in the fish tissues, was used as an indicator of the trophic exposure to the seaweed and related to the plasma metabolic profiles. The profiles appeared clearly influenced by the sampling period beside the content of caulerpin, while the analyses also supported a moderate alteration of lipid and choline metabolism related to the Caulerpa-based diet. PMID:26058009

  17. Reconsidering the activation entropy for anomerization of glucose and mannose in water studied by NMR spectroscopy

    NASA Astrophysics Data System (ADS)

    Kosaka, Ami; Aida, Misako; Katsumoto, Yukiteru

    2015-08-01

    The anomerization of monosaccharides is a very important process to understand how their stereoisomers are stabilized in aqueous solutions. For glucose and mannose, it has been known that α- and β-anomers of hexopyranose exist as the major components. In order to examine the anomerization pathway for glucose and mannose in aqueous solutions, it is indispensable to determine the thermodynamic parameters such as the activation energy, the activation Gibbs free energy (ΔG‡), enthalpy (ΔH‡), and entropy (ΔS‡). Although several research groups reported these quantities in aqueous solution, they have still been controversial especially for ΔS‡. In this paper, we employ 1H NMR spectroscopy for monitoring the population of both α- and β-anomers of glucose and mannose. The contribution of ΔS‡ to ΔG‡ for glucose in water is estimated to be ca. 30%, while that for mannose is 8.0%. The large difference in ΔS‡ suggests that the anomerization pathway is not the same for glucose and mannose.

  18. Thermodynamic Study on the Protonation Reactions of Glyphosate in Aqueous Solution: Potentiometry, Calorimetry and NMR spectroscopy.

    PubMed

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

    2016-03-10

    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. PMID:26862689

  19. Insights into the molecular basis of action of the AT1 antagonist losartan using a combined NMR spectroscopy and computational approach.

    PubMed

    Zervou, Maria; Cournia, Zoe; Potamitis, Constantinos; Patargias, George; Durdagi, Serdar; Grdadolnik, Simona Golic; Mavromoustakos, Thomas

    2014-03-01

    The drug:membrane interactions for the antihypertensive AT1 antagonist losartan, the prototype of the sartans class, are studied herein using an integrated approach. The pharmacophore arrangement of the drug was revealed by rotating frame nuclear Overhauser effect spectroscopy (2D ROESY) NMR spectroscopy in three different environments, namely water, dimethyl sulfoxide (DMSO), and sodium dodecyl sulfate (SDS) micellar solutions mimicking conditions of biological transport fluids and membrane lipid bilayers. Drug association with micelles was monitored by diffusion ordered spectroscopy (2D DOSY) and drug:micelle intermolecular interactions were characterized by ROESY spectroscopy. The localisation of the drug in the micellar environment was investigated by introducing 5-doxyl and 16-doxyl stearic acids. The use of spin labels confirmed that losartan resides close to the micelle:water interface with the hydroxymethyl group and the tetrazole heterocyclic aromatic ring facing the polar surface with the potential to interact with SDS charged polar head groups in order to increase amphiphilic interactions. The spontaneous insertion, the diffusion pathway and the conformational features of losartan were monitored by Molecular Dynamics (MD) simulations in a modeled SDS micellar aggregate environment and a long exploratory MD run (580ns) in a phospholipid dipalmitoylphosphatidylcholine (DPPC) bilayer with the AT1 receptor embedded. MD simulations were in excellent agreement with experimental results and further revealed the molecular basis of losartan:membrane interactions in atomic-level detail. This applied integrated approach aims to explore the role of membranes in losartan's pathway towards the AT1 receptor. PMID:24374319

  20. Structural investigation of BaOsbnd B2O3sbnd P2O5 glasses by NMR and Raman spectroscopy

    NASA Astrophysics Data System (ADS)

    Koudelka, Ladislav; Kalenda, Petr; Mošner, Petr; Černošek, Zdeněk; Montagne, Lionel; Revel, Bertrand

    2016-09-01

    Glasses of the ternary system BaOsbnd B2O3sbnd P2O5 were prepared and studied in broad concentration limits covering the whole vitrification domain: 20-50 mol% BaO, 0-40 mol% B2O3 and 20-60 mol% P2O5. Their structure was studied with combinations of Raman spectroscopy, 31P MAS NMR spectroscopy and 11B MAS NMR spectroscopy. The obtained results are discussed in several compositional lines A: (100-x)Ba(PO3)2sbnd xB2O3, B: 40BaOsbnd yB2O3sbnd (60-y)P2O5, C: (50-z)BaOsbnd zB2O3sbnd 50P2O5, D: (60-w)BaOsbnd wB2O3sbnd 40P2O5 and E: uBaOsbnd 40B2O3sbnd (60-u)P2O5. Boron oxide incorporates into the phosphate network in the form of BO4 and BO3 groups and increases their glass transition temperature. Nevertheless, the increase in Tg is only steep within the region of 0-20 mol% B2O3 reaching a maximum at the glasses with ∼30 mol% B2O3. In the lines A, B and E a decrease in the P2O5 and an increase of B2O3 content results in the shortening of phosphate chains with decreasing P2O5 content; these changes are most pronounced in line B with a constant BaO content. In lines C and D with a constant P2O5 content a decrease in the BaO content results, in contrast, in the reverse transformation of phosphate structural units in the direction Q1 → Q2 → Q3 as detected from Raman spectra and 31P MAS NMR spectra. 11B MAS NMR spectra revealed that only BO4 units are present in the glasses with 0-20 mol% B2O3. In the glasses of the E series the fraction of BO3 units increases with a decreasing P2O5 content. By the decomposition of the 11B MAS NMR spectra it is possible to estimate the fractions of basic structural units formed by boron - B(OP)3O, B(OP)2O2 and BO3 in all the glasses of the glass forming region.

  1. Structure of the propeptide of prothrombin containing the. gamma. -carboxylation recognition site determined by two-dimensional NMR spectroscopy

    SciTech Connect

    Sanford, D.G.; Sudmeier, J.L.; Bachovchin, W.W.; Kanagy, C.; Furie, B.C.; Furie, B. )

    1991-10-15

    The propeptides of the vitamin K dependent blood clotting and regulatory proteins contain a {gamma}-carboxylation recognition site that directs precursor forms of these proteins for posttranslational {gamma}-carboxylation. Peptides corresponding to the propeptide of prothrombin were synthesized and examined by circular dichroism (CD) and nuclear magnetic resonance spectroscopy (NMR). CD spectra indicate that these peptides have little or no secondary structure in aqueous solutions but that the addition of trifluoroethanol induces or stabilizes a structure containing {alpha}-helical character. The maximum helical content occurs at 35-40% trifluoroethanol. This trifluoroethanol-stabilized structure was solved by two-dimensional NMR spectroscopy. The NMR results demonstrate that residues {minus}13 to {minus}3 form an amphipathic {alpha}-helix. NMR spectra indicate that a similar structure is present at 5C, in the absence of trifluoroethanol. Of the residues previously implicated in defining the {gamma}-carboxylation recognition site, four residues ({minus}18, {minus}17, {minus}16, and {minus}15) are adjacent to the helical region and one residue ({minus}10) is located within the helix. The potential role of the amphipathic {alpha}-helix in the {gamma}-carboxylation recognition site is discussed.

  2. Characterization of the biochemical effects of 1-nitronaphthalene in rats using global metabolic profiling by NMR spectroscopy and pattern recognition.

    PubMed

    Azmi, J; Connelly, J; Holmes, E; Nicholson, J K; Shore, R F; Griffin, J L

    2005-01-01

    Metabolic fingerprints, in the form of patterns of high-concentration endogenous metabolites, of 1-nitronaphthalene (NN)-induced lung toxicity have been elucidated in bronchoalveolar lavage fluid (BALF), urine, blood plasma, and intact lung and liver tissue using NMR spectroscopy-based metabolic profiling. A single dose of NN (75 mg kg(-1)) was administered orally to Sprague-Dawley rats. BALF and lung tissue were obtained 24 h after dosing from these animals and matched control rats post-mortem. High-resolution (1)H-NMR spectroscopy of BALF samples indicated that NN caused increases in concentrations of choline, amino acids (leucine, isoleucine and alanine) and lactate together with decreased concentrations of succinate, citrate, creatine, creatinine and glucose. In addition, the intact lung weights were higher in the NN-treated group (p<0.01), consistent with pulmonary oedema. The NMR-detected perturbations indicated that NN induces a perturbation in energy metabolism in both lung and liver tissue, as well as surfactant production and osmolyte levels in the lungs. As well as reporting the first NMR spectroscopic combined examination of BALF and intact lung, this study indicates that such holistic approaches to investigating mechanisms of lung toxicity may be of value in evaluating disease progression or the effects of therapeutic intervention in pulmonary conditions such as surfactant disorders or asthma. PMID:16308265

  3. Accurate quantitative 13C NMR spectroscopy: repeatability over time of site-specific 13C isotope ratio determination.

    PubMed

    Caytan, Elsa; Botosoa, Eliot P; Silvestre, Virginie; Robins, Richard J; Akoka, Serge; Remaud, Gérald S

    2007-11-01

    The stability over time (repeatability) for the determination of site-specific 13C/12C ratios at natural abundance by quantitative 13C NMR spectroscopy has been tested on three probes: enriched bilabeled [1,2-13C2]ethanol; ethanol at natural abundance; and vanillin at natural abundance. It is shown in all three cases that the standard deviation for a series of measurements taken every 2-3 months over periods between 9 and 13 months is equal to or smaller than the standard deviation calculated from 5-10 replicate measurements made on a single sample. The precision which can be achieved using the present analytical 13C NMR protocol is higher than the prerequisite value of 1-2 per thousand for the determination of site-specific 13C/12C ratios at natural abundance (13C-SNIF-NMR). Hence, this technique permits the discrimination of very small variations in 13C/12C ratios between carbon positions, as found in biogenic natural products. This observed stability over time in 13C NMR spectroscopy indicates that further improvements in precision will depend primarily on improved signal-to-noise ratio. PMID:17900175

  4. Structure of the propeptide of prothrombin containing the gamma-carboxylation recognition site determined by two-dimensional NMR spectroscopy.

    PubMed

    Sanford, D G; Kanagy, C; Sudmeier, J L; Furie, B C; Furie, B; Bachovchin, W W

    1991-10-15

    The propeptides of the vitamin K dependent blood clotting and regulatory proteins contain a gamma-carboxylation recognition site that directs precursor forms of these proteins for posttranslational gamma-carboxylation. Peptides corresponding to the propeptide of prothrombin were synthesized and examined by circular dichroism (CD) and nuclear magnetic resonance spectroscopy (NMR). CD spectra indicate that these peptides have little or no secondary structure in aqueous solutions but that the addition of trifluoroethanol induces or stabilizes a structure containing alpha-helical character. The maximum helical content occurs at 35-40% trifluoroethanol. This trifluoroethanol-stabilized structure was solved by two-dimensional NMR spectroscopy. The NMR results demonstrate that residues -13 to -3 form an amphipathic alpha-helix. NMR spectra indicate that a similar structure is present at 5 degrees C, in the absence of trifluoroethanol. Of the residues previously implicated in defining the gamma-carboxylation recognition site, four residues (-18, -17, -16, and -15) are adjacent to the helical region and one residue (-10) is located within the helix. The potential role of the amphipathic alpha-helix in the gamma-carboxylation recognition site is discussed. PMID:1911775

  5. Characterization of a multicomponent lithium lithiate from a combined x-ray diffraction, NMR spectroscopy, and computational approach.

    PubMed

    Pöppler, Ann-Christin; Granitzka, Markus; Herbst-Irmer, Regine; Chen, Yu-Sheng; Iversen, Bo B; John, Michael; Mata, Ricardo A; Stalke, Dietmar

    2014-11-24

    An unusual lithium lithiate [Li(diglyme)2][(diglyme)Li2(C4H3S)3], made up from three carbanions, two lithium cations, and a single donor base molecule in the anion and a single lithium cation, coordinated by two donor base molecules, is investigated in a combined study including X-ray diffraction, NMR spectroscopy and computational approaches in solution and the solid state. While the multicomponent lithiate is the only species present in the solid state, solution NMR spectroscopy and computational methods were employed to identify a second species in solution. The dimer [(diglyme)Li(C4H3S)]2 coexists with the lithiate in solution in a 1:1 ratio, the more the higher the polarity of the solvent is. Only the combination of this multitude of methods provides a firm picture of the whole. PMID:25284593

  6. Rapid approach to identify the presence of Arabica and Robusta species in coffee using 1H NMR spectroscopy.

    PubMed

    Monakhova, Yulia B; Ruge, Winfried; Kuballa, Thomas; Ilse, Maren; Winkelmann, Ole; Diehl, Bernd; Thomas, Freddy; Lachenmeier, Dirk W

    2015-09-01

    NMR spectroscopy was used to verify the presence of Arabica and Robusta species in coffee. Lipophilic extracts of authentic roasted and green coffees showed the presence of established markers for Robusta (16-O-methylcafestol (16-OMC)) and for Arabica (kahweol). The integration of the 16-OMC signal (δ 3.165 ppm) was used to estimate the amount of Robusta in coffee blends with an approximate limit of detection of 1-3%. The method was successfully applied for the analysis of 77 commercial coffee samples (coffee pods, coffee capsules, and coffee beans). Furthermore, principal component analysis (PCA) was applied to the spectra of lipophilic and aqueous extracts of 20 monovarietal authentic samples. Clusters of the two species were observed. NMR spectroscopy can be used as a rapid prescreening tool to discriminate Arabica and Robusta coffee species before the confirmation applying the official method. PMID:25842325

  7. Fast characterization of functionalized silica materials by silicon-29 surface-enhanced NMR spectroscopy using dynamic nuclear polarization.

    PubMed

    Lelli, Moreno; Gajan, David; Lesage, Anne; Caporini, Marc A; Vitzthum, Veronika; Miéville, Pascal; Héroguel, Florent; Rascón, Fernando; Roussey, Arthur; Thieuleux, Chloé; Boualleg, Malika; Veyre, Laurent; Bodenhausen, Geoffrey; Copéret, Christophe; Emsley, Lyndon

    2011-02-23

    We demonstrate fast characterization of the distribution of surface bonding modes and interactions in a series of functionalized materials via surface-enhanced nuclear magnetic resonance spectroscopy using dynamic nuclear polarization (DNP). Surface-enhanced silicon-29 DNP NMR spectra were obtained by using incipient wetness impregnation of the sample with a solution containing a polarizing radical (TOTAPOL). We identify and compare the bonding topology of functional groups in materials obtained via a sol-gel process and in materials prepared by post-grafting reactions. Furthermore, the remarkable gain in time provided by surface-enhanced silicon-29 DNP NMR spectroscopy (typically on the order of a factor 400) allows the facile acquisition of two-dimensional correlation spectra. PMID:21280606

  8. (19) F NMR Spectroscopy as a Highly Sensitive Method for the Direct Monitoring of Confined Crystallization within Nanoporous Materials.

    PubMed

    Nartowski, Karol P; Malhotra, Diksha; Hawarden, Lucy E; Sibik, Juraj; Iuga, Dinu; Zeitler, J Axel; Fábián, László; Khimyak, Yaroslav Z

    2016-07-25

    The introduction of fluorine into the structure of pharmaceuticals has been an effective strategy for tuning their pharmacodynamic properties, with more than 40 new drugs entering the market in the last 15 years. In this context, (19) F NMR spectroscopy can be viewed as a useful method for investigating the host-guest chemistry of pharmaceuticals in nanosized drug-delivery systems. Although the interest in confined crystallization, nanosized devices, and porous catalysts is gradually increasing, understanding of the complex phase behavior of organic molecules confined within nanochambers or nanoreactors is still lacking. Using (19) F magic-angle-spinning NMR spectroscopy, we obtained detailed mechanistic insight into the crystallization of flufenamic acid (FFA) in a confined environment of mesoporous silica materials with different pore diameters (3.2-29 nm), providing direct experimental evidence for the formation of a molecular-liquid-like layer besides crystalline confined FFA form I. PMID:27272008

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

    PubMed

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

    2016-03-01

    The ligand capping of phosphonic acid functionalized CdSe/ZnS core-shell quantum dots (QDs) was investigated with a combination of solution and solid-state (31) P nuclear magnetic resonance (NMR) spectroscopy. Two phosphonic acid ligands were used in the synthesis of the QDs, tetradecylphosphonic acid and ethylphosphonic acid. Both alkyl phosphonic acids showed broad liquid and solid-state (31) P NMR resonances for the bound ligands, indicative of heterogeneous binding to the QD surface. In order to quantify the two ligand populations on the surface, ligand exchange facilitated by phenylphosphonic acid resulted in the displacement of the ethylphosphonic acid and tetradecylphosphonic acid and allowed for quantification of the free ligands using (31) P liquid-state NMR. After washing away the free ligand, two broad resonances were observed in the liquids' (31) P NMR corresponding to the alkyl and aromatic phosphonic acids. The washed samples were analyzed via solid-state (31) P NMR, which confirmed the ligand populations on the surface following the ligand exchange process. Copyright © 2015 John Wiley & Sons, Ltd. PMID:26639792

  10. Fragment-Linking Approach Using (19)F NMR Spectroscopy To Obtain Highly Potent and Selective Inhibitors of β-Secretase.

    PubMed

    Jordan, John B; Whittington, Douglas A; Bartberger, Michael D; Sickmier, E Allen; Chen, Kui; Cheng, Yuan; Judd, Ted

    2016-04-28

    Fragment-based drug discovery (FBDD) has become a widely used tool in small-molecule drug discovery efforts. One of the most commonly used biophysical methods in detecting weak binding of fragments is nuclear magnetic resonance (NMR) spectroscopy. In particular, FBDD performed with (19)F NMR-based methods has been shown to provide several advantages over (1)H NMR using traditional magnetization-transfer and/or two-dimensional methods. Here, we demonstrate the utility and power of (19)F-based fragment screening by detailing the identification of a second-site fragment through (19)F NMR screening that binds to a specific pocket of the aspartic acid protease, β-secretase (BACE-1). The identification of this second-site fragment allowed the undertaking of a fragment-linking approach, which ultimately yielded a molecule exhibiting a more than 360-fold increase in potency while maintaining reasonable ligand efficiency and gaining much improved selectivity over cathepsin-D (CatD). X-ray crystallographic studies of the molecules demonstrated that the linked fragments exhibited binding modes consistent with those predicted from the targeted screening approach, through-space NMR data, and molecular modeling. PMID:26978477

  11. Stellar Spectroscopy during Exoplanet Transits: Revealing structures across stellar surfaces

    NASA Astrophysics Data System (ADS)

    Dravins, Dainis; Ludwig, Hans-Günter; Dahlén, Erik

    2015-08-01

    Exoplanet transits permit to study stellar surface portions that successively become hidden behind the planet. Differential spectroscopy between various transit phases reveals spectra of those stellar surface segments that were hidden. The deduced center-to-limb behavior of stellar spectral line shapes, asymmetries and wavelength shifts enables detailed tests of 3-dimensional hydrodynamic models of stellar atmospheres, such that are required for any precise determination of abundances or seismic properties. Such models can now be computed for widely different classes of stars (including metal-poor ones and white dwarfs), but have been feasible to test and verify only for the Sun with its resolved surface structure. Exoplanet transits may also occur across features such as starspots, whose magnetic signatures will be retrieved from spectra of sufficient fidelity.Knowing the precise background stellar spectra, also properties of exoplanet atmospheres are better constrained: e.g., the Rossiter-McLaughlin effect becomes resolved as not only a simple change of stellar wavelength, but as a variation of the full line profiles and their asymmetries.Such studies are challenging since exoplanets cover only a tiny fraction of the stellar disk. Current work, analyzing sequences of high-fidelity ESO UVES spectra, demonstrate that such spatially resolved stellar spectra can already be (marginally) retrieved in a few cases with the brightest host stars. Already in a near future, ongoing exoplanet surveys are likely to find further bright hosts that will enable such studies for various stellar types. http://arxiv.org/abs/1408.1402

  12. Determination of the time course of an enzymatic reaction by 1H NMR spectroscopy: hydroxynitrile lyase catalysed transhydrocyanation

    NASA Astrophysics Data System (ADS)

    Hickel, A.; Gradnig, G.; Griengl, H.; Schall, M.; Sterk, H.

    1996-01-01

    The time course of the enzyme catalysed transhydrocyanation of benzaldehyde to give ( S)-mandelonitrile was investigated using a hydroxynitrile lyase from Hevea brasiliensis as catalyst and acetone cyanohydrin as cyanide donor. Employing special techniques it was possible to apply 1H NMR spectroscopy in aqueous medium to monitor the concentration changes of all substrates and products. By this technique strong evidence for inhibition of the enzyme at higher substrate concentrations was obtained.

  13. Metabolomics-Based Study of Logarithmic and Stationary Phases of Promastigotes in Leishmania major by 1H NMR Spectroscopy

    PubMed Central

    Arjmand, Mohammad; Madrakian, Azadeh; Khalili, Ghader; Najafi, Ali; Zamani, Zahra; Akbari, Ziba

    2016-01-01

    Background: Cutaneous leishmaniasis is one of the most important parasitic diseases in humans. In this disease, one of the responsible organisms is Leishmania major, which is transmitted by sandfly vector. There are specific differences in biochemical profiles and metabolite pathways in logarithmic and stationary phases of Leishmania parasites. In the present study, 1H NMR spectroscopy was used to examine the metabolites outliers in the logarithmic and stationary phases of promastigotes in L. major to enlighten more about the transmission mechanism in metacyclogenesis of L. major. Methods: Promastigote was cultured, logarithmic and stationary phases were separated by the peanut agglutinin, and cell metabolites were extracted. 1H NMR spectroscopy was applied, and outliers were analyzed using principal component analysis. Results: The most altered metabolites in stationary and logarithmic phases were limited to citraconic acid, isopropylmalic acid, L-leucine, ornithine, caprylic acid, capric acid, and acetic acid. Conclusion: 1H NMR spectroscopy could play an important role in the characterization of metabolites in biochemical pathways during a metacyclogenesis process. These metabolites and their pathways can help in exploiting a transmission mechanism in metacyclogenesis, and outcoming data might be used in the metabolic network reconstruction of L. major modeling. PMID:26592771

  14. Use of nuclear magnetic resonance (NMR) spectroscopy for the analysis of chemical warfare agents and their degradation products in enviornmental samples

    SciTech Connect

    Szafraniec, L.L.; Beaudry, W.T.

    1995-06-01

    Nuclear magnetic resonance (NMR) spectroscopy is one of the most powerful analytical techniques for elucidating the molecular structure of organic compounds. In environmental samples, the identification and detection of chemical warfare related compounds is best accomplished using high field high resolution NMR. This paper describes the experimental procedures.

  15. Improving Assessment of Lipoprotein Profile in Type 1 Diabetes by 1H NMR Spectroscopy

    PubMed Central

    Brugnara, Laura; Mallol, Roger; Ribalta, Josep; Vinaixa, Maria; Murillo, Serafín; Casserras, Teresa; Guardiola, Montse; Vallvé, Joan Carles; Kalko, Susana G.; Correig, Xavier; Novials, Anna

    2015-01-01

    Patients with type 1 diabetes (T1D) present increased risk of cardiovascular disease (CVD). The aim of this study is to improve the assessment of lipoprotein profile in patients with T1D by using a robust developed method 1H nuclear magnetic resonance spectroscopy (1H NMR), for further correlation with clinical factors associated to CVD. Thirty patients with T1D and 30 non-diabetes control (CT) subjects, matched for gender, age, body composition (DXA, BMI, waist/hip ratio), regular physical activity levels and cardiorespiratory capacity (VO2peak), were analyzed. Dietary records and routine lipids were assessed. Serum lipoprotein particle subfractions, particle sizes, and cholesterol and triglycerides subfractions were analyzed by 1H NMR. It was evidenced that subjects with T1D presented lower concentrations of small LDL cholesterol, medium VLDL particles, large VLDL triglycerides, and total triglycerides as compared to CT subjects. Women with T1D presented a positive association with HDL size (p<0.005; R = 0.601) and large HDL triglycerides (p<0.005; R = 0.534) and negative (p<0.005; R = -0.586) to small HDL triglycerides. Body fat composition represented an important factor independently of normal BMI, with large LDL particles presenting a positive correlation to total body fat (p<0.005; R = 0.505), and total LDL cholesterol and small LDL cholesterol a positive correlation (p<0.005; R = 0.502 and R = 0.552, respectively) to abdominal fat in T1D subjects; meanwhile, in CT subjects, body fat composition was mainly associated to HDL subclasses. VO2peak was negatively associated (p<0.005; R = -0.520) to large LDL-particles only in the group of patients with T1D. In conclusion, patients with T1D with adequate glycemic control and BMI and without chronic complications presented a more favourable lipoprotein profile as compared to control counterparts. In addition, slight alterations in BMI and/or body fat composition showed to be relevant to provoking alterations in

  16. Parallel NMR spectroscopy with simultaneous detection of (1) H and (19) F nuclei.

    PubMed

    Kovacs, Helena; Kupče, Ēriks

    2016-07-01

    Recording NMR signals of several nuclear species simultaneously by using parallel receivers provides more information from a single measurement and at the same time increases the measurement sensitivity per unit time. Here we present a comprehensive series of the most frequently used NMR experiments modified for simultaneous direct detection of two of the most sensitive NMR nuclei - (1) H and (19) F. We hope that the presented material will stimulate interest in and further development of this technique. PMID:27021630

  17. Determination of intramolecular hydrogen bonds in amikacin in water solution by NMR spectroscopy

    NASA Astrophysics Data System (ADS)

    Gaggelli, Elena; Gaggelli, Nicola; Maccotta, Antonella; Valensin, Gianni; Marini, Domenico; Di Cocco, Maria Enrica; Delfini, Maurizio

    1995-10-01

    An NMR investigation has been carried out on amikacin in water solution in the physiological pH range. Two-dimenstional heterocorrelated maps provide 1H NMR chemical shifts from the unambiguous assignment of the 13C NMR spectrum. Reorientational dynamics at the molecular level are interpreted in terms of a pseudoisotropic motion with a correlation time of 0.17 ns at 300 K. The pH and temperature dependences of 13C NMR chemical shifts are interpreted to delineate protonation equilibria (all p Ks are determined) and to assess the occurrence of two intermolecular hydrogen bonds, which are confirmed by molecular modelling.

  18. Solid state 31P MAS NMR spectroscopy and conductivity measurements on NbOPO4 and H3PO4 composite materials

    NASA Astrophysics Data System (ADS)

    Risskov Sørensen, Daniel; Nielsen, Ulla Gro; Skou, Eivind M.

    2014-11-01

    A systematic study of composite powders of niobium oxide phosphate (NbOPO4) and phosphoric acid (H3PO4) has been performed in order to characterize the material's ability to perform as an electrolyte material in medium temperature fuel cells and electrolyzers. Powders of H3PO4 contents between 13.1 and 74.2 M% were produced and characterized with powder X-ray diffraction, 31P MAS NMR and impedance spectroscopy. NMR revealed that a significant degree of dehydration and vaporization of H3PO4 takes place above 200 °C, and increases with temperature. At 500 °C the NbOPO4 and H3PO4 has reacted to form niobium pyrophosphate (Nb2P4O15). Impedance spectroscopy showed an increase in conductivity with increasing acid concentration, whereas the conductivity decreased slightly with increasing temperature. The highest conductivity measured was 2.5·10-3 S/cm for a sample containing 74.2 M% of H3PO4. Lastly, it was shown that NbOPO4 has no significant conductivity of its own.

  19. Mg-25 ultra-high field solid state NMR spectroscopy and first principles calculations of magnesium compounds.

    PubMed

    Pallister, Peter J; Moudrakovski, Igor L; Ripmeester, John A

    2009-12-28

    Due to sensitivity problems, (25)Mg remains a largely under-explored nucleus in solid state NMR spectroscopy. In this work at an ultrahigh magnetic field of 21.1 T, we have studied at natural abundance the (25)Mg solid state (SS) NMR spectra for a number of previously unreported magnesium compounds with known crystal structures. Some previously reported compounds have been revisited to clarify the spectra that were obtained at lower fields and were either not sufficiently resolved, or misinterpreted. First principles calculations of the (25)Mg SS NMR parameters have been carried out using plane wave basis sets and periodic boundary conditions (CASTEP) and the results are compared with experimental data. The calculations produce the (25)Mg absolute shielding scale and give us insight into the relationship between the NMR and structural parameters. At 21.1 T the effects of the quadrupolar interactions are reduced significantly and the sensitivity and accuracy in determining chemicals shifts and quadrupole coupling parameters improve dramatically. Although T(1) measurements were not performed explicitly, these proved to be longer than assumed in much of the previously reported work. We demonstrate that the chemical shift range of magnesium in diamagnetic compounds may approach 200 ppm. Most commonly, however, the observed shifts are between -15 and +25 ppm. Quadrupolar effects dominate the (25)Mg spectra of magnesium cations in non-cubic environments. The chemical shift anisotropy appears to be rather small and only in a few cases could the contribution of the CSA be detected reliably. A good correspondence between the calculated shielding constants and experimental chemical shifts was obtained, demonstrating the good potential of computational methods in spectroscopic assignments of solid state (25)Mg NMR spectroscopy. PMID:20024420

  20. Compositional differences among Chinese soy sauce types studied by (13)C NMR spectroscopy coupled with multivariate statistical analysis.

    PubMed

    Kamal, Ghulam Mustafa; Wang, Xiaohua; Bin Yuan; Wang, Jie; Sun, Peng; Zhang, Xu; Liu, Maili

    2016-09-01

    Soy sauce a well known seasoning all over the world, especially in Asia, is available in global market in a wide range of types based on its purpose and the processing methods. Its composition varies with respect to the fermentation processes and addition of additives, preservatives and flavor enhancers. A comprehensive (1)H NMR based study regarding the metabonomic variations of soy sauce to differentiate among different types of soy sauce available on the global market has been limited due to the complexity of the mixture. In present study, (13)C NMR spectroscopy coupled with multivariate statistical data analysis like principle component analysis (PCA), and orthogonal partial least square-discriminant analysis (OPLS-DA) was applied to investigate metabonomic variations among different types of soy sauce, namely super light, super dark, red cooking and mushroom soy sauce. The main additives in soy sauce like glutamate, sucrose and glucose were easily distinguished and quantified using (13)C NMR spectroscopy which were otherwise difficult to be assigned and quantified due to serious signal overlaps in (1)H NMR spectra. The significantly higher concentration of sucrose in dark, red cooking and mushroom flavored soy sauce can directly be linked to the addition of caramel in soy sauce. Similarly, significantly higher level of glutamate in super light as compared to super dark and mushroom flavored soy sauce may come from the addition of monosodium glutamate. The study highlights the potentiality of (13)C NMR based metabonomics coupled with multivariate statistical data analysis in differentiating between the types of soy sauce on the basis of level of additives, raw materials and fermentation procedures. PMID:27343582

  1. Clinoptilolite and heulandite structural differences as revealed by multinuclear nuclear magnetic resonance spectroscopy

    SciTech Connect

    Ward, R.L.; McKague, H.L. )

    1994-01-27

    Wide-line proton NMR has revealed differences in the water environment in two zeolitic isomorphs: clinoptilolite and heulandite. The proton spectrum of clinoptilolite is Gaussian in shape, while that of heulandite is a (reduced splitting) Pake doublet. Studies of clinoptilolite from five different locations and heulandite from nine different sites agree with this observation. These results suggest a simple nondestructive NMR method for distinguishing heulandite from clinoptilolite. Dehydration experiments are particularly informative. Proton line widths of clinoptilolite as a function of the dehydration temperature reveal three types of water binding, none being absorbed water. Similar studies with heulandite reveal a change from the Pake doublet to a Gaussian, which is probably associated with the heulandite to heulandite B transformation. [sup 27]Al and [sup 29]Si NMR studies of clinoptilolite indicate a change in framework structure and/or cation binding with dehydration. [sup 27]Al NMR of heulandite exhibits an increase in line width with dehydration temperature to 175[degrees]C. At this temperature the increase stops and the line width remains constant to 215[degrees]C, the maximum temperature studied. This agrees with the proton studies and is attributed to the heulandite to heulandite B transformation. [sup 29]Si NMR of heulandite reveals a framework structural change and/or cation binding with dehydration. All of these observations are reversible upon rehydration. 21 refs., 9 figs.

  2. Lithium ion diffusion in Li β-alumina single crystals measured by pulsed field gradient NMR spectroscopy

    SciTech Connect

    Chowdhury, Mohammed Tareque Takekawa, Reiji; Iwai, Yoshiki; Kuwata, Naoaki; Kawamura, Junichi

    2014-03-28

    The lithium ion diffusion coefficient of a 93% Li β-alumina single crystal was measured for the first time using pulsed field gradient (PFG) NMR spectroscopy with two different crystal orientations. The diffusion coefficient was found to be 1.2 × 10{sup −11} m{sup 2}/s in the direction perpendicular to the c axis at room temperature. The Li ion diffusion coefficient along the c axis direction was found to be very small (6.4 × 10{sup −13} m{sup 2}/s at 333 K), which suggests that the macroscopic diffusion of the Li ion in the β-alumina crystal is mainly two-dimensional. The diffusion coefficient for the same sample was also estimated using NMR line narrowing data and impedance measurements. The impedance data show reasonable agreement with PFG-NMR data, while the line narrowing measurements provided a lower value for the diffusion coefficient. Line narrowing measurements also provided a relatively low value for the activation energy and pre-exponential factor. The temperature dependent diffusion coefficient was obtained in the temperature range 297–333 K by PFG-NMR, from which the activation energy for diffusion of the Li ion was estimated. The activation energy obtained by PFG-NMR was smaller than that obtained by impedance measurements, which suggests that thermally activated defect formation energy exists for 93% Li β-alumina single crystals. The diffusion time dependence of the diffusion coefficient was observed for the Li ion in the 93% Li β-alumina single crystal by means of PFG-NMR experiments. Motion of Li ion in fractal dimension might be a possible explanation for the observed diffusion time dependence of the diffusion coefficient in the 93% Li β–alumina system.

  3. Organic Spectroscopy Laboratory: Utilizing IR and NMR in the Identification of an Unknown Substance

    ERIC Educational Resources Information Center

    Glagovich, Neil M.; Shine, Timothy D.

    2005-01-01

    A laboratory experiment that emphasizes the interpretation of both infrared (IR) and nuclear magnetic resonance (NMR) spectra in the elucidation of the structure of an unknown compound was developed. The method helps students determine [to the first power]H- and [to the thirteenth power]C-NMR spectra from the structures of compounds and to…

  4. Establishing resolution-improved NMR spectroscopy in high magnetic fields with unknown spatiotemporal variations.

    PubMed

    Zhang, Zhiyong; Smith, Pieter E S; Cai, Shuhui; Zheng, Zhenyao; Lin, Yulan; Chen, Zhong

    2015-12-28

    A half-century quest for higher magnetic fields has been an integral part of the progress undergone in the Nuclear Magnetic Resonance (NMR) study of materials' structure and dynamics. Because 2D NMR relies on systematic changes in coherences' phases as a function of an encoding time varied over a series of independent experiments, it generally cannot be applied in temporally unstable fields. This precludes most NMR methods from being used to characterize samples situated in hybrid or resistive magnets that are capable of achieving extremely high magnetic field strength. Recently, "ultrafast" NMR has been developed into an effective and widely applicable methodology enabling the acquisition of a multidimensional NMR spectrum in a single scan; it can therefore be used to partially mitigate the effects of temporally varying magnetic fields. Nevertheless, the strong interference of fluctuating fields with the spatial encoding of ultrafast NMR still severely restricts measurement sensitivity and resolution. Here, we introduce a strategy for obtaining high resolution NMR spectra that exploits the immunity of intermolecular zero-quantum coherences (iZQCs) to field instabilities and inhomogeneities. The spatial encoding of iZQCs is combined with a J-modulated detection scheme that removes the influence of arbitrary field inhomogeneities during acquisition. This new method can acquire high-resolution one-dimensional NMR spectra in large inhomogeneous and fluctuating fields, and it is tested with fields experimentally modeled to mimic those of resistive and resistive-superconducting hybrid magnets. PMID:26723664

  5. Establishing resolution-improved NMR spectroscopy in high magnetic fields with unknown spatiotemporal variations

    SciTech Connect

    Zhang, Zhiyong; Cai, Shuhui; Zheng, Zhenyao; Lin, Yulan E-mail: lylfj2005@xmu.edu.cn; Chen, Zhong E-mail: lylfj2005@xmu.edu.cn; Smith, Pieter E. S.

    2015-12-28

    A half-century quest for higher magnetic fields has been an integral part of the progress undergone in the Nuclear Magnetic Resonance (NMR) study of materials’ structure and dynamics. Because 2D NMR relies on systematic changes in coherences’ phases as a function of an encoding time varied over a series of independent experiments, it generally cannot be applied in temporally unstable fields. This precludes most NMR methods from being used to characterize samples situated in hybrid or resistive magnets that are capable of achieving extremely high magnetic field strength. Recently, “ultrafast” NMR has been developed into an effective and widely applicable methodology enabling the acquisition of a multidimensional NMR spectrum in a single scan; it can therefore be used to partially mitigate the effects of temporally varying magnetic fields. Nevertheless, the strong interference of fluctuating fields with the spatial encoding of ultrafast NMR still severely restricts measurement sensitivity and resolution. Here, we introduce a strategy for obtaining high resolution NMR spectra that exploits the immunity of intermolecular zero-quantum coherences (iZQCs) to field instabilities and inhomogeneities. The spatial encoding of iZQCs is combined with a J-modulated detection scheme that removes the influence of arbitrary field inhomogeneities during acquisition. This new method can acquire high-resolution one-dimensional NMR spectra in large inhomogeneous and fluctuating fields, and it is tested with fields experimentally modeled to mimic those of resistive and resistive-superconducting hybrid magnets.

  6. Establishing resolution-improved NMR spectroscopy in high magnetic fields with unknown spatiotemporal variations

    NASA Astrophysics Data System (ADS)

    Zhang, Zhiyong; Smith, Pieter E. S.; Cai, Shuhui; Zheng, Zhenyao; Lin, Yulan; Chen, Zhong

    2015-12-01

    A half-century quest for higher magnetic fields has been an integral part of the progress undergone in the Nuclear Magnetic Resonance (NMR) study of materials' structure and dynamics. Because 2D NMR relies on systematic changes in coherences' phases as a function of an encoding time varied over a series of independent experiments, it generally cannot be applied in temporally unstable fields. This precludes most NMR methods from being used to characterize samples situated in hybrid or resistive magnets that are capable of achieving extremely high magnetic field strength. Recently, "ultrafast" NMR has been developed into an effective and widely applicable methodology enabling the acquisition of a multidimensional NMR spectrum in a single scan; it can therefore be used to partially mitigate the effects of temporally varying magnetic fields. Nevertheless, the strong interference of fluctuating fields with the spatial encoding of ultrafast NMR still severely restricts measurement sensitivity and resolution. Here, we introduce a strategy for obtaining high resolution NMR spectra that exploits the immunity of intermolecular zero-quantum coherences (iZQCs) to field instabilities and inhomogeneities. The spatial encoding of iZQCs is combined with a J-modulated detection scheme that removes the influence of arbitrary field inhomogeneities during acquisition. This new method can acquire high-resolution one-dimensional NMR spectra in large inhomogeneous and fluctuating fields, and it is tested with fields experimentally modeled to mimic those of resistive and resistive-superconducting hybrid magnets.

  7. Self-radiation effects and glassy nature of magnetic transition in AmO2 revealed by O17-NMR

    NASA Astrophysics Data System (ADS)

    Tokunaga, Yo; Nishi, Tsuyoshi; Nakada, Masami; Itoh, Akinori; Sakai, Hironori; Kambe, Shinsaku; Homma, Yoshiya; Honda, Fuminori; Aoki, Dai; Walstedt, Russell E.

    2014-06-01

    The magnetic phase transition near T0=8.5 K in americium dioxide (AmO2) has been investigated microscopically by means of O17 NMR. To avoid complexities arising from sample aging associated with the α decay of Am243, all measurements have been performed within 40 days after sample synthesis. Even during such a short period, however, a rapid change of NMR line shape has been observed at 1.5 K, suggesting that the ground state of AmO2 is very sensitive to disorder. We have also confirmed the loss of O17 NMR signal intensity over a wide temperature range below T0, and more than half of oxygen nuclei are undetectable at 1.5 K. This behavior reveals the persistence of slow and distributed spin fluctuations down to temperatures well below T0. In the paramagnetic state, strong NMR line broadening and spatially inhomogeneous spin fluctuations have been observed. The results are all indicative of short-range, spin-glass-like character for the magnetic transition in this system.

  8. Lithological control on gas hydrate saturation as revealed by signal classification of NMR logging data

    NASA Astrophysics Data System (ADS)

    Bauer, Klaus; Kulenkampff, Johannes; Henninges, Jan; Spangenberg, Erik

    2015-09-01

    In this paper, nuclear magnetic resonance (NMR) downhole logging data are analyzed with a new strategy to study gas hydrate-bearing sediments in the Mackenzie Delta (NW Canada). In NMR logging, transverse relaxation time (T2) distribution curves are usually used to determine single-valued parameters such as apparent total porosity or hydrocarbon saturation. Our approach analyzes the entire T2 distribution curves as quasi-continuous signals to characterize the rock formation. We apply self-organizing maps, a neural network clustering technique, to subdivide the data set of NMR curves into classes with a similar and distinctive signal shape. The method includes (1) preparation of data vectors, (2) unsupervised learning, (3) cluster definition, and (4) classification and depth mapping of all NMR signals. Each signal class thus represents a specific pore size distribution which can be interpreted in terms of distinct lithologies and reservoir types. A key step in the interpretation strategy is to reconcile the NMR classes with other log data not considered in the clustering analysis, such as gamma ray, hydrate saturation, and other logs. Our results defined six main lithologies within the target zone. Gas hydrate layers were recognized by their low signal amplitudes for all relaxation times. Most importantly, two subtypes of hydrate-bearing shaly sands were identified. They show distinct NMR signals and differ in hydrate saturation and gamma ray values. An inverse linear relationship between hydrate saturation and clay content was concluded. Finally, we infer that the gas hydrate is not grain coating, but rather, pore filling with matrix support is the preferred growth habit model for the studied formation.

  9. Investigation of interaction parameters in mixed micelle using pulsed field gradient NMR spectroscopy.

    PubMed

    Gharibi, H; Javadian, S; Sohrabi, B; Behjatmanesh, R

    2005-05-01

    Pulsed field gradient NMR spectroscopy was used to determine the partitioning of surfactant between monomeric and micellar forms in a mixed CTAB (hexadecyltetramethylammonium bromide) and Triton X-100 [p-(1,1,3-tetramethylbutyl)polyoxyethylene] system. In addition, potentiometric and surface tension measurements were used to determine the free concentration of ionic surfactant and the critical micelle concentration (CMC) of mixtures of n-alkyltrimethylammonium bromide (C(n)TAB, n=12, 14, 16, 18) and Triton X-100. Regular solution theory cannot describe the behavior of the activity coefficient and the excess Gibbs free energy of mixtures of ionic and nonionic surfactants. To overcome these shortcomings, we developed a new model that combines Van Laar expressions and the theory of nonrandom mixing in mixed micelles. The Van Laar expressions contain an additional parameter, rho, which reflects differences in the size of the components of the mixture. Nonrandom mixing theory was introduced to describe nonrandom mixing in mixed micelles. This effect was modeled by a packing parameter, P*. The proposed model provided a good description of the behavior of binary surfactant mixtures. The results indicated that head group size and packing constraints are important contributors to nonideal surfactant behavior. In addition, the results showed that as the chain length of the C(n)TAB molecule in C(n)TAB/Triton X-100 mixtures was increased, the head group size parameter remained constant, but the interaction and packing parameters increased. Increase of the temperature caused an increase in the interaction parameter beta and a decrease in the packing parameter (P*). PMID:15797433

  10. Improving the resolution in proton-detected through-space heteronuclear multiple quantum correlation NMR spectroscopy

    NASA Astrophysics Data System (ADS)

    Shen, Ming; Trébosc, J.; Lafon, O.; Pourpoint, F.; Hu, Bingwen; Chen, Qun; Amoureux, J.-P.

    2014-08-01

    Connectivities and proximities between protons and low-gamma nuclei can be probed in solid-state NMR spectroscopy using two-dimensional (2D) proton-detected heteronuclear correlation, through Heteronuclear Multiple Quantum Correlation (HMQC) pulse sequence. The indirect detection via protons dramatically enhances the sensitivity. However, the spectra are often broadened along the indirect F1 dimension by the decay of heteronuclear multiple-quantum coherences under the strong 1H-1H dipolar couplings. This work presents a systematic comparison of the performances of various decoupling schemes during the indirect t1 evolution period of dipolar-mediated HMQC (D-HMQC) experiment. We demonstrate that 1H-1H dipolar decoupling sequences during t1, such as symmetry-based schemes, phase-modulated Lee-Goldburg (PMLG) and Decoupling Using Mind-Boggling Optimization (DUMBO), provide better resolution than continuous wave 1H irradiation. We also report that high resolution requires the preservation of 1H isotropic chemical shifts during the decoupling sequences. When observing indirectly broad spectra presenting numerous spinning sidebands, the D-HMQC sequence must be fully rotor-synchronized owing to the rotor-synchronized indirect sampling and dipolar recoupling sequence employed. In this case, we propose a solution to reduce artefact sidebands caused by the modulation of window delays before and after the decoupling application during the t1 period. Moreover, we show that 1H-1H dipolar decoupling sequence using Smooth Amplitude Modulation (SAM) minimizes the t1-noise. The performances of the various decoupling schemes are assessed via numerical simulations and compared to 2D 1H-{13C} D-HMQC experiments on [U-13C]-L-histidineṡHClṡH2O at various magnetic fields and Magic Angle spinning (MAS) frequencies. Great resolution and sensitivity enhancements resulting from decoupling during t1 period enable the detection of heteronuclear correlation between aliphatic protons and

  11. High-field localized 1H NMR spectroscopy in the anesthetized and in the awake monkey.

    PubMed

    Pfeuffer, Josef; Juchem, Christoph; Merkle, Hellmut; Nauerth, Arno; Logothetis, Nikos K

    2004-12-01

    Localized cerebral in vivo 1H NMR spectroscopy (MRS) was performed in the anesthetized as well as the awake monkey using a novel vertical 7 T/60 cm MR system. The increased sensitivity and spectral dispersion gained at high field enabled the quantification of up to 16 metabolites in 0.1- to 1-ml volumes. Quantification was accomplished by using simulations of 18 metabolite spectra and a macromolecule (MM) background spectrum consisting of 12 components. Major cerebral metabolites (concentrations >3 mM) such as glutamate (Glu), N-acetylaspartate (NAA), creatine (Cr)/phosphocreatine (PCr) and myo-inositol (Ins) were identified with an error below 3%; most other metabolites were quantified with errors in the order of 10%. Metabolite ratios were 1.39:1 for total NAA, 1.38:1 for glutamate (Glu)/glutamine (Gln) and 0.09:1 for cholines (Cho) relative to total Cr. Taurine (Tau) was detectable at concentrations lower than 1 mM, while lactate (Lac) remained below the detection limit. The spectral dispersion was sufficient to separate metabolites of similar spectral patterns, such as Gln and Glu, N-acetylaspartylglutamate (NAAG) and NAA, and PCr-Cr. MRS in the awake monkey required the development and refinement of acquisition and correction strategies to minimize magnetic susceptibility artifacts induced by respiration and movement of the mouth or body. Periods with major motion artifacts were rejected, while a frequency/phase correction was performed on the remaining single spectra before averaging. In resting periods, both spectral amplitude and line width, that is, the voxel shim, were unaffected permitting reliable measurements. The corrected spectra obtained from the awake monkey afforded the reliable detection of 6-10 cerebral metabolites of 1-ml volumes. PMID:15707786

  12. Impact of Adenovirus infection in host cell metabolism evaluated by (1)H-NMR spectroscopy.

    PubMed

    Silva, Ana Carina; P Teixeira, Ana; M Alves, Paula

    2016-08-10

    Adenovirus-based vectors are powerful vehicles for gene transfer applications in vaccination and gene therapy. Although highly exploited in the clinical setting, key aspects of the adenovirus biology are still not well understood, in particular the subversion of host cell metabolism during viral infection and replication. The aim of this work was to gain insights on the metabolism of two human cell lines (HEK293 and an amniocyte-derived cell line, 1G3) after infection with an adenovirus serotype 5 vector (AdV5). In order to profile metabolic alterations, we used (1)H-NMR spectroscopy, which allowed the quantification of 35 metabolites in cell culture supernatants with low sample preparation and in a relatively short time. Significant differences between both cell lines in non-infected cultures were identified, namely in glutamine and acetate metabolism, as well as by-product secretion. The main response to AdV5 infection was an increase in glucose consumption and lactate production rates. Moreover, cultures performed with or without glutamine supplementation confirmed the exhaustion of this amino acid as one of the main causes of lower AdV5 production at high cell densities (10- and 1.5-fold less specific yields in HEK293 and 1G3 cells, respectively), and highlighted different degrees of glutamine dependency of adenovirus replication in each cell line. The observed metabolic alterations associated with AdV5 infection and specificity of the host cell line can be useful for targeted bioprocess optimization. PMID:27215342

  13. Local environment and composition of magnesium gallium layered double hydroxides determined from solid-state {sup 1}H and {sup 71}Ga NMR spectroscopy

    SciTech Connect

    Petersen, Line Boisen; Lipton, Andrew S.; Zorin, Vadim; Nielsen, Ulla Gro

    2014-11-15

    Ordering of gallium(III) in a series of magnesium gallium (MgGa) layered double hydroxides (LDHs), [Mg{sub 1−x}Ga{sub x}(OH){sub 2}(NO{sub 3}){sub x}·yH{sub 2}O] was investigated using solid-state {sup 1}H and {sup 71}Ga NMR spectroscopy as well as powder X-ray diffraction. Three different proton environments from Mg{sub 3}-OH, Mg{sub 2}Ga-OH and intergallery water molecules were assigned and quantified using ({sup 1}H,{sup 71}Ga) HETCOR and {sup 1}H MAS NMR. A single {sup 71}Ga site originating from the unique Ga site in the MgGa LDH's was observed in {sup 71}Ga MAS and 3QMAS NMR spectra. Both {sup 1}H MAS NMR spectra recorded at 21.1 T (900 MHz) and elemental analysis show that the synthesized MgGa LDH's had a lower Mg:Ga ratio than that of the starting reactant solution. The origin of this is the formation of soluble [Ga(OH){sub 4}]{sup −} complexes formed during synthesis, and not due to formation of insoluble gallium (oxy)hydroxides. No sign of Ga-O-Ga connectivities or defects were detected for the MgGa LDH's. - Graphical abstract: Two types of hydroxides groups are observed in magnesium gallium layered double hydroxides revealing an ordering of Ga in the cation layer. - Highlights: • Ga is ordered in our magnesium gallium layered double hydroxides. • Ga depletion due to formation of soluble Ga complexes during synthesis. • No sign of Ga rich regions in magnesium gallium LDHs. • Solid state {sup 1}H and {sup 71}Ga give detailed insight into the structure.

  14. Understanding the Mechanism of Prosegment-catalyzed Folding by Solution NMR Spectroscopy*

    PubMed Central

    Wang, Shenlin; Horimoto, Yasumi; Dee, Derek R.; Yada, Rickey Y.

    2014-01-01

    Multidomain protein folding is often more complex than a two-state process, which leads to the spontaneous folding of the native state. Pepsin, a zymogen-derived enzyme, without its prosegment (PS), is irreversibly denatured and folds to a thermodynamically stable, non-native conformation, termed refolded pepsin, which is separated from native pepsin by a large activation barrier. While it is known that PS binds refolded pepsin and catalyzes its conversion to the native form, little structural details are known regarding this conversion. In this study, solution NMR was used to elucidate the PS-catalyzed folding mechanism by examining the key equilibrium states, e.g. native and refolded pepsin, both in the free and PS-bound states, and pepsinogen, the zymogen form of pepsin. Refolded pepsin was found to be partially structured and lacked the correct domain-domain structure and active-site cleft formed in the native state. Analysis of chemical shift data revealed that upon PS binding refolded pepsin folds into a state more similar to that of pepsinogen than to native pepsin. Comparison of pepsin folding by wild-type and mutant PSs, including a double mutant PS, indicated that hydrophobic interactions between residues of prosegment and refolded pepsin lower the folding activation barrier. A mechanism is proposed for the binding of PS to refolded pepsin and how the formation of the native structure is mediated. PMID:24265313

  15. Novel insights from NMR spectroscopy into seasonal changes in the composition of dissolved organic matter exported to the Bering Sea by the Yukon River

    USGS Publications Warehouse

    Cao, Xiaoyan; Aiken, George R.; Spencer, Robert G. M.; Butler, Kenna; Mao, Jingdong; Schmidt-Rohr, Klaus

    2016-01-01

    Seasonal (spring freshet, summer–autumn, and winter) variability in the chemical composition of dissolved organic matter (DOM) from the Yukon River was determined using advanced one- and two-dimensional (2D) solid-state NMR spectroscopy, coupled with isotopic measurements and UV–visible spectroscopy. Analyses were performed on two major DOM fractions, the hydrophobic organic acid (HPOA) and transphilic organic acid (TPIA) fractions obtained using XAD resins. Together these two fractions comprised 64–74% of the total DOM. Carboxyl-rich alicyclic molecules (CRAM) accounted for the majority of carbon atoms in the HPOA (63–77%) and TPIA (54–78%) samples, and more so in winter and summer than in spring samples. 2D and selective NMR data revealed association of abundant nonprotonated O-alkyl and quaternary alkyl C (OCnp, OCnpO and Cq, 13–17% of HPOA and 15–20% of TPIA) and isolated O–CH structures with CRAM, which were not recognized in previous studies. Spectral editing and 2D NMR allowed for the discrimination of carbohydrate-like O-alkyl C from non-carbohydrate O-alkyl C. Whereas two spring freshet TPIA samples contained carbohydrate clusters such as carboxylated carbohydrates (16% and 26%), TPIA samples from other seasons or HPOA samples mostly had small amounts (<8%) of sugar rings dispersed in a nonpolar alkyl environment. Though nonprotonated aromatic C represented the largest fraction of aromatic C in all HPOA/TPIA isolates, only a small fraction (∼5% in HPOA and 3% in TPIA) was possibly associated with dissolved black carbon. Our results imply a relatively stable portion of DOM exported by the Yukon River across different seasons, due to the predominance of CRAM and their associated nonprotonated C–O and O–C–O structures, and elevated reactivity (bio- and photo-lability) of spring DOM due to the presence of terrestrial inputs enriched in carbohydrates and aromatic structures.

  16. Novel insights from NMR spectroscopy into seasonal changes in the composition of dissolved organic matter exported to the Bering Sea by the Yukon River

    NASA Astrophysics Data System (ADS)

    Cao, Xiaoyan; Aiken, George R.; Spencer, Robert G. M.; Butler, Kenna; Mao, Jingdong; Schmidt-Rohr, Klaus

    2016-05-01

    Seasonal (spring freshet, summer-autumn, and winter) variability in the chemical composition of dissolved organic matter (DOM) from the Yukon River was determined using advanced one- and two-dimensional (2D) solid-state NMR spectroscopy, coupled with isotopic measurements and UV-visible spectroscopy. Analyses were performed on two major DOM fractions, the hydrophobic organic acid (HPOA) and transphilic organic acid (TPIA) fractions obtained using XAD resins. Together these two fractions comprised 64-74% of the total DOM. Carboxyl-rich alicyclic molecules (CRAM) accounted for the majority of carbon atoms in the HPOA (63-77%) and TPIA (54-78%) samples, and more so in winter and summer than in spring samples. 2D and selective NMR data revealed association of abundant nonprotonated O-alkyl and quaternary alkyl C (OCnp, OCnpO and Cq, 13-17% of HPOA and 15-20% of TPIA) and isolated O-CH structures with CRAM, which were not recognized in previous studies. Spectral editing and 2D NMR allowed for the discrimination of carbohydrate-like O-alkyl C from non-carbohydrate O-alkyl C. Whereas two spring freshet TPIA samples contained carbohydrate clusters such as carboxylated carbohydrates (16% and 26%), TPIA samples from other seasons or HPOA samples mostly had small amounts (<8%) of sugar rings dispersed in a nonpolar alkyl environment. Though nonprotonated aromatic C represented the largest fraction of aromatic C in all HPOA/TPIA isolates, only a small fraction (∼5% in HPOA and 3% in TPIA) was possibly associated with dissolved black carbon. Our results imply a relatively stable portion of DOM exported by the Yukon River across different seasons, due to the predominance of CRAM and their associated nonprotonated C-O and O-C-O structures, and elevated reactivity (bio- and photo-lability) of spring DOM due to the presence of terrestrial inputs enriched in carbohydrates and aromatic structures.

  17. Quantitative Determination of Methylcyclohexanone Mixtures Using 13C NMR Spectroscopy: A Project for an Advanced Chemistry Laboratory

    NASA Astrophysics Data System (ADS)

    Lefevre, Joseph W.; Silveira, Augustine, Jr.

    2000-01-01

    The percentage composition of mixtures of four methylcyclohexanones was determined using 13C NMR spectroscopy as a quantitative analytical method. The data were acquired using standard broadband proton decoupling and inverse-gated decoupling, the latter done both with and without the paramagnetic relaxation reagent chromium(III) acetylacetonate [Cr(acac)3]. The standard broadband decoupled spectrum resulted in percentages far from the actual values owing to the varying nuclear Overhauser enhancements (NOEs) and spin-lattice relaxation times (T1's) of the various carbon atoms. These effects were eliminated in the inverse-gated experiments, and the results were very close to the actual percentages. Before examining the mixtures, the students studied a pure sample of 2-methylcyclohexanone. They assigned the 13C spectrum and determined the T1 of the carbonyl group both with and without Cr(acac)3 using the inversion-recovery method. Then a five-times-T1 delay was inserted between pulses in all subsequent inverse-gated decoupling experiments. This project provides students with valuable experience with modern NMR techniques. These include COrrelated SpectroscopY (COSY), Distortionless Enhancement by Polarization Transfer (DEPT) spectroscopy, HETeronuclear CORrelated (HETCOR) spectroscopy, T1 determination, standard broadband versus inverse-gated decoupling, and the addition of a paramagnetic relaxation reagent to dramatically shorten both the T

  18. High-field NMR spectroscopy and FTICR mass spectrometry: powerful discovery tools for the molecular level characterization of marine dissolved organic matter

    NASA Astrophysics Data System (ADS)

    Hertkorn, N.; Harir, M.; Koch, B. P.; Michalke, B.; Schmitt-Kopplin, P.

    2013-03-01

    High-performance, non-target, high-resolution organic structural spectroscopy was applied to solid phase extracted marine dissolved organic matter (SPE-DOM) isolated from four different depths in the open South Atlantic Ocean off the Angola coast (3° E, 18° S; Angola Basin) and provided molecular level information with extraordinary coverage and resolution. Sampling was performed at depths of 5 m (Angola Current; near-surface photic zone), 48 m (Angola Current; fluorescence maximum), 200 m (still above Antarctic Intermediate Water, AAIW; upper mesopelagic zone) and 5446 m (North Atlantic Deep Water, NADW; abyssopelagic, ~30 m above seafloor) and produced SPE-DOM with near 40% carbon yield and beneficial nuclear magnetic resonance (NMR) relaxation properties, a crucial prerequisite for the acquisition of NMR spectra with excellent resolution. 1H and 13C NMR spectra of all four marine SPE-DOM showed smooth bulk envelopes, reflecting intrinsic averaging from massive signal overlap, with a few percent of visibly resolved signatures and variable abundances for all major chemical environments. The abundance of singly oxygenated aliphatics and acetate derivatives in 1H NMR spectra declined from surface to deep marine SPE-DOM, whereas C-based aliphatics and carboxyl-rich alicyclic molecules (CRAM) increased in abundance. Surface SPE-DOM contained fewer methyl esters than all other samples, likely a consequence of direct exposure to sunlight. Integration of 13C NMR spectra revealed continual increase of carboxylic acids and ketones from surface to depth, reflecting a progressive oxygenation, with concomitant decline of carbohydrate-related substructures. Aliphatic branching increased with depth, whereas the fraction of oxygenated aliphatics declined for methine, methylene and methyl carbon. Lipids in the oldest SPE-DOM at 5446 m showed a larger share of ethyl groups and methylene carbon than observed in the other samples. Two-dimensional NMR spectra showed exceptional

  19. A Novel MHC-I Surface Targeted for Binding by the MCMV m06 Immunoevasin Revealed by Solution NMR.

    PubMed

    Sgourakis, Nikolaos G; May, Nathan A; Boyd, Lisa F; Ying, Jinfa; Bax, Ad; Margulies, David H

    2015-11-27

    As part of its strategy to evade detection by the host immune system, murine cytomegalovirus (MCMV) encodes three proteins that modulate cell surface expression of major histocompatibility complex class I (MHC-I) molecules: the MHC-I homolog m152/gp40 as well as the m02-m16 family members m04/gp34 and m06/gp48. Previous studies of the m04 protein revealed a divergent Ig-like fold that is unique to immunoevasins of the m02-m16 family. Here, we engineer and characterize recombinant m06 and investigate its interactions with full-length and truncated forms of the MHC-I molecule H2-L(d) by several techniques. Furthermore, we employ solution NMR to map the interaction footprint of the m06 protein on MHC-I, taking advantage of a truncated H2-L(d), "mini-H2-L(d)," consisting of only the α1α2 platform domain. Mini-H2-L(d) refolded in vitro with a high affinity peptide yields a molecule that shows outstanding NMR spectral features, permitting complete backbone assignments. These NMR-based studies reveal that m06 binds tightly to a discrete site located under the peptide-binding platform that partially overlaps with the β2-microglobulin interface on the MHC-I heavy chain, consistent with in vitro binding experiments showing significantly reduced complex formation between m06 and β2-microglobulin-associated MHC-I. Moreover, we carry out NMR relaxation experiments to characterize the picosecond-nanosecond dynamics of the free mini-H2-L(d) MHC-I molecule, revealing that the site of interaction is highly ordered. This study provides insight into the mechanism of the interaction of m06 with MHC-I, suggesting a structural manipulation of the target MHC-I molecule at an early stage of the peptide-loading pathway. PMID:26463211

  20. Concentration Profiling in Rat Tissue by High-Resolution Magic-Angle Spinning NMR Spectroscopy: Investigation of a Model Drug

    PubMed Central

    Lucas, Laura H.; Wilson, Sarah F.; Lunte, Craig E.; Larive, Cynthia K.

    2008-01-01

    The utility of high-resolution magic-angle spinning (HR-MAS) NMR for studying drug delivery in whole tissues was explored by dosing female Sprague–Dawley rats with topical or injectable benzoic acid (BA). In principle, HR-MAS NMR permits the detection of both intra- and extracellular compounds. This is an advantage over the previous detection of topically applied BA using microdialysis coupled to HPLC/UV as microdialysis samples only the extracellular space. Skin and muscle samples were analyzed by 1H HR-MAS NMR, and BA levels were determined using an external standard solution added to the sample rotor. One to two percent of the BA topical dose was detected in the muscle, showing that BA penetrated through the dermal and subcutaneous layers. Since BA was not detected in the muscle in the microdialysis studies, the NMR spectra revealed the intracellular localization of BA. The amount of BA detected in muscle after subcutaneous injection correlated with the distance from the dosing site. Overall, the results suggest that HR-MAS NMR can distinguish differences in the local concentration of BA varying with tissue type, dosage method, and tissue proximity to the dosing site. The results illustrate the potential of this technique for quantitative analysis of drug delivery and distribution and the challenges to be addressed as the method is refined. PMID:15859619

  1. Natural abundance 17O DNP two-dimensional and surface-enhanced NMR spectroscopy

    SciTech Connect

    Perras, Frédéric A.; Kobayashi, Takeshi; Pruski, Marek

    2015-06-22

    Due to its extremely low natural abundance and quadrupolar nature, the 17O nuclide is very rarely used for spectroscopic investigation of solids by NMR without isotope enrichment. Additionally, the applicability of dynamic nuclear polarization (DNP), which leads to sensitivity enhancements of 2 orders of magnitude, to 17O is wrought with challenges due to the lack of spin diffusion and low polarization transfer efficiency from 1H. Here, we demonstrate new DNP-based measurements that extend 17O solid-state NMR beyond its current capabilities. The use of the PRESTO technique instead of conventional 1H–17O cross-polarization greatly improves the sensitivity and enables the facile measurement of undistorted line shapes and two-dimensional 1H–17O HETCOR NMR spectra as well as accurate internuclear distance measurements at natural abundance. This was applied for distinguishing hydrogen-bonded and lone 17O sites on the surface of silica gel; the one-dimensional spectrum of which could not be used to extract such detail. As a result, this greatly enhanced sensitivity has enabled, for the first time, the detection of surface hydroxyl sites on mesoporous silica at natural abundance, thereby extending the concept of DNP surface-enhanced NMR spectroscopy to the 17O nuclide.

  2. Precision high-throughput proton NMR spectroscopy of human urine, serum, and plasma for large-scale metabolic phenotyping.

    PubMed

    Dona, Anthony C; Jiménez, Beatriz; Schäfer, Hartmut; Humpfer, Eberhard; Spraul, Manfred; Lewis, Matthew R; Pearce, Jake T M; Holmes, Elaine; Lindon, John C; Nicholson, Jeremy K

    2014-10-01

    Proton nuclear magnetic resonance (NMR)-based metabolic phenotyping of urine and blood plasma/serum samples provides important prognostic and diagnostic information and permits monitoring of disease progression in an objective manner. Much effort has been made in recent years to develop NMR instrumentation and technology to allow the acquisition of data in an effective, reproducible, and high-throughput approach that allows the study of general population samples from epidemiological collections for biomarkers of disease risk. The challenge remains to develop highly reproducible methods and standardized protocols that minimize technical or experimental bias, allowing realistic interlaboratory comparisons of subtle biomarker information. Here we present a detailed set of updated protocols that carefully consider major experimental conditions, including sample preparation, spectrometer parameters, NMR pulse sequences, throughput, reproducibility, quality control, and resolution. These results provide an experimental platform that facilitates NMR spectroscopy usage across different large cohorts of biofluid samples, enabling integration of global metabolic profiling that is a prerequisite for personalized healthcare. PMID:25180432

  3. Reconstitution of the Cytb5 -CytP450 Complex in Nanodiscs for Structural Studies using NMR Spectroscopy.

    PubMed

    Zhang, Meng; Huang, Rui; Ackermann, Rose; Im, Sang-Choul; Waskell, Lucy; Schwendeman, Anna; Ramamoorthy, Ayyalusamy

    2016-03-24

    Cytochrome P450s (P450s) are a superfamily of enzymes responsible for the catalysis of a wide range of substrates. Dynamic interactions between full-length membrane-bound P450 and its redox partner cytochrome b5 (cytb5 ) have been found to be important for the enzymatic activity of P450. However, the stability of the circa 70 kDa membrane-bound complex in model membranes renders high-resolution structural NMR studies particularly difficult. To overcome these challenges, reconstitution of the P450-cytb5 complex in peptide-based nanodiscs, containing no detergents, has been demonstrated, which are characterized by size exclusion chromatography and NMR spectroscopy. In addition, NMR experiments are used to identify the binding interface of the P450-cytb5 complex in the nanodisc. This is the first successful demonstration of a protein-protein complex in a nanodisc using NMR structural studies and should be useful to obtain valuable structural information on membrane-bound protein complexes. PMID:26924779

  4. Identification and quantification of major steviol glycosides in Stevia rebaudiana purified extracts by 1H NMR spectroscopy.

    PubMed

    Pieri, Valerio; Belancic, Andrea; Morales, Susana; Stuppner, Hermann

    2011-05-11

    The use of (1)H NMR spectroscopy for the characterization of Stevia rebaudiana extracts is presented. The developed method allows qualitative and quantitative determination of the major steviol glycosides in purified extracts and fractions obtained from various stages of the purification process. Moreover, it proved to be a powerful tool to differentiate between glycosides which are naturally occurring in the stevia plant and artifacts formed in the course of the manufacturing process. Identification of steviol glycosides was achieved by the use of 2D NMR techniques, whereas quantification is based on qHNMR using anthracene as internal standard. The solvent mixture pyridine-d(5)-DMSO-d(6) (6:1) enabled satisfactory separation of the signals to be integrated. Validation of the method was performed in terms of specificity, precision, accuracy, linearity, robustness, and stability. Quantitative results were compared to those obtained with the JECFA HPLC-UV method and were found to be in reasonable agreement. NMR analysis does not rely on the use of reference compounds and enables significantly faster analysis compared to HPLC-UV. Thus, NMR represents a feasible alternative to HPLC-based methods for the quality control of Stevia rebaudiana extracts. PMID:21417451

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

    PubMed

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

    2012-12-01

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

  6. Detection of Potential TNA and RNA Nucleoside Precursors in a Prebiotic Mixture by Pure Shift Diffusion-Ordered NMR Spectroscopy

    PubMed Central

    Islam, Saidul; Aguilar, Juan A; Powner, Matthew W; Nilsson, Mathias; Morris, Gareth A; Sutherland, John D

    2013-01-01

    In the context of prebiotic chemistry, one of the characteristics of mixed nitrogenous-oxygenous chemistry is its propensity to give rise to highly complex reaction mixtures. There is therefore an urgent need to develop improved spectroscopic techniques if onerous chromatographic separations are to be avoided. One potential avenue is the combination of pure shift methodology, in which NMR spectra are measured with greatly improved resolution by suppressing multiplet structure, with diffusion-ordered spectroscopy, in which NMR signals from different species are distinguished through their different rates of diffusion. Such a combination has the added advantage of working with intact mixtures, allowing analyses to be carried out without perturbing mixtures in which chemical entities are part of a network of reactions in equilibrium. As part of a systems chemistry approach towards investigating the self-assembly of potentially prebiotic small molecules, we have analysed the complex mixture arising from mixing glycolaldehyde and cyanamide, in a first application of pure shift DOSY NMR to the characterisation of a partially unknown reaction composition. The work presented illustrates the potential of pure shift DOSY to be applied to chemistries that give rise to mixtures of compounds in which the NMR signal resolution is poor. The direct formation of potential RNA and TNA nucleoside precursors, amongst other adducts, was observed. These preliminary observations may have implications for the potentially prebiotic assembly chemistry of pyrimidine threonucleotides, and therefore of TNA, by using recently reported chemistries that yield the activated pyridimidine ribonucleotides. PMID:23371787

  7. Recoupling of chemical shift anisotropy by R-symmetry sequences in magic angle spinning NMR spectroscopy

    NASA Astrophysics Data System (ADS)

    Hou, Guangjin; Byeon, In-Ja L.; Ahn, Jinwoo; Gronenborn, Angela M.; Polenova, Tatyana

    2012-10-01

    13C and 15N chemical shift (CS) interaction is a sensitive probe of structure and dynamics in a wide variety of biological and inorganic systems, and in the recent years several magic angle spinning NMR approaches have emerged for residue-specific measurements of chemical shift anisotropy (CSA) tensors in uniformly and sparsely enriched proteins. All of the currently existing methods are applicable to slow and moderate magic angle spinning (MAS) regime, i.e., MAS frequencies below 20 kHz. With the advent of fast and ultrafast MAS probes capable of spinning frequencies of 40-100 kHz, and with the superior resolution and sensitivity attained at such high frequencies, development of CSA recoupling techniques working under such conditions is necessary. In this work, we present a family of R-symmetry based pulse sequences for recoupling of 13C/15N CSA interactions that work well in both natural abundance and isotopically enriched systems. We demonstrate that efficient recoupling of either first-rank (σ1) or second-rank (σ2) spatial components of CSA interaction is attained with appropriately chosen γ-encoded RNnv symmetry sequences. The advantage of these γ-encoded RNnv-symmetry based CSA (RNCSA) recoupling schemes is that they are suitable for CSA recoupling under a wide range of MAS frequencies, including fast MAS regime. Comprehensive analysis of the recoupling properties of these RNnv symmetry sequences reveals that the σ1-CSA recoupling symmetry sequences exhibit large scaling factors; however, the partial homonuclear dipolar Hamiltonian components are symmetry allowed, which makes this family of sequences suitable for CSA measurements in systems with weak homonuclear dipolar interactions. On the other hand, the γ-encoded symmetry sequences for σ2-CSA recoupling have smaller scaling factors but they efficiently suppress the homonuclear dipole-dipole interactions. Therefore, the latter family of sequences is applicable for measurements of CSA parameters in

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

    NASA Astrophysics Data System (ADS)

    Singh, Girija S.; Pheko, Tshepo

    2008-08-01

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

  9. Magic Angle Spinning NMR Reveals Sequence-Dependent Structural Plasticity, Dynamics, and the Spacer Peptide 1 Conformation in HIV-1 Capsid Protein Assemblies

    SciTech Connect

    Han, Yun; Hou, Guangjin; Suiter, Christopher L.; Ahn, Jinwoo; Byeon, In-Ja L.; Lipton, Andrew S.; Burton, Sarah D.; Hung, Ivan; Gorkov, Peter L.; Gan, Zhehong; Brey, William W.; Rice, David M.; Gronenborn, Angela M.; Polenova, Tatyana E.

    2013-11-27

    Maturation of HIV-1 virus into an infectious virion requires cleavage of the Gag polyprotein into its constituent domains and formation of a conical capsid core that encloses viral RNA and a small complement of proteins for replication. The final step of this process is the cleavage of the SP1 peptide from the CA-SP1 maturation intermediate, which triggers the condensation of the CA protein into a conical capsid. The mechanism of this step, including the conformation of the SP1 peptide in CA-SP1, is under intense debate. In this report, we examine the tubular assemblies of CA and the CA-SP1 maturation intermediate using Magic Angle Spinning NMR spectroscopy. At the magnetic fields of 19.9 T and above, tubular CA and CA-SP1 assemblies yield outstanding-quality 2D and 3D MAS NMR spectra, which are amenable to resonance assignments and detailed structural characterization. Dipolar- and scalar-based correlation experiments unequivocally indicate that SP1 peptide is in a random coil conformation and mobile in the assembled CA-SP1. Analysis of two sequence variants reveals that remarkably, the conformation of SP1 tail, of the functionally important CypA loop, and of the loop preceding helix 8 are sequence dependent and modulated by the residue variations at distal sites. These findings challenge the role of SP1 as a conformational switch in the maturation process and establish sequence-dependent conformational plasticity in CA.

  10. NMR structural studies reveal a novel protein fold for MerB, the organomercurial lyase involved in the bacterial mercury resistance system.

    PubMed

    Di Lello, Paola; Benison, Gregory C; Valafar, Homayoun; Pitts, Keith E; Summers, Anne O; Legault, Pascale; Omichinski, James G

    2004-07-01

    Mercury resistant bacteria have developed a system of two enzymes (MerA and MerB), which allows them to efficiently detoxify both ionic and organomercurial compounds. The organomercurial lyase (MerB) catalyzes the protonolysis of the carbon-mercury bond resulting in the formation of ionic mercury and a reduced hydrocarbon. The ionic mercury [Hg(II)] is subsequently reduced to the less reactive elemental mercury [Hg(0)] by a specific mercuric reductase (MerA). To better understand MerB's unique enzymatic activity, we used nuclear magnetic resonance (NMR) spectroscopy to determine the structure of the free enzyme. MerB is characterized by a novel protein fold consisting of three noninteracting antiparallel beta-sheets surrounded by six alpha-helices. By comparing the NMR data of free MerB and the MerB/Hg/DTT complex, we identified a set of residues that likely define a Hg/DTT binding site. These residues cluster around two cysteines (C(96) and C(159)) that are crucial to MerB's catalytic activity. A detailed analysis of the structure revealed the presence of an extensive hydrophobic groove adjacent to this Hg/DTT binding site. This extensive hydrophobic groove has the potential to interact with the hydrocarbon moiety of a wide variety of substrates and may explain the broad substrate specificity of MerB. PMID:15222745

  11. In vivo1H NMR spectroscopy of the human brain at 9.4 T: Initial results

    NASA Astrophysics Data System (ADS)

    Deelchand, Dinesh Kumar; Moortele, Pierre-François Van de; Adriany, Gregor; Iltis, Isabelle; Andersen, Peter; Strupp, John P.; Thomas Vaughan, J.; Uğurbil, Kâmil; Henry, Pierre-Gilles

    2010-09-01

    In vivo proton NMR spectroscopy allows non-invasive detection and quantification of a wide range of biochemical compounds in the brain. Higher field strength is generally considered advantageous for spectroscopy due to increased signal-to-noise and increased spectral dispersion. So far 1H NMR spectra have been reported in the human brain up to 7 T. In this study we show that excellent quality short echo time STEAM and LASER 1H NMR spectra can be measured in the human brain at 9.4 T. The information content of the human brain spectra appears very similar to that measured in the past decade in rodent brains at the same field strength, in spite of broader linewidth in human brain. Compared to lower fields, the T1 relaxation times of metabolites were slightly longer while T2 relaxation values of metabolites were shorter (<100 ms) at 9.4 T. The linewidth of the total creatine (tCr) resonance at 3.03 ppm increased linearly with magnetic field (1.35 Hz/T from 1.5 T to 9.4 T), with a minimum achievable tCr linewidth of around 12.5 Hz at 9.4 T. At very high field, B0 microsusceptibility effects are the main contributor to the minimum achievable linewidth.

  12. 1H HR-MAS NMR Spectroscopy and the Metabolite Determination of Typical Foods in Mediterranean Diet

    PubMed Central

    Corsaro, Carmelo; Mallamace, Domenico; Vasi, Sebastiano; Ferrantelli, Vincenzo; Dugo, Giacomo; Cicero, Nicola

    2015-01-01

    NMR spectroscopy has become an experimental technique widely used in food science. The experimental procedures that allow precise and quantitative analysis on different foods are relatively simple. For a better sensitivity and resolution, NMR spectroscopy is usually applied to liquid sample by means of extraction procedures that can be addressed to the observation of particular compounds. For the study of semisolid systems such as intact tissues, High-Resolution Magic Angle Spinning (HR-MAS) has received great attention within the biomedical area and beyond. Metabolic profiling and metabolism changes can be investigated both in animal organs and in foods. In this work we present a proton HR-MAS NMR study on the typical vegetable foods of Mediterranean diet such as the Protected Geographical Indication (PGI) cherry tomato of Pachino, the PGI Interdonato lemon of Messina, several Protected Designation of Origin (PDO) extra virgin olive oils from Sicily, and the Traditional Italian Food Product (PAT) red garlic of Nubia. We were able to identify and quantify the main metabolites within the studied systems that can be used for their characterization and authentication. PMID:26495154

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

    PubMed

    Lesot, Philippe; Baillif, Vincent; Billault, Isabelle

    2008-04-15

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

  14. Si-29 NMR spectroscopy of naturally-shocked quartz from Meteor Crater, Arizona: Correlation to Kieffer's classification scheme

    NASA Technical Reports Server (NTRS)

    Boslough, M. B.; Cygan, R. T.; Kirkpatrick, R. J.

    1993-01-01

    We have applied solid state Si-29 nuclear magnetic resonance (NMR) spectroscopy to five naturally-shocked Coconino Sandstone samples from Meteor Crater, Arizona, with the goal of examining possible correlations between NMR spectral characteristics and shock level. This work follows our observation of a strong correlation between the width of a Si-29 resonance and peak shock pressure for experimentally shocked quartz powders. The peak width increase is due to the shock-induced formation of amorphous silica, which increases as a function of shock pressure over the range that we studied (7.5 to 22 GPa). The Coconino Sandstone spectra are in excellent agreement with the classification scheme of Kieffer in terms of presence and approximate abundances of quartz, coesite, stishovite, and glass. We also observe a new resonance in two moderately shocked samples that we have tentatively identified with silicon in tetrahedra with one hydroxyl group in a densified form of amorphous silica.

  15. Selective detection and complete identification of triglycerides in cortical bone by high-resolution (1)H MAS NMR spectroscopy.

    PubMed

    Mroue, Kamal H; Xu, Jiadi; Zhu, Peizhi; Morris, Michael D; Ramamoorthy, Ayyalusamy

    2016-07-28

    Using (1)H-based magic angle spinning solid-state NMR spectroscopy, we report an atomistic-level characterization of triglycerides in compact cortical bone. By suppressing contributions from immobile molecules present in bone, we show that a (1)H-based constant-time uniform-sign cross-peak (CTUC) two-dimensional COSY-type experiment that correlates the chemical shifts of protons can selectively detect a mobile triglyceride layer as the main component of small lipid droplets embedded on the surface of collagen fibrils. High sensitivity and resolution afforded by this NMR approach could be potentially utilized to investigate the origin of triglycerides and their pathological roles associated with bone fractures, diseases, and aging. PMID:27374353

  16. An investigation of catalytic active phase-support interactions by IR, NMR and x-ray absorption spectroscopies

    SciTech Connect

    Haller, G.L.

    1992-09-01

    Active catalytic phases (metal, mixed metals, oxide or mixed oxides) interacting with oxide support on which the active phase is dispersed can affect the percentage exposed, the morphology of supported particles, the degree of reducibility of cations, etc., in a variety of ways. Our objective is to characterize the physical chemistry of the active phase-oxide support interaction by spectroscopic methods and to correlate this structure with catalytic function. Two catalytic systems and their associated techniques (x-ray absorption and NMR) are discussed in this progress report. Firstly, the interaction of Pt-Ni supported on silica and L-zeolite are characterized and compared by x-ray absorption spectroscopy (EXAFS). Secondly, we present both experimental and calculational developments of NMR for the investigation of amorphous silica-alumina catalysts and/or supports.

  17. NMR spectroscopy applied to the Cultural Heritage: a preliminary study on ancient wood characterisation

    NASA Astrophysics Data System (ADS)

    Viel, S.; Capitani, D.; Proietti, N.; Ziarelli, F.; Segre, A. L.

    High and low resolution solid state NMR methods have been applied to characterise a few samples of ancient wood. In an ancient larch wood sample, by applying 1H low resolution NMR methods as a function of the temperature, the average pore size and its distribution have been determined. In addition, high resolution NMR techniques have allowed addressing of the question of the proximity of water pools to cellulose and lignin. In particular, a model can be hypothesized in which water pools are surrounded by thin layers of amorphous cellulose and/or lignin while the crystalline domains of cellulose surround the layers of amorphous cellulose. Preliminary results obtained using a fully non invasive and portable NMR unilateral relaxometer, the Eureka-Mouse10 (EM10), are reported. This instrumentation is shown to be perfectly suitable for characterizing degradation in ancient wood samples.

  18. Titration of Alanine Monitored by NMR Spectroscopy: A Biochemistry Laboratory Experiment

    ERIC Educational Resources Information Center

    Waller, Francis J.; And Others

    1977-01-01

    The experiment described here involves simultaneous monitoring of pH and NMR chemical shifts during an aqueous titration of alpha- and beta-alanine. This experiment is designed for use in an undergraduate biochemistry course. (MR)

  19. Powder-XRD and (14) N magic angle-spinning solid-state NMR spectroscopy of some metal nitrides.

    PubMed

    Kempgens, Pierre; Britton, Jonathan

    2016-05-01

    Some metal nitrides (TiN, ZrN, InN, GaN, Ca3 N2 , Mg3 N2 , and Ge3 N4 ) have been studied by powder X-ray diffraction (XRD) and (14) N magic angle-spinning (MAS) solid-state NMR spectroscopy. For Ca3 N2 , Mg3 N2 , and Ge3 N4 , no (14) N NMR signal was observed. Low speed (νr  = 2 kHz for TiN, ZrN, and GaN; νr  = 1 kHz for InN) and 'high speed' (νr  = 15 kHz for TiN; νr  = 5 kHz for ZrN; νr  = 10 kHz for InN and GaN) MAS NMR experiments were performed. For TiN, ZrN, InN, and GaN, powder-XRD was used to identify the phases present in each sample. The number of peaks observed for each sample in their (14) N MAS solid-state NMR spectrum matches perfectly well with the number of nitrogen-containing phases identified by powder-XRD. The (14) N MAS solid-state NMR spectra are symmetric and dominated by the quadrupolar interaction. The envelopes of the spinning sidebands manifold are Lorentzian, and it is concluded that there is a distribution of the quadrupolar coupling constants Qcc 's arising from structural defects in the compounds studied. Copyright © 2015 John Wiley & Sons, Ltd. PMID:26687421

  20. NMR-Based Metabolic Profiling Reveals Neurochemical Alterations in the Brain of Rats Treated with Sorafenib.

    PubMed

    Du, Changman; Shao, Xue; Zhu, Ruiming; Li, Yan; Zhao, Qian; Fu, Dengqi; Gu, Hui; Kong, Jueying; Luo, Li; Long, Hailei; Deng, Pengchi; Wang, Huijuan; Hu, Chunyan; Zhao, Yinglan; Cen, Xiaobo

    2015-11-01

    Sorafenib, an active multi-kinase inhibitor, has been widely used as a chemotherapy drug to treat advanced clear-cell renal cell carcinoma patients. In spite of the relative safety, sorafenib has been shown to exert a negative impact on cognitive functioning in cancer patients, specifically on learning and memory; however, the underlying mechanism remains unclear. In this study, an NMR-based metabolomics approach was applied to investigate the neurochemical effects of sorafenib in rats. Male rats were once daily administrated with 120 mg/kg sorafenib by gavage for 3, 7, and 28 days, respectively. NMR-based metabolomics coupled with histopathology examinations for hippocampus, prefrontal cortex (PFC), and striatum were performed. The (1)H NMR spectra data were analyzed by using multivariate pattern recognition techniques to show the time-dependent biochemical variations induced by sorafenib. Excellent separation was obtained and distinguishing metabolites were observed between sorafenib-treated and control rats. A total of 36 differential metabolites in hippocampus of rats treated with sorafenib were identified, some of which were significantly changed. Furthermore, these modified metabolites mainly reflected the disturbances in neurotransmitters, energy metabolism, membrane, and amino acids. However, only a few metabolites in PFC and striatum were altered by sorafenib. Additionally, no apparent histological changes in these three brain regions were observed in sorafenib-treated rats. Together, our findings demonstrate the disturbed metabonomics pathways, especially, in hippocampus, which may underlie the sorafenib-induced cognitive deficits in patients. This work also shows the advantage of NMR-based metabolomics over traditional approach on the study of biochemical effects of drugs. PMID:26233726