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Sample records for 13c chemical shifts

  1. A procedure to validate and correct the 13C chemical shift calibration of RNA datasets

    Chemical shifts reflect the structural environment of a certain nucleus and can be used to extract structural and dynamic information. Proper calibration is indispensable to extract such information from chemical shifts. Whereas a variety of procedures exist to verify the chemical shift calibration for proteins, no such procedure is available for RNAs to date. We present here a procedure to analyze and correct the calibration of 13C NMR data of RNAs. Our procedure uses five 13C chemical shifts as a reference, each of them found in a narrow shift range in most datasets deposited in the Biological Magnetic Resonance Bank. In 49 datasets we could evaluate the 13C calibration and detect errors or inconsistencies in RNA 13C chemical shifts based on these chemical shift reference values. More than half of the datasets (27 out of those 49) were found to be improperly referenced or contained inconsistencies. This large inconsistency rate possibly explains that no clear structure–13C chemical shift relationship has emerged for RNA so far. We were able to recalibrate or correct 17 datasets resulting in 39 usable 13C datasets. 6 new datasets from our lab were used to verify our method increasing the database to 45 usable datasets. We can now search for structure–chemical shift relationships with this improved list of 13C chemical shift data. This is demonstrated by a clear relationship between ribose 13C shifts and the sugar pucker, which can be used to predict a C2′- or C3′-endo conformation of the ribose with high accuracy. The improved quality of the chemical shift data allows statistical analysis with the potential to facilitate assignment procedures, and the extraction of restraints for structure calculations of RNA.

  2. Four-Component Relativistic DFT Calculations of (13)C Chemical Shifts of Halogenated Natural Substances.

    Casella, Girolamo; Bagno, Alessandro; Komorovsky, Stanislav; Repisky, Michal; Saielli, Giacomo

    2015-12-14

    We have calculated the (13)C NMR chemical shifts of a large ensemble of halogenated organic molecules (81 molecules for a total of 250 experimental (13)C NMR data at four different levels of theory), ranging from small rigid organic compounds, used to benchmark the performance of various levels of theory, to natural substances of marine origin with conformational degrees of freedom. Carbon atoms bonded to heavy halogen atoms, particularly bromine and iodine, are known to be rather challenging when it comes to the prediction of their chemical shifts by quantum methods, due to relativistic effects. In this paper, we have applied the state-of-the-art four-component relativistic density functional theory for the prediction of such NMR properties and compared the performance with two-component and nonrelativistic methods. Our results highlight the necessity to include relativistic corrections within a four-component description for the most accurate prediction of the NMR properties of halogenated organic substances. PMID:26541625

  3. Using Neural Networks for 13C NMR Chemical Shift Prediction-Comparison with Traditional Methods

    Meiler, Jens; Maier, Walter; Will, Martin; Meusinger, Reinhard

    2002-08-01

    Interpretation of 13C chemical shifts is essential for structure elucidation of organic molecules by NMR. In this article, we present an improved neural network approach and compare its performance to that of commonly used approaches. Specifically, our recently proposed neural network ( J. Chem. Inf. Comput. Sci. 2000, 40, 1169-1176) is improved by introducing an extended hybrid numerical description of the carbon atom environment, resulting in a standard deviation (std. dev.) of 2.4 ppm for an independent test data set of ˜42,500 carbons. Thus, this neural network allows fast and accurate 13C NMR chemical shift prediction without the necessity of access to molecule or fragment databases. For an unbiased test dataset containing 100 organic structures the accuracy of the improved neural network was compared to that of a prediction method based on the HOSE code ( hierarchically ordered spherical description of environment) using S PECI NFO. The results show the neural network predictions to be of quality (std. dev.=2.7 ppm) comparable to that of the HOSE code prediction (std. dev.=2.6 ppm). Further we compare the neural network predictions to those of a wide variety of other 13C chemical shift prediction tools including incremental methods (C HEMD RAW, S PECT OOL), quantum chemical calculation (G AUSSIAN, C OSMOS), and HOSE code fragment-based prediction (S PECI NFO, ACD/CNMR, P REDICTI T NMR) for the 47 13C-NMR shifts of Taxol, a natural product including many structural features of organic substances. The smallest standard deviations were achieved here with the neural network (1.3 ppm) and S PECI NFO (1.0 ppm).

  4. Determination of the Orientation and Dynamics of Ergosterol in Model Membranes Using Uniform 13C Labeling and Dynamically Averaged 13C Chemical Shift Anisotropies as Experimental Restraints

    Soubias, O.; Jolibois, F.; Massou, S.; Milon, A.; Réat, V.

    2005-01-01

    A new strategy was established to determine the average orientation and dynamics of ergosterol in dimyristoylphosphatidylcholine model membranes. It is based on the analysis of chemical shift anisotropies (CSAs) averaged by the molecular dynamics. Static 13C CSA tensors were computed by quantum chemistry, using the gauge-including atomic-orbital approach within Hartree-Fock theory. Uniformly 13C-labeled ergosterol was purified from Pichia pastoris cells grown on labeled methanol. After reconstitution into dimyristoylphosphatidylcholine lipids, the complete 1H and 13C assignment of ergosterol's resonances was performed using a combination of magic-angle spinning two-dimensional experiments. Dynamically averaged CSAs were determined by standard side-band intensity analysis for isolated 13C resonances (C3 and ethylenic carbons) and by off-magic-angle spinning experiments for other carbons. A set of 18 constraints was thus obtained, from which the sterol's molecular order parameter and average orientation could be precisely defined. The validity of using computed CSAs in this strategy was verified on cholesterol model systems. This new method allowed us to quantify ergosterol's dynamics at three molar ratios: 16 mol % (Ld phase), 30 mol % (Lo phase), and 23 mol % (mixed phases). Contrary to cholesterol, ergosterol's molecular diffusion axis makes an important angle (14°) with the inertial axis of the rigid four-ring system. PMID:15923221

  5. Comprehensive signal assignment of 13C-labeled lignocellulose using multidimensional solution NMR and 13C chemical shift comparison with solid-state NMR.

    Komatsu, Takanori; Kikuchi, Jun

    2013-09-17

    A multidimensional solution NMR method has been developed using various pulse programs including HCCH-COSY and (13)C-HSQC-NOESY for the structural characterization of commercially available (13)C labeled lignocellulose from potatoes (Solanum tuberosum L.), chicory (Cichorium intybus), and corn (Zea mays). This new method allowed for 119 of the signals in the (13)C-HSQC spectrum of lignocelluloses to be assigned and was successfully used to characterize the structures of lignocellulose samples from three plants in terms of their xylan and xyloglucan structures, which are the major hemicelluloses in angiosperm. Furthermore, this new method provided greater insight into fine structures of lignin by providing a high resolution to the aromatic signals of the β-aryl ether and resinol moieties, as well as the diastereomeric signals of the β-aryl ether. Finally, the (13)C chemical shifts assigned in this study were compared with those from solid-state NMR and indicated the presence of heterogeneous dynamics in the polysaccharides where rigid cellulose and mobile hemicelluloses moieties existed together. PMID:24010724

  6. 13C chemical shift anisotropies for carbonate ions in cement minerals and the use of 13C, 27Al and 29Si MAS NMR in studies of Portland cement including limestone additions

    13C isotropic chemical shifts and chemical shift anisotropy parameters have been determined for a number of inorganic carbonates relevant in cement chemistry from slow-speed 13C MAS or 13C(1H) CP/MAS NMR spectra (9.4 T or 14.1 T) for 13C in natural abundance. The variation in the 13C chemical shift parameters is relatively small, raising some doubts that different carbonate species in Portland cement-based materials may not be sufficiently resolved in 13C MAS NMR spectra. However, it is shown that by combining 13C MAS and 13C(1H) CP/MAS NMR carbonate anions in anhydrous and hydrated phases can be distinguished, thereby providing valuable information about the reactivity of limestone in cement blends. This is illustrated for three cement pastes prepared from an ordinary Portland cement, including 0, 16, and 25 wt.% limestone, and following the hydration for up to one year. For these blends 29Si MAS NMR reveals that the limestone filler accelerates the hydration for alite and also results in a smaller fraction of tetrahedrally coordinated Al incorporated in the C-S-H phase. The latter result is more clearly observed in 27Al MAS NMR spectra of the cement–limestone blends and suggests that dissolved aluminate species in the cement–limestone blends readily react with carbonate ions from the limestone filler, forming calcium monocarboaluminate hydrate. -- Highlights: •13C chemical shift anisotropies for inorganic carbonates from 13C MAS NMR. •Narrow 13C NMR chemical shift range (163–171 ppm) for inorganic carbonates. •Anhydrous and hydrated carbonate species by 13C MAS and 13C(1H) CP/MAS NMR. •Limestone accelerates the hydration for alite in Portland – limestone cements. •Limestone reduces the amount of aluminium incorporated in the C-S-H phase

  7. Fragment-based (13)C nuclear magnetic resonance chemical shift predictions in molecular crystals: An alternative to planewave methods.

    Hartman, Joshua D; Monaco, Stephen; Schatschneider, Bohdan; Beran, Gregory J O

    2015-09-14

    We assess the quality of fragment-based ab initio isotropic (13)C chemical shift predictions for a collection of 25 molecular crystals with eight different density functionals. We explore the relative performance of cluster, two-body fragment, combined cluster/fragment, and the planewave gauge-including projector augmented wave (GIPAW) models relative to experiment. When electrostatic embedding is employed to capture many-body polarization effects, the simple and computationally inexpensive two-body fragment model predicts both isotropic (13)C chemical shifts and the chemical shielding tensors as well as both cluster models and the GIPAW approach. Unlike the GIPAW approach, hybrid density functionals can be used readily in a fragment model, and all four hybrid functionals tested here (PBE0, B3LYP, B3PW91, and B97-2) predict chemical shifts in noticeably better agreement with experiment than the four generalized gradient approximation (GGA) functionals considered (PBE, OPBE, BLYP, and BP86). A set of recommended linear regression parameters for mapping between calculated chemical shieldings and observed chemical shifts are provided based on these benchmark calculations. Statistical cross-validation procedures are used to demonstrate the robustness of these fits. PMID:26374002

  8. Fragment-based 13C nuclear magnetic resonance chemical shift predictions in molecular crystals: An alternative to planewave methods

    We assess the quality of fragment-based ab initio isotropic 13C chemical shift predictions for a collection of 25 molecular crystals with eight different density functionals. We explore the relative performance of cluster, two-body fragment, combined cluster/fragment, and the planewave gauge-including projector augmented wave (GIPAW) models relative to experiment. When electrostatic embedding is employed to capture many-body polarization effects, the simple and computationally inexpensive two-body fragment model predicts both isotropic 13C chemical shifts and the chemical shielding tensors as well as both cluster models and the GIPAW approach. Unlike the GIPAW approach, hybrid density functionals can be used readily in a fragment model, and all four hybrid functionals tested here (PBE0, B3LYP, B3PW91, and B97-2) predict chemical shifts in noticeably better agreement with experiment than the four generalized gradient approximation (GGA) functionals considered (PBE, OPBE, BLYP, and BP86). A set of recommended linear regression parameters for mapping between calculated chemical shieldings and observed chemical shifts are provided based on these benchmark calculations. Statistical cross-validation procedures are used to demonstrate the robustness of these fits

  9. 13C-NMR chemical shift databases as a quick tool to evaluate structural models of humic substances

    Nyrop Albers, Christian; Hansen, Poul Erik

    2010-01-01

    Models for humic and fulvic acids are discussed based on 13C liquid state NMR spectra combined with results from elemental analysis and titration studies. The analysis of NMR spectra is based on a full reconstruction of the NMR spectrum done with help of 13C-NMR data bases by adding up chemical s...

  10. Backbone and stereospecific (13)C methyl Ile (δ1), Leu and Val side-chain chemical shift assignments of Crc.

    Sharma, Rakhi; Sahu, Bhubanananda; Ray, Malay K; Deshmukh, Mandar V

    2015-04-01

    Carbon catabolite repression (CCR) allows bacteria to selectively assimilate a preferred compound among a mixture of several potential carbon sources, thus boosting growth and economizing the cost of adaptability to variable nutrients in the environment. The RNA-binding catabolite repression control (Crc) protein acts as a global post-transcriptional regulator of CCR in Pseudomonas species. Crc triggers repression by inhibiting the expression of genes involved in transport and catabolism of non-preferred substrates, thus indirectly favoring assimilation of preferred one. We report here a nearly complete backbone and stereospecific (13)C methyl side-chain chemical shift assignments of Ile (δ1), Leu and Val of Crc (~ 31 kDa) from Pseudomonas syringae Lz4W. PMID:24496608

  11. NMR spectroscopy of organic compounds of selenium and tellurium. Communication 9. Chemical shifts of 13C in isological series of unsaturated ethers, sulfides, selenides and tellurides

    The effects of heteroatoms Eh(Eh=O, S, Se, Te) on 13C chemical shifts in eleven isological series of R1-Eh-R2 unsaturated compounds are compared. A linear relation between 13C nuclei screening and tEh electronegativity is observed. An assumption is suggested that both likeness of the effects of 6A and 7A group elements on 13C chemical shifts of R1 and R2 substituents and their difference for elements of the 4A group are caused by unbonded interactions of the substituents with unshared electron pairs of heteroatoms

  12. Molecular structure and vibrational bands and 13C chemical shift assignments of both enmein-type diterpenoids by DFT study

    Wang, Tao; Wu, Yi fang; Wang, Xue liang

    2014-01-01

    We report here theoretical and experimental studies on the molecular structure and vibrational and NMR spectra of both natural enmein type diterpenoids molecule (6, 7-seco-ent-kaurenes enmein type), isolated from the leaves of Isodon japonica (Burm.f.) Hara var. galaucocalyx (maxin) Hara. The optimized geometry, total energy, NMR chemical shifts and vibrational wavenumbers of epinodosinol and epinodosin have been determined using B3LYP method with 6-311G (d,p) basis set. A complete vibrational assignment is provided for the observed IR spectra of studied compounds. The calculated wavenumbers and 13C c.s. are in an excellent agreement with the experimental values. Quantum chemical calculations at the B3LYP/6-311G (d,p) level of theory have been carried out on studied compounds to obtain a set of molecular electronic properties (MEP,HOMO, LUMO and gap energies ΔEg). Electrostatic potential surfaces have been mapped over the electron density isosurfaces to obtain information about the size, shape, charge density distribution and chemical reactivity of the molecules.

  13. Chemical Constituents of Lecythispisonis (Lecythidaceae)--A New Saponin and Complete 1H and 13C Chemical Shift Assignments.

    Duarte, Rennê C; Matos, Carlos R R; Braz-Filho, Raimundo; Mathias, Leda

    2015-06-01

    A novel triterpenoid saponin 3-O-β-D-glucuronopyranosyl-(1' --> 3)-2α,19α-dihydroxyolean-12-en-28-oic acid [3-O-β-D-glucuronopyranosyl-(1' --> 3)-arjunic acid, 1], ten known compounds [six triterpenoids: α-amyrin (2), β-amyrin (3), germanicol (4), lupeol (5), friedelin (6), friedelanol (7); four steroids--campesterol (8), stigmasterol (9), sitosterol (10), cholesterol (11)], and a long chain alcohol n-eicosan-1-ol (12) were identified in the bark of Lecythis pisonis. The structures were established by 1D and 2D NMR spectroscopy (1H and 13C-NMR, DEPTQ, 1H-1H-COSY, NOESY, HSQC and HMBC), low (CG-MS) and high resolution mass spectrometry (HR-ESI-MS), and infrared (IR) spectral data involving comparison with the literature. PMID:26197504

  14. Secondary structural analysis of proteins based on 13C chemical shift assignments in unresolved solid-state NMR spectra enhanced by fragmented structure database

    Magic-angle-spinning solid-state 13C NMR spectroscopy is useful for structural analysis of non-crystalline proteins. However, the signal assignments and structural analysis are often hampered by the signal overlaps primarily due to minor structural heterogeneities, especially for uniformly-13C,15N labeled samples. To overcome this problem, we present a method for assigning 13C chemical shifts and secondary structures from unresolved two-dimensional 13C–13C MAS NMR spectra by spectral fitting, named reconstruction of spectra using protein local structures (RESPLS). The spectral fitting was conducted using databases of protein fragmented structures related to 13Cα, 13Cβ, and 13C′ chemical shifts and cross-peak intensities. The experimental 13C–13C inter- and intra-residue correlation spectra of uniformly isotope-labeled ubiquitin in the lyophilized state had a few broad peaks. The fitting analysis for these spectra provided sequence-specific Cα, Cβ, and C′ chemical shifts with an accuracy of about 1.5 ppm, which enabled the assignment of the secondary structures with an accuracy of 79 %. The structural heterogeneity of the lyophilized ubiquitin is revealed from the results. Test of RESPLS analysis for simulated spectra of five different types of proteins indicated that the method allowed the secondary structure determination with accuracy of about 80 % for the 50–200 residue proteins. These results demonstrate that the RESPLS approach expands the applicability of the NMR to non-crystalline proteins exhibiting unresolved 13C NMR spectra, such as lyophilized proteins, amyloids, membrane proteins and proteins in living cells.

  15. Other compounds isolated from Simira glaziovii and the {sup 1}H and {sup 13}C NMR chemical shift assignments of new 1-epi-castanopsol

    Araujo, Marcelo F. de; Vieira, Ivo J. Curcino [Universidade Federal Rural do Rio de Janeiro, Seropedica, RJ (Brazil). Dept. de Quimica; Braz-Filho, Raimundo [Universidade Estadual do Norte Fluminense (UENF), Campos dos Goytacases, RJ (Brazil). Centro de Ciencias Tecnologicas. Lab. de Ciencias Quimicas; Carvalho, Mario G. de, E-mail: mgeraldo@ufrrj.br [Universidade Federal do Rio de Janeiro (NPPN/UFRJ), RJ (Brazil). Centro de Ciencias da Saude. Nucleo de Pesquisa em Produtos Naturais

    2012-07-01

    A new triterpene, 1-epi-castanopsol, besides eleven known compounds: sitosterol, stigmasterol, campesterol, lupeol, lupenone, simirane B, syringaresinol, scopoletin, isofraxidin, 6,7,8-trimethoxycoumarin and harman, were isolated from the wood of Simira glaziovii. The structures of the known compounds were defined by 1D, 2D {sup 1}H, {sup 13}C NMR spectra data analyses and comparison with literature data. The detailed spectral data analyses allowed the definition of the structure of the new 1-epi isomer of castanopsol and performance of {sup 1}H and {sup 13}C NMR chemical shift assignments. (author)

  16. Other compounds isolated from Simira glaziovii and the 1H and 13C NMR chemical shift assignments of new 1-epi-castanopsol

    A new triterpene, 1-epi-castanopsol, besides eleven known compounds: sitosterol, stigmasterol, campesterol, lupeol, lupenone, simirane B, syringaresinol, scopoletin, isofraxidin, 6,7,8-trimethoxycoumarin and harman, were isolated from the wood of Simira glaziovii. The structures of the known compounds were defined by 1D, 2D 1H, 13C NMR spectra data analyses and comparison with literature data. The detailed spectral data analyses allowed the definition of the structure of the new 1-epi isomer of castanopsol and performance of 1H and 13C NMR chemical shift assignments. (author)

  17. 1H, 13C and 13N chemical shifts and 1H-15N and 13C-15N heteronuclear spin-spin coupling constants n the NMR spectra of 5-substituted furfural oximes

    The 1H, 13C, and 15N NMR spectra of 15N-enriched 5-substituted furfural oximes were investigated. It was shown that the chemical shifts of the ring atoms and the oxime group correlate satisfactorily with the F and R substituent constants, whereas their sensitivity to the effect of the substituents is lower than in monosubstituted furan derivatives. The constants of spin-spin coupling between the ring protons and the oxime group were determined. An analysis of the 1H-1H spin-spin coupling constants (SSCC) on the basis of their stereospecificity indicates that the E isomers have primarily an s-trans conformation in polar dimethyl sulfoxide, whereas the Z isomers, on the other hand, have an s-cis conformation. The signs of the direct and geminal 13C-15N SSCC were determined for 5-trimethylsilylfurfural oxime

  18. The Effect of Molecular Conformation on the Accuracy of Theoretical (1)H and (13)C Chemical Shifts Calculated by Ab Initio Methods for Metabolic Mixture Analysis.

    Chikayama, Eisuke; Shimbo, Yudai; Komatsu, Keiko; Kikuchi, Jun

    2016-04-14

    NMR spectroscopy is a powerful method for analyzing metabolic mixtures. The information obtained from an NMR spectrum is in the form of physical parameters, such as chemical shifts, and construction of databases for many metabolites will be useful for data interpretation. To increase the accuracy of theoretical chemical shifts for development of a database for a variety of metabolites, the effects of sets of conformations (structural ensembles) and the levels of theory on computations of theoretical chemical shifts were systematically investigated for a set of 29 small molecules in the present study. For each of the 29 compounds, 101 structures were generated by classical molecular dynamics at 298.15 K, and then theoretical chemical shifts for 164 (1)H and 123 (13)C atoms were calculated by ab initio quantum chemical methods. Six levels of theory were used by pairing Hartree-Fock, B3LYP (density functional theory), or second order Møller-Plesset perturbation with 6-31G or aug-cc-pVDZ basis set. The six average fluctuations in the (1)H chemical shift were ±0.63, ± 0.59, ± 0.70, ± 0.62, ± 0.75, and ±0.66 ppm for the structural ensembles, and the six average errors were ±0.34, ± 0.27, ± 0.32, ± 0.25, ± 0.32, and ±0.25 ppm. The results showed that chemical shift fluctuations with changes in the conformation because of molecular motion were larger than the differences between computed and experimental chemical shifts for all six levels of theory. In conclusion, selection of an appropriate structural ensemble should be performed before theoretical chemical shift calculations for development of an accurate database for a variety of metabolites. PMID:26963288

  19. Automated prediction of 15N, 13Cα, 13Cβ and 13C' chemical shifts in proteins using a density functional database

    A database of peptide chemical shifts, computed at the density functional level, has been used to develop an algorithm for prediction of 15N and 13C shifts in proteins from their structure; the method is incorporated into a program called SHIFTS (version 4.0). The database was built from the calculated chemical shift patterns of 1335 peptides whose backbone torsion angles are limited to areas of the Ramachandran map around helical and sheet configurations. For each tripeptide in these regions of regular secondary structure (which constitute about 40% of residues in globular proteins) SHIFTS also consults the database for information about sidechain torsion angle effects for the residue of interest and for the preceding residue, and estimates hydrogen bonding effects through an empirical formula that is also based on density functional calculations on peptides. The program optionally searches for alternate side-chain torsion angles that could significantly improve agreement between calculated and observed shifts. The application of the program on 20 proteins shows good consistency with experimental data, with correlation coefficients of 0.92, 0.98, 0.99 and 0.90 and r.m.s. deviations of 1.94, 0.97, 1.05, and 1.08 ppm for 15N, 13Cα, 13Cβ and 13C', respectively. Reference shifts fit to protein data are in good agreement with 'random-coil' values derived from experimental measurements on peptides. This prediction algorithm should be helpful in NMR assignment, crystal and solution structure comparison, and structure refinement

  20. 1H and 13C NMR Chemical Shift Assignments and Conformational Analysis for the Two Diastereomers of the Vitamin K Epoxide Reductase Inhibitor Brodifacoum

    Proton and 13C NMR chemical shift assignments and 1H-1H scalar couplings for the two diastereomers of the vitamin K epoxide reductase (VKOR) inhibitor brodifacoum have been determined from acetone solutions containing both diastereomers. Data were obtained from homo- and heteronuclear correlation spectra acquired at 1H frequencies of 750 and 900 MHz over a 268-303 K temperature range. Conformations inferred from scalar coupling and 1-D NOE measurements exhibit large differences between the diastereomers. Pacific Northwest National Laboratory is operated by Battelle for the US Department of Energy.

  1. Fractional enrichment of proteins using [2-{sup 13}C]-glycerol as the carbon source facilitates measurement of excited state {sup 13}Cα chemical shifts with improved sensitivity

    Ahlner, Alexandra; Andresen, Cecilia; Khan, Shahid N. [Linköping University, Division of Chemistry, Department of Physics, Chemistry and Biology (Sweden); Kay, Lewis E. [The University of Toronto, Departments of Molecular Genetics, Biochemistry and Chemistry, One King’s College Circle (Canada); Lundström, Patrik, E-mail: patlu@ifm.liu.se [Linköping University, Division of Chemistry, Department of Physics, Chemistry and Biology (Sweden)

    2015-07-15

    A selective isotope labeling scheme based on the utilization of [2-{sup 13}C]-glycerol as the carbon source during protein overexpression has been evaluated for the measurement of excited state {sup 13}Cα chemical shifts using Carr–Purcell–Meiboom–Gill (CPMG) relaxation dispersion (RD) experiments. As expected, the fractional incorporation of label at the Cα positions is increased two-fold relative to labeling schemes based on [2-{sup 13}C]-glucose, effectively doubling the sensitivity of NMR experiments. Applications to a binding reaction involving an SH3 domain from the protein Abp1p and a peptide from the protein Ark1p establish that accurate excited state {sup 13}Cα chemical shifts can be obtained from RD experiments, with errors on the order of 0.06 ppm for exchange rates ranging from 100 to 1000 s{sup −1}, despite the small fraction of {sup 13}Cα–{sup 13}Cβ spin-pairs that are present for many residue types. The labeling approach described here should thus be attractive for studies of exchanging systems using {sup 13}Cα spin probes.

  2. DFT Studies on Thermal Stabilities,Electronic Structures, and 13C Chemical Shifts of C24O2 Based on Fullerene C24(D6)

    WANG Zhen; ZHANG Jing

    2011-01-01

    Quantum chemical calculations on some possible equilibrium geometries of C2402 isomers derived from C24 (D6) and C240 have been performed using density functional theory (DFT) method. The geometric and electronic structures as well as the relative energies and thermal stabilities of various C2402 isomers at the ground state have been calculated at the B3LYP/6-31G(d) level of theory. And the 1,4,2,5-C2402 isomer was found to be the most stable geometry where two oxygen atoms were added to the longest carbon-carbon bonds in the same pentagon from a thermodynamic point of view. Based on the optimized neutral geometries, the vertical ionization potential and vertical electron affinity have been obtained. Meanwhile, the vibrational frequencies,IR spectrum, and 13C chemical shifts of various C2402 isomers have been calculated and analyzed.

  3. Influence of substituents on chemical shift of {delta}({sup 13}C) in the series of 5-methyl-5H-indole [2,3-b]quinoline derivatives; Wplyw podstawnikow na przesuniecie chemiczne {sigma}({sup 13}C) w serii pochodnych 5-metylo-5H-indolo-[2,3-b]chinoliny

    Kamienska-Trela, K.; Kania, L.; Kaczmarek, L. [Inst. Chemii Organicznej, Polska Akademia Nauk, Warsaw (Poland)

    1994-12-31

    {sup 13}C NMR spectra of series of 5-methyl-5H-indole quinoline substituted with different groups and their number have been measured. The influence of steric and electronic properties of substituents on observed chemical shifts of {sup 13}C nuclei have been discussed. 1 fig., 1 tab.

  4. Probing structural patterns of ion association and solvation in mixtures of imidazolium ionic liquids with acetonitrile by means of relative (1)H and (13)C NMR chemical shifts.

    Marekha, Bogdan A; Kalugin, Oleg N; Bria, Marc; Idrissi, Abdenacer

    2015-09-21

    Mixtures of ionic liquids (ILs) with polar aprotic solvents in different combinations and under different conditions (concentration, temperature etc.) are used widely in electrochemistry. However, little is known about the key intermolecular interactions in such mixtures depending on the nature of the constituents and mixture composition. In order to systematically address the intermolecular interactions, the chemical shift variation of (1)H and (13)C nuclei has been followed in mixtures of imidazolium ILs 1-n-butyl-3-methylimidazolium tetrafluoroborate (BmimBF4), 1-n-butyl-3-methylimidazolium hexafluorophosphate (BmimPF6), 1-n-butyl-3-methylimidazolium trifluoromethanesulfonate (BmimTfO) and 1-n-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide (BmimTFSI) with molecular solvent acetonitrile (AN) over the entire composition range at 300 K. The concept of relative chemical shift variation is proposed to assess the observed effects on a unified and unbiased scale. We have found that hydrogen bonds between the imidazolium ring hydrogen atoms and electronegative atoms of anions are stronger in BmimBF4 and BmimTfO ILs than those in BmimTFSI and BmimPF6. Hydrogen atom at position 2 of the imidazolium ring is substantially more sensitive to interionic hydrogen bonding than those at positions 4-5 in the case of BmimTfO and BmimTFSI ILs. These hydrogen bonds are disrupted upon dilution in AN due to ion dissociation which is more pronounced at high dilutions. Specific solvation interactions between AN molecules and IL cations are poorly manifested. PMID:26278514

  5. Determination of the Tautomeric Equilibria of Pyridoyl Benzoyl -Diketones in the Liquid and Solid State through the use of Deuterium Isotope Effects on 1H and 13C NMR Chemical Shifts and Spin Coupling Constants

    Hansen, Poul Erik; Borisov, Eugeny V.; Lindon, John C.

    2015-01-01

    The tautomeric equilibria for 2-pyridoyl-, 3-pyridoyl-, and 4-pyridoyl-benzoyl methane have been investigated using deuterium isotope effects on 1H and 13C chemical shifts both in the liquid and the solid state. Equilibria are established both in the liquid and the solid state. In addition, in th...

  6. Plakilactones G and H from a marine sponge. Stereochemical determination of highly flexible systems by quantitative NMR-derived interproton distances combined with quantum mechanical calculations of 13C chemical shifts

    Simone Di Micco

    2013-12-01

    Full Text Available In this paper the stereostructural investigation of two new oxygenated polyketides, plakilactones G and H, isolated from the marine sponge Plakinastrella mamillaris collected at Fiji Islands, is reported. The stereostructural studies began on plakilactone H by applying an integrated approach of the NOE-based protocol and quantum mechanical calculations of 13C chemical shifts. In particular, plakilactone H was used as a template to extend the application of NMR-derived interproton distances to a highly flexible molecular system with simultaneous assignment of four non-contiguous stereocenters. Chemical derivatization and quantum mechanical calculations of 13C on plakilactone G along with a plausible biogenetic interconversion between plakilactone G and plakilactone H allowed us to determine the absolute configuration in this two new oxygenated polyketides.

  7. (1)H, (13)C, and (15)N chemical shift assignments of cyanobacteriochrome NpR6012g4 in the green-absorbing photoproduct state.

    Lim, Sunghyuk; Yu, Qinhong; Rockwell, Nathan C; Martin, Shelley S; Lagarias, J Clark; Ames, James B

    2016-04-01

    Cyanobacteriochromes (CBCRs) are cyanobacterial photosensory proteins with a tetrapyrrole (bilin) chromophore that belong to the phytochrome superfamily. Like phytochromes, CBCRs photoconvert between two photostates with distinct spectral properties. NpR6012g4 from Nostoc punctiforme is a model system for widespread CBCRs with conserved red/green photocycles. Atomic-level structural information for the photoproduct state in this subfamily is not known. Here, we report NMR backbone chemical shift assignments of the light-activated state of NpR6012g4 (BMRB no. 26577) as a first step toward determining its atomic resolution structure. PMID:26537963

  8. (1)H, (15)N and (13)C chemical shift assignment of the Gram-positive conjugative transfer protein TraHpIP501.

    Fercher, Christian; Keller, Walter; Zangger, Klaus; Helge Meyer, N

    2016-04-01

    Conjugative transfer of DNA represents the most important transmission pathway in terms of antibiotic resistance and virulence gene dissemination among bacteria. TraH is a putative transfer protein of the type IV secretion system (T4SS) encoded by the Gram-positive (G+) conjugative plasmid pIP501. This molecular machine involves a multi-protein core complex spanning the bacterial envelope thereby serving as a macromolecular secretion channel. Here, we report the near complete (1)H, (13)C and (15)N resonance assignment of a soluble TraH variant comprising the C-terminal domain. PMID:26559076

  9. Iboga alkaloids from Peschiera affinis (Apocynaceae) - unequivocal {sup 1}H and {sup 13}C chemical shift assignments: antioxidant activity; Alcaloides iboga de Peschiera affinis (Apocynaceae) - atribuicao inequivoca dos deslocamentos quimicos dos atomos de hidrogenio e carbono: atividade antioxidante

    Santos, Allana Kellen L.; Magalhaes, Ticiane S.; Monte, Francisco Jose Q.; Mattos, Marcos Carlos de; Oliveira, Maria Conceicao F. de; Almeida, Maria Mozarina B.; Lemos, Telma L.G.; Braz-Filho, Raimundo [Universidade Federal do Ceara (UFC), Fortaleza, CE (Brazil). Dept. de Quimica Organica e Inorganica], e-mail: tlemos@dqoi.ufc.br

    2009-07-01

    Six known alkaloids iboga type and the triterpene {alpha}- and {beta}-amyrin acetate were isolated from the roots and stems of Peschiera affinis. Their structures were characterized on the basis of spectral data mainly NMR and mass spectra. 1D and 2D NMR spectra were also used to unequivocal {sup 1}H and {sup 13}C chemical shift assignments of alkaloids. The ethanolic extract of roots, alkaloidic and no-alkaloidic fractions and iso-voacristine hydroxyindolenine and voacangine were evaluated for their antioxidative properties using an autographic assay based on {beta}-carotene bleaching on TLC plates, and also spectrophotometric detection by reduction of the stable DPPH (2,2-diphenyl-1-picrylhydrazyl) free radical. (author)

  10. Structure-based predictions of 13C-NMR chemical shifts for a series of 2-functionalized 5-(methylsulfonyl)-1-phenyl-1H-indoles derivatives using GA-based MLR method

    Ghavami, Raouf; Sadeghi, Faridoon; Rasouli, Zolikha; Djannati, Farhad

    2012-12-01

    Experimental values for the 13C NMR chemical shifts (ppm, TMS = 0) at 300 K ranging from 96.28 ppm (C4' of indole derivative 17) to 159.93 ppm (C4' of indole derivative 23) relative to deuteride chloroform (CDCl3, 77.0 ppm) or dimethylsulfoxide (DMSO, 39.50 ppm) as internal reference in CDCl3 or DMSO-d6 solutions have been collected from literature for thirty 2-functionalized 5-(methylsulfonyl)-1-phenyl-1H-indole derivatives containing different substituted groups. An effective quantitative structure-property relationship (QSPR) models were built using hybrid method combining genetic algorithm (GA) based on stepwise selection multiple linear regression (SWS-MLR) as feature-selection tools and correlation models between each carbon atom of indole derivative and calculated descriptors. Each compound was depicted by molecular structural descriptors that encode constitutional, topological, geometrical, electrostatic, and quantum chemical features. The accuracy of all developed models were confirmed using different types of internal and external procedures and various statistical tests. Furthermore, the domain of applicability for each model which indicates the area of reliable predictions was defined.

  11. Complete assignment of 1H, 13C and 15N chemical shifts for bovine β-lactoglobulin: Secondary structure and topology of the native state is retained in a partially unfolded form

    Although β-lactoglobulin (β-LG) has been studied extensively for more than 50 years, its physical properties in solution are not yet understood fully in terms of its three-dimensional (3D) structure. For example, despite a recent high-resolution crystal structure, it is still not clear why the two common variants of bovine β-LG which differ by just two residues have different aggregation properties during milk processing. We have conducted solution-state NMR studies on a recombinant form of the A variant of β-LG at low pH conditions where the protein is partially unfolded and exists as a monomer rather than a dimer. Using a13 C,15N-labelled sample, expressed in Pichia pastoris, we have employed the standard combination of 3D heteronuclear NMR techniques to obtain near complete assignments of proton, carbon and nitrogen resonances. Using a novel pulse sequence we were able to obtain additional assignments, in particular those of methyl groups in residues preceding proline within the sequence. From chemical shifts and on the basis of inter-residue NOEs, we have inferred the secondary structure and topology of monomeric β-LG A. It includes eight antiparallel β-strands arranged in a barrel, flanked by an α-helix, which is typical of a member of the lipocalin family. A detailed comparison with the crystal structure of the dimeric form (for a mixture of A and B variants) at pH 6.5 reveals a close resemblance in both secondary structure and overall topology. Both forms have a ninth β-strand which, at the higher pH, forms part of the dimer interface. These studies represent the first full NMR assignment of β-LG and will form the basis for a complete characterisation of the solution structure and dynamics of this protein and its variants

  12. Constituintes químicos de Ottonia corcovadensis Miq. da floresta Amazônica: atribuição dos deslocamentos químicos dos átomos de hidrogênio e carbono Chemical constituents of Ottonia corcovadensis Miq. from Amazon forest: ¹h and 13c chemical shift assignments

    Valdir A. Facundo

    2004-02-01

    Full Text Available In an ethanolic extract of leaves of Ottonia corcovadensis (Piperaceae were identified sixteen terpenoids of essential oil and the three flavonoids 3',4',5,5',7-pentamethoxyflavone (1, 3',4',5,7-tetramethoxyflavone (2 and 5-hydroxy-3',4',5',7-tetramethoxyflavone (3 and cafeic acid (4. Two amides (5 and 6 were isolated from an ethanolic extract of the roots. The structures were established by spectral analysis, meanly NMR (1D and 2D and mass spectra. Extensive NMR analysis was also used to complete ¹H and 13C chemical shift assignments of the flavonoids and amides. The components of the essential oil were identified by computer library search, retention indices and visual interpretation of mass spectra.

  13. Synthesis and GIAO NMR Calculations for Some Novel 4-Heteroarylidenamino-4,5-dihydro-1H-1,2,4-triazol-5-one Derivatives: Comparison of Theoretical and Experimental 1Hand 13C- Chemical Shifts

    Haci Baykara

    2005-08-01

    Full Text Available Abstract: 3-Alkyl(aryl-4-amino-4,5-dihydro-1H-1,2,4-triazol-5-ones (1 reacted with 5-methylfuran-2-carboxyaldehyde to afford the corresponding 3-alkyl(aryl-4-(5-methyl-2-furylmethylenamino-4,5-dihydro-1H-1,2,4-triazol-5-ones (2. Four newly synthesized compounds have been characterized by elemental analyses, IR, 1H-NMR, 13C-NMR and UV spectral data. In addition, isotropic 1H- and 13C-nuclear magnetic shielding constants of compounds 3 were calculated by employing the direct implementation of the gaugeincluding-atomic-orbital (GIAO method at the B3LYP density functional and HF levels of the theory. The geometry of each compound has been optimized using a 6-311G basis set. Nuclear shielding constants were also calculated by using 6-311G basis set. Theoretical values are compared to the experimental data.

  14. Relationship between 13C NMR Chemical Shifts of Alkanes and Ionicity Index and Polarizability Effect Index%离子性指数、极化效应指数与烷烃13C NMR化学位移的关系研究

    聂长明; 李忠海; 文松年

    2002-01-01

    定义了烷烃分子中碳原子的离子性指数(INI),用离子性指数(INI)、极化效应指数(PEI)及NiH(i=α,β,γ)结构信息参数研究了烷烃的13C NMR化学位移模型.结果表明,烷烃13C NMR化学位移(CS)可用下式来定量描述:CS=194.6156-37.7394(INI)+98.6505(ΣPEI)+27.1630(INI/ΣPEI)-652.910(ΣPEI/INI)+0.7735NαH+2.2468NβH-0.1742NγH用上式估算了304个碳原子的化学位移,平均绝对误差仅为0.77 δ,标准差0.9860δ,预测值与实验值非常吻合.

  15. Efficient Total Chemical Synthesis of (13) C=(18) O Isotopomers of Human Insulin for Isotope-Edited FTIR.

    Dhayalan, Balamurugan; Fitzpatrick, Ann; Mandal, Kalyaneswar; Whittaker, Jonathan; Weiss, Michael A; Tokmakoff, Andrei; Kent, Stephen B H

    2016-03-01

    Isotope-edited two-dimensional Fourier transform infrared spectroscopy (2 D FTIR) can potentially provide a unique probe of protein structure and dynamics. However, general methods for the site-specific incorporation of stable (13) C=(18) O labels into the polypeptide backbone of the protein molecule have not yet been established. Here we describe, as a prototype for the incorporation of specific arrays of isotope labels, the total chemical synthesis-via a key ester insulin intermediate-of 97 % enriched [(1-(13) C=(18) O)Phe(B24) ] human insulin: stable-isotope labeled at a single backbone amide carbonyl. The amino acid sequence as well as the positions of the disulfide bonds and the correctly folded structure were unambiguously confirmed by the X-ray crystal structure of the synthetic protein molecule. In vitro assays of the isotope labeled [(1-(13) C=(18) O)Phe(B24) ] human insulin showed that it had full insulin receptor binding activity. Linear and 2 D IR spectra revealed a distinct red-shifted amide I carbonyl band peak at 1595 cm(-1) resulting from the (1-(13) C=(18) O)Phe(B24) backbone label. This work illustrates the utility of chemical synthesis to enable the application of advanced physical methods for the elucidation of the molecular basis of protein function. PMID:26715336

  16. Benchmarks for the 13C NMR chemical shielding tensors in peptides in the solid state

    Czernek, Jiří; Pawlak, Tomasz; Potrzebowski, Marek J.

    2012-02-01

    The benchmark set is proposed, which comprises 126 principal elements of chemical shielding tensors, and the respective isotropic chemical shielding values, of all 42 13C nuclei in crystalline Tyr-D-Ala-Phe and Tyr-Ala-Phe tripeptides with known, but highly dissimilar structures. These data are obtained by both the NMR measurements and the density functional theory in the pseudopotential plane-wave scheme. Using the CASTEP program, several computational strategies are employed, for which the level of agreement between calculations and experiment is established. This set is mainly intended for the validation of methods capable of predicting the 13C NMR parameters in solid-state systems.

  17. Random coil chemical shift for intrinsically disordered proteins

    Kjærgaard, Magnus; Brander, Søren; Poulsen, Flemming Martin

    2011-01-01

    Secondary chemical shift analysis is the main NMR method for detection of transiently formed secondary structure in intrinsically disordered proteins. The quality of the secondary chemical shifts is dependent on an appropriate choice of random coil chemical shifts. We report random coil chemical....... Temperature has a non-negligible effect on the (13)C random coil chemical shifts, so temperature coefficients are reported for the random coil chemical shifts to allow extrapolation to other temperatures. The pH dependence of the histidine random coil chemical shifts is investigated in a titration series...

  18. Protein Chemical Shift Prediction

    Larsen, Anders S

    2014-01-01

    The protein chemical shifts holds a large amount of information about the 3-dimensional structure of the protein. A number of chemical shift predictors based on the relationship between structures resolved with X-ray crystallography and the corresponding experimental chemical shifts have been developed. These empirical predictors are very accurate on X-ray structures but tends to be insensitive to small structural changes. To overcome this limitation it has been suggested to make chemical shift predictors based on quantum mechanical(QM) calculations. In this thesis the development of the QM derived chemical shift predictor Procs14 is presented. Procs14 is based on 2.35 million density functional theory(DFT) calculations on tripeptides and contains corrections for hydrogen bonding, ring current and the effect of the previous and following residue. Procs14 is capable at performing predictions for the 13CA, 13CB, 13CO, 15NH, 1HN and 1HA backbone atoms. In order to benchmark Procs14, a number of QM NMR calculatio...

  19. Quantifying the chemical composition of soil organic carbon with solid-state 13C NMR

    Baldock, J. A.; Sanderman, J.

    2011-12-01

    The vulnerability of soil organic carbon (SOC) to biological decomposition and mineralisation to CO2 is defined at least partially by its chemical composition. Highly aromatic charcoal-like SOC components are more stable to biological decomposition than other forms of carbon including cellulose. Solid-state 13C NMR has gained wide acceptance as a method capable of defining SOC chemical composition and mathematical fitting processes have been developed to estimate biochemical composition. Obtaining accurate estimates depends on an ability to quantitatively detect all carbon present in a sample. Often little attention has been paid to defining the proportion of organic carbon present in a soil that is observable in solid-state 13C NMR analyses of soil samples. However, if such data is to be used to inform carbon cycling studies, it is critical that quantitative assessments of SOC observability be undertaken. For example, it is now well established that a significant discrimination exists against the detection of the low proton content polyaromatic structures typical of charcoal using cross polarisation 13C NMR analyses. Such discrimination does not exist where direct polarisation analyses are completed. In this study, the chemical composition of SOC as defined by cross polarisation and direct polarisation13C NMR analyses will be compared for Australian soils collected from under a diverse range of agricultural managements and climatic conditions. Results indicate that where significant charcoal C contents exist, it is highly under-represented in the acquired CP spectra. For some soils, a discrimination against alkyl carbon was also evident. The ability to derive correction factors to compensate for such discriminations will be assessed and presented.

  20. Characterising ontogenetic niche shifts in Nile crocodile using stable isotope (δ13C, δ15N) analyses of scute keratin.

    Radloff, Frans G T; Hobson, Keith A; Leslie, Alison J

    2012-09-01

    Nile crocodiles undergo a three to five order of magnitude increase in body size during their lifespan. This shift coincides with a change in resource and habitat use which influences the strength, type and symmetry of interactions with other species. Identifying size-specific crocodile groups displaying similar traits is important for conservation planning. Here, we illustrate how stable carbon (δ(13) C) and nitrogen (δ(15) N) isotope analysis of scute keratin, together with breakpoint modelling analysis can be used to characterise ontogenetic niche shifts. Using a sample set of 238 crocodiles from the Okavango Delta, Botswana (35-463 cm total length), we found prominent size-related changes in the scute keratin δ(13) C and δ(15) N profiles close to 40 and 119 cm snout-vent length. The first shift corroborated the findings of a traditional stomach-content study conducted on the same population at the same time, and the second conformed to known crocodile ecology. This approach can be used as a first approximation to identify size-specific groups within crocodile populations, and these can then be investigated further using isotopic or other methods. PMID:22462522

  1. Structure and dynamics of poly(ethylene- co-1,5-hexadiene) as studied by solid state 13C NMR and quantum chemical calculations

    Kurosu, Hiromichi; Yamamoto, Yuuri; Fujikawa, Aki; Kawabata, Emika; Sone, Masato; Naga, Naofumi

    2009-03-01

    Poly(ethylene- co-1,5-hexadiene) with 1,5-hexadiene (HD) contents of 1.8, 8.1, 9.7 and 20.3% was prepared by copolymerization of ethylene and HD involving intermolecular cyclization. Higher-order structures and dynamics of these samples were studied by solid state NMR and quantum chemistry. The 13C solid state NMR spectra and 13C spin-lattice relaxation time ( T1) of the samples were measured. The observed 13C CP/MAS and PST/MAS NMR spectra for all samples were decomposed into six peaks. The cyclopentane units incorporated in the main chain of polyethylene affected not only the crystalline structure but also the noncrystalline structure. This causes a trans-rich conformation in the noncrystalline region. Even in the melt-quenched samples, incorporation of the cyclopentane structure into the polyethylene chain suppresses the increase in the gauche structure in the noncrystalline region. Based on the 13C chemical shift of the methylene carbon, the low cyclopentane content sample assumes an orthorhombic crystal structure, and the high cyclopentane content samples assume a hexagonal-type chain packing. 13C spin-lattice relaxation times show that the crystalline region of the low cyclopentane content sample has two regions with different mobility, although the high cyclopentane content samples have only one region with a high mobility for each peak. Furthermore, quantum chemical calculations for the 13C NMR shieldings were carried out for precise assignment of the peaks.

  2. Retrospective characterization of ontogenetic shifts in killer whale diets via δ13C and δ15N analysis of teeth

    Newsome, Seth D.; Etnier, Michael A.; Monson, Daniel H.; Fogel, Marilyn L.

    2009-01-01

    Metabolically inert, accretionary structures such as the dentin growth layers in teeth provide a life history record of individual diet with near-annual resolution. We constructed ontogenetic ??13C and ??15N profiles by analyzing tooth dentin growth layers from 13 individual killer whales Orcinus orca collected in the eastern northeast Pacific Ocean between 1961 and 2003. The individuals sampled were 6 to 52 yr old, representing 2 ecotypes-resident and transient - collected across ???25?? of latitude. The average isotopic values of transient individuals (n = 10) are consistent with a reliance on mammalian prey, while the average isotopic values of residents (n = 3) are consistent with piscivory. Regardless of ecotype, most individuals show a decrease in ??15N values of ???2.5% through the first 3 yr of life, roughly equivalent to a decrease of one trophic level. We interpret this as evidence of gradual weaning, after which, ontogenetic shifts in isotopic values are highly variable. A few individuals (n = 2) maintained relatively stable ??15N and ??13C values throughout the remainder of their lives, whereas ??15N values of most (n = 11) increased by ???1.5%, suggestive of an ontogenetic increase in trophic level. Significant differences in mean ??13C and ??15N values among transients collected off California suggest that individuality in prey preferences may be prevalent within this ecotype. Our approach provides retrospective individual life history and dietary information that cannot be obtained through traditional field observations of free-ranging and elusive species such as killer whales, including unique historic ecological information that pre-dates modern studies. By providing insights into individual diet composition, stable isotope analysis of teeth and/or bones may be the only means of evaluating a number of hypothesized historical dietary shifts in killer whales of the northeast Pacific Ocean. ?? Inter-Research 2009.

  3. Application of 13C NMR spectroscopy to characterize organic chemical components of decomposing coarse woody debris from different climatic regions

    Takuya Hishinuma

    2015-04-01

    Full Text Available Solid-state 13C nuclear magnetic resonance (NMR spectroscopy was applied to coarse woody debris (CWD in different stages of decomposition and collected from forest floor of a subtropical, a cool temperate, and a subalpine forest in Japan. The purpose was to test its applicability to characterize organic chemical composition of CWD of broad-leaved and coniferous trees from different climatic conditions. O-alkyl-C, mainly representing carbohydrates, was the predominant component of CWD at the three sites, accounting for 43.5-58.1% of the NMR spectra. Generally, the relative area under the signals for aromatic-C and phenolic-C, mainly representing lignin, increased, whereas the relative area for O-alkyl-C decreased, as the decay class advanced. The relative area under NMR chemical shift regions was significantly correlated with the chemical properties examined with proximate analyses. That is, O-alkyl-C and di-O-alkyl-C NMR signal areas were positively correlated with the volumetric density of CWD and the content of total carbohydrates. Methoxyl-C, aromatic-C, phenolic-C, carboxyl-C, and carbonyl-C were positively correlated with the contents of acid-unhydrolyzable residues (lignin, tannins, and cutin and nitrogen. Lignin-C calculated from NMR signals increased, and polysaccharide-C decreased, with the decay class of CWD at the three study sites. A review of previous studies on 13C NMR spectroscopy for decomposing CWD suggested further needs of its application to broad-leaved trees from tropical and subtropical regions.

  4. {sup 13}C structuring shifts for the analysis of model {beta}-hairpins and {beta}-sheets in proteins: diagnostic shifts appear only at the cross-strand H-bonded residues

    Shu, Irene; Scian, Michele; Stewart, James M.; Kier, Brandon L.; Andersen, Niels H., E-mail: andersen@chem.washington.edu [University of Washington, Department of Chemistry (United States)

    2013-08-15

    The present studies have shown that {sup 13}C=O, {sup 13}C{sup {alpha}} and {sup 13}C{sup {beta}} of H-bonded strand residues in {beta}-hairpins provide additional probes for quantitating the extent of folding in {beta}-hairpins and other {beta}-sheet models. Large differences in the structuring shifts (CSDs) of these {sup 13}C sites in H-bonded versus non-H-bonded sites are observed: the differences between H-bonded and non-H-bonded sites are greater than 1.2 ppm for all three {sup 13}C probes. This prompts us to suggest that efforts to determine the extent of hairpin folding from {sup 13}C shifts should be based exclusively on the observation at the cross-strand H-bonded sites. Furthermore, the statistics suggest the {sup 13}C Prime and {sup 13}C{sup {beta}}CSDs will provide the best differentiation with 100 %-folded CSD values approaching -2.6 and +3 ppm, respectively, for the H-bonded sites. These conclusions can be extended to edge-strands of protein {beta}-sheets. Our survey of reported {sup 13}C shifts in {beta}-proteins indicates that some of the currently employed random coil values need to be adjusted, particularly for ionization-induced effects.

  5. Changes in chemical composition of litter during decomposition: a review of published 13C NMR spectra

    Cepáková, Šárka; Frouz, Jan

    2015-01-01

    Roč. 15, č. 3 (2015), s. 805-815. ISSN 0718-9516 Grant ostatní: GAJU(CZ) GAJU/04-146/2013P; GA ČR(CZ) GAP504/12/1288 Institutional support: RVO:60077344 Keywords : 13C CPMAS NMR * litter decomposition * litter quality * soil organic matter Subject RIV: DF - Soil Science Impact factor: 0.680, year: 2014

  6. Applications of the 18O-isotope shift on 13C and 15N nuclear magnetic resonance spectroscopy to the study of bioorganic reaction mechanisms

    The study of reactions involving the formation and cleavage of carbon-oxygen or nitrogen-oxygen bonds has been significantly aided by recent demonstrations of the generality and characteristics of the 18O-isotope shift in 13C and 15N nuclear magnetic resonance spectroscopy. In many instances, the magnitudes of the 18O-induced isotopic shifts are sufficiently large as to permit the use of even modest NMR instrumentation and natural abundance 13C. Studies involving less soluble compounds, higher molecular weight materials or relatively rapid reactions may often be carried out using 13C enrichment. Because NMR spectroscopy is non-destructive, it has proven to be extremely useful in the study of natural product biosynthetic pathways. Another area where important applications are being made is in the study of enzymatic and non-enzymatic reaction mechanisms. The characteristics of the 18O isotope shift in 13C NMR spectroscopy are reviewed. Several examples from the work of other groups in the area of natural product biosynthesis are briefly mentioned. This is followed by a number of illustrative applications in the area of bioorganic and enzymatic reaction mechanism that have been examined in our laboratory. The enzymatic examples include acid phosphatases, epoxide hydratase, acetylcholinesterase and asparaginase. 20 refs.; 1 figure

  7. Galactic Chemical Evolution and solar s-process abundances: dependence on the 13C-pocket structure

    Bisterzo, S; Gallino, R; Wiescher, M; Käppeler, F

    2014-01-01

    We study the s-process abundances (A > 90) at the epoch of the solar-system formation. AGB yields are computed with an updated neutron capture network and updated initial solar abundances. We confirm our previous results obtained with a Galactic Chemical Evolution (GCE) model: (i) as suggested by the s-process spread observed in disk stars and in presolar meteoritic SiC grains, a weighted average of s-process strengths is needed to reproduce the solar s-distribution of isotopes with A > 130; (ii) an additional contribution (of about 25%) is required in order to represent the solar s-process abundances of isotopes from A = 90 to 130. Furthermore, we investigate the effect of different internal structures of the 13C-pocket, which may affect the efficiency of the 13C(a, n)16O reaction, the major neutron source of the s-process. First, keeping the same 13C profile adopted so far, we modify by a factor of two the mass involved in the pocket; second, we assume a flat 13C profile in the pocket, and we test again the...

  8. 13C-NMR of diterpenes with pimarane skeleton

    The effect of substituent groups on the chemical shift of carbons using nuclear magnetic resonance spectra of carbon 13 (13C-NMR) is discussed. Diterpenes having pimarane skeleton, isolated from plants of Velloziaceae family are analysed. (ARHC)

  9. 13C structuring shifts for the analysis of model β-hairpins and β-sheets in proteins: diagnostic shifts appear only at the cross-strand H-bonded residues

    The present studies have shown that 13C=O, 13Cα and 13Cβ of H-bonded strand residues in β-hairpins provide additional probes for quantitating the extent of folding in β-hairpins and other β-sheet models. Large differences in the structuring shifts (CSDs) of these 13C sites in H-bonded versus non-H-bonded sites are observed: the differences between H-bonded and non-H-bonded sites are greater than 1.2 ppm for all three 13C probes. This prompts us to suggest that efforts to determine the extent of hairpin folding from 13C shifts should be based exclusively on the observation at the cross-strand H-bonded sites. Furthermore, the statistics suggest the 13C′ and 13CβCSDs will provide the best differentiation with 100 %-folded CSD values approaching −2.6 and +3 ppm, respectively, for the H-bonded sites. These conclusions can be extended to edge-strands of protein β-sheets. Our survey of reported 13C shifts in β-proteins indicates that some of the currently employed random coil values need to be adjusted, particularly for ionization-induced effects

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

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

  11. Primidone - An antiepileptic drug - characterisation by quantum chemical and spectroscopic (FTIR, FT-Raman, 1H, 13C NMR and UV-Visible) investigations

    Arjunan, V.; Santhanam, R.; Subramanian, S.; Mohan, S.

    2013-05-01

    The solid phase FTIR and FT-Raman spectra of primidone were recorded in the regions 4000-400 cm-1 and 4000-100 cm-1, respectively. The vibrational spectra were analysed and the observed fundamentals were assigned and analysed. The experimental wavenumbers were compared with the theoretical scaled vibrational wavenumbers determined by DFT methods. The Raman intensities were also determined with B3LYP/6-31G(d,p) method. The total electron density and molecular electrostatic potential surface of the molecule were constructed by using B3LYP/6-311++G(d,p) method to display electrostatic potential (electron + nuclei) distribution. The HOMO and LUMO energies were measured. Natural bond orbital analysis of primidone has been performed to indicate the presence of intramolecular charge transfer. The 1H and 13C NMR spectra were recorded and the chemical shifts of the molecule were calculated.

  12. Diazanaphthalenes: A 13C NMR investigation on the site of protonation and pKa values

    Weijer, van de Peter; Thijsse, Hans; Meer, van der Douwe

    1976-01-01

    The pH dependence of the 13C chemical shifts (δ) of the diazanaphthalenes has been recorded. From this dependence the pKa values have been determined using the Henderson-Hasselbach equation. The change in 13C chemical shifts under the influence of nitrogen protonation (Δδ) has been predicted using t

  13. Synthesis of [5,6-13C2, 1-14C]olivetolic acid, methyl [1'-13C]olivetolate and [5,6-13C2, 1-14C]cannabigerolic acid

    Potential advanced intermediates in the biosynthesis of delta9-tetrahydrocannabinol, the major psychoactive principle of marijuana, have been synthesized labeled with two contiguous 13C atoms and 14C. Methyl [5,6-13C2, 1-14C]olivetolate was prepared from lithium [13C2]acetylide and dimethyl [2-14C]malonate. Reaction with geranyl bromide afforded methyl [5,6-13C2, 1-14C]cannabigerolate, and hydrolysis of these methyl esters with lithium propyl mercaptide yielded the corresponding labeled acids. The 13C-13C couplings observable in the 13C NMR spectra of these 13C-enriched compounds and their synthetic precursors are recorded. Methyl [1'-14C]olivetolate was prepared from 13CO2 to confirm assignments of the 13C chemical shifts in the pentyl side chain of these compounds. (author)

  14. Counterion influence on chemical shifts in strychnine salts

    Metaxas, Athena E.; Cort, John R.

    2013-05-01

    The highly toxic plant alkaloid strychnine is often isolated in the form of the anion salt of its protonated tertiary amine. Here we characterize the relative influence of different counterions on 1H and 13C chemical shifts in several strychnine salts in D2O, methanol-d4 (CD3OD) and chloroform-d (CDCl3) solvents. In organic solvents, but not in water, substantial variation in chemical shifts of protons near the tertiary amine was observed among different salts. These secondary shifts reveal differences in the way each anion influences electronic structure within the protonated amine. The distributions of secondary shifts allow salts to be easily distinguished from each other as well as from the free base form. The observed effects are much greater in organic solvents than in water. Slight concentration-dependence in chemical shifts of some protons near the amine was observed for two salts in CDCl3, but this effect is small compared to the influence of the counterion. Distinct chemical shifts in different salt forms of the same compound may be useful as chemical forensic signatures for source attribution and sample matching of alkaloids such as strychnine and possibly other organic acid and base salts.

  15. Counterion influence on chemical shifts in strychnine salts.

    Metaxas, Athena E; Cort, John R

    2013-05-01

    The highly toxic plant alkaloid strychnine is often isolated in the form of the anion salt of its protonated tertiary amine. Here, we characterize the relative influence of different counterions on (1)H and (13)C chemical shifts in several strychnine salts in D2O, methanol-d4 (CD3OD), and chloroform-d (CDCl3) solvents. In organic solvents but not in water, substantial variation in chemical shifts of protons near the tertiary amine was observed among different salts. These secondary shifts reveal differences in the way each anion influences electronic structure within the protonated amine. The distributions of secondary shifts allow salts to be easily distinguished from each other as well as from the free base form. Slight concentration dependence in chemical shifts of some protons near the amine was observed for two salts in CDCl3, but this effect is small compared with the influence of the counterion. Distinct chemical shifts in different salt forms of the same compound may be useful as chemical forensic signatures for source attribution and sample matching of alkaloids such as strychnine and possibly other organic acid and base salts. PMID:23495106

  16. A Short History of Three Chemical Shifts

    Nagaoka, Shin-ichi

    2007-01-01

    A short history of chemical shifts in nuclear magnetic resonance (NMR), electron spectroscopy for chemical analysis (ESCA) and Mossbauer spectroscopy, which are useful for chemical studies, is described. The term chemical shift is shown to have originated in the mistaken assumption that nuclei of a given element would all undergo resonance at the…

  17. Applications of Chemical Shift Imaging to Marine Sciences

    Haakil Lee

    2010-08-01

    Full Text Available The successful applications of magnetic resonance imaging (MRI in medicine are mostly due to the non-invasive and non-destructive nature of MRI techniques. Longitudinal studies of humans and animals are easily accomplished, taking advantage of the fact that MRI does not use harmful radiation that would be needed for plain film radiographic, computerized tomography (CT or positron emission (PET scans. Routine anatomic and functional studies using the strong signal from the most abundant magnetic nucleus, the proton, can also provide metabolic information when combined with in vivo magnetic resonance spectroscopy (MRS. MRS can be performed using either protons or hetero-nuclei (meaning any magnetic nuclei other than protons or 1H including carbon (13C or phosphorus (31P. In vivo MR spectra can be obtained from single region ofinterest (ROI or voxel or multiple ROIs simultaneously using the technique typically called chemical shift imaging (CSI. Here we report applications of CSI to marine samples and describe a technique to study in vivo glycine metabolism in oysters using 13C MRS 12 h after immersion in a sea water chamber dosed with [2-13C]-glycine. This is the first report of 13C CSI in a marine organism.

  18. Soil organic degradation: bridging the gap between Rock-Eval pyrolysis and chemical characterization (CPMAS 13C NMR)

    Albrecht, Remy; Sebag, David; Verrecchia, Eric

    2013-04-01

    Being a source of mineral nutrients, organic matter contributes to soil chemical fertility and acts on soil physical fertility through its role in soil structure. Soil organic matter (SOM) is a key component of soils. Despite the paramount importance of SOM, information on its chemistry and behaviour in soils is incomplete. Numerous methods are used to characterize and monitor OM dynamics in soils using different approaches (Kogel-Knabner, 2000). Two of the main approaches are evaluated and compared in this study. Rock-Eval pyrolysis (RE pyrolysis) provides a description of a SOM's general evolution using its thermal resistance. The second tool (13C CPMAS NMR) aims to give precise and accurate chemical information on OM characterization. The RE pyrolysis technique was designed for petroleum exploration (Lafargue et al., 1998) and because of its simplicity, it has been applied to a variety of other materials such as soils or Recent sediments (Disnar et al., 2000; Sebag, 2006). Recently, RE pyrolysis became a conventional tool to study OM dynamics in soils. In RE pyrolysis, a peak deconvolution is applied to the pyrolysis signal in order to get four main components related to major classes of organic constituents. These components differ in origin and resistance to pyrolysis: labile biological constituents (F1), resistant biological constituents (F2), immature non-biotic constituents (F3) and a mature refractory fraction (F4) (Sebag, 2006; Coppard, 2006). Main advantages of the technique are its repeatability, and rapidity to provide an overview of OM properties and stocks. However, do the four major classes used in the literature reflect a pertinent chemical counterpart? To answer this question, we used 13C Nuclear Magnetic Resonance Spectroscopy in the solid state (13C CPMAS NMR) to collect direct information on structural and conformational characteristics of OM. NMR resonances were assigned to chemical structures according to five dominant forms: alkyl C, O

  19. Chemical Synthesis of Deoxynivalenol-3-β-d-[13C6]-glucoside and Application in Stable Isotope Dilution Assays

    Katharina Habler

    2016-06-01

    Full Text Available Modified mycotoxins have been gaining importance in recent years and present a certain challenge in LC-MS/MS analysis. Due to the previous lack of a labeled isotopologue of the modified mycotoxin deoxynivalenol-3-glucoside, in our study we synthesized the first 13C-labeled internal standard. Therefore, we used the Königs-Knorr method to synthesize deoxynivalenol-3-β-d-[13C6]-glucoside originated from unlabeled deoxynivalenol and [13C6]-labeled glucose. Using the synthesized isotopically-labeled standard deoxynivalenol-3-β-d-[13C6]-glucoside and the purchased labeled standard [13C15]-deoxynivalenol, a stable isotope dilution LC-MS/MS method was firstly developed for deoxynivalenol-3-glucoside and deoxynivalenol in beer. The preparation and purification of beer samples was based on a solid phase extraction. The validation data of the newly developed method gave satisfying results. Intra- and interday precision studies revealed relative standard deviations below 0.5% and 7%, respectively. The recoveries ranged for both analytes between 97% and 112%. The stable isotope dilution assay was applied to various beer samples from four different countries. In summary, deoxynivalenol-3-glucoside and deoxynivalenol mostly appeared together in varying molar ratios but were quantified in rather low contents in the investigated beers.

  20. SPARTA+: a modest improvement in empirical NMR chemical shift prediction by means of an artificial neural network

    Shen Yang; Bax, Ad, E-mail: bax@nih.go [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States)

    2010-09-15

    NMR chemical shifts provide important local structural information for proteins and are key in recently described protein structure generation protocols. We describe a new chemical shift prediction program, SPARTA+, which is based on artificial neural networking. The neural network is trained on a large carefully pruned database, containing 580 proteins for which high-resolution X-ray structures and nearly complete backbone and {sup 13}C{sup {beta}} chemical shifts are available. The neural network is trained to establish quantitative relations between chemical shifts and protein structures, including backbone and side-chain conformation, H-bonding, electric fields and ring-current effects. The trained neural network yields rapid chemical shift prediction for backbone and {sup 13}C{sup {beta}} atoms, with standard deviations of 2.45, 1.09, 0.94, 1.14, 0.25 and 0.49 ppm for {delta}{sup 15}N, {delta}{sup 13}C', {delta}{sup 13}C{sup {alpha}}, {delta}{sup 13}C{sup {beta}}, {delta}{sup 1}H{sup {alpha}} and {delta}{sup 1}H{sup N}, respectively, between the SPARTA+ predicted and experimental shifts for a set of eleven validation proteins. These results represent a modest but consistent improvement (2-10%) over the best programs available to date, and appear to be approaching the limit at which empirical approaches can predict chemical shifts.

  1. Comprehensive quantum chemical and spectroscopic (FTIR, FT-Raman, 1H, 13C NMR) investigations of O-desmethyltramadol hydrochloride an active metabolite in tramadol - An analgesic drug

    Arjunan, V.; Santhanam, R.; Marchewka, M. K.; Mohan, S.

    2014-03-01

    O-desmethyltramadol is one of the main metabolites of tramadol widely used clinically and has analgesic activity. The FTIR and FT-Raman spectra of O-desmethyl tramadol hydrochloride are recorded in the solid phase in the regions 4000-400 cm-1 and 4000-100 cm-1, respectively. The observed fundamentals are assigned to different normal modes of vibration. Theoretical studies have been performed as its hydrochloride salt. The structure of the compound has been optimised with B3LYP method using 6-31G** and cc-pVDZ basis sets. The optimised bond length and bond angles are correlated with the X-ray data. The experimental wavenumbers were compared with the scaled vibrational frequencies determined by DFT methods. The IR and Raman intensities are determined with B3LYP method using cc-pVDZ and 6-31G(d,p) basic sets. The total electron density and molecular electrostatic potential surfaces of the molecule are constructed by using B3LYP/cc-pVDZ method to display electrostatic potential (electron + nuclei) distribution. The electronic properties HOMO and LUMO energies were measured. Natural bond orbital analysis of O-desmethyltramadol hydrochloride has been performed to indicate the presence of intramolecular charge transfer. The 1H and 13C NMR chemical shifts of the molecule have been anlysed.

  2. Sc3CH@C80: selective (13)C enrichment of the central carbon atom.

    Junghans, Katrin; Rosenkranz, Marco; Popov, Alexey A

    2016-05-01

    Sc3CH@C80 is synthesized and characterized by (1)H, (13)C, and (45)Sc NMR. A large negative chemical shift of the proton, -11.73 ppm in the Ih and -8.79 ppm in the D5h C80 cage isomers, is found. (13)C satellites in the (1)H NMR spectrum enabled indirect determination of the (13)C chemical shift for the central carbon at 173 ± 1 ppm. Intensity of the satellites allowed determination of the (13)C content for the central carbon atom. This unique possibility is applied to analyze the cluster/cage (13)C distribution in mechanistic studies employing either (13)CH4 or (13)C powder to enrich Sc3CH@C80 with (13)C. PMID:27109443

  3. Prediction of hydrogen and carbon chemical shifts from RNA using database mining and support vector regression

    The Biological Magnetic Resonance Data Bank (BMRB) contains NMR chemical shift depositions for over 200 RNAs and RNA-containing complexes. We have analyzed the 1H NMR and 13C chemical shifts reported for non-exchangeable protons of 187 of these RNAs. Software was developed that downloads BMRB datasets and corresponding PDB structure files, and then generates residue-specific attributes based on the calculated secondary structure. Attributes represent properties present in each sequential stretch of five adjacent residues and include variables such as nucleotide type, base-pair presence and type, and tetraloop types. Attributes and 1H and 13C NMR chemical shifts of the central nucleotide are then used as input to train a predictive model using support vector regression. These models can then be used to predict shifts for new sequences. The new software tools, available as stand-alone scripts or integrated into the NMR visualization and analysis program NMRViewJ, should facilitate NMR assignment and/or validation of RNA 1H and 13C chemical shifts. In addition, our findings enabled the re-calibration a ring-current shift model using published NMR chemical shifts and high-resolution X-ray structural data as guides

  4. Prediction of hydrogen and carbon chemical shifts from RNA using database mining and support vector regression.

    Brown, Joshua D; Summers, Michael F; Johnson, Bruce A

    2015-09-01

    The Biological Magnetic Resonance Data Bank (BMRB) contains NMR chemical shift depositions for over 200 RNAs and RNA-containing complexes. We have analyzed the (1)H NMR and (13)C chemical shifts reported for non-exchangeable protons of 187 of these RNAs. Software was developed that downloads BMRB datasets and corresponding PDB structure files, and then generates residue-specific attributes based on the calculated secondary structure. Attributes represent properties present in each sequential stretch of five adjacent residues and include variables such as nucleotide type, base-pair presence and type, and tetraloop types. Attributes and (1)H and (13)C NMR chemical shifts of the central nucleotide are then used as input to train a predictive model using support vector regression. These models can then be used to predict shifts for new sequences. The new software tools, available as stand-alone scripts or integrated into the NMR visualization and analysis program NMRViewJ, should facilitate NMR assignment and/or validation of RNA (1)H and (13)C chemical shifts. In addition, our findings enabled the re-calibration a ring-current shift model using published NMR chemical shifts and high-resolution X-ray structural data as guides. PMID:26141454

  5. Prediction of hydrogen and carbon chemical shifts from RNA using database mining and support vector regression

    Brown, Joshua D.; Summers, Michael F. [University of Maryland Baltimore County, Howard Hughes Medical Institute (United States); Johnson, Bruce A., E-mail: bruce.johnson@asrc.cuny.edu [University of Maryland Baltimore County, Department of Chemistry and Biochemistry (United States)

    2015-09-15

    The Biological Magnetic Resonance Data Bank (BMRB) contains NMR chemical shift depositions for over 200 RNAs and RNA-containing complexes. We have analyzed the {sup 1}H NMR and {sup 13}C chemical shifts reported for non-exchangeable protons of 187 of these RNAs. Software was developed that downloads BMRB datasets and corresponding PDB structure files, and then generates residue-specific attributes based on the calculated secondary structure. Attributes represent properties present in each sequential stretch of five adjacent residues and include variables such as nucleotide type, base-pair presence and type, and tetraloop types. Attributes and {sup 1}H and {sup 13}C NMR chemical shifts of the central nucleotide are then used as input to train a predictive model using support vector regression. These models can then be used to predict shifts for new sequences. The new software tools, available as stand-alone scripts or integrated into the NMR visualization and analysis program NMRViewJ, should facilitate NMR assignment and/or validation of RNA {sup 1}H and {sup 13}C chemical shifts. In addition, our findings enabled the re-calibration a ring-current shift model using published NMR chemical shifts and high-resolution X-ray structural data as guides.

  6. Geometric effects on carbon-13 chemical shifts

    In the course of our investigations on carbon-13 chemical shifts of tetracyclic dodecanes, we managed to show that a large number of chemical shift differences between members of the series and models provided by bicyclic analogs could be attributed to steric effects. There are examples, however, where this is clearly not the case. In order to investigate apparent anomalies we calculated structures of interest and looked into the relationships between molecular geometry and chemical shifts. As the assignment of some of the key structures in these analysis were made by comparison with model compounds and crucial experiments that could remove ambiguities were missing, we prepared and interpreted two spectra which are presented

  7. MR chemical shift imaging of human atheroma

    The lipid content of atheromatous plaques has been measured with chemical shift MR imaging by taking advantage of the different resonance frequencies of protons in lipid and water. Fifteen postmortem aortic specimens of the human descending aorta and the aortae of seven patients with documented peripheral vascular disease were studied at 0.5 T. Spin-echo images were used to localize the lesions before acquisition of the chemical shift images. The specimens were examined histologically, and the lipid distribution in the plaque showed good correlation with the chemical shift data. Validation in vivo and clinical applications remain to be established

  8. Four-dimensional 13C/13C-edited nuclear Overhauser Enhancement Spectroscopy of a protein in solution: Application to interleukin 1β

    A four-dimensional 13C/13C-edited NOESY experiment is described which dramatically improves the resolution of protein NMR spectra and enables the straightforward assignment of nuclear Overhauser effects involving aliphatic and/or aromatic protons in larger proteins. The experiment is demonstrated for uniformly (>95%) 13C-labeled interleukin 1β, a protein of 153 residues and 17.4 kDa, which plays a key role in the immune response. NOEs between aliphatic and/or aromatic protons are first spread out into a third dimension by the 13C chemical shift of the carbon atom attached to the originating proton and subsequently into a fourth dimension by the 13C chemical shift of the carbon atom attached to the destination proton. Thus, each NOE cross peak is labeled by four chemical shifts. By this means, ambiguities in the assignment of NOEs that arise from chemical shift overlap and degeneracy are completely removed. Further, NOEs between protons with the same chemical shifts can readily be detected providing their attached carbon atoms have different 13C chemical shifts. The design of the pulse sequence requires special care to minimize the level of artifacts arising from undesired coherence transfer pathways, and in particular those associated with diagonal peaks which correspond to magnetization that has not been transferred from one proton to another. The 4D 13C/13C-edited NOESY experiment is characterized by high sensitivity as the through-bond transfer steps involve the large 1JCH (130 Hz) couplings, and it is possible to obtain high-quality spectra on 1-2 mM samples of 13C-labeled protein in as little as 3 days. This experiment should open up the application of protein structure determination by NMR to a large number of medium-sized proteins (150-300 residues) of biological interest

  9. Determination of refractory organic matter in marine sediments by chemical oxidation, analytical pyrolysis and solid-state 13C nuclear magnetic resonance spectroscopy

    Rosa Arranz, José M. de la; González-Pérez, José Antonio; Hatcher, Patrick G; Knicker, Heike; González-Vila, Francisco Javier

    2008-01-01

    Seeking to quantify the amount of refractory organic matter (ROM), which includes black carbon-like material (BC), in marine sediments, we have applied a two-step procedure that consists of a chemical oxidation with sodium chlorite of the demineralized sediments followed by integration of the aromatic C region in the remaining residues by solid-state 13C nuclear magnetic resonance (NMR) spectroscopy. The efficacy for lignin removal was tested by analytical pyrolysis in the presence of tetrame...

  10. A simple graphical approach to predict local residue conformation using NMR chemical shifts and density functional theory.

    Shaghaghi, Hoora; Ebrahimi, Hossein Pasha; Fathi, Fariba; Bahrami Panah, Niloufar; Jalali-Heravi, Mehdi; Tafazzoli, Mohsen

    2016-05-30

    The dependency of amino acid chemical shifts on φ and ψ torsion angle is, independently, studied using a five-residue fragment of ubiquitin and ONIOM(DFT:HF) approach. The variation of absolute deviation of (13) C(α) chemical shifts relative to φ dihedral angle is specifically dependent on secondary structure of protein not on amino acid type and fragment sequence. This dependency is observed neither on any of (13) C(β) , and (1) H(α) chemical shifts nor on the variation of absolute deviation of (13) C(α) chemical shifts relative to ψ dihedral angle. The (13) C(α) absolute deviation chemical shifts (ADCC) plots are found as a suitable and simple tool to predict secondary structure of protein with no requirement of highly accurate calculations, priori knowledge of protein structure and structural refinement. Comparison of Full-DFT and ONIOM(DFT:HF) approaches illustrates that the trend of (13) C(α) ADCC plots are independent of computational method but not of basis set valence shell type. © 2016 Wiley Periodicals, Inc. PMID:26940760

  11. /sup 13/C-NMR of diterpenes with rosane skeleton

    da Cunha Pinto, A.; Garcez, W.S.; Ficara, M.L.G.; Vasconcelos, T.C.; Pereira, A.L.; Gomes, L.N.L.F.; Frechiani, M.doC.; Patitucci, M.L. (Rio de Janeiro Univ. (Brazil). Nucleo de Pesquisas de Produtos Naturais)

    1982-03-01

    /sup 13/C-NMR data of three diterpenoids with rosane skeleton isolated from Vellozia candida Mikan, and of their oxidated and acetylated derivatives are presented. The main effects caused by small structural differences are discussed and used in the assignment of the chemical shifts of all carbons.

  12. 13C NMR of diterpenes with isopimarane structure

    Several effects of the Δ sup(8(9)) double bond on the 13C NMR data of isopimarane diterpenoids are discussed, including chemical shifts and acetilation of the C-7 Hydroxyl radical on the above mentioned double bond. (C.L.B.)

  13. 13C nuclear magnetic resonance study of the complexation of calcium by taurine

    13C Nuclear magnetic resonance chemical shifts, 1J/sub c-c/ scalar coupling constants, spin-lattice relaxation times, and nuclear Overhauser effects were determined for taurine-[1, 2 13C] and a taurine-[1 13C] and taurine-[2 13C] mixture in the presence and absence of calcium. Comparison of taurine titration shifts to values for related compounds reveals some unusual electronic properties of the taurine molecule. Stability constants of 1:1 calcium complexes with taurine zwitterions and anions, as well as their 13C chemical shifts, were obtained by least squares analysis of titration curves measured in the presence of calcium. The stability constants of calcium-taurine complexes were significantly lower than previous values and led to estimates that only approximately one percent of intracellular calcium of mammalian myocardial cells would exist in a taurine complex

  14. Synchronous negative carbon isotope shifts in marine and terrestrial biomarkers at the onset of the early Aptian oceanic anoxic event 1a: Evidence for the release of 13C-depleted carbon into the atmosphere

    van Breugel, Yvonne; Schouten, Stefan; Tsikos, Harilaos; Erba, Elisabetta; Price, Gregory D.; Sinninghe Damsté, Jaap S.

    2007-03-01

    A common feature of records of the early Aptian oceanic anoxic event (OAE) 1a is the sharp negative δ13C excursion displayed in both carbonate and organic matter at the onset of this event. A synchronous negative δ13C excursion has also been noted for terrestrial organic matter. This negative excursion has been attributed to either an injection of 13C-depleted light carbon into the atmosphere or, in case of marine sediments, recycling of 13C-depleted CO2. However, most studies were done on separate cores, and no information on the relative timing of the negative spikes in terrestrial versus marine records has been obtained. Here we examine early Aptian core sections from two geographically distal sites (Italy and the mid-Pacific) to elucidate the causes and relative timing of this negative "spike." At both sites, increased organic carbon (Corg) and decreased bulk carbonate contents characterize the interval recording OAE 1a (variously referred to as the "Selli event"). The organic material within the "Selli level" is immature and of autochthonous origin. Measured δ13C values of marine and terrestrial biomarkers largely covary with those of bulk organic carbon, with lowest values recorded at the base of the organic-rich section. By contrast, sediments enveloping the "Selli level" exhibit very low Corg contents, and their extractable Corg is predominantly of allochthonous origin. Hydrous pyrolysis techniques used to obtain an autochthonous, pre-Selli δ13C value for algal-derived pristane from corresponding sample material yielded a negative δ13C shift of up to 4‰. A negative δ13C shift of similar magnitude was also measured for the terrigenous n-alkanes. The results are collectively best explained by means of a massive, syndepositional, rapid input of 13C-depleted carbon into the atmosphere and surface oceans, likely delivered either via methane produced from the dissociation of sedimentary clathrates or perhaps by widespread thermal metamorphism of Corg

  15. Conformationally selective multidimensional chemical shift ranges in proteins from a PACSY database purged using intrinsic quality criteria.

    Fritzsching, Keith J; Hong, Mei; Schmidt-Rohr, Klaus

    2016-02-01

    We have determined refined multidimensional chemical shift ranges for intra-residue correlations ((13)C-(13)C, (15)N-(13)C, etc.) in proteins, which can be used to gain type-assignment and/or secondary-structure information from experimental NMR spectra. The chemical-shift ranges are the result of a statistical analysis of the PACSY database of >3000 proteins with 3D structures (1,200,207 (13)C chemical shifts and >3 million chemical shifts in total); these data were originally derived from the Biological Magnetic Resonance Data Bank. Using relatively simple non-parametric statistics to find peak maxima in the distributions of helix, sheet, coil and turn chemical shifts, and without the use of limited "hand-picked" data sets, we show that ~94% of the (13)C NMR data and almost all (15)N data are quite accurately referenced and assigned, with smaller standard deviations (0.2 and 0.8 ppm, respectively) than recognized previously. On the other hand, approximately 6% of the (13)C chemical shift data in the PACSY database are shown to be clearly misreferenced, mostly by ca. -2.4 ppm. The removal of the misreferenced data and other outliers by this purging by intrinsic quality criteria (PIQC) allows for reliable identification of secondary maxima in the two-dimensional chemical-shift distributions already pre-separated by secondary structure. We demonstrate that some of these correspond to specific regions in the Ramachandran plot, including left-handed helix dihedral angles, reflect unusual hydrogen bonding, or are due to the influence of a following proline residue. With appropriate smoothing, significantly more tightly defined chemical shift ranges are obtained for each amino acid type in the different secondary structures. These chemical shift ranges, which may be defined at any statistical threshold, can be used for amino-acid type assignment and secondary-structure analysis of chemical shifts from intra-residue cross peaks by inspection or by using a provided

  16. RefDB: A database of uniformly referenced protein chemical shifts

    RefDB is a secondary database of reference-corrected protein chemical shifts derived from the BioMagResBank (BMRB). The database was assembled by using a recently developed program (SHIFTX) to predict protein 1H, 13C and 15N chemical shifts from X-ray or NMR coordinate data of previously assigned proteins. The predicted shifts were then compared with the corresponding observed shifts and a variety of statistical evaluations performed. In this way, potential mis-assignments, typographical errors and chemical referencing errors could be identified and, in many cases, corrected. This approach allows for an unbiased, instrument-independent solution to the problem of retrospectively re-referencing published protein chemical shifts. Results from this study indicate that nearly 25% of BMRB entries with 13C protein assignments and 27% of BMRB entries with 15N protein assignments required significant chemical shift reference readjustments. Additionally, nearly 40% of protein entries deposited in the BioMagResBank appear to have at least one assignment error. From this study it evident that protein NMR spectroscopists are increasingly adhering to recommended IUPAC 13C and 15N chemical shift referencing conventions, however, approximately 20% of newly deposited protein entries in the BMRB are still being incorrectly referenced. This is cause for some concern. However, the utilization of RefDB and its companion programs may help mitigate this ongoing problem. RefDB is updated weekly and the database, along with its associated software, is freely available at http://redpoll.pharmacy.ualberta.ca and the BMRB website

  17. The study of a monocotyledon abscission zone using microscopic, chemical, enzymatic and solid state 13C CP/MAS NMR analyses.

    Henderson, J; Davies, H A; Heyes, S J; Osborne, D J

    2001-01-01

    We have investigated distinguishing features in cells of the abscission zone of a monocotyledon fruit, the oil palm Elaeis guineensis. The cell walls of the abscission zone and the subtending mesocarp and pedicel have been analysed by light and transmission electron microscopy, by chemical methods and by solid state 13C CP/MAS NMR spectroscopy. Results show that these abscission zone cells have specific characteristics which include high levels of unmethylated pectin in the walls and an inducible (x35) polygalacturonase enzyme expression. Together these findings help to explain the localised precision of cell separation events. PMID:11219806

  18. Biosynthetic uniform 13C,15N-labelling of zervamicin IIB. Complete 13C and 15N NMR assignment.

    Ovchinnikova, Tatyana V; Shenkarev, Zakhar O; Yakimenko, Zoya A; Svishcheva, Natalia V; Tagaev, Andrey A; Skladnev, Dmitry A; Arseniev, Alexander S

    2003-01-01

    Zervamicin IIB is a member of the alpha-aminoisobutyric acid containing peptaibol antibiotics. A new procedure for the biosynthetic preparation of the uniformly 13C- and 15N-enriched peptaibol is described This compound was isolated from the biomass of the fungus-producer Emericellopsis salmosynnemata strain 336 IMI 58330 obtained upon cultivation in the totally 13C, 15N-labelled complete medium. To prepare such a medium the autolysed biomass and the exopolysaccharides of the obligate methylotrophic bacterium Methylobacillus flagellatus KT were used. This microorganism was grown in totally 13C, 15N-labelled minimal medium containing 13C-methanol and 15N-ammonium chloride as the only carbon and nitrogen sources. Preliminary NMR spectroscopic analysis indicated a high extent of isotope incorporation (> 90%) and led to the complete 13C- and 15N-NMR assignment including the stereospecific assignment of Aib residues methyl groups. The observed pattern of the structurally important secondary chemical shifts of 1H(alpha), 13C=O and 13C(alpha) agrees well with the previously determined structure of zervamicin IIB in methanol solution. PMID:14658801

  19. Protein backbone chemical shifts predicted from searching a database for torsion angle and sequence homology

    Chemical shifts of nuclei in or attached to a protein backbone are exquisitely sensitive to their local environment. A computer program, SPARTA, is described that uses this correlation with local structure to predict protein backbone chemical shifts, given an input three-dimensional structure, by searching a newly generated database for triplets of adjacent residues that provide the best match in φ/ψ/χ1 torsion angles and sequence similarity to the query triplet of interest. The database contains 15N, 1HN, 1Hα, 13Cα, 13Cβ and 13C' chemical shifts for 200 proteins for which a high resolution X-ray (≤2.4 A) structure is available. The relative importance of the weighting factors for the φ/ψ/χ1 angles and sequence similarity was optimized empirically. The weighted, average secondary shifts of the central residues in the 20 best-matching triplets, after inclusion of nearest neighbor, ring current, and hydrogen bonding effects, are used to predict chemical shifts for the protein of known structure. Validation shows good agreement between the SPARTA-predicted and experimental shifts, with standard deviations of 2.52, 0.51, 0.27, 0.98, 1.07 and 1.08 ppm for 15N, 1HN, 1Hα, 13Cα, 13Cβ and 13C', respectively, including outliers

  20. Conformationally selective multidimensional chemical shift ranges in proteins from a PACSY database purged using intrinsic quality criteria

    Fritzsching, Keith J., E-mail: kfritzsc@brandeis.edu [Brandeis University, Department of Chemistry (United States); Hong, Mei [Massachusetts Institute of Technology, Department of Chemistry (United States); Schmidt-Rohr, Klaus, E-mail: srohr@brandeis.edu [Brandeis University, Department of Chemistry (United States)

    2016-02-15

    We have determined refined multidimensional chemical shift ranges for intra-residue correlations ({sup 13}C–{sup 13}C, {sup 15}N–{sup 13}C, etc.) in proteins, which can be used to gain type-assignment and/or secondary-structure information from experimental NMR spectra. The chemical-shift ranges are the result of a statistical analysis of the PACSY database of >3000 proteins with 3D structures (1,200,207 {sup 13}C chemical shifts and >3 million chemical shifts in total); these data were originally derived from the Biological Magnetic Resonance Data Bank. Using relatively simple non-parametric statistics to find peak maxima in the distributions of helix, sheet, coil and turn chemical shifts, and without the use of limited “hand-picked” data sets, we show that ∼94 % of the {sup 13}C NMR data and almost all {sup 15}N data are quite accurately referenced and assigned, with smaller standard deviations (0.2 and 0.8 ppm, respectively) than recognized previously. On the other hand, approximately 6 % of the {sup 13}C chemical shift data in the PACSY database are shown to be clearly misreferenced, mostly by ca. −2.4 ppm. The removal of the misreferenced data and other outliers by this purging by intrinsic quality criteria (PIQC) allows for reliable identification of secondary maxima in the two-dimensional chemical-shift distributions already pre-separated by secondary structure. We demonstrate that some of these correspond to specific regions in the Ramachandran plot, including left-handed helix dihedral angles, reflect unusual hydrogen bonding, or are due to the influence of a following proline residue. With appropriate smoothing, significantly more tightly defined chemical shift ranges are obtained for each amino acid type in the different secondary structures. These chemical shift ranges, which may be defined at any statistical threshold, can be used for amino-acid type assignment and secondary-structure analysis of chemical shifts from intra

  1. Conformationally selective multidimensional chemical shift ranges in proteins from a PACSY database purged using intrinsic quality criteria

    We have determined refined multidimensional chemical shift ranges for intra-residue correlations (13C–13C, 15N–13C, etc.) in proteins, which can be used to gain type-assignment and/or secondary-structure information from experimental NMR spectra. The chemical-shift ranges are the result of a statistical analysis of the PACSY database of >3000 proteins with 3D structures (1,200,207 13C chemical shifts and >3 million chemical shifts in total); these data were originally derived from the Biological Magnetic Resonance Data Bank. Using relatively simple non-parametric statistics to find peak maxima in the distributions of helix, sheet, coil and turn chemical shifts, and without the use of limited “hand-picked” data sets, we show that ∼94 % of the 13C NMR data and almost all 15N data are quite accurately referenced and assigned, with smaller standard deviations (0.2 and 0.8 ppm, respectively) than recognized previously. On the other hand, approximately 6 % of the 13C chemical shift data in the PACSY database are shown to be clearly misreferenced, mostly by ca. −2.4 ppm. The removal of the misreferenced data and other outliers by this purging by intrinsic quality criteria (PIQC) allows for reliable identification of secondary maxima in the two-dimensional chemical-shift distributions already pre-separated by secondary structure. We demonstrate that some of these correspond to specific regions in the Ramachandran plot, including left-handed helix dihedral angles, reflect unusual hydrogen bonding, or are due to the influence of a following proline residue. With appropriate smoothing, significantly more tightly defined chemical shift ranges are obtained for each amino acid type in the different secondary structures. These chemical shift ranges, which may be defined at any statistical threshold, can be used for amino-acid type assignment and secondary-structure analysis of chemical shifts from intra-residue cross peaks by inspection or by using a provided

  2. Comparative Analysis of the Chemical Composition of Mixed and Pure Cultures of Green Algae and Their Decomposed Residues by 13C Nuclear Magnetic Resonance Spectroscopy

    Zelibor, J. L.; Romankiw, L.; Hatcher, P. G.; Colwell, R. R.

    1988-01-01

    It is known that macromolecular organic matter in aquatic environments, i.e., humic substances, is highly aliphatic. These aliphatic macromolecules, predominantly paraffinic in structure, are prevalent in marine and lacustrine sediments and are believed to originate from algae or bacteria. A comparative study of mixed and pure cultures of green algae and their decomposed residues was performed by using solid-state 13C nuclear magnetic resonance spectroscopy as the primary analytical method. Results obtained in this study confirm the presence of components that are chemically refractory and that are defined as alghumin and hydrolyzed alghumin. These were detected in heterogeneous, homogeneous, and axenic biomasses composed of several genera of Chlorophyta. Although the chemical composition of algal biomass varied with culture conditions, the chemical structure of the alghumin and hydrolyzed alghumin, demonstrated by 13C nuclear magnetic resonance spectroscopy appeared to be constant for members of the Chlorophyta examined in this study. The alghumin was dominated by carbohydrate-carbon, with minor amounts of amide or carboxyl carbon and paraffinic carbon, the latter surviving strong hydrolysis by 6 N HCI (hydrolyzed alghumin). Bacterial decomposition of heterogeneous algal biomass labeled with 13C was conducted under both aerobic and anaerobic conditions to determine chemical structure and stability of the refractory material. The refractory fraction ranged from 33% in aerobic to 44% in anaerobic cultures. The refractory fraction recovered from either aerobic or anaerobic degradation comprised 40% alghumin, which represented an enrichment by 10% relative to the proportion of alghumin derived from whole cells of algae. The paraffinic component in the hydrolyzed alghumin of whole algal cells was found to be 1.8% and increased to 5.1 and 6.9% after aerobic and anaerobic bacterial degradation, respectively. It is concluded that members of the Chlorophyta contain a

  3. Accessible surface area from NMR chemical shifts

    Hafsa, Noor E.; Arndt, David; Wishart, David S., E-mail: david.wishart@ualberta.ca [University of Alberta, Department of Computing Science (Canada)

    2015-07-15

    Accessible surface area (ASA) is the surface area of an atom, amino acid or biomolecule that is exposed to solvent. The calculation of a molecule’s ASA requires three-dimensional coordinate data and the use of a “rolling ball” algorithm to both define and calculate the ASA. For polymers such as proteins, the ASA for individual amino acids is closely related to the hydrophobicity of the amino acid as well as its local secondary and tertiary structure. For proteins, ASA is a structural descriptor that can often be as informative as secondary structure. Consequently there has been considerable effort over the past two decades to try to predict ASA from protein sequence data and to use ASA information (derived from chemical modification studies) as a structure constraint. Recently it has become evident that protein chemical shifts are also sensitive to ASA. Given the potential utility of ASA estimates as structural constraints for NMR we decided to explore this relationship further. Using machine learning techniques (specifically a boosted tree regression model) we developed an algorithm called “ShiftASA” that combines chemical-shift and sequence derived features to accurately estimate per-residue fractional ASA values of water-soluble proteins. This method showed a correlation coefficient between predicted and experimental values of 0.79 when evaluated on a set of 65 independent test proteins, which was an 8.2 % improvement over the next best performing (sequence-only) method. On a separate test set of 92 proteins, ShiftASA reported a mean correlation coefficient of 0.82, which was 12.3 % better than the next best performing method. ShiftASA is available as a web server ( http://shiftasa.wishartlab.com http://shiftasa.wishartlab.com ) for submitting input queries for fractional ASA calculation.

  4. Accessible surface area from NMR chemical shifts

    Accessible surface area (ASA) is the surface area of an atom, amino acid or biomolecule that is exposed to solvent. The calculation of a molecule’s ASA requires three-dimensional coordinate data and the use of a “rolling ball” algorithm to both define and calculate the ASA. For polymers such as proteins, the ASA for individual amino acids is closely related to the hydrophobicity of the amino acid as well as its local secondary and tertiary structure. For proteins, ASA is a structural descriptor that can often be as informative as secondary structure. Consequently there has been considerable effort over the past two decades to try to predict ASA from protein sequence data and to use ASA information (derived from chemical modification studies) as a structure constraint. Recently it has become evident that protein chemical shifts are also sensitive to ASA. Given the potential utility of ASA estimates as structural constraints for NMR we decided to explore this relationship further. Using machine learning techniques (specifically a boosted tree regression model) we developed an algorithm called “ShiftASA” that combines chemical-shift and sequence derived features to accurately estimate per-residue fractional ASA values of water-soluble proteins. This method showed a correlation coefficient between predicted and experimental values of 0.79 when evaluated on a set of 65 independent test proteins, which was an 8.2 % improvement over the next best performing (sequence-only) method. On a separate test set of 92 proteins, ShiftASA reported a mean correlation coefficient of 0.82, which was 12.3 % better than the next best performing method. ShiftASA is available as a web server ( http://shiftasa.wishartlab.com http://shiftasa.wishartlab.com ) for submitting input queries for fractional ASA calculation

  5. Intermolecular interactions in nuclear magnetic resonance: medium shifts of the 1H and 13C nuclei in methane in the gas phase and in solution and of gaseous 3He

    An analysis has been carried out of the continuum and the binary collision models used in the description of NMR solvent shifts caused by Van der Waals intermolecular interactions. The basic assumption underlying the models, i.e. σ sub(w)= -BE2 (I) is examined. The possible effects on I of such phenomena as B anisotropy and field gradients are discussed, as well as the inadequacy of I in representing the true intermolecular shielding. A new expression for E2 is proposed, which in connection with I forms the bais of a modified binary collision model. The new E2 expression takes into account the dynamic character of the interaction. The major obstacle to the binary collision model, the requirement for accurate parameters for the intermolecular potential employed in the statistical-mechanical averaging, is alleviated by the establishment of priority rules to be used in the selection of these paramters. The proposed binary collision model and a collision model are used to interpret the 1H and 13C medium shifts of methane in the gas phase and in solution. The proton shift data conform equally well to either model; the 13C data indicate that a large solvent-dependent term contributes to the observed medium shifts in addition to I. Proton and 13C B parameters of methane in the gas phase and in solution are discussed. Preliminary results of 3He medium shifts as a function of gas density are presented. An extracted B parameter based on the proposed binary collision model appears to agree well with the result of a quantum-mechanical calculation of B for a 3He atom in a uniform static electric field. (LL)

  6. Sequence correction of random coil chemical shifts: correlation between neighbor correction factors and changes in the Ramachandran distribution

    Kjærgaard, Magnus; Poulsen, Flemming Martin

    2011-01-01

    this study, we use random coil peptides containing glutamine instead of glycine to determine the random coil chemical shifts and the neighbor correction factors. The resulting correction factors correlate to changes in the populations of the major wells in the Ramachandran plot, which demonstrates that...... changes in the conformational ensemble are an important source of neighbor effects in disordered proteins. Glutamine derived random coil chemical shifts and correction factors modestly improve our ability to predict (13)C chemical shifts of intrinsically disordered proteins compared to existing datasets......Random coil chemical shifts are necessary for secondary chemical shift analysis, which is the main NMR method for identification of secondary structure in proteins. One of the largest challenges in the determination of random coil chemical shifts is accounting for the effect of neighboring residues...

  7. Hyperfine structure in the J = 1-0 transitions of DCO+, DNC, and HN13C: astronomical observations and quantum-chemical calculations

    van der Tak, Floris; Harding, Michael; Gauss, Jürgen

    2009-01-01

    We have observed the rotational ground-state (J = 1-0) transitions of DCO+, HN13C and DNC with the IRAM 30m telescope toward the dark cloud LDN 1512 which has exceptionally narrow lines permitting hyperfine splitting to be resolved in part. The measured splittings of 50-300 kHz are used to derive nuclear quadrupole and spin-rotation parameters for these species. The measurements are supplemented by high-level quantum-chemical calculations using coupled-cluster techniques and large atomic-orbital basis sets. We find eQq = +151.12 (400) kHz and C_I = -1.12 (43) kHz for DCO+, eQq = 272.5 (51) kHz for HN13C, and eQq(D) = 265.9 (83) kHz and eQq(N) = 288.2 (71) kHz for DNC. The numbers for DNC are consistent with previous laboratory data, while our constants for DCO+ are somewhat smaller than previous results based on astronomical data. For both DCO+ and DNC, our results are more accurate than previous determinations. Our results are in good agreement with the corresponding best theoretical estimates. We also deriv...

  8. Protein Structure Determination Using Chemical Shifts

    Christensen, Anders Steen

    In this thesis, a protein structure determination using chemical shifts is presented. The method is implemented in the open source PHAISTOS protein simulation framework. The method combines sampling from a generative model with a coarse-grained force field and an energy function that includes che...... residues. For Rhodopsin (225 residues) a structure is found at 2.5 Å CA-RMSD from the experimental X-ray structure, and a structure is determined for the Savinase protein (269 residues) with 2.9 Å CA-RMSD from the experimental X-ray structure....

  9. Chemical shift MR imaging of the skin

    MR imaging with conventional spin-echo pulse sequences has not found wide application in the evaluation of skin pathology. This paper reports that this study was designed to determine the value of chemical shift imaging (CSI) compared with conventional pulse sequences for the noninvasive evaluation of connective tissue and neoplastic disease of the skin and underlying fascia. The studies were acquired in patients and volunteers on a whole-body system at 1.5 T and small surface coils. Comparisons were made between T1- and T2-weighted gradient-echo, spin-echo, and hybrid lipid and water-suppressed CSI series (Chopper-Dixon combined with frequency-selective pulse). CSI improves detail in the hypodermis by eliminating unwanted (lipid) signal and chemical shift misregistration artifact. The detail of water-based signal is improved in the deeper layers of the skin by improved tissue contrast and elimination of the disturbing adjacent dominant fat-based signal. MR imaging has the potential to provide information that can complement skin biopsy. A more optimal choice of pulse sequences can improve the sensitivity of MR imaging to water-based pathology and allow noninvasive visualization of deep layers. The CSI sequences may be useful in the evaluation of infiltrative and neoplastic disease of the skin, particularly as they are adapted into microimaging methods with local gradient coils

  10. Enhanced conformational space sampling improves the prediction of chemical shifts in proteins.

    Markwick, Phineus R L; Cervantes, Carla F; Abel, Barrett L; Komives, Elizabeth A; Blackledge, Martin; McCammon, J Andrew

    2010-02-01

    A biased-potential molecular dynamics simulation method, accelerated molecular dynamics (AMD), was combined with the chemical shift prediction algorithm SHIFTX to calculate (1)H(N), (15)N, (13)Calpha, (13)Cbeta, and (13)C' chemical shifts of the ankyrin repeat protein IkappaBalpha (residues 67-206), the primary inhibitor of nuclear factor kappa-B (NF-kappaB). Free-energy-weighted molecular ensembles were generated over a range of acceleration levels, affording systematic enhancement of the conformational space sampling of the protein. We have found that the predicted chemical shifts, particularly for the (15)N, (13)Calpha, and (13)Cbeta nuclei, improve substantially with enhanced conformational space sampling up to an optimal acceleration level. Significant improvement in the predicted chemical shift data coincides with those regions of the protein that exhibit backbone dynamics on longer time scales. Interestingly, the optimal acceleration level for reproduction of the chemical shift data has previously been shown to best reproduce the experimental residual dipolar coupling (RDC) data for this system, as both chemical shift data and RDCs report on an ensemble and time average in the millisecond range. PMID:20063881

  11. Cationic Closo-carboranes 2. Do computed 11B and 13C NMR chemical shifts support their experimental availability?

    Hnyk, Drahomír; Jayasree, E.G.

    2013-01-01

    Roč. 34, č. 8 (2013), s. 656-661. ISSN 0192-8651 R&D Projects: GA ČR GAP208/10/2269 Institutional support: RVO:61388980 Keywords : boron clusters * weakly-coordinating cations * 11B NMR * dynamic electron correlation Subject RIV: CA - Inorganic Chemistry Impact factor: 3.601, year: 2013

  12. Further conventions for NMR shielding and chemical shifts (IUPAC Recommendations 2008)

    Harris, R.K. [University of Durham, Durham (United Kingdom). Dept. of Chemistry; Becker, E.D. [National Institutes of Health, Bethesda, MD (United States); Menezes, S.M. Cabral de [PETROBRAS, Rio de Janeiro, RJ (Brazil). Centro de Pesquisas (CENPES); Granger, P. [University Louis Pasteur, Strasbourg (France). Inst. of Chemistry; Hoffman, R.E. [The Hebrew University of Jerusalem, Safra Campus, Jerusalem (Israel). Dept. of Organic Chemistry; Zilm, K.W., E-mail: r.k.harris@durham.ac.uk [Yale University, New Haven, CT (United States). Dept. of Chemistry

    2008-07-01

    IUPAC has published a number of recommendations regarding the reporting of nuclear magnetic resonance (NMR) data, especially chemical shifts. The most recent publication [Pure Appl. Chem. 73, 1795 (2001)] recommended that tetramethylsilane (TMS) serve as a universal reference for reporting the shifts of all nuclides, but it deferred recommendations for several aspects of this subject. This document first examines the extent to which the {sup 1}H shielding in TMS itself is subject to change by variation in temperature, concentration, and solvent. On the basis of recently published results, it has been established that the shielding of TMS in solution [along with that of sodium-3- (trimethylsilyl)propanesulfonate, DSS, often used as a reference for aqueous solutions] varies only slightly with temperature but is subject to solvent perturbations of a few tenths of a part per million (ppm). Recommendations are given for reporting chemical shifts under most routine experimental conditions and for quantifying effects of temperature and solvent variation, including the use of magnetic susceptibility corrections and of magic-angle spinning (MAS). This document provides the first IUPAC recommendations for referencing and reporting chemical shifts in solids, based on high-resolution MAS studies. Procedures are given for relating {sup 13}C NMR chemical shifts in solids to the scales used for high resolution studies in the liquid phase. The notation and terminology used for describing chemical shift and shielding tensors in solids are reviewed in some detail, and recommendations are given for best practice. (author)

  13. Further conventions for NMR shielding and chemical shifts (IUPAC Recommendations 2008)

    IUPAC has published a number of recommendations regarding the reporting of nuclear magnetic resonance (NMR) data, especially chemical shifts. The most recent publication [Pure Appl. Chem. 73, 1795 (2001)] recommended that tetramethylsilane (TMS) serve as a universal reference for reporting the shifts of all nuclides, but it deferred recommendations for several aspects of this subject. This document first examines the extent to which the 1H shielding in TMS itself is subject to change by variation in temperature, concentration, and solvent. On the basis of recently published results, it has been established that the shielding of TMS in solution [along with that of sodium-3- (trimethylsilyl)propanesulfonate, DSS, often used as a reference for aqueous solutions] varies only slightly with temperature but is subject to solvent perturbations of a few tenths of a part per million (ppm). Recommendations are given for reporting chemical shifts under most routine experimental conditions and for quantifying effects of temperature and solvent variation, including the use of magnetic susceptibility corrections and of magic-angle spinning (MAS). This document provides the first IUPAC recommendations for referencing and reporting chemical shifts in solids, based on high-resolution MAS studies. Procedures are given for relating 13C NMR chemical shifts in solids to the scales used for high resolution studies in the liquid phase. The notation and terminology used for describing chemical shift and shielding tensors in solids are reviewed in some detail, and recommendations are given for best practice. (author)

  14. Selective diagonal-free 13C,13C-edited aliphatic–aromatic NOESY experiment with non-uniform sampling

    A band-selective aromatic–aliphatic C,C-edited four-dimensional NOESY experiment is proposed here. Its key advantage is the absence of auto-correlation signals which makes it very attractive for joint use with non-uniform sampling. It is demonstrated here that the sensitivity of the experiment is not significantly affected by utilization of selective pulses (for either aromatic-13C or aliphatic-13C spins). The method was applied to the sample of E32Q mutant of human S100A1 protein, a homodimer of total molecular mass ∼20 kDa. High-resolution 4D spectra were obtained from ∼1.5 % of sampling points required conventionally. It is shown that superior resolution facilitates unambiguous assignment of observed aliphatic–aromatic cross-peaks. Additionally, the addition of aliphatic-13C dimension enables to resolve peaks with degenerated aliphatic 1H chemical shifts. All observed cross-peaks were validated against previously determined 3D structure of E32Q mutant of S100A1 protein (PDB 2LHL). The increased reliability of structural constraints obtained from the proposed high-resolution 4D 13C(ali),13C(aro)-edited NOESY can be exploited in the automated protocols of structure determination of proteins

  15. Synthesis of 13C-labeled methanol

    A novel convenient method for the synthesis of 13C-methanol was described. 13C- methanol was prepared by means of catalytic hydrogenation, and then as-synthesized methanol solution was further purified in a microscale high-efficient rectification column. The chemical purity of 13C-methanol was more than 99.5%. The synthetic route was featured by mild conditions and high yields of more than 90% based on isotopic substrate consumed. The product was characterized by GC-MS and 1H NMR, and the 13C abundance of 13C- methanol was more than 97%. Compared with the raw materials, the reduction of relative isotopic abundance of product was less than 1%. (authors)

  16. Backbone dynamics of a model membrane protein: measurement of individual amide hydrogen-exchange rates in detergent-solubilized M13 coat protein using 13C NMR hydrogen/deuterium isotope shifts

    Hydrogen-exchange rates have been measured for individual assigned amide protons in M13 coat protein, a 50-residue integral membrane protein, using a 13C nuclear magnetic resonance (NMR) equilibrium isotope shift technique. The locations of the more rapidly exchanging amides have been determined. In D2O solutions, a peptide carbonyl resonance undergoes a small upfield isotope shift (0.08-0.09 ppm) from its position in H2O solutions; in 1:1 H2O/D2O mixtures, the carbonyl line shape is determined by the exchange rate at the adjacent nitrogen atom. M13 coat protein was labeled biosynthetically with 13C at the peptide carbonyls of alanine, glycine, phenylalanine, proline, and lysine, and the exchange rates of 12 assigned amide protons in the hydrophilic regions were measured as a function of pH by using the isotope shift method. This equilibrium technique is sensitive to the more rapidly exchanging protons which are difficult to measure by classical exchange-out experiments. In proteins, structural factors, notably H bonding, can decrease the exchange rate of an amide proton by many orders of magnitude from that observed in the freely exposed amides of model peptides such as poly(DL-alanine). With corrections for sequence-related inductive effects, the retardation of amide exchange in sodium dodecyl sulfate solubilized coat protein has been calculated with respect to poly(DL-alanine). The most rapidly exchanging protons, which are retarded very little or not at all, are shown to occur at the N- and C-termini of the molecule. A model of the detergent-solubilized coat protein is constructed from these H-exchange data which is consistent with circular dichroism and other NMR results

  17. Chemical structures of coal lithotypes before and after CO2 adsorption as investigated by advanced solid-state 13C nuclear magnetic resonance spectroscopy

    Cao, X.; Mastalerz, Maria; Chappell, M.A.; Miller, L.F.; Li, Y.; Mao, J.

    2011-01-01

    Four lithotypes (vitrain, bright clarain, clarain, and fusain) of a high volatile bituminous Springfield Coal from the Illinois Basin were characterized using advanced solid-state 13C nuclear magnetic resonance (NMR) spectroscopy. The NMR techniques included quantitative direct polarization/magic angle spinning (DP/MAS), cross polarization/total sideband suppression (CP/TOSS), dipolar dephasing, CHn selection, and recoupled C-H long-range dipolar dephasing techniques. The lithotypes that experienced high-pressure CO2 adsorption isotherm analysis were also analyzed to determine possible changes in coal structure as a result of CO2 saturation at high pressure and subsequent evacuation. The main carbon functionalities present in original vitrain, bright clarain, clarain and fusain were aromatic carbons (65.9%-86.1%), nonpolar alkyl groups (9.0%-28.9%), and aromatic C-O carbons (4.1%-9.5%). Among these lithotypes, aromaticity increased in the order of clarain, bright clarain, vitrain, and fusain, whereas the fraction of alkyl carbons decreased in the same order. Fusain was distinct from other three lithotypes in respect to its highest aromatic composition (86.1%) and remarkably small fraction of alkyl carbons (11.0%). The aromatic cluster size in fusain was larger than that in bright clarain. The lithotypes studied responded differently to high pressure CO2 saturation. After exposure to high pressure CO2, vitrain and fusain showed a decrease in aromaticity but an increase in the fraction of alkyl carbons, whereas bright clarain and clarain displayed an increase in aromaticity but a decrease in the fraction of alkyl carbons. Aromatic fused-rings were larger for bright clarain but smaller for fusain in the post-CO2 adsorption samples compared to the original lithotypes. These observations suggested chemical CO2-coal interactions at high pressure and the selectivity of lithotypes in response to CO2 adsorption. ?? 2011 Elsevier B.V.

  18. Calculation of NMR chemical shifts. 7. Gauge-invariant INDO method

    Fukui, H.; Miura, K.; Hirai, A.

    A gauge-invariant INDO method based on the coupled Hartree-Fuck perturbation theory is presented and applied to the calculation of 1H and 13C chemical shifts of hydrocarbons including ring compounds. Invariance of the diamagnetic and paramagnetic shieldings with respect to displacement of the coordinate origin is discussed. Comparison between calculated and experimental results exhibits fairly good agreement, provided that the INDO parameters of Ellis et al. (J. Am. Chem. Soc.94, 4069 (1972)) are used with the inclusion of all multicenter one-electron integrals.

  19. Comprehensive quantum chemical and spectroscopic (FTIR, FT-Raman, 1H, 13C NMR) investigations of (1,2-epoxyethyl)benzene and (1,2-epoxy-2-phenyl)propane

    Arjunan, V.; Anitha, R.; Devi, L.; Mohan, S.; Yang, Haifeng

    2015-01-01

    Aromatic epoxides are causative factors for mutagenic and carcinogenic activity of polycyclic arenes. The 1,2- or 2,3-epoxy compounds are widely used to a considerable extent in the textile, plastics, pharmaceutical, cosmetics, detergent and photochemical industries. The FTIR and FT-Raman spectra of (1,2-epoxyethyl)benzene and (1,2-epoxy-2-phenyl)propane are recorded in the regions 4000-400 cm-1 and 4000-100 cm-1, respectively. The observed fundamentals are assigned to different normal modes of vibration. The structure of the compound has been optimised with B3LYP method using 6-311++G** and cc-pVTZ basis sets. The IR and Raman intensities are determined. The total electron density and molecular electrostatic potential surfaces of the molecule are constructed by using B3LYP/6-311++G(d,p) method to display electrostatic potential (electron + nuclei) distribution. The electronic properties HOMO and LUMO energies were measured. Natural bond orbital analysis of the compounds has been performed to indicate the presence of intramolecular charge transfer. The 1H and 13C NMR chemical shifts of the molecules have been analysed.

  20. Utilization of lysine {sup 13}C-methylation NMR for protein-protein interaction studies

    Hattori, Yoshikazu; Furuita, Kyoko [Osaka University, Institute for Protein Research (Japan); Ohki, Izuru, E-mail: i-ooki@bs.naist.jp [Nara Institute of Science and Technology (NAIST), Graduate School of Biological Sciences (Japan); Ikegami, Takahisa [Osaka University, Institute for Protein Research (Japan); Fukada, Harumi [Osaka Prefecture University, Graduate School of Life and Environmental Sciences (Japan); Shirakawa, Masahiro [Kyoto University, Graduate School of Engineering (Japan); Fujiwara, Toshimichi; Kojima, Chojiro, E-mail: kojima@protein.osaka-u.ac.jp [Osaka University, Institute for Protein Research (Japan)

    2013-01-15

    Chemical modification is an easy way for stable isotope labeling of non-labeled proteins. The reductive {sup 13}C-methylation of the amino group of the lysine side-chain by {sup 13}C-formaldehyde is a post-modification and is applicable to most proteins since this chemical modification specifically and quickly proceeds under mild conditions such as 4 Degree-Sign C, pH 6.8, overnight. {sup 13}C-methylation has been used for NMR to study the interactions between the methylated proteins and various molecules, such as small ligands, nucleic acids and peptides. Here we applied lysine {sup 13}C-methylation NMR to monitor protein-protein interactions. The affinity and the intermolecular interaction sites of methylated ubiquitin with three ubiquitin-interacting proteins were successfully determined using chemical-shift perturbation experiments via the {sup 1}H-{sup 13}C HSQC spectra of the {sup 13}C-methylated-lysine methyl groups. The lysine {sup 13}C-methylation NMR results also emphasized the importance of the usage of side-chain signals to monitor the intermolecular interaction sites, and was applicable to studying samples with concentrations in the low sub-micromolar range.

  1. Utilization of lysine 13C-methylation NMR for protein–protein interaction studies

    Chemical modification is an easy way for stable isotope labeling of non-labeled proteins. The reductive 13C-methylation of the amino group of the lysine side-chain by 13C-formaldehyde is a post-modification and is applicable to most proteins since this chemical modification specifically and quickly proceeds under mild conditions such as 4 °C, pH 6.8, overnight. 13C-methylation has been used for NMR to study the interactions between the methylated proteins and various molecules, such as small ligands, nucleic acids and peptides. Here we applied lysine 13C-methylation NMR to monitor protein–protein interactions. The affinity and the intermolecular interaction sites of methylated ubiquitin with three ubiquitin-interacting proteins were successfully determined using chemical-shift perturbation experiments via the 1H–13C HSQC spectra of the 13C-methylated-lysine methyl groups. The lysine 13C-methylation NMR results also emphasized the importance of the usage of side-chain signals to monitor the intermolecular interaction sites, and was applicable to studying samples with concentrations in the low sub-micromolar range.

  2. 13C-NMR Data of Diterpenes Isolated from Aristolochia Species

    Antônio Flávio de Carvalho Alcântara

    2009-03-01

    Full Text Available The genus Aristolochia,an important source of physiologically active compounds that belong to different chemical classes, is the subject of research in numerous pharmacological and chemical studies. This genus contains a large number of terpenoid compounds, particularly diterpenes. This work presents a compilation of the 13C-NMR data of 57 diterpenoids described between 1981 and 2007 which were isolated from Aristolochia species. The compounds are arranged skeletonwise in each section, according to their structures, i.e., clerodane, labdane, and kaurane derivatives. A brief discussion on the 13C chemical shifts of these diterpenes is also included.

  3. /sup 13/C NMR of diterpenes with isopimarane structure. Part 2: effects involving the double bond. delta. sup(8(9))

    Cunha Pinto, A. da; Lima Pereira, A. de (Rio de Janeiro Univ. (Brazil). Nucleo de Pesquisas de Produtos Naturais)

    1984-01-01

    Several effects of the ..delta.. sup(8(9)) double bond on the /sup 13/C NMR data of isopimarane diterpenoids are discussed, including chemical shifts and acetylation of the C-7 hydroxyl radical on the above mentioned double bond.

  4. Chemical structures of swine-manure chars produced under different carbonization conditions investigated by advanced solid-state 13C nuclear magnetic resonance (NMR) spectroscopy

    Two types of swine manure chars, hydrothermally-produced hydrochar and slow-pyrolysis pyrochar, and their raw swine manure solid were characterized using advanced 13C solid-state nuclear magnetic resonance (NMR) spectroscopy. Compared with the parent raw swine manure, both hydrochars and pyrochar di...

  5. Conditions to obtain precise and true measurements of the intramolecular 13C distribution in organic molecules by isotopic 13C nuclear magnetic resonance spectrometry

    Highlights: • Evaluation of the trueness and precision criteria of isotopic 13C NMR spectrometry. • Use of bi-labelled [1,2-13C2]acetic acid to determine the performance of the instrumental response. • Inter-calibration of the 13C intramolecular composition of acetic acid using the technique GC-Py–irm-MS. - Abstract: Intramolecular 13C composition gives access to new information on the (bio) synthetic history of a given molecule. Isotopic 13C NMR spectrometry provides a general tool for measuring the position-specific 13C content. As an emerging technique, some aspects of its performance are not yet fully delineated. This paper reports on (i) the conditions required to obtain satisfactory trueness and precision for the determination of the internal 13C distribution, and (ii) an approach to determining the “absolute” position-specific 13C content. In relation to (i), a precision of <1% can be obtained whatever the molecule on any spectrometer, once quantitative conditions are met, in particular appropriate proton decoupling efficiency. This performance is a prerequisite to the measurement of isotope fractionation either on the transformed or residual compound when a chemical reaction or process is being studied. The study of the trueness has revealed that the response of the spectrometer depends on the 13C frequency range of the studied molecule, i.e. the chemical shift range. The “absolute value” and, therefore, the trueness of the 13C NMR measurements has been assessed on acetic acid and by comparison to the results obtained on the fragments from COOH and CH3 by isotopic mass spectrometry coupled to a pyrolysis device (GC-Py–irm-MS), this technique being the reference method for acetic acid. Of the two NMR spectrometers used in this work, one gave values that corresponded to those obtained by GC-Py–irm-MS (thus, the “true” value) while the other showed a bias, which was dependent to the range covered by the resonance frequencies of the

  6. Conditions to obtain precise and true measurements of the intramolecular {sup 13}C distribution in organic molecules by isotopic {sup 13}C nuclear magnetic resonance spectrometry

    Bayle, Kevin [EBSI Team, Interdisciplinary Chemistry: Synthesis, Analysis, Modelling (CEISAM), University of Nantes-CNRS UMR 6230, 2 Rue de la Houssinière, BP 92208, F-44322, Nantes Cedex 3 (France); Gilbert, Alexis [Department of Environmental Chemistry and Engineering, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8503 (Japan); Earth–Life Science Institute, Tokyo Institute of Technology, Meguro, Tokyo 152-8551 (Japan); Julien, Maxime [EBSI Team, Interdisciplinary Chemistry: Synthesis, Analysis, Modelling (CEISAM), University of Nantes-CNRS UMR 6230, 2 Rue de la Houssinière, BP 92208, F-44322, Nantes Cedex 3 (France); Yamada, Keita [Department of Environmental Chemistry and Engineering, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8503 (Japan); Silvestre, Virginie; Robins, Richard J.; Akoka, Serge [EBSI Team, Interdisciplinary Chemistry: Synthesis, Analysis, Modelling (CEISAM), University of Nantes-CNRS UMR 6230, 2 Rue de la Houssinière, BP 92208, F-44322, Nantes Cedex 3 (France); Yoshida, Naohiro [Department of Environmental Chemistry and Engineering, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8503 (Japan); Earth–Life Science Institute, Tokyo Institute of Technology, Meguro, Tokyo 152-8551 (Japan); Remaud, Gérald S., E-mail: gerald.remaud@univ-nantes.fr [EBSI Team, Interdisciplinary Chemistry: Synthesis, Analysis, Modelling (CEISAM), University of Nantes-CNRS UMR 6230, 2 Rue de la Houssinière, BP 92208, F-44322, Nantes Cedex 3 (France)

    2014-10-10

    Highlights: • Evaluation of the trueness and precision criteria of isotopic {sup 13}C NMR spectrometry. • Use of bi-labelled [1,2-{sup 13}C{sub 2}]acetic acid to determine the performance of the instrumental response. • Inter-calibration of the {sup 13}C intramolecular composition of acetic acid using the technique GC-Py–irm-MS. - Abstract: Intramolecular {sup 13}C composition gives access to new information on the (bio) synthetic history of a given molecule. Isotopic {sup 13}C NMR spectrometry provides a general tool for measuring the position-specific {sup 13}C content. As an emerging technique, some aspects of its performance are not yet fully delineated. This paper reports on (i) the conditions required to obtain satisfactory trueness and precision for the determination of the internal {sup 13}C distribution, and (ii) an approach to determining the “absolute” position-specific {sup 13}C content. In relation to (i), a precision of <1% can be obtained whatever the molecule on any spectrometer, once quantitative conditions are met, in particular appropriate proton decoupling efficiency. This performance is a prerequisite to the measurement of isotope fractionation either on the transformed or residual compound when a chemical reaction or process is being studied. The study of the trueness has revealed that the response of the spectrometer depends on the {sup 13}C frequency range of the studied molecule, i.e. the chemical shift range. The “absolute value” and, therefore, the trueness of the {sup 13}C NMR measurements has been assessed on acetic acid and by comparison to the results obtained on the fragments from COOH and CH{sub 3} by isotopic mass spectrometry coupled to a pyrolysis device (GC-Py–irm-MS), this technique being the reference method for acetic acid. Of the two NMR spectrometers used in this work, one gave values that corresponded to those obtained by GC-Py–irm-MS (thus, the “true” value) while the other showed a bias, which was

  7. Histidine side-chain dynamics and protonation monitored by {sup 13}C CPMG NMR relaxation dispersion

    Hass, Mathias A. S. [Leiden University, Institute of Chemistry (Netherlands); Yilmaz, Ali [University of Copenhagen, Department of Medicinal Chemistry, Faculty of Pharmaceutical Sciences (Denmark); Christensen, Hans E. M. [Technical University of Denmark, Department of Chemistry (Denmark); Led, Jens J. [University of Copenhagen, Department of Chemistry (Denmark)], E-mail: led@kiku.dk

    2009-08-15

    The use of {sup 13}C NMR relaxation dispersion experiments to monitor micro-millisecond fluctuations in the protonation states of histidine residues in proteins is investigated. To illustrate the approach, measurements on three specifically {sup 13}C labeled histidine residues in plastocyanin (PCu) from Anabaena variabilis (A.v.) are presented. Significant Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion is observed for {sup 13}C{sup {epsilon}}{sup 1} nuclei in the histidine imidazole rings of A.v. PCu. The chemical shift changes obtained from the CPMG dispersion data are in good agreement with those obtained from the chemical shift titration experiments, and the CPMG derived exchange rates agree with those obtained previously from {sup 15}N backbone relaxation measurements. Compared to measurements of backbone nuclei, {sup 13}C{sup {epsilon}}{sup 1} dispersion provides a more direct method to monitor interchanging protonation states or other kinds of conformational changes of histidine side chains or their environment. Advantages and shortcomings of using the {sup 13}C{sup {epsilon}}{sup 1} dispersion experiments in combination with chemical shift titration experiments to obtain information on exchange dynamics of the histidine side chains are discussed.

  8. Identification of helix capping and {beta}-turn motifs from NMR chemical shifts

    Shen Yang; Bax, Ad, E-mail: bax@nih.gov [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States)

    2012-03-15

    We present an empirical method for identification of distinct structural motifs in proteins on the basis of experimentally determined backbone and {sup 13}C{sup {beta}} chemical shifts. Elements identified include the N-terminal and C-terminal helix capping motifs and five types of {beta}-turns: I, II, I Prime , II Prime and VIII. Using a database of proteins of known structure, the NMR chemical shifts, together with the PDB-extracted amino acid preference of the helix capping and {beta}-turn motifs are used as input data for training an artificial neural network algorithm, which outputs the statistical probability of finding each motif at any given position in the protein. The trained neural networks, contained in the MICS (motif identification from chemical shifts) program, also provide a confidence level for each of their predictions, and values ranging from ca 0.7-0.9 for the Matthews correlation coefficient of its predictions far exceed those attainable by sequence analysis. MICS is anticipated to be useful both in the conventional NMR structure determination process and for enhancing on-going efforts to determine protein structures solely on the basis of chemical shift information, where it can aid in identifying protein database fragments suitable for use in building such structures.

  9. Probabilistic Approach to Determining Unbiased Random-coil Carbon-13 Chemical Shift Values from the Protein Chemical Shift Database

    We describe a probabilistic model for deriving, from the database of assigned chemical shifts, a set of random coil chemical shift values that are 'unbiased' insofar as contributions from detectable secondary structure have been minimized (RCCSu). We have used this approach to derive a set of RCCSu values for 13Cα and 13Cβ for 17 of the 20 standard amino acid residue types by taking advantage of the known opposite conformational dependence of these parameters. We present a second probabilistic approach that utilizes the maximum entropy principle to analyze the database of 13Cα and 13Cβ chemical shifts considered separately; this approach yielded a second set of random coil chemical shifts (RCCSmax-ent). Both new approaches analyze the chemical shift database without reference to known structure. Prior approaches have used either the chemical shifts of small peptides assumed to model the random coil state (RCCSpeptide) or statistical analysis of chemical shifts associated with structure not in helical or strand conformation (RCCSstruct-stat). We show that the RCCSmax-ent values are strikingly similar to published RCCSpeptide and RCCSstruct-stat values. By contrast, the RCCSu values differ significantly from both published types of random coil chemical shift values. The differences (RCCSpeptide-RCCSu) for individual residue types show a correlation with known intrinsic conformational propensities. These results suggest that random coil chemical shift values from both prior approaches are biased by conformational preferences. RCCSu values appear to be consistent with the current concept of the 'random coil' as the state in which the geometry of the polypeptide ensemble samples the allowed region of (φ,ψ)-space in the absence of any dominant stabilizing interactions and thus represent an improved basis for the detection of secondary structure. Coupled with the growing database of chemical shifts, this probabilistic approach makes it possible to refine

  10. 13 C signal attribution of 5-bromine-2(2'-thienyl)thiophene

    This work has carried out a study of C-H coupling constants in oligothiophenes, through 1 H and 13 C NMR spectra analysis. Nuclear magnetic resonance spectroscopy have been used in order to characterize the molecular structure of them. Chemical shifts were also studied and spectral data have been shown and analysed

  11. Probabilistic validation of protein NMR chemical shift assignments

    Data validation plays an important role in ensuring the reliability and reproducibility of studies. NMR investigations of the functional properties, dynamics, chemical kinetics, and structures of proteins depend critically on the correctness of chemical shift assignments. We present a novel probabilistic method named ARECA for validating chemical shift assignments that relies on the nuclear Overhauser effect data. ARECA has been evaluated through its application to 26 case studies and has been shown to be complementary to, and usually more reliable than, approaches based on chemical shift databases. ARECA is available online at http://areca.nmrfam.wisc.edu/ http://areca.nmrfam.wisc.edu/

  12. Probabilistic validation of protein NMR chemical shift assignments

    Dashti, Hesam [University of Wisconsin-Madison, Graduate Program in Biophysics, Biochemistry Department (United States); Tonelli, Marco; Lee, Woonghee; Westler, William M.; Cornilescu, Gabriel [University of Wisconsin-Madison, Biochemistry Department, National Magnetic Resonance Facility at Madison (United States); Ulrich, Eldon L. [University of Wisconsin-Madison, BioMagResBank, Biochemistry Department (United States); Markley, John L., E-mail: markley@nmrfam.wisc.edu, E-mail: jmarkley@wisc.edu [University of Wisconsin-Madison, Biochemistry Department, National Magnetic Resonance Facility at Madison (United States)

    2016-01-15

    Data validation plays an important role in ensuring the reliability and reproducibility of studies. NMR investigations of the functional properties, dynamics, chemical kinetics, and structures of proteins depend critically on the correctness of chemical shift assignments. We present a novel probabilistic method named ARECA for validating chemical shift assignments that relies on the nuclear Overhauser effect data. ARECA has been evaluated through its application to 26 case studies and has been shown to be complementary to, and usually more reliable than, approaches based on chemical shift databases. ARECA is available online at http://areca.nmrfam.wisc.edu/ http://areca.nmrfam.wisc.edu/.

  13. A polymer-based magnetic resonance tracer for visualization of solid tumors by 13C spectroscopic imaging.

    Yoshikazu Suzuki

    Full Text Available Morphological imaging precedes lesion-specific visualization in magnetic resonance imaging (MRI because of the superior ability of this technique to depict tissue morphology with excellent spatial and temporal resolutions. To achieve lesion-specific visualization of tumors by MRI, we investigated the availability of a novel polymer-based tracer. Although the 13C nucleus is a candidate for a detection nucleus because of its low background signal in the body, the low magnetic resonance sensitivity of the nucleus needs to be resolved before developing a 13C-based tracer. In order to overcome this problem, we enriched polyethylene glycol (PEG, a biocompatible polymer, with 13C atoms. 13C-PEG40,000 (13C-PEG with an average molecular weight of 40 kDa emitted a single 13C signal with a high signal-to-noise ratio due to its ability to maintain signal sharpness, as was confirmed by in vivo investigation, and displayed a chemical shift sufficiently distinct from that of endogenous fat. 13C-PEG40,000 intravenously injected into mice showed long retention in circulation, leading to its effective accumulation in tumors reflecting the well-known phenomenon that macromolecules accumulate in tumors because of leaky tumor capillaries. These properties of 13C-PEG40,000 allowed visualization of tumors in mice by 13C spectroscopic imaging. These findings suggest that a technique based on 13C-PEG is a promising strategy for tumor detection.

  14. In vivo single-shot (13)C spectroscopic imaging of hyperpolarized metabolites by spatiotemporal encoding

    Schmidt, Rita; Laustsen, Christoffer; Dumez, Jean-Nicolas;

    2014-01-01

    necessary. Several approaches have been customized for hyperpolarized (13)C MRI, including CSI with a center-out k-space encoding, EPSI, and spectrally selective pulses in combination with spiral EPI acquisitions. Recent studies have described the potential of single-shot alternatives based on...... spatiotemporal encoding (SPEN) principles, to derive chemical-shift images within a sub-second period. By contrast to EPSI, SPEN does not require oscillating acquisition gradients to deliver chemical-shift information: its signal encodes both spatial as well as chemical shift information, at no extra cost in...

  15. Study of the fusion reaction 13C+13C

    The fusion reaction 13C+13C has been studied, it must allow, by comparisons with the system 12C+13C already studied to determine how the presence of a supplementary nucleon in the interaction nuclei of the entrance channel affects the energy dependence of the reaction cross section. The reaction 13C+13C has been studied for incident energies E(CM)=3.05 - 6.88 MeV and no resonant structure seems to appear in the coulombian energies. The reaction products are identified by the energy of their gamma transition using a germanium detector situated at zero degree with respect to the incident beam at approximately 1 cm from the target

  16. SPARTA+: a modest improvement in empirical NMR chemical shift prediction by means of an artificial neural network

    NMR chemical shifts provide important local structural information for proteins and are key in recently described protein structure generation protocols. We describe a new chemical shift prediction program, SPARTA+, which is based on artificial neural networking. The neural network is trained on a large carefully pruned database, containing 580 proteins for which high-resolution X-ray structures and nearly complete backbone and 13Cβ chemical shifts are available. The neural network is trained to establish quantitative relations between chemical shifts and protein structures, including backbone and side-chain conformation, H-bonding, electric fields and ring-current effects. The trained neural network yields rapid chemical shift prediction for backbone and 13Cβ atoms, with standard deviations of 2.45, 1.09, 0.94, 1.14, 0.25 and 0.49 ppm for δ15N, δ13C', δ13Cα, δ13Cβ, δ1Hα and δ1HN, respectively, between the SPARTA+ predicted and experimental shifts for a set of eleven validation proteins. These results represent a modest but consistent improvement (2-10%) over the best programs available to date, and appear to be approaching the limit at which empirical approaches can predict chemical shifts.

  17. Determination of the DNA sugar pucker using 13C NMR spectroscopy

    Solid-state 13C NMR spectroscopy of a series of crystalline nucleosides and nucleotides allows direct measurement of the effect of the deoxyribose ring conformation on the carbon chemical shift. It is found that 3'-endo conformers have 3' and 5' chemical shifts significantly (5-10 ppm) upfield of comparable 3'-exo and 2'-endo conformers. The latter two conformers may be distinguished by smaller but still significant differences in the carbon chemical shifts at the C-2' and C-4' positions. High-resolution solid-state NMR of three modifications of fibrous calf thymus DNA shows that these trends are maintained in high-molecular-weight DNA and confirms that the major ring pucker in A-DNA is 3'-endo, while both B-DNA and C-DNA are largely 2'-endo. The data show that 13C NMR spectroscopy is a straightforward and useful probe of DNA ring pucker in both solution and the solid state

  18. LAMPF polarized 13C targets

    Ethylene glycol, 1-butanol, and toluene highly enriched in 13C have been used at LAMPF to produce dynamically polarized 13C targets for scattering experiments with protons and pions. Preparation of the materials and characteristic properties of these targets are described. 17 refs., 1 fig

  19. Conformational propensities of intrinsically disordered proteins from NMR chemical shifts

    The realization that a protein can be fully functional even in the absence of a stable three-dimensional structure has motivated a large number of studies describing the conformational behaviour of these proteins at atomic resolution. Here, we review recent advances in the determination of local structural propensities of intrinsically disordered proteins (IDPs) from experimental NMR chemical shifts. A mapping of the local structure in IDPs is of paramount importance in order to understand the molecular details of complex formation, in particular, for IDPs that fold upon binding or undergo structural transitions to pathological forms of the same protein. We discuss experimental strategies for the spectral assignment of IDPs, chemical shift prediction algorithms and the generation of representative structural ensembles of IDPs on the basis of chemical shifts. Additionally, we highlight the inherent degeneracies associated with the determination of IDP sub-state populations from NMR chemical shifts alone. (authors)

  20. Synthesis and applications of 13C glycerol

    The authors are currently developing new synthetic routes to the various isotopomers of glycerol. Labeled glycerol is useful for 13C enrichment of biomolecules. However, traditional methods of glycerol synthesis are not easily adapted for isotopic enrichment or have poor overall yields (12-15%). In addition, the use of glycerol for enrichment can be prohibitively expensive and its availability depends on the level of demand. The authors have developed a short de novo synthesis of [U-13C]glycerol from carbon dioxide (∼53% overall yield for four steps) and are currently examining the feasibility of synthesizing site-specific 13C labeled glycerol and dihydroxyacetone (DHA) from methanol and carbon dioxide. The authors have examined the enzymatic conversion of [U-13C]glycerol to glyceraldehyde-3-monophosphate or dihydroxyacetone monophosphate (DHAP) with yields ranging from 25-50% (as determined by NMR spectroscopy). The authors are also pursuing the chemical conversion of 13C labeled DHA to DHAP and the results are presented. Labeled DHAP is a possible enzymatic precursor for both labeled 2-deoxyribose and 2-deoxyribonucleic acids

  1. Simultaneous hyperpolarized (13)C-pyruvate MRI and (18)F-FDG-PET in cancer (hyperPET)

    Borgwardt, Henrik Gutte; Hansen, Adam E; Henriksen, Sarah T; Johannesen, Helle H; Ardenkjær-Larsen, Jan Henrik; Vignaud, Alexandre; Hansen, Anders E; Børresen, Betina; Klausen, Thomas L; Wittekind, Anne-Mette N; Gillings, Nic; Kristensen, Annemarie T; Clemmensen, Andreas; Højgaard, Liselotte; Kjær, Andreas

    2015-01-01

    23 mL hyperpolarized (13)C-pyruvate. Peak heights of (13)C-pyruvate and (13)C-lactate were quantified using a general linear model. Anatomic (1)H-MRI included axial and coronal T1 vibe, coronal T2-tse and axial T1-tse with fat saturation following gadolinium injection. In the tumor we found clearly...... have named this concept hyper PET. Intravenous injection of the hyperpolarized (13)C-pyruvate results in an increase of (13)C-lactate, (13)C-alanine and (13)C-CO2 ((13)C-HCO3) resonance peaks relative to the tissue, disease and the metabolic state probed. Accordingly, with dynamic nuclear polarization...... local recurrence of a liposarcoma on the right forepaw was imaged using a combined PET/MR clinical scanner. PET was performed as a single-bed, 10 min acquisition, 107 min post injection of 310 MBq (18)F-FDG. (13)C-chemical shift imaging (CSI) was performed just after FDG-PET and 30 s post injection of...

  2. Degradation of mangrove tissues by arboreal termites (Nasutitermes acajutlae) and their role in the mangrove C cycle (Puerto Rico): Chemical characterization and organic matter provenance using bulk δ13C, C/N, alkaline CuO oxidation-GC/MS, and solid-state 13C NMR

    Vane, Christopher H.; Kim, Alexander W.; Moss-Hayes, Vicky; Snape, Colin E.; Diaz, Miguel Castro; Khan, Nicole S.; Engelhart, Simon E.; Horton, Benjamin P.

    2013-08-01

    Arboreal termites are wood decaying organisms that play an important role in the first stages of C cycling in mangrove systems. The chemical composition of Rhizophora mangle, Avicennia germinans, and Laguncularia racemosa leaf, stem, and pneumatophore tissues as well as associated sediments was compared to that of nests of the termite Nasutitermes acajutlae. Nests gave δ13C values of -26.1 to -27.2‰ (±0.1) and C/N of 43.3 (±2.0) to 98.6 (±16.2) which were similar to all stem and pneumatophores but distinct from mangrove leaves or sediments. Organic matter processed by termites yielded lignin phenol concentrations (Λ, lambda) that were 2-4 times higher than stem or pneumatophores and 10-20 times higher than that of leaves or sediments, suggesting that the nests were more resistant to biodegradation than the mangrove vegetation source. 13C NMR revealed that polysaccharide content of mangrove tissues (50-69% C) was higher than that of the nests (46-51% C). Conversely, lignin accounted for 16.2-19.6% C of nest material, a threefold increase relative to living mangrove tissues; a similar increase in aromatic methoxyl content was also observed in the nests. Lipids (aliphatic and paraffinic moieties) were also important but rather variable chemical components of all three mangrove species, representing between 13.5 and 28.3% of the C content. Termite nests contained 3.14 Mg C ha-1 which represents approximately 2% of above ground C storage in mangroves, a value that is likely to increase upon burial due to their refractory chemical composition.

  3. Complete 1H and 13C NMR assignments and anti fungal activity of two 8-hydroxy flavonoids in mixture

    A mixture of the two new flavonols 8-hydroxy-3, 4', 5, 6, 7-pentamethoxyflavone (1) and 8-hydroxy-3, 3', 4', 5, 6, 7-hexamethoxyflavone (2) was isolated from a commercial sample of Citrus aurantifolia. An array of one- (1H NMR, {1H} -13C NMR, and APT-13C NMR) and two-dimensional NMR techniques (COSY, NOESY, HMQC and HMBC) was used to achieve the structural elucidation and the complete 1H and 13C chemical shift assignments of these natural compounds. In addition, the antifungal activity of these compounds against phytopathogenic and human pathogenic fungi was investigated. (author)

  4. An evaluation of chemical shift index-based secondary structure determination in proteins: Influence of random coil chemical shifts

    Mielke, S.P.; Krishnan, V.V. [Biophysics Graduate Group, University of California, Davis (United States)], E-mail: krish@llnl.gov

    2004-10-15

    Random coil chemical shifts are commonly used to detect protein secondary structural elements in chemical shift index (CSI) calculations. Though this technique is widely used and seems reliable for folded proteins, the choice of reference random coil chemical shift values can significantly alter the outcome of secondary structure estimation. In order to evaluate these effects, we present a comparison of secondary structure content calculated using CSI, based on five different reference random coil chemical shift value sets, to that derived from three-dimensional structures. Our results show that none of the reference random coil data sets chosen for evaluation fully reproduces the actual secondary structures. Among the reference values generally available to date, most tend to be good estimators only of helices. Based on our evaluation, we recommend the experimental values measured by Schwarzinger et al. (2000), and statistical values obtained by Lukin et al. (1997), as good estimators of both helical and sheet content.

  5. Bayesian inference of protein structure from chemical shift data

    Bratholm, Lars Andersen; Christensen, Anders Steen; Hamelryck, Thomas Wim; Jensen, Jan Halborg

    2015-01-01

    Protein chemical shifts are routinely used to augment molecular mechanics force fields in protein structure simulations, with weights of the chemical shift restraints determined empirically. These weights, however, might not be an optimal descriptor of a given protein structure and predictive model...... chain Monte Carlo simulations of three small proteins (ENHD, Protein G and the SMN Tudor Domain) using the PROFASI force field and the chemical shift predictor CamShift. Using a clustering-criterion for identifying the best structure, together with the addition of a solvent exposure scoring term, the......, result in overall better convergence to the native fold, suggesting that both types of distribution might be useful in different aspects of the protein structure prediction....

  6. Bayesian inference of protein structure from chemical shift data

    Lars A. Bratholm

    2015-03-01

    Full Text Available Protein chemical shifts are routinely used to augment molecular mechanics force fields in protein structure simulations, with weights of the chemical shift restraints determined empirically. These weights, however, might not be an optimal descriptor of a given protein structure and predictive model, and a bias is introduced which might result in incorrect structures. In the inferential structure determination framework, both the unknown structure and the disagreement between experimental and back-calculated data are formulated as a joint probability distribution, thus utilizing the full information content of the data. Here, we present the formulation of such a probability distribution where the error in chemical shift prediction is described by either a Gaussian or Cauchy distribution. The methodology is demonstrated and compared to a set of empirically weighted potentials through Markov chain Monte Carlo simulations of three small proteins (ENHD, Protein G and the SMN Tudor Domain using the PROFASI force field and the chemical shift predictor CamShift. Using a clustering-criterion for identifying the best structure, together with the addition of a solvent exposure scoring term, the simulations suggests that sampling both the structure and the uncertainties in chemical shift prediction leads more accurate structures compared to conventional methods using empirical determined weights. The Cauchy distribution, using either sampled uncertainties or predetermined weights, did, however, result in overall better convergence to the native fold, suggesting that both types of distribution might be useful in different aspects of the protein structure prediction.

  7. Valence neutrons' role in the collisions 13C+12C and 13C+13C

    The resonant behaviour is not limited to collisions between α-like nuclei: resonance structures have been observed in the direct channels for the 13C+12C and 13C+13C collisions; in the contrary, the resonances observed in the fusion channels are not so pronounced as in the 12C+12C case: the valence neutrons increase the number of reaction channels and the density of states in the states in the compound nuclei, the resonances are therefore 'washed out' and it is difficult to observe them experimentally

  8. Magnetic resonance butterfly coils: Design and application for hyperpolarized 13C studies

    Giovannetti, Giulio; Frijia, Francesca; Attanasio, Simona;

    2013-01-01

    Hyperpolarized 13C magnetic resonance spectroscopy in pig models enables cardiac metabolism assessment and provides a powerful tool for heart physiology studies, although the low molar concentration of derivate metabolites gives rise to technological limitations in terms of data quality. The design...... coil throughout the volume of interest for cardiac imaging in pig. Experimental SNR-vs-depth profiles, extracted from the [1-13C]acetate phantom chemical shift image (CSI), permitted to highlight the performance of the proposed coils configuration. © 2013 Elsevier Ltd. All rights reserved....

  9. 13 C and 31 P NMR use in phosphinite synthesis and rhodium cationic catalysts accompaniment

    Several studies on rigid cyclic frameworks have been developed recently. This work shows the use of 13 C and 31 P NMR analysis for identifying and characterizing the molecular structures of phosphinites, thiophosphinites and rhodium catalysts. The phosphinites were synthesized and rhodium complexes prepared from them, aiming the catalysts synthesis for hydrogenation processes. Synthesizing phosphinites and thiophosphinites, alcohols on their racemic form were used, therefore, the catalysts were obtained as diasteroisomers. 13 C and 31 P NMR data are discussed in details and chemical shifts are also analysed

  10. Improving the chemical shift dispersion of multidimensional NMR spectra of intrinsically disordered proteins

    Bermel, Wolfgang [Bruker BioSpin GmbH (Germany); Bruix, Marta [Consejo Superior de Investigaciones Cientificas, Instituto de Quimica Fisica ' ' Rocasolano' ' (Spain); Felli, Isabella C., E-mail: felli@cerm.unifi.it [University of Florence, Department of Chemistry ' Ugo Shiff' (Italy); Kumar, M.V. Vasantha [University of Florence, Magnetic Resonance Center (Italy); Pierattelli, Roberta, E-mail: pierattelli@cerm.unifi.it [University of Florence, Department of Chemistry ' Ugo Shiff' (Italy); Serrano, Soraya [Consejo Superior de Investigaciones Cientificas, Instituto de Quimica Fisica ' ' Rocasolano' ' (Spain)

    2013-03-15

    Intrinsically disordered proteins (IDPs) have recently attracted the attention of the scientific community challenging the well accepted structure-function paradigm. In the characterization of the dynamic features of proteins nuclear magnetic resonance spectroscopy (NMR) is a strategic tool of investigation. However the peculiar properties of IDPs, with the lack of a unique 3D structure and their high flexibility, have a strong impact on NMR observables (low chemical shift dispersion, efficient solvent exchange broadening) and thus on the quality of NMR spectra. Key aspects to be considered in the design of new NMR experiments optimized for the study of IDPs are discussed. A new experiment, based on direct detection of {sup 13}C{sup {alpha}}, is proposed.

  11. Application of unsymmetrical indirect covariance NMR methods to the computation of the (13)C (15)N HSQC-IMPEACH and (13)C (15)N HMBC-IMPEACH correlation spectra.

    Martin, Gary E; Hilton, Bruce D; Irish, Patrick A; Blinov, Kirill A; Williams, Antony J

    2007-10-01

    Utilization of long-range (1)H--(15)N heteronuclear chemical shift correlation has continually grown in importance since the first applications were reported in 1995. More recently, indirect covariance NMR methods have been introduced followed by the development of unsymmetrical indirect covariance processing methods. The latter technique has been shown to allow the calculation of hyphenated 2D NMR data matrices from more readily acquired nonhyphenated 2D NMR spectra. We recently reported the use of unsymmetrical indirect covariance processing to combine (1)H--(13)C GHSQC and (1)H--(15)N GHMBC long-range spectra to yield a (13)C--(15)N HSQC-HMBC chemical shift correlation spectrum that could not be acquired in a reasonable period of time without resorting to (15)N-labeled molecules. We now report the unsymmetrical indirect covariance processing of (1)H--(13)C GHMBC and (1)H--(15)N IMPEACH spectra to afford a (13)C--(15)N HMBC-IMPEACH spectrum that has the potential to span as many as six to eight bonds. Correlations for carbon resonances long-range coupled to a protonated carbon in the (1)H--(13)C HMBC spectrum are transferred via the long-range (1)H--(15)N coupling pathway in the (1)H--(15)N IMPEACH spectrum to afford a much broader range of correlation possibilities in the (13)C--(15)N HMBC-IMPEACH correlation spectrum. The indole alkaloid vincamine is used as a model compound to illustrate the application of the method. PMID:17729230

  12. Data requirements for reliable chemical shift assignments in deuterated proteins

    The information required for chemical shift assignments in large deuterated proteins was investigated using a Monte Carlo approach (Hitchens et al., 2002). In particular, the consequences of missing amide resonances on the reliability of assignments derived from Cα and CO or from Cα and Cβ chemical shifts was investigated. Missing amide resonances reduce both the number of correct assignments as well as the confidence in these assignments. More significantly, a number of undetectable errors can arise when as few as 9% of the amide resonances are missing from the spectra. However, the use of information from residue specific labeling as well as local and long-range distance constraints improves the reliability and extent of assignment. It is also shown that missing residues have only a minor effect on the assignment of protein-ligand complexes using Cα and CO chemical shifts and Cα inter-residue connectivity, provided that the known chemical shifts of the unliganded protein are utilized in the assignment process

  13. Phenyl galactopyranosides – {sup 13}C CPMAS NMR and conformational analysis using genetic algorithm

    Wałejko, Piotr, E-mail: pwalejko@uwb.edu.pl [University of Bialystok, Institute of Chemistry, Pilsudskiego 11/4, 15-443 Bialystok (Poland); Paradowska, Katarzyna, E-mail: katarzyna.paradowska@wum.edu.pl [Medical University of Warsaw, Faculty of Pharmacy, Department of Physical Chemistry, Banacha 1, 02-097 Warsaw (Poland); Bukowicki, Jarosław [Medical University of Warsaw, Faculty of Pharmacy, Department of Physical Chemistry, Banacha 1, 02-097 Warsaw (Poland); Witkowski, Stanisław [University of Bialystok, Institute of Chemistry, Pilsudskiego 11/4, 15-443 Bialystok (Poland); Wawer, Iwona [Medical University of Warsaw, Faculty of Pharmacy, Department of Physical Chemistry, Banacha 1, 02-097 Warsaw (Poland)

    2015-08-18

    Highlights: • The structures of phenyl galactosides were studied by {sup 13}C CPMAS NMR. • The GAAGS method was used in conformational analysis of phenyl galactosides. • The rotation of the aglycone was investigated. • {sup 13}C CPMAS NMR supported by GIAO DFT calculations was used as a verification method. - Abstract: Structural analyses of four compounds (phenyl 2,3,4,6-tetra-O-acetyl-β-D-galactopyranoside (1), phenyl β-D-galactopyranoside (2), phenyl 2,3,4,6-tetra-O-acetyl-α-D-galactopyranoside (3) and phenyl α-D-galactopyranoside (4)) have been performed using solid-state {sup 13}C MAS NMR spectroscopy and theoretical methods. Conformational analysis involved grid search and genetic algorithm (GAAGS). Low-energy conformers found by GAAGS were further optimized by DFT and chemical shifts were calculated using GIAO/DFT approach. {sup 13}C CPMAS NMR chemical shift of carbon C2 is indicative of the glycoside torsional angle. Separated or merged resonances of C2 and C6 suggest free rotation of phenyl ring in the solid phase.

  14. Phenyl galactopyranosides – 13C CPMAS NMR and conformational analysis using genetic algorithm

    Highlights: • The structures of phenyl galactosides were studied by 13C CPMAS NMR. • The GAAGS method was used in conformational analysis of phenyl galactosides. • The rotation of the aglycone was investigated. • 13C CPMAS NMR supported by GIAO DFT calculations was used as a verification method. - Abstract: Structural analyses of four compounds (phenyl 2,3,4,6-tetra-O-acetyl-β-D-galactopyranoside (1), phenyl β-D-galactopyranoside (2), phenyl 2,3,4,6-tetra-O-acetyl-α-D-galactopyranoside (3) and phenyl α-D-galactopyranoside (4)) have been performed using solid-state 13C MAS NMR spectroscopy and theoretical methods. Conformational analysis involved grid search and genetic algorithm (GAAGS). Low-energy conformers found by GAAGS were further optimized by DFT and chemical shifts were calculated using GIAO/DFT approach. 13C CPMAS NMR chemical shift of carbon C2 is indicative of the glycoside torsional angle. Separated or merged resonances of C2 and C6 suggest free rotation of phenyl ring in the solid phase

  15. CO{sub H}(N)CACB experiments for assigning backbone resonances in {sup 13}C/{sup 15}N-labeled proteins

    Astrof, Nathan; Bracken, Clay; Cavanagh, John; Palmer, Arthur G

    1998-05-15

    A triple resonance NMR experiment, denoted CO{sub H}(N)CACB, correlates{sup 1}H{sup N} and {sup 13}CO spins with the{sup 13}C{sup {alpha}} and{sup 13}C{sup {beta}} spins of adjacent amino acids. The pulse sequence is an 'out-and-back' design that starts with{sup 1}H{sup N} magnetization and transfers coherence via the {sup 15}N spin simultaneously to the {sup 13}CO and{sup 13}C{sup {alpha}} spins, followed by transfer to the{sup 13}C{sup {beta}} spin. Two versions of the sequence are presented: one in which the {sup 13}CO spins are frequency labeled during an incremented t{sub 1} evolution period prior to transfer of magnetization from the {sup 13}C{sup {alpha}} to the{sup 13}C{sup {beta}} resonances, and one in which the{sup 13}CO spins are frequency labeled in a constant-time manner during the coherence transfer to and from the{sup 13}C{sup {beta}} resonances. Because {sup 13}COand {sup 15}N chemical shifts are largely uncorrelated, the technique will be especially useful when degeneracy in the{sup 1}H{sup N}-{sup 15}N chemical shifts hinders resonance assignment. The CO{sub H}(N)CACB experiment is demonstrated using uniformly {sup 13}C/{sup 15}N-labeled ubiquitin.

  16. Pressure dependence of backbone chemical shifts in the model peptides Ac-Gly-Gly-Xxx-Ala-NH2.

    Erlach, Markus Beck; Koehler, Joerg; Crusca, Edson; Kremer, Werner; Munte, Claudia E; Kalbitzer, Hans Robert

    2016-06-01

    For a better understanding of nuclear magnetic resonance (NMR) detected pressure responses of folded as well as unstructured proteins the availability of data from well-defined model systems are indispensable. In this work we report the pressure dependence of chemical shifts of the backbone atoms (1)H(α), (13)C(α) and (13)C' in the protected tetrapeptides Ac-Gly-Gly-Xxx-Ala-NH2 (Xxx one of the 20 canonical amino acids). Contrary to expectation the chemical shifts of these nuclei have a nonlinear dependence on pressure in the range from 0.1 to 200 MPa. The polynomial pressure coefficients B 1 and B 2 are dependent on the type of amino acid studied. The coefficients of a given nucleus show significant linear correlations suggesting that the NMR observable pressure effects in the different amino acids have at least partly the same physical cause. In line with this observation the magnitude of the second order coefficients of nuclei being direct neighbors in the chemical structure are also weakly correlated. PMID:27335085

  17. The Effect of Solvent Accessible Surface on Hammett-Type Dependencies of Infinite Dilution 29Si and 13C NMR Shifts in Ring Substituted Silylated Phenols Dissolved in Chloroform and Acetone

    Blechta, Vratislav; Šabata, Stanislav; Sýkora, Jan; Hetflejš, Jiří; Soukupová, Ludmila; Schraml, Jan

    2012-01-01

    Roč. 50, č. 2 (2012), s. 128-134. ISSN 0749-1581 R&D Projects: GA AV ČR IAA400720706; GA ČR GA203/06/0738 Institutional research plan: CEZ:AV0Z40720504 Keywords : 1H NMR * 13C NMR * 29Si NMR Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 1.528, year: 2012

  18. Solid state NMR of proteins at high MAS frequencies: symmetry-based mixing and simultaneous acquisition of chemical shift correlation spectra

    Bellstedt, Peter [Fritz Lipmann Institute, Biomolecular NMR spectroscopy, Leibniz Institute for Age Research (Germany); Herbst, Christian [Ubon Ratchathani University, Department of Physics, Faculty of Science (Thailand); Haefner, Sabine; Leppert, Joerg; Goerlach, Matthias; Ramachandran, Ramadurai, E-mail: raman@fli-leibniz.de [Fritz Lipmann Institute, Biomolecular NMR spectroscopy, Leibniz Institute for Age Research (Germany)

    2012-12-15

    We have carried out chemical shift correlation experiments with symmetry-based mixing sequences at high MAS frequencies and examined different strategies to simultaneously acquire 3D correlation spectra that are commonly required in the structural studies of proteins. The potential of numerically optimised symmetry-based mixing sequences and the simultaneous recording of chemical shift correlation spectra such as: 3D NCAC and 3D NHH with dual receivers, 3D NC Prime C and 3D C Prime NCA with sequential {sup 13}C acquisitions, 3D NHH and 3D NC Prime H with sequential {sup 1}H acquisitions and 3D CANH and 3D C'NH with broadband {sup 13}C-{sup 15}N mixing are demonstrated using microcrystalline samples of the {beta}1 immunoglobulin binding domain of protein G (GB1) and the chicken {alpha}-spectrin SH3 domain.

  19. Organometallic derivatives of furan. LII. Synthesis of carbofunctional furylsilanes and their 1H, 13C, and 29Si NMR spectroscopic and quantum-chemical investigation

    Under the standard conditions for the synthesis of furan compounds it is possible to obtain the carbofunctional derivatives of silylated furfural with retention of the trimethylsilyl group in the ring. By NMR and CNDO/2 LCAO MO methods and also as a result of the investigation of the chemical characteristics of silylated furfural and its carbofunctional derivatives it was established that the introduction of a trimethylsilyl group at position 5 of the furan ring does not change the reactivity of the carbofunctional substituents at position 2. The electronic effects of the substituents are hardly transmitted through the furan ring at all. The effect of substituents in the carbofunctional furylsilanes on the electronic structure of the ring is additive

  20. Improving 3D structure prediction from chemical shift data

    We report advances in the calculation of protein structures from chemical shift nuclear magnetic resonance data alone. Our previously developed method, CS-Rosetta, assembles structures from a library of short protein fragments picked from a large library of protein structures using chemical shifts and sequence information. Here we demonstrate that combination of a new and improved fragment picker and the iterative sampling algorithm RASREC yield significant improvements in convergence and accuracy. Moreover, we introduce improved criteria for assessing the accuracy of the models produced by the method. The method was tested on 39 proteins in the 50–100 residue size range and yields reliable structures in 70 % of the cases. All structures that passed the reliability filter were accurate (<2 Å RMSD from the reference)

  1. Calculations of NMR chemical shifts with APW-based methods

    Laskowski, Robert; Blaha, Peter

    2012-01-01

    We present a full potential, all electron augmented plane wave (APW) implementation of first-principles calculations of NMR chemical shifts. In order to obtain the induced current we follow a perturbation approach [Pickard and Mauri, Phys. Rev. BPRBMDO1098-012110.1103/PhysRevB.63.245101 63, 245101 (2001)] and extended the common APW + local orbital (LO) basis by several LOs at higher energies. The calculated all-electron current is represented in traditional APW manner as Fourier series in the interstitial region and with a spherical harmonics representation inside the nonoverlapping atomic spheres. The current is integrated using a “pseudocharge” technique. The implementation is validated by comparison of the computed chemical shifts with some “exact” results for spherical atoms and for a set of solids and molecules with available published data.

  2. Improving 3D structure prediction from chemical shift data

    Schot, Gijs van der [Utrecht University, Computational Structural Biology, Bijvoet Center for Biomolecular Research, Faculty of Science-Chemistry (Netherlands); Zhang, Zaiyong [Technische Universitaet Muenchen, Biomolecular NMR and Munich Center for Integrated Protein Science, Department Chemie (Germany); Vernon, Robert [University of Washington, Department of Biochemistry (United States); Shen, Yang [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States); Vranken, Wim F. [VIB, Department of Structural Biology (Belgium); Baker, David [University of Washington, Department of Biochemistry (United States); Bonvin, Alexandre M. J. J., E-mail: a.m.j.j.bonvin@uu.nl [Utrecht University, Computational Structural Biology, Bijvoet Center for Biomolecular Research, Faculty of Science-Chemistry (Netherlands); Lange, Oliver F., E-mail: oliver.lange@tum.de [Technische Universitaet Muenchen, Biomolecular NMR and Munich Center for Integrated Protein Science, Department Chemie (Germany)

    2013-09-15

    We report advances in the calculation of protein structures from chemical shift nuclear magnetic resonance data alone. Our previously developed method, CS-Rosetta, assembles structures from a library of short protein fragments picked from a large library of protein structures using chemical shifts and sequence information. Here we demonstrate that combination of a new and improved fragment picker and the iterative sampling algorithm RASREC yield significant improvements in convergence and accuracy. Moreover, we introduce improved criteria for assessing the accuracy of the models produced by the method. The method was tested on 39 proteins in the 50-100 residue size range and yields reliable structures in 70 % of the cases. All structures that passed the reliability filter were accurate (<2 A RMSD from the reference)

  3. Anisotropy of the fluorine chemical shift tensor in UF6

    An 19F magnetic resonance study of polycrystalline UF6 is presented. The low temperature complex line can be analyzed as the superposition of two distinct lines, which is attributed to a distortion of the UF6 octahedron in the solid. The shape of the two components is studied. Their width is much larger than the theoretical dipolar width, and must be explained by large anisotropies of the fluorine chemical shift tensors. The resulting shape functions of the powder spectra are determined. The values of the parameters of the chemical shift tensors yield estimates of the characters of the U-F bonds, and this gives some information on the ground state electronic wave function of the UF6 molecule in the solid. (author)

  4. Magnetic shift of the chemical freezeout and electric charge fluctuations

    Fukushima, Kenji

    2016-01-01

    We discuss the effect of a strong magnetic field on the chemical freezeout points in the ultra-relativistic heavy-ion collision. As a result of the inverse magnetic catalysis or the magnetic inhibition, the crossover onset to hot and dense matter out of quarks and gluons should be shifted to a lower temperature. To quantify this shift we employ the hadron resonance gas model and an empirical condition for the chemical freezeout. We point out that the charged particle abundances are significantly affected by the magnetic field so that the electric charge fluctuation is largely enhanced especially at high baryon density. The charge conservation partially cancels the enhancement but our calculation shows that the electric charge fluctuation could serve as a magnetometer.

  5. Estimation of optical chemical shift in nuclear spin optical rotation

    Highlights: • Analytical theory of nuclear spin optical rotation (NSOR) is further developed. • Derive formula of NSOR ratio R between different nuclei in a same molecule. • Calculated results of R agree with the experiments. • Analyze influence factors on R and chemical distinction by NSOR. - Abstract: A recently proposed optical chemical shift in nuclear spin optical rotation (NSOR) is studied by theoretical comparison of NSOR magnitude between chemically non-equivalent or different element nuclei in the same molecule. Theoretical expressions of the ratio R between their NSOR magnitudes are derived by using a known semi-empirical formula of NSOR. Taking methanol, tri-ethyl-phosphite and 2-methyl-benzothiazole as examples, the ratios R are calculated and the results approximately agree with the experiments. Based on those, the important influence factors on R and chemical distinction by NSOR are discussed

  6. Chemical-shift MRI of exogenous lipoid pneumonia

    Cox, J.E.; Choplin, R.H.; Chiles, C. [Wake Forest Univ., Winston-Salem, NC (United States)

    1996-05-01

    Exogenous lipoid pneumonia results from the aspiration or inhalation of fatty substances, such as mineral oil found in laxatives or nasal medications containing liquid paraffin. We present standard and lipid-sensitive (chemical-shift) MR findings in a patient with histologically confirmed lipoid pneumonia. The loss of signal intensity in an area of airspace disease on opposed-phase imaging was considered specific for the presence of lipid. 14 refs., 3 figs.

  7. Simultaneous hyperpolarized (13)C-pyruvate MRI and (18)F-FDG-PET in cancer (hyperPET)

    Gutte Borgwardt, Henrik; Hansen, Adam E; Henriksen, Sarah T;

    2015-01-01

    In this paper we demonstrate, for the first time, the feasibility of a new imaging concept - combined hyperpolarized (13)C-pyruvate magnetic resonance spectroscopic imaging (MRSI) and (18)F-FDG-PET imaging. This procedure was performed in a clinical PET/MRI scanner with a canine cancer patient. We...... have named this concept hyper PET. Intravenous injection of the hyperpolarized (13)C-pyruvate results in an increase of (13)C-lactate, (13)C-alanine and (13)C-CO2 ((13)C-HCO3) resonance peaks relative to the tissue, disease and the metabolic state probed. Accordingly, with dynamic nuclear polarization...... local recurrence of a liposarcoma on the right forepaw was imaged using a combined PET/MR clinical scanner. PET was performed as a single-bed, 10 min acquisition, 107 min post injection of 310 MBq (18)F-FDG. (13)C-chemical shift imaging (CSI) was performed just after FDG-PET and 30 s post injection of...

  8. Molecular structure, vibrational and 13C NMR spectra of two ent-kaurenes spirolactone type diterpenoids rabdosinate and rabdosin B: A combined experimental and density functional methods

    Wang, Tao; Wang, Xueliang

    2015-01-01

    The title compounds, rabdosinate and rabdosin B, were isolated from the leaves of Isodon japonica, and characterized by IR-NMR spectroscopy. The molecular geometry, vibrational frequencies and gauge including atomic orbital (GIAO-13C) chemical shift values of the title compounds have been calculated by using DFT/B3LYP method with 6-311++G(d,p) basis set. In addition, obtained results were related to the linear regression of experimental 13C NMR chemical shifts values. The integral equation formalism polarized continuum model (IEFPCM) was used in treating chloroform solvation effects on optimized structural parameters and 13C chemical shifts. Besides, molecular electrostatic potential (MEP), HOMO-LUMO analysis were performed by the B3LYP method.

  9. A study of the molecular conformations and the vibrational, 1H and 13C NMR spectra of the anticancer drug tamoxifen and triphenylethylene

    Badawi, Hassan M.; Khan, Ibrahim

    2016-08-01

    The structural stability and the vibrational spectra of the anticancer drug tamoxifen and triphenylethylene were investigated by the DFT B3LYP/6-311G (d,p) calculations. Tamoxifen and triphenylethylene were predicted to exist predominantly as non-planar structures. The vibrational frequencies and the 1H and 13C NMR chemical shifts of the low energy structures of tamoxifen and triphenylethylene were computed at the DFT B3LYP level of theory. Complete vibrational assignments were provided by combined theoretical and experimental data of tamoxifen and triphenylethylene. The 1H and 13C NMR spectra of both molecules were interpreted by experimental and DFT calculated chemical shifts of the two molecules. The RMSD between experimental and theoretical 1H and 13C chemical shifts for tamoxifen is 0.29 and 4.72 ppm, whereas for triphenylethylene, it is 0.16 and 2.70 ppm, respectively.

  10. Proton-detected 3D 1H/13C/1H correlation experiment for structural analysis in rigid solids under ultrafast-MAS above 60 kHz

    Zhang, Rongchun; Nishiyama, Yusuke; Ramamoorthy, Ayyalusamy

    2015-10-01

    A proton-detected 3D 1H/13C/1H chemical shift correlation experiment is proposed for the assignment of chemical shift resonances, identification of 13C-1H connectivities, and proximities of 13C-1H and 1H-1H nuclei under ultrafast magic-angle-spinning (ultrafast-MAS) conditions. Ultrafast-MAS is used to suppress all anisotropic interactions including 1H-1H dipolar couplings, while the finite-pulse radio frequency driven dipolar recoupling (fp-RFDR) pulse sequence is used to recouple dipolar couplings among protons and the insensitive nuclei enhanced by polarization transfer technique is used to transfer magnetization between heteronuclear spins. The 3D experiment eliminates signals from non-carbon-bonded protons and non-proton-bonded carbons to enhance spectral resolution. The 2D (F1/F3) 1H/1H and 2D 13C/1H (F2/F3) chemical shift correlation spectra extracted from the 3D spectrum enable the identification of 1H-1H proximity and 13C-1H connectivity. In addition, the 2D (F1/F2) 1H/13C chemical shift correlation spectrum, incorporated with proton magnetization exchange via the fp-RFDR recoupling of 1H-1H dipolar couplings, enables the measurement of proximities between 13C and even the remote non-carbon-bonded protons. The 3D experiment also gives three-spin proximities of 1H-1H-13C chains. Experimental results obtained from powder samples of L-alanine and L-histidine ṡ H2O ṡ HCl demonstrate the efficiency of the 3D experiment.

  11. Increased resolution of aromatic cross peaks using alternate {sup 13}C labeling and TROSY

    Milbradt, Alexander G. [AstraZeneca Discovery Sciences, Structure and Biophysics UK (United Kingdom); Arthanari, Haribabu [Harvard Medical School, Department of Biological Chemistry and Molecular Pharmacology (United States); Takeuchi, Koh [National Institute of Advanced Industrial Science and Technology, Biomedicinal Information Research Center and Molecular Profiling Research Center for Drug Discovery (Japan); Boeszoermenyi, Andras; Hagn, Franz; Wagner, Gerhard, E-mail: gerhard-wagner@hms.harvard.edu [Harvard Medical School, Department of Biological Chemistry and Molecular Pharmacology (United States)

    2015-07-15

    For typical globular proteins, contacts involving aromatic side chains would constitute the largest number of distance constraints that could be used to define the structure of proteins and protein complexes based on NOE contacts. However, the {sup 1}H NMR signals of aromatic side chains are often heavily overlapped, which hampers extensive use of aromatic NOE cross peaks. Some of this overlap can be overcome by recording {sup 13}C-dispersed NOESY spectra. However, the resolution in the carbon dimension is rather low due to the narrow dispersion of the carbon signals, large one-bond carbon–carbon (C–C) couplings, and line broadening due to chemical shift anisotropy (CSA). Although it has been noted that the CSA of aromatic carbons could be used in TROSY experiments for enhancing resolution, this has not been used much in practice because of complications arising from large aromatic one-bond C–C couplings, and 3D or 4D carbon dispersed NOESY are typically recorded at low resolution hampering straightforward peak assignments. Here we show that the aromatic TROSY effect can optimally be used when employing alternate {sup 13}C labeling using 2-{sup 13}C glycerol, 2-{sup 13}C pyruvate, or 3-{sup 13}C pyruvate as the carbon source. With the elimination of the strong one-bond C–C coupling, the TROSY effect can easily be exploited. We show that {sup 1}H–{sup 13}C TROSY spectra of alternately {sup 13}C labeled samples can be recorded at high resolution, and we employ 3D NOESY aromatic-TROSY spectra to obtain valuable intramolecular and intermolecular cross peaks on a protein complex.

  12. Characterization of a Mixture of CO2 Adsorption Products in Hyperbranched Aminosilica Adsorbents by (13)C Solid-State NMR.

    Moore, Jeremy K; Sakwa-Novak, Miles A; Chaikittisilp, Watcharop; Mehta, Anil K; Conradi, Mark S; Jones, Christopher W; Hayes, Sophia E

    2015-11-17

    Hyperbranched amine polymers (HAS) grown from the mesoporous silica SBA-15 (hereafter "SBA-15-HAS") exhibit large capacities for CO2 adsorption. We have used static in situ and magic-angle spinning (MAS) ex situ (13)C nuclear magnetic resonance (NMR) to examine the adsorption of CO2 by SBA-15-HAS. (13)C NMR distinguishes the signal of gas-phase (13)CO2 from that of the chemisorbed species. HAS polymers possess primary, secondary, and tertiary amines, leading to multiple chemisorption reaction outcomes, including carbamate (RnNCOO(-)), carbamic acid (RnNCOOH), and bicarbonate (HCO3(-)) moieties. Carbamates and bicarbonate fall within a small (13)C chemical shift range (162-166 ppm), and a mixture was observed including carbamic acid and carbamate, the former disappearing upon evacuation of the sample. By examining the (13)C-(14)N dipolar coupling through low-field (B0 = 3 T) (13)C{(1)H} cross-polarization MAS NMR, carbamate is confirmed through splitting of the (13)C resonance. A third species that is either bicarbonate or a second carbamate is evident from bimodal T2 decay times of the ∼163 ppm peak, indicating the presence of two species comprising that single resonance. The mixture of products suggests that (1) the presence of amines and water leads to bicarbonate being present and/or (2) the multiple types of amine sites in HAS permit formation of chemically distinct carbamates. PMID:26477882

  13. 40 CFR 721.6505 - Polymers of C13C15 oxoalcohol ethoxolates.

    2010-07-01

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

  14. Substituent effects on 61Ni NMR chemical shifts

    Bühl, Michael; Peters, Dietmund; Herges, Rainer

    2009-01-01

    Ni-61 chemical shifts of Ni(all-trans-cdt) L (cdt = cyclododecatriene, L = none, CO, PMe3), Ni(CO)(4), Ni(C2H4)(2)(PMe3), Ni(cod)(2) (cod = cyclooctadiene) and Ni(PX3)(4) (X = Me, F, Cl) are computed at the GIAO (gauge-including atomic orbitals), BPW91, B3LYP and BHandHLYP levels, using BP86-optimised geometries and an indirect referencing scheme. For this set of compounds, substituent effects on delta(Ni-61) are better described with hybrid functionals than with the pure BPW91 functional. On...

  15. 13C NMR of methane in an AlPO4-11 molecular sieve: Exchange effects and shielding anisotropy

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

    1998-12-01

    13C NMR spectra of 13CH4 in an AlPO4-11 molecular sieve reveal exchange effects between adsorbed and nonadsorbed methane gas. An application of pulsed field gradients is introduced to decrease nonadsorbed and exchanging gas signals in order to extract the chemical shift anisotropy line shape of the adsorbed gas. The resulting 13C shielding anisotropy of methane is compared to existing value for methane in related SAPO-11 material. Less anisotropic shielding is observed in AlPO4-11, most likely due to the lack of charge-compensating cations.

  16. Toward dynamic isotopomer analysis in the rat brain in vivo: automatic quantitation of 13C NMR spectra using LCModel

    Henry, Pierre-Gilles; Oz, Gülin; Provencher, Stephen; Gruetter, Rolf

    2003-01-01

    The LCModel method was adapted to analyze localized in vivo (13)C NMR spectra obtained from the rat brain in vivo at 9.4 T. Prior knowledge of chemical-shifts, J-coupling constants and J-evolution was included in the analysis. Up to 50 different isotopomer signals corresponding to 10 metabolites were quantified simultaneously in 400 microl volumes in the rat brain in vivo during infusion of [1,6-(13)C(2)]glucose. The analysis remained accurate even at low signal-to-noise ratio of the order of...

  17. Backbone and Ile-δ1, Leu, Val Methyl 1H, 13C and 15N NMR chemical shift assignments for human interferon-stimulated gene 15 protein

    Yin, Cuifeng; Aramini, James M.; Ma, LiChung; Cort, John R.; Swapna, G.V.T.; Krug, R. M.; Montelione, Gaetano

    2011-10-01

    Human interferon-stimulated gene 15 protein (ISG15), also called ubiquitin cross-reactive protein (UCRP), is the first identified ubiquitin-like protein containing two ubiquitin-like domains fused in tandem. The active form of ISG15 is conjugated to target proteins via the C-terminal glycine residue through an isopeptide bond in a manner similar to ubiquitin. The biological role of ISG15 is strongly associated with the modulation of cell immune function, and there is mounting evidence suggesting that many viral pathogens evade the host innate immune response by interfering with ISG15 conjugation to both host and viral proteins in a variety of ways. Here we report nearly complete backbone 1HN, 15N, 13CO, and 13Ca, as well as side chain 13Cb, methyl (Ile-d1, Leu, Val), amide (Asn, Gln), and indole NH (Trp) NMR resonance assignments for the 157-residue human ISG15 protein. These resonance assignments provide the basis for future structural and functional solution NMR studies of the biologically important human ISG15 protein.

  18. NMR chemical shifts in amino acids: Effects of environments, electric field, and amine group rotation

    The authors present calculations of NMR chemical shifts in crystalline phases of some representative amino acids such as glycine, alanine, and alanyl-alanine. To get an insight on how different environments affect the chemical shifts, they study the transition from the crystalline phase to completely isolated molecules of glycine. In the crystalline limit, the shifts are dominated by intermolecular hydrogen-bonds. In the molecular limit, however, dipole electric field effects dominate the behavior of the chemical shifts. They show that it is necessary to average the chemical shifts in glycine over geometries. Tensor components are analyzed to get the angle dependent proton chemical shifts, which is a more refined characterization method

  19. (13) C-TmDOTA as versatile thermometer compound for solid-state NMR of hydrated lipid bilayer membranes.

    Umegawa, Yuichi; Tanaka, Yuya; Nobuaki, Matsumori; Murata, Michio

    2016-03-01

    Recent advances in solid-state nuclear magnetic resonance (NMR) techniques, such as magic angle spinning and high-power decoupling, have dramatically increased the sensitivity and resolution of NMR. However, these NMR techniques generate extra heat, causing a temperature difference between the sample in the rotor and the variable temperature gas. This extra heating is a particularly crucial problem for hydrated lipid membrane samples. Thus, to develop an NMR thermometer that is suitable for hydrated lipid samples, thulium-1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetate (TmDOTA) was synthesized and labeled with (13) C (i.e., (13) C-TmDOTA) to increase the NMR sensitivity. The complex was mixed with a hydrated lipid membrane, and the system was subjected to solid-state NMR and differential scanning calorimetric analyses. The physical properties of the lipid bilayer and the quality of the NMR spectra of the membrane were negligibly affected by the presence of (13) C-TmDOTA, and the (13) C chemical shift of the complex exhibited a large-temperature dependence. The results demonstrated that (13) C-TmDOTA could be successfully used as a thermometer to accurately monitor temperature changes induced by (1) H decoupling pulses and/or by magic angle spinning and the temperature distribution of the sample inside the rotor. Thus, (13) C-TmDOTA was shown to be a versatile thermometer for hydrated lipid assemblies. Copyright © 2015 John Wiley & Sons, Ltd. PMID:26460094

  20. Correlations of the chemical shift on fasly rotating biological solids by means of NMR spectroscopy; Korrelationen der chemischen Verschiebung an schnell rotierenden biologischen Festkoerpern mittels NMR-Spektroskopie

    Herbst, Christian

    2010-04-27

    The basic aim of the thesis was the development and improvement of homo- and heteronuclear feedback sequences for the generation of correlation spectra of the chemical shift. In a first step the possibility of the acquisition of {sup 13}C-{sup 13} correlation spectra of the chemical shift by means of inversion pulses with low RF power factor was studied. Furthermore it was shown that broad-band phase-modulated inversion and universal rotational pulses can be constructed by means of global optimization procedures like the genetic algorithms under regardment of the available RF field strength. By inversion, universal rotational, and 360 pulses as starting values of the optimization efficient homonuclear CN{sub n}{sup {nu}} and RN{sub n}{sup {nu}} mixing sequences as well as heteronuclear RN{sub n}{sup {nu}{sub s},{nu}{sub k}} feedback sequences were generated. The satisfactory power of the numerically optimized sequences was shown by means of the simulation as well by means of correlation experiments of the chemical shift of L-histidine, L-arginine, and the (CUG){sub 97}-RNA. This thesis deals furthermore with the possibility to acquire simultaneously different signals with several receivers. By means of numerically optimized RN{sub n}{sup {nu}{sub s},{nu}{sub k}} pulse sequences both {sup 15}N-{sup 13}C and {sup 13}C-{sup 15}N correlation spectra were simultaneously generated. Furthermore it could be shown that the simultaneous acquisition of 3D-{sup 15}N-{sup 13}C-{sup 13}C and {sup 13}C-{sup 15}N-({sup 1}H)-{sup 1}H correlation spectra is possible. By this in only one measurement process resonance assignments can be met and studies of the global folding performed. A further application of several receivers is the simultaneous acquisition of CHHC, NHHN, NHHC, as well as CHHN spectra. By such experiments it is possible to characterize the hydrogen-bonding pattern and the glycosidic torsion angle {sup {chi}} in RNA. This was demonstrated by means of the (CUG){sub 97

  1. (13)C NMR Studies, Molecular Order, and Mesophase Properties of Thiophene Mesogens.

    Veeraprakash, B; Lobo, Nitin P; Narasimhaswamy, T

    2015-12-01

    Three-ring mesogens with a core comprising thiophene linked to one phenyl ring directly and to the other via flexible ester are synthesized with terminal alkoxy chains to probe the mesophase properties and find the molecular order. The phenyl thiophene link in the core offers a comparison of the mesophase features with the molecular shape of the mesogen. The synthesized mesogens display enantiotropic polymesomorphism and accordingly nematic, smectic A, smectic C and smectic B mesophases are perceived depending upon the terminal chain length. For some of the homologues, monotropic higher order smectic phases such as smectic F and crystal E are also witnessed. The existence of polymesomorphism are originally observed by HOPM and DSC and further confirmed by powder X-ray diffraction studies. For the C8 homologue, high resolution solid state (13)C NMR spectroscopy is employed to find the molecular structure in the liquid crystalline phase and using the 2D SLF technique, the (13)C-(1)H dipolar couplings are extracted to calculate the order parameter. By comparing the ratio of local order of thiophene as well as phenyl rings, we establish the bent-core shape of the mesogen. Importantly, for assigning the carbon chemical shifts of the core unit of aligned C8 mesogen, the (13)C NMR measured in mesophase of the synthetic intermediate is employed. Thus, the proposed approach addresses the key step in the spectral assignment of target mesogens with the use of (13)C NMR data of mesomorphic intermediate. PMID:26551439

  2. Computational Assignment of Chemical Shifts for Protein Residues

    Bratholm, Lars A

    2013-01-01

    Fast and accurate protein structure prediction is one of the major challenges in structural biology, biotechnology and molecular biomedicine. These fields require 3D protein structures for rational design of proteins with improved or novel properties. X-ray crystallography is the most common approach even with its low success rate, but lately NMR based approaches have gained popularity. The general approach involves a set of distance restraints used to guide a structure prediction, but simple NMR triple-resonance experiments often provide enough structural information to predict the structure of small proteins. Previous protein folding simulations that have utilised experimental data have weighted the experimental data and physical force field terms more or less arbitrarily, and the method is thus not generally applicable to new proteins. Furthermore a complete and near error-free assignment of chemical shifts obtained by the NMR experiments is needed, due to the static, or deterministic, assignment. In this ...

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

    The use of 13C NMR relaxation dispersion experiments to monitor micro-millisecond fluctuations in the protonation states of histidine residues in proteins is investigated. To illustrate the approach, measurements on three specifically 13C labeled histidine residues in plastocyanin (PCu) from Anabaena variabilis (A.v.) are presented. Significant Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion is observed for 13Cε1 nuclei in the histidine imidazole rings of A.v. PCu. The chemical shift changes obtained from the CPMG dispersion data are in good agreement with those obtained from the chemical shift titration experiments, and the CPMG derived exchange rates agree with those obtained previously from 15N backbone relaxation measurements. Compared to measurements of backbone nuclei, 13Cε1 dispersion provides a more direct method to monitor interchanging protonation states or other kinds of conformational changes of histidine side chains or their environment. Advantages and shortcomings of using the 13Cε1 dispersion experiments in combination with chemical shift titration experiments to obtain information on exchange dynamics of the histidine side chains are discussed

  4. Accurate calculation of (31)P NMR chemical shifts in polyoxometalates.

    Pascual-Borràs, Magda; López, Xavier; Poblet, Josep M

    2015-04-14

    We search for the best density functional theory strategy for the determination of (31)P nuclear magnetic resonance (NMR) chemical shifts, δ((31)P), in polyoxometalates. Among the variables governing the quality of the quantum modelling, we tackle herein the influence of the functional and the basis set. The spin-orbit and solvent effects were routinely included. To do so we analysed the family of structures α-[P2W18-xMxO62](n-) with M = Mo(VI), V(V) or Nb(V); [P2W17O62(M'R)](n-) with M' = Sn(IV), Ge(IV) and Ru(II) and [PW12-xMxO40](n-) with M = Pd(IV), Nb(V) and Ti(IV). The main results suggest that, to date, the best procedure for the accurate calculation of δ((31)P) in polyoxometalates is the combination of TZP/PBE//TZ2P/OPBE (for NMR//optimization step). The hybrid functionals (PBE0, B3LYP) tested herein were applied to the NMR step, besides being more CPU-consuming, do not outperform pure GGA functionals. Although previous studies on (183)W NMR suggested that the use of very large basis sets like QZ4P were needed for geometry optimization, the present results indicate that TZ2P suffices if the functional is optimal. Moreover, scaling corrections were applied to the results providing low mean absolute errors below 1 ppm for δ((31)P), which is a step forward in order to confirm or predict chemical shifts in polyoxometalates. Finally, via a simplified molecular model, we establish how the small variations in δ((31)P) arise from energy changes in the occupied and virtual orbitals of the PO4 group. PMID:25738630

  5. Solid state 13C NMR characterisation study on fourth generation Ziegler-Natta catalysts.

    Heikkinen, Harri; Liitiä, Tiina; Virkkunen, Ville; Leinonen, Timo; Helaja, Tuulamari; Denifl, Peter

    2012-01-01

    In this study, solid state (13)C NMR spectroscopy was utilised to characterize and identify the metal-ester coordination in active fourth generation (phthalate) Ziegler-Natta catalysts. It is known that different donors affect the active species in ZN catalysts. However, there is still limited data available of detailed molecular information how the donors and the active species are interplaying. One of the main goals of this work was to get better insight into the interactions of donor and active species. Based on the anisotropy tensor values (δ(11), δ(22), δ(33)) from low magic-angle spinning (MAS) (13)C NMR spectra in combination with chemical shift anisotropy (CSA) calculations (δ(aniso) and η), both the coordinative metal (Mg/Ti) and the symmetry of this interaction between metal and the internal donor in the active catalyst (MgCl(2)/TiCl(4)/electron donor) system could be identified. PMID:22425229

  6. Host-guest interactions in fluorinated polymer electrolytes: A 7Li-13C NMR study

    Mustarelli, P.; Quartarone, E.; Capiglia, C.; Tomasi, C.; Ferloni, P.; Magistris, A.

    1999-08-01

    Gel-type electrolytes based on fluorinated polymers are of interest for electrochemical devices. We present a 7Li-13C solid-state NMR and modulated differential scanning calorimetry (MDSC) study of gel electrolytes based on a copolymer poly(vinylidene fluoride) (PVdF)-hexafluoropropylene (HFP) activated with a nonaqueous solution ethylene carbonate (EC)-propylene carbonate (PC)-LiN(CF3SO2)2. We show that the narrowing of the Li lineshape is decoupled from the glass transition. The behavior of the longitudinal relaxation times, T1, confirms that the host polymer matrix simply behaves like a quasiinert cage for the solution. These results are confirmed by 13C NMR at the magic angle (MAS) data, which show that the presence of the polymer does not significantly affect the chemical shift changes induced in the EC/PC carbons by the imide salt.

  7. Measuring changes in substrate utilization in the myocardium in response to fasting using hyperpolarized [1-(13)C]butyrate and [1-(13)C]pyruvate.

    Bastiaansen, Jessica A M; Merritt, Matthew E; Comment, Arnaud

    2016-01-01

    Cardiac dysfunction is often associated with a shift in substrate preference for ATP production. Hyperpolarized (HP) (13)C magnetic resonance spectroscopy (MRS) has the unique ability to detect real-time metabolic changes in vivo due to its high sensitivity and specificity. Here a protocol using HP [1-(13)C]pyruvate and [1-(13)C]butyrate is used to measure carbohydrate versus fatty acid metabolism in vivo. Metabolic changes in fed and fasted Sprague Dawley rats (n = 36) were studied at 9.4 T after tail vein injections. Pyruvate and butyrate competed for acetyl-CoA production, as evidenced by significant changes in [(13)C]bicarbonate (-48%), [1-(13)C]acetylcarnitine (+113%), and [5-(13)C]glutamate (-63%), following fasting. Butyrate uptake was unaffected by fasting, as indicated by [1-(13)C]butyrylcarnitine. Mitochondrial pseudoketogenesis facilitated the labeling of the ketone bodies [1-(13)C]acetoacetate and [1-(13)C]β-hydroxybutyryate, without evidence of true ketogenesis. HP [1-(13)C]acetoacetate was increased in fasting (250%) but decreased during pyruvate co-injection (-82%). Combining HP (13)C technology and co-administration of separate imaging agents enables noninvasive and simultaneous monitoring of both fatty acid and carbohydrate oxidation. This protocol illustrates a novel method for assessing metabolic flux through different enzymatic pathways simultaneously and enables mechanistic studies of the changing myocardial energetics often associated with disease. PMID:27150735

  8. ¹³C solid-state NMR analysis of the most common pharmaceutical excipients used in solid drug formulations, Part I: Chemical shifts assignment.

    Pisklak, Dariusz Maciej; Zielińska-Pisklak, Monika Agnieszka; Szeleszczuk, Łukasz; Wawer, Iwona

    2016-04-15

    Solid-state NMR is an excellent and useful method for analyzing solid-state forms of drugs. In the (13)C CP/MAS NMR spectra of the solid dosage forms many of the signals originate from the excipients and should be distinguished from those of active pharmaceutical ingredient (API). In this work the most common pharmaceutical excipients used in the solid drug formulations: anhydrous α-lactose, α-lactose monohydrate, mannitol, sucrose, sorbitol, sodium starch glycolate type A and B, starch of different origin, microcrystalline cellulose, hypromellose, ethylcellulose, methylcellulose, hydroxyethylcellulose, sodium alginate, magnesium stearate, sodium laurilsulfate and Kollidon(®) were analyzed. Their (13)C CP/MAS NMR spectra were recorded and the signals were assigned, employing the results (R(2): 0.948-0.998) of GIPAW calculations and theoretical chemical shifts. The (13)C ssNMR spectra for some of the studied excipients have not been published before while for the other signals in the spectra they were not properly assigned or the assignments were not correct. The results summarize and complement the data on the (13)C ssNMR analysis of the most common pharmaceutical excipients and are essential for further NMR studies of API-excipient interactions in the pharmaceutical formulations. PMID:26845204

  9. Synthesis of 13C-labelled medroxyprogesterone acetate with three 13C isotopes [1

    17α-hydroxyprogesterone was condensed with phenyl acetate 13C2 in the presence of sodium hydride. Treatment with acetic and hydrochloric acids and acetylation gave 17α-acetoxyprogesterone 13C2. Treatment with tetrabromomethane 13C and hydrogenation yielded medroxyprogesterone acetate with three 13C isotopes. (U.K.)

  10. Synthesis of /sup 13/C-labelled medroxyprogesterone acetate with three /sup 13/C isotopes (1)

    Rao, P.N.; Damodaran, K.M. (Southwest Foundation for Research and Education, San Antonio, TX (USA))

    1982-03-01

    17..cap alpha..-hydroxyprogesterone was condensed with phenyl acetate /sup 13/C/sub 2/ in the presence of sodium hydride. Treatment with acetic and hydrochloric acids and acetylation gave 17..cap alpha..-acetoxyprogesterone /sup 13/C/sub 2/. Treatment with tetrabromomethane /sup 13/C and hydrogenation yielded medroxyprogesterone acetate with three /sup 13/C isotopes.

  11. 13C GIAO DFT calculation as a tool for configuration prediction of N-O group in saturated heterocyclic N-oxides

    Pohl, Radek; Potmischil, F.; Dračínský, Martin; Vaněk, Václav; Slavětínská, Lenka; Buděšínský, Miloš

    2012-01-01

    Roč. 50, č. 6 (2012), s. 415-423. ISSN 0749-1581 R&D Projects: GA ČR GA203/09/1919 Institutional research plan: CEZ:AV0Z40550506 Keywords : NMR * 13C * 1H * saturated heterocyclic N-oxides * chemical shift calculations * DFT Subject RIV: CC - Organic Chemistry Impact factor: 1.528, year: 2012

  12. Design of a quadrature surface coil for hyperpolarized 13C MRS cardiac metabolism studies in pigs

    Giovannetti, G.; Frijia, F.; Hartwig, V.;

    2013-01-01

    coil performance evaluation in terms of coil resistance, sample-induced resistance and magnetic field pattern. Experimental SNR-vs.-depth profiles, extracted from the [1-13C]acetate phantom chemical shift image (CSI), showed good agreement with the theoretical SNR-vs.-depth profiles. Moreover, the...... performance of the quadrature coil was compared with the single TX/RX circular and TX/RX butterfly coil, in order to verify the advantage of the proposed configuration over the single coils throughout the volume of interest for cardiac imaging in pig. Finally, the quadrature surface coil was tested by...

  13. Assignment of the side-chain 1H and 13C resonances of interleukin-1β using double- and triple-resonance heteronuclear three-dimensional NMR spectroscopy

    The assignment of the aliphatic 1H and 13C resonances of IL-1β, a protein of 153 residues and molecular mass 17.4 kDa, is presented by use of a number of novel three-dimensional (3D) heteronuclear NMR experiments which rely on large heteronuclear one-bond J couplings to transfer magnetization and establish through-bond connectivities. These 3D NMR experiments circumvent problems traditionally associated with the application of conventional 2D 1H-1H correlation experiments to proteins of this size, in particular the extensive chemical shift overlap which precludes the interpretation of the spectra and the reduced sensitivity arising from 1H line widths that are often significantly larger than the 1H-1H J couplings. The assignment proceeds in two stages. In the first step the 13Cα chemical shifts are correlated with the NH and 15N chemical shifts by a 3D triple-resonance NH-15N-13Cα (HNCA) correlation experiment which reveals both intraresidue NH(i)-15N(i)-13Cα(i) and some weaker interresidue NH(i)-15N(i)-Cα(i-1) correlations, the former via intraresidue one-bond 1JNCα and the latter via interresidue two-bond 2HNCα couplings. The second step involves the identification of side-chain spin systems by 3D 1H-13C-13C-1H correlated (HCCH-COSY) and 3D 1H-13C-13C-1H total correlated (HCCH-TOCSY) spectroscopy, the latter making use of isotropic mixing of 13C magnetization to obtain relayed connectivities along the side chains. The authors were able to obtain complete 1H and 13C side-chain assignments for all residues, with the exception of 4 (out of a total of 15) lysine residues for which partial assignments were obtained

  14. Random coil chemical shifts in acidic 8 M urea: Implementation of random coil shift data in NMRView

    Studies of proteins unfolded in acid or chemical denaturant can help in unraveling events during the earliest phases of protein folding. In order for meaningful comparisons to be made of residual structure in unfolded states, it is necessary to use random coil chemical shifts that are valid for the experimental system under study. We present a set of random coil chemical shifts obtained for model peptides under experimental conditions used in studies of denatured proteins. This new set, together with previously published data sets, has been incorporated into a software interface for NMRView, allowing selection of the random coil data set that fits the experimental conditions best

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

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

    2016-05-10

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

  16. Pitfalls of adrenal imaging with chemical shift MRI

    Chemical shift (CS) MRI of the adrenal glands exploits the different precessional frequencies of fat and water protons to differentiate the intracytoplasmic lipid-containing adrenal adenoma from other adrenal lesions. The purpose of this review is to illustrate both technical and interpretive pitfalls of adrenal imaging with CS MRI and emphasize the importance of adherence to strict technical specifications and errors that may occur when other imaging features and clinical factors are not incorporated into the diagnosis. When performed properly, the specificity of CS MRI for the diagnosis of adrenal adenoma is over 90%. Sampling the in-phase and opposed-phase echoes in the correct order and during the same breath-hold are essential requirements, and using the first echo pair is preferred, if possible. CS MRI characterizes more adrenal adenomas then unenhanced CT but may be non-diagnostic in a proportion of lipid-poor adenomas; CT washout studies may be able to diagnose these lipid-poor adenomas. Other primary and secondary adrenal tumours and supra-renal disease entities may contain lipid or gross fat and mimic adenoma or myelolipoma. Heterogeneity within an adrenal lesion that contains intracytoplasmic lipid could be due to myelolipoma, lipomatous metaplasia of adenoma, or collision tumour. Correlation with previous imaging, other imaging features, clinical history, and laboratory investigations can minimize interpretive errors

  17. Diagnostic value of chemical shift artifact in distinguishing benign lymphadenopathy

    Purpose: Today, distinguishing metastatic lymph nodes from secondary benign inflammatory ones via using non-invasive methods is increasingly favorable. In this study, the diagnostic value of chemical shift artifact (CSA) in magnetic resonance imaging (MRI) was evaluated to distinguish benign lymphadenopathy. Subjects and methods: A prospective intraindividual internal review board-approved study was carried out on 15 men and 15 women having lymphadenopathic lesions in different locations of the body who underwent contrast-enhanced dynamic MR imaging at 1.5 T. Then, the imaging findings were compared with pathology reports, using the statistics analyses. Results: Due to the findings of the CSA existence in MRI, a total of 56.7% of the studied lesions (17 of 30) were identified as benign lesions and the rest were malignant, whereas the pathology reports distinguished twelve malignant and eighteen benign cases. Furthermore, the CSA findings comparing the pathology reports indicated that CSA, with confidence of 79.5%, has a significant diagnostic value to differentiate benign lesions from malignant ones. Conclusion: Our study demonstrated that CSA in MR imaging has a suitable diagnostic potential nearing readiness for clinical trials. Furthermore, CSA seems to be a feasible tool to differentiate benign lymph nodes from malignant ones; however, further studies including larger numbers of patients are required to confirm our results.

  18. 13C CPMAS NMR Studies of Anthocyanidins and their Glucosides

    Anthocyanins are responsible for red, purple or blue colours of flower petals and can be found in red or black fruits and berries. Many foods, especially red grapes and wines, aronia or blueberries contain large amounts of anthocyanins. Their health beneficial effects are related to antioxidant and radical scavenging properties. Structural analysis of anthocyanins by NMR are few, owing to the difficulty in obtaining analysable spectra for unstable, interconverting compounds, available in small amounts. Compounds studied by us were isolated from fruits and berries. 13C CPMAS NMR spectra were recorded on a Bruker DSX-400 spectrometer for solid chlorides of: cyanidin, cyanidin 3-O-glucoside, cyanidin 3,5-O-diglucoside, pelargonidin and pelargonidin 3-O-glucoside. Dipolar dephased and short contact pulse sequences were used as an aid in the assignment of resonances in CPMAS spectra of solids. Inspection of the spectra indicates that anthocyanidins are in the form of flavylium (cationic) and not in form of the chalcone.: the resonance of C2 appears at ca. 160 ppm and C3 at ca. 135 ppm, whereas C ring opening produces C2 = O, for which chemical shift of ca. 180 ppm can be expected. A comparison of experimental (CPMAS) and predicted (GIAO DFT) shielding constants for cyanidin provided information about the orientation of OH groups, twist angle of aromatic ring B and the localization of the chloride anion.(author)

  19. Unambiguous assigning of the signals of the nuclear magnetic resonance spectra of {sup 1} H and {sup 13} C of monoterpenes using computational methods; Asignacion inequivoca de las senales del espectro de resonancia magnetica nuclear de {sup 1} H y {sup 13} C de monoterpenos empleando metodos computacionales

    Cortes, F.; Cuevas, G.; Tenorio, J.; Rochin, A.L. [Universidad Nacional Autonoma de Mexico, Instituto de Quimica, A.P. 70213, 04510 Mexico D.F. (Mexico)

    2000-07-01

    Ab initio calculations, within the frame of Density Functional Theory were carried out on camphene and {alpha}-pinene. The {sup 1} H and {sup 13} C shifts were estimated according to the recently developed Sum-Over-States Density Functional Perturbation Theory (SOS-DFPT) as implemented in a modified deMon-KS program. The calculations not only reproduced the observed NMR chemical shifts, quantitatively in the case of {sup 1} H nuclei and qualitatively in the case of {sup 13} C nuclei, but also allow assigning unambiguously the signal on these spectra. (Author)

  20. Revisiting the metathesis of 13C-monolabeled ethane

    Maury, Olivier

    2010-12-13

    The metathesis of 13C-monolabeled ethane leads to the parallel occurrence of degenerate and productive reactions, affording the statistical distribution of the various product isotopomers, which can be rationalized in terms of a mechanistic reaction scheme combining both processes. © 2010 American Chemical Society.

  1. Proton-detected 3D {sup 1}H/{sup 13}C/{sup 1}H correlation experiment for structural analysis in rigid solids under ultrafast-MAS above 60 kHz

    Zhang, Rongchun; Ramamoorthy, Ayyalusamy, E-mail: ramamoor@umich.edu [Biophysics and Department of Chemistry, The University of Michigan, Ann Arbor, Michigan 48109-1055 (United States); Nishiyama, Yusuke [JEOL RESONANCE Inc., Musashino, Akishima, Tokyo 196-8558 (Japan); RIKEN CLST-JEOL Collaboration Center, RIKEN, Yokohama, Kanagawa 230-0045 (Japan)

    2015-10-28

    A proton-detected 3D {sup 1}H/{sup 13}C/{sup 1}H chemical shift correlation experiment is proposed for the assignment of chemical shift resonances, identification of {sup 13}C-{sup 1}H connectivities, and proximities of {sup 13}C-{sup 1}H and {sup 1}H-{sup 1}H nuclei under ultrafast magic-angle-spinning (ultrafast-MAS) conditions. Ultrafast-MAS is used to suppress all anisotropic interactions including {sup 1}H-{sup 1}H dipolar couplings, while the finite-pulse radio frequency driven dipolar recoupling (fp-RFDR) pulse sequence is used to recouple dipolar couplings among protons and the insensitive nuclei enhanced by polarization transfer technique is used to transfer magnetization between heteronuclear spins. The 3D experiment eliminates signals from non-carbon-bonded protons and non-proton-bonded carbons to enhance spectral resolution. The 2D (F1/F3) {sup 1}H/{sup 1}H and 2D {sup 13}C/{sup 1}H (F2/F3) chemical shift correlation spectra extracted from the 3D spectrum enable the identification of {sup 1}H-{sup 1}H proximity and {sup 13}C-{sup 1}H connectivity. In addition, the 2D (F1/F2) {sup 1}H/{sup 13}C chemical shift correlation spectrum, incorporated with proton magnetization exchange via the fp-RFDR recoupling of {sup 1}H-{sup 1}H dipolar couplings, enables the measurement of proximities between {sup 13}C and even the remote non-carbon-bonded protons. The 3D experiment also gives three-spin proximities of {sup 1}H-{sup 1}H-{sup 13}C chains. Experimental results obtained from powder samples of L-alanine and L-histidine ⋅ H{sub 2}O ⋅ HCl demonstrate the efficiency of the 3D experiment.

  2. 19-Fluorine nuclear magnetic resonance chemical shift variability in trifluoroacetyl species

    Sloop, Joseph

    2013-01-01

    Joseph C SloopSchool of Science and Technology, Georgia Gwinnett College, Lawrenceville, GA, USAAbstract: This review examines the variability of chemical shifts observed in 19-fluorine (19F) nuclear magnetic resonance spectra for the trifluoroacetyl (TFA) functional group. The range of 19F chemical shifts reported spectra for the TFA group varies generally from −85 to −67 ppm relative to CFCl3. The literature revealed several factors that impact chemical shifts of the TFA...

  3. Synthesis of encainide-13C hydrochloride from 2-nitrobenzaldehyde-formyl-13C

    A facile synthesis of 2-nitrobenzaldehyde-formyl-13C was developed. This compound was converted to the labelled antiarrhythmic agent, encainide-13C hydrochloride, 4-methoxy-N-[2-(1-methyl-2-piperidinyl)ethyl-1-13C]phenyl]benzamide hydrochloride. (author)

  4. Synthesis and applications of {sup 13}C glycerol

    Stocking, E.; Khalsa, O.; Martinez, R.A.; Silks, L.A. III [Los Alamos National Laboratory, NM (United States)

    1994-12-01

    Due in part to the use of labeled glycerol for the {sup 13}C enrichment of biomolecules, we are currently developing new synthetic routes to various isotopomers of glycerol. Judging from our experience, traditional methods of glycerol synthesis are not easily adapted for isotopic enrichment and/or have poor overall yields (12 to 15%). Furthermore, the use of glycerol for enrichment can be prohibitively expensive and its availability is limited by the level of demand. We are presently developing a short de novo synthesis of glycerol from carbon dioxide ({approximately}53% overall yield for four steps) and are examining the feasibility of synthesizing site-specific {sup 13}C-labeled glycerol and dihydroxyacetone (DHA) from labeled methanol and carbon dioxide. One application of {sup 13}C glycerol we have examined is enzymatic conversion of glycerol to glyceraldehyde-3-monophosphate or dihydroxyacetone monophosphate (DHAP) with yields ranging from 25 to 50% (as determined by NMR spectroscopy). We are also pursuing the chemical conversion of {sup 13}C-labeled DHA to DHAP. We are especially interested in {sup 13}C-labeled DHAP because we are investigating its use as a chemo-enzymatic precursor for both labeled 2-deoxyribose and 2-deoxyribonucleic acids.

  5. Neutron halo state of 13C

    2001-01-01

    Angular distributions for the 12C(d, p)13C transfer reactionshave been measured at Ed = 11.8 MeV, and compared with those of the DWBA calculations. By means of this comparison, density distributions of the last neutron in the ground state and the first 1/2+ state of 13C are extracted. The properties of these states in 13C have also been studied in the framework of the nonlinear relativistic mean-field theory with NL-SH parameters. It is found that the first 1/2+ state in 13C is a neutron halo state shown by both the experimental and theoretical density distributions of the last neutron.

  6. Dereplication of depsides from the lichen Pseudevernia furfuracea by centrifugal partition chromatography combined to {sup 13}C nuclear magnetic resonance pattern recognition

    Oettl, Sarah K. [Institute of Pharmacy/Pharmacognosy, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innrain 80–82, 6020 Innsbruck (Austria); Hubert, Jane, E-mail: jane.hubert@univ-reims.fr [Institut de Chimie Moléculaire de Reims (UMR CNRS 7312), SFR CAP' sANTE, UFR de Pharmacie, Université de Reims Champagne-Ardenne, BP 1039, 51687 Reims Cedex 2 (France); Nuzillard, Jean-Marc [Institut de Chimie Moléculaire de Reims (UMR CNRS 7312), SFR CAP' sANTE, UFR de Pharmacie, Université de Reims Champagne-Ardenne, BP 1039, 51687 Reims Cedex 2 (France); Stuppner, Hermann [Institute of Pharmacy/Pharmacognosy, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innrain 80–82, 6020 Innsbruck (Austria); Renault, Jean-Hugues [Institut de Chimie Moléculaire de Reims (UMR CNRS 7312), SFR CAP' sANTE, UFR de Pharmacie, Université de Reims Champagne-Ardenne, BP 1039, 51687 Reims Cedex 2 (France); Rollinger, Judith M. [Institute of Pharmacy/Pharmacognosy, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innrain 80–82, 6020 Innsbruck (Austria)

    2014-10-10

    Highlights: • The major depsides of a lichen extract were directly identified within mixtures. • The initial extract was rapidly fractionated by CPC in the pH-zone refining mode. • Hierarchical clustering of {sup 13}C NMR signals resulted in the identification of depside molecular skeletons. • {sup 13}C chemical shift clusters were assigned to structures using a {sup 13}C NMR database. • Six depsides were unambiguously identified by this approach. - Abstract: Lichens produce a diversity of secondary metabolites, among them depsides comprised of two or more hydroxybenzoic acid units linked by ester, ether, or C-C-bonds. During classic solid support-based purification processes, depsides are often hydrolyzed and in many cases time, consuming procedures result only in the isolation of decomposition products. In an attempt to avoid extensive purification steps while maintaining metabolite structure integrity, we propose an alternative method to identify the major depsides of a lichen crude extract (Pseudevernia furfuracea var. ceratea (Ach.) D. Hawksw., Parmeliaceae) directly within mixtures. Exploiting the acidic character of depsides and differences in polarity, the extract was fractionated by centrifugal partition chromatography in the pH-zone refining mode resulting in twelve simplified mixtures of depsides. After {sup 13}C nuclear magnetic resonance analysis of the produced fractions, the major molecular structures were directly identified within the fraction series by using a recently developed pattern recognition method, which combines spectral data alignment and hierarchical clustering analysis. The obtained clusters of {sup 13}C chemical shifts were assigned to their corresponding molecular structures with the help of an in-house {sup 13}C NMR chemical shift database, resulting in six unambiguously identified compounds, namely methyl β-orcinolcarboxylate (1), atranorin (2), 5-chloroatranorin (3), olivetol carboxylic acid (4), olivetoric acid (5

  7. Dereplication of depsides from the lichen Pseudevernia furfuracea by centrifugal partition chromatography combined to 13C nuclear magnetic resonance pattern recognition

    Highlights: • The major depsides of a lichen extract were directly identified within mixtures. • The initial extract was rapidly fractionated by CPC in the pH-zone refining mode. • Hierarchical clustering of 13C NMR signals resulted in the identification of depside molecular skeletons. • 13C chemical shift clusters were assigned to structures using a 13C NMR database. • Six depsides were unambiguously identified by this approach. - Abstract: Lichens produce a diversity of secondary metabolites, among them depsides comprised of two or more hydroxybenzoic acid units linked by ester, ether, or C-C-bonds. During classic solid support-based purification processes, depsides are often hydrolyzed and in many cases time, consuming procedures result only in the isolation of decomposition products. In an attempt to avoid extensive purification steps while maintaining metabolite structure integrity, we propose an alternative method to identify the major depsides of a lichen crude extract (Pseudevernia furfuracea var. ceratea (Ach.) D. Hawksw., Parmeliaceae) directly within mixtures. Exploiting the acidic character of depsides and differences in polarity, the extract was fractionated by centrifugal partition chromatography in the pH-zone refining mode resulting in twelve simplified mixtures of depsides. After 13C nuclear magnetic resonance analysis of the produced fractions, the major molecular structures were directly identified within the fraction series by using a recently developed pattern recognition method, which combines spectral data alignment and hierarchical clustering analysis. The obtained clusters of 13C chemical shifts were assigned to their corresponding molecular structures with the help of an in-house 13C NMR chemical shift database, resulting in six unambiguously identified compounds, namely methyl β-orcinolcarboxylate (1), atranorin (2), 5-chloroatranorin (3), olivetol carboxylic acid (4), olivetoric acid (5), and olivetonide (6)

  8. Carbon-13 magnetic resonance chemical shift additivity relationships of clinically used furocoumarins and furchromones

    The natural abundance carbon-13 nuclear magnetic resonance spectra of various clinically used furocoumarins and furochromones have been studied. The assignments of carbon chemical shift values were based on the theory of chemical shift, additivity rules, SFORD spectra and model compounds. (author)

  9. Global Fold of Human Cannabinoid Type 2 Receptor Probed by Solid-State 13C-, 15N-MAS NMR and Molecular Dynamics Simulations

    Kimura, Tomohiro; Vukoti, Krishna; Lynch, Diane L.; Hurst, Dow P.; Grossfield, Alan; Pitman, Michael C.; Reggio, Patricia H.; Yeliseev, Alexei A.; Gawrisch, Klaus

    2013-01-01

    The global fold of human cannabinoid type 2 (CB2) receptor in the agonist-bound active state in lipid bilayers was investigated by solid-state 13C- and 15N magic-angle spinning (MAS) NMR, in combination with chemical-shift prediction from a structural model of the receptor obtained by microsecond-long molecular dynamics (MD) simulations. Uniformly 13C-, and 15N-labeled CB2 receptor was expressed in milligram quantities by bacterial fermentation, purified, and functionally reconstituted into l...

  10. Short-term d13C changes in cultivated soils from Mexico

    Lounejeva, E.; Etchevers, J.; Morales Puente, P.; Cienfuegos Alvarado, E.; Sedov, S.; Solleiro, E.; Hidalgo, C.

    2007-05-01

    The soils of the Mexican Volcanic Belt are part of ecosystems subjected to strong human impact during the last six centuries. One measurable characteristic of the soil is the stable carbon isotopic relation of the soil organic matter (SOM) or d13C. The d13C SOM parameter is a genetic characteristic of soil reflecting the relative proportion of C3 and C4 that comes from colonizing plants having different photosynthetic C pathway and is used as a high-spatial resolution tool to infer paleoenvironmental changes.The d13C mean signatures of C3 and C4 plants are -27 and -13 %o, respectively. This work focuses on short-term changes in d13C on soils subjected to controlled agricultural practices during 2002-2005 in two sites of Mexico with similar annual precipitation and temperature. The tepetate was broken up 20y ago and ameliorated with fertilizers and organic matter. In both sites three experimental treatments consisting of traditional soil management and two variations of this one were evaluated. Traditional treatment implies low fertilizer and any chemical input, sowing annual crops during the rainy season and, in general, using low energy input. The crops planted were: legumes C3, oat C3, and a mixture of maizeC4 and beanC3, and wheatC3. The Improved and Organic treatments, had higher input of N and P as chemical fertilizers, and of organic manure (manure or compost), respectively. Soil samples were collected from the plow layer in Tlaxcala and in Michoacán, before C4 maize was planted. An Andisol from a pine-oak (C3 species) forest close to the Atecuaro site was also sampled up to 40 cm. This soil was considered a reference site not recently influenced by human activity. To analyze the d13C ratios of the SOM carbonate free samples, a routine combustion method and mass spectrometry (Finnigan MAT250) were used. In both agricultural sites a general excess of C3 species over C4 was evidenced through a mass balance equation derived from experimental d13C values

  11. Enhanced spectral resolution in RNA HCP spectra for measurement of 3JC2'P and 3JC4'P couplings and 31P chemical shift changes upon weak alignment

    The 'out-and-back' 3D HCP experiment, using gradient- and sensitivity-enhanced detection, provides a convenient method for assignment of the 31P NMR spectra and accurate measurement of the 31P chemical shifts of ribonucleic acids. The 13C resolution in such spectra can be doubled, at the cost of a 50% reduction in sensitivity, by combining 13C evolution during the 13C-31P de- and rephasing periods. The multiple connectivities observable for a given 31P, including correlations to the intranucleotide C5'H2 and C4'H groups, and the C2'H, C3'H and C4'H groups of the preceding nucleotide, permit independent measurements of the 31P shift. The 13C spectrum of these groups is typically crowded for an RNA molecule in isotropic solution and overlap becomes more problematic in media used to achieve partial alignment. However, many of these correlations are resolvable in the combined-evolution HCP spectrum. The difference in 31P chemical shift between isotropic solution and a medium containing liquid crystalline Pf1 provides information on the orientation of phosphate groups. The intensities measured in the 3D HCP spectrum, obtained for an isotropic sample, yield values for the 3JC2'P and 3JC4'P couplings, thereby providing important restraints for the backbone torsion angles ε and β. The experiments are illustrated for a uniformly 13C-enriched, 24-residue stem-loop RNA sequence, and results for the helical stem region show close agreement between observed Δδ(31P) values and those predicted for a model A-form RNA helix when using a uniform 31P CSA tensor. This confirms that Δδ(31P) values can be used directly as restraints in refining nucleic acid structures

  12. Retrobiosynthetic NMR studies with 13C-labeled glucose. Formation of gallic acid in plants and fungi

    The biosynthesis of gallic acid was studied in cultures of the fungus Phycomyces blakesleeanus and in leaves of the tree Rhus typhina. Fungal cultures were grown with [1-13C]glucose or with a mixture of unlabeled glucose and [U-13C6]glucose. Young leaves of R. typhina were kept in an incubation chamber and were supplied with a solution containing a mixture of unlabeled glucose and [U-13C6]glucose via the leaf stem. Isotope distributions in isolated gallic acid and aromatic amino acids were analyzed by one-dimensional 1H and 13C NMR spectroscopy. A quantitative analysis of the complex isotopomer composition of metabolites was obtained by deconvolution of the 13C13C coupling multiplets using numerical simulation methods. This approach required the accurate analysis of heavy isotope chemical shift effects in a variety of different isotopomers and the analysis of long range 13C13C coupling constants. The resulting isotopomer patterns were interpreted using a retrobiosynthetic approach based on a comparison between the isotopomer patterns of gallic acid and tyrosine. The data show that both in the fungus and in the plant all carbon atoms of gallic acid are biosynthetically equivalent to carbon atoms of shikimate. Notably, the carboxylic group of gallic acid is derived from the carboxylic group of an early intermediate of the shikimate pathway and not from the side chain of phenylalanine or tyrosine. It follows that the committed precursor of gallic acid is an intermediate of the shikimate pathway prior to prephenate or arogenate, most probably 5-dehydroshikimate. A formation of gallic acid via phenylalanine, the lignin precursor, caffeic acid, or 3,4, 5-trihydroxycinnamic acid can be ruled out as major pathways in the fungus and in young leaves of R. typhina. The incorporation of uniformly 13C-labeled glucose followed by quantitative NMR analysis of isotopomer patterns is suggested as a general method for biosynthetic studies. As shown by the plant experiment, this

  13. Method of evaluating chemical shifts of X-ray emission lines in molecules and solids

    Lomachuk, Yuriy V.; Titov, Anatoly V.

    2013-01-01

    Method of evaluating chemical shifts of X-ray emission lines for sufficiently heavy atoms (beginning from period 4 elements) in chemical compounds is developed. This method is based on the pseudopotential model and one-center restoration method (to reconstruct the proper electronic structure in heavy-atom cores). The approximations of instantaneous transition and frozen inner core spinors of the atom are used for derivation of an expression for chemical shift as a difference between mean valu...

  14. Inferential protein structure determination and refinement using fast, electronic structure based backbone amide chemical shift predictions

    Christensen, Anders S

    2015-01-01

    This report covers the development of a new, fast method for calculating the backbone amide proton chemical shifts in proteins. Through quantum chemical calculations, structure-based forudsiglese the chemical shift for amidprotonen in protein has been parameterized. The parameters are then implemented in a computer program called Padawan. The program has since been implemented in protein folding program Phaistos, wherein the method andvendes to de novo folding of the protein structures and to refine the existing protein structures.

  15. High resolution 4D HPCH experiment for sequential assignment of 13C-labeled RNAs via phosphodiester backbone

    The three-dimensional structure determination of RNAs by NMR spectroscopy requires sequential resonance assignment, often hampered by assignment ambiguities and limited dispersion of 1H and 13C chemical shifts, especially of C4′/H4′. Here we present a novel through-bond 4D HPCH NMR experiment involving phosphate backbone where C4′–H4′ correlations are resolved along the 1H3′–31P spectral planes. The experiment provides high peak resolution and effectively removes ambiguities encountered during assignments. Enhanced peak dispersion is provided by the inclusion of additional 31P and 1H3′ dimensions and constant-time evolution of chemical shifts. High spectral resolution is obtained by using non-uniform sampling in three indirect dimensions. The experiment fully utilizes the isotopic 13C-labeling with evolution of C4′ carbons. Band selective 13C inversion pulses are used to achieve selectivity and prevent signal dephasing due to the C4′–C3′ and C4′–C5′ homonuclear couplings. Multiple quantum line narrowing is employed to minimize sensitivity loses. The 4D HPCH experiment is verified and successfully applied to a non-coding 34-nt RNA consisting typical structure elements and a 14-nt RNA hairpin capped by cUUCGg tetraloop

  16. High resolution 4D HPCH experiment for sequential assignment of {sup 13}C-labeled RNAs via phosphodiester backbone

    Saxena, Saurabh; Stanek, Jan [University of Warsaw, Faculty of Chemistry, Biological and Chemical Research Centre (Poland); Cevec, Mirko; Plavec, Janez [National Institute of Chemistry, Slovenian NMR Centre (Slovenia); Koźmiński, Wiktor, E-mail: kozmin@chem.uw.edu.pl [University of Warsaw, Faculty of Chemistry, Biological and Chemical Research Centre (Poland)

    2015-11-15

    The three-dimensional structure determination of RNAs by NMR spectroscopy requires sequential resonance assignment, often hampered by assignment ambiguities and limited dispersion of {sup 1}H and {sup 13}C chemical shifts, especially of C4′/H4′. Here we present a novel through-bond 4D HPCH NMR experiment involving phosphate backbone where C4′–H4′ correlations are resolved along the {sup 1}H3′–{sup 31}P spectral planes. The experiment provides high peak resolution and effectively removes ambiguities encountered during assignments. Enhanced peak dispersion is provided by the inclusion of additional {sup 31}P and {sup 1}H3′ dimensions and constant-time evolution of chemical shifts. High spectral resolution is obtained by using non-uniform sampling in three indirect dimensions. The experiment fully utilizes the isotopic {sup 13}C-labeling with evolution of C4′ carbons. Band selective {sup 13}C inversion pulses are used to achieve selectivity and prevent signal dephasing due to the C4′–C3′ and C4′–C5′ homonuclear couplings. Multiple quantum line narrowing is employed to minimize sensitivity loses. The 4D HPCH experiment is verified and successfully applied to a non-coding 34-nt RNA consisting typical structure elements and a 14-nt RNA hairpin capped by cUUCGg tetraloop.

  17. Alterations in chemical shifts and exchange broadening upon peptide boronic acid inhibitor binding to α-lytic protease

    α-Lytic protease, a bacterial serine protease of 198 aminoacids (19800 Da), has been used as a model system for studies of catalytic mechanism, structure-function relationships, and more recently for studies of pro region-assisted protein folding. We have assigned the backbones of the enzyme alone, and of its complex with the tetrahedral transition state mimic N-tert-butyloxycarbonyl-Ala-Pro-boroVal, using double- and triple-resonance 3D NMR spectroscopy on uniformly15N- and 13C/15N-labeled protein.Changes in backbone chemical shifts between the uncomplexed and inhibited form of the protein are correlated with distance from the inhibitor, the displacement of backbone nitrogens, and change in hydrogen bond strength upon inhibitor binding (derived from previously solved crystal structures).A comparison of the solution secondary structure of the uninhibited enzyme with that of the X-ray structure reveals no significant differences.Significant line broadening, indicating intermediate chemical exchange, was observed in many of the active site amides (including three broadened to invisibility), and in a majority of cases the broadening was reversed upon addition of the inhibitor. Implications and possible mechanisms of this line broadening are discussed

  18. Correlation of chemical shifts predicted by molecular dynamics simulations for partially disordered proteins

    There has been a longstanding interest in being able to accurately predict NMR chemical shifts from structural data. Recent studies have focused on using molecular dynamics (MD) simulation data as input for improved prediction. Here we examine the accuracy of chemical shift prediction for intein systems, which have regions of intrinsic disorder. We find that using MD simulation data as input for chemical shift prediction does not consistently improve prediction accuracy over use of a static X-ray crystal structure. This appears to result from the complex conformational ensemble of the disordered protein segments. We show that using accelerated molecular dynamics (aMD) simulations improves chemical shift prediction, suggesting that methods which better sample the conformational ensemble like aMD are more appropriate tools for use in chemical shift prediction for proteins with disordered regions. Moreover, our study suggests that data accurately reflecting protein dynamics must be used as input for chemical shift prediction in order to correctly predict chemical shifts in systems with disorder

  19. A robust algorithm for optimizing protein structures with NMR chemical shifts

    Berjanskii, Mark; Arndt, David; Liang, Yongjie; Wishart, David S., E-mail: david.wishart@ualberta.ca [University of Alberta, Department of Computing Science (Canada)

    2015-11-15

    Over the past decade, a number of methods have been developed to determine the approximate structure of proteins using minimal NMR experimental information such as chemical shifts alone, sparse NOEs alone or a combination of comparative modeling data and chemical shifts. However, there have been relatively few methods that allow these approximate models to be substantively refined or improved using the available NMR chemical shift data. Here, we present a novel method, called Chemical Shift driven Genetic Algorithm for biased Molecular Dynamics (CS-GAMDy), for the robust optimization of protein structures using experimental NMR chemical shifts. The method incorporates knowledge-based scoring functions and structural information derived from NMR chemical shifts via a unique combination of multi-objective MD biasing, a genetic algorithm, and the widely used XPLOR molecular modelling language. Using this approach, we demonstrate that CS-GAMDy is able to refine and/or fold models that are as much as 10 Å (RMSD) away from the correct structure using only NMR chemical shift data. CS-GAMDy is also able to refine of a wide range of approximate or mildly erroneous protein structures to more closely match the known/correct structure and the known/correct chemical shifts. We believe CS-GAMDy will allow protein models generated by sparse restraint or chemical-shift-only methods to achieve sufficiently high quality to be considered fully refined and “PDB worthy”. The CS-GAMDy algorithm is explained in detail and its performance is compared over a range of refinement scenarios with several commonly used protein structure refinement protocols. The program has been designed to be easily installed and easily used and is available at http://www.gamdy.ca http://www.gamdy.ca.

  20. A robust algorithm for optimizing protein structures with NMR chemical shifts

    Over the past decade, a number of methods have been developed to determine the approximate structure of proteins using minimal NMR experimental information such as chemical shifts alone, sparse NOEs alone or a combination of comparative modeling data and chemical shifts. However, there have been relatively few methods that allow these approximate models to be substantively refined or improved using the available NMR chemical shift data. Here, we present a novel method, called Chemical Shift driven Genetic Algorithm for biased Molecular Dynamics (CS-GAMDy), for the robust optimization of protein structures using experimental NMR chemical shifts. The method incorporates knowledge-based scoring functions and structural information derived from NMR chemical shifts via a unique combination of multi-objective MD biasing, a genetic algorithm, and the widely used XPLOR molecular modelling language. Using this approach, we demonstrate that CS-GAMDy is able to refine and/or fold models that are as much as 10 Å (RMSD) away from the correct structure using only NMR chemical shift data. CS-GAMDy is also able to refine of a wide range of approximate or mildly erroneous protein structures to more closely match the known/correct structure and the known/correct chemical shifts. We believe CS-GAMDy will allow protein models generated by sparse restraint or chemical-shift-only methods to achieve sufficiently high quality to be considered fully refined and “PDB worthy”. The CS-GAMDy algorithm is explained in detail and its performance is compared over a range of refinement scenarios with several commonly used protein structure refinement protocols. The program has been designed to be easily installed and easily used and is available at http://www.gamdy.ca http://www.gamdy.ca

  1. Mineral Moessbauer spectroscopy: correlations between chemical shift and quadrupole splitting parameters

    The variety of coordination numbers, symmetries, distortions and ligand environments in thermally-stable iron-bearing minerals provide wide ranges of chemical shift (δ) and quadrupole splitting (Δ) parameters, which serve to characterize the crystal chemistries and site occupancies of Fe2+ and Fe3+ ions in minerals of terrestrial and extraterrestrial origins. Correlations between ferrous and ferric chemical shifts enable thermally-induced electron delocalization behavior in mixed-valence Fe2+-Fe3+ minerals to be identified, while chemical shift versus quadrupole splitting correlations serve to identify nanophase ferric oxides and oxyhydroxides in oxidized minerals and in meteorites subjected to aqueous oxidation before and after they arrived on Earth. (orig.)

  2. Protein structure validation and refinement using amide proton chemical shifts derived from quantum mechanics

    Christensen, Anders Steen; Linnet, Troels Emtekær; Borg, Mikael;

    2013-01-01

    We present the ProCS method for the rapid and accurate prediction of protein backbone amide proton chemical shifts - sensitive probes of the geometry of key hydrogen bonds that determine protein structure. ProCS is parameterized against quantum mechanical (QM) calculations and reproduces high level...... QM results obtained for a small protein with an RMSD of 0.25 ppm (r = 0.94). ProCS is interfaced with the PHAISTOS protein simulation program and is used to infer statistical protein ensembles that reflect experimentally measured amide proton chemical shift values. Such chemical shift...

  3. Prediction of proton chemical shifts in RNA - Their use in structure refinement and validation

    An analysis is presented of experimental versus calculated chemical shifts of the non-exchangeable protons for 28 RNA structures deposited in the Protein Data Bank, covering a wide range of structural building blocks. We have used existing models for ring-current and magnetic-anisotropy contributions to calculate the proton chemical shifts from the structures. Two different parameter sets were tried: (i) parameters derived by Ribas-Prado and Giessner-Prettre (GP set) [(1981) J. Mol. Struct.,76, 81-92.]; (ii) parameters derived by Case [(1995) J. Biomol. NMR, 6, 341-346]. Both sets lead to similar results. The detailed analysis was carried using the GP set. The root-mean-square-deviation between the predicted and observed chemical shifts of the complete database is 0.16 ppm with a Pearson correlation coefficient of 0.79. For protons in the usually well-defined A-helix environment these numbers are, 0.08 ppm and 0.96, respectively. As a result of this good correspondence, a reliable analysis could be made of the structural dependencies of the 1H chemical shifts revealing their physical origin. For example, a down-field shift of either H2' or H3' or both indicates a high-syn/syn χ-angle. In an A-helix it is essentially the 5'-neighbor that affects the chemical shifts of H5, H6 and H8 protons. The H5, H6 and H8 resonances can therefore be assigned in an A-helix on the basis of their observed chemical shifts. In general, the chemical shifts were found to be quite sensitive to structural changes. We therefore propose that a comparison between calculated and observed 1H chemical shifts is a good tool for validation and refinement of structures derived from NOEs and J-couplings

  4. Coal structure at reactive sites by sup 1 H- sup 13 C- sup 19 F double cross polarization (DCP)/MAS sup 13 C NMR spectroscopy

    Hagaman, E.W.; Woody, M.C. (Oak Ridge National Lab., TN (USA))

    1989-01-01

    The solid state NMR technique, {sup 1}H-{sup 13}C-{sup 31}P double cross polarization (DCP)/MAS {sup 13}C-NMR spectroscopy, uses the direct dipolar interaction between {sup 13}C-{sup 31}P spin pairs in organophosphorus substances to identify the subset of carbons within a spherical volume element of 0.4 nm radius centered on the {sup 31}P atom. In combination with chemical manipulation of coals designed to introduce phosphorus containing functionality into the organic matrix, the NMR experiment becomes a method to examine selectively the carbon bonding network at the reactive sites in the coal. This approach generates a statistical structure description of the coal at the reaction centers in contrast to bulk carbon characterization using conventional {sup 1}H-{sup 13}C CP/MAS {sup 13}C NMR spectroscopy. 3 refs.

  5. The electric dipole moment of $^{13}$C

    Yamanaka, Nodoka; Hiyama, Emiko; Funaki, Yasuro

    2016-01-01

    We calculate for the first time the electric dipole moment (EDM) of $^{13}$C generated by the isovector CP-odd pion exchange nuclear force in the $\\alpha$-cluster model, which describes well the structures of low lying states of the $^{13}$C nucleus. The linear dependence of the EDM of $^{13}$C on the neutron EDM and the isovector CP-odd nuclear coupling is found to be $d_{^{13}{\\rm C}} = -0.33 d_n - 0.0012 \\bar G_\\pi^{(1)}$. The linear enhancement factor of the CP-odd nuclear coupling is smaller than that of the deuteron, due to the difference of the structure between the $1/2^-_1$ state and the opposite parity ($1/2^+$) states. We clarify the role of the structure played in the enhancement of the EDM. This result provides good guiding principles to search for other nuclei with large enhancement factor. We also mention the role of the EDM of $^{13}$C in determining the new physics beyond the standard model.

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

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

    2013-09-01

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

  7. Combined Effects of Noise and Shift Work on Workers’ Physiological Parameters in a Chemical Industry

    M. Motamedzade; S. Ghazaiee

    2003-01-01

    This study was conducted to determine the combined effects of noise and shift work on physiological parameters including body temperature, heart rate and blood pressure. This study was performed in a chemical industry in Tehran in 1993. The workers’ physiological parameters was recorded at the beginning and at the end of all work shifts. Groups under study included : day workers (n=115) , day workers with continuous noise exposure (n=44) , two-shift workers without...

  8. PPM-One: a static protein structure based chemical shift predictor

    Li, Dawei; Brüschweiler, Rafael, E-mail: bruschweiler.1@osu.edu [The Ohio State University, Campus Chemical Instrument Center (United States)

    2015-07-15

    We mined the most recent editions of the BioMagResDataBank and the protein data bank to parametrize a new empirical knowledge-based chemical shift predictor of protein backbone atoms using either a linear or an artificial neural network model. The resulting chemical shift predictor PPM-One accepts a single static 3D structure as input and emulates the effect of local protein dynamics via interatomic steric contacts. Furthermore, the chemical shift prediction was extended to most side-chain protons and it is found that the prediction accuracy is at a level allowing an independent assessment of stereospecific assignments. For a previously established set of test proteins some overall improvement was achieved over current top-performing chemical shift prediction programs.

  9. Chemical shifts and coupling constants of C8H10N4O2

    Jain, M.

    This document is part of Subvolume D3 `Chemical Shifts and Coupling Constants for Carbon-13: Heterocycles' of Volume 35 `Nuclear Magnetic Resonance (NMR) Data' of Landolt-Börnstein Group III `Condensed Matter'

  10. Quantitative chemical-shift MR imaging cutoff value: Benign versus malignant vertebral compression – Initial experience

    Dalia Z. Zidan

    2014-09-01

    Conclusion: Quantitative chemical shift MR imaging could be a valuable addition to standard MR imaging techniques and represent a rapid problem solving tool in differentiating benign from malignant vertebral compression, especially in patients with known primary malignancies.

  11. PPM-One: a static protein structure based chemical shift predictor

    We mined the most recent editions of the BioMagResDataBank and the protein data bank to parametrize a new empirical knowledge-based chemical shift predictor of protein backbone atoms using either a linear or an artificial neural network model. The resulting chemical shift predictor PPM-One accepts a single static 3D structure as input and emulates the effect of local protein dynamics via interatomic steric contacts. Furthermore, the chemical shift prediction was extended to most side-chain protons and it is found that the prediction accuracy is at a level allowing an independent assessment of stereospecific assignments. For a previously established set of test proteins some overall improvement was achieved over current top-performing chemical shift prediction programs

  12. {sup 1}H and {sup 13}C NMR spectroscopy of 5-methyl-5H-indole-[2,3-b]quinoline; Spektroskopia {sup 1}H i {sup 13}C NMR 5-metylo-5H-indole-[2,3-b]chinoliny

    Kamienska-Trela, K.; Kania, L.; Kaczmarek, L. [Inst. Chemii Organicznej, Polska Akademia Nauk, Warsaw (Poland)

    1994-12-31

    {sup 1}H and {sup 13}C NMR spectra of 5-methyl-5H-indole quinoline have been measured in CDCl{sub 3} solution. The full assignation of resonant signals observed for this compound has been done. Also the chemical shifts {delta}({sup 1}H) and {delta}({sup 13}C) have been determined. That parameters as being tightly dependent on electronic density in molecule are very important also from the view point of biological activity of investigated compound. 3 refs, 1 fig., 1 tab.

  13. Supramolecular chemical shift reagents inducing conformational transitions: NMR analysis of carbohydrate homooligomer mixtures

    Beeren, Sophie; Meier, Sebastian

    2015-01-01

    We introduce the concept of supramolecular chemical shift reagents as a tool to improve signal resolution for the NMR analysis of homooligomers. Non-covalent interactions with the shift reagent can constrain otherwise flexible analytes inducing a conformational transition that results in signal...

  14. AFNMR: automated fragmentation quantum mechanical calculation of NMR chemical shifts for biomolecules

    We evaluate the performance of the automated fragmentation quantum mechanics/molecular mechanics approach (AF-QM/MM) on the calculation of protein and nucleic acid NMR chemical shifts. The AF-QM/MM approach models solvent effects implicitly through a set of surface charges computed using the Poisson–Boltzmann equation, and it can also be combined with an explicit solvent model through the placement of water molecules in the first solvation shell around the solute; the latter substantially improves the accuracy of chemical shift prediction of protons involved in hydrogen bonding with solvent. We also compare the performance of AF-QM/MM on proteins and nucleic acids with two leading empirical chemical shift prediction programs SHIFTS and SHIFTX2. Although the empirical programs outperform AF-QM/MM in predicting chemical shifts, the differences are in some cases small, and the latter can be applied to chemical shifts on biomolecules which are outside the training set employed by the empirical programs, such as structures containing ligands, metal centers, and non-standard residues. The AF-QM/MM described here is implemented in version 5 of the SHIFTS software, and is fully automated, so that only a structure in PDB format is required as input

  15. AFNMR: automated fragmentation quantum mechanical calculation of NMR chemical shifts for biomolecules

    Swails, Jason [Rutgers University, Department of Chemistry and Chemical Biology and BioMaPS Institute (United States); Zhu, Tong; He, Xiao, E-mail: xiaohe@phy.ecnu.edu.cn [East China Normal University, State Key Laboratory of Precision Spectroscopy, Institute of Theoretical and Computational Science (China); Case, David A., E-mail: case@biomaps.rutgers.edu [Rutgers University, Department of Chemistry and Chemical Biology and BioMaPS Institute (United States)

    2015-10-15

    We evaluate the performance of the automated fragmentation quantum mechanics/molecular mechanics approach (AF-QM/MM) on the calculation of protein and nucleic acid NMR chemical shifts. The AF-QM/MM approach models solvent effects implicitly through a set of surface charges computed using the Poisson–Boltzmann equation, and it can also be combined with an explicit solvent model through the placement of water molecules in the first solvation shell around the solute; the latter substantially improves the accuracy of chemical shift prediction of protons involved in hydrogen bonding with solvent. We also compare the performance of AF-QM/MM on proteins and nucleic acids with two leading empirical chemical shift prediction programs SHIFTS and SHIFTX2. Although the empirical programs outperform AF-QM/MM in predicting chemical shifts, the differences are in some cases small, and the latter can be applied to chemical shifts on biomolecules which are outside the training set employed by the empirical programs, such as structures containing ligands, metal centers, and non-standard residues. The AF-QM/MM described here is implemented in version 5 of the SHIFTS software, and is fully automated, so that only a structure in PDB format is required as input.

  16. Chemical shift MRI can aid in the diagnosis of indeterminate skeletal lesions of the spine

    Douis, H. [University Hospital Birmingham, Department of Radiology, Birmingham (United Kingdom); Royal Orthopaedic Hospital, Department of Radiology, Birmingham (United Kingdom); Davies, A.M. [Royal Orthopaedic Hospital, Department of Radiology, Birmingham (United Kingdom); Jeys, L. [Royal Orthopaedic Hospital, Department of Orthopaedic Oncology, Birmingham (United Kingdom); Sian, P. [Royal Orthopaedic Hospital, Department of Spinal Surgery and Spinal Oncology, Birmingham (United Kingdom)

    2016-04-15

    To evaluate the role of chemical shift MRI in the characterisation of indeterminate skeletal lesions of the spine as benign or malignant. Fifty-five patients (mean age 54.7 years) with 57 indeterminate skeletal lesions of the spine were included in this retrospective study. In addition to conventional MRI at 3 T which included at least sagittal T1WI and T2WI/STIR sequences, patients underwent chemical shift MRI. A cut-off value with a signal drop-out of 20 % was used to differentiate benign lesions from malignant lesions (signal drop-out <20 % being malignant). There were 45 benign lesions and 12 malignant lesions. Chemical shift imaging correctly diagnosed 33 of 45 lesions as benign and 11 of 12 lesions as malignant. In contrast, there were 12 false positive cases and 1 false negative case based on chemical shift MRI. This yielded a sensitivity of 91.7 %, a specificity of 73.3 %, a negative predictive value of 97.1 %, a positive predictive value of 47.8 % and a diagnostic accuracy of 82.5 %. Chemical shift MRI can aid in the characterisation of indeterminate skeletal lesions of the spine in view of its high sensitivity in diagnosing malignant lesions. Chemical shift MRI can potentially avoid biopsy in a considerable percentage of patients with benign skeletal lesions of the spine. (orig.)

  17. Chemical shift MRI can aid in the diagnosis of indeterminate skeletal lesions of the spine

    To evaluate the role of chemical shift MRI in the characterisation of indeterminate skeletal lesions of the spine as benign or malignant. Fifty-five patients (mean age 54.7 years) with 57 indeterminate skeletal lesions of the spine were included in this retrospective study. In addition to conventional MRI at 3 T which included at least sagittal T1WI and T2WI/STIR sequences, patients underwent chemical shift MRI. A cut-off value with a signal drop-out of 20 % was used to differentiate benign lesions from malignant lesions (signal drop-out <20 % being malignant). There were 45 benign lesions and 12 malignant lesions. Chemical shift imaging correctly diagnosed 33 of 45 lesions as benign and 11 of 12 lesions as malignant. In contrast, there were 12 false positive cases and 1 false negative case based on chemical shift MRI. This yielded a sensitivity of 91.7 %, a specificity of 73.3 %, a negative predictive value of 97.1 %, a positive predictive value of 47.8 % and a diagnostic accuracy of 82.5 %. Chemical shift MRI can aid in the characterisation of indeterminate skeletal lesions of the spine in view of its high sensitivity in diagnosing malignant lesions. Chemical shift MRI can potentially avoid biopsy in a considerable percentage of patients with benign skeletal lesions of the spine. (orig.)

  18. From NMR chemical shifts to amino acid types: Investigation of the predictive power carried by nuclei

    An approach to automatic prediction of the amino acid type from NMR chemical shift values of its nuclei is presented here, in the frame of a model to calculate the probability of an amino acid type given the set of chemical shifts. The method relies on systematic use of all chemical shift values contained in the BioMagResBank (BMRB). Two programs were designed, one (BMRB stats) for extracting statistical chemical shift parameters from the BMRB and another one (RESCUE2) for computing the probabilities of each amino acid type, given a set of chemical shifts. The Bayesian prediction scheme presented here is compared to other methods already proposed: PROTYP (Grzesiek and Bax, J. Biomol. NMR, 3, 185-204, 1993) RESCUE (Pons and Delsuc, J. Biomol. NMR, 15, 15-26, 1999) and PLATON (Labudde et al., J. Biomol. NMR, 25, 41-53, 2003) and is found to be more sensitive and more specific. Using this scheme, we tested various sets of nuclei. The two nuclei carrying the most information are Cβ and Hβ, in agreement with observations made in Grzesiek and Bax, 1993. Based on four nuclei: Hβ, Cβ, Cα and C', it is possible to increase correct predictions to a rate of more than 75%. Taking into account the correlations between the nuclei chemical shifts has only a slight impact on the percentage of correct predictions: indeed, the largest correlation coefficients display similar features on all amino acids

  19. Ontogenetic shift in response to prey-derived chemical cues in prairie rattlesnakes Crotalus viridis viridis

    Anthony J. SAVIOLA, David CHISZAR, Stephen P. MACKESSY

    2012-08-01

    Full Text Available Snakes often have specialized diets that undergo a shift from one prey type to another depending on the life stage of the snake. Crotalus viridis viridis (prairie rattlesnake takes different prey at different life stages, and neonates typically prey on ectotherms, while adults feed almost entirely on small endotherms. We hypothesized that elevated rates of tongue flicking to chemical stimuli should correlate with particular prey consumed, and that this response shifts from one prey type to another as individuals age. To examine if an ontogenetic shift in response to chemical cues occurred, we recorded the rate of tongue flicking for 25 neonate, 20 subadult, and 20 adult (average SVL = 280.9, 552, 789.5 mm, respectively wild-caught C. v. viridis to chemical stimuli presented on a cotton-tipped applicator; water-soluble cues from two ectotherms (prairie lizard, Sceloporus undulatus, and house gecko, Hemidactylus frenatus, two endotherms (deer mouse, Peromyscus maniculatus and lab mouse, Mus musculus, and water controls were used. Neonates tongue flicked significantly more to chemical cues of their common prey, S. undulatus, than to all other chemical cues; however, the response to this lizard’s chemical cues decreased in adult rattlesnakes. Subadults tongue flicked with a higher rate of tongue flicking to both S. undulatus and P. maniculatus than to all other treatments, and adults tongue flicked significantly more to P. maniculatus than to all other chemical cues. In addition, all three sub-classes demonstrated a greater response for natural prey chemical cues over chemical stimuli of prey not encountered in the wild (M. musculus and H. frenatus. This shift in chemosensory response correlated with the previously described ontogenetic shifts in C. v. viridis diet. Because many vipers show a similar ontogenetic shift in diet and venom composition, we suggest that this shift in prey cue discrimination is likely a general phenomenon among viperid

  20. Alpha Resonant States in 13C

    The 9Be(6Li,d)13C reaction was used to investigate alpha resonant states in 13C up to 15 MeV of excitation. The reaction was measured at a bombarding energy of 25.5 MeV employing the Sao Paulo Pelletron-Enge-Spectrograph facility and the nuclear emulsion detection technique. An energy resolution of 50 keV was obtained. Several narrow alpha resonant states not previously measured were detected, in particular the one at the (3α+n) threshold populated by an L = 2 transfer, revealing a 9Be+α component for the 1/2- cluster state candidate at this threshold. Experimental angular distributions are presented in comparison with DWBA predictions.

  1. A preliminary investigation of 13C background in 13C-urea breath test

    During the 13C-urea breath test which is used for diagnosis of the helicobacter pylori infection (HP), the 13C background values are measured in 495 normal donors in Beijing, Shandong, Jiangsu and Guizhou. The fluctuation is less than 0.2% for these areas and is about 0.1% within the same area. Through replacing of the individual 13C background values by the averaged values from local areas, the coincident rate for diagnosis of HP is higher than 98%

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

    Zhang, Rongchun; Mroue, Kamal H.; Ramamoorthy, Ayyalusamy, E-mail: ramamoor@umich.edu [Biophysics and Department of Chemistry, The University of Michigan, Ann Arbor, Michigan 48109-1055 (United States)

    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

  3. 1H and 13C NMR studies of palladium(2) and platinium(2) complexes with S-Methyl-L-Cysteine

    Our recent 1H NMR studies on Pd(2)-S-Methyl-L-Cysteine(SMC) complexes have shown that the use of a conformational analysis to establish the complexed species existing in solution may provide clearer results than considering the proton chemical shift only. However, the use of the vicinal coupling constant of ABC spectrum of αCH-βCH2 proton unit to estimate the rotational isomer fractions, may contain some ambiguity, especially on the proton assignment of the methylene group. For this reason 13C NMR method has been applied to study these systems. (author)

  4. Applications of artificial intelligence techniques to organic chemistry. Study on 13C NMR of steroids using computer

    This work describes the utilization of two groups of programs in searching for characteristic signals of NMR 13C steroidal compounds. The first group of programs used data bases with the spectral data and a methodology that enables the choice and the search of substructures. The chemical shifts and multiplicities for each specific substructure are used as rules to identify different types and subtypes of steroidal compounds. The second one was built to apply the rules formulated by the first group of programs and to foresee any skeletal based on a spectral analysis. (author)

  5. Effect of shifting cultivation on soil physical and chemical properties in Bandarban hill district, Bangladesh

    Khandakar Showkat Osman; M. Jashimuddin; S. M. Sirajul Haque; Sohag Miah

    2013-01-01

    This study reports the effects of shifting cultivation at slashing stage on soil physicochemical properties at Bandarban Sadar Upazila in Chittagong Hill Tracts of Bangladesh. At this initial stage of shifting cultivation no general trend was found for moisture content, maximum water holding capacity, field capacity, dry and moist bulk density, parti-cle density for some chemical properties between shifting cultivated land and forest having similar soil texture. Organic matter was significantly (p≤0.05) lower in 1-year and 3-year shifting cultivated lands and higher in 2-year shifting cultivation than in adjacent natural forest. Significant differences were also found for total N, exchangeable Ca, Mg and K and in CEC as well as for available P. Slashed area showed higher soil pH. Deterioration in land quality starts from burning of slashing materials and continues through subsequent stages of shifting cultivation.

  6. Method for evaluating chemical shifts of x-ray emission lines in molecules and solids

    Lomachuk, Yuriy V.; Titov, Anatoly V.

    2013-12-01

    A method of evaluating chemical shifts of x-ray emission lines for period four and heavier elements is developed. This method is based on the relativistic pseudopotential model and one-center restoration approach [Int. J. Quantum Chem.IJQCB20020-760810.1002/qua.20418 104, 223 (2005)] to recover a proper electronic structure in heavy-atom cores after the pseudopotential simulation of chemical compounds. The approximations of instantaneous transition and frozen core are presently applied to derive an expression for chemical shift as a difference between mean values of certain effective operator. The method allows one to avoid evaluation of small quantities (chemical shifts ˜0.01-1 eV) as differences of very large values (transition energies ˜1-100 keV in various compounds). The results of our calculations of chemical shifts for the Kα1, Kα2, and L transitions of group-14 metal cations with respect to neutral atoms are presented. Calculations of Kα1-line chemical shifts for the Pb core transitions in PbO and PbF2 with respect to those in the Pb atom are also performed and discussed. The accuracy of approximations used is estimated and the quality of the calculations is analyzed.

  7. Method of evaluating chemical shifts of X-ray emission lines in molecules and solids

    Lomachuk, Yuriy V

    2013-01-01

    Method of evaluating chemical shifts of X-ray emission lines for sufficiently heavy atoms (beginning from period 4 elements) in chemical compounds is developed. This method is based on the pseudopotential model and one-center restoration method (to reconstruct the proper electronic structure in heavy-atom cores). The approximations of instantaneous transition and frozen inner core spinors of the atom are used for derivation of an expression for chemical shift as a difference between mean values of some effective operator. The method allows one to avoid evaluating small values (chemical shifts ~ 0.01{\\div}1 eV) as differences of very large values (transition energies ~ 1{\\div}100 keV in various compounds). The results of our calculations of chemical shifts for the K_{\\alpha1,2} and L transitions of the group 14 metal cations with respect to neutral atoms are presented. The calculations of chemical shift of K_{\\alpha1}-line in the Pb-core transition within PbO and PbF_2 with respect to the neutral Pb are also p...

  8. Aspects of reaction of N-oxide radical with ethers in 13C NMR spectrum

    The stable radical N-oxide 2,2,6,6-tetramethylpiperidine was dissolved in ethers. The 13C NMR spectra were recorded in the temperature 313K at the frequency 22,625 MHz on the spectrometers with Fourier transformation. The dissolution of the radical in ether caused the contact shifts in NMR spectra. The shifts were measured. (A.S.)

  9. Structural characteristics of marine sedimentary humic acids by CP/MAS sup(13)C NMR spectroscopy

    Sardessai, S.; Wahidullah, S.

    Humic acids from sediments of different depositional environments have been studied by solid-state sup(13)C NMR and the results compared with the traditional wet chemical analysis. Results obtained are well in agreement with the previous literature...

  10. Characterisation of black carbon-rich samples by (13)C solid-state nuclear magnetic resonance.

    Novotny, Etelvino H; Hayes, Michael H B; Deazevedo, Eduardo R; Bonagamba, Tito J

    2006-09-01

    There are difficulties in quantifying and characterising the organic matter (OM) in soils that contain significant amounts of partially oxidised char or charcoal materials. The anthropogenic black carbon (BC), such as that found in the Terra Preta de Indio soils of the Amazon region, is a good example of the OM that is difficult to analyse in such soils. (13)C direct polarisation/magic angle spinning (DP/MAS) at high MAS frequency, (1)H-(13)C cross polarisation (CP)/MAS with total suppression of spinning sidebands (TOSS), and chemical shift anisotropy (CSA) filter nuclear magnetic resonance techniques have been applied successfully for quantifying the different components of OM. However, because pyrogenic materials present strong local magnetic susceptibility heterogeneities, the use of CSA-filter and TOSS make the pulse sequences very sensitive to imperfections in the pi pulses. In this study, the DP/MAS pulse sequence was replaced by a CP with a radio frequency ramp--variable amplitude CP (VACP)--VACP/MAS pulse sequence, and composite pi pulses were used in the CSA-filter and TOSS pulse sequences. In that way, the component functionalities in a humic acid from a BC soil were successfully determined. The spectrometer time needed was greatly decreased by employing this VACP/MAS technique. This development provides an accurate method for characterising BC-rich samples from different origins. PMID:16688435

  11. Characterisation of black carbon-rich samples by 13C solid-state nuclear magnetic resonance

    Novotny, Etelvino H.; Hayes, Michael H. B.; Deazevedo, Eduardo R.; Bonagamba, Tito J.

    2006-09-01

    There are difficulties in quantifying and characterising the organic matter (OM) in soils that contain significant amounts of partially oxidised char or charcoal materials. The anthropogenic black carbon (BC), such as that found in the Terra Preta de Índio soils of the Amazon region, is a good example of the OM that is difficult to analyse in such soils. 13C direct polarisation/magic angle spinning (DP/MAS) at high MAS frequency, 1H-13C cross polarisation (CP)/MAS with total suppression of spinning sidebands (TOSS), and chemical shift anisotropy (CSA) filter nuclear magnetic resonance techniques have been applied successfully for quantifying the different components of OM. However, because pyrogenic materials present strong local magnetic susceptibility heterogeneities, the use of CSA-filter and TOSS make the pulse sequences very sensitive to imperfections in the π pulses. In this study, the DP/MAS pulse sequence was replaced by a CP with a radio frequency ramp—variable amplitude CP (VACP)—VACP/MAS pulse sequence, and composite π pulses were used in the CSA-filter and TOSS pulse sequences. In that way, the component functionalities in a humic acid from a BC soil were successfully determined. The spectrometer time needed was greatly decreased by employing this VACP/MAS technique. This development provides an accurate method for characterising BC-rich samples from different origins.

  12. A comparative study of the 13C(p,p')13C and 13C(p,n)13N reactions at Ep = 35 MeV

    Differential cross sections were measured at Ep = 35 MeV for the 13C(p,n) and 13C(p,p') reactions leading to the four low-lying states in the mirror nuclei 13N and 13C. In addition, the analyzing powers were measured for the 13C(p,p') reaction. The data are generally well accounted for by DWBA calculations except for the 13C(p,p')13C(3.09 MeV, 1/2+) reaction, for which the calculations can not even reproduce the qualitative features of the data. A comparison of the (p,n) and the (p,p') results suggests that the isoscalar part of the 13C(g.s., 1/2-) → 13C(3.09 MeV, 1/2+) transition is not correctly described by currently available shell-model wave functions. (author)

  13. Differential diagnosis of adrenal masses by chemical shift and dynamic gadolinium enhanced MR imaging

    Chemical shift MRI is widely used for identifying adenomas, but it is not a perfect method. We determined whether combined dynamic MRI methods can lead to improved diagnostic accuracy. Fifty-seven adrenal masses were examined by chemical shift and dynamic MR imaging using 2 MR systems. The masses included 38 adenomas and 19 non-adenomas. In chemical shift MRI studies, the signal intensity index (SI) was calculated, and the lesions classified into 5 types in the dynamic MRI studies. Of the 38 adenomas studied, 37 had an SI greater than 0. In the dynamic MRI, 34 of 38 adenomas showed a benign pattern (type 1). If the SI for the adenomas in the chemical shift MRI was considered to be greater than 0, the positive predictive value was 0.9, and the negative predictive value was 0.94 and κ=0.79. If type 1 was considered to indicate adenomas in the dynamic MRI, the corresponding values were 0.94, 0.81 and κ=0.77 respectively. The results obtained when the 2 methods were combined were 1, 0.95 and κ=0.96 respectively. The chemical shift MRI was found to be useful for identifying adenomas in most cases. If the adrenal mass had a low SI (0< SI<5), dynamic MRI was also found to be helpful for making a differential diagnosis. (author)

  14. Prediction algorithm for amino acid types with their secondary structure in proteins (PLATON) using chemical shifts

    Labudde, D.; Leitner, D.; Krueger, M.; Oschkinat, H. [Forschungsinstitut fuer Molekulare Pharmakologie (Germany)], E-mail: oschkinat@fmp-berlin.de

    2003-01-15

    The algorithm PLATON is able to assign sets of chemical shifts derived from a single residue to amino acid types with its secondary structure (amino acid species). A subsequent ranking procedure using optionally two different penalty functions yields predictions for possible amino acid species for the given set of chemical shifts. This was demonstrated in the case of the {alpha}-spectrin SH3 domain and applied to 9 further protein data sets taken from the BioMagRes database. A database consisting of reference chemical shift patterns (reference CSPs) was generated from assigned chemical shifts of proteins with known 3D-structure. This reference CSP database is used in our approach for extracting distributions of amino acid types with their most likely secondary structure elements (namely {alpha}-helix, {beta}-sheet, and coil) for single amino acids by comparison with query CSPs. Results obtained for the 10 investigated proteins indicates that the percentage of correct amino acid species in the first three positions in the ranking list, ranges from 71.4% to 93.2% for the more favorable penalty function. Where only the top result of the ranking list for these 10 proteins is considered, 36.5% to 83.1% of the amino acid species are correctly predicted. The main advantage of our approach, over other methods that rely on average chemical shift values is the ability to increase database content by incorporating newly derived CSPs, and therefore to improve PLATON's performance over time.

  15. Protein structure validation and refinement using amide proton chemical shifts derived from quantum mechanics.

    Anders S Christensen

    Full Text Available We present the ProCS method for the rapid and accurate prediction of protein backbone amide proton chemical shifts--sensitive probes of the geometry of key hydrogen bonds that determine protein structure. ProCS is parameterized against quantum mechanical (QM calculations and reproduces high level QM results obtained for a small protein with an RMSD of 0.25 ppm (r = 0.94. ProCS is interfaced with the PHAISTOS protein simulation program and is used to infer statistical protein ensembles that reflect experimentally measured amide proton chemical shift values. Such chemical shift-based structural refinements, starting from high-resolution X-ray structures of Protein G, ubiquitin, and SMN Tudor Domain, result in average chemical shifts, hydrogen bond geometries, and trans-hydrogen bond ((h3J(NC' spin-spin coupling constants that are in excellent agreement with experiment. We show that the structural sensitivity of the QM-based amide proton chemical shift predictions is needed to obtain this agreement. The ProCS method thus offers a powerful new tool for refining the structures of hydrogen bonding networks to high accuracy with many potential applications such as protein flexibility in ligand binding.

  16. Protein structure validation and refinement using amide proton chemical shifts derived from quantum mechanics

    Christensen, Anders S; Borg, Mikael; Boomsma, Wouter; Lindorff-Larsen, Kresten; Hamelryck, Thomas; Jensen, Jan H

    2013-01-01

    We present the ProCS method for the rapid and accurate prediction of protein backbone amide proton chemical shifts - sensitive probes of the geometry of key hydrogen bonds that determine protein structure. ProCS is parameterized against quantum mechanical (QM) calculations and reproduces high level QM results obtained for a small protein with an RMSD of 0.25 ppm (r = 0.94). ProCS is interfaced with the PHAISTOS protein simulation program and is used to infer statistical protein ensembles that reflect experimentally measured amide proton chemical shift values. Such chemical shift-based structural refinements, starting from high-resolution X-ray structures of Protein G, ubiquitin, and SMN Tudor Domain, result in average chemical shifts, hydrogen bond geometries, and trans-hydrogen bond (h3JNC') spin-spin coupling constants that are in excellent agreement with experiment. We show that the structural sensitivity of the QM-based amide proton chemical shift predictions is needed to refine protein structures to this...

  17. Prediction algorithm for amino acid types with their secondary structure in proteins (PLATON) using chemical shifts

    The algorithm PLATON is able to assign sets of chemical shifts derived from a single residue to amino acid types with its secondary structure (amino acid species). A subsequent ranking procedure using optionally two different penalty functions yields predictions for possible amino acid species for the given set of chemical shifts. This was demonstrated in the case of the α-spectrin SH3 domain and applied to 9 further protein data sets taken from the BioMagRes database. A database consisting of reference chemical shift patterns (reference CSPs) was generated from assigned chemical shifts of proteins with known 3D-structure. This reference CSP database is used in our approach for extracting distributions of amino acid types with their most likely secondary structure elements (namely α-helix, β-sheet, and coil) for single amino acids by comparison with query CSPs. Results obtained for the 10 investigated proteins indicates that the percentage of correct amino acid species in the first three positions in the ranking list, ranges from 71.4% to 93.2% for the more favorable penalty function. Where only the top result of the ranking list for these 10 proteins is considered, 36.5% to 83.1% of the amino acid species are correctly predicted. The main advantage of our approach, over other methods that rely on average chemical shift values is the ability to increase database content by incorporating newly derived CSPs, and therefore to improve PLATON's performance over time

  18. Alpha-cluster structure in 13C

    We study the structure of low-lying states of 13C with a microscopic cluster model. In addition to the 3α-n model space, the breaking effect of one of the α-clusters due to the spin-orbit interaction is also taken into account. The iso-scalar E0 transition probabilities from the ground 1/2- state to the excited 1/2- states have been shown to be large associated with the cluster structure of these states. However the values are small due to the effect of one additional valence neutron compared to the case of the second 0+ state in 12C. (author)

  19. Isotope effects on chemical shifts in the study of intramolecular hydrogen bonds

    Hansen, Poul Erik

    2015-01-01

    The paper deals with the use of isotope effects on chemical shifts in characterizing intramolecular hydrogen bonds. Both so-called resonance-assisted (RAHB) and non-RAHB systems are treated. The importance of RAHB will be discussed. Another very important issue is the borderline between “static......” and tautomeric systems. Isotope effects on chemical shifts are particularly useful in such studies. All kinds of intramolecular hydrogen bonded systems will be treated, typical hydrogen bond donors: OH, NH, SH and NH+, typical acceptors C=O, C=N, C=S C=N−. The paper will be deal with both secondary...... and primary isotope effects on chemical shifts. These two types of isotope effects monitor the same hydrogen bond, but from different angles...

  20. Detection of initiation sites in protein folding of the four helix bundle ACBP by chemical shift analysis

    Modig, K.; Jürgensen, Vibeke Würtz; Lindorff-Larsen, K.;

    2007-01-01

    A simple alternative method for obtaining "random coil" chemical shifts by intrinsic referencing using the protein's own peptide sequence is presented. These intrinsic random coil backbone shifts were then used to calculate secondary chemical shifts, that provide important information on the resi...

  1. Pulse NMR in solids: chemical shift, lead fluoride, and thorium hydride

    The fluorine chemical shift of a single crystal CaF2 was measured up to 4 kilobar at room temperature using multiple pulse NMR. The pressure dependence of the shift is found to be --1.7 +- 1 ppM/kbar, while an overlap model predicts a shift of --0.46 ppM/kbar.The chemical shift tensor is separated into ''geometrical'' and ''chemical'' contributions, and comparison of the proposed model calculations with recent data on hydroxyl proton chemical shift tensors shows that the geometrical portion accounts for the qualitative features of the measured tensors. A study of fluoride ion motion in β-PbF2 doped with NaF was conducted by measurement of the 19F transverse relaxation time (T2), spin lattice relaxation time (T1) and the spin lattice relaxation time in the rotating frame (T/sub 1r). Two samples of Th4H15, prepared under different conditions but both having the proper ratio of H/Th (to within 1 percent), were studied. The structure of the Th4H15 suggested by x-ray measurements is confirmed through a moment analysis of the rigid lattice line shape

  2. Multisite Kinetic Modeling of 13C Metabolic MR Using [1-13C]Pyruvate

    Hyperpolarized 13C imaging allows real-time in vivo measurements of metabolite levels. Quantification of metabolite conversion between [1-13C]pyruvate and downstream metabolites [1-13C]alanine, [1-13C]lactate, and [13C]bicarbonate can be achieved through kinetic modeling. Since pyruvate interacts dynamically and simultaneously with its downstream metabolites, the purpose of this work is the determination of parameter values through a multisite, dynamic model involving possible biochemical pathways present in MR spectroscopy. Kinetic modeling parameters were determined by fitting the multisite model to time-domain dynamic metabolite data. The results for different pyruvate doses were compared with those of different two-site models to evaluate the hypothesis that for identical data the uncertainty of a model and the signal-to-noise ratio determine the sensitivity in detecting small physiological differences in the target metabolism. In comparison to the two-site exchange models, the multisite model yielded metabolic conversion rates with smaller bias and smaller standard deviation, as demonstrated in simulations with different signal-to-noise ratio. Pyruvate dose effects observed previously were confirmed and quantified through metabolic conversion rate values. Parameter interdependency allowed an accurate quantification and can therefore be useful for monitoring metabolic activity in different tissues

  3. Multisite Kinetic Modeling of 13C Metabolic MR Using [1-13C]Pyruvate

    Pedro A. Gómez Damián

    2014-01-01

    Full Text Available Hyperpolarized 13C imaging allows real-time in vivo measurements of metabolite levels. Quantification of metabolite conversion between [1-13C]pyruvate and downstream metabolites [1-13C]alanine, [1-13C]lactate, and [13C]bicarbonate can be achieved through kinetic modeling. Since pyruvate interacts dynamically and simultaneously with its downstream metabolites, the purpose of this work is the determination of parameter values through a multisite, dynamic model involving possible biochemical pathways present in MR spectroscopy. Kinetic modeling parameters were determined by fitting the multisite model to time-domain dynamic metabolite data. The results for different pyruvate doses were compared with those of different two-site models to evaluate the hypothesis that for identical data the uncertainty of a model and the signal-to-noise ratio determine the sensitivity in detecting small physiological differences in the target metabolism. In comparison to the two-site exchange models, the multisite model yielded metabolic conversion rates with smaller bias and smaller standard deviation, as demonstrated in simulations with different signal-to-noise ratio. Pyruvate dose effects observed previously were confirmed and quantified through metabolic conversion rate values. Parameter interdependency allowed an accurate quantification and can therefore be useful for monitoring metabolic activity in different tissues.

  4. An automated system designed for large scale NMR data deposition and annotation: application to over 600 assigned chemical shift data entries to the BioMagResBank from the Riken Structural Genomics/Proteomics Initiative internal database

    Biomolecular NMR chemical shift data are key information for the functional analysis of biomolecules and the development of new techniques for NMR studies utilizing chemical shift statistical information. Structural genomics projects are major contributors to the accumulation of protein chemical shift information. The management of the large quantities of NMR data generated by each project in a local database and the transfer of the data to the public databases are still formidable tasks because of the complicated nature of NMR data. Here we report an automated and efficient system developed for the deposition and annotation of a large number of data sets including 1H, 13C and 15N resonance assignments used for the structure determination of proteins. We have demonstrated the feasibility of our system by applying it to over 600 entries from the internal database generated by the RIKEN Structural Genomics/Proteomics Initiative (RSGI) to the public database, BioMagResBank (BMRB). We have assessed the quality of the deposited chemical shifts by comparing them with those predicted from the PDB coordinate entry for the corresponding protein. The same comparison for other matched BMRB/PDB entries deposited from 2001–2011 has been carried out and the results suggest that the RSGI entries greatly improved the quality of the BMRB database. Since the entries include chemical shifts acquired under strikingly similar experimental conditions, these NMR data can be expected to be a promising resource to improve current technologies as well as to develop new NMR methods for protein studies.

  5. What can we learn by computing 13Cα chemical shifts for X-ray protein models?

    The room-temperature X-ray structures of two proteins, solved at 1.8 and 1.9 Å resolution, are used to investigate whether a set of conformations, rather than a single X-ray structure, provides better agreement with both the X-ray data and the observed 13Cα chemical shifts in solution. The room-temperature X-ray structures of ubiquitin and of the RNA-binding domain of nonstructural protein 1 of influenza A virus solved at 1.8 and 1.9 Å resolution, respectively, were used to investigate whether a set of conformations rather than a single X-ray structure provides better agreement with both the X-ray data and the observed 13Cα chemical shifts in solution. For this purpose, a set of new conformations for each of these proteins was generated by fitting them to the experimental X-ray data deposited in the PDB. For each of the generated structures, which show R and Rfree factors similar to those of the deposited X-ray structure, the 13Cα chemical shifts of all residues in the sequence were computed at the DFT level of theory. The sets of conformations were then evaluated by their ability to reproduce the observed 13Cα chemical shifts by using the conformational average root-mean-square-deviation (ca-r.m.s.d.). For ubiquitin, the computed set of conformations is a better representation of the observed 13Cα chemical shifts in terms of the ca-r.m.s.d. than a single X-ray-derived structure. However, for the RNA-binding domain of nonstructural protein 1 of influenza A virus, consideration of an ensemble of conformations does not improve the agreement with the observed 13Cα chemical shifts. Whether an ensemble of conformations rather than any single structure is a more accurate representation of a protein structure in the crystal as well as of the observed 13Cα chemical shifts is determined by the dispersion of coordinates, in terms of the all-atom r.m.s.d. among the generated models; these generated models satisfy the experimental X-ray data with accuracy as good as

  6. Proton Magnetic Resonance and Human Thyroid Neoplasia III. Ex VivoChemical-Shift Microimaging

    Rutter, Allison; Künnecke, Basil; Dowd, Susan; Russell, Peter; Delbridge, Leigh; Mountford, Carolyn E.

    1996-03-01

    Magnetic-resonance chemical-shift microimaging, with a spatial resolution of 40 × 40 μm, is a modality which can detect alterations to cellular chemistry and hence markers of pathological processes in human tissueex vivo.This technique was used as a chemical microscope to assess follicular thyroid neoplasms, lesions which are unsatisfactorily investigated using standard histopathological techiques or water-based magnetic-resonance imaging. The chemical-shift images at the methyl frequency (0.9 ppm) identify chemical heterogeneity in follicular tumors which are histologically homogeneous. The observed changes to cellular chemistry, detectable in foci of approximately 100 cells or less, support the existence of a preinvasive state hitherto unidentified by current pathological techniques.

  7. Stereoselective synthesis of L-[4-13C]carnitine

    The stereoselective synthesis of L-[4-13C]carnitine was achieved in 5 steps. The label was introduced from K13CN into an easily separated diastereomeric pair of 3-deoxy-D-[1-13C]aldohexoses. Reductive amination of the labeled aldohexose yielded the corresponding D-1-(dimethylamino)[1-13C]alditol which was oxidized in two steps and alkylated with iodomethane to yield L-[4-13C]carnitine. The stereochemical integrity at C-2 of the 3-deoxy-D-[1-13C]glucose precursor was maintained throughout the synthesis of L-[4-13C]carnitine. (author)

  8. Parameter-free calculation of K alpha chemical shifts for Al, Si, and Ge oxides

    Lægsgaard, Jesper

    2001-01-01

    The chemical shifts of the K alpha radiation line from Al, Si, and Ge ions between their elemental and oxide forms are calculated within the framework of density functional theory using ultrasoft pseudopotentials. It is demonstrated that this theoretical approach yields quantitatively accurate re...... implanted in silica are found to be in excellent agreement with experimental data, providing support for the proposed atomic geometry....

  9. Database proton NMR chemical shifts for RNA signal assignment and validation

    The Biological Magnetic Resonance Data Bank contains NMR chemical shift depositions for 132 RNAs and RNA-containing complexes. We have analyzed the 1H NMR chemical shifts reported for non-exchangeable protons of residues that reside within A-form helical regions of these RNAs. The analysis focused on the central base pair within a stretch of three adjacent base pairs (BP triplets), and included both Watson–Crick (WC; G:C, A:U) and G:U wobble pairs. Chemical shift values were included for all 43 possible WC-BP triplets, as well as 137 additional triplets that contain one or more G:U wobbles. Sequence-dependent chemical shift correlations were identified, including correlations involving terminating base pairs within the triplets and canonical and non-canonical structures adjacent to the BP triplets (i.e. bulges, loops, WC and non-WC BPs), despite the fact that the NMR data were obtained under different conditions of pH, buffer, ionic strength, and temperature. A computer program (RNAShifts) was developed that enables convenient comparison of RNA 1H NMR assignments with database predictions, which should facilitate future signal assignment/validation efforts and enable rapid identification of non-canonical RNA structures and RNA-ligand/protein interaction sites.

  10. Chemical shifts in transition metal dithiocarbamates from infrared and X-ray photoelectron spectroscopies

    Payne, R.; Magee, R. J.; Liesegang, J.

    1982-11-01

    Measurements of the IR stretching frequencies of the NC and MS bonds in transition-metal (M) dithiocarbamates show significant correlation with measurement of core level XPS chemical shifts. This is believed to be the first demonstration of such a correlation for a series of solid-phase compounds.

  11. Automated assignment of NMR chemical shifts based on a known structure and 4D spectra.

    Trautwein, Matthias; Fredriksson, Kai; Möller, Heiko M; Exner, Thomas E

    2016-08-01

    Apart from their central role during 3D structure determination of proteins the backbone chemical shift assignment is the basis for a number of applications, like chemical shift perturbation mapping and studies on the dynamics of proteins. This assignment is not a trivial task even if a 3D protein structure is known and needs almost as much effort as the assignment for structure prediction if performed manually. We present here a new algorithm based solely on 4D [(1)H,(15)N]-HSQC-NOESY-[(1)H,(15)N]-HSQC spectra which is able to assign a large percentage of chemical shifts (73-82 %) unambiguously, demonstrated with proteins up to a size of 250 residues. For the remaining residues, a small number of possible assignments is filtered out. This is done by comparing distances in the 3D structure to restraints obtained from the peak volumes in the 4D spectrum. Using dead-end elimination, assignments are removed in which at least one of the restraints is violated. Including additional information from chemical shift predictions, a complete unambiguous assignment was obtained for Ubiquitin and 95 % of the residues were correctly assigned in the 251 residue-long N-terminal domain of enzyme I. The program including source code is available at https://github.com/thomasexner/4Dassign . PMID:27484442

  12. Ab Initio Calculations of Deuterium Isotope Effects on Chemical Shifts of Salt-Bridged Lysines

    Ullah, Saif; Ishimoto, Takayoshi; Williamson, Mike P.;

    2011-01-01

    Deuterium isotope effects measure the change in chemical shift on substitution of a proton by deuterium. They have been calculated by direct treatment of the H/D nuclear quantum effect using a multicomponent ab initio molecular orbital method based on a non-Born−Oppenheimer approximation. This me...

  13. Using NMR chemical shifts to calculate the propensity for structural order and disorder in proteins

    Tamiola, Kamil; Mulder, Frans A. A.

    2012-01-01

    NMR spectroscopy offers the unique possibility to relate the structural propensities of disordered proteins and loop segments of folded peptides to biological function and aggregation behaviour. Backbone chemical shifts are ideally suited for this task, provided that appropriate reference data are a

  14. Sequence-specific assignment of histidine and tryptophan ring 1H, 13C and 15N resonances in 13C/15N- and 2H/13C/15N-labelled proteins

    Methods are described to correlate aromatic 1Hδ2/13Cδ2 or 1Hε1/15Nε1 with aliphatic 13Cβ chemical shifts of histidine and tryptophan residues, respectively. The pulse sequences exclusively rely on magnetization transfers via one-bond scalar couplings and employ [15N, 1H]- and/or [13C, 1H]-TROSY schemes to enhance sensitivity. In the case of histidine imidazole rings exhibiting slow HN-exchange with the solvent, connectivities of these proton resonances with β-carbons can be established as well. In addition, their correlations to ring carbons can be detected in a simple [15N, 1H]-TROSY-H(N)Car experiment, revealing the tautomeric state of the neutral ring system. The novel methods are demonstrated with the 23-kDa protein xylanase and the 35-kDa protein diisopropylfluorophosphatase, providing nearly complete sequence-specific resonance assignments of their histidine δ-CH and tryptophan ε-NH groups

  15. Combining ambiguous chemical shift mapping with structure-based backbone and NOE assignment from 15N-NOESY

    Jang, Richard

    2011-01-01

    Chemical shift mapping is an important technique in NMRbased drug screening for identifying the atoms of a target protein that potentially bind to a drug molecule upon the molecule\\'s introduction in increasing concentrations. The goal is to obtain a mapping of peaks with known residue assignment from the reference spectrum of the unbound protein to peaks with unknown assignment in the target spectrum of the bound protein. Although a series of perturbed spectra help to trace a path from reference peaks to target peaks, a one-to-one mapping generally is not possible, especially for large proteins, due to errors, such as noise peaks, missing peaks, missing but then reappearing, overlapped, and new peaks not associated with any peaks in the reference. Due to these difficulties, the mapping is typically done manually or semi-automatically. However, automated methods are necessary for high-throughput drug screening. We present PeakWalker, a novel peak walking algorithm for fast-exchange systems that models the errors explicitly and performs many-to-one mapping. On the proteins: hBclXL, UbcH5B, and histone H1, it achieves an average accuracy of over 95% with less than 1.5 residues predicted per target peak. Given these mappings as input, we present PeakAssigner, a novel combined structure-based backbone resonance and NOE assignment algorithm that uses just 15N-NOESY, while avoiding TOCSY experiments and 13C- labeling, to resolve the ambiguities for a one-toone mapping. On the three proteins, it achieves an average accuracy of 94% or better. Copyright © 2011 ACM.

  16. Elucidating the Link between NMR Chemical Shifts and Electronic Structure in d(0) Olefin Metathesis Catalysts.

    Halbert, Stéphanie; Copéret, Christophe; Raynaud, Christophe; Eisenstein, Odile

    2016-02-24

    The nucleophilic carbon of d(0) Schrock alkylidene metathesis catalysts, [M] = CHR, display surprisingly low downfield chemical shift (δiso) and large chemical shift anisotropy. State-of-the-art four-component relativistic calculations of the chemical shift tensors combined with a two-component analysis in terms of localized orbitals allow a molecular-level understanding of their orientations, the magnitude of their principal components (δ11 > δ22 > δ33) and associated δiso. This analysis reveals the dominating influence of the paramagnetic contribution yielding a highly deshielded alkylidene carbon. The largest paramagnetic contribution, which originates from the coupling of alkylidene σMC and π*MC orbitals under the action of the magnetic field, is analogous to that resulting from coupling σCC and π*CC in ethylene; thus, δ11 is in the MCH plane and is perpendicular to the MC internuclear direction. The higher value of carbon-13 δiso in alkylidene complexes relative to ethylene is thus due to the smaller energy gap between σMC and π*MC vs this between σCC and π*CC in ethylene. This effect also explains why the highest value of δiso is observed for Mo and the lowest for Ta, the values for W and Re being in between. In the presence of agostic interaction, the chemical shift tensor principal components orientation (δ22 or δ33 parallel or perpendicular to πMX) is influenced by the MCH angle because it determines the orientation of the alkylidene CHR fragment relative to the MC internuclear axis. The orbital analysis shows how the paramagnetic terms, understood with a localized bond model, determine the chemical shift tensor and thereby δiso. PMID:26787258

  17. Synthesis and structural analysis of 13C-fatty acids

    2000-01-01

    The 13C-labeled fatty acids octanoic-1-13C acid and palmitic-l-13C acid were synthetically prepared from Ba 13CO3. The yield of the former was more than 90% and that of the latter was above 85%. MS, IR, 1H-NMR and 13NMR were performed to analyze the structures of the two 13C-fatty acids, compared with their unlabeled fatty acids.

  18. 1H, 15N and 13C NMR resonance assignment, secondary structure and global fold of the FMN-binding domain of human cytochrome P450

    The FMN-binding domain of human NADPH-cytochrome P450 reductase,corresponding to exons 3-;7, has been expressed at high level in an active form and labelled with 13C and 15N. Most of the backbone and aliphatic side-chain 1H, 15Nand 13C resonances have been assigned using heteronuclear double- and triple-resonance methods, together with a semiautomatic assignment strategy. The secondary structure as estimated from the chemical shift index and NOE connectivities consists of six α-helices and fiveβ-strands. The global fold was deduced from the long-range NOE sun ambiguously assigned in a 4D 13C-resolved HMQC-NOESY-HMQC spectrum. The fold is of the alternating α/β type, with the fiveβ-strands arranged into a parallel β-sheet. The secondary structure and global fold are very similar to those of the bacterial flavodoxins, but the FMN-binding domain has an extra short helix in place of a loop, and an extra helix at the N-terminus (leading to the membrane anchordomain in the intact P450 reductase). The experimental constraints were combined with homology modelling to obtain a structure of the FMN-bindingdomain satisfying the observed NOE constraints. Chemical shift comparisons showed that the effects of FMN binding and of FMN reduction are largely localised at the binding site

  19. A study of the experimental and theoretical infrared, Raman, 1H and 13C NMR spectra of the biochemicals valeric and valproic acids

    Badawi, Hassan M.; Förner, Wolfgang; Ali, Shaikh A.

    2014-10-01

    The structural stability, vibrational, 1H and 13C NMR spectra of valeric and valproic acids were investigated by the B3LYP calculations with the 6-311G** basis set. Valeric acid is predicted to exist predominantly in the planar cis form (80% abundance). Valproic acid is predicted to have an equilibrium mixture of 68% gauche-1 and 32% gauche-2 structures at 298.15 K. The spectral feature of the Osbnd H stretching mode in the infrared spectra of both acids suggests the presence of strong H-bonding in the condensed phase of valeric acid and weak H-bonding in the case of valproic acid. The harmonic and anharmonic vibrational wavenumbers were computed at the B3LYP level of theory and tentative vibrational assignments were provided on the basis of combined theoretical and experimental infrared and Raman data of the molecules. Not all of the calculated anharmonic wavenumbers showed a consistent trend with the observed wavenumbers. The 1H and 13C NMR spectra of both acids were interpreted by experimental and DFT calculated chemical shifts of the two acids. The RMSD between experimental and theoretical 1H and 13C chemical shifts for valeric acid is 1.8 and 3.8 ppm, whereas for valproic acid, it is 1.4 and 4.5 ppm, respectively.

  20. The conformational stability, solvation and the assignments of the experimental infrared, Raman, 1H and 13C NMR spectra of the local anesthetic drug lidocaine

    Badawi, Hassan M.; Förner, Wolfgang; Ali, Shaikh A.

    2015-05-01

    The structure, vibrational and 1H and 13C NMR spectra of the local anesthetic drug lidocaine were investigated by the B3LYP/6-311G∗∗ calculations. The molecule was predicted to have the non-planar cis (NCCN ∼ 0°) structures being about 2-6 kcal/mol lower in energy than the corresponding trans (NCCN ∼ 180°) forms. The calculated NCCN (9.6°) and CNCC (-132.2°) torsional angles were in a good qualitative agreement with the reported X-ray angles (3.1 and 13.0°, -102.67 and -77.9°, respectively, for H-bonded dimers). The Gibbs energy of solution of lidocaine in formamide, water, dimethylsulfoxide, acetonitrile, methanol, ethanol and chloroform solutions was estimated at the B3LYP level. The predicted affinity of lidocaine toward the alcohols, acetonitrile and chloroform solutions was in excellent agreement with the reported experimental solubility of the drug in organic solvents. The analysis of the observed vibrational spectra is consistent with the presence of lidocaine in only one conformation at room temperature. The 1H and 13C NMR spectra of lidocaine were interpreted by experimental and DFT calculated chemical shifts of the drug. The RMSD between experimental and theoretical 1H and 13C chemical shifts for lidocaine is 0.47 and 8.26 ppm, respectively.

  1. Solution behavior and complete 1H and 13C NMR assignments of the coenzyme B12 derivative (5'-deoxyadenosyl)cobinamide using modern 2D NMR experiments, including 600-MHz 1H NMR data

    Two-dimensional (2D) NMR methods have been used to assign completely the 1H and 13C NMR spectra of the (5'-deoxyadenosyl)cobinamide cation (AdoCbi+) in D2O. Most of the 1H spectral assignments were made by using 2D homonuclear shift correlation spectroscopy (COSY), homonuclear Hartmann-Hahn spectroscopy (HOHAHA), absorption-mode (phase sensitive) 2D nuclear Overhauser effect (NOE) spectroscopy, and spin-locked NOE spectroscopy (also called ROESY, for rotating-frame Overhauser enhancement spectroscopy). Most of the protonated carbon resonances were assigned by using 1H-detected heteronuclear multiple-quantum coherence (HMQC) spectroscopy. The nonprotonated carbon resonances, as well as the remaining unassigned 1H and 13C NMR signals, were assigned from long-range 1H-13C connectivities determined from 1H-detected multiple-bond heteronuclear multiple-quantum coherence spectroscopy (HMBC). Comparison of the 13C chemical shifts and 1H NOEs of AdoCbi+ with those of coenzyme B12 ((5'-deoxyadenosyl)cobalamin) and its benzimidazole-protonated, base-off form indicates that the electronic properties and structure of AdoCbi+ are similar to that of coenzyme B12 in the protonated, base-off form. The 13C chemical shifts of most of the carbons of AdoCbi+ do not vary significantly from those of base-off, benzimidazole-protonated coenzyme B12, indicating that the electronic environment of the corrin ring is also similar in both compounds. However, significant differences in the chemical shifts of some of the corresponding carbons of the b, d, e, and f corrin side chains in AdoCbi+ and in base-off, benzimidazole-protonated coenzyme B12 indicate that the positions of these side chains may be different in AdoCbi+ compared to base-off coenzyme B12

  2. Noninvasive Temperature Mapping With MRI Using Chemical Shift Water-Fat Separation

    Soher, Brian J.; Wyatt, Cory; Reeder, Scott B.; MacFall, James R.

    2010-01-01

    Tissues containing both water and lipids, e.g., breast, confound standard MR proton reference frequency-shift methods for mapping temperatures due to the lack of temperature-induced frequency shift in lipid protons. Generalized Dixon chemical shift–based water-fat separation methods, such as GE’s iterative decomposition of water and fat with echo asymmetry and least-squares estimation method, can result in complex water and fat images. Once separated, the phase change over time of the water s...

  3. Accuracy and precision of protein–ligand interaction kinetics determined from chemical shift titrations

    NMR-monitored chemical shift titrations for the study of weak protein–ligand interactions represent a rich source of information regarding thermodynamic parameters such as dissociation constants (KD) in the micro- to millimolar range, populations for the free and ligand-bound states, and the kinetics of interconversion between states, which are typically within the fast exchange regime on the NMR timescale. We recently developed two chemical shift titration methods wherein co-variation of the total protein and ligand concentrations gives increased precision for the KD value of a 1:1 protein–ligand interaction (Markin and Spyracopoulos in J Biomol NMR 53: 125–138, 2012). In this study, we demonstrate that classical line shape analysis applied to a single set of 1H–15N 2D HSQC NMR spectra acquired using precise protein–ligand chemical shift titration methods we developed, produces accurate and precise kinetic parameters such as the off-rate (koff). For experimentally determined kinetics in the fast exchange regime on the NMR timescale, koff ∼ 3,000 s−1 in this work, the accuracy of classical line shape analysis was determined to be better than 5 % by conducting quantum mechanical NMR simulations of the chemical shift titration methods with the magnetic resonance toolkit GAMMA. Using Monte Carlo simulations, the experimental precision for koff from line shape analysis of NMR spectra was determined to be 13 %, in agreement with the theoretical precision of 12 % from line shape analysis of the GAMMA simulations in the presence of noise and protein concentration errors. In addition, GAMMA simulations were employed to demonstrate that line shape analysis has the potential to provide reasonably accurate and precise koff values over a wide range, from 100 to 15,000 s−1. The validity of line shape analysis for koff values approaching intermediate exchange (∼100 s−1), may be facilitated by more accurate KD measurements from NMR-monitored chemical shift

  4. PACSY, a relational database management system for protein structure and chemical shift analysis

    PACSY (Protein structure And Chemical Shift NMR spectroscopY) is a relational database management system that integrates information from the Protein Data Bank, the Biological Magnetic Resonance Data Bank, and the Structural Classification of Proteins database. PACSY provides three-dimensional coordinates and chemical shifts of atoms along with derived information such as torsion angles, solvent accessible surface areas, and hydrophobicity scales. PACSY consists of six relational table types linked to one another for coherence by key identification numbers. Database queries are enabled by advanced search functions supported by an RDBMS server such as MySQL or PostgreSQL. PACSY enables users to search for combinations of information from different database sources in support of their research. Two software packages, PACSY Maker for database creation and PACSY Analyzer for database analysis, are available from http://pacsy.nmrfam.wisc.eduhttp://pacsy.nmrfam.wisc.edu.

  5. Identifying Stereoisomers by ab-initio Calculation of Secondary Isotope Shifts on NMR Chemical Shieldings

    Karl-Heinz Böhm

    2014-04-01

    Full Text Available We present ab-initio calculations of secondary isotope effects on NMR chemical shieldings. The change of the NMR chemical shift of a certain nucleus that is observed if another nucleus is replaced by a different isotope can be calculated by computing vibrational corrections on the NMR parameters using electronic structure methods. We demonstrate that the accuracy of the computational results is sufficient to even distinguish different conformers. For this purpose, benchmark calculations for fluoro(2-2Hethane in gauche and antiperiplanar conformation are carried out at the HF, MP2 and CCSD(T level of theory using basis sets ranging from double- to quadruple-zeta quality. The methodology is applied to the secondary isotope shifts for 2-fluoronorbornane in order to resolve an ambiguity in the literature on the assignment of endo- and exo-2-fluoronorbornanes with deuterium substituents in endo-3 and exo-3 positions, also yielding insight into mechanistic details of the corresponding synthesis.

  6. Substituent Chemical Shifts of (E)-1-Aryl-3-thienylpropen-1-ones

    Substituent chemical shifts were examined for the 2- and 3-thiophene derivatives of chalcone and compared to the thiophene series of derivatives with the phenyl series. The chemical shift values for the α-carbons of the enones showed and inverse correlation with the Hammett σ values, but the correlation coefficients were moderate (r = 0.836 - 0.878). On the other hand, the β-carbons showed a normal correlation with excellent correlation coefficients (r = 0.994). The absolute magnitude of the ρ values for the α-carbon are about half of those of the β-carbon. The observation may be the result of a through-space transition of the electronic effect of the substituents in addition to the through bond transition

  7. 1H chemical shift imaging characterization of human brain tumor and edema

    Longitudinal (T1) and transverse (T2) relaxation times of metabolites in human brain tumor, peritumoral edema, and unaffected brain tissue were assessed from point resolved spectroscopy (PRESS) 1H chemical shift imaging results at different repetition times (TR=1500 and 5000 ms; T1: n=19) and echo times (TE=135 and 270 ms; T2: n=7). Metabolite T1 and T2 relaxation times in unaffected brain tissue corresponded with those published for healthy volunteers. T2 relaxation times were reduced in tumor (choline, N-acetyl aspartate) and edema (choline, creatine) compared with unaffected brain tissue (p1H chemical shift imaging is most suited in the use of choline elevation as tumor marker. (orig.)

  8. Protein backbone and sidechain torsion angles predicted from NMR chemical shifts using artificial neural networks

    A new program, TALOS-N, is introduced for predicting protein backbone torsion angles from NMR chemical shifts. The program relies far more extensively on the use of trained artificial neural networks than its predecessor, TALOS+. Validation on an independent set of proteins indicates that backbone torsion angles can be predicted for a larger, ≥90 % fraction of the residues, with an error rate smaller than ca 3.5 %, using an acceptance criterion that is nearly two-fold tighter than that used previously, and a root mean square difference between predicted and crystallographically observed (φ, ψ) torsion angles of ca 12º. TALOS-N also reports sidechain χ1 rotameric states for about 50 % of the residues, and a consistency with reference structures of 89 %. The program includes a neural network trained to identify secondary structure from residue sequence and chemical shifts

  9. Protein backbone and sidechain torsion angles predicted from NMR chemical shifts using artificial neural networks

    Shen Yang; Bax, Ad, E-mail: bax@nih.gov [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States)

    2013-07-15

    A new program, TALOS-N, is introduced for predicting protein backbone torsion angles from NMR chemical shifts. The program relies far more extensively on the use of trained artificial neural networks than its predecessor, TALOS+. Validation on an independent set of proteins indicates that backbone torsion angles can be predicted for a larger, {>=}90 % fraction of the residues, with an error rate smaller than ca 3.5 %, using an acceptance criterion that is nearly two-fold tighter than that used previously, and a root mean square difference between predicted and crystallographically observed ({phi}, {psi}) torsion angles of ca 12 Masculine-Ordinal-Indicator . TALOS-N also reports sidechain {chi}{sup 1} rotameric states for about 50 % of the residues, and a consistency with reference structures of 89 %. The program includes a neural network trained to identify secondary structure from residue sequence and chemical shifts.

  10. Relationship between electrophilicity index, Hammett constant and nucleus-independent chemical shift

    M Elango; R Parthasarathi; G Karthik Narayanan; A Md Sabeelullah; U Sarkar; N S Venkatasubramaniyan; V Subramanian; P K Chattaraj

    2005-01-01

    Inter-relationships between the electrophilicity index (), Hammett constant (ó) and nucleusindependent chemical shift (NICS (1) - NICS value one å ngstrom above the ring centre) have been investigated for a series of meta- and para-substituted benzoic acids. Good linear relationships between Hammett constant vs electrophilicity and Hammett constant vs NICS (1) values have been observed. However, the variation of NICS (1) against shows only a low correlation coefficient.

  11. Chemical shifts and EXAFS in some rare-earth metals and compounds

    The positions of the Lsub(111) absorption edge and accompanying Kossel and EXAFS oscillations of terbium, dysprosium and holmium in metals and compounds (acetate, carbonate, chloride, fluoride, nitrate, oxalate, oxide, phosphate and sulphate) have been measured. The chemical shifts of the main edge range from about 1 eV to about 10 eV and the EXAFS are observed up to about 150 eV. (author)

  12. Effect of 13C enrichment in the glassing matrix on dynamic nuclear polarization of [1-13C]pyruvate

    Lumata, Lloyd; Kovacs, Zoltan; Malloy, Craig; Sherry, A. Dean; Merritt, Matthew

    2011-01-01

    Dimethyl sulfoxide (DMSO) can effectively form a glassy matrix necessary for dynamic nuclear polarization (DNP) experiments. We tested the effects of 13C enrichment in DMSO on DNP of [1-13C]pyruvate doped with trityl radical OX063Me. We found that the polarization build-up time τ of pyruvate in 13C-labelled DMSO glassing solution is twice as fast as the unenriched DMSO while the NMR enhancement was unchanged. This indicates that 13C-13C spin diffusion is a limiting factor in the kinetics of d...

  13. Late Quaternary biomass changes from 13C measurements in a highland peatbog from Equatorial Africa (Burundi)

    Stable carbon isotope ratios of total organic matter were measured in two cores collected from the Kashiru peatbog in Burundi, Equatorial Africa. The record, which spans at least the last 40,000 yr, documents the C3-C4 biomass balance in the organic sediment. Among the major modern peat formers, most plants are C3 species and are characterized by δ13C values of -25.5 ± 2.3% (vs PDB). The C4 plants, which are characterized by higher δ13C values (-11.3 ± 0.7%) belong to the Gramineae (Miscanthidium sp.) and Cyperaceae families (Cyperus latifolius, C. papyrus, Pycreus nigricans). In the fossil record, δ13C values of total organic matter vary between -28 and -15% in response to the relative fluxes of C3 and C4 plants. Before 30,000 yr B.P., low δ13C values (-23.5 ± 1.1%) match high arboreal pollen contents. From 30,000 to 15,000 yr B.P., higher δ13C values (-17.6 ± 1.1%) correspond to a significant increase in percentages of grass pollen. During this episode, a short and sharp shift toward lighter carbon isotopic compositions at 21,000 yr B.P. is synchronous with higher input of arboreal pollen. From 15,000 to 12,000 yr B.P., the 13C content decreases (δ13C = -22.9 ± 1.4%). This shift, which cannot be explained by an increase in the arboreal vegetation, could be explained by the spreading of C3 Gramineae or C3 Cyperaceae. The interval from 12,000 to 7000 yr B.P. is poorly documented in these cores due to much lower organic matter accumulation. Low δ13C values (δ13C = -25.2 ± 1.3%) are observed from 7000 to 5000 yr B.P., when the pollen data show development of C3 mountain forest. The Late Holocene is characterized by a mixed C3-C4 organic matter accumulation (δ13C = -20.9 ± 1.6%). This study depicts a change in the dominant photosynthetic pathway among the herbaceous components, notably at the glacial-interglacial transition, when C3 plants were favored by increased water supply and/or higher atmospheric CO2 concentration. (author)

  14. Systematic comparison of sets of (13)C NMR spectra that are potentially identical. Confirmation of the configuration of a cuticular hydrocarbon from the cane beetle Antitrogus parvulus.

    Basar, Norazah; Damodaran, Krishnan; Liu, Hao; Morris, Gareth A; Sirat, Hasnah M; Thomas, Eric J; Curran, Dennis P

    2014-08-15

    A systematic process is introduced to compare (13)C NMR spectra of two (or more) candidate samples of known structure to a natural product sample of unknown structure. The process is designed for the case where the spectra involved can reasonably be expected to be very similar, perhaps even identical. It is first validated by using published (13)C NMR data sets for the natural product 4,6,8,10,16,18-hexamethyldocosane. Then the stereoselective total syntheses of two candidate isomers of the related 4,6,8,10,16-pentamethyldocosane natural product are described, and the process is applied to confidently assign the configuration of the natural product as (4S,6R,8R,10S,16S). This is accomplished even though the chemical shift differences between this isomer and its (16R)-epimer are only ±5-10 ppb (±0.005-0.01 ppm). PMID:25019530

  15. Accurate measurements of 13C-13C distances in uniformly 13C-labeled proteins using multi-dimensional four-oscillating field solid-state NMR spectroscopy

    Application of sets of 13C-13C internuclear distance restraints constitutes a typical key element in determining the structure of peptides and proteins by magic-angle-spinning solid-state NMR spectroscopy. Accurate measurements of the structurally highly important 13C-13C distances in uniformly 13C-labeled peptides and proteins, however, pose a big challenge due to the problem of dipolar truncation. Here, we present novel two-dimensional (2D) solid-state NMR experiments capable of extracting distances between carbonyl (13C′) and aliphatic (13Caliphatic) spins with high accuracy. The method is based on an improved version of the four-oscillating field (FOLD) technique [L. A. Straasø, M. Bjerring, N. Khaneja, and N. C. Nielsen, J. Chem. Phys. 130, 225103 (2009)] which circumvents the problem of dipolar truncation, thereby offering a base for accurate extraction of internuclear distances in many-spin systems. The ability to extract reliable accurate distances is demonstrated using one- and two-dimensional variants of the FOLD experiment on uniformly 13C,15N-labeled-L-isoleucine. In a more challenging biological application, FOLD 2D experiments are used to determine a large number of 13C′-13Caliphatic distances in amyloid fibrils formed by the SNNFGAILSS fibrillating core of the human islet amyloid polypeptide with uniform 13C,15N-labeling on the FGAIL fragment

  16. Overall structure and sugar dynamics of a DNA dodecamer from homo- and heteronuclear dipolar couplings and 31P chemical shift anisotropy

    The solution structure of d(CGCGAATTCGCG)2 has been determined on the basis of an exceptionally large set of residual dipolar couplings. In addition to the heteronuclear 13C-1H and 15N-1H and qualitative homonuclear 1H-1H dipolar couplings, previously measured in bicelle medium, more than 300 quantitative 1H-1H and 22 31P-1H dipolar restraints were obtained in liquid crystalline Pf1 medium, and 22 31P chemical shift anisotropy restraints. High quality DNA structures can be obtained solely on the basis of these new restraints, and these structures are in close agreement with those calculated previously on the basis of 13C-1H and 15N-1H dipolar couplings. In the newly calculated structures, 31P-1H dipolar and 3JsubH3'Psub couplings and 31P CSA data restrain the phosphodiester backbone torsion angles. The final structure represents a quite regular B-form helix with a modest bending of ∼10 deg., which is essentially independent of whether or not electrostatic terms are used in the calculation. Combined, the number of homo- and heteronuclear dipolar couplings significantly exceeds the number of degrees of freedom in the system. Results indicate that the dipolar coupling data cannot be fit by a single structure, but are compatible with the presence of rapid equilibria between C2'-endo and C3'-endo deoxyribose puckers (sugar switching). The C2'-H2'/H2'' dipolar couplings in B-form DNA are particularly sensitive to sugar pucker and yield the largest discrepancies when fit to a single structure. To resolve these discrepancies, we suggest a simplified dipolar coupling analysis that yields N/S equilibria for the ribose sugar puckers, which are in good agreement with previous analyses of NMR JHH couplings, with a population of the minor C3'-endo form higher for pyrimidines than for purines

  17. Biosynthesis and identification of 13C-labeled starch

    Biosynthesis of 13C-labeled starch was examined by using a small-scale apparatus. Tobacco leaves were placed in the cylindric photosynthesis chamber (14φx50 cm). After preincubation for 30 h in the dark, incubation with 13C-labeled CO2 was carried out for 48 h under irradiation with fluorescent lights. Labeled starch was extracted from the leaves and was purified. About 500 mg of 13C-labeled starch can be obtained from 50 g of the leaves. The 13C-abundance of the starch formed by the incubation was determined to be 82.0-92.0 atom % by mass spectrometry. (author)

  18. On the bathochromic shift of the absorption by astaxanthin in crustacyanin: a quantum chemical study

    Durbeej, Bo; Eriksson, Leif A.

    2003-06-01

    The structural origin of the bathochromic shift assumed by the electronic absorption spectrum of protein-bound astaxanthin, the carotenoid that upon binding to crustacyanin is responsible for the blue colouration of lobster shell, is investigated by means of quantum chemical methods. The calculations suggest that the bathochromic shift is largely due to one of the astaxanthin C4 keto groups being hydrogen-bonded to a histidine residue of the surrounding protein, and that the effect of this histidine is directly dependent on its protonation state. Out of the different methodologies (CIS, TD-DFT, and ZINDO/S) employed to calculate wavelengths of maximum absorption, the best agreement with experimental data is obtained using the semiempirical ZINDO/S method.

  19. The thermal desorption of CO2 from amine carbamate solutions for the 13C isotope enrichment

    Dronca, S.; Varodi, C.; Gligan, M.; Stoia, V.; Baldea, A.; Hodor, I.

    2012-02-01

    The CO2 desorption from amine carbamate in non-aqueous solvents is of major importance for isotopic enrichment of 13C. A series of experiments were carried out in order to set up the conditions for the CO2 desorption. For this purpose, a laboratory- scale plant for 13C isotope separation by chemical exchange between CO2 and amine carbamate was designed and used. The decomposition of the carbamate solution was mostly produced in the desorber and completed in the boiler. Two different-length desorbers were used, at different temperatures and liquid flow rates of the amine-non-aqueous solvent solutions. The residual CO2 was determined by using volumetric and gaschromatographic methods. These results can be used for enrichment of 13C by chemical exchange between CO2 and amine carbamate in nonaqueous solvents.

  20. Assigning large proteins in the solid state: a MAS NMR resonance assignment strategy using selectively and extensively 13C-labelled proteins

    In recent years, solid-state magic-angle spinning nuclear magnetic resonance spectroscopy (MAS NMR) has been growing into an important technique to study the structure of membrane proteins, amyloid fibrils and other protein preparations which do not form crystals or are insoluble. Currently, a key bottleneck is the assignment process due to the absence of the resolving power of proton chemical shifts. Particularly for large proteins (approximately >150 residues) it is difficult to obtain a full set of resonance assignments. In order to address this problem, we present an assignment method based upon samples prepared using [1,3-13C]- and [2-13C]-glycerol as the sole carbon source in the bacterial growth medium (so-called selectively and extensively labelled protein). Such samples give rise to higher quality spectra than uniformly [13C]-labelled protein samples, and have previously been used to obtain long-range restraints for use in structure calculations. Our method exploits the characteristic cross-peak patterns observed for the different amino acid types in 13C-13C correlation and 3D NCACX and NCOCX spectra. An in-depth analysis of the patterns and how they can be used to aid assignment is presented, using spectra of the chicken α-spectrin SH3 domain (62 residues), αB-crystallin (175 residues) and outer membrane protein G (OmpG, 281 residues) as examples. Using this procedure, over 90% of the Cα, Cβ, C' and N resonances in the core domain of αB-crystallin and around 73% in the flanking domains could be assigned (excluding 24 residues at the extreme termini of the protein)

  1. Assigning large proteins in the solid state: a MAS NMR resonance assignment strategy using selectively and extensively {sup 13}C-labelled proteins

    Higman, Victoria A. [Leibniz-Institut fuer Molekulare Pharmakologie (Germany); Flinders, Jeremy [Genentech, Inc., Structural Biology Department (United States); Hiller, Matthias; Jehle, Stefan; Markovic, Stefan; Fiedler, Sebastian; Rossum, Barth-Jan van; Oschkinat, Hartmut [Leibniz-Institut fuer Molekulare Pharmakologie (Germany)], E-mail: oschkinat@fmp-berlin.de

    2009-08-15

    In recent years, solid-state magic-angle spinning nuclear magnetic resonance spectroscopy (MAS NMR) has been growing into an important technique to study the structure of membrane proteins, amyloid fibrils and other protein preparations which do not form crystals or are insoluble. Currently, a key bottleneck is the assignment process due to the absence of the resolving power of proton chemical shifts. Particularly for large proteins (approximately >150 residues) it is difficult to obtain a full set of resonance assignments. In order to address this problem, we present an assignment method based upon samples prepared using [1,3-{sup 13}C]- and [2-{sup 13}C]-glycerol as the sole carbon source in the bacterial growth medium (so-called selectively and extensively labelled protein). Such samples give rise to higher quality spectra than uniformly [{sup 13}C]-labelled protein samples, and have previously been used to obtain long-range restraints for use in structure calculations. Our method exploits the characteristic cross-peak patterns observed for the different amino acid types in {sup 13}C-{sup 13}C correlation and 3D NCACX and NCOCX spectra. An in-depth analysis of the patterns and how they can be used to aid assignment is presented, using spectra of the chicken {alpha}-spectrin SH3 domain (62 residues), {alpha}B-crystallin (175 residues) and outer membrane protein G (OmpG, 281 residues) as examples. Using this procedure, over 90% of the C{alpha}, C{beta}, C' and N resonances in the core domain of {alpha}B-crystallin and around 73% in the flanking domains could be assigned (excluding 24 residues at the extreme termini of the protein)

  2. Interactions of D-cellobiose with selected chloride salts: A 13C NMR and FT-IR study

    Amarasekara, Ananda S.; Wiredu, Bernard

    2016-04-01

    The interactions of cellulose model compound D-cellobiose with chloride salts of Zn2 +, Ca2 +, Li+, Sn2 +, La3 +, Mg2 +, K+ and NH4+ were evaluated by measuring the 13C NMR chemical shift changes (Δδ) of the disaccharide due to the addition of salts in D2O. The KCl and NH4Cl showed similar Δδ changes due to interactions only with the Cl- anion. Whereas other chloride salts showed interactions with both cation and anion. Among these salts the total interactions are in the order: Zn2 + > Sn2 + > Li+ > Ca2 + ~ La3 + > Mg2 +. The FT-IR spectra of D-cellobiose-chloride salt 1:2 mixtures also indicate that KCl and NH4Cl interacts similarly with D-cellobiose in the solid state.

  3. A broad deglacial δ13C minimum event in planktonic foraminiferal records in the Okinawa Trough

    2002-01-01

    The equatorial Pacific upwelling zone has been suspected of playing an important role in the global atmospheric CO2 changes associated with glacial-interglacial cycles.In order to assess the influencing scope of the surface water deglacial δ13C minimum in the tropical Iow-latitude Pacific,the core DGKS9603, collected from the middle Okinawa Trough, was examined for δ13C records of planktonic foraminifera N. dutertrei and G. ruber. The planktonic foraminiferal δ13C records show a clear decreasing event from 20 to 6 cal. kaBP., which is characterized by long duration of about 14 ka and amplitude shift of 0.4 × 10-3. Its minimum value occurred at 15.7 cai kaBP. The event shows fairly synchrony with the surface water deglacial δ13C minimum identiffed in the tropical Pacific and its marginal seas. Because there is no evidence in planktonic foraminiferal fauna and δ18O records for upwelling and river runoff enhancement,the broad deglacial δ13C minimum event in planktonic foraminiferal records revealed in core DGKS9603 might have been the direct influencing result of the deglacial surface water of the tropical Pacific. The identification for the event in the Okinawa Trough provides new evidence that the water evolution in the tropical low-latitude Pacific plays a key role in large regional, even global carbon cycle.

  4. Simulations of Xe-129 NMR chemical shift of atomic xenon dissolved in liquid benzene

    Standara, Stanislav; Kulhánek, P.; Marek, R.; Horníček, Jan; Bouř, Petr; Straka, Michal

    2011-01-01

    Roč. 129, 3/5 (2011), s. 677-684. ISSN 1432-881X R&D Projects: GA ČR GA203/09/2037; GA ČR GAP208/11/0105 Grant ostatní: AV ČR(CZ) M200550902; European Reintegration Grant(XE) 230955; European Community(XE) 205872 Institutional research plan: CEZ:AV0Z40550506 Keywords : Xe-129 NMR chemical shift * dynamical averaging * density functional theory * Breit-Pauli perturbation theory * relativistic effects Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.162, year: 2011

  5. Three model space experiments on chemical reactions. [Gibbs adsorption, equilibrium shift and electrodeposition

    Grodzka, P.; Facemire, B.

    1977-01-01

    Three investigations conducted aboard Skylab IV and Apollo-Soyuz involved phenomena that are of interest to the biochemistry community. The formaldehyde clock reaction and the equilibrium shift reaction experiments conducted aboard Apollo Soyuz demonstrate the effect of low-g foams or air/liquid dispersions on reaction rate and chemical equilibrium. The electrodeposition reaction experiment conducted aboard Skylab IV demonstrate the effect of a low-g environment on an electrochemical displacement reaction. The implications of the three space experiments for various applications are considered.

  6. Model analysis of influences of the high-temperature reactor on location shifting in chemical industry

    An analysis is presented of the influences of High-Temperature Reactor on probable location shifting of big chemical plants, in the future. This is done by a spatial location model, that includes an investigation on 116 industrial locations within the first six countries of Common Market. The results of a computerized program show differences in location qualities when furnished either with traditional or with nuclear energy systems. In addition to location factor energy some other important factors, as subventions, taxes, labour, and transport costs are analysed, and their influence on industrial location is quantified. (orig.)

  7. NMR Chemical Shift Ranges of Urine Metabolites in Various Organic Solvents.

    Görling, Benjamin; Bräse, Stefan; Luy, Burkhard

    2016-01-01

    Signal stability is essential for reliable multivariate data analysis. Urine samples show strong variance in signal positions due to inter patient differences. Here we study the exchange of the solvent of a defined urine matrix and how it affects signal and integral stability of the urinary metabolites by NMR spectroscopy. The exchange solvents were methanol, acetonitrile, dimethyl sulfoxide, chloroform, acetone, dichloromethane, and dimethyl formamide. Some of these solvents showed promising results with a single batch of urine. To evaluate further differences between urine samples, various acid, base, and salt solutions were added in a defined way mimicking to some extent inter human differences. Corresponding chemical shift changes were monitored. PMID:27598217

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

    Abou-Hamad, E.

    2011-10-10

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

  9. Specific 13C labeling of leucine, valine and isoleucine methyl groups for unambiguous detection of long-range restraints in protein solid-state NMR studies

    Fasshuber, Hannes Klaus; Demers, Jean-Philippe; Chevelkov, Veniamin; Giller, Karin; Becker, Stefan; Lange, Adam

    2015-03-01

    Here we present an isotopic labeling strategy to easily obtain unambiguous long-range distance restraints in protein solid-state NMR studies. The method is based on the inclusion of two biosynthetic precursors in the bacterial growth medium, α-ketoisovalerate and α-ketobutyrate, leading to the production of leucine, valine and isoleucine residues that are exclusively 13C labeled on methyl groups. The resulting spectral simplification facilitates the collection of distance restraints, the verification of carbon chemical shift assignments and the measurement of methyl group dynamics. This approach is demonstrated on the type-three secretion system needle of Shigella flexneri, where 49 methyl-methyl and methyl-nitrogen distance restraints including 10 unambiguous long-range distance restraints could be collected. By combining this labeling scheme with ultra-fast MAS and proton detection, the assignment of methyl proton chemical shifts was achieved.

  10. 1H and 13C NMR spectra, structure and physicochemical features of phenyl acridine-9-carboxylates and 10-methyl-9-(phenoxycarbonyl)acridinium trifluoromethanesulphonates--alkyl substituted in the phenyl fragment.

    Krzymiński, K; Malecha, P; Zadykowicz, B; Wróblewska, A; Błażejowski, J

    2011-01-01

    The 1H and 13C NMR spectra of twelve phenyl acridine-9-carboxylates--alkyl-substituted in the phenyl fragment--and their 10-methyl-9-(phenoxycarbonyl)acridinium salts dissolved in CD3CN, CD3OD, CDCl3 and DMSO-d6 were recorded in order to examine the influence of the structure of these compounds and the properties of the solvents on chemical shifts and 1H-(1)H coupling constants. Experimental data were compared with 1H and 13C chemical shifts predicted at the GIAO/DFT level of theory for DFT(B3LYP)/6-31G** optimised geometries of molecules, as well as with values of 1H chemical shifts and 1H-(1)H coupling constants, estimated using ACD/HNMR database software to ensure that the assignment was correct. To investigate the relations between chemical shifts and selected structural or physicochemical characteristics of the target compounds, the values of several of these parameters were determined at the DFT or HF levels of theory. The HOMO and LUMO energies obtained at the HF level yielded the ionisation potentials and electron affinities of molecules. The DFT method provided atomic partial charges, dipole moments, LCAO coefficients of pz LUMO of selected C atoms, and angles reflecting characteristic structural features of the compounds. It was found that the experimentally determined 1H and 13C chemical shifts of certain atoms relate to the predicted dipole moments, the angles between the acridine and phenyl moieties, and the LCAO coefficients of the pz LUMO of the C atoms believed to participate in the initial step of the oxidation of the target compounds. The spectral and physicochemical characteristics of the target compounds were investigated in the context of their chemiluminogenic ability. PMID:21134782

  11. Hydrothermal carbon from biomass: structural differences between hydrothermal and pyrolyzed carbons via 13C solid state NMR.

    Falco, Camillo; Perez Caballero, Fernando; Babonneau, Florence; Gervais, Christel; Laurent, Guillaume; Titirici, Maria-Magdalena; Baccile, Niki

    2011-12-01

    The objective of this paper is to better describe the structure of the hydrothermal carbon (HTC) process and put it in relationship with the more classical pyrolytic carbons. Indeed, despite the low energetic impact and the number of applications described so far for HTC, very little is known about the structure, reaction mechanism, and the way these materials relate to coals. Are HTC and calcination processes equivalent? Are the structures of the processed materials related to each other in any way? Which is the extent of polyaromatic hydrocarbons (PAH) inside HTC? In this work, the effect of hydrothermal treatment and pyrolysis are compared on glucose, a good model carbohydrate; a detailed single-quantum double-quantum (SQ-DQ) solid state (13)C NMR study of the HTC and calcined HTC is used to interpret the spectral region corresponding to the signal of furanic and arene groups. These data are compared to the spectroscopic signatures of calcined glucose, starch, and xylose. A semiquantitative analysis of the (13)C NMR spectra provides an estimation of the furanic-to-arene ratio which varies from 1:1 to 4:1 according to the processing conditions and carbohydrate employed. In addition, we formulate some hypothesis, validated by DFT (density functional theory) modeling associated with (13)C NMR chemical shifts calculations, about the possible furan-rich structural intermediates that occur in the coalification process leading to condensed polyaromatic structures. In combination with a broad parallel study on the HTC processing conditions effect on glucose, cellulose, and raw biomass (Falco, C.; Baccile, N.; Titirici, M.-M. Green Chem., 2011, DOI: 10.1039/C1GC15742F), we propose a broad reaction scheme and in which we show that, through HTC, it is possible to tune the furan-to-arene ratio composing the aromatic core of the produced HTC carbons, which is not possible if calcination is used alone, in the temperature range below 350 °C. PMID:22050004

  12. The influence of analytical and technological procedures on the 13C/12C isotope ratio of orange oil compounds

    The influence of chromatographic and technological procedures on the 13C-isotope value of flavour compounds from orange oils was investigated. In order to avoid misinterpretations of isotopic data, quantitative yields during sample clean-up must be ascertained. Ordinary as well as deterpenated orange oils were not influenced by the technological processing. In the case of special products containing single compounds concentrated up to more than 70%, a shift in the 13C/12C-isotope ratio was detectable. (orig.)

  13. 13C solution NMR spectra of poly(ether)urethanes. Technical memorandum

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

  14. 11B, 13C-NMR study of the complex formation of phenylboronate with catechol and L-dopa

    In the solution of phenylboronic acid and either catechol or L-dopa at various pH, the equilibrium between phenylboronate anion and catechol or L-dopa to form the anionic complex has been demonstrated by the existence of 11B-NMR signals for the complex and either phenylboronate anion or phenylboronic acid. By the pH dependence of the 11B-NMR chemical shift of phenylboronate-phenylboronic acid solution, the ionization constant of phenylboronic acid (pKa) has been estimated as 8.90. By the 11B-NMR spectra at pH below 7, the complex formation constant, log K, has been obtained as 4.5 for catechol, and as 4.6 for L-dopa. The 13C-NMR spectra have also demonstrated the complex formations, but in the pH 8 and 9 solution of phenylboronic acid and L-dopa, the 13C-NMR signal of carbonyl carbon of L-dopa disappeared. (author)

  15. Hyperpolarized 13C NMR lifetimes in the liquid-state: relating structures and T1 relaxation times

    Parish, Christopher; Niedbalski, Peter; Hashami, Zohreh; Fidelino, Leila; Kovacs, Zoltan; Lumata, Lloyd

    Among the various attempts to solve the insensitivity problem in nuclear magnetic resonance (NMR), the physics-based technique dissolution dynamic nuclear polarization (DNP) is probably the most successful method of hyperpolarization or amplifying NMR signals. Using this technique, liquid-state NMR signal enhancements of several thousand-fold are expected for low-gamma nuclei such as carbon-13. The lifetimes of these hyperpolarized 13C NMR signals are directly related to their 13C spin-lattice relaxation times T1. Depending upon the 13C isotopic location, the lifetimes of hyperpolarized 13C compounds can range from a few seconds to minutes. In this study, we have investigated the hyperpolarized 13C NMR lifetimes of several 13C compounds with various chemical structures from glucose, acetate, citric acid, naphthalene to tetramethylallene and their deuterated analogs at 9.4 T and 25 deg C. Our results show that the 13C T1s of these compounds can range from a few seconds to more than 60 s at this field. Correlations between the chemical structures and T1 relaxation times will be discussed and corresponding implications of these results on 13C DNP experiments will be revealed. US Dept of Defense Award No. W81XWH-14-1-0048 and Robert A. Welch Foundation Grant No. AT-1877.

  16. Optimal voxel size for measuring global gray and white matter proton metabolite concentrations using chemical shift imaging

    Hanson, Lars Peter Grüner; Adalsteinsson, E; Pfefferbaum, A;

    2000-01-01

    Quantification of gray and white matter levels of spectroscopically visible metabolites can provide important insights into brain development and pathological conditions. Chemical shift imaging offers a gain in efficiency for estimation of global gray and white matter metabolite concentrations co...

  17. 13C-NMR assignment, structure, and dynamics of deoxyoligonucleotides

    The unique spectral properties of 13C-NMR for studying nucleic acids and some of the important features of 13C-NMR in oligonucleotide studies are demostrated. The main difficulty in studying oligonucleotides by 13C-NMR and recent improvements in NMR instrumentation and advances in oligonucleotide synthesis are presented. The high resolution 13C-NMR spectra, T1 relaxation times and NOEs were measured for duplex of the self-complementary oligo-DNAs: d(CG)3 and d(GGTATACC) are studied. The target of this study is to developed a systematic 13C-NMR spectral assignment and to investigate the structure and dynamics of these two sequences by this techniques. (M.J.C.)

  18. Use of 13C measurements in humus dynamics studies

    The humic substances of the Ol and Ah horizons of a Spodo-Dystric Cambisol were characterized by exclusion chromatography on controlled pore glass followed by determination of the natural 13C/12C ratios by mass spectrometry. A significant correlation of the molecular weight of the humic substances and the δ13C values was observed. Fractions with higher molecular weight have less negative δ13C values. This relationship holds only for the humic and fulvic acids. In both horizons the non-humic substances and the very small humic substances (Kd > 0.80) were isotopically heavier than the humic substances of the second maximum (brown humic and fulvic acids). The low molecular weight organic substances of the Ol horizon showed a higher δ13C value than all other fractions. These results indicate that the non-humic substances are easily attacked by microorganismus and are therefore richer in 13C. (authors)

  19. Studies and characterization of in natura and benzylated sisal by using CPMAS 13C NMR

    Delignificated and benzylated sisal fibers were characterized by CPMAS 13 C NMR. In this study were analyzed the structure of the fiber before and after chemical treatments via delignification and benzylation processes. We observed that after delignification of sisal fiber, cellulose chains become more disordered and exposed which increases benzylation reaction efficiency. However, for not delignificated fibers their constituents decreases benzylation reaction efficiency. (author)

  20. Qualitative Study of Substituent Effects on NMR 15N and 17O Chemical Shifts

    Contreras, Rubén H.; Llorente, Tomás; Pagola, Gabriel I.; Bustamante, Manuel G.; Pasqualini, Enrique E.; Melo, Juan I.; Tormena, Cláudio F.

    2009-08-01

    A qualitative approach to analyze the electronic origin of substituent effects on the paramagnetic part of chemical shifts is described and applied to few model systems, where its potentiality can be appreciated. The formulation of this approach is based on the following grounds. The influence of different inter- or intramolecular interactions on a second-order property can be qualitatively predicted if it can be known how they affect the main virtual excitations entering into that second-order property. A set of consistent approximations are introduced in order to analyze the behavior of occupied and virtual orbitals that define some experimental trends of magnetic shielding constants. This approach is applied first to study the electronic origin of methyl-β substituent effects on both 15N and 17O chemical shifts, and afterward it is applied to a couple of examples of long-range substituent effects originated in charge transfer interactions such as the conjugative effect in aromatic compounds and σ-hyperconjugative interactions in saturated multicyclic compounds.

  1. Qualitative study of substituent effects on NMR (15)N and (17)O chemical shifts.

    Contreras, Rubén H; Llorente, Tomás; Pagola, Gabriel I; Bustamante, Manuel G; Pasqualini, Enrique E; Melo, Juan I; Tormena, Cláudio F

    2009-09-10

    A qualitative approach to analyze the electronic origin of substituent effects on the paramagnetic part of chemical shifts is described and applied to few model systems, where its potentiality can be appreciated. The formulation of this approach is based on the following grounds. The influence of different inter- or intramolecular interactions on a second-order property can be qualitatively predicted if it can be known how they affect the main virtual excitations entering into that second-order property. A set of consistent approximations are introduced in order to analyze the behavior of occupied and virtual orbitals that define some experimental trends of magnetic shielding constants. This approach is applied first to study the electronic origin of methyl-beta substituent effects on both (15)N and (17)O chemical shifts, and afterward it is applied to a couple of examples of long-range substituent effects originated in charge transfer interactions such as the conjugative effect in aromatic compounds and sigma-hyperconjugative interactions in saturated multicyclic compounds. PMID:19685922

  2. Stereoelectronic effects on 1H nuclear magnetic resonance chemical shifts in methoxybenzenes

    Lambert, Maja; Olsen, Lars; Jaroszewski, Jerzy W

    2006-01-01

    differences are due to different conformational behavior of the OH and OCH3 groups; while the ortho-disubstituted OH group remains planar in polyphenols due to hydrogen bonding and conjugative stabilization, the steric congestion in ortho-disubstituted anisoles outweighs the conjugative effects and forces the......Investigation of all O-methyl ethers of 1,2,3-benzenetriol and 4-methyl-1,2,3-benzenetriol (3-16) by 1H NMR spectroscopy and density-functional calculations disclosed practically useful conformational effects on 1H NMR chemical shifts in the aromatic ring. While the conversion of phenol (2) to...... Ar-OCH3 torsion out of the ring plane, resulting in large stereoelectronic effects on the chemical shift of Hpara. Conformational searches and geometry optimizations for 3-16 at the B3LYP/6-31G** level, followed by B3LYP/6-311++G(2d,2p) calculations for all low-energy conformers, gave excellent...

  3. Characteristic coupling constants 1J(13C-13C) of some mesoionic methylides contaIning a diphenyltetrazolium ring

    Jazwinski, Jaroslaw; Kozminski, Wtktor; stefaniak, Lech; Webl, Graham A.

    1994-01-01

    1J(13C-13C) data are presented for some Types A and B tetrazoliwn methylides. The results show a large amoWlt of double bond character for the C5-C6 bond which is significantly reduced upon protonation. A similar decrease in bond order is noted for the C6-C8 bond following protonation.

  4. Accurate quantitative 13C NMR spectroscopy: repeatability over time of site-specific 13C isotope ratio determination.

    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

  5. An improved procedure for the synthesis of DL-[2-[sup 13]C]-glutamic acid

    Potrzebowski, M.J.; Stolowich, N.J.; Scott, A.I. (Texas A and M Univ., College Station, TX (United States). Dept. of Chemistry)

    1990-03-01

    A convenient two-step chemical synthesis of DL-[2-[sup 13]C]-glutamic acid from methyl acrylate and diethylacetamidomalonate is described. Synthesis of the Michael adduct (III) was effected in quantitative yield by employing strong amino bases as catalysts. The reactivities of three such catalysts, tetramethyl guanidine (TMG), 1,8-diazobicyclo [5,4,0]-undec-7-ene (1,5-5) (DBU) and 1,5-diazobicyclo [4,3,0] non-5-ene (DBN) were compared by [sup 13]C NMR and all are shown to catalyse the reaction quantitatively, however at markedly different rates. (Author).

  6. A Method to Constrain Genome-Scale Models with 13C Labeling Data.

    Héctor García Martín

    2015-09-01

    Full Text Available Current limitations in quantitatively predicting biological behavior hinder our efforts to engineer biological systems to produce biofuels and other desired chemicals. Here, we present a new method for calculating metabolic fluxes, key targets in metabolic engineering, that incorporates data from 13C labeling experiments and genome-scale models. The data from 13C labeling experiments provide strong flux constraints that eliminate the need to assume an evolutionary optimization principle such as the growth rate optimization assumption used in Flux Balance Analysis (FBA. This effective constraining is achieved by making the simple but biologically relevant assumption that flux flows from core to peripheral metabolism and does not flow back. The new method is significantly more robust than FBA with respect to errors in genome-scale model reconstruction. Furthermore, it can provide a comprehensive picture of metabolite balancing and predictions for unmeasured extracellular fluxes as constrained by 13C labeling data. A comparison shows that the results of this new method are similar to those found through 13C Metabolic Flux Analysis (13C MFA for central carbon metabolism but, additionally, it provides flux estimates for peripheral metabolism. The extra validation gained by matching 48 relative labeling measurements is used to identify where and why several existing COnstraint Based Reconstruction and Analysis (COBRA flux prediction algorithms fail. We demonstrate how to use this knowledge to refine these methods and improve their predictive capabilities. This method provides a reliable base upon which to improve the design of biological systems.

  7. Impact of Ho(3+)-doping on (13)C dynamic nuclear polarization using trityl OX063 free radical.

    Kiswandhi, Andhika; Niedbalski, Peter; Parish, Christopher; Kaur, Pavanjeet; Martins, André; Fidelino, Leila; Khemtong, Chalermchai; Song, Likai; Sherry, A Dean; Lumata, Lloyd

    2016-08-21

    We have investigated the effects of Ho-DOTA doping on the dynamic nuclear polarization (DNP) of [1-(13)C] sodium acetate using trityl OX063 free radical at 3.35 T and 1.2 K. Our results indicate that addition of 2 mM Ho-DOTA on 3 M [1-(13)C] sodium acetate sample in 1 : 1 v/v glycerol : water with 15 mM trityl OX063 improves the DNP-enhanced (13)C solid-state nuclear polarization by a factor of around 2.7-fold. Similar to the Gd(3+) doping effect on (13)C DNP, the locations of the positive and negative (13)C maximum polarization peaks in the (13)C microwave DNP sweep are shifted towards each other with the addition of Ho-DOTA on the DNP sample. W-band electron spin resonance (ESR) studies have revealed that while the shape and linewidth of the trityl OX063 ESR spectrum was not affected by Ho(3+)-doping, the electron spin-lattice relaxation time T1 of trityl OX063 was prominently reduced at cryogenic temperatures. The reduction of trityl OX063 electron T1 by Ho-doping is linked to the (13)C DNP improvement in light of the thermodynamic picture of DNP. Moreover, the presence of Ho-DOTA in the dissolution liquid at room temperature has negligible reduction effect on liquid-state (13)C T1, in contrast to Gd(3+)-doping which drastically reduces the (13)C T1. The results here suggest that Ho(3+)-doping is advantageous over Gd(3+) in terms of preservation of hyperpolarized state-an important aspect to consider for in vitro and in vivo NMR or imaging (MRI) experiments where a considerable preparation time is needed to administer the hyperpolarized (13)C liquid. PMID:27424954

  8. Water-fat imaging and general chemical shift imaging with spectrum modeling

    An, Li

    Water-fat chemical shift imaging (CSI) has been an active research area in magnetic resonance imaging (MRI) since the early 1980's. There are two main reasons for water- fat imaging. First, water-fat imaging can serve as a fat- suppression method. Removing the usually bright fatty signals not only extends the useful dynamic range of an image, but also allows better visualization of lesions or injected contrast, and removes chemical shift artifacts, which may contribute to improved diagnosis. Second, quantification of water and fat provides useful chemical information for characterizing tissues such as bone marrow, liver, and adrenal masses. A milestone in water- fat imaging is the Dixon method that can produce separate water and fat images with only two data acquisitions. In practice, however, the Dixon method is not always successful due to field inhomogeneity problems. In recent years, many variations of the Dixon method have been proposed to overcome the field inhomogeneity problem. In general, these methods can at best separate water and fat without identifying the two because the water and fat magnetization vectors are sampled symmetrically, only parallel and anti-parallel. Furthermore, these methods usually depend on two-dimensional phase unwrapping which itself is sensitive to noise and artifacts, and becomes unreliable when the images have disconnected tissues in the field-of-view (FOV). We will first introduce the basic principles of nuclear magnetic resonance (NMR) and magnetic resonance imaging (MRI) in chapter 1, and briefly review the existing water-fat imaging techniques in chapter 2. In chapter 3, we will introduce a new method for water-fat imaging. With three image acquisitions, a general direct phase encoding (DPE) of the chemical shift information is achieved, which allows an unambiguous determination of water and fat on a pixel by pixel basis. Details of specific implementations and noise performance will be discussed. Representative results

  9. Chemical potential shift in organic field-effect transistors identified by soft X-ray operando nano-spectroscopy

    Nagamura, Naoka; Kitada, Yuta; Tsurumi, Junto; Matsui, Hiroyuki; Horiba, Koji; Honma, Itaru; Takeya, Jun; Oshima, Masaharu

    2015-06-01

    A chemical potential shift in an organic field effect transistor (OFET) during operation has been revealed by soft X-ray operando nano-spectroscopy analysis performed using a three-dimensional nanoscale electron-spectroscopy chemical analysis system. OFETs were fabricated using ultrathin (3 ML or 12 nm) single-crystalline C10-DNBDT-NW films on SiO2 (200 nm)/Si substrates with a backgate electrode and top source/drain Au electrodes, and C 1s line profiles under biasing at the backgate and drain electrodes were measured. When applying -30 V to the backgate, there is C 1s core level shift of 0.1 eV; this shift can be attributed to a chemical potential shift corresponding to band bending by the field effect, resulting in p-type doping.

  10. Chemical potential shift in organic field-effect transistors identified by soft X-ray operando nano-spectroscopy

    A chemical potential shift in an organic field effect transistor (OFET) during operation has been revealed by soft X-ray operando nano-spectroscopy analysis performed using a three-dimensional nanoscale electron-spectroscopy chemical analysis system. OFETs were fabricated using ultrathin (3 ML or 12 nm) single-crystalline C10-DNBDT-NW films on SiO2 (200 nm)/Si substrates with a backgate electrode and top source/drain Au electrodes, and C 1s line profiles under biasing at the backgate and drain electrodes were measured. When applying −30 V to the backgate, there is C 1s core level shift of 0.1 eV; this shift can be attributed to a chemical potential shift corresponding to band bending by the field effect, resulting in p-type doping

  11. Chemical potential shift in organic field-effect transistors identified by soft X-ray operando nano-spectroscopy

    Nagamura, Naoka, E-mail: NAGAMURA.Naoka@nims.go.jp; Kitada, Yuta; Honma, Itaru [Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577 (Japan); Tsurumi, Junto; Matsui, Hiroyuki; Takeya, Jun [Department of Advanced Materials Science, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8561 (Japan); Horiba, Koji [Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba, Ibaraki 305-0801 (Japan); Oshima, Masaharu [Synchrotron Radiation Research Organization, The University of Tokyo, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198 (Japan)

    2015-06-22

    A chemical potential shift in an organic field effect transistor (OFET) during operation has been revealed by soft X-ray operando nano-spectroscopy analysis performed using a three-dimensional nanoscale electron-spectroscopy chemical analysis system. OFETs were fabricated using ultrathin (3 ML or 12 nm) single-crystalline C10-DNBDT-NW films on SiO{sub 2} (200 nm)/Si substrates with a backgate electrode and top source/drain Au electrodes, and C 1s line profiles under biasing at the backgate and drain electrodes were measured. When applying −30 V to the backgate, there is C 1s core level shift of 0.1 eV; this shift can be attributed to a chemical potential shift corresponding to band bending by the field effect, resulting in p-type doping.

  12. Liquid chromatography combined with mass spectrometry for 13C isotopic analysis in life science research.

    Godin, Jean-Philippe; Fay, Laurent-Bernard; Hopfgartner, Gérard

    2007-01-01

    Among the different disciplines covered by mass spectrometry, measurement of (13)C/(12)C isotopic ratio crosses a large section of disciplines from a tool revealing the origin of compounds to more recent approaches such as metabolomics and proteomics. Isotope ratio mass spectrometry (IRMS) and molecular mass spectrometry (MS) are the two most mature techniques for (13)C isotopic analysis of compounds, respectively, for high and low-isotopic precision. For the sample introduction, the coupling of gas chromatography (GC) to either IRMS or MS is state of the art technique for targeted isotopic analysis of volatile analytes. However, liquid chromatography (LC) also needs to be considered as a tool for the sample introduction into IRMS or MS for (13)C isotopic analyses of non-volatile analytes at natural abundance as well as for (13)C-labeled compounds. This review presents the past and the current processes used to perform (13)C isotopic analysis in combination with LC. It gives particular attention to the combination of LC with IRMS which started in the 1990's with the moving wire transport, then subsequently moved to the chemical reaction interface (CRI) and was made commercially available in 2004 with the wet chemical oxidation interface (LC-IRMS). The LC-IRMS method development is also discussed in this review, including the possible approaches for increasing selectivity and efficiency, for example, using a 100% aqueous mobile phase for the LC separation. In addition, applications for measuring (13)C isotopic enrichments using atmospheric pressure LC-MS instruments with a quadrupole, a time-of-flight, and an ion trap analyzer are also discussed as well as a LC-ICPMS using a prototype instrument with two quadrupoles. PMID:17853432

  13. Geochemical Approach to Archaeal Ecology: δ13C of GDGTs

    Lichtin, S.; Warren, C.; Pearson, A.; Pagani, M.

    2015-12-01

    Over the last decade and a half, glycerol dialkyl glycerol tetraethers (GDGTs) have increasingly been used to reconstruct environmental temperatures; proxies like TEX86 that correlate the relative abundance of these archaeal cell membrane lipids to sea surface temperature are omnipresent in paleoclimatology literature. While it has become common to make claims about past temperatures using GDGTs, our present understanding of the organisms that synthesize the compounds is still quite limited. The generally accepted theory states that microorganisms like the Thaumarchaeota modify the structure of membrane lipids to increase intermolecular interactions, strengthening the membrane at higher temperatures. Yet to date, culture experiments have been largely restricted to a single species, Nitrosopumilus maritimes, and recent studies on oceanic archaeal rRNA have revealed that these biomarkers are produced in diverse, heterogeneous, and site-specific communities. This brings up questions as to whether different subclasses of GDGTs, and all subsequent proxies, represent adaptation within a single organismal group or a shift in community composition. To investigate whether GDGTs with different chain structures, from the simple isoprenoidal GDGT-0 to Crenarchaeol with its many cyclopentane groups, are sourced from archaea with similar or disparate metabolic pathways—and if that information is inherited in GDGTs trapped in marine sediments—this study examines the stable carbon isotope values (δ13C) of GDGTs extracted from the uppermost meters of sediment in the Orca Basin, Gulf of Mexico, using spooling-wire microcombustion isotope-ratio mass spectrometer (SWiM-IRMS), tackling a fundamental assumption of the TEX86 proxy that influences the way we perceive the veracity of existing temperature records.

  14. Reassigning the Structures of Natural Products Using NMR Chemical Shifts Computed with Quantum Mechanics: A Laboratory Exercise

    Palazzo, Teresa A.; Truong, Tiana T.; Wong, Shirley M. T.; Mack, Emma T.; Lodewyk, Michael W.; Harrison, Jason G.; Gamage, R. Alan; Siegel, Justin B.; Kurth, Mark J.; Tantillo, Dean J.

    2015-01-01

    An applied computational chemistry laboratory exercise is described in which students use modern quantum chemical calculations of chemical shifts to assign the structure of a recently isolated natural product. A pre/post assessment was used to measure student learning gains and verify that students demonstrated proficiency of key learning…

  15. 1H MAS, 13C CP/MAS, and 2H NMR spectra studies of piperidinium p-chlorobenzoate

    Anomalous H/D isotope effects were detected in the 1H MAS NMR spectra of piperidinium p-chlorobenzoate (C5H10NH 2+⋅ ClC6H4COO − ) upon deuterium substitution of hydrogen atoms which form two kinds of N-H⋯O H-bonds in the crystal; in contrast to these spectra, only slight chemical shifts were recorded in 13C CP/MAS NMR spectra. 2H NMR spectrum of the deuterated sample show quadrupole coupling constants of 148 and 108 kHz, and reveal that there are a few motions contributing to the electric-field modulation of the 2H nucleus. The 1H MAS NMR spectra of piperidinium p-chlrobenzoate-d16 (C5D10ND 2+⋅ ClC6D4COO − ) and -d14 (C5D10NH 2+⋅ ClC6D4COO − ) revealed that the change in the envelope is caused by chemical shifts of each signal upon deuteration. Calculations based on the density-functional-theory showed that the N-H distance along the crystallographic a-axis mainly contributes to the anomalous isotope effects on 1H MAS NMR envelopes.

  16. 1D 13C-NMR Data as Molecular Descriptors in Spectra — Structure Relationship Analysis of Oligosaccharides

    Florbela Pereira

    2012-03-01

    Full Text Available Spectra-structure relationships were investigated for estimating the anomeric configuration, residues and type of linkages of linear and branched trisaccharides using 13C-NMR chemical shifts. For this study, 119 pyranosyl trisaccharides were used that are trimers of the α or β anomers of D-glucose, D-galactose, D-mannose, L-fucose or L-rhamnose residues bonded through a or b glycosidic linkages of types 1→2, 1→3, 1→4, or 1→6, as well as methoxylated and/or N-acetylated amino trisaccharides. Machine learning experiments were performed for: (1 classification of the anomeric configuration of the first unit, second unit and reducing end; (2 classification of the type of first and second linkages; (3 classification of the three residues: reducing end, middle and first residue; and (4 classification of the chain type. Our previously model for predicting the structure of disaccharides was incorporated in this new model with an improvement of the predictive power. The best results were achieved using Random Forests with 204 di- and trisaccharides for the training set—it could correctly classify 83%, 90%, 88%, 85%, 85%, 75%, 79%, 68% and 94% of the test set (69 compounds for the nine tasks, respectively, on the basis of unassigned chemical shifts.

  17. 1H, 13C and 15N NMR spectral and X-ray structural studies of 2-arylsulfonylamino-5-chlorobenzophenones

    Six 2-(4-R-phenylsulfonylamino)-5-chlorobenzophenones were prepared and their 1H, 13C and 15N NMR spectra recorded and assigned. The dependence between the chemical shift of the amide proton and Hammett σ substituent constants is of the V type. Substituent effect on the chemical shift of the amide nitrogen atom was found insignificant. X-ray analysis shows that the terminal benzene rings in 2-(4-nitro-phenylsulfonylamino)-5-chlorobenzophenones are located close to each other. They are not, however, parallel, dihedral angle between them being equal to 10.86 deg (MP2/6-31G**//HF/6-31G** ab initio calculations show this to be 20.44 deg). This shows that the mutual orientation of two benzene rings in the molecule of this compound is caused by the π-π stacking. It is additionally reinforced by the intramolecular NH...O=C hydrogen bond. Except the dihedral angle between the benzene rings, X-ray determined structure of 2-(4-nitro-phenylsulfonylamino)-5-chlorobenzophenones is very similar to this optimized by the ab initio calculations. (author)

  18. IRMS detection of testosterone manipulated with 13C labeled standards in human urine by removing the labeled 13C

    Highlights: • 13C labeled testosterone can be used to adjust the isotope ratio of testosterone. • The novel testosterone cannot be detected by the regular IRMS method in doping test. • A method was explored to remove the labeled 13C. • The established method can be used to detect the manipulated testosterone. - Abstract: Isotope ratio mass spectrometry (IRMS) is applied to confirm testosterone (T) abuse by determining the carbon isotope ratios (δ13C value). However, 13C labeled standards can be used to control the δ13C value and produce manipulated T which cannot be detected by the current method. A method was explored to remove the 13C labeled atom at C-3 from the molecule of androsterone (Andro), the metabolite of T in urine, to produce the resultant (A-nor-5α-androstane-2,17-dione, ANAD). The difference in δ13C values between Andro and ANAD (Δδ13CAndro–ANAD, ‰) would change significantly in case manipulated T is abused. Twenty-one volunteers administered T manipulated with different 13C labeled standards. The collected urine samples were analyzed with the established method, and the maximum value of Δδ13CAndro–ANAD post ingestion ranged from 3.0‰ to 8.8‰. Based on the population reference, the cut-off value of Δδ13CAndro–ANAD for positive result was suggested as 1.2‰. The developed method could be used to detect T manipulated with 3-13C labeled standards

  19. 13C fractionation in soil as connected with microbial metabolism

    Šantrůčková, Hana; Šmejkalová, M.; Uhlířová, Eva

    Interlaken : Paul Scherrer Institut, 2004. s. 35. [SIBAE-BASIN Conference, Partitioning of fluxes between the biosphere across spatial scales. 01.04.2004-03.04.2004, Interlaken] Keywords : 13C fractionation * soil * microbial metabolism Subject RIV: EH - Ecology, Behaviour

  20. Anomalous 13C enrichment in modern marine organic carbon

    Arthur, M.A.; Dean, W.E.; Claypool, G.E.

    1985-01-01

    Marine organic carbon is heavier isotopically (13C enriched) than most land-plant or terrestrial organic C1. Accordingly, ??13C values of organic C in modern marine sediments are routinely interpreted in terms of the relative proportions of marine and terrestrial sources of the preserved organic matter2,3. When independent geochemical techniques are used to evaluate the source of organic matter in Cretaceous or older rocks, those rocks containing mostly marine organic C are found typically to have lighter (more-negative) ??13C values than rocks containing mostly terrestrial organic C. Here we conclude that marine photosynthesis in mid-Cretaceous and earlier oceans generally resulted in a greater fractionation of C isotopes and produced organic C having lighter ??13C values. Modern marine photosynthesis may be occurring under unusual geological conditions (higher oceanic primary production rates, lower PCO2) that limit dissolved CO2 availability and minimize carbon isotope fractionation4. ?? 1985 Nature Publishing Group.

  1. Study of wavelength-shifting chemicals for use in large-scale water Cherenkov detectors

    Sweany, M; Bernstein, A; Dazeley, S; Dunmore, J; Felde, J; Svoboda, R; Tripathi, S M

    2011-09-21

    Cherenkov detectors employ various methods to maximize light collection at the photomultiplier tubes (PMTs). These generally involve the use of highly reflective materials lining the interior of the detector, reflective materials around the PMTs, or wavelength-shifting sheets around the PMTs. Recently, the use of water-soluble wavelength-shifters has been explored to increase the measurable light yield of Cherenkov radiation in water. These wave-shifting chemicals are capable of absorbing light in the ultravoilet and re-emitting the light in a range detectable by PMTs. Using a 250 L water Cherenkov detector, we have characterized the increase in light yield from three compounds in water: 4-Methylumbelliferone, Carbostyril-124, and Amino-G Salt. We report the gain in PMT response at a concentration of 1 ppm as: 1.88 {+-} 0.02 for 4-Methylumbelliferone, stable to within 0.5% over 50 days, 1.37 {+-} 0.03 for Carbostyril-124, and 1.20 {+-} 0.02 for Amino-G Salt. The response of 4-Methylumbelliferone was modeled, resulting in a simulated gain within 9% of the experimental gain at 1 ppm concentration. Finally, we report an increase in neutron detection performance of a large-scale (3.5 kL) gadolinium-doped water Cherenkov detector at a 4-Methylumbelliferone concentration of 1 ppm.

  2. Study of wavelength-shifting chemicals for use in large-scale water Cherenkov detectors

    Cherenkov detectors employ various methods to maximize light collection at the photomultiplier tubes (PMTs). These generally involve the use of highly reflective materials lining the interior of the detector, reflective materials around the PMTs, or wavelength-shifting sheets around the PMTs. Recently, the use of water-soluble wavelength-shifters has been explored to increase the measurable light yield of Cherenkov radiation in water. These wave-shifting chemicals are capable of absorbing light in the ultraviolet and re-emitting the light in a range detectable by PMTs. Using a 250 L water Cherenkov detector, we have characterized the increase in light yield from three compounds in water: 4-Methylumbelliferone, Carbostyril-124, and Amino-G Salt. We report the gain in PMT response at a concentration of 1 ppm as 1.88±0.02 for 4-Methylumbelliferone, stable within 0.5% over 50 days, 1.37±0.03 for Carbostyril-124, and 1.20±0.02 for Amino-G Salt. The response of 4-Methylumbelliferone was modeled, resulting in a simulated gain within 9% of the experimental gain at 1 ppm concentration. Finally, we report an increase in neutron detection performance of a large-scale (3.5 kL) gadolinium-doped water Cherenkov detector at a 4-Methylumbelliferone concentration of 1 ppm.

  3. Study of wavelength-shifting chemicals for use in large-scale water Cherenkov detectors

    Sweany, M; Dazeley, S; Dunmore, J; Felde, J; Svoboda, R; Tripathi, M

    2011-01-01

    Cherenkov detectors employ various methods to maximize light collection at the photomultiplier tubes (PMTs). These generally involve the use of highly reflective materials lining the interior of the detector, reflective materials around the PMTs, or wavelength-shifting sheets around the PMTs. Recently, the use of water-soluble wavelength-shifters has been explored to increase the measurable light yield of Cherenkov radiation in water. These wave-shifting chemicals are capable of absorbing light in the ultravoilet and re-emitting the light in a range detectable by PMTs. Using a 250 L water Cherenkov detector, we have characterized the increase in light yield from three compounds in water: 4-Methylumbelliferone, Carbostyril-124, and Amino-G Salt. We report the gain in PMT response at a concentration of 1 ppm as: 1.88 $\\pm$ 0.02 for 4-Methylumbelliferone, stable to within 0.5% over 50 days, 1.37 $\\pm$ 0.03 for Carbostyril-124, and 1.20 $\\pm$ 0.02 for Amino-G Salt. The response of 4-Methylumbelliferone was modele...

  4. Clinical application of 1H-chemical-shift imaging (CSI) to brain diseases

    An H-1 chemical shift imaging (CSI) was developed as part of the clinical MRI system, by which magnetic resonance spectra (MRS) can be obtained from multiple small voxels and metabolite distribution in the brain can be visualized. The present study was to determine the feasibility and clinical potential of using an H-1 CSI. The device used was a Magnetom H 15 apparatus. The study population was comprised of 25 healthy subjects, 20 patients with brain tumor, 4 with ischemic disease, and 6 with miscellaneous degenerative disease. The H-1 CSI was obtained by the 3-dimensional Fourier transformation. After suppressing the lipid signal by the inversion-recovery method and the water signal by the chemical-shift selective pulse with a following dephasing gradient, 2-directional 16 x 16 phase encodings were applied to the 16 x 16∼18 x 18 cm field of view, in which a 8 x 8 x 2∼10 x 10 x 2 cm area was selected by the stimulated echo or spin-echo method. The metabolite mapping and its contour mapping were created by using the curve-fitted area, with interpolation to the 256 x 256 matrix. In the healthy group, high resolution spectra for N-acetyl aspartate (NAA), creatine, choline (Cho), and glutamine/glutamate were obtained from each voxel; and metabolite mapping and contour mapping also clearly showed metabolite distribution in the brain. In the group of brain tumor, an increased Cho and lactate and loss of NAA were observed, along with heterogeneity within the tumor and changes in the surrounding tissue; and there was a good correlation between lactate peak and tumor malignancy. The group of ischemic and degenerative disease had a decreased NAA and increased lactate on both spectra and metabolite mapping, depending on disease stage. These findings indicated that H-1 CSI is helpful for detecting spectra over the whole brain, as well as for determining metabolite distribution. (N.K.)

  5. Cluster states in 13C and 11B

    The cluster structures of the excited states in 11B and 13C were discussed by measuring the isoscalar monopole strengths in the inelastic α scattering at Eα = 388 MeV. It was found that the 1/22-, 1/23-, and 1/24- states in 13C are candidates for the α cluster states with a 3α + n molecular configuration. (author)

  6. Hyperpolarized 13C MR for Molecular Imaging of Prostate Cancer

    Wilson, David M.; Kurhanewicz, John

    2014-01-01

    Hyperpolarization using dissolution dynamic nuclear polarization has emerged as a versatile method to dramatically improve the MR signal of low-sensitivity nuclei. This technique facilitates the study of real-time metabolism in vitro and in vivo using 13C-enriched substrates and has been applied to numerous models of human disease. In particular, several mechanisms underlying prostate cancer have been interrogated using hyperpolarized 13C MR spectroscopy. This review highlights key metabolic ...

  7. An in Vivo 13C NMR Analysis of the Anaerobic Yeast Metabolism of 1-13C-Glucose

    Giles, Brent J.; Matsche, Zenziwe; Egeland, Ryan D.; Reed, Ryan A.; Morioka, Scott S.; Taber, Richard L.

    1999-11-01

    A biochemistry laboratory experiment that studies the dynamics of the anaerobic yeast metabolism of 1-13C-D-glucose via NMR is described. Fleischmann's Active Dry yeast, under anaerobic conditions, produces primarily 2-13C-ethanol and some 1-13C-glycerol as end products. An experiment is described in which the yeast is subjected to osmotic shock from an increasing sodium chloride concentration. Under these conditions, the yeast increases the ratio of glycerol to ethanol. The experiment can be accomplished in a single laboratory period.

  8. EI Mass Spectrometry investigation of 13C and 15N labelling of cyanobacteria neurotoxins anatoxin-a and homoanatoxin-a

    Full text: Former 13C NMR investigations by Hemscheidt et al. have shown that cyanobacteria are able to incorporate by biosynthesis 13C labels from acetate and glutamate into the neurotoxins anatoxin-a and homoanatoxin-a. The main results of these investigations are the facts that the 13C isotopes of doubly labelled acetate incorporate into carbon atoms nr.3-4, 2-10, 8-1 and 11 of anatoxin-a and homoanatoxin-a, that the 13C labels of 13C5-glutamate incorporate into carbon atoms no. 5, 6, 7, 8 and 1, while the other carbon atoms remain unlabeled. There was also NMR evidence of competition for carbon atoms no. 8 and 1, as the presence of glutamate suppresses incorporation from acetate to these atoms. EI mass spectra were recorded using GC/MS on anatoxin-a and homoanatoxin-a extracts from the PCC6506 cyanobacteria strain of Oscillatoria grown in media containing 13C2-acetate alone and combined with unlabeled glutamate, 13C515N-glutamate, 13C615N4-arginine, 13C415N-aspartic acid and 13C6-glucose. The mass spectra confirm the NMR results obtained for acetate and glutamate, showing corresponding shifts of the ion masses. The results show that the 15N label is lost in early stages and not incorporated. 13C615N4-arginine transmits all six C labels into the toxins while 13C415N-aspartic acid and 13C6-glucose did not contribute at all to the formation of labelled anatoxin-a and homoanatoxin-a. The isotope shifts observed in the mass spectra indicated the origin of the main fragment ions. (author)

  9. Testing compound-specific δ13C of amino acids in mussels as a new approach to determine the average 13C values of primary production in littoral ecosystems

    Vokhshoori, N. L.; Larsen, T.; McCarthy, M.

    2012-12-01

    Compound-specific isotope analysis of amino acids (CSI-AA) is a technique used to decouple trophic enrichment patterns from source changes at the base of the food web. With this new emerging tool, it is possible to precisely determine both trophic position and δ15N or δ13C source values in higher feeding organisms. While most work to date has focused on nitrogen (N) isotopic values, early work has suggested that δ13C CSI-AA has great potential as a new tracer both to a record δ13C values of primary production (unaltered by trophic transfers), and also to "fingerprint" specific carbon source organisms. Since essential amino acids (EAA) cannot be made de novo in metazoans but must be obtained from diet, the δ13C value of the primary producer is preserved through the food web. Therefore, the δ13C values of EAAs act as a unique signature of different primary producers and can be used to fingerprint the dominant carbon (C) source driving primary production at the base of the food web. In littoral ecosystems, such as the California Upwelling System (CUS), the likely dominant C sources of suspended particulate organic matter (POM) pool are kelp, upwelling phytoplankton or estuarine phytoplankton. While bulk isotopes of C and N are used extensively to resolve relative consumer hierarchy or shifting diet in a food web, we found that the δ13C bulk values in mussels cannot distinguish exact source in littoral ecosystems. Here we show 15 sites within the CUS, between Cape Blanco, OR and La Jolla, CA where mussels were sampled and analyzed for both bulk δ13C and CSI-AA. We found no latitudinal trends, but rather average bulk δ13C values for the entire coastal record were highly consistent (-15.7 ± 0.9‰). The bulk record would suggest either nutrient provisioning from kelp or upwelled phytoplankton, but 13C-AA fingerprinting confines these two sources to upwelling. This suggests that mussels are recording integrated coastal phytoplankton values, with the enriched

  10. Analysis Method for Isotope Abundance of 13C-urea

    In order to better control the effective content of 13C in 13C-urea reagent, the technique and the conditions for converting 13C-urea sample into the sample gas used in gas isotopic mass spectrometry detection by means of nitrite oxidation method and high temperature burning method were investigated. The results showed that the 13CO2 gas obtained from nitrite oxidation method with 2 mg 13C-urea samples and that from high temperature burning method with 1 mg 13C-urea samples can satisfy the demand of the mass spectrometer detection. The sodium nitrite reagent dosage, the reaction temperature and the reaction time of the sample gas preparation, as well as the treatment effect of copper oxide reagent etc.were sought experimentally. The high abundance 13C-urea testing was completed, the calculation and expression of the detection data were also determined, and the standard deviation were less than ±0.07%. (authors)

  11. Abundance anomaly of the 13C species of CCH

    Sakai, N.; Saruwatari, O.; Sakai, T.; Takano, S.; Yamamoto, S.

    2010-03-01

    Aims: We have observed the N = 1-0 lines of CCH and its 13C isotopic species toward a cold dark cloud, TMC-1 and a star-forming region, L1527, to investigate the 13C abundances and formation pathways of CCH. Methods: The observations have been carried out with the IRAM 30 m telescope. Results: We have successfully detected the lines of 13CCH and C13CH toward the both sources and found a significant intensity difference between the two 13C isotopic species. The [C13CH] /[13CCH] abundance ratios are 1.6 ± 0.4 (3σ) and 1.6 ± 0.1 (3σ) for TMC-1 and L1527, respectively. The abundance difference between C13CH and 13CCH means that the two carbon atoms of CCH are not equivalent in the formation pathway. On the other hand, the [CCH]/[C13CH] and [CCH]/[13CCH] ratios are evaluated to be larger than 170 and 250 toward TMC-1, and to be larger than 80 and 135 toward L1527, respectively. Therefore, both of the 13C species are significantly diluted in comparison with the interstellar 12C/13C ratio of 60. The dilution is discussed in terms of a behavior of 13C in molecular clouds.

  12. Trends in stomatal density and 13C/12C ratios of Pinus flexilis needles during last glacial-interglacial cycle

    Measurements of stomatal density and delta 13C of limber pine (Pinus flexilis) needles (leaves) preserved in pack rat middens from the Great Basin reveal shifts in plant physiology and leaf morphology during the last 30,000 years. Sites were selected so as to offset glacia to Holocene climatic differences and thus to isolate the effects of changing atmospheric CO2 levels. Stomatal density decreased approximately 17 percent and delta 13C decreased approximately 1.5 per ml during deglaciation from 15,000 to 12,000 years ago, concomitant with a 30 percent increase in atmospheric CO2. Water-use efficiency increased approximately 15 percent during deglaciation, if temperature and humidity were held constant and the proxy values for CO2 and delta 13C of past atmospheres are accurate. The delta 13C variations may help constrain hypotheses about the redistribution of carbon between the atmosphere and biosphere during the last glacial-interglacial cycle

  13. Simple, efficient protocol for enzymatic synthesis of uniformly 13C, 15N-labeled DNA for heteronuclear NMR studies.

    Masse, J.E.; Bortmann, P; Dieckmann, T.; Feigon, J

    1998-01-01

    The use of uniformly 13C,15N-labeled RNA has greatly facilitated structural studies of RNA oligonucleotides by NMR. Application of similar methodologies for the study of DNA has been limited, primarily due to the lack of adequate methods for sample preparation. Methods for both chemical and enzymatic synthesis of DNA oligonucleotides uniformly labeled with 13C and/or 15N have been published, but have not yet been widely used. We have developed a modified procedure for preparing uniformly 13C,...

  14. A simplified 13C-Urea breath test (13C-UBT) in the diagnosis of Helicobacter pylori (HP) infection

    Rahman, T.; Bartholomeusz, F.D. L.; Bellon, M.S.; Chatterton, B.E. [Royal Adelaide Hospital, Adelaide. SA (Australia). Department of Nuclear Medicine

    1998-06-01

    Full text: The Urea Breath Test (UBT) is an accurate, noninvasive means of assessing the presence of Helicobacter pylori in the stomach. Two tests are currently available, using 13C- and 14C-labelled urea, respectively. 13C is a nonradioactive isotope, unlike 14C, but the 13C-UBT is technically more challenging. The aim of this study was to determine the accuracy of a simplified 13C-UBT with no test meal, using the 14C-UBT as the previously validated standard. 76 studies were performed on 72 patients; 4 patients performed the test twice. 28 patients were female, 44 male. The mean age was 51.1 years (range 23-86 years). 42 patients presented for post-eradication follow up, and 30 for initial diagnosis. All subjects underwent a 14C-UBT with a 15 minute sample. The 13C-UBT was then performed without a test meal and the breath samples obtained at baseline and 20 minutes. Of the 14C-UBT studies, 27 were positive, ranging from 1372 to 10,987 DPM (Normal <1000 DPM), and 49 were negative, range 177-946 DPM. 26 of the 13C-UBT studies were positive, with a Delta value ranging from 4.29-47.89 (Normal: Delta <3.5), and 50 were negative, range -0.20-2.80. There were 1 false-positive and 2 false-negative 13-UBT studies. This yielded a sensitivity of 92.6% and specificity of 98.0% for the simplified 13C-UBT. From these results we conclude that the simplified 13C-UBT is an accurate means of detecting the presence of Helicobacter pylori within the stomach

  15. A simplified 13C-Urea breath test (13C-UBT) in the diagnosis of Helicobacter pylori (HP) infection

    Full text: The Urea Breath Test (UBT) is an accurate, noninvasive means of assessing the presence of Helicobacter pylori in the stomach. Two tests are currently available, using 13C- and 14C-labelled urea, respectively. 13C is a nonradioactive isotope, unlike 14C, but the 13C-UBT is technically more challenging. The aim of this study was to determine the accuracy of a simplified 13C-UBT with no test meal, using the 14C-UBT as the previously validated standard. 76 studies were performed on 72 patients; 4 patients performed the test twice. 28 patients were female, 44 male. The mean age was 51.1 years (range 23-86 years). 42 patients presented for post-eradication follow up, and 30 for initial diagnosis. All subjects underwent a 14C-UBT with a 15 minute sample. The 13C-UBT was then performed without a test meal and the breath samples obtained at baseline and 20 minutes. Of the 14C-UBT studies, 27 were positive, ranging from 1372 to 10,987 DPM (Normal <1000 DPM), and 49 were negative, range 177-946 DPM. 26 of the 13C-UBT studies were positive, with a Delta value ranging from 4.29-47.89 (Normal: Delta <3.5), and 50 were negative, range -0.20-2.80. There were 1 false-positive and 2 false-negative 13-UBT studies. This yielded a sensitivity of 92.6% and specificity of 98.0% for the simplified 13C-UBT. From these results we conclude that the simplified 13C-UBT is an accurate means of detecting the presence of Helicobacter pylori within the stomach

  16. Delta /sup 13/C fractionation in Tarbela dam fish

    The paper focuses on the study of naturally occurring /sup 13/C fractionation in Tarbela dam fish. Craig noted that gamma /sup 13/C values for animal tissues fall in the range as their food supply. DeNiro and Epstein demonstrated clearly that the carbon isotope composition of an animal greatly depends on its diet. The above mentioned statements were observed while studying the isotopic composition of carbon in different parts of the fish. Living fish was purchased from the Haripur side of the Tarbela lake. Different portions were separated and fish diet was collected from the fish stomach. Samples were dried in the oven at 40-50 deg. C for five days. Ground, homogenized and ignited with research grade oxygen at 900-1000 deg. C. CO and CO /sub 2/ were produced and CO was converted to CO/sub 2/ by circulation over CuO gauge furnace at 900 deg. C. CO/sub 2/ was purified using 70 deg. C slush and analyzed on Varian Mat (GD-150) mass spectrometer for gamma /sup 13/C measurements. The results show that fish flesh sup/13 C value is nearly similar to fish diet gamma /sup 13/C. gamma /sup 13/C values to different parts of the fish departed from that of the diet in the sequence: fish swim bladder (-22.04) >ribs (2-22.26)>skin (122.91)>diet (123.22)>flesh (-23.40)> vertebral column (-24.07). It is concluded that diet is easily metabolized in the fish flesh and skin tissues through blood streams without causing any pronounced fractionation. Fractionation was observed in the fish endo skeleton system due to which fish ribs become enriched in gamma /sup 13/C than vertebral column. Fractionation was also detected in visceral muscles (swim bladder) of the fish as comparison with somatic axial trunk muscle (fish flesh). (author)

  17. 1 H and 13 C NMR of phenyl barbiturilidene

    The condensation of barbituric acids with aromatic aldehydes gives the phenyl barbiturilidenes, which are studied as intermediary compounds in the synthesis of new heterocyclic compounds for pharmaceutical use. One of the most characteristic reactions of these compounds is the Michael type addition reaction, in the exocyclic carbon-carbon double binding. The reaction with 2,4-di nitrophenyl hydrazine reaction is been used as a test of this type of reactivity, which supplies the respective hydrazone and barbituric acid. In this work, preliminary studies have been performed for establishing correlations between the Brown parameter (σ+), the chemical shifts (δ) of the barbiturilidene atoms involved in the reaction, and their reactivities

  18. Chemical shifts of the X-ray L3 absorption edge of europium in its trivalent halides

    Position of the Eu-L3 absorption edge has been studied in pure metal and in its trivalent halides, EuF3, EuCl3, EuBr3, and EuI3, employing a simple X-ray spectrometer with an LiF single crystal as the analyser. A linear relationship was established between the chemical shift and the effective charge on the absorbing rare earth atom. The chemical shifts have also been correlated to Moessbauer isomer shifts. The results have been discussed in terms of nature of chemical bonding, effective atomic charge on the absorbing atom and some other parameters relevant to the immediate local environment of the absorbing atom. (author)

  19. Attainable entanglement of unitary transformed thermal states in liquid-state nuclear magnetic resonance with the chemical shift

    Ota, Y; Ohba, I; Yoshida, N; Mikami, Shuji; Ohba, Ichiro; Ota, Yukihiro; Yoshida, Noriyuki

    2006-01-01

    Recently, Yu, Brown, and Chuang [Phys. Rev. A {\\bf 71}, 032341 (2005)] investigated the entanglement attainable from unitary transformed thermal states in liquid-state nuclear magnetic resonance (NMR). Their research gave an insight into the role of the entanglement in a liquid-state NMR quantum computer. Moreover, they attempted to reveal the role of mixed-state entanglement in quantum computing. However, they assumed that the Zeeman energy of each nuclear spin which corresponds to a qubit takes a common value for all; there is no chemical shift. In this paper, we research a model with the chemical shifts and analytically derive the physical parameter region where unitary transformed thermal states are entangled, by the positive partial transposition (PPT) criterion with respect to any bipartition. We examine the effect of the chemical shifts on the boundary between the separability and the nonseparability, and find it is negligible.

  20. Shifts in microbial and chemical patterns within the marine sponge Aplysina aerophoba during a disease outbreak.

    Webster, Nicole S; Xavier, Joana R; Freckelton, Marnie; Motti, Cherie A; Cobb, Rose

    2008-12-01

    The microbial community composition in affected and unaffected portions of diseased sponges and healthy control sponges of Aplysina aerophoba was assessed to ascertain the role of microbes in the disease process. Sponge secondary metabolites were also examined to assess chemical shifts in response to infection. The microbial profile and aplysinimine levels in unaffected tissue near the lesions closely reflected those of healthy sponge tissue, indicating a highly localized disease process. DGGE detected multiple sequences that were exclusively present in diseased sponges. Most notably, a Deltaproteobacteria sequence with high homology to a coral black band disease strain was detected in all sponge lesions and was absent from all healthy and unaffected regions of diseased sponges. Other potential pathogens identified by DGGE include an environmental Cytophaga strain and a novel Epsilonproteobacteria strain with no known close relatives. The disease process also caused a major shift in prokaryote community structure at a very high taxonomic level. Using 16S rRNA gene sequence analysis, only the diseased sponges were found to contain sequences belonging to the Epsilonproteobacteria and Firmicutes, and there was a much greater number of Bacteroidetes sequences within the diseased sponges. In contrast, only the healthy sponges contained sequences corresponding to the cyanobacteria and 'OP1' candidate division, and the healthy sponges were dominated by Chloroflexi and Gammaproteobacteria sequences. Overall bacterial diversity was found to be considerably higher in diseased sponges than in healthy sponges. These results provide a platform for future cultivation-based experiments to isolate the putative pathogens from A. aerophoba and perform re-infection trials to define the disease aetiology. PMID:18783385

  1. Nuclear magnetic resonance shielding constants and chemical shifts in linear 199Hg compounds: a comparison of three relativistic computational methods.

    Arcisauskaite, Vaida; Melo, Juan I; Hemmingsen, Lars; Sauer, Stephan P A

    2011-07-28

    We investigate the importance of relativistic effects on NMR shielding constants and chemical shifts of linear HgL(2) (L = Cl, Br, I, CH(3)) compounds using three different relativistic methods: the fully relativistic four-component approach and the two-component approximations, linear response elimination of small component (LR-ESC) and zeroth-order regular approximation (ZORA). LR-ESC reproduces successfully the four-component results for the C shielding constant in Hg(CH(3))(2) within 6 ppm, but fails to reproduce the Hg shielding constants and chemical shifts. The latter is mainly due to an underestimation of the change in spin-orbit contribution. Even though ZORA underestimates the absolute Hg NMR shielding constants by ∼2100 ppm, the differences between Hg chemical shift values obtained using ZORA and the four-component approach without spin-density contribution to the exchange-correlation (XC) kernel are less than 60 ppm for all compounds using three different functionals, BP86, B3LYP, and PBE0. However, larger deviations (up to 366 ppm) occur for Hg chemical shifts in HgBr(2) and HgI(2) when ZORA results are compared with four-component calculations with non-collinear spin-density contribution to the XC kernel. For the ZORA calculations it is necessary to use large basis sets (QZ4P) and the TZ2P basis set may give errors of ∼500 ppm for the Hg chemical shifts, despite deceivingly good agreement with experimental data. A Gaussian nucleus model for the Coulomb potential reduces the Hg shielding constants by ∼100-500 ppm and the Hg chemical shifts by 1-143 ppm compared to the point nucleus model depending on the atomic number Z of the coordinating atom and the level of theory. The effect on the shielding constants of the lighter nuclei (C, Cl, Br, I) is, however, negligible. PMID:21806118

  2. A scientific workflow framework for (13)C metabolic flux analysis.

    Dalman, Tolga; Wiechert, Wolfgang; Nöh, Katharina

    2016-08-20

    Metabolic flux analysis (MFA) with (13)C labeling data is a high-precision technique to quantify intracellular reaction rates (fluxes). One of the major challenges of (13)C MFA is the interactivity of the computational workflow according to which the fluxes are determined from the input data (metabolic network model, labeling data, and physiological rates). Here, the workflow assembly is inevitably determined by the scientist who has to consider interacting biological, experimental, and computational aspects. Decision-making is context dependent and requires expertise, rendering an automated evaluation process hardly possible. Here, we present a scientific workflow framework (SWF) for creating, executing, and controlling on demand (13)C MFA workflows. (13)C MFA-specific tools and libraries, such as the high-performance simulation toolbox 13CFLUX2, are wrapped as web services and thereby integrated into a service-oriented architecture. Besides workflow steering, the SWF features transparent provenance collection and enables full flexibility for ad hoc scripting solutions. To handle compute-intensive tasks, cloud computing is supported. We demonstrate how the challenges posed by (13)C MFA workflows can be solved with our approach on the basis of two proof-of-concept use cases. PMID:26721184

  3. Carbonyl 13C NMR spectrum of basin pancreatic trypsin inhibitor: resonance assignments by selective amide hydrogen isotope labeling and detection of isotope effects on 13C nuclear shielding

    The carbonyl region of the natural abundance 13C nuclear magnetic resonance (NMR) spectrum of basic pancreatic trypsin inhibitor is examined, and 65 of the 66 expected signals are characterized at varying pH and temperature. Assignments are reported for over two-thirds of the signals, including those of all buried backbone amide groups with slow proton exchange and all side-chain carbonyl groups. This is the first extensively assigned carbonyl spectrum for any protein. A method for carbonyl resonance assignments utilizing amide proton exchange and isotope effects on nuclear shielding is described in detail. The assignments are made by establishing kinetic correlation between effects of amide proton exchange observed in the carbonyl 13C region with development of isotope effects and in the amide proton region with disappearance of preassigned resonances. Several aspects of protein structure and dynamics in solution may be investigated by carbonyl 13C NMR spectroscopy. Some effects of side-chain primary amide group hydrolysis are described. The main interest is on information about intramolecular hydrogen-bond energies and changes in the protein due to amino acid replacements by chemical modification or genetic engineering

  4. GCE and solar S-process abundances. Dependence on the 13C-pocket structure

    We study the s-process abundances (A>90) at the epoch of the formation of the solar-system as the outcome of nucleosynthesis occurring in AGB stars of various initial masses and metallicities. AGB yields are computed with an updated neutron capture network and updated initial solar abundances. We use a Galactic Chemical Evolution (GCE) code based on, slightly modified accounting for the new determination of the age of the Universe (13.8 Gyr [3]) and solar abundances by [4]. At present, one of the most problematic issues of AGB stellar models is the formation of the 13C-pocket, where the major neutron source of the s-process (the 13C(α, n)16O reaction) burns radiatively. Indeed, the internal structure of the 13C-pocket may depend on the stellar characteristic (e.g., AGB initial mass and metallicity), and on the interplay between physical mechanisms that may compete in the star itself (e.g., rotation, magnetic fields, gravity waves). Because of the present uncertainties, we adopt in our AGB models a free parametrization of the 13C-pocket as has been done by [1]: this approximation allow us to investigate the impact of different internal structures of the 13C-pocket on the GCE s-distribution. We discuss our results in the light of the most recent studies.We follow the chemical evolution of several elements (e.g., α, Zr, Ba, Eu) along the stellar age and metallicity, comparing our results with the most update spectroscopic observations (e.g., [11,12]). (author)

  5. Inclusion of 13C and D in protonated acetylene

    Fortenberry, Ryan C.; Roueff, Evelyne; Lee, Timothy J.

    2016-04-01

    The rovibrational spectrum of cyclic, protonated acetylene has been established. The improvement in modern telescopes coupled with the different branching ratios in reaction models welcomes study of 13C-substitution for C2H3+. Quartic force fields (QFFs) have been previously utilized to predict the antisymmetric HCCH stretch in standard c-C2H3+ to within 0.1 cm-1 of experiment and are employed here to generate rovibrational insights for the 13C isotopologues. The zero-point energies are also given for the cyclic and 'Y'-shaped isomers for both 13C and D substitutions. Vibrational intensities and the dipole moments are provided in order to characterize more fully this simple cation.

  6. {sup 13}C relaxation in an RNA hairpin

    King, G.C. [Univ. of South Wales, Kensington (Australia)]|[Rice Univ., Houston, TX (United States); Akratos, C. [Univ. of South Wales, Kensington (Australia); Xi, Z.; Michnica, M.J. [Rice Univ., Houston, TX (United States)

    1994-12-01

    This initial survey of {sup 13}C relaxation in the {triangle}TAR RNA element has generated a number of interesting results that should prove generally useful for future studies. The most readily comparable study in the literature monitored {sup 13}C relaxation of the methyl groups from unusual bases in tRNA{sup Phe}. The study, which used T{sub 1} and NOE data only, reported order parameters for the methyl group axis that ranged between 0.51 and 0.97-a range similar to that observed here. However, they reported a breakdown of the standard order parameter analysis at higher (118-MHz {sup 13}C) frequencies, which should serve to emphasize the need for a thorough exploration of suitable motional models.

  7. Magnetic Resonance Imaging with Hyperpolarized 13C Contrast Agents

    Gordon, Jeremy W.

    Hyperpolarized 13C substrates offer the potential to non-invasively image metabolism and enzymatic activity. However, hyperpolarization introduces a number of difficulties, and imaging is hampered by non-equilibrium magnetization and the need for spectral encoding. There is therefore a need for fast and RF efficient spectral imaging techniques. This work presents a number of new methods that can be used to improve polarization, increase RF efficiency and improve modeling accuracy in hyperpolarized 13C experiments. In particular, a novel encoding and reconstruction algorithm is presented that can generate spatially and spectrally resolved images with a single RF excitation and echo time. This reconstruction framework increases data acquisition efficiency, enabling accelerated acquisition speed, preserved polarization, and/or improved temporal or spatial resolution. Overall, the methods enumerated in this dissertation have the potential to improve modeling accuracy and to mitigate the conventional tradeoffs between SNR, spatial resolution, and temporal resolution that govern image quality in hyperpolarized 13C experiments.

  8. Solid state 13C NMR analysis of Brazilian cretaceous ambers

    13C cross polarization with magic angle spinning nuclear magnetic resonance (13C CPMAS NMR) spectra have been obtained for the first time to three Cretaceous amber samples from South America. The samples were dated to Lower Cretaceous and collected in sediments from the Amazonas, Araripe and Reconcavo basins, Brazil. All samples have very similar spectra, consistent with a common paleobotanical source. Some aspects of the spectra suggest a relationship between Brazilian ambers and Araucariaceae family, such as intense resonances at 38-39 ppm. All samples are constituted by polylabdane structure associated to Class Ib resins, constituted by polymers of labdanoid diterpenes. Finally, information concerning some structural changes during maturation, such as isomerization of Δ8(17) and Δ12(13) unsaturations, were obtained by 13C NMR analyses. The results concerning botanical affinities are in accordance with previous results obtained by gas chromatography-mass spectrometry (GC-MS). (author)

  9. Solid state CP/MAS 13C n.m.r. analysis of particle size and density fractions of soil incubated with uniformly labelled 13C-glucose

    A soil incubated for 34 days in the absence (control) and presence (treated) of uniformly labelled 13C-glucose was dispersed using an ultrasonic probe and fractionated by sedimentation in water and a polytungstate solution of density 2.0 Mg m-3. Solid state CP/MAS 13C n.m.r. (cross polarization/magic angle spinning 13C nuclear magnetic resonance) spectroscopy was used to characterize the chemical structure of the native soil organic carbon and the residual substrate carbon in the fractions of the control and treated soils. To obtain quantitative results it was essential to determine the spin lattice relaxation time in a rotating frame of the individual carbon types in the spectra as the relaxation behaviour of the native organic material in the clay fraction was different from that of the residual substrate carbon. The residual substrate carbon was found to accumulate in predominantly alkyl and O-alkyl structures in both fractions. However, significant amounts of acetal and carboxyl carbon were also observed in the clay fraction. Little if any aromatic or phenolic carbon was synthesized by the soil microorganisms utilizing substrate carbon. Dipolar dephasing CP/MAS 13C n.m.r. experiments were also performed and allowed the proportion of each type of carbon which was protonated and nonprotonated to be estimated. Essentially all of the O-alkyl and acetal carbon, 25-40% of the aromatic carbon and 66-80% of the alkyl carbon was protonated in the fractions isolated from the treated soil. 24 refs., 4 figs., 2 tabs

  10. Transport and imaging of brute-force 13C hyperpolarization

    Hirsch, Matthew L.; Smith, Bryce A.; Mattingly, Mark; Goloshevsky, Artem G.; Rosay, Melanie; Kempf, James G.

    2015-12-01

    We demonstrate transport of hyperpolarized frozen 1-13C pyruvic acid from its site of production to a nearby facility, where a time series of 13C images was acquired from the aqueous dissolution product. Transportability is tied to the hyperpolarization (HP) method we employ, which omits radical electron species used in other approaches that would otherwise relax away the HP before reaching the imaging center. In particular, we attained 13C HP by 'brute-force', i.e., using only low temperature and high-field (e.g., T water and obtaining a 13C image of the hyperpolarized, dilute, aqueous product (∼0.01% 13C polarization, a >100-fold gain over thermal signals in the 1 T scanner). An annealing step, prior to polarizing the sample, was also key for increasing T1 ∼ 30-fold during transport. In that time, HP was maintained using only modest cryogenics and field (T ∼ 60 K and B = 1.3 T), for T1(13C) near 5 min. Much greater time and distance (with much smaller losses) may be covered using more-complete annealing and only slight improvements on transport conditions (e.g., yielding T1 ∼ 5 h at 30 K, 2 T), whereas even intercity transfer is possible (T1 > 20 h) at reasonable conditions of 6 K and 2 T. Finally, it is possible to increase the overall enhancement near d-DNP levels (i.e., 102-fold more) by polarizing below 100 mK, where nanoparticle agents are known to hasten T1 buildup by 100-fold, and to yield very little impact on T1 losses at temperatures relevant to transport.

  11. Phosphorus-31, 15N, and 13C NMR of glyphosate: Comparison of pH titrations to the herbicidal dead-end complex with 5-enolpyruvoylshikimate-3-phosphate synthase

    The herbicidal dead-end ternary complex (ES3PGlyph) of glyphosate [N-(phosphonomethyl)glycine] with 5-enolpyruvoylshikimate-3-phosphate synthase (EPSPS) and the substrate shikimate 3-phosphate (S3P) has been characterized by 31P, 15N, and 13C NMR. The NMR spectra of EPSPS-bound glyphosate show unique chemical shifts (δ) for each of the three nuclei. By 31P NMR, glyphosate in the dead-end complex is a distinct species 3.5 ppm downfield from free glyphosate. The 13C signal of glyphosate in the dead-end complex is shifted 4 ppm downfield from that of free glyphosate. The 15N signal for glyphosate (99%) in the dead-end complex is 5 ppm further downfield than that of any free zwitterionic species and 10 ppm downfield from that of the average free species at pH 10.1. The structures of each ionic state of glyphosate are modeled with force field calculations by using MacroModel. A correlation is made for the 31P δ and the C-P-O bond angle, and the 13C and 15N δ values are postulated to be related to C-C-O and C-N-C bond angles, respectively. The downfield 31P chemical shift perturbation for S3P in the EPSPS binary complex is consistent with ionization of the 3-phosphate of S3P upon binding. Comparison with the S3P 31P δ vs pH titration curve specifies predominantly the dianion of the 3-phosphate in the ES3P binary complex, while the ES3PGlyph complex indicates net protonation at the 3-phosphate. Chemical shift perturbations of this latter type may be explained by changes in the O-P-O bond angle

  12. Comparison of Computed Tomography Histogram Analysis and Chemical-Shift Magnetic Resonance Imaging for Adrenal Mass Characterization

    Background: Computed tomography (CT) histogram analysis and chemical-shift magnetic resonance imaging (MRI) are currently used modalities for adrenal mass characterization. However, it is not yet clear which modality can be regarded as most sensitive in terms of adrenal mass characterization. Purpose: To prospectively compare CT histogram analysis and chemical-shift MRI in the characterization of adrenal masses. Material and Methods: Between May 2007 and November 2008, 93 patients (45 males, 48 females; mean age 56.7 years, range 22-85 years) with 109 adrenal masses prospectively underwent both unenhanced CT and chemical-shift MRI examinations. These masses consisted of 67 adenomas and 42 metastases. Histogram analysis was applied with a circular region of interest (ROI) that recorded mean attenuation, total number of pixels, number of negative pixels, and the percentage of negative pixels on unenhanced CT images for each adrenal mass. In the CT histogram analysis, a 10% negative pixel threshold for unenhanced CT was calculated. In chemical-shift MRI, signal intensity drop between in-phase and opposed-phase images was quantitatively calculated so that adrenal-to-spleen chemical-shift ratios and adrenal signal intensity indexes were determined for each of the adrenal masses. A mass was regarded as an adenoma if it contained more than 10% negative pixels by CT histogram analysis, showed an adrenal-to-spleen chemical-shift ratio of less than 0.71, and had an adrenal signal intensity index of more than 16.5% by chemical-shift MRI. The results were compared to reveal which method was most sensitive in the diagnosis of adrenal masses and whether or not a correlation exists between these two modalities. Final diagnoses were based on imaging follow-up of minimum 6 months, biopsy, surgery, and adrenal washout study. Results: On unenhanced CT examinations, all of the 67 adenomas and 21 out of 42 metastases exhibited negative pixels. None of the metastases showed more than 10

  13. Comparison of Computed Tomography Histogram Analysis and Chemical-Shift Magnetic Resonance Imaging for Adrenal Mass Characterization

    Halefoglu, A.M.; Yasar, A.; Bas, N.; Ozel, A.; Erturk, S.M.; Basak, M. (Dept. of Radiology, Sisli Etfal Training and Research Hospital, Sisli, Istanbul (Turkey))

    2009-11-15

    Background: Computed tomography (CT) histogram analysis and chemical-shift magnetic resonance imaging (MRI) are currently used modalities for adrenal mass characterization. However, it is not yet clear which modality can be regarded as most sensitive in terms of adrenal mass characterization. Purpose: To prospectively compare CT histogram analysis and chemical-shift MRI in the characterization of adrenal masses. Material and Methods: Between May 2007 and November 2008, 93 patients (45 males, 48 females; mean age 56.7 years, range 22-85 years) with 109 adrenal masses prospectively underwent both unenhanced CT and chemical-shift MRI examinations. These masses consisted of 67 adenomas and 42 metastases. Histogram analysis was applied with a circular region of interest (ROI) that recorded mean attenuation, total number of pixels, number of negative pixels, and the percentage of negative pixels on unenhanced CT images for each adrenal mass. In the CT histogram analysis, a 10% negative pixel threshold for unenhanced CT was calculated. In chemical-shift MRI, signal intensity drop between in-phase and opposed-phase images was quantitatively calculated so that adrenal-to-spleen chemical-shift ratios and adrenal signal intensity indexes were determined for each of the adrenal masses. A mass was regarded as an adenoma if it contained more than 10% negative pixels by CT histogram analysis, showed an adrenal-to-spleen chemical-shift ratio of less than 0.71, and had an adrenal signal intensity index of more than 16.5% by chemical-shift MRI. The results were compared to reveal which method was most sensitive in the diagnosis of adrenal masses and whether or not a correlation exists between these two modalities. Final diagnoses were based on imaging follow-up of minimum 6 months, biopsy, surgery, and adrenal washout study. Results: On unenhanced CT examinations, all of the 67 adenomas and 21 out of 42 metastases exhibited negative pixels. None of the metastases showed more than 10

  14. Chemical shift imaging and localised magnetic resonance spectroscopy in full-term asphyxiated neonates

    Diagnosis of brain lesions after birth anoxia-ischemia is essential for appropriate management. Clinical evaluation is not sufficient. MRI has been proven to provide useful information. To compare abnormalities observed with MRI, including diffusion-weighted imaging (DWI), localised magnetic resonance spectroscopy (MRS) and chemical shift imaging (CSI) and correlate these findings with the clinical outcome. Fourteen full-term neonates with birth asphyxia were studied. MRI, MRS and CSI were performed within the first 4 days of life. Lesions observed with DWI were correlated with outcome, but the apparent diffusion coefficient (ADC) did improve diagnostic confidence. The mean value of Lac/Cr for the neonates with a favourable outcome was statically lower than for those who died (0.22 vs 1.04; P = 0.01). The same results were observed for the Lac/NAA ratio (0.21 vs 1.23; P = 0.01). Data obtained with localised MRS and CSI were correlated for the ratio N-acetyl-aspartate/choline, but not for the other metabolites. No correlation was found between the ADC values and the metabolite ratios. Combination of these techniques could be helpful in our understanding of the physiopathological events occurring in neonates with asphyxia. (orig.)

  15. Repeatability of long and short echo-time in vivo proton chemical-shift imaging

    We carried out long (145 ms) and short (25 ms) echo time spectroscopic imaging of the brain (chemical-shift imaging, CSI) on two occasions 1 week apart on 15 healthy individuals. We found coefficients of variation (CVs) generally in the range 10-25% for long and 15-30% for short echo-time measurements. The CVs of metabolite ratios were higher by about 5-10%. Limits of agreement (defined as mean±2 SD of the week 1-week 2 differences) were wider at the shorter echo time. The modest repeatability may be due in part to the difficulty of repositioning spectroscopic voxels at a scale of 1 mm. The generally higher CVs and wider limits of agreement at TE25 ms suggest that the increased spectral complexity more than offsets the theoretical advantage of increased signal at short echo-times. Analysis of variance general linear modelling of metabolites and metabolite ratios showed that, in general, the subject, region of the brain and hemisphere were more important than the occasion in explaining the variability of results. Unless information on short-T2 metabolites is specifically required, better results can probably be achieved with longer echo-times. The magnitude of the CVs needs to be taken into account in the calculation of sample size for cross-sectional or linear studies. (orig.)

  16. Clinical evaluation of the cerebral energy metabolism with 31P chemical shift imaging in neurosurgical disorders

    Cerebral energy metabolism was evaluated by means of 31P chemical shift imaging (CSI) using the 2.0 T whole-body MRIS system. 31P CSI was carried out by means of Spectroscopic Imaging by Dephasing Amplitude Changing method, four-dimensional CSI, and three-dimensional CSI. Twenty three patients with cerebral infarction and 21 patients with hypertensive intracerebral hemorrhage were examined. In cerebral infarction, an acute infarction was seen as a low-signal area in the PCr and ATP images and as a high-signal area in the Pi image. A subacute and chronic infarction was seen as a low-signal area in all the images -- 31P, PCr, ATP, Pi, PDE and PME. Intracellular acidosis was noticed within 2 days after onset. The intracellular pH became alkaline at the subacute and chronic stages of infarction. The chronological changes in the phosphorus metabolites were evaluated by means of these methods. In hypertensive intracerebral hemorrhage, hematoma and perifocal edema in the acute stage were seen as low-signal areas in the 31P, PCr, and ATP images, and as high-signal areas in the Pi image. In the chronic stage, a hematoma was seen as a low-signal area in all the images -- 31P, PCr, ATP and Pi. 31P CSI is thus a practical tool for studying phosphate metabolites clinically. Changes in the phosphorus metabolism relative to the anatomy of interest were detected by the use of these methods. (author)

  17. Correlation of 1H NMR Chemical Shift for Aqueous Solutions by Statistical Associating Fluid Theory Association Model

    许波; 李浩然; 王从敏; 许映杰; 韩世钧

    2005-01-01

    1H NMR chemical shifts of binary aqueous mixtures of acylamide, alcohol, dimethyl sulphoxide (DMSO), and acetone are correlated by statistical associating fluid theory (SAFT) association model. The comparison between SAFT association model and Wilson equation shows that the former is better for dealing with aqueous solutions. Finally, the specialties of both models are discussed.

  18. Optimal voxel size for measuring global gray and white matter proton metabolite concentrations using chemical shift imaging

    Hanson, Lars Peter Grüner; Adalsteinsson, E; Pfefferbaum, A; Spielman, D.M.

    2000-01-01

    Quantification of gray and white matter levels of spectroscopically visible metabolites can provide important insights into brain development and pathological conditions. Chemical shift imaging offers a gain in efficiency for estimation of global gray and white matter metabolite concentrations co...... concentration error (<15%). Magn Reson Med 44:10-18, 2000....

  19. Direct 13C NMR Detection in HPLC Hyphenation Mode

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

    2012-01-01

    is indubitable in simplifying structural elucidations. In the current study, we demonstrated direct (13)C NMR detection of triterpenoids from a Ganoderma lucidum extract in hyphenation mode. The combined advantage of a cryogenically cooled probe, miniaturization, and multiple trapping enabled the...

  20. Cardiac metabolism measured noninvasively by hyperpolarized 13C MRI

    Golman, K.; Petersson, J.S.; Magnusson, P.;

    2008-01-01

    was almost absent (0.2-11%) and the alanine signal was reduced (27-51%). Due to image-folding artifacts the data obtained for lactate were inconclusive. These studies demonstrate that cardiac metabolic imaging with hyperpolarized 1-(13)C-pyruvate is feasible. The changes in concentrations of the...

  1. Spectral editing for in vivo 13C magnetic resonance spectroscopy

    Xiang, Yun; Shen, Jun

    2012-01-01

    In vivo detection of carboxylic/amide carbons is a promising technique for studying cerebral metabolism and neurotransmission due to the very low RF power required for proton decoupling. In the carboxylic/amide region, however, there is severe spectral overlap between acetate C1 and glutamate C5, complicating studies that use acetate as an astroglia-specific substrate. There are no known in vivo MRS techniques that can spectrally resolve acetate C1 and glutamate C5 singlets. In this study, we propose to spectrally separate acetate C1 and glutamate C5 by a two-step J-editing technique after introducing homonuclear 13C- 13C scalar coupling between carboxylic/amide carbons and aliphatic carbons. By infusing [1,2- 13C 2]acetate instead of [1- 13C]acetate the acetate doublet can be spectrally edited because of the large separation between acetate C2 and glutamate C4 in the aliphatic region. This technique can be applied to studying acetate transport and metabolism in brain in the carboxylic/amide region without spectral interference.

  2. Does the Shuram δ13C excursion record Ediacaran oxygenation?

    Husson, J. M.; Maloof, A. C.; Schoene, B.; Higgins, J. A.

    2013-12-01

    The most negative carbon isotope excursion in Earth history is found in carbonate rocks of the Ediacaran Period (635-542 Ma). Known colloquially as the the 'Shuram' excursion, workers have long noted its tantalizing, broad concordance with the rise of abundant macro-scale fossils in the rock record, variously interpreted as animals, giant protists, macro-algae and lichen, and known as the 'Ediacaran Biota.' Thus, the Shuram excursion has been interpreted by many in the context of a dramatically changing redox state of the Ediacaran oceans - e.g., a result of methane cycling in a low O2 atmosphere, the final destruction of a large pool of recalcitrant dissolved organic carbon (DOC), and the step-wise oxidation of the Ediacaran oceans. More recently, diagenetic interpretations of the Shuram excursion - e.g. sedimentary in-growth of very δ13C depleted authigenic carbonates, meteoric alteration of Ediacaran carbonates, late-stage burial diagenesis - have challenged the various Ediacaran redox models. A rigorous geologic context is required to discriminate between these explanatory models, and determine whether the Shuram excursion can be used to evaluate terminal Neoproterozoic oxygenation. Here, we present chemo-stratigraphic data (δ13C, δ18O, δ44/42Ca and redox sensitive trace element abundances) from 12 measured sections of the Ediacaran-aged Wonoka Formation (Fm.) of South Australia that require a syn-depositional age for the extraordinary range of δ13C values (-12 to +4‰) observed in the formation. In some locations, the Wonoka Fm. is ~700 meters (m) of mixed shelf limestones and siliclastics that record the full 16 ‰ δ13C excursion in a remarkably consistent fashion across 100s of square kilometers of basin area. Fabric-altering diagenesis, where present, occurs at the sub-meter vertical scale, only results in sub-permil offsets in δ13C and cannot be used to explain the full δ13C excursion. In other places, the Wonoka Fm. is host to deep (1 km

  3. Internal motions in yeast phenylalanine transfer RNA from 13C NMR relaxation rates of modified base methyl groups: a model-free approach

    Internal motions at specific locations through yeast phenylalanine tRNA were measured by using nucleic acid biosynthetically enriched in 13C at modified base methyl groups. Carbon NMR spectra of isotopically enriched tRNA/sup Phe/ reveal 12 individual peaks for 13 of the 14 methyl groups known to be present. The two methyls of N2, N2-dimethylguanosine (m22G-26) have indistinguishable resonances, whereas the fourteenth methyl bound to ring carbon-11 of the hypermodified nucleoside 3' adjacent to the anticodon, wyosine (Y-37), does not come from the [methyl-13C] methionine substrate. Assignments to individual nucleosides within the tRNA were made on the basis of chemical shifts of the mononucleosides and correlation of 13C resonances with proton NMR chemical shifts via two-dimensional heteronuclear proton-carbon correlation spectroscopy. Values of 13C longitudinal relaxation (T1) and the nuclear Overhauser enhancements (NOE) were determined at 22.5, 75.5, and 118 MHz for tRNA/sup Phe/ in a physiological buffer solution with 10 mM MgCl2, at 220C. These data were used to extract two physical parameters that define the system with regard to fast internal motion: the generalized order parameters (S2) and effective correlation times (tau/sub e/) for internal motion of the C-H internuclear vectors. For all methyl groups the generalized order parameter varied from 0.057 to 0.108, compared with the value of 0.111 predicted for a rapidly spinning methyl group rigidly mounted on a spherical macromolecule. Values of tau/sub e/ ranged from 4 to 16 ps, generally shorter times than measured in other work for amino acid methyl groups in several proteins. Somewhat surprising was the finding that the two methyl esters terminating the Y-37 side chain have order parameters similar to those of other methyls in tRNA and only 25% less than that for a methyl directly bonded to the base

  4. A comparison of chemical shift sensitivity of trifluoromethyl tags: optimizing resolution in {sup 19}F NMR studies of proteins

    Ye, Libin; Larda, Sacha Thierry; Frank Li, Yi Feng [University of Toronto, UTM, Department of Chemistry (Canada); Manglik, Aashish [Stanford University School of Medicine, Department of Molecular and Cellular Physiology (United States); Prosser, R. Scott, E-mail: scott.prosser@utoronto.ca [University of Toronto, UTM, Department of Chemistry (Canada)

    2015-05-15

    The elucidation of distinct protein conformers or states by fluorine ({sup 19}F) NMR requires fluorinated moieties whose chemical shifts are most sensitive to subtle changes in the local dielectric and magnetic shielding environment. In this study we evaluate the effective chemical shift dispersion of a number of thiol-reactive trifluoromethyl probes [i.e. 2-bromo-N-(4-(trifluoromethyl)phenyl)acetamide (BTFMA), N-(4-bromo-3-(trifluoromethyl)phenyl)acetamide (3-BTFMA), 3-bromo-1,1,1-trifluoropropan-2-ol (BTFP), 1-bromo-3,3,4,4,4-pentafluorobutan-2-one (BPFB), 3-bromo-1,1,1-trifluoropropan-2-one (BTFA), and 2,2,2-trifluoroethyl-1-thiol (TFET)] under conditions of varying polarity. In considering the sensitivity of the {sup 19}F NMR chemical shift to the local environment, a series of methanol/water mixtures were prepared, ranging from relatively non-polar (MeOH:H{sub 2}O = 4) to polar (MeOH:H{sub 2}O = 0.25). {sup 19}F NMR spectra of the tripeptide, glutathione ((2S)-2-amino-4-{[(1R)-1-[(carboxymethyl)carbamoyl] -2-sulfanylethyl]carbamoyl}butanoic acid), conjugated to each of the above trifluoromethyl probes, revealed that the BTFMA tag exhibited a significantly greater range of chemical shift as a function of solvent polarity than did either BTFA or TFET. DFT calculations using the B3LYP hybrid functional and the 6-31G(d,p) basis set, confirmed the observed trend in chemical shift dispersion with solvent polarity.

  5. {sup 1}H MR chemical shift imaging detection of phenylalanine in patients suffering from phenylketonuria (PKU)

    Sijens, Paul E.; Oudkerk, Matthijs [University Hospital Groningen, Department of Radiology, Hanzeplein 1, P.O. Box 30001, Groningen (Netherlands); Reijngoud, Dirk-Jan; Spronsen, Francjan J. van [University Hospital Groningen, Department of Pediatrics, Groningen (Netherlands); Leenders, Klaas L. [University Hospital Groningen, Department of Neurology, Groningen (Netherlands); Valk, Harold W. de [University Medical Centre of Utrecht, Department of Internal Medicine, Utrecht (Netherlands)

    2004-10-01

    Short echo time single voxel methods were used in previous MR spectroscopy studies of phenylalanine (Phe) levels in phenylketonuria (PKU) patients. In this study, apparent T{sub 2} relaxation time of the 7.3-ppm Phe multiplet signal in the brain of PKU patients was assessed in order to establish which echo time would be optimal. {sup 1}H chemical shift imaging (CSI) examinations of a transverse plain above the ventricles of the brain were performed in 10 PKU patients and 11 persons not suffering from PKU at 1.5 T, using four echo times (TE 20, 40, 135 and 270 ms). Phe was detectable only when the signals from all CSI voxels were summarized. In patients suffering from PKU the T{sub 2} relaxation times of choline, creatine and N-acetyl aspartate (NAA) were similar to those previously reported for healthy volunteers (between 200 and 325 ms). The T{sub 2} of Phe in brain tissue was 215{+-}120 ms (standard deviation). In the PKU patients the brain tissue Phe concentrations were 141{+-}69 {mu}M as opposed to 58{+-}23 {mu}M in the persons not suffering from PKU. In the detection of Phe, MR spectroscopy performed at TE 135 or 270 ms is not inferior to that performed at TE 20 or 40 ms (all previous studies). Best results were obtained at TE=135 ms, relating to the fact that at that particular TE, the visibility of a compound with a T{sub 2} of 215 ms still is good, while interfering signals from short-TE compounds are negligible. (orig.)

  6. Quantification of fat using chemical shift imaging and 1H-MR spectroscopy in phantom model

    Objective: To evaluate the accuracy of chemical shift imaging (CSI) and MR spectroscopy (MRS) for fat quantification in phantom model. Methods: Eleven phantoms were made according to the volume percentage of fat ranging from 0 to 100% with an interval of 10%. The fat concentration in the phantoms were measured respectively by CSI and MRS and compared using one-sample t test. The correlation between the two methods was also analyzed. The concentration of saturated fatty acids (FS), unsaturated fatty acids (FU) and the poly, unsaturation degree (PUD) were calculated by using MRS. Results: The fat concentration was (48.0±1.0)%, (57.0±0.5)%, (67.3±0.6)%, (77.3± 0.6)%, (83.3±0.6)% and (91.0±1.0)% respectively with fat volume of 50% to 100% by CSI. The fat concentration was (8.3±0.6)%, (16.3±0.7)%, (27.7±0.6)%, (36.0±1.0)%, (43.5± 0.6)% and (56.5±1.0)% respectively with fat volume of 10% to 60% by MRS, the fat concentration were underestimated by CSI and MRS (P<0.05), and had high linear correlation with the real concentration in phantoms (CSI: r=0.998, MRS: r=0.996, P<0.01). There was also a linear correlation between two methods (r=0.992, P<0.01) but no statistically significant difference (paired- samples t test, t=-0.125, P=0.903). By using MRS, the relative ratio of FS and FU in fat were 0. 15 and 0.85, the PUD was 0.0325, respectively, and highly consistent with these in phantoms. Conclusion: Both CSI and MRS are efficient and accurate methods in fat quantification at 7.0 T MR. (authors)

  7. Female sea lamprey shift orientation toward a conspecific chemical cue to escape a sensory trap

    Brant, Cory O.; Johnson, Nicholas; Li, Ke; Buchinger, Tyler J.; Li, Weiming

    2016-01-01

    The sensory trap model of signal evolution hypothesizes that signalers adapt to exploit a cue used by the receiver in another context. Although exploitation of receiver biases can result in conflict between the sexes, deceptive signaling systems that are mutually beneficial drive the evolution of stable communication systems. However, female responses in the nonsexual and sexual contexts may become uncoupled if costs are associated with exhibiting a similar response to a trait in both contexts. Male sea lamprey (Petromyzon marinus) signal with a mating pheromone, 3-keto petromyzonol sulfate (3kPZS), which may be a match to a juvenile cue used by females during migration. Upstream movement of migratory lampreys is partially guided by 3kPZS, but females only move toward 3kPZS with proximal accuracy during spawning. Here, we use in-stream behavioral assays paired with gonad histology to document the transition of female preference for juvenile- and male-released 3kPZS that coincides with the functional shift of 3kPZS as a migratory cue to a mating pheromone. Females became increasingly biased toward the source of synthesized 3kPZS as their maturation progressed into the reproductive phase, at which point, a preference for juvenile odor (also containing 3kPZS naturally) ceased to exist. Uncoupling of female responses during migration and spawning makes the 3kPZS communication system a reliable means of synchronizing mate search. The present study offers a rare example of a transition in female responses to a chemical cue between nonsexual and sexual contexts, provides insights into the origins of stable communication signaling systems.

  8. Application of 13C-stable isotope probing to identify RDX-degrading microorganisms in groundwater

    We employed stable isotope probing (SIP) with 13C-labeled hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) to identify active microorganisms responsible for RDX biodegradation in groundwater microcosms. Sixteen different 16S rRNA gene sequences were derived from microcosms receiving 13C-labeled RDX, suggesting the presence of microorganisms able to incorporate carbon from RDX or its breakdown products. The clones, residing in Bacteroidia, Clostridia, α-, β- and δ-Proteobacteria, and Spirochaetes, were different from previously described RDX degraders. A parallel set of microcosms was amended with cheese whey and RDX to evaluate the influence of this co-substrate on the RDX-degrading microbial community. Cheese whey stimulated RDX biotransformation, altered the types of RDX-degrading bacteria, and decreased microbial community diversity. Results of this study suggest that RDX-degrading microorganisms in groundwater are more phylogenetically diverse than what has been inferred from studies with RDX-degrading isolates. Highlights: •SIP identified sixteen groundwater bacteria capable of using RDX and/or its metabolites as a carbon source. •The RDX degraders in groundwater are phylogenetically diverse and different from known RDX degraders. •Cheese whey induced community shift and altered diversity of the RDX-degrading microorganisms over time. -- RDX-degrading bacteria in contaminated groundwater, identified by SIP with 13C-labeled RDX, are phylogenetically diverse and different from known RDX degraders

  9. Isotopic variability of cave bears (δ15N, δ13C) across Europe during MIS 3

    Krajcarz, Magdalena; Pacher, Martina; Krajcarz, Maciej T.; Laughlan, Lana; Rabeder, Gernot; Sabol, Martin; Wojtal, Piotr; Bocherens, Hervé

    2016-01-01

    Collagen, the organic fraction of bone, records the isotopic parameters of consumed food for carbon (δ13C) and nitrogen (δ15N). This relationship of isotopic signature between diet and tissue is an important tool for the study of dietary preferences of modern and fossil animal species. Since the first information on the isotopic signature of cave bear was reported, numerous data from Europe have become available. The goal of this work is to track the geographical variation of cave bear collagen isotopic values in Europe during Marine Isotopic Stage 3 (about 60,000-25,000 yr BP). In this study the results of new δ13C and δ15N isotopic analyses of cave bear collagen from four Central-Eastern European sites are presented, as well as a review of all published isotopic data for cave bears of the same period. The main conclusion is a lack of geographical East-West pattern in the variations of δ13C and δ15N values of cave bear collagen. Moreover, no relationship was found between cave bear taxonomy and isotopic composition. The cave bears from Central-Eastern Europe exhibit δ13C and δ15N values near the average of the range of Central, Western and Southern European cave bears. Despite the fact that most cave bear sites follow an altitudinal gradient, separate groups of sites exhibit shift in absolute values of δ13C, what disturbs an altitude-related isotopic pattern. The most distinct groups are: high Alpine sites situated over 1500 m a.s.l. - in terms of δ13C; and two Romanian sites Peştera cu Oase and Urşilor - in case of δ15N. Although the cave bear isotopic signature is driven by altitude, the altitudinal adjustment of isotopic data is not enough to explain the isotopic dissimilarity of these cave bears. The unusually high δ15N signature of mentioned Romanian sites is an isolated case in Europe. Cave bears from relatively closely situated Central-Eastern European sites and other Romanian sites are more similar to Western European than to Romanian

  10. Anomalous chemical shifts in X-ray photoelectron spectra of sulfur-containing compounds of silver (I) and (II)

    Highlights: • Ag 3d5/2 binding energy for Ag(II)SO4 is as large as 370.1 eV. • This is the largest value ever measured for a silver (II) compound. • Large shift is connected with the extreme oxidizing nature of Ag(II) species. • Ag(I)2S2O7 exhibits both positive and negative shifts with respect to metallic Ag. • Two distinct Ag(I) sites are responsible for large BE difference of 3.6 eV. - Abstract: Anomalous chemical shifts, i.e. cases when binding energy decreases with the increase of the oxidation state, have been well-documented for selected compounds of silver, and well understood based on analysis of initial- and final-state effects in the XPS spectra. Here we report two examples of even more exotic behaviour of chemical shifts for two silver compounds. The first one is Ag2S2O7 which exhibits both positive and negative substantial shifts with respect to metallic Ag for two distinct Ag(I) sites in its crystal structure, which differ by as much as 3.6 eV. Another is AgSO4, a rare example of oxo silver (II) salt, which exhibits “normal” chemical shift but the Ag 3d5/2 binding energy takes the largest value measured for a silver (II) compound (370.1 eV). This property is connected predominantly with the extremely strongly oxidizing nature of Ag(II) species

  11. Anomalous chemical shifts in X-ray photoelectron spectra of sulfur-containing compounds of silver (I) and (II)

    Grzelak, A. [Faculty of Chemistry, University of Warsaw, Pasteur 1, 02093 Warsaw (Poland); Jaroń, T. [Centre of New Technologies, University of Warsaw, Żwirki i Wigury 93, 02089 Warsaw (Poland); Mazej, Z. [Department of Inorganic Chemistry and Technology, Jožef Stefan Institute, Jamova 39, SI-1000 Ljubljana (Slovenia); Michałowski, T. [Faculty of Chemistry, University of Warsaw, Pasteur 1, 02093 Warsaw (Poland); Centre of New Technologies, University of Warsaw, Żwirki i Wigury 93, 02089 Warsaw (Poland); Szarek, P. [Centre of New Technologies, University of Warsaw, Żwirki i Wigury 93, 02089 Warsaw (Poland); Grochala, W., E-mail: w.grochala@cent.uw.edu.pl [Faculty of Chemistry, University of Warsaw, Pasteur 1, 02093 Warsaw (Poland); Centre of New Technologies, University of Warsaw, Żwirki i Wigury 93, 02089 Warsaw (Poland)

    2015-07-15

    Highlights: • Ag 3d{sub 5/2} binding energy for Ag(II)SO{sub 4} is as large as 370.1 eV. • This is the largest value ever measured for a silver (II) compound. • Large shift is connected with the extreme oxidizing nature of Ag(II) species. • Ag(I){sub 2}S{sub 2}O{sub 7} exhibits both positive and negative shifts with respect to metallic Ag. • Two distinct Ag(I) sites are responsible for large BE difference of 3.6 eV. - Abstract: Anomalous chemical shifts, i.e. cases when binding energy decreases with the increase of the oxidation state, have been well-documented for selected compounds of silver, and well understood based on analysis of initial- and final-state effects in the XPS spectra. Here we report two examples of even more exotic behaviour of chemical shifts for two silver compounds. The first one is Ag{sub 2}S{sub 2}O{sub 7} which exhibits both positive and negative substantial shifts with respect to metallic Ag for two distinct Ag(I) sites in its crystal structure, which differ by as much as 3.6 eV. Another is AgSO{sub 4}, a rare example of oxo silver (II) salt, which exhibits “normal” chemical shift but the Ag 3d{sub 5/2} binding energy takes the largest value measured for a silver (II) compound (370.1 eV). This property is connected predominantly with the extremely strongly oxidizing nature of Ag(II) species.

  12. In Situ 13C NMR at Elevated-Pressures and -Temperatures Investigating the Conversion of CO2 to Magnesium and Calcium Carbonate Minerals

    Surface, J. A.; Conradi, M. S.; Skemer, P. A.; Hayes, S. E.

    2013-12-01

    We have constructed specialized NMR hardware to conduct in situ elevated-pressure, elevated-temperature 13C NMR studies of unmixed heterogeneous mixtures of solids, liquids, gases, and supercritical fluids. Specifically, our aim is to monitor CO2 uptake in both ultramafic rocks and in more porous geological materials to understand the mechanisms of chemisorption as a function of temperature, pressure and pH. In this in situ NMR probe, we are able to simulate processes at geologically relevant fluid pressures and temperatures, monitoring the kinetics of CO2 conversion to carbonates. The in situ NMR experiments consist of heterogeneous mixtures of rock, salty brine solution, and moderate pressure CO2 gas at elevated temperatures. The purpose of studying these reactions is to determine efficacy of carbonate formation in various geological reservoirs. Via 13C NMR, we have spectroscopically characterized and quantified the conversion of CO2 to magnesium carbonate and calcium carbonate minerals. When CO2 reacts with the calcium or magnesium in a mineral or rock sample, the 13C chemical shift, linewidth, lineshape, and relaxation times change dramatically. This change can be monitored in situ and provide instantaneous and continuous characterization that maps the chemistry that is taking place. For example, on the pathway to MgCO3 formation, there are a number of phases of Mg(OH)x(H2O)y(CO3)z that are apparent via NMR spectroscopy. We will demonstrate that NMR can be used for quantitative characterization of multiple metastable mineral phases in pure forms and in mixtures. Results are confirmed via powder XRD and Raman spectroscopy of aquo- hydro- carbonato- magnesium species and calcium carbonate species. We also have monitored the 13C spectroscopy to analyze the phase of CO2 (liquid, supercritical, or gas) and its conversion into other forms, such as bicarbonate and carbonate species, providing a "window" into the in situ pH of the reacting system. Reference: 'In Situ

  13. Single voxel localization for dynamic hyperpolarized 13C MR spectroscopy

    Chen, Albert P.; Cunningham, Charles H.

    2015-09-01

    The PRESS technique has been widely used to achieve voxel localization for in vivo1H MRS acquisitions. However, for dynamic hyperpolarized 13C MRS experiments, the transition bands of the refocusing pulses may saturate the pre-polarized substrate spins flowing into the voxel. This limitation may be overcome by designing refocusing pulses that do not perturb the resonance of the hyperpolarized substrate, but selectively refocuses the spins of the metabolic products. In this study, a PRESS pulse sequence incorporating spectral-spatial refocusing pulses that have a stop band ('notch') at the substrate resonance is tested in vivo using hyperpolarized [1-13C]pyruvate. Higher metabolite SNR was observed in experiments using the spectral-spatial refocusing pulses as compared to conventional refocusing pulses.

  14. Alpha-resonant states in {sup 13}C

    Borello-Lewin, T.; Rodrigues, M.R.D.; Horodynski-Matsushigue, L.B.; Duarte, J.L.M.; Rodrigues, C.L.; Souza, M.A.; Miyake, H. [Universidade de Sao Paulo (IF/USP), SP (Brazil). Inst. de Fisica; Cunsolo, A.; Cappuzzello, F. [Universita di Catania (Italy); Istituto Nazionali di Fisica Nucleare (INFN), Catania (Italy). Lab. Nazionali del Sud; Ukita, G.M. [Universidade de Santo Amaro (UNISA), Sao Paulo, SP (Brazil). Faculty of Psychology

    2010-07-01

    Full text: The research program in progress aims to achieve a better understanding of the alpha-clustering phenomenon in light (x{alpha} + {nu}) nuclei. The {sup 9}Be({sup 6}Li,d){sup 13}C reaction was used in the present work to investigate alpha resonant states in {sup 13}C up to 15 MeV of excitation. The data have been taken at a bombarding energy of 25.5 MeV employing the Sao Paulo Pelletron-Enge-Spectrograph facility and the nuclear emulsion detection technique. The plates covered 100 cm along the focal surface and spectra were measured at seven scattering angles, between 3 deg and 20 degrees in the laboratory frame. The resolution of 50 keV allowed for the separation of the resonant contributions to the known 7/2{sup -} at 10.753 MeV and (5/2{sup -}) at 10.818 MeV {sup 13}C states. Particularly interesting is the the narrow alpha resonance seen at E{sub x} = 12.3 MeV close the (3{alpha} + n) threshold, not previously measured, populated by an L = 2 transfer. Detected, near this threshold by alpha inelastic scattering, a large E0 isoscalar transition, the signature of a spatially developed 1/2{sup -} cluster-state, was reported by T. Kawabata. The L = 2 transfer agrees with the 1/2{sup -} attribution. The present work is underway. Taking the benefit of the use of the emulsion plates and applying the track selective reading methodology, at least other three narrow alpha resonances in {sup 13}C up to 15 MeV of excitation, not previously measured, were detected. (author)

  15. Deconvolution of the tree ring based delta13C record

    We assumed that the tree-ring based 13C/12C record constructed by Freyer and Belacy (1983) to be representative of the fossil fuel and forest-soil induced 13C/12C change for atmospheric CO2. Through the use of a modification of the Oeschger et al. ocean model, we have computed the contribution of the combustion of coal, oil, and natural gas to this observed 13C/12C change. A large residual remains when the tree-ring-based record is corrected for the contribution of fossil fuel CO2. A deconvolution was performed on this residual to determine the time history and magnitude of the forest-soil reservoir changes over the past 150 years. Several important conclusions were reached. (1) The magnitude of the integrated CO2 input from these sources was about 1.6 times that from fossil fuels. (2) The forest-soil contribution reached a broad maximum centered at about 1900. (3) Over the 2 decade period covered by the Mauna Loa atmospheric CO2 content record, the input from forests and soils was about 30% that from fossil fuels. (4) The 13C/12C trend over the last 20 years was dominated by the input of fossil fuel CO2. (5) The forest-soil release did not contribute significantly to the secular increase in atmospheric CO2 observed over the last 20 years. (6) The pre-1850 atmospheric p2 values must have been in the range 245 to 270 x 10-6 atmospheres

  16. Galactose oxidation using 13C in healthy and galactosemic children

    D.R. Resende-Campanholi; Porta, G.; Ferrioli, E.; Pfrimer, K.; L.A. Del Ciampo; J.S. Camelo Junior

    2015-01-01

    Galactosemia is an inborn error of galactose metabolism that occurs mainly as the outcome of galactose-1-phosphate uridyltransferase (GALT) deficiency. The ability to assess galactose oxidation following administration of a galactose-labeled isotope (1-13C-galactose) allows the determination of galactose metabolism in a practical manner. We aimed to assess the level of galactose oxidation in both healthy and galactosemic Brazilian children. Twenty-one healthy children and seven children with ...

  17. In vivo 13C MRS studies of carbohydrate metabolism

    The work described in this thesis was performed by the author, except where indicated, within the Magnetic Resonance Centre at the University of Nottingham during the period between October 1999 and October 2002. Although much is known about the major pathways of carbohydrate metabolism, there is still much to be learnt about the exact mechanisms of many of these pathways. Of particular interest is how these pathways are modified under different physiological conditions and in diseased states. 13C NMR spectroscopy provides a non-invasive means for studying carbohydrate metabolism in vivo, and the work presented within this thesis gives two such examples of this in human subjects. Natural abundance 13C NMR spectroscopy was used to measure glycogen levels in gastrocnemius muscle. The diurnal changes in response to mixed meals were measured in both type 2 diabetic subjects and age and weight matched controls. Metabolic studies were performed to complement the NMR measurements. The data obtained in these studies show the effect of the failure of muscle glucose storage upon post-prandial hyperglycaemia despite a supra-normal increase in plasma insulin in type 2 diabetes. 13C NMR spectroscopy was also used to study cerebral metabolism. Accumulation of 13C label into glutamate and glutamine following infusion of [113C] glucose allows the determination of the rates of the TCA cycle (FTCA) and neurotransmitter cycling (Fcyc). These rates were measured in the visual cortex under control and activated conditions. The increases seen in FTCA upon activation, together with the lack of label accumulation in lactate, suggest that cerebral glucose metabolism is oxidative, even during strong activation. No conclusion can be made as to whether or not a similar increase is seen in Fcyc due to the large associated errors in these values. (author)

  18. 13C-NMR of forest soil lipids

    Almendros Martín, Gonzalo; Tinoco, Pilar; González-Vila, Francisco Javier; Lüdemann, H.-D.; Sanz Perucha, Jesús; Velasco de Pedro, F.

    2001-01-01

    Molecular characterization of soil lipids often provides valuable biogeochemical information about the impact of vegetation, microorganisms, and abiotic factors on the soil C sequestration process. The total lipid extracted with petroleum ether from nine soils developed under three types of Mediterranean forest (stone pine (Pinus pinea L.), evergreen oak (Quercus rotundifolia L.), and Spanish juniper (Juniperus thurifera L)) has been analyzed by high-resolution 13C nuclear magnetic resonance ...

  19. Evaluation of vertebral bone marrow fat content by chemical-shift MRI in osteoporosis

    To quantitatively evaluate vertebral bone marrow fat content and investigate its association with osteoporosis with chemical-shift magnetic resonance imaging (CS-MRI). Fifty-six female patients (age range 50-65 years) with varying bone mineral densities as documented with dual x-ray absorptiometry (DXA) were prospectively included in the study. According to the DXA results, the patients were grouped as normal bone density, osteopenic, or osteoporotic. In order to calculate fat content, the lumbar region was visualized in the sagittal plane by CS-MRI sequence. ''Region of interest'' (ROI)s were placed within L3 vertebral bodies and air (our reference point) at different time points by different radiologists. Fat content was calculated through ''signal intensity (SI) suppression rate'' and ''SI Index''. The quantitative values were compared statistically with those obtained from DXA examinations. Kruskal-Wallis, and Mann-Whitney U tests were used for comparisons between groups. The reliability of the measurements performed by two radiologists was evaluated with the ''intraclass correlation coefficient''. This study was approved by an institutional review board and all participants provided informed consent to participate in the study. Eighteen subjects with normal bone density (mean T score, 0.39 ± 1.3 [standard deviation]), 20 subjects with osteopenia (mean T score, -1.79 ± 0.38), and 18 subjects with osteoporosis (mean T score, -3 ± 0.5) were determined according to DXA results. The median age was 55.9 (age range 50-64 years) in the normal group, 55.5 (age range 50-64 years) in the osteopenic group, and 55.1 (age range 50-65 years) in the osteoporotic group (p = 0.872). In the CS-MRI examination, the values of ''SI suppression ratio'' and ''SI Index'' (median [min:max]) were calculated by the first and second reader, independently. There was no statistically significant difference between the groups with regard to vertebral bone marrow fat content (p > 0

  20. PEDOGENIC CARBONATE δ13C AND ENVIRONMENTAL PRECIPITATION CONDITIONS

    Marcella Catoni

    2011-12-01

    Full Text Available Carbon isotopic analysis is a useful tool for investigating paleoenvironments, as the pedogenic carbonate δ13C is related to δ13CSOM and to the proportions of C3/C4 plants. In this work we interpreted the paleoenvironmental conditions at the time of carbonate precipitation in soils formed under different climates and during different geological ages. Samples were taken from a Bk (PR1, Holocene and from two Bkm horizons (PR2 and PR3, Pleistocene. When the mean δ13C plant values and the most plausible paleotemperatures were used in the evaluation, PR1 showed a lower percentage of C4 plants (48% than Pleistocene soils (~53%, in agreement with paleoclimate changes. When instead the δ13C values of current plants were used for PR1, C4 plants ranged from 59 (12°C to 66% (18°C, suggesting two possible interpretations: either plant species changed during the Holocene, or the plant mean values normally used in the literature are not suitable for Pleistocene reconstructions

  1. Galactose oxidation using 13C in healthy and galactosemic children

    Galactosemia is an inborn error of galactose metabolism that occurs mainly as the outcome of galactose-1-phosphate uridyltransferase (GALT) deficiency. The ability to assess galactose oxidation following administration of a galactose-labeled isotope (1-13C-galactose) allows the determination of galactose metabolism in a practical manner. We aimed to assess the level of galactose oxidation in both healthy and galactosemic Brazilian children. Twenty-one healthy children and seven children with galactosemia ranging from 1 to 7 years of age were studied. A breath test was used to quantitate 13CO2 enrichment in exhaled air before and at 30, 60, and 120 min after the oral administration of 7 mg/kg of an aqueous solution of 1-13C-galactose to all children. The molar ratios of 13CO2 and 12CO2 were quantified by the mass/charge ratio (m/z) of stable isotopes in each air sample by gas-isotope-ratio mass spectrometry. In sick children, the cumulative percentage of 13C from labeled galactose (CUMPCD) in the exhaled air ranged from 0.03% at 30 min to 1.67% at 120 min. In contrast, healthy subjects showed a much broader range in CUMPCD, with values from 0.4% at 30 min to 5.58% at 120 min. The study found a significant difference in galactose oxidation between children with and without galactosemia, demonstrating that the breath test is useful in discriminating children with GALT deficiencies

  2. Predicting 15N chemical shifts in proteins using the preceding residue-specific individual shielding surfaces from φ, ψi-1, and χ1torsion angles

    Empirical shielding surfaces are most commonly used to predict chemical shifts in proteins from known backbone torsion angles, φ and ψ. However, the prediction of 15N chemical shifts using this technique is significantly poorer, compared to that for the other nuclei such as 1Hα, 13Cα, and 13Cβ. In this study, we investigated the effects from the preceding residue and the side-chain geometry, χ1, on 15N chemical shifts by statistical methods. For an amino acid sequence XY, the 15N chemical shift of Y is expressed as a function of the amino acid types of X and Y, as well as the backbone torsion angles, φ and ψi-1. Accordingly, 380 empirical 'Preceding Residue Specific Individual (PRSI)' 15N chemical shift shielding surfaces, representing all the combinations of X and Y (except for Y=Pro), were built and used to predict 15N chemical shift from φ and ψi-1. We further investigated the χ1 effects, which were found to account for differences in 15N chemical shifts by ∼5 ppm for amino acids Val, Ile, Thr, Phe, His, Tyr, and Trp. Taking the χ1 effects into account, the χ1-calibrated PRSI shielding surfaces (XPRSI) were built and used to predict 15N chemical shifts for these amino acids. We demonstrated that 15N chemical shift predictions are significantly improved by incorporating the preceding residue and χ1 effects. The present PRSI and XPRSI shielding surfaces were extensively compared with three recently published programs, SHIFTX (Neal et al., 2003), SHIFTS (Xu and Case, 2001 and 2002), and PROSHIFT (Meiler, 2003) on a set of ten randomly selected proteins. A set of Java programs using XPRSI shielding surfaces to predict 15N chemical shifts in proteins were developed and are freely available for academic users at http://www.pronmr.com or by sending email to one of the authors Yunjun Wang

  3. Halogen effect on structure and 13C NMR chemical shift of 3,6-disubstituted-N-alkyl carbazoles

    Radula-Janik, Klaudia; Kupka, Teobald; Ejsmont, Krzysztof; Daszkiewicz, Zdzislaw; Sauer, Stephan P. A.

    2013-01-01

    Structures of selected 3,6-dihalogeno-N-alkyl carbazole derivatives were calculated at the B3LYP/6-311++G(3df,2pd) level of theory and their 13C NMR isotropic nuclear shieldings were predicted using density functional theory (DFT). The model compounds contained 9H-, N-methyl and N-ethyl derivatives....... The relativistic effect of Br and I atoms on nuclear shieldings was modeled using the spin-orbit ZORA method. Significant heavy atom shielding effects for the carbon atom directly bonded with bromine and iodine were observed (~ -10 and ~ -30 ppm while the other carbon shifts were practically...

  4. A Paradigm Shift: Supply Chain Collaboration and Competition in and between Europe’s Chemical Clusters

    Wassenhove, Luk; Lebreton, Baptiste; Letizia, Paolo

    2007-01-01

    textabstractWith the attention of the chemical industry focused on exploiting the low cost feedstocks in the Middle East and the growth markets of Brazil, Russia, India, China and South East Asia, this report provides a timely reminder to policy makers, chemical companies and logistics service providers of the significant opportunities for improving business potential in Europe’s chemical clusters. Europe is still the largest, most sophisticated global market for chemical products, with a wel...

  5. Determination of nuclear distances and chemical-shift anisotropy from 1H MAS NMR sideband patterns of surface OH groups

    Fenzke, Dieter; Hunger, Michael; Pfeifer, Harry

    A procedure is described which allows a separate determination of the proton-aluminum distance and of the chemical-shift anisotropy for the bridging OH groups of crystalline molecular sieves from their 'H MAS NMR sideband patterns. For the bridging OH groups which point into the 6-rings of the framework (line "c"), the 1H- 27Al distance could be determined to be 0.237 ± 0.004 and 0.234 ± 0.004 nm for molecular sieves of type H-Y and SAPO-5, respectively. In contrast, for the bridging OH groups of the 12-rings (line "b"), the corresponding distances are equal and distinctly larger, 0.248 ± 0.004 nm. Within the limits of error, the values of the chemical-shift anisotropy are equal (about 19 ± 2 ppm) except for line b of SAPO-5, which exhibits a much smaller value of 14.5 ± 2 ppm.

  6. Dynamics of the carbohydrate chains attached to the Fc portion of immunoglobulin G as studied by NMR spectroscopy assisted by selective 13C labeling of the glycans

    A systematic method for 13C labeling of the glycan of immunoglobulin G for NMR study has been developed. A mouse immunoglobulin of subclass IgG2b has been used for the experiment. On the basis of chemical shift and linewidth data, it has been concluded that (1) the mobility of the carbohydrate chain in IgG2b is comparable to that of the backbone polypeptide chain with the exception of the galactose residue at the nonreducing end of the Manα1-3 branch, which is extremely mobile and (2) agalactosylation does not induce any significant change in the mobility. The results obtained indicate that even in the agalactosyl form the glycans are buried in the protein. Biological significance of the NMR results obtained is also briefly discussed

  7. Multiple pancreatic metastases from clear cell renal carcinoma: diagnosis with chemical shift magnetic resonance imaging before surgery

    We present a case in which multiple pancreatic tumours were diagnosed as metastatic clear cell renal carcinomas with chemical shift MRI (CSI) before surgery. Radiologists may be unable to recognize the loss of intensity on CSI macroscopically. We believe that it is useful to make subtraction images and calculate signal intensity on CSI, even if the lesions are multiple metastatic tumours Copyright (2005) Blackwell Publishing Asia Pty Ltd

  8. Application of data mining tools for classification of protein structural class from residue based averaged NMR chemical shifts.

    Kumar, Arun V; Ali, Rehana F M; Cao, Yu; Krishnan, V V

    2015-10-01

    The number of protein sequences deriving from genome sequencing projects is outpacing our knowledge about the function of these proteins. With the gap between experimentally characterized and uncharacterized proteins continuing to widen, it is necessary to develop new computational methods and tools for protein structural information that is directly related to function. Nuclear magnetic resonance (NMR) provides powerful means to determine three-dimensional structures of proteins in the solution state. However, translation of the NMR spectral parameters to even low-resolution structural information such as protein class requires multiple time consuming steps. In this paper, we present an unorthodox method to predict the protein structural class directly by using the residue's averaged chemical shifts (ACS) based on machine learning algorithms. Experimental chemical shift information from 1491 proteins obtained from Biological Magnetic Resonance Bank (BMRB) and their respective protein structural classes derived from structural classification of proteins (SCOP) were used to construct a data set with 119 attributes and 5 different classes. Twenty four different classification schemes were evaluated using several performance measures. Overall the residue based ACS values can predict the protein structural classes with 80% accuracy measured by Matthew correlation coefficient. Specifically protein classes defined by mixed αβ or small proteins are classified with >90% correlation. Our results indicate that this NMR-based method can be utilized as a low-resolution tool for protein structural class identification without any prior chemical shift assignments. PMID:25758094

  9. Predicting Heats of Explosion of Nitroaromatic Compounds through NBO Charges and 15N NMR Chemical Shifts of Nitro Groups

    Ricardo Infante-Castillo

    2012-01-01

    Full Text Available This work presents a new quantitative model to predict the heat of explosion of nitroaromatic compounds using the natural bond orbital (NBO charge and 15N NMR chemical shifts of the nitro groups (15NNitro as structural parameters. The values of the heat of explosion predicted for 21 nitroaromatic compounds using the model described here were compared with experimental data. The prediction ability of the model was assessed by the leave-one-out cross-validation method. The cross-validation results show that the model is significant and stable and that the predicted accuracy is within 0.146 MJ kg−1, with an overall root mean squared error of prediction (RMSEP below 0.183 MJ kg−1. Strong correlations were observed between the heat of explosion and the charges (R2 = 0.9533 and 15N NMR chemical shifts (R2 = 0.9531 of the studied compounds. In addition, the dependence of the heat of explosion on the presence of activating or deactivating groups of nitroaromatic explosives was analyzed. All calculations, including optimizations, NBO charges, and 15NNitro NMR chemical shifts analyses, were performed using density functional theory (DFT and a 6-311+G(2d,p basis set. Based on these results, this practical quantitative model can be used as a tool in the design and development of highly energetic materials (HEM based on nitroaromatic compounds.

  10. Distinguishing between cystic teratomas and endometriomas of the ovary using chemical shift gradient echo magnetic resonance imaging

    Ishijima Hideyuki; Ishizaka Hiroshi; Inoue Tomio [Gunma University Hospital, Gunma (Japan). Depts. of Diagnostic Radiaology and Nuclear Medicine

    1996-02-01

    The purpose of this study was to evaluate the efficacy of chemical shift gradient echo magnetic resonance imaging (MRI) in distinguishing between cystic teratomas and endometriomas of the ovary, using a 1.5 T magnet. The study included 22 patients with 31 ovarian lesions (15 cystic teratomas and 16 endometriomas), which showed high signal intensity on T1-weighted spin echo images. Chemical shift gradient echo images with three different echo times (TE = 2.5, 4.5 and 6.5 ms) were obtained in all cases. Indices were calculated on the basis of the signal intensities of lesions on the chemical shift gradient echo images. All endometriomas had signal intensity indices of less than 2.1, while all cystic teratomas had signal intensity indices of 18.1 or greater. It was concluded that the method used in this study presents the following advantages: the acquisition time is short; it needs no special software; and it does not depend on magnetic field homogeneity. 11 refs., 4 figs.

  11. Chemical shift of Mn and Cr K-edges in X-ray absorption spectroscopy with synchrotron radiation

    D Joseph; A K Yadav; S N Jha; D Bhattacharyya

    2013-11-01

    Mn and Cr K X-ray absorption edges were measured in various compounds containing Mn in Mn2+, Mn3+ and Mn4+ oxidation states and Cr in Cr3+ and Cr6+ oxidation states. Few compounds possess tetrahedral coordination in the 1st shell surrounding the cation while others possess octahedral coordination. Measurements have been carried out at the energy dispersive EXAFS beamline at INDUS-2 Synchrotron Radiation Source at Raja Ramanna Centre for Advanced Technology, Indore. Energy shifts of ∼8–16 eV were observed for Mn K edge in the Mn-compounds while a shift of 13–20 eV was observed for Cr K edge in Cr-compounds compared to values in elementalMn and Cr, respectively. The different chemical shifts observed for compounds having the same oxidation state of the cation but different anions or ligands show the effect of different chemical environments surrounding the cations in determining their X-ray absorption edges in the above compounds. The above chemical effect has been quantitatively described by determining the effective charges on Mn and Cr cations in the above compounds.

  12. Solid-state 13C NMR analysis of Lower Cretaceous Baganuur (Mongolia) lignite

    Erdenetsogt, B.; Lee, I.; Lee, S.; Ko, Y.

    2009-12-01

    The transformation of plant matter into peat and coal has two steps, called the biochemical and geochemical stages of coalification. Biochemical coalification begins with the accumulation of dead vegetable matter and ends at the rank of subbituminous coal. The rank of Baganuur lignite ranges from lignite to subbituminous coal. It is transition between biochemical and physico-chemical coalification stages. The changes of chemical structure of coal during the transition between above mentioned two stages were studied by solid state CP/MAS 13C NMR. The most predominant alteration is the disappearance of the resonances from oxygenated aliphatic carbons (63 ppm), protonated aromatic carbons (114 ppm), oxygen-substituted aromatic carbons (144 ppm) and carbonyl carbons (195 ppm). In addition, the intensity of resonances from methoxyl carbons (56 ppm) and oxygenated aliphatic carbons (72 ppm) decreased. While the intensities of resonance from aliphatic (30 ppm), protonated aromatic (125 ppm) and carboxyl carbon (174 ppm) increased or remained almost constant. The relative percent of O-substituted aromatic carbons decreased by ~25% mainly due to the intensity loss of the peak at 144 ppm, indicating removal of O-containing functional groups substituted to aromatic carbons. It is consistent with the decreased relative percent (~75%) of the peak at 114 ppm from protonated aromatic carbons nearby oxygen-substituted aromatic carbons. In addition, the resonance from 125 ppm was shifted to 128 ppm and its relative area increased by ~20%, indicating replacement of O-substituent of aromatic rings by hydrogen or carbon. Protonated aromatic carbons at least two bond away from an oxygen-substituted aromatic carbons give a resonance at 125 ppm and carbon-substituted aromatic carbons give a resonance at 130-132 ppm. With the increase relative percent of C-substituted aromatic carbons, their resonance were overlapped with protonated aromatic carbons and shifted to higher ppm. A decreasing

  13. Solid-state 13C NMR study of banana liquid crystals - 3: Alkyl-tail-group packing environments of an acute-angle bent-core molecule in the hexagonal columnar and cubic phases

    Kurosu, Hiromichi; Endo, Yumi; Kimura, Saori; Hashimoto, Tomoko; Harada, Motoi; Lee, Eun-Woo; Sone, Masato; Watanabe, Junji; Kang, Sungmin

    2016-02-01

    Solid-state 13C nuclear magnetic resonance (NMR) measurements were performed on the hexagonal columnar and cubic phases of an acute-angle banana-shaped molecule, N(1,7)-S30. In the hexagonal columnar phase, three peaks appear at the NMR chemical shifts assigned to the internal methylene carbons of alkyl tails, indicating that the two alkyl tails have different packing structures, and one of the tails has two different conformations within a single molecule. Combined cross-polarization/magic-angle spinning and pulse saturation transfer/magic-angle spinning measurements show that one of the alkyl chains is located inside and the other is located outside the columnar structure. In the cubic phase, pulse saturation transfer/magic-angle spinning measurement shows that only one peak appears at the NMR chemical shifts assigned to the internal methylene carbons of alkyl tails, indicating that both of the alkyl chains are located outside the cubic structure.

  14. Soil nitrogen mineralisation and organic matter composition revealed by 13C NMR spectroscopy under repeated prescribed burning in eucalypt forests of south-east Queensland

    The effects of burning on in situ extractable nitrogen (NH+4-N+NO-3-N) and net N mineralisation following scheduled fuel reduction burns in repeatedly burnt dry and wet sclerophyll forest sites in south-east Queensland were assessed. In addition, soil organic matter composition in the wet sclerophyll site was assessed by 13C NMR spectroscopy. The results showed that at the dry sclerophyll site, extractable N and net N mineralisation for 1 year were largely unaffected by burning, while at the wet sclerophyll site, these parameters decreased. 13C NMR analysis of soil samples from the wet sclerophyll site revealed that there was a significant reduction in the proportion of O-alkyl (alkoxy/carbohydrate) C with increasing burning frequency. Statistically significant effects on the other chemical shift regions were not detected. The ratio of alkyl C to O-alkyl C, a proposed index of organic matter decomposition, increased with increasing burning frequency. A high ratio of alkyl C to O-alkyl C suggests low amounts of carbohydrates relative to waxes and cutins, which could in turn lead to slower mineralisation. The findings are in accord with this hypothesis. There were significant linear relationships between cumulative N mineralisation for 1 year and the proportions of alkyl C and O-alkyl C, and the ratio of alkyl C/O-alkyl C. Thus, in addition to reductions in substrate quantity (low organic C and total N for burnt soils), there was also an alteration of substrate quality as revealed by 13C NMR spectroscopy which is reflected in low N mineralisation. Copyright (1999) CSIRO Publishing

  15. Chiral effects on the /sup 13/C resonances of. cap alpha. -tocopherol and related compounds. A novel illustration of Newman's rule of six

    Brownstein, S.; Burton, G.W.; Hughes, L.; Ingold, K.U.

    1989-02-03

    The 100-MHz /sup 13/C NMR spectrum of (2R,4'R,8'R)-..cap alpha..-tocopherol (natural vitamin E) has been completely assigned with the aid of a number of selectively deuteriated (2R,4'R,8'R)-..cap alpha..-tocopherols. The /sup 13/C NMR spectrum of (2RS,4'RS,8'RS)-..cap alpha..-tocopherol (all-racemic, synthetic vitamin E) has also been measured. Many of the individual carbons in this all-racemic mixture of eight ..cap alpha..-tocopherol stereoisomers give more than one resonance with eight of the carbons (2-CH/sub 3/, 2',3',4',4'-CH/sub 3/, 5', 8', and 9') giving the maximum number of four resonances from each of the four enantiomeric pairs; these resonances have also been assigned. The structurally related 5'-hydroxy-2-(4',8',12'-trimethyltridecyl)-2,4,6,7-tetramethyl-2,3,-dihydrobenzofuran (HTDBF) has been synthesized for the first time in the 2R,4'R,8'R and 2S,4'R,8'R configurations and their /sup 13/C resonances have been assigned. In its all-racemic form this compound also shows up to four resonances from a single carbon. Related observations have been made with phytol and isophytol. A careful examination of these chirally induced chemical shift differences for the individual carbon atoms, ..delta.., reveals a bond-alternation effect with maxima at a separation of one, three, and five bonds from the closest chiral center and with the maximum at a five-bond separation being greater than that at a three-bond separation. 32 references, 2 figures, 4 tables.

  16. Chiral effects on the 13C resonances of α-tocopherol and related compounds. A novel illustration of Newman's rule of six

    The 100-MHz 13C NMR spectrum of (2R,4'R,8'R)-α-tocopherol (natural vitamin E) has been completely assigned with the aid of a number of selectively deuteriated (2R,4'R,8'R)-α-tocopherols. The 13C NMR spectrum of (2RS,4'RS,8'RS)-α-tocopherol (all-racemic, synthetic vitamin E) has also been measured. Many of the individual carbons in this all-racemic mixture of eight α-tocopherol stereoisomers give more than one resonance with eight of the carbons (2-CH3, 2',3',4',4'-CH3, 5', 8', and 9') giving the maximum number of four resonances from each of the four enantiomeric pairs; these resonances have also been assigned. The structurally related 5'-hydroxy-2-(4',8',12'-trimethyltridecyl)-2,4,6,7-tetramethyl-2,3,-dihydrobenzofuran (HTDBF) has been synthesized for the first time in the 2R,4'R,8'R and 2S,4'R,8'R configurations and their 13C resonances have been assigned. In its all-racemic form this compound also shows up to four resonances from a single carbon. Related observations have been made with phytol and isophytol. A careful examination of these chirally induced chemical shift differences for the individual carbon atoms, Δ, reveals a bond-alternation effect with maxima at a separation of one, three, and five bonds from the closest chiral center and with the maximum at a five-bond separation being greater than that at a three-bond separation. 32 references, 2 figures, 4 tables

  17. (H)N(COCA)NH and HN(COCA)NH experiments for 1H-15N backbone assignments in 13C/15N-labeled proteins

    Bracken, Clay; Palmer, Arthur G. III [Columbia University, Department of Biochemistry and Molecular Biophysics (United States); Cavanagh, John [New York State Department of Health, NMR Structural Biology Facility, Wadsworth Center (United States)

    1997-01-15

    Triple resonance HN(COCA)NH pulse sequences for correlating 1H(i), 15N(i),1H(i-1), and 15N(i-1) spins that utilize overlapping coherence transfer periods provide increased sensitivity relative to pulse sequences that utilize sequential coherence transfer periods. Although the overlapping sequence elements reduce the overall duration of the pulse sequences, the principal benefit derives from a reduction in the number of 180 deg. pulses. Two versions of the technique are presented: a 3D (H)N(COCA)NH experiment that correlates 15N(i),1H(i-1), and 15N(i-1) spins, and a 3D HN(COCA)NH experiment that correlates 1H(i), 15N(i),1H(i-1), and 15N(i-1) spins by simultaneously encoding the 1H(i) and 15N(i) chemical shifts during the t1 evolution period. The methods are demonstrated on a 13C/15N-enriched sample of the protein ubiquitin and are easily adapted for application to 2H/13C/15N-enriched proteins.

  18. Studies on molecular motion in lyotropic mesophases of hexaethylene glycol dodecyl ether-D2O system by 13C nuclear magnetic resonance

    The 13C spin-lattice relaxation time(T1) and the resonance line width corresponding to T2 * were measured for each of the carbons in hexaethylene glycol dodecyl ether-water(D2O) system, which exists as two distinct lyotropic mesophases(neat and middle phase). The line width is very narrow in the isotropic state, such as in organic solvents and in a lower concentration aqueous solution, whereas in a mesophase and in a higher concentration aqueous solution, the line width of the alkyl chain was broadened. Here the line widths for glycol carbons were about an order of magnitude smaller than for an alkyl chain, demonstrating the difference of molecular motion. The chemical shifts of the alkyl chain in the middle phase were different from those in the isotropic state; this difference was clearly shown in the spectrum of the middle/isotropic coexistent phase. 13C-T1 was not sensitive enough to differentiate between the isotropic and the lyotropic phase at room temperature. It was found that T1 did not equal T2 * for any of the methylene carbons, the difference being most marked for the terminal methyl carbon in the alkyl chain. The orientational order in the phases had an influence on the T2 * values. (author)

  19. XRD, FTIR and 13C CP/ MAS NMR Studies of Composite Comprising Poly(vinyl acetate)- silylated Si-MCM-41

    A composite structure based on silylated MCM-41 and Poly(vinyl acetate) (PVAc) was synthesized via solution intercalation. Poly(vinyl acetate)-silylated Si- MCM-41 composite were characterized by XRD, FTIR spectroscopy and 13C CP/ MAS NMR in order to determine the compatibility between PVAc and the silicate host. XRD study reveals that the framework of silylated Si-MCM-41 was not altered upon incorporation of PVAc. FTIR study showed that characteristic peak assigned to carbonyl group in PVAc was observed around 1741.6 cm-1 for all the composites indicating the presence of PVAc in the silylated Si-MCM-41. 13C CP/ MAS NMR showed the increase of line width of the peak assigned to C=O carbonyl group indicating the increase in randomness of polymer chains in confined space. The shifting of the C=O carbonyl groups is a sign of the change in chemical environment of the carbonyl owing to the interaction of PVAc with the silica matrix of silylated Si-MCM-41. (author)

  20. Short hydrogen bonds in salts of dicarboxylic acids; structural correlations from solid-state 13C and 2H NMR spectroscopy

    Kalsbeek, Nicoline; Schaumburg, Kjeld; Larsen, Sine

    1993-10-01

    Solid-state 13C and 2H NMR spectra are found to very suitable for characterizing the short Osbnd H...O hydrogen bonds observed in acid salts of dicarboxylic acids. The majority of the investigated compounds are acid salts of malonic, succinic and tartaric acid with monovalent cations derived from alkali metals and small aliphatic amines. They include systems with symmetric and asymmetric hydrogen bonds. Accurate structural information about their geometry is available from low-temperature X-ray diffraction data. The 13C chemical shifts of the C atoms in the different carboxy groups display a linear variation with the absolute difference between the two Csbnd O bond lengths. Theoretical ab initio calculations for model systems showed that the nuclear quadrupole coupling constant NQCC for 2H increases with increasing asymmetry of the hydrogen-bonded system. NQCC values for 2H in the short symmetric hydrogen-bonded systems are in the range 53-59 kHz compared with the larger values of up to 166kHz found in systems with longer asymmetric hydrogen bonds. The 2H NQCC values display a perfect linear dependence on the asymmetry of the hydrogen bond. 2H NQCC decreases with decreasing temperature in the symmetric hydrogen bonds showing that the corresponding potential has a single well.

  1. Cyanoacetylene and its /sup 13/C species: Evidence against relative isotope fractionation and improved /sup 12/C//sup 13/C abundance ratios

    Wannier, P.G.; Linke, R.A.

    1978-12-15

    We use the J=9..-->..8 transitions of HCCCN and its /sup 13/C substituted species to obtain several results in Sgr B2 and Ori A. In Sgr B2 we test for relative isotope fractionation among the three carbon sites in HCCCN and find none to a level of +- 5%. We verify that HCCCN has low opacity in both sources and derive /sup 12/C//sup 13/C isotope ratios of 50 (Ori A) and 22 (Sgr B2), an indication of galactic evolution of this important ratio. That the Orion ''plateau'' feature is especially prominent in HCCCN indicates a surprisingly large polyatomic molecule abundance for this energetic source. Our spectra also yield information about other chemical species, including a new transition of NH/sub 2/CN, an improved frequency of U81505, and a new unidentified line U79220. In addition, sensitive upper limits for NH/sub 2/CN, CH/sub 2/CO, and HNO in the Orion ''spike'' source imply that this cloud is relatively deficient in these species.

  2. Monitoring CO[subscript 2] Fixation Using GC-MS Detection of a [superscript 13]C-Label

    Hammond, Daniel G.; Bridgham, April; Reichert, Kara; Magers, Martin

    2010-01-01

    Much of our understanding of metabolic pathways has resulted from the use of chemical and isotopic labels. In this experiment, a heavy isotope of carbon, [superscript 13]C, is used to label the product of the well-known RuBisCO enzymatic reaction. This is a key reaction in photosynthesis that converts inorganic carbon to organic carbon; a process…

  3. Galactose oxidation using (13)C in healthy and galactosemic children.

    Resende-Campanholi, D R; Porta, G; Ferrioli, E; Pfrimer, K; Ciampo, L A Del; Junior, J S Camelo

    2015-03-01

    Galactosemia is an inborn error of galactose metabolism that occurs mainly as the outcome of galactose-1-phosphate uridyltransferase (GALT) deficiency. The ability to assess galactose oxidation following administration of a galactose-labeled isotope (1-(13)C-galactose) allows the determination of galactose metabolism in a practical manner. We aimed to assess the level of galactose oxidation in both healthy and galactosemic Brazilian children. Twenty-one healthy children and seven children with galactosemia ranging from 1 to 7 years of age were studied. A breath test was used to quantitate (13)CO2 enrichment in exhaled air before and at 30, 60, and 120 min after the oral administration of 7 mg/kg of an aqueous solution of 1-(13)C-galactose to all children. The molar ratios of (13)CO2 and (12)CO2 were quantified by the mass/charge ratio (m/z) of stable isotopes in each air sample by gas-isotope-ratio mass spectrometry. In sick children, the cumulative percentage of (13)C from labeled galactose (CUMPCD) in the exhaled air ranged from 0.03% at 30 min to 1.67% at 120 min. In contrast, healthy subjects showed a much broader range in CUMPCD, with values from 0.4% at 30 min to 5.58% at 120 min. The study found a significant difference in galactose oxidation between children with and without galactosemia, demonstrating that the breath test is useful in discriminating children with GALT deficiencies. PMID:25608239

  4. Galactose oxidation using 13C in healthy and galactosemic children

    D.R. Resende-Campanholi

    2015-03-01

    Full Text Available Galactosemia is an inborn error of galactose metabolism that occurs mainly as the outcome of galactose-1-phosphate uridyltransferase (GALT deficiency. The ability to assess galactose oxidation following administration of a galactose-labeled isotope (1-13C-galactose allows the determination of galactose metabolism in a practical manner. We aimed to assess the level of galactose oxidation in both healthy and galactosemic Brazilian children. Twenty-one healthy children and seven children with galactosemia ranging from 1 to 7 years of age were studied. A breath test was used to quantitate 13CO2 enrichment in exhaled air before and at 30, 60, and 120 min after the oral administration of 7 mg/kg of an aqueous solution of 1-13C-galactose to all children. The molar ratios of 13CO2 and 12CO2 were quantified by the mass/charge ratio (m/z of stable isotopes in each air sample by gas-isotope-ratio mass spectrometry. In sick children, the cumulative percentage of 13C from labeled galactose (CUMPCD in the exhaled air ranged from 0.03% at 30 min to 1.67% at 120 min. In contrast, healthy subjects showed a much broader range in CUMPCD, with values from 0.4% at 30 min to 5.58% at 120 min. The study found a significant difference in galactose oxidation between children with and without galactosemia, demonstrating that the breath test is useful in discriminating children with GALT deficiencies.

  5. Compartmentation of glycogen metabolism revealed from 13C isotopologue distributions

    Marin de Mas Igor

    2011-10-01

    Full Text Available Abstract Background Stable isotope tracers are used to assess metabolic flux profiles in living cells. The existing methods of measurement average out the isotopic isomer distribution in metabolites throughout the cell, whereas the knowledge of compartmental organization of analyzed pathways is crucial for the evaluation of true fluxes. That is why we accepted a challenge to create a software tool that allows deciphering the compartmentation of metabolites based on the analysis of average isotopic isomer distribution. Results The software Isodyn, which simulates the dynamics of isotopic isomer distribution in central metabolic pathways, was supplemented by algorithms facilitating the transition between various analyzed metabolic schemes, and by the tools for model discrimination. It simulated 13C isotope distributions in glucose, lactate, glutamate and glycogen, measured by mass spectrometry after incubation of hepatocytes in the presence of only labeled glucose or glucose and lactate together (with label either in glucose or lactate. The simulations assumed either a single intracellular hexose phosphate pool, or also channeling of hexose phosphates resulting in a different isotopic composition of glycogen. Model discrimination test was applied to check the consistency of both models with experimental data. Metabolic flux profiles, evaluated with the accepted model that assumes channeling, revealed the range of changes in metabolic fluxes in liver cells. Conclusions The analysis of compartmentation of metabolic networks based on the measured 13C distribution was included in Isodyn as a routine procedure. The advantage of this implementation is that, being a part of evaluation of metabolic fluxes, it does not require additional experiments to study metabolic compartmentation. The analysis of experimental data revealed that the distribution of measured 13C-labeled glucose metabolites is inconsistent with the idea of perfect mixing of hexose

  6. Synthesis of ring-13C-labelled and ring-demethylated retinals

    Efficient synthetic schemes are described for the preparation of the required mono- and di-13C labelled retinals based on simple 13C labelled starting materials. Results from solid-state 13C-NMR spectroscopic studies of the various ring-13C labelled bacteriorhodopsins and rhodopsins are discussed. 404 refs.; 74 figs.; 16 tabs

  7. Hyperpolarized 1-13C Pyruvate Imaging of Porcine Cardiac Metabolism shift by GIK Intervention

    Søvsø Szocska Hansen, Esben; Tougaard, Rasmus Stilling; Mikkelsen, Emmeli;

    Cardiac metabolism has gained considerable attention worldwide lately, both as a diagnostic and prognostication tool, as well as a novel target for treatment. As human trials involving hyperpolarized MR in the heart are imminent, we employed a clinically relevant, large animal model, and sought to...

  8. Cluster states and alpha particle condensation in 13C

    The structure of 13C is studied with the semi-microscopic cluster model, 3α+n orthogonality condition model (OCM). The energy spectra of four 1/2- states and three 1/2+ states up to Ex ~ 13 MeV are successfully reproduced, in particular, three monopole transition strengths are in fair agreement with the observed ones. We discuss the cluster states and alpha particle condensation in the 1/2± states appearing around the 12C+n, 9Be+α and 3α+n thresholds. (author)

  9. A (nearly) complete experimental linelist for 13C16O2, 16O13C18O, 16O13C17O, 13C18O2 and 17O13C18O by high-sensitivity CW-CRDS spectroscopy between 5851 and 7045 cm-1

    An experimental database for the 13C16O2, 16O13C18O, 16O13C17O, 13C18O2 and 17O13C18O isotopologues of carbon dioxide has been constructed on the basis of the high-sensitivity absorption spectrum of carbon dioxide with 99% enrichment in 13C recorded by CW-cavity ring down spectroscopy (CW-CRDS) between 5851 and 7045 cm-1. As a result of the achieved sensitivity (typical noise equivalent absorption αmin∼2-5x10-10 cm-1) combined with the high linearity and dynamics (more than four decades) of the CW-CRDS technique, the amount of spectroscopic information contained in these spectra was considerable. A total of 8639 transitions of the 13C16O2, 16O13C18O, 16O13C17O, 13C18O2 and 17O13C18O isotopologues with line strength as low as 5x10-29 cm/molecule were assigned. They belong to a total of 150 bands, while less than 20 bands were previously reported by Fourier transform spectroscopy. The excellent agreement between the predictions of the effective operators model and the observations has allowed using an automatic search program to assign the weaker lines observed in the congested spectrum. The spectroscopic parameters of the vibrational upper levels were obtained from a fit of the measured line positions. A number of resonance interactions were observed; in particular, several occurrences of interpolyad anharmonic couplings not included in the polyad model of effective Hamiltonian, were found to affect a few bands of the 16O13C18O and 16O13C17O isotopologues. In the list of 8639 transitions, which are provided as Supplementary material, line positions are experimental values (typical uncertainty in the order of 1x10-3 cm-1), while line strengths were calculated at 296 K by using the effective operators approach (typical uncertainty in the order of 5%). In the case of the 13C16O2 isotopologue, the reported transitions represent 99.65% of the total absorbance in the region considered

  10. Study of xanthates reaction from cellulose and polypeptides by 13 C NMR in the solid state

    This work has aimed to study chemical reactions of p-nitro benzyl cellulose xanthate (CelXNB) and 2,4-dinitrophenyl cellulose xanthate (CelXDNP) with amines, which produced cellulose thio carbamates. These compounds were characterized and identified by 13 C NMR in the solid state. The following reactions were also studied: CelXNB and poly alanine, CelXNB and lysozyme, CelXDNP and poly alanine, and CelXDNP and lysozyme. Then, their NMR spectra have been presented and analysed

  11. Real-time cardiac metabolism assessed with hyperpolarized [1-13C]acetate in a large-animal model

    Flori, Alessandra; Liserani, Matteo; Frijia, Francesca;

    2015-01-01

    Dissolution-dynamic nuclear polarization (dissolution-DNP) for magnetic resonance (MR) spectroscopic imaging has recently emerged as a novel technique for noninvasive studies of the metabolic fate of biomolecules in vivo. Since acetate is the most abundant extra- and intracellular short-chain fatty...... acid, we focused on [1-13C]acetate as a promising candidate for a chemical probe to study the myocardial metabolism of a beating heart. The dissolution-DNP procedure of Na[1-13C]acetate for in vivo cardiac applications with a 3 T MR scanner was optimized in pigs during bolus injection of doses of up to...

  12. Study of diabetes using naturally enriched 13C-glucose

    Following the work undertaken by Duchesne et al. since 1968, results from the use of a new method in the area of glucose metabolism are presented. Because of differences in their photosynthetic pathway, some vegetables, e.g., maize and sugarcane, are a little richer in 13C than most common foodstuffs. This weak, but significant, enrichment allows the use of maize glucose as a natural and nonradioactive tracer. In this procedure the variations of the 13C/12C ratio of exhaled CO2 are measured by mass spectrometry. By this method, we can follow, in man, the complete conversion of an oral glucose load into CO2 during a glucose tolerance test. At the same time, measurements of blood glucose and of respiratory quotient are made. They permit a useful comparison of the level of glucose in blood, the total amount of glucose consumed, and the fraction of exogenous glucose burned in the hours following oral administration. New information was obtained from these studies concerning glucose metabolism. The method was used in normal subjects and in obese and diabetic patients. Some of the diabetics were receiving an oral antidiabetic treatment. Significant differences were obtained in these cases, not only between them but also with the information given by the classical methods

  13. Isotopic separation of 13C by selective photodissociation of formaldehyde

    The aim of this work is to study the feasibility of the 13C isotopic separation by UV laser spectroscopy. The spectra of H212CO and H213CO have been recorded by a Fourier transform spectrometer between 28000 and 34000 cm-1. From these data has been carried out a systematic study of some lines by laser spectroscopy. The selectivity measurements have been compared with the obtained enrichment factors. Thus has been revealed in a quantitative way, the importance of the isotopic re-mixture phenomena and of the selectivity loss. The best enrichment factor has been measured at 29935,56 cm-1 (band: (2,14,1)). A final percentage of 42,1 % has been obtained in a reproducible way for 13C. The evolution of the enrichment factor has been characterized for a pressure range between 4,4 and 43 mbar. Above the radical dissociation threshold, it has not be possible to show a positive effect of NO on the enrichment factor. This negative result has been explained by a detailed kinetic study of the radical reactions (available literature). This experimental study has been completed by a bibliographic synthesis for understanding the formaldehyde photochemistry. All the processes able to influence the performance of this isotopic separation process have been gathered in this work in an exhaustive way. The radical dissociation threshold of H213CO have been calculated from molecular constants of the literature and from known thermodynamic data for H212CO. (O.M.)

  14. Solid-, Solution-, and Gas-state NMR Monitoring of 13C-Cellulose Degradation in an Anaerobic Microbial Ecosystem

    Yasuhiro Date

    2013-07-01

    Full Text Available Anaerobic digestion of biomacromolecules in various microbial ecosystems is influenced by the variations in types, qualities, and quantities of chemical components. Nuclear magnetic resonance (NMR spectroscopy is a powerful tool for characterizing the degradation of solids to gases in anaerobic digestion processes. Here we describe a characterization strategy using NMR spectroscopy for targeting the input solid insoluble biomass, catabolized soluble metabolites, and produced gases. 13C-labeled cellulose produced by Gluconacetobacter xylinus was added as a substrate to stirred tank reactors and gradually degraded for 120 h. The time-course variations in structural heterogeneity of cellulose catabolism were determined using solid-state NMR, and soluble metabolites produced by cellulose degradation were monitored using solution-state NMR. In particular, cooperative changes between the solid NMR signal and 13C-13C/13C-12C isotopomers in the microbial degradation of 13C-cellulose were revealed by a correlation heat map. The triple phase NMR measurements demonstrated that cellulose was anaerobically degraded, fermented, and converted to methane gas from organic acids such as acetic acid and butyric acid.

  15. Forward modeling of fluctuating dietary 13C signals to validate 13C turnover models of milk and milk components from a diet-switch experiment.

    Alexander Braun

    Full Text Available Isotopic variation of food stuffs propagates through trophic systems. But, this variation is dampened in each trophic step, due to buffering effects of metabolic and storage pools. Thus, understanding of isotopic variation in trophic systems requires knowledge of isotopic turnover. In animals, turnover is usually quantified in diet-switch experiments in controlled conditions. Such experiments usually involve changes in diet chemical composition, which may affect turnover. Furthermore, it is uncertain if diet-switch based turnover models are applicable under conditions with randomly fluctuating dietary input signals. Here, we investigate if turnover information derived from diet-switch experiments with dairy cows can predict the isotopic composition of metabolic products (milk, milk components and feces under natural fluctuations of dietary isotope and chemical composition. First, a diet-switch from a C3-grass/maize diet to a pure C3-grass diet was used to quantify carbon turnover in whole milk, lactose, casein, milk fat and feces. Data were analyzed with a compartmental mixed effects model, which allowed for multiple pools and intra-population variability, and included a delay between feed ingestion and first tracer appearance in outputs. The delay for milk components and whole milk was ~12 h, and that of feces ~20 h. The half-life (t½ for carbon in the feces was 9 h, while lactose, casein and milk fat had a t½ of 10, 18 and 19 h. The (13C kinetics of whole milk revealed two pools, a fast pool with a t½ of 10 h (likely representing lactose, and a slower pool with a t½ of 21 h (likely including casein and milk fat. The diet-switch based turnover information provided a precise prediction (RMSE ~0.2 ‰ of the natural (13C fluctuations in outputs during a 30 days-long period when cows ingested a pure C3 grass with naturally fluctuating isotope composition.

  16. 13C/12C isotope ratios in the organic matter forming the mucilaginous aggregates in the northern Adriatic Sea

    The occurrence of large mucilaginous aggregates is frequent during summer periods in the Northern Adriatic Sea. Their formation is not recurrent every summer but there are cluster of events as in 1988, 1989, 1991 and 1997, 1998, 2000, 2001 and 2002. Different aggregate size and morphologies have been described ranging from cm size marine snow to meters long clouds. Kilometers long layers may form at pycnoclines or at surface as a consequence of the accumulation of the aggregates. Riverine inputs produce 13C depleted organic matter in contrast to 13C enriched autochthonous marine organic matter. The δ13C is an indicator of the terrestrial (δ13C from -30 to -25 per mille versus VPDB) or marine (δ13C -23 to -15 per mille versus VPDB) origin of particulate organic matter. Humic substances may form as a consequence of the degradation of terrestrial organic matter or of phytoplankton. The δ13C values of humic substances range from -21.8 per mille to -22.8 per mille for open ocean humic substances and -22.8 per mille to 23.7 per mille for coastal humic substances. In order to establish the origin of the aggregates sampled during summer 2000, 2001 and 2002, the chemical characterization and the isotopic composition of organic carbon in different aggregates, plankton and humic substances were performed. The composition of the aggregates depends on the nature of the matter involved in the aggregation, therefore the δ13C of mucilage and humic fraction can explain the origin of the phenomenon. The mucilaginous aggregates were dialyzed on a CelluSep3500 membrane with a 3500 nominal weight cut off and freeze dried. The δ13C were analyzed by Isotope Ratio Mass Spectrometer (Delta Plus, Thermo Finnigan). Elemental analysis indicated in the aggregates: 11.1/29.4% of organic carbon, 2.8/5.0% of inorganic carbon and 0.7/3.7% of nitrogen. In order to characterize the nature of organic fraction of the aggregate, humic substance were extracted according to the method of

  17. Elucidating the trophodynamics of four coral reef fishes of the Solomon Islands using δ15N and δ13C

    Greenwood, N. D. W.; Sweeting, C. J.; Polunin, N. V. C.

    2010-09-01

    Size-related diet shifts are important characteristics of fish trophodynamics. Here, body size-related changes in muscle δ15N and δ13C of four coral reef fishes, Acanthurus nigrofuscus (herbivore), Chaetodon lunulatus (corallivore) , Chromis xanthura (planktivore) and Plectropomus leopardus (piscivore) were investigated at two locations in the Solomon Islands. All four species occupied distinct isotopic niches and the concurrent δ13C' values of C. xanthura and P. leopardus suggested a common planktonic production source. Size-related shifts in δ15N, and thus trophic level, were observed in C. xanthura, C. lunulatus and P. leopardus, and these trends varied between location, indicating spatial differences in trophic ecology. A literature review of tropical fishes revealed that positive δ15N-size trends are common while negative δ15N-size trends are rare. Size-δ15N trends fall into approximately equal groups representing size-based feeding within a food chain, and that associated with a basal resource shift and occurs in conjunction with changes in production source, indicated by δ13C. The review also revealed large scale differences in isotope-size trends and this, combined with small scale location differences noted earlier, highlights a high degree of plasticity in the reef fishes studied. This suggests that trophic size analysis of reef fishes would provide a productive avenue to identify species potentially vulnerable to reef impacts as a result of constrained trophic behaviour.

  18. Linear correlation of the barriers to pyramidal inversion of phosphorus with the 31P chemical shifts of acylphosphines

    The dependence of the inversion barriers (ΔG) of phosphorus compounds directly on a parameter of the inversion center, i.e., the chemical shift of the nucleus (delta31 P) were studied. The possibility of such an approach was justified by the correlation both of ΔG, and of delta31 P for phosphorus compounds with one and the same characteristics (the bond angles and electronegativities of the substituent). The acylphosphines (I-IX) were investigated in the range of variation of ΔG, accessible to dynamic NMR and in a fairly wide range of delta31 P

  19. Gradient-echo in-phase and opposed-phase chemical shift imaging: Role in evaluating bone marrow

    Chemical shift imaging (CSI) provides valuable information for assessing the bone marrow, while adding little to total examination time. In this article, we review the uses of CSI for evaluating bone marrow abnormalities. CSI can be used for differentiating marrow-replacing lesions from a range of non-marrow-replacing processes, although the sequence is associated with technical limitations and pitfalls. Particularly at 3 T, susceptibility artefacts are prevalent, and optimal technical parameters must be implemented with appropriate choices for echo times

  20. 1H to 13C Energy Transfer in Solid State NMR Spectroscopy of Natural Organic Systems

    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

  1. Metabolism and transport studies of exogenous compounds thanks to 13C uniform isotopic enrichment

    The study of many exogenous compounds does not raise difficulties when they are isolated, purified and in quantities sufficient for the usual detection methods used in biology (Chromatography, NMR, Mass Spectrometry, etc). When they are found in a biological fluid (blood, urines,..), they are often in infinitesimal amount such as the effect of their biological matrices or the background noise that make their detection and their quantification very delicate. The use of internal standards uniformly enriched with carbon 13 and/or nitrogen 15 makes it possible to obtain a signal more easily recognizable and identifiable thanks to the presence of the isotopes (peaks shifted in a mass spectrum for example). This is why, complementary to the analytical and biochemical studies of zearalenone (ZEN) metabolism, we were interested in building mass spectra of molecules enriched (rates between 0 and 1) by various isotopes (13C, 15N, 18O and 2H). In parallel we studied the influence of the 13C enrichment on the reactivity of a given molecule, from a theoretical and an experimental point of view. (author)

  2. 13C NMR spectra of trimethylene oxide and sulphide

    The 13C NMR spectra of trimethylene oxide and trimethylene sulphide have been recorded and analysed as second-order spectra. The values of all the C-H coupling constants with their signs are reported. The signs of the C-H coupling constants in trimethylene oxide were determined by selective irradiation experiments and theoretical calculations, while in trimethylene sulphide the signs were obtained directly from the analysis. The one-bond C-H coupling constants are approximately 3 Hz greater in trimethylene oxide than in trimethylene sulphide, while the absolute values of the two-bond and three-bond coupling constants, 2Jsub(cβH) and 3Jsub(CαH), are bout 1 Hz greater in the latter molecule. (orig.)

  3. 13C NMR studies of the molecular flexibility of antidepressants

    The solution dynamics of a series of clinically potent antidepressants have been investigated by measuring 13C NMR relaxation parameters. Correlation times and internal motional rates were calculated from spin-lattice relaxation times and nuclear Overhauser effects for the protonated carbons in mianserin, imipramine-like antidepressants, and amitriptyline-like antidepressants. These data were interpreted in terms of overall molecular tumbling, internal rotations, and inherent flexibility of these structures. Of particular interest was the conformational variability of the tricyclic nucleus of the tricyclic antidepressants, where the data indicated a fivefold difference in mobility of the dimethylene bridge of imipramine-like antidepressants relative to amitriptyline-like compounds. The implications of such a difference in internal motions is discussed in relation to previous NMR studies and to the reported differences in pharmacological activity of these antidepressants

  4. Millimeter and submillimeter wave spectra of 13C-glycolaldehydes

    Haykal, I.; Motiyenko, R. A.; Margulès, L.; Huet, T. R.

    2013-01-01

    Context. Glycolaldehyde (CH2OHCHO) is the simplest sugar and an important intermediate in the path toward forming more complex biologically relevant molecules. Astronomical surveys of interstellar molecules, such as those available with the very sensitive ALMA telescope, require preliminary laboratory investigations of the microwave and submillimeter-wave spectra of molecular species including new isotopologs - to identify these in the interstellar media. Aims: To achieve the detection of the 13C isotopologs of glycolaldehyde in the interstellar medium, their rotational spectra in the millimeter and submillimeter-wave regions were studied. Methods: The spectra of 13CH2OHCHO and CH2OH13CHO were recorded in the 150-945 GHz spectral range in the laboratory using a solid-state submillimeter-wave spectrometer in Lille. The observed line frequencies were measured with an accuracy of 30 kHz up to 700 GHz and of 50 kHz above 700 GHz. We analyzed the spectra with a standard Watson Hamiltonian. Results: About 10 000 new lines were identified for each isotopolog. The spectroscopic parameters were determined for the ground- and the three lowest vibrational states up to 945 and 630 GHz. Previous microwave assignments of 13CH2OHCHO were not confirmed. Conclusions: The provided line-lists and sets of molecular parameters meet the needs for a first astrophysical search of 13C-glycolaldehydes. Full Tables 3 and 4 are only available at the CDS via anonymous ftp to cdsarc.u-strasbg.fr (130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/549/A96

  5. Oligomeric complexes of some heteroaromatic ligands and aromatic diamines with rhodium and molybdenum tetracarboxylates: 13C and 15N CPMAS NMR and density functional theory studies.

    Leniak, Arkadiusz; Kamieński, Bohdan; Jaźwiński, Jarosław

    2015-05-01

    Seven new oligomeric complexes of 4,4'-bipyridine; 3,3'-bipyridine; benzene-1,4-diamine; benzene-1,3-diamine; benzene-1,2-diamine; and benzidine with rhodium tetraacetate, as well as 4,4'-bipyridine with molybdenum tetraacetate, have been obtained and investigated by elemental analysis and solid-state nuclear magnetic resonance spectroscopy, (13)C and (15)N CPMAS NMR. The known complexes of pyrazine with rhodium tetrabenzoate, benzoquinone with rhodium tetrapivalate, 4,4'-bipyridine with molybdenum tetrakistrifluoroacetate and the 1 : 1 complex of 2,2'-bipyridine with rhodium tetraacetate exhibiting axial-equatorial ligation mode have been obtained as well for comparison purposes. Elemental analysis revealed 1 : 1 complex stoichiometry of all complexes. The (15)N CPMAS NMR spectra of all new complexes consist of one narrow signal, indicating regular uniform structures. Benzidine forms a heterogeneous material, probably containing linear oligomers and products of further reactions. The complexes were characterized by the parameter complexation shift Δδ (Δδ = δcomplex  - δligand). This parameter ranged from around -40 to -90 ppm in the case of heteroaromatic ligands, from around -12 to -22 ppm for diamines and from -16 to -31 ppm for the complexes of molybdenum tetracarboxylates with 4,4'-bipyridine. The experimental results have been supported by a density functional theory computation of (15)N NMR chemical shifts and complexation shifts at the non-relativistic Becke, three-parameter, Perdew-Wang 91/[6-311++G(2d,p), Stuttgart] and GGA-PBE/QZ4P levels of theory and at the relativistic scalar and spin-orbit zeroth order regular approximation/GGA-PBE/QZ4P level of theory. Nucleus-independent chemical shifts have been calculated for the selected compounds. PMID:25614975

  6. 2H and 13C tracer studies of ethanol metabolism by Fourier transform 13C[2H, 1H] NMR difference spectroscopy

    A novel form of NMR difference spectroscopy has been developed to monitor low levels of deuterium incorporation in steroids resulting from ethanol metabolism. Ethanol specifically labeled with 13C and/or 2H was administered to bile fistula rats, and bile acids were collected, derivatized and separated. Subtracting 13C [1H] spectra from 13C[2H,1H] spectra of such samples, where the brackets imply complete noise decoupling of the indicated nuclei, results in difference spectra. These spectra display 13C resonances only from 13C spins which are J-coupled to 2H spins. Particular sites and extents of 2H incorporation along the steroid skeletons could thus be evaluated and compared with GC-MS analysis. A practical lower limit of approximately 20 nanomoles of 13C--2H couples could be observed using this technique, through use of sample microcells, quadrature detection and long-term signal averaging

  7. Apparent rate constant mapping using hyperpolarized [1-(13) C]pyruvate

    Khegai, O.; Schulte, R. F.; Janich, M. A.;

    2014-01-01

    Hyperpolarization of [1-13C]pyruvate in solution allows real-time measurement of uptake and metabolism using MR spectroscopic methods. After injection and perfusion, pyruvate is taken up by the cells and enzymatically metabolized into downstream metabolites such as lactate, alanine, and bicarbonate...... the build-up of downstream metabolites from the pyruvate substrate) and (ii) an effective decay rate (summarizing signal depletion due to repetitive excitation, T1-relaxation and backward conversion). The presented spectral and kinetic quantification were experimentally verified in vitro and in vivo...... shift frequencies are automatically estimated using a matching pursuit algorithm. Second, a time-discretized formulation of the two-site exchange kinetic model is used to quantify metabolite signal dynamics by two characteristic rate constants in the form of (i) an apparent build-up rate (quantifying...

  8. IRMS detection of testosterone manipulated with {sup 13}C labeled standards in human urine by removing the labeled {sup 13}C

    Wang, Jingzhu, E-mail: wangjingzhu@chinada.cn [National Anti-Doping Laboratory, China Anti-Doping Agency, Beijing (China); Yang, Rui [Sport Science College, Beijing Sport University Beijing, Beijing (China); Yang, Wenning [School of Pharmacy, Beijing University of Chinese Medicine, Beijing (China); Liu, Xin; Xing, Yanyi; Xu, Youxuan [National Anti-Doping Laboratory, China Anti-Doping Agency, Beijing (China)

    2014-12-10

    Highlights: • {sup 13}C labeled testosterone can be used to adjust the isotope ratio of testosterone. • The novel testosterone cannot be detected by the regular IRMS method in doping test. • A method was explored to remove the labeled {sup 13}C. • The established method can be used to detect the manipulated testosterone. - Abstract: Isotope ratio mass spectrometry (IRMS) is applied to confirm testosterone (T) abuse by determining the carbon isotope ratios (δ{sup 13}C value). However, {sup 13}C labeled standards can be used to control the δ{sup 13}C value and produce manipulated T which cannot be detected by the current method. A method was explored to remove the {sup 13}C labeled atom at C-3 from the molecule of androsterone (Andro), the metabolite of T in urine, to produce the resultant (A-nor-5α-androstane-2,17-dione, ANAD). The difference in δ{sup 13}C values between Andro and ANAD (Δδ{sup 13}C{sub Andro–ANAD}, ‰) would change significantly in case manipulated T is abused. Twenty-one volunteers administered T manipulated with different {sup 13}C labeled standards. The collected urine samples were analyzed with the established method, and the maximum value of Δδ{sup 13}C{sub Andro–ANAD} post ingestion ranged from 3.0‰ to 8.8‰. Based on the population reference, the cut-off value of Δδ{sup 13}C{sub Andro–ANAD} for positive result was suggested as 1.2‰. The developed method could be used to detect T manipulated with 3-{sup 13}C labeled standards.

  9. Accurate Measurements of Heteronuclear 13C-1H Coupling Constants by Phase-sensitive HMQC and HSQC Spectra%应用相敏HMQC和HSQC谱准确测定异核碳-氢偶合常数

    丁克洋

    2001-01-01

    Phase-sensitive HMQC(Heteronuclear Multiple-Quantum Coherence) and HSQC(Heteronuclear Single-Quantum Coherence) experiments with t1-noise reduction are proposed for the accurate measurement of heteronuclear one-bond 13C-1H coupling constants. The resulting 2D spectra give anti-phase splittings of heteronuclear one-bond couplings along ω2-dimension, so that the precision of coupling constant measurement is less subject to the residual t1-noise. By combining use of data-fitting procedure on a spectrum with enough digital resolution and signal-to-noise ratio, a precision of about 0.03 Hz can be achieved in the measurement of heteronuclear one-bond coupling constants. The proposed method can be very useful for the study of residual dipolar couplings caused by the alignment in high magnetic field and the dynamic frequency shift caused by the cross-correlation between chemical shift and spin dipolar interactions.

  10. The Influence of Plant Litter on Soil Water Repellency: Insight from 13C NMR Spectroscopy

    Cesarano, Gaspare; Incerti, Guido; Bonanomi, Giuliano

    2016-01-01

    Soil water repellency (SWR, i.e. reduced affinity for water owing to the presence of organic hydrophobic coatings on soil particles) has relevant hydrological implications because low rates of infiltration enhance water runoff, and untargeted diffusion of fertilizers and pesticides. Previous studies investigated the occurrence of SWR in ecosystems with different vegetation cover but did not clarify its relationships with litter biochemical quality. Here, we investigated the capability of different plant litter types to induce SWR by using fresh and decomposed leaf materials from 12 species, to amend a model sandy soil over a year-long microcosm experiment. Water repellency, measured by the Molarity of an Ethanol Droplet (MED) test, was tested for the effects of litter species and age, and compared with litter quality assessed by 13C-CPMAS NMR in solid state and elemental chemical parameters. All litter types were highly water repellent, with MED values of 18% or higher. In contrast, when litter was incorporated into the soil, only undecomposed materials induced SWR, but with a large variability of onset and peak dynamics among litter types. Surprisingly, SWR induced by litter addition was unrelated to the aliphatic fraction of litter. In contrast, lignin-poor but labile C-rich litter, as defined by O-alkyl C and N-alkyl and methoxyl C of 13C-CPMAS NMR spectral regions, respectively, induced a stronger SWR. This study suggests that biochemical quality of plant litter is a major controlling factor of SWR and, by defining litter quality with 13C-CPMAS NMR, our results provide a significant novel contribution towards a full understanding of the relationships between plant litter biochemistry and SWR. PMID:27022916

  11. Spectral density mapping at multiple magnetic fields suitable for 13C NMR relaxation studies

    Kadeřávek, Pavel; Zapletal, Vojtěch; Fiala, Radovan; Srb, Pavel; Padrta, Petr; Přecechtělová, Jana Pavlíková; Šoltésová, Mária; Kowalewski, Jozef; Widmalm, Göran; Chmelík, Josef; Sklenář, Vladimír; Žídek, Lukáš

    2016-05-01

    Standard spectral density mapping protocols, well suited for the analysis of 15N relaxation rates, introduce significant systematic errors when applied to 13C relaxation data, especially if the dynamics is dominated by motions with short correlation times (small molecules, dynamic residues of macromolecules). A possibility to improve the accuracy by employing cross-correlated relaxation rates and on measurements taken at several magnetic fields has been examined. A suite of protocols for analyzing such data has been developed and their performance tested. Applicability of the proposed protocols is documented in two case studies, spectral density mapping of a uniformly labeled RNA hairpin and of a selectively labeled disaccharide exhibiting highly anisotropic tumbling. Combination of auto- and cross-correlated relaxation data acquired at three magnetic fields was applied in the former case in order to separate effects of fast motions and conformational or chemical exchange. An approach using auto-correlated relaxation rates acquired at five magnetic fields, applicable to anisotropically moving molecules, was used in the latter case. The results were compared with a more advanced analysis of data obtained by interpolation of auto-correlated relaxation rates measured at seven magnetic fields, and with the spectral density mapping of cross-correlated relaxation rates. The results showed that sufficiently accurate values of auto- and cross-correlated spectral density functions at zero and 13C frequencies can be obtained from data acquired at three magnetic fields for uniformly 13C -labeled molecules with a moderate anisotropy of the rotational diffusion tensor. Analysis of auto-correlated relaxation rates at five magnetic fields represents an alternative for molecules undergoing highly anisotropic motions.

  12. Aspects regarding at 13C isotope separation column control using Petri nets system

    Boca, M. L.; Ciortea, M. E.

    2015-11-01

    This paper is intended to show that Petri nets can be also applicable in the chemical industry. It used linear programming, modeling underlying Petri nets, especially discrete event systems for isotopic separation, the purpose of considering and control events in real-time through graphical representations. In this paper it is simulate the control of 13C Isotope Separation column using Petri nets. The major problem with 13C comes from the difficulty of obtaining it and raising its natural fraction. Carbon isotopes can be obtained using many methods, one of them being the cryogenic distillation of carbon monoxide. Some few aspects regarding operating conditions and the construction of such cryogenic plants are known today, and even less information are available as far as the separation process modeling and control are concerned. In fact, the efficient control of the carbon monoxide distillation process represents a necessity for large-scale 13C production. Referring to a classic distillation process, some models for carbon isotope separation have been proposed, some based on mass, component and energy balance equations, some on the nonlinear wave theory or the Cohen equations. For modeling the system it was used Petri nets because in this case it is deal with discrete event systems. In use of the non-timed and with auxiliary times Petri model, the transport stream was divided into sections and these sections will be analyzed successively. Because of the complexity of the system and the large amount of calculations required it was not possible to analyze the system as a unitary whole. A first attempt to model the system as a unitary whole led to the blocking of the model during simulation, because of the large processing times.

  13. The Influence of Plant Litter on Soil Water Repellency: Insight from 13C NMR Spectroscopy.

    Gaspare Cesarano

    Full Text Available Soil water repellency (SWR, i.e. reduced affinity for water owing to the presence of organic hydrophobic coatings on soil particles has relevant hydrological implications because low rates of infiltration enhance water runoff, and untargeted diffusion of fertilizers and pesticides. Previous studies investigated the occurrence of SWR in ecosystems with different vegetation cover but did not clarify its relationships with litter biochemical quality. Here, we investigated the capability of different plant litter types to induce SWR by using fresh and decomposed leaf materials from 12 species, to amend a model sandy soil over a year-long microcosm experiment. Water repellency, measured by the Molarity of an Ethanol Droplet (MED test, was tested for the effects of litter species and age, and compared with litter quality assessed by 13C-CPMAS NMR in solid state and elemental chemical parameters. All litter types were highly water repellent, with MED values of 18% or higher. In contrast, when litter was incorporated into the soil, only undecomposed materials induced SWR, but with a large variability of onset and peak dynamics among litter types. Surprisingly, SWR induced by litter addition was unrelated to the aliphatic fraction of litter. In contrast, lignin-poor but labile C-rich litter, as defined by O-alkyl C and N-alkyl and methoxyl C of 13C-CPMAS NMR spectral regions, respectively, induced a stronger SWR. This study suggests that biochemical quality of plant litter is a major controlling factor of SWR and, by defining litter quality with 13C-CPMAS NMR, our results provide a significant novel contribution towards a full understanding of the relationships between plant litter biochemistry and SWR.

  14. The Influence of Plant Litter on Soil Water Repellency: Insight from 13C NMR Spectroscopy.

    Cesarano, Gaspare; Incerti, Guido; Bonanomi, Giuliano

    2016-01-01

    Soil water repellency (SWR, i.e. reduced affinity for water owing to the presence of organic hydrophobic coatings on soil particles) has relevant hydrological implications because low rates of infiltration enhance water runoff, and untargeted diffusion of fertilizers and pesticides. Previous studies investigated the occurrence of SWR in ecosystems with different vegetation cover but did not clarify its relationships with litter biochemical quality. Here, we investigated the capability of different plant litter types to induce SWR by using fresh and decomposed leaf materials from 12 species, to amend a model sandy soil over a year-long microcosm experiment. Water repellency, measured by the Molarity of an Ethanol Droplet (MED) test, was tested for the effects of litter species and age, and compared with litter quality assessed by 13C-CPMAS NMR in solid state and elemental chemical parameters. All litter types were highly water repellent, with MED values of 18% or higher. In contrast, when litter was incorporated into the soil, only undecomposed materials induced SWR, but with a large variability of onset and peak dynamics among litter types. Surprisingly, SWR induced by litter addition was unrelated to the aliphatic fraction of litter. In contrast, lignin-poor but labile C-rich litter, as defined by O-alkyl C and N-alkyl and methoxyl C of 13C-CPMAS NMR spectral regions, respectively, induced a stronger SWR. This study suggests that biochemical quality of plant litter is a major controlling factor of SWR and, by defining litter quality with 13C-CPMAS NMR, our results provide a significant novel contribution towards a full understanding of the relationships between plant litter biochemistry and SWR. PMID:27022916

  15. Application of δ13C and δ15N isotopic signatures of organic matter fractions sequentially separated from adjacent arable and forest soils to identify carbon stabilization mechanisms

    Kayler, Z.E.; Kaiser, M; Gessler, A.; Ellerbrock, R. H.; M. Sommer

    2011-01-01

    Identifying the chemical mechanisms behind soil carbon bound in organo-mineral complexes is necessary to determine the degree to which soil organic carbon is stabilized belowground. Analysis of δ13C and δ15N isotopic signatures of stabilized OM fractions along with soil mineral characteristics may yield important information about OM-mineral associations and their processing history. We anlayzed the δ13C and δ15N isotopic signatures from two organic matter (OM) fractio...

  16. The 'Nuts and Bolts' of 13C NMR Spectroscopy at Elevated-Pressures and -Temperatures for Monitoring In Situ CO2 Conversion to Metal Carbonates

    Moore, J. K.; Surface, J. A.; Skemer, P. A.; Conradi, M. S.; Hayes, S. E.

    2013-12-01

    We will present details of newly-constructed specialized NMR designed to conduct in situ elevated-pressure, elevated-temperature 13C NMR studies on unmixed slurries of minerals in the presence of CO2 or other gases. This static probe is capable of achieving 300 bar, 300C conditions, and it is designed to spectroscopically examine 13C signals in mixtures of solids, liquids, gases, and supercritical fluids. Ultimately, our aim is to monitor CO2 uptake in both ultramafic rocks and in more porous geological materials to understand the mechanisms of chemisorption as a function of temperature, pressure and pH. We will give details of the hardware setup, and we will show a variety of static in situ NMR, as well as ex situ 'magic-angle spinning' NMR to show the analyses that are possible of minerals in pure form and in mixtures. In addition, specific NMR pulse sequences, techniques, and modeling will be described in detail. In this in situ NMR probe, we are able to simulate processes at geologically relevant fluid pressures and temperatures, monitoring the kinetics of CO2 conversion to carbonates. The in situ NMR experiments consist of heterogeneous mixtures of rock, salty brine solution, and moderate pressure CO2 gas at elevated temperatures. The purpose of studying these reactions is to determine conditions that affect the efficacy of carbonate formation in various targeted geological reservoirs (i.e., peroditite, or others). Via 13C NMR, we have spectroscopically characterized and quantified the conversion of CO2 to magnesium carbonate and calcium carbonate minerals, including metastable intermediates (such as hydromagnesite, or dypingite in the case of magnesium carbonate species, or vaterite in the case of calcium carbonate species). Such species are distinguishable from a combination of the 13C isotropic chemical shift, the static 13C lineshape, and changes in spin-lattice (T1) relaxation times. We will demonstrate that NMR can be used for quantitative

  17. Anisotropy of the Chemical Shift Tensor for Fluorines in UF6 : Application to the Fluorine Atom Movement Model

    R. Blinc et al. have made an initial study of polycrystalline uranium hexafluoride using the magnetic resonance of fluorine at 40 Mc/s. The low-temperattire spectrum (t 6 octahedron has one long axis and two short axes, the fluorine atoms are divided among two different types of site. The change in the spectrum with temperature (coalescence of the two lines) suggests movement of the fluorine atoms between the two types of site. By repeating these experiments at 56.4 Mc/s and 94 Mc/s, we have been able to demonstrate the existence of considerable axial anisotropy of the chemical shift tensor (about 650 ppm). The absorption line obtained for a powder in these conditions is complex, and to study it we must envisage a line-shape function f(h), which is the probability that a grain of powder is so orientated that it resonates for the value h of the field. In the absence of movement (low-temperature spectrum) the line-shape function for each of the two lines (corresponding to the two types of site) is of the form obtained for equivalent atoms. It is known that the parameters of chemical shift tensors give information on chemical bond character. We are thus led, for example, to attribute a considerable ionic character (I ≃ 1/2) to the bonds between the uranium and the two most distant fluorine atoms. In the presence of movement the line-shape function is very different, and depends on the type of movement. For UF6, study of the shape of the single line (t > 20°C) in cases where we have anisotropy, shows that the fluorine atoms of the same molecule interchange with each other, each atom remaining in each of the positions for about 5 μsec at 30°C, with an activation energy of about 0.5 eV. (author)

  18. Proton exchange and temperature studies of pyrazole in dimethyl-d6 sulfoxide by 13C NMR

    The 13C NMR shifts of all the carbons in pyrazole have been observed at room temperature. This paper reports the kinetic data available from the temperature-induced collapse of the C-3, C-5 NMR peaks. ΔG2+ similarly ordered 7.0 kcal/mol, and ΔS2+ similarly ordered -25.0 cal/deg for the virtual tautomerism of pyrazole in SO-d6. Temperature-induced 13C DM shofts for the solvent and for pyrazole were also determined to be +1.47 x 10-3 and +2.0 x 10-3 ppM/deg for C-4 and the center of the C-3, C-5 peaks, respectively. The solvent shift for 13C with temperature is +11.59 +- 10-3 ppM/deg for the CD3 in DM SO-d6 and +3.22 x 10-3 ppM/deg for the deuterium in Me2SO-d6. Rapid exchange of pyrazole observed earlier by several workers in the solvent Me2SO-d6 is attributed to acid impurities present in previous samples. 3 tables

  19. The synthesis of [2-13C]2-nitropropane at room temperature and at atmospheric pressure

    Jacquemijns M; Zomer G

    1990-01-01

    In this report the synthesis of [2-13C]2-nitropropane at room temperature is described. [2-13C]Acetone was converted into the oxime with hydroxy hydrochloridelamine and sodium carbonate. Treatment with hypobromic acid resulted in 2-13C]2-bromo-2-nitropropane. Hydrogenation with sodium borohydride gave [2-13C]2-nitropropane in 14,3% overall yield.

  20. The synthesis of [2-13C]2-nitropropane at room temperature and at atmospheric pressure

    Jacquemijns M; Zomer G

    1990-01-01

    In this report the synthesis of [2-13C]2-nitropropane at room temperature is described. [2-13C]Acetone was converted into the oxime with hydroxy hydrochloridelamine and sodium carbonate. Treatment with hypobromic acid resulted in 2-13C]2-bromo-2-nitropropane. Hydrogenation with sodium borohydride

  1. High-field dissolution dynamic nuclear polarization of [1-13C]pyruvic acid

    Yoshihara, Hikari A. I.; Can, Emine; Karlsson, Magnus;

    2016-01-01

    [1-13C]pyruvate is the most widely used hyperpolarized metabolic magnetic resonance imaging agent. Using a custom-built 7.0 T polarizer operating at 1.0 K and trityl radical-doped [1-13C]pyruvic acid, unextrapolated solution-state 13C polarization greater than 60% was measured after dissolution a...

  2. Espiritu Santo, Vanuatu Stable Isotope (delta 18O, delta 13C) Data for 1806 to 1979

    National Oceanic and Atmospheric Administration, Department of Commerce — Site: Espiritu Santo Island, Vanuatu, 15S, 167E. 173 year record of d18O and d13C. Variable names: QSR Age, QSR 13C, QSR 18O, GRL Age, GRL Qtrly 13C, GRL Qtrly 18O,...

  3. High-throughput hyperpolarized 13C metabolic investigations using a multi-channel acquisition system

    Lee, Jaehyuk; Ramirez, Marc S.; Walker, Christopher M.; Chen, Yunyun; Yi, Stacey; Sandulache, Vlad C.; Lai, Stephen Y.; Bankson, James A.

    2015-11-01

    Magnetic resonance imaging and spectroscopy of hyperpolarized (HP) compounds such as [1-13C]-pyruvate have shown tremendous potential for offering new insight into disease and response to therapy. New applications of this technology in clinical research and care will require extensive validation in cells and animal models, a process that may be limited by the high cost and modest throughput associated with dynamic nuclear polarization. Relatively wide spectral separation between [1-13C]-pyruvate and its chemical endpoints in vivo are conducive to simultaneous multi-sample measurements, even in the presence of a suboptimal global shim. Multi-channel acquisitions could conserve costs and accelerate experiments by allowing acquisition from multiple independent samples following a single dissolution. Unfortunately, many existing preclinical MRI systems are equipped with only a single channel for broadband acquisitions. In this work, we examine the feasibility of this concept using a broadband multi-channel digital receiver extension and detector arrays that allow concurrent measurement of dynamic spectroscopic data from ex vivo enzyme phantoms, in vitro anaplastic thyroid carcinoma cells, and in vivo in tumor-bearing mice. Throughput and the cost of consumables were improved by up to a factor of four. These preliminary results demonstrate the potential for efficient multi-sample studies employing hyperpolarized agents.

  4. δ 13C evidence that high primary productivity delayed recovery from end-Permian mass extinction

    Meyer, K. M.; Yu, M.; Jost, A. B.; Kelley, B. M.; Payne, J. L.

    2011-02-01

    Euxinia was widespread during and after the end-Permian mass extinction and is commonly cited as an explanation for delayed biotic recovery during Early Triassic time. This anoxic, sulfidic episode has been ascribed to both low- and high-productivity states in the marine water column, leaving the causes of euxinia and the mechanisms underlying delayed recovery poorly understood. Here we use isotopic analysis to examine the changing chemical structure of the water column through the recovery interval and thereby better constrain paleoproductivity. The δ 13C of limestones from 5 stratigraphic sections in south China displays a negative gradient of approximately 4‰ from shallow-to-deep water facies within the Lower Triassic. This intense gradient declines within Spathian and lowermost Middle Triassic strata, coincident with accelerated biotic recovery and carbon cycle stabilization. Model simulations show that high nutrient levels and a vigorous biological pump are required to sustain such a large gradient in δ 13C, indicating that Early Triassic ocean anoxia and delayed recovery of benthic animal ecosystems resulted from too much productivity rather than too little.

  5. Liver fat quantification: Comparison of dual-echo and triple-echo chemical shift MRI to MR spectroscopy

    Satkunasingham, Janakan; Besa, Cecilia [Department of Radiology, Body MRI, Icahn School of Medicine at Mount Sinai, One Gustave Levy Place, New York, NY 10029 (United States); Translational and Molecular Imaging Institute, Icahn School of Medicine at Mount Sinai, One Gustave Levy Place, New York, NY 10029 (United States); Bane, Octavia [Translational and Molecular Imaging Institute, Icahn School of Medicine at Mount Sinai, One Gustave Levy Place, New York, NY 10029 (United States); Shah, Ami [Department of Radiology, Body MRI, Icahn School of Medicine at Mount Sinai, One Gustave Levy Place, New York, NY 10029 (United States); Oliveira, André de; Gilson, Wesley D.; Kannengiesser, Stephan [Siemens AG, Healthcare Sector, Erlangen (Germany); Taouli, Bachir, E-mail: bachir.taouli@mountsinai.org [Department of Radiology, Body MRI, Icahn School of Medicine at Mount Sinai, One Gustave Levy Place, New York, NY 10029 (United States); Translational and Molecular Imaging Institute, Icahn School of Medicine at Mount Sinai, One Gustave Levy Place, New York, NY 10029 (United States)

    2015-08-15

    Highlights: • We present a large cohort of patients who underwent dual and triple echo chemical shift imaging against multi-echo T{sub 2} corrected MR spectroscopy (MRS) for liver fat quantification. • Our data suggests that a triple-echo sequence is highly accurate for detection of liver fat, even in the presence of T{sub 2}{sup *} shortening, with minor discrepancies when compared with the advanced fat quantification method. - Abstract: Purpose: To assess the diagnostic value of MRI using dual-echo (2PD) and triple-echo (3PD) chemical shift imaging for liver fat quantification against multi-echo T{sub 2} corrected MR spectroscopy (MRS) used as the reference standard, and examine the effect of T{sub 2}{sup *} imaging on accuracy of MRI for fat quantification. Materials and methods: Patients who underwent 1.5 T liver MRI that incorporated 2PD, 3PD, multi-echo T{sub 2}{sup *} and MRS were included in this IRB approved prospective study. Regions of interest were placed in the liver to measure fat fraction (FF) with 2PD and 3PD and compared with MRS-FF. A random subset of 25 patients with a wide range of MRS-FF was analyzed with an advanced FF calculation method, to prove concordance with the 3PD. The statistical analysis included correlation stratified according to T{sub 2}{sup *}, Bland-Altman analysis, and calculation of diagnostic accuracy for detection of MRS-FF > 6.25%. Results: 220 MRI studies were identified in 217 patients (mean BMI 28.0 ± 5.6). 57/217 (26.2%) patients demonstrated liver steatosis (MRS-FF > 6.25%). Bland-Altman analysis revealed strong agreement between 3PD and MRS (mean ± 1.96 SD: −0.5% ± 4.6%) and weaker agreement between 2PD and MRS (4.7% ± 16.0%). Sensitivity of 3PD for diagnosing FF> 6.25% was higher than that of 2PD. 3PD-FF showed minor discrepancies (coefficient of variation <10%) from FF measured with the advanced method. Conclusion: Our large series study validates the use of 3PD chemical shift sequence for detection of

  6. Liver fat quantification: Comparison of dual-echo and triple-echo chemical shift MRI to MR spectroscopy

    Highlights: • We present a large cohort of patients who underwent dual and triple echo chemical shift imaging against multi-echo T2 corrected MR spectroscopy (MRS) for liver fat quantification. • Our data suggests that a triple-echo sequence is highly accurate for detection of liver fat, even in the presence of T2* shortening, with minor discrepancies when compared with the advanced fat quantification method. - Abstract: Purpose: To assess the diagnostic value of MRI using dual-echo (2PD) and triple-echo (3PD) chemical shift imaging for liver fat quantification against multi-echo T2 corrected MR spectroscopy (MRS) used as the reference standard, and examine the effect of T2* imaging on accuracy of MRI for fat quantification. Materials and methods: Patients who underwent 1.5 T liver MRI that incorporated 2PD, 3PD, multi-echo T2* and MRS were included in this IRB approved prospective study. Regions of interest were placed in the liver to measure fat fraction (FF) with 2PD and 3PD and compared with MRS-FF. A random subset of 25 patients with a wide range of MRS-FF was analyzed with an advanced FF calculation method, to prove concordance with the 3PD. The statistical analysis included correlation stratified according to T2*, Bland-Altman analysis, and calculation of diagnostic accuracy for detection of MRS-FF > 6.25%. Results: 220 MRI studies were identified in 217 patients (mean BMI 28.0 ± 5.6). 57/217 (26.2%) patients demonstrated liver steatosis (MRS-FF > 6.25%). Bland-Altman analysis revealed strong agreement between 3PD and MRS (mean ± 1.96 SD: −0.5% ± 4.6%) and weaker agreement between 2PD and MRS (4.7% ± 16.0%). Sensitivity of 3PD for diagnosing FF> 6.25% was higher than that of 2PD. 3PD-FF showed minor discrepancies (coefficient of variation <10%) from FF measured with the advanced method. Conclusion: Our large series study validates the use of 3PD chemical shift sequence for detection of liver fat in the clinical environment, even in the presence of

  7. Characterization of interface abruptness and material properties in catalytically grown III-V nanowires: exploiting plasmon chemical shift

    We have studied the assessment of chemical composition changes in III-V heterostructured semiconductor nanowires (NWs) with nanometric spatial resolution using transmission electron microscopy methods. These materials represent a challenge for conventional spectroscopy techniques due to their high sensitivity to electron beam irradiation. Radiation damage strongly limits the exposure time to a few (5-10) s, which reduces the sensitivity of the traditionally used x-ray spectroscopy. The rather low counting statistics results in significant errors bars for EDS chemical quantification (5-10%) and interface width determination (few nanometers). Plasmon chemical shift is ideal in this situation, as its measurement requires very short exposure times (∼100 ms) and the plasmon peak energy can be measured with high precision (∼20 meV in this work). This high sensitivity allows the detection of subtle changes (1-2%) in composition or even the detection of a small plasmon energy (33 ± 7) meV change along usually assumed pure and homogeneous InAs segments. We have applied this approach to measure interface widths in heterostructure InAs/InP NWs grown using metal catalysts and also to determine the timescale (∼10 s) in which beam irradiation induces material damage in these wires. In particular, we have detected small As concentrations (4.4 ± 0.5)% in the final InP segment close to the Au catalyst, which leads to the conclusion that As diffuses through the metal nanoparticle during growth.

  8. Acetylcholinesterase(AChE)-catalyzed hydrolysis of long-chain thiocholine esters:shift to a new chemical mechanism

    The kinetic and chemical mechanisms of AChE-catalyzed hydrolysis of short-chain thiocholine esters are relatively well documented. Up to propanoylthiocholine (PrTCh) the chemical mechanism is general acid-base catalysis by the active site catalytic triad. The chemical mechanism for the enzyme-catalyzed butyrylthio-choline(BuTCh) hydrolysis shifts to a parallel mechanism in which general base catalysis by E199 of direct water attack to the carbonyl carbon of the substrate. (Selwood, T., et al. J. Am. Chem. Soc. 1993, 115, 10477-10482) The long chain thiocholine esters such as hexanoylthiocholine (HexTCh), heptanoylthiocholine (HepTCh), and octanoylthiocholine (OcTCh) are hydrolyzed by electric eel acetylcholinesterase (AChE). The kinetic parameters are determined to show that these compounds have a lower Michaelis constant than BuTCh and the pH-Rate profile showed that the mechanism is similar to that of BuTCh hydrolysis. The solvent isotope effect and proton inventory of AChE-catalyzed hydrolysis of HexTCh showed that one proton transfer is involved in the transition state of the acylation stage. The relationship between the dipole moment and the Michaelis constant of the long chain thiocholine esters showed that the dipole moment is the most important factor for the binding of a substrate to the enzyme active site

  9. Acetylcholinesterase(AChE)-catalyzed hydrolysis of long-chain thiocholine esters:shift to a new chemical mechanism

    Jung, Dai Il; Shin, Young Ju [Donga Univ., Busan (Korea, Republic of); Lee, Eun Seok; Lee, Bong Ho [Hanbat National Univ., Daejon (Korea, Republic of); Moon, Tae Sung; Yoon, Chang No [Korea Institute of Science and Technology, Seoul (Korea, Republic of)

    2003-01-01

    The kinetic and chemical mechanisms of AChE-catalyzed hydrolysis of short-chain thiocholine esters are relatively well documented. Up to propanoylthiocholine (PrTCh) the chemical mechanism is general acid-base catalysis by the active site catalytic triad. The chemical mechanism for the enzyme-catalyzed butyrylthio-choline(BuTCh) hydrolysis shifts to a parallel mechanism in which general base catalysis by E199 of direct water attack to the carbonyl carbon of the substrate. (Selwood, T., et al. J. Am. Chem. Soc. 1993, 115, 10477-10482) The long chain thiocholine esters such as hexanoylthiocholine (HexTCh), heptanoylthiocholine (HepTCh), and octanoylthiocholine (OcTCh) are hydrolyzed by electric eel acetylcholinesterase (AChE). The kinetic parameters are determined to show that these compounds have a lower Michaelis constant than BuTCh and the pH-Rate profile showed that the mechanism is similar to that of BuTCh hydrolysis. The solvent isotope effect and proton inventory of AChE-catalyzed hydrolysis of HexTCh showed that one proton transfer is involved in the transition state of the acylation stage. The relationship between the dipole moment and the Michaelis constant of the long chain thiocholine esters showed that the dipole moment is the most important factor for the binding of a substrate to the enzyme active site.

  10. δ13C-CH4 reveals CH4 variations over oceans from mid-latitudes to the Arctic

    Yu, Juan; Xie, Zhouqing; Sun, Liguang; Kang, Hui; He, Pengzhen; Xing, Guangxi

    2015-09-01

    The biogeochemical cycles of CH4 over oceans are poorly understood, especially over the Arctic Ocean. Here we report atmospheric CH4 levels together with δ13C-CH4 from offshore China (31°N) to the central Arctic Ocean (up to 87°N) from July to September 2012. CH4 concentrations and δ13C-CH4 displayed temporal and spatial variation ranging from 1.65 to 2.63 ppm, and from -50.34% to -44.94% (mean value: -48.55 ± 0.84%), respectively. Changes in CH4 with latitude were linked to the decreasing input of enriched δ13C and chemical oxidation by both OH and Cl radicals as indicated by variation of δ13C. There were complex mixing sources outside and inside the Arctic Ocean. A keeling plot showed the dominant influence by hydrate gas in the Nordic Sea region, while the long range transport of wetland emissions were one of potentially important sources in the central Arctic Ocean. Experiments comparing sunlight and darkness indicate that microbes may also play an important role in regional variations.

  11. Determination of fructose metabolic pathways in normal and fructose-intolerant children: A 13C NMR study using [U-13C]fructose

    An inborn deficiency in the ability of aldolase B to split fructose 1-phosphate is found in humans with hereditary fructose intolerance (HFI). A stable isotope procedure to elucidate the mechanism of conversion of fructose to glucose in normal children and in HFI children has been developed. A constant infusion of D-[U-13C]fructose was given nasogastrically to control and to HFI children. Hepatic fructose conversion to glucose was estimated by examination of 13C NMR spectra of plasma glucose. Significantly lower values (∼3-fold) for fructose conversion to glucose were obtained for the HFI patients as compared to the controls. A quantitative determination of the metabolic pathways of fructose conversion to glucose was derived from 13C NMR measurement of plasma [13C]glucose isotopomer populations. The finding of isotopomer populations of three adjacent 13C atoms at glucose C-4 (13C3-13C4-13C5) suggests that there is a direct pathway from fructose, by-passing fructose-1-phosphate aldolase, to fructose 1,6-bisphosphate. The metabolism of fructose by fructose-1-phosphate aldolase activity accounts for only ∼50% of the total amount of hepatic fructose conversion to glucose. In view of the marked decline by 67% in synthesis of glucose from fructose in HFI subjects found in this study, the extent of [13C]glucose formation from a trace amount of [U-13C]fructose infused into the patient can be used as a safe and noninvasive diagnostic test for inherent faulty fructose metabolism

  12. Chemical structure elucidation from ¹³C NMR chemical shifts: efficient data processing using bipartite matching and maximal clique algorithms.

    Koichi, Shungo; Arisaka, Masaki; Koshino, Hiroyuki; Aoki, Atsushi; Iwata, Satoru; Uno, Takeaki; Satoh, Hiroko

    2014-04-28

    Computer-assisted chemical structure elucidation has been intensively studied since the first use of computers in chemistry in the 1960s. Most of the existing elucidators use a structure-spectrum database to obtain clues about the correct structure. Such a structure-spectrum database is expected to grow on a daily basis. Hence, the necessity to develop an efficient structure elucidation system that can adapt to the growth of a database has been also growing. Therefore, we have developed a new elucidator using practically efficient graph algorithms, including the convex bipartite matching, weighted bipartite matching, and Bron-Kerbosch maximal clique algorithms. The utilization of the two matching algorithms especially is a novel point of our elucidator. Because of these sophisticated algorithms, the elucidator exactly produces a correct structure if all of the fragments are included in the database. Even if not all of the fragments are in the database, the elucidator proposes relevant substructures that can help chemists to identify the actual chemical structures. The elucidator, called the CAST/CNMR Structure Elucidator, plays a complementary role to the CAST/CNMR Chemical Shift Predictor, and together these two functions can be used to analyze the structures of organic compounds. PMID:24655374

  13. NMR chemical shift analysis of the conformational transition between the monomer and tetramer of melittin in an aqueous solution.

    Miura, Yoshinori

    2016-05-01

    It is known that melittin in an aqueous solution undergoes a conformational transition between the monomer and tetramer by variation in temperature. The transition correlates closely with isomers of the proline residue; monomeric melittin including a trans proline peptide bond (trans-monomer) is involved directly in the transition, whereas monomeric melittin having a cis proline peptide bond (cis-monomer) is virtually not. The transition has been explored by using nuclear magnetic resonance spectroscopy in order to clarify the stability of the tetrameric conformation and the cooperativity of the transition. In the light of temperature dependence of chemical shifts of resonances from the isomeric monomers, we qualitatively estimate the temperature-, salt-, and concentration-dependence of the relative equilibrium populations of the trans-monomer and tetramer, and show that the tetramer has a maximum conformational stability at 30-45 °C and that the transition cooperativity is very low. PMID:26658745

  14. Topological Constraints on Chain-Folding Structure of Semicrystalline Polymer as Studied by 13C-13C Double Quantum NMR

    Hong, Youlee; Miyoshi, Toshikazu

    Chain-folding process is a prominent feature of long polymer chains during crystallization. Over the last half century, much effort has been paid to reveal the chain trajectory. Even though various chain-folding models as well as theories of crystallization at molecule levels have been proposed, they could be not reconciled due to the limited experimental evidences. Recent development of double quantum NMR with selective isotope labeling identified the chain-trajectory of 13C labeled isotactic poly(1-butene). The systematic experiments covered a wide range of parameters, i.e. kinetics, concentration, and molecular weight (Mw) . It was demonstrated that i) adjacent re-entry site was invariant as a function of crystallization temperature (Tc) , concentration, andMw, ii) long-range order of adjacent re-entry sequence is independence of kinetics at a given concentration while it decreased with increasing the polymer concentration at a given Tc due to the increased interruption between the chains, and iii) high Mw chains led to the multilayer folded structures in single crystals, but the melt state induced the identical short adjacent sequences of long and short polymer over a wide range of Tc due to the entanglements. The behaviors indicated that the topological restriction plays significant roles in the chain-folding process rather than the kinetics. The proposed framework to control the chain-folding structure presents a new perspective into the chain organization by either the intra- or inter-chain interaction. National Science Foundation Grants DMR-1105829 and 1408855.

  15. Synthesis of [8,9,10,11-13C4]leukotriene C4

    A ''one pot'' reduction of ethyl [1,2-13C2]bromoacetate with diisobutylaluminium hydride in dichloromethane, followed by reaction with triphenylphosphine, then triethylamine, yields [1,2-13C2]formylmethylenetriphenylphosphorane. Consecutive Wittig reactions of [1,2-13C2]formylmethylenetriphenylphosphorane with methyl 5(S),6(R)-epoxy-6-formylhexanoate and subsequent Wittig reactions with Z-3-nonen-1-triphenylphosphorane yields [8,9,10,11-13C4]LTA4 methyl ester, which is readily converted to [8,9,10,11-13C4]LTC4. (author)

  16. Modified 13C-urea breath test and the detection of helicobacter pylori

    The 13C-urea breath test (13C-UBT) is one of the most important non-invasive methods for detecting Helicobacter pylori infection. This examination is innocuous, simple, highly accurate. While the major drawback of 13C-UBT is the higher cost compared with other methods which hold back its widely using. The author review focuses on the most recent advances in the machines used to measure the 13C isotope and on the most important improvements about the UBT, such as the use of lower dose 13C-urea tablet or capsule, the modification of test meal, a shortened collection time of exhalation sample and so on

  17. Microscopic structures of ionic liquids 1-ethyl-3-methylimidazolium tetrafluoroborate in water probed by the relative chemical shift

    2010-01-01

    The relative chemical shifts (△δ) △δwere put forward to investigate the microscopic structure of 1-ethyl-3-methyl-imidazolium tetrafluoroborate (EmimBF4) during the dilution process with water.The concentration-dependent △δ(C2)H-(C4)H,△δ(C2)H-(C5)H and △δ(C4)H-(C5)H were analyzed.The results reveal that the variations of the microscopic structures of three aromatic protons are inconsistent.The strength of the H-bond between water and three aromatic protons follows the order:(C2)H···O > (C4)H···O > (C5)H···O.The concentration-dependent △δ(C6)H-(C7)H and △δ(C6)H-(C8)H indicate the formation of the H-bonds of (Calkyl)H···O is impossible,and more water is located around (C6)H than around (C7)H or (C8)H.The concentration-dependent △δ(C2)H-(C4)H and △δ(C2)H-(C5)H both increase rapidly when xwater > 0.9 or so,suggesting the ionic pairs of EmimBF4 are dissociated rapidly.The turning points of concentration-dependent △δ(C2)H-(C4)H and △δ(C2)H-(C5)H indicate that some physical properties of the EmimBF4/water mixtures also change at the corresponding concentration point.The microscopic structures of EmimBF4 in water could be clearly detected by the relative chemical shifts.

  18. Quantitative evaluation of vertebral marrow adipose tissue in postmenopausal female using MRI chemical shift-based water–fat separation

    Aim: To investigate the feasibility of assessing vertebral marrow adipose tissue using a magnetic resonance imaging (MRI) chemical shift-based water–fat separation technique at 3 T. Material and methods: A modified Dixon technique was performed to obtain the vertebral marrow fat fraction (FF) in a study of 58 postmenopausal females (age range 49.2–77.4 years), including 24 normal bone density, 19 osteopaenia, and 15 osteoporosis as documented with dual-energy X-ray absorptiometry. The reliability of FF measurements performed by two radiologists independently was evaluated with the intraclass correlation coefficient (ICC). Ten participants were scanned twice to assess the reproducibility of FF measurements. FF values were compared between each vertebral level and between groups. Results: The mean coefficient of variation of FF measurements was 2.1%. According to the ICC, the measurements were reliable (ICC = 0.900 for normal bone density, ICC = 0.937 for osteopaenia and ICC = 0.909 for osteoporosis, p < 0.001 for all). There was an inverse association between mean FF at L1–L4 vertebrae and lumbar spine BMD (r = −0.459, p = 0.006), which remained significant even after controlling for confounders (age, height, and body weight). FF values at different vertebral levels were significantly correlated to each other (r = 0.703–0.921, p < 0.05 for all). There was a general trend toward increased marrow adiposity for more inferior vertebral bodies. Patients with osteopaenia and osteoporosis had a higher marrow fat content compared with normal bone mass after adjusting for confounders, although no significant differences in each vertebral level and average marrow fat content were found between the osteopaenia and osteoporosis groups. Conclusion: Chemical shift-based water–fat separation enables the quantitation of vertebral marrow adiposity with excellent reproducibility, which appears to be a useful method to provide complementary information to osteoporosis

  19. Thickness-Dependent Binding Energy Shift in Few-Layer MoS2 Grown by Chemical Vapor Deposition.

    Lin, Yu-Kai; Chen, Ruei-San; Chou, Tsu-Chin; Lee, Yi-Hsin; Chen, Yang-Fang; Chen, Kuei-Hsien; Chen, Li-Chyong

    2016-08-31

    The thickness-dependent surface states of MoS2 thin films grown by the chemical vapor deposition process on the SiO2-Si substrates are investigated by X-ray photoelectron spectroscopy. Raman and high-resolution transmission electron microscopy suggest the thicknesses of MoS2 films to be ranging from 3 to 10 layers. Both the core levels and valence band edges of MoS2 shift downward ∼0.2 eV as the film thickness increases, which can be ascribed to the Fermi level variations resulting from the surface states and bulk defects. Grainy features observed from the atomic force microscopy topographies, and sulfur-vacancy-induced defect states illustrated at the valence band spectra imply the generation of surface states that causes the downward band bending at the n-type MoS2 surface. Bulk defects in thick MoS2 may also influence the Fermi level oppositely compared to the surface states. When Au contacts with our MoS2 thin films, the Fermi level downshifts and the binding energy reduces due to the hole-doping characteristics of Au and easy charge transfer from the surface defect sites of MoS2. The shift of the onset potentials in hydrogen evolution reaction and the evolution of charge-transfer resistances extracted from the impedance measurement also indicate the Fermi level varies with MoS2 film thickness. The tunable Fermi level and the high chemical stability make our MoS2 a potential catalyst. The observed thickness-dependent properties can also be applied to other transition-metal dichalcogenides (TMDs), and facilitates the development in the low-dimensional electronic devices and catalysts. PMID:27488185

  20. Local deposition of {sup 13}C tracer in the JET MKII-HD divertor

    Likonen, Jari, E-mail: jari.likonen@vtt.fi [Association EURATOM-TEKES, VTT, PO Box 1000, 02044 VTT, Espoo (Finland); Airila, M.I.; Coad, J.P.; Hakola, A.; Koivuranta, S.; Ahonen, E. [Association EURATOM-TEKES, VTT, PO Box 1000, 02044 VTT, Espoo (Finland); Alves, E.; Barradas, N. [Instituto Tecnológico e Nuclear, Sacavém 2686-953 (Portugal); Widdowson, A. [EURATOM/CCFE Fusion Association, Culham Science Centre, Abingdon, Oxon OX14 3DB (United Kingdom); Rubel, M. [Alfvén Laboratory, Royal Institute of Technology, Association EURATOM-VR, 100 44 Stockholm (Sweden); Brezinsek, S. [Institute of Energy and Climate Research – Plasma Physics, Forschungszentrum Jülich GmbH, Association EURATOM-FZJ, Partner in the Trilateral Euregio Cluster, D-52425 Jülich (Germany); Groth, M. [Association EURATOM-TEKES, Aalto University, 02015 Espoo (Finland)

    2013-07-15

    Migration and deposition of {sup 13}C have been investigated at JET by injecting {sup 13}C-labelled methane at the outer divertor base at the end of the 2009 campaign. The {sup 13}C deposition profile was measured with enhanced proton scattering (EPS) and secondary ion mass spectrometry (SIMS) techniques. A strong toroidal deposition band for {sup 13}C was observed experimentally on each of the analysed four outer divertor floor tiles. In addition, {sup 13}C was also found on the vertical edge of load bearing tile (LBT) and at the bottom of the LBT tile facing the puffing hole. Local {sup 13}C migration in the vicinity of the injection location was modelled by the ERO code. The ERO simulations also produced the strong toroidal {sup 13}C deposition band but there is strong deposition also on the vertical edge of the LBT tile and elsewhere on the horizontal part of the outer divertor floor tile.

  1. Solid-state /sup 13/C NMR and X-ray diffraction of dermatan sulfate

    Winter, W.T.; Taylor, M.G.; Stevens, E.S.; Morris, E.R.; Rees, D.A.

    1986-05-29

    Dermatan sulfate in the solid state has been studied by /sup 13/C CP/MAS nmr and X-ray diffraction in order to establish the ring conformation of the L-iduronate moiety. The solid state nmr spectrum is similar to the solution spectrum obtained previously, indicating that a ring conformation at least approximating to /sup 1/C/sub 4/ predominates in the solid state. X-ray powder diffraction data from the same sample indicate the presence of the 8-fold helix form previously observed by fiber diffraction, and interpreted in terms of a /sup 4/C/sub 1/ ring form. A likely explanation of the results is that a distorted /sup 1/C/sub 4/ L-iduronate ring conformation, not considered in the initial X-ray analysis, may emerge to provide a satisfactory interpretation of all available physical-chemical data.

  2. Solid-state 13C NMR and X-ray diffraction of dermatan sulfate

    Dermatan sulfate in the solid state has been studied by 13C CP/MAS nmr and X-ray diffraction in order to establish the ring conformation of the L-iduronate moiety. The solid state nmr spectrum is similar to the solution spectrum obtained previously, indicating that a ring conformation at least approximating to 1C4 predominates in the solid state. X-ray powder diffraction data from the same sample indicate the presence of the 8-fold helix form previously observed by fiber diffraction, and interpreted in terms of a 4C1 ring form. A likely explanation of the results is that a distorted 1C4 L-iduronate ring conformation, not considered in the initial X-ray analysis, may emerge to provide a satisfactory interpretation of all available physical-chemical data

  3. Computational Platform for Flux Analysis Using 13C-Label Tracing- Phase I SBIR Final Report

    Van Dien, Stephen J.

    2005-04-12

    Isotopic label tracing is a powerful experimental technique that can be combined with metabolic models to quantify metabolic fluxes in an organism under a particular set of growth conditions. In this work we constructed a genome-scale metabolic model of Methylobacterium extorquens, a facultative methylotroph with potential application in the production of useful chemicals from methanol. A series of labeling experiments were performed using 13C-methanol, and the resulting distribution of labeled carbon in the proteinogenic amino acids was determined by mass spectrometry. Algorithms were developed to analyze this data in context of the metabolic model, yielding flux distributions for wild-type and several engineered strains of M. extorquens. These fluxes were compared to those predicted by model simulation alone, and also integrated with microarray data to give an improved understanding of the metabolic physiology of this organism.

  4. Synthesis and quality control of {sup 13}C-enriched urea for Helicobacter pylori (HP) diagnosis

    Sant Ana Filho, Carlos R.; Tavares, Claudineia R.O.; Ferreira, Andre V.; Prestes, Cleber V.; Bendassolli, Jose A., E-mail: jab@cena.usp.br [Centro de Energia Nuclear na Agricultura (CENA/USP), Piracicaba, SP (Brazil)

    2013-08-01

    The aim of the study was to synthesize the urea ({sup 13}CO(NH{sub 2}){sub 2}), with 99% {sup 13}C atoms, and to perform a quality analysis for the diagnosis (breath test) of Helicobacter pylori. Furthermore, the process was submitted to economic analysis. The reaction was performed in a stainless steel reactor, lined with polytetrafluoroethylene, under low pressure and temperature. The synthesis method was shown to be appropriate (2.35 g; 81.9% yield), evidenced by physico-chemical and microbiological results, according to Brazilian legislation. The production and diagnosis costs were competitive compared with national and international market values, rendering this a valuable tool in clinical medicine. (author)

  5. Acetylcholinesterase-catalyzed acetate - water oxygen exchange studied by 13C-NMR

    The kinetics of the oxygen exchange reaction between [l-13C,18O2]acetate and H216O catalyzed by homogeneous acetyl-cholinesterase from the electric eel, Electrophorus electricus, was studied using the 18O-isotope-induced shift on 13C-nuclear magnetic resonance spectra. Pseudo-first-order rate constants for the exchange reactions were determined at pH values from 4.5 to 8. The exchange reaction exhibits a maximum at pH 5.8. The apparent catalytic rate constant for the exchange reaction is 102 to 104 times smaller than that for the deacylation of the acetyl-enzyme intermediate over the pH range tested. Oxygen exchange occurs by a random sequential pathway rather than by multiple (coupled) exchange. The inhibition of acetylcholinesterase by sodium acetate showed a sigmoidal dependence on pH, with K/sub i/ increasing 2.5 orders of magnitude over the pH range. Protonation of an active site residue having an apparent pKa of 6.8 is associated with an increase in acetate binding. Deacylation also exhibits a sigmoidal dependence on [H+]. The experimental data fits titration curves with inflection points at 5.0 +/- 0.3 and 6.7 +/-0.1. Results support the role of histidine in acetylation of the active site serine, but the conjugate base of another active site residue with a pKa of 5.0 appears necessary for maximal catalytic activity in both the deacylation and exchange reactions

  6. Chemical shift measurements of chlorine K X-ray spectra using a high-resolution PIXE system

    A high-efficiency high-resolution wavelength-dispersive spectrograph with a von-Hamos configuration was developed for chemical state identification of elements in environmental samples using PIXE analysis. To evaluate the performance of this system, chlorine K X-ray spectra for NaCl, NH4Cl and polyvinylchloride (PVC) targets were measured and compared. Also, to study the applicability to environmental mixed samples, mixtures of NaCl and NH4Cl with different mixing ratios were measured. Through observation of Cl Kα1 X-ray from NaCl, the energy resolution of the system was determined to be 1.1 eV. For the NaCl sample, a Kβx line was observed at an energy, which is higher than that of the Kβ main peak by 2 eV, whereas no Kβx emission was observed for the NH4Cl sample. The chemical shift of the Kβ main peak for PVC relative to that for NaCl was about 1.2 eV. For NaCl-NH4Cl mixture targets, the relative intensity of Kβx satellite to the Kβ main line provided an indication of mixing ratio. Energies and relative intensity of Cl Kβ X-ray satellites for NaCl and NH4Cl samples calculated by a simple molecular-orbital method agreed only qualitatively with the experimental results

  7. Site-specific {sup 13}C content by quantitative isotopic {sup 13}C Nuclear Magnetic Resonance spectrometry: A pilot inter-laboratory study

    Chaintreau, Alain; Fieber, Wolfgang; Sommer, Horst [Firmenich SA, Corporate R and D Division, P.O. Box 239, 1211 Geneva 8 (Switzerland); Gilbert, Alexis; Yamada, Keita [Department of Environmental Chemistry and Engineering, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8503 (Japan); Yoshida, Naohiro [Department of Environmental Chemistry and Engineering, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8503 (Japan); Earth-Life Science Institute, Tokyo Institute of Technology, Meguro, Tokyo 152-8551 (Japan); Pagelot, Alain [Bruker Biospin SAS, 34 rue de l‘Industrie, 67166 Wissembourg Cedex (France); Moskau, Detlef; Moreno, Aitor [Bruker Biospin AG, Industriestrasse 26, 8117 Fällanden (Switzerland); Schleucher, Jürgen [Department of Medical Biochemistry and Biophysics, Umeå University, S-90187 Umeå (Sweden); Reniero, Fabiano; Holland, Margaret; Guillou, Claude [European Commission, Joint Research Centre – Institute for Health and Consumer Protection, via E. Fermi 2749, I-21027 Ispra (Italy); Silvestre, Virginie; Akoka, Serge [EBSI team, Interdisciplinary Chemistry: Synthesis, Analysis, Modelling (CEISAM), University of Nantes-CNRS UMR 6230, 2 rue de la Houssinière, BP 92208, F-44322 Nantes cedex 3 (France); Remaud, Gérald S., E-mail: gerald.remaud@univ-nantes.fr [EBSI team, Interdisciplinary Chemistry: Synthesis, Analysis, Modelling (CEISAM), University of Nantes-CNRS UMR 6230, 2 rue de la Houssinière, BP 92208, F-44322 Nantes cedex 3 (France)

    2013-07-25

    Graphical abstract: -- Highlights: •First ring test on isotopic {sup 13}C NMR spectrometry. •Evaluation of the intra- and inter-variability of the NMR spectrometers used. •Definition of a protocol for qualification of the performance of the spectrometer. -- Abstract: Isotopic {sup 13}C NMR spectrometry, which is able to measure intra-molecular {sup 13}C composition, is of emerging demand because of the new information provided by the {sup 13}C site-specific content of a given molecule. A systematic evaluation of instrumental behaviour is of importance to envisage isotopic {sup 13}C NMR as a routine tool. This paper describes the first collaborative study of intra-molecular {sup 13}C composition by NMR. The main goals of the ring test were to establish intra- and inter-variability of the spectrometer response. Eight instruments with different configuration were retained for the exercise on the basis of a qualification test. Reproducibility at the natural abundance of isotopic {sup 13}C NMR was then assessed on vanillin from three different origins associated with specific δ{sup 13}C{sub i} profiles. The standard deviation was, on average, between 0.9 and 1.2‰ for intra-variability. The highest standard deviation for inter-variability was 2.1‰. This is significantly higher than the internal precision but could be considered good in respect of a first ring test on a new analytical method. The standard deviation of δ{sup 13}C{sub i} in vanillin was not homogeneous over the eight carbons, with no trend either for the carbon position or for the configuration of the spectrometer. However, since the repeatability for each instrument was satisfactory, correction factors for each carbon in vanillin could be calculated to harmonize the results.

  8. Development of multicomponent hybrid density functional theory with polarizable continuum model for the analysis of nuclear quantum effect and solvent effect on NMR chemical shift

    We have developed the multicomponent hybrid density functional theory [MC-(HF+DFT)] method with polarizable continuum model (PCM) for the analysis of molecular properties including both nuclear quantum effect and solvent effect. The chemical shifts and H/D isotope shifts of the picolinic acid N-oxide (PANO) molecule in chloroform and acetonitrile solvents are applied by B3LYP electron exchange-correlation functional for our MC-(HF+DFT) method with PCM (MC-B3LYP/PCM). Our MC-B3LYP/PCM results for PANO are in reasonable agreement with the corresponding experimental chemical shifts and isotope shifts. We further investigated the applicability of our method for acetylacetone in several solvents

  9. Biosynthetically directed fractional 13C labeling facilitates identification of Phe and Tyr aromatic signals in proteins

    Analysis of 2D [13C,1H]-HSQC spectra of biosynthetic fractionally 13C labeled proteins is a reliable, straightforward means to obtain stereospecific assignments of Val and Leu methyl sites in proteins. Herein we show that the same fractionally labeled protein sample facilitates observation and identification of Phe and Tyr aromatic signals. This is the case, in part, because the fractional 13C labeling yields aromatic rings in which some of the 13C-13C J-couplings, present in uniformly labeled samples, are absent. Also, the number of homonuclear J-coupling partners differs for the δ-, ε- and ζ-carbons. This enabled us to vary their signal intensities in distinctly different ways by appropriately setting the 13C constant-time period in 2D [13C,1H]-HSQC spectra. We illustrate the application of this approach to an 18 kDa protein, c-VIAF, a modulator of apoptosis. In addition, we show that cancellation of the aromatic 13C CSA and 13C-1H dipolar interactions can be fruitfully utilized in the case of the fractionally labeled sample to obtain high resolution 13C constant-time spectra with good sensitivity

  10. Performance evaluation of quantitative adiabatic (13)C NMR pulse sequences for site-specific isotopic measurements.

    Thibaudeau, Christophe; Remaud, Gérald; Silvestre, Virginie; Akoka, Serge

    2010-07-01

    (2)H/(1)H and (13)C/(12)C site-specific isotope ratios determined by NMR spectroscopy may be used to discriminate pharmaceutically active ingredients based on the synthetic process used in production. Extending the Site-specific Natural Isotope Fractionation NMR (SNIF-NMR) method to (13)C is highly beneficial for complex organic molecules when measurements of (2)H/(1)H ratios lead to poorly defined molecular fingerprints. The current NMR methodology to determine (13)C/(12)C site-specific isotope ratios suffers from poor sensitivity and long experimental times. In this work, several NMR pulse sequences based on polarization transfer were evaluated and optimized to measure precise quantitative (13)C NMR spectra within a short time. Adiabatic 180 degrees (1)H and (13)C pulses were incorporated into distortionless enhancement by polarization transfer (DEPT) and refocused insensitive nuclei enhanced by polarization transfer (INEPT) to minimize the influence of 180 degrees pulse imperfections and of off-resonance effects on the precision of the measured (13)C peak areas. The adiabatic DEPT sequence was applied to draw up a precise site-specific (13)C isotope profile of ibuprofen. A modified heteronuclear cross-polarization (HCP) experiment featuring (1)H and (13)C spin-locks with adiabatic 180 degrees pulses is also introduced. This sequence enables efficient magnetization transfer across a wide (13)C frequency range although not enough for an application in quantitative (13)C isotopic analysis. PMID:20527737

  11. Individual protein balance strongly influences δ15N and δ13C values in Nile tilapia, Oreochromis niloticus

    Gaye-Siessegger, Julia; Focken, Ulfert; Abel, Hansjörg; Becker, Klaus

    Although stable isotope ratios in animals have often been used as indicators of the trophic level and for the back-calculation of diets, few experiments have been done under standardized laboratory conditions to investigate factors influencing δ15N and δ13C values. An experiment using Nile tilapia [Oreochromis niloticus (L.)] was therefore carried out to test the effect of different dietary protein contents (35.4, 42.3, and 50.9%) on δ15N and δ13C values of the whole tilapia. The fish were fed the isoenergetic and isolipidic semi-synthetic diets at a relatively low level. δ15N and δ13C values of the lipid-free body did not differ between the fish fed the diets with different protein contents, but the trophic shift for N and C isotopes decreased with increasing protein accretion in the individual fish, for N from 6.5‰ to 4‰ and for C in the lipid-free body from 4‰ to 2.5‰. This is the first study showing the strong influence of the individual protein balance to the degree to which the isotopic signature of dietary protein was modified in tissue protein of fish. The extrapolation of the trophic level or the reconstruction of the diet of an animal from stable isotope ratios without knowledge of the individual physiological condition and the feeding rate may lead to erroneous results.

  12. 13C metabolic flux analysis at a genome-scale.

    Gopalakrishnan, Saratram; Maranas, Costas D

    2015-11-01

    Metabolic models used in 13C metabolic flux analysis generally include a limited number of reactions primarily from central metabolism. They typically omit degradation pathways, complete cofactor balances, and atom transition contributions for reactions outside central metabolism. This study addresses the impact on prediction fidelity of scaling-up mapping models to a genome-scale. The core mapping model employed in this study accounts for (75 reactions and 65 metabolites) primarily from central metabolism. The genome-scale metabolic mapping model (GSMM) (697 reaction and 595 metabolites) is constructed using as a basis the iAF1260 model upon eliminating reactions guaranteed not to carry flux based on growth and fermentation data for a minimal glucose growth medium. Labeling data for 17 amino acid fragments obtained from cells fed with glucose labeled at the second carbon was used to obtain fluxes and ranges. Metabolic fluxes and confidence intervals are estimated, for both core and genome-scale mapping models, by minimizing the sum of square of differences between predicted and experimentally measured labeling patterns using the EMU decomposition algorithm. Overall, we find that both topology and estimated values of the metabolic fluxes remain largely consistent between core and GSM model. Stepping up to a genome-scale mapping model leads to wider flux inference ranges for 20 key reactions present in the core model. The glycolysis flux range doubles due to the possibility of active gluconeogenesis, the TCA flux range expanded by 80% due to the availability of a bypass through arginine consistent with labeling data, and the transhydrogenase reaction flux was essentially unresolved due to the presence of as many as five routes for the inter-conversion of NADPH to NADH afforded by the genome-scale model. By globally accounting for ATP demands in the GSMM model the unused ATP decreased drastically with the lower bound matching the maintenance ATP requirement. A non

  13. An optimized buffer system for NMR-based urinary metabonomics with effective pH control, chemical shift consistency and dilution minimization.

    Xiao, Chaoni; Hao, Fuhua; Qin, Xiaorong; Wang, Yulan; Tang, Huiru

    2009-05-01

    NMR-based metabonomics has been widely employed to understand the stressor-induced perturbations to mammalian metabolism. However, inter-sample chemical shift variations for metabolites remain an outstanding problem for effective data mining. In this work, we systematically investigated the effects of pH and ionic strength on the chemical shifts for a mixture of 9 urinary metabolites. We found that the chemical shifts were decreased with the rise of pH but increased with the increase of ionic strength, which probably resulted from the pH- and ionic strength-induced alteration to the ionization equilibrium for the function groups. We also found that the chemical shift variations for most metabolites were reduced to less than 0.004 ppm when the pH was 7.1-7.7 and the salt concentration was less than 0.15 M. Based on subsequent optimization to minimize chemical shift variation, sample dilution and maximize the signal-to-noise ratio, we proposed a new buffer system consisting of K(2)HPO(4) and NaH(2)PO(4) (pH 7.4, 1.5 M) with buffer-urine volume ratio of 1 : 10 for human urinary metabonomic studies; we suggest that the chemical shifts for the proton signals of citrate and aromatic signals of histidine be corrected prior to multivariate data analysis especially when high resolution data were employed. Based on these, an optimized sample preparation method has been developed for NMR-based urinary metabonomic studies. PMID:19381385

  14. High accuracy NMR chemical shift corrected for bulk magnetization as a tool for structural elucidation of dilutable microemulsions. Part 1 - Proof of concept.

    Hoffman, Roy E; Darmon, Eliezer; Aserin, Abraham; Garti, Nissim

    2016-02-01

    In microemulsions, changes in droplet size and shape and possible transformations occur under various conditions. They are difficult to characterize by most analytical tools because of their nano-sized structure and dynamic nature. Several methods are usually combined to obtain reliable information, guiding the scientist in understanding their physical behavior. We felt that there is a need for a technique that complements those in use today in order to provide more information on the microemulsion behavior, mainly as a function of dilution with water. The improvement of NMR chemical shift measurements independent of bulk magnetization effects makes it possible to study the very weak intermolecular chemical shift effects. In the present study, we used NMR high resolution magic angle spinning to measure the chemical shift very accurately, free of bulk magnetization effects. The chemical shift of microemulsion components is measured as a function of the water content in order to validate the method in an interesting and promising, U-type dilutable microemulsion, which had been previously studied by a variety of techniques. Phase transition points of the microemulsion (O/W, bicontinuous, W/O) and changes in droplet shape were successfully detected using high-accuracy chemical shift measurements. We analyzed the results and found them to be compatible with the previous studies, paving the way for high-accuracy chemical shifts to be used for the study of other microemulsion systems. We detected two transition points along the water dilution line of the concentrate (reverse micelles) corresponding to the transition from swollen W/O nano-droplets to bicontinuous to the O/W droplets along with the changes in the droplets' sizes and shapes. The method seems to be in excellent agreement with other previously studied techniques and shows the advantage of this easy and valid technique. PMID:25113928

  15. 13C NMR Quantitative Study-Part 1: Relationships between the Conformation of Amino Acids, Peptide, Carboxylic Acids and Integration Intensity of 13C NMR

    2001-01-01

    @@ In proton broad band decoupling 13C NMR, carbon atoms have different integration intensity because of NOE effects and their different relaxation time(T1), thus it makes a 13C NMR quantitative analyses very difficult. To acquire a 3C NMR quantitative analyses, a gated decoupling with suppressed NOE technology, i.e., an inversed gated decoupling pulse (IGDP), must be used. In IGDP relay time (tR) between two acquisition cycles must be more than 5T1, the time needed for a acquisition cycles is so long that makes the total 13C NMR quantitative analyses time much longer. For this reason, the 13C NMR quantitative analyses is paid less attention.

  16. 13C NMR Quantitative Study-Part 1: Relationships between the Conformation of Amino Acids, Peptide, Carboxylic Acids and Integration Intensity of 13C NMR

    TIAN; JinPing

    2001-01-01

    In proton broad band decoupling 13C NMR, carbon atoms have different integration intensity because of NOE effects and their different relaxation time(T1), thus it makes a 13C NMR quantitative analyses very difficult. To acquire a 3C NMR quantitative analyses, a gated decoupling with suppressed NOE technology, i.e., an inversed gated decoupling pulse (IGDP), must be used. In IGDP relay time (tR) between two acquisition cycles must be more than 5T1, the time needed for a acquisition cycles is so long that makes the total 13C NMR quantitative analyses time much longer. For this reason, the 13C NMR quantitative analyses is paid less attention.  ……

  17. 13C and 15N fractionation of CH4/N2 mixtures during photochemical aerosol formation: Relevance to Titan

    Sebree, Joshua A.; Stern, Jennifer C.; Mandt, Kathleen E.; Domagal-Goldman, Shawn D.; Trainer, Melissa G.

    2016-05-01

    The ratios of the stable isotopes that comprise each chemical species in Titan's atmosphere provide critical information towards understanding the processes taking place within its modern and ancient atmosphere. Several stable isotope pairs, including 12C/13C and 14N/15N, have been measured in situ or probed spectroscopically by Cassini-borne instruments, space telescopes, or through ground-based observations. Current attempts to model the observed isotope ratios incorporate fractionation resulting from atmospheric diffusion, hydrodynamic escape, and primary photochemical processes. However, the effect of a potentially critical pathway for isotopic fractionation - organic aerosol formation and subsequent deposition onto the surface of Titan - has not been considered due to insufficient data regarding fractionation during aerosol formation. To better understand the nature of this process, we have conducted a laboratory study to measure the isotopic fractionation associated with the formation of Titan aerosol analogs, commonly referred to as 'tholins', via far-UV irradiation of several methane (CH4) and dinitrogen (N2) mixtures. Analysis of the δ13C and δ15N isotopic signatures of the photochemical aerosol products using an isotope ratio mass spectrometer (IRMS) show that fractionation direction and magnitude are dependent on the initial bulk composition of the gas mixture. In general, the aerosols showed enrichment in 13C and 14N, and the observed fractionation trends can provide insight into the chemical mechanisms controlling photochemical aerosol formation.

  18. Kankan diamonds (Guinea) III: δ13C and nitrogen characteristics of deep diamonds

    Stachel, T.; Harris, J. W.; Aulbach, S.; Deines, P.

    Diamonds from the Kankan area in Guinea formed over a large depth profile beginning within the cratonic mantle lithosphere and extending through the asthenosphere and transition zone into the lower mantle. The carbon isotopic composition, the concentration of nitrogen impurities and the nitrogen aggregation level of diamonds representing this entire depth range have been determined. Peridotitic and eclogitic diamonds of lithospheric origin from Kankan have carbon isotopic compositions (δ13C: peridotitic -5.4 to -2.2‰ eclogitic -19.7 to -0.7‰) and nitrogen characteristics (N: peridotitic 17-648 atomic ppm; eclogitic 0-1,313 atomic ppm; aggregation from IaA to IaB) which are generally typical for diamonds of these two suites worldwide. Geothermobarometry of peridotitic and eclogitic inclusion parageneses (worldwide sources) indicates that both suites formed under very similar conditions within the cratonic lithosphere, which is not consistent with a derivation of diamonds with light carbon isotopic composition from subducted organic matter within subducting oceanic slabs. Diamonds containing majorite garnet inclusions fall to the isotopically heavy side (δ13C: -3.1‰ to +0.9‰) of the worldwide diamond population. Nitrogen contents are low (0-126 atomic ppm) and one of the two nitrogen-bearing diamonds shows such a low level of nitrogen aggregation (30% B-centre) that it cannot have been exposed to ambient temperatures of the transition zone (>=1,400 °C) for more than 0.2 Ma. This suggests rapid upward transport and formation of some Kankan diamonds pene-contemporaneous to Cretaceous kimberlite activity. Similar to these diamonds from the asthenosphere and the transition zone, lower mantle diamonds show a small shift towards isotopic heavy compositions (-6.6 to -0.5‰, mode at -3.5‰). As already observed for other mines, the nitrogen contents of lower mantle diamonds were below detection (using FTIRS). The mutual shift of sublithospheric diamonds towards

  19. Application of compound specific 13C isotope investigations of chlorinated hydrocarbons in contaminated groundwaters

    Full text: Chlorinated hydrocarbons are one of the most common pollutants found in groundwater. Due to complex contamination situations with overlapping contamination plumes the assessment of the organic contaminants requires the installation of expensive observation wells and high analytical effort. Here the determination of the stable isotope ratio 13C/12C of the organic compounds offers a promising and efficient tool to investigate the origin and the biodegradation characteristics of the chlorinated hydrocarbons in groundwater. The application of the method is based on characteristic isotope fingerprints, differing in chlorinated solvents. This isotope fingerprint is derived from different production pathways and is not influenced by transport or by retardation processes in the underground. Due to the fact, that two different contaminations can easily be distinguished by isotope ratios, an improved distinction of spatially and temporally different contamination plumes might be possible. In course of biologically mediated degradation processes a shift of the isotope ratios between the precursor and the product can frequently be observed, such as with denitrification or sulfate reduction processes. The isotope fractionation is due to a preferential reaction of the bonds formed by the lighter isotopes and leads to a progressive enrichment of the heavy isotopes in the precursor while the product becomes depleted in the heavy isotopes. Biological degradation of the highly chlorinated hydrocarbons is due to a co-metabolic dechlorinisation. Tetrachloroethene (PCE) for example degrades under anoxic conditions via trichloroethene (TCE) to cis-1,2-dichloroethene (cDCE). Subsequent degradation to vinyl chloride (VC) and ethene may appear under aerobic as well as reducing environments depending on the site specific conditions. In several laboratory studies it has been shown, that biodegradation of the chlorinated hydrocarbons is accompanied by an isotope fractionation of

  20. Estimation of glucose carbon recycling in children with glycogen storage disease: A 13C NMR study using [U-13C]glucose

    A stable isotope procedure to estimate hepatic glucose carbon recycling and thereby elucidate the mechanism by which glucose is produced in patients lacking glucose 6-phosphatase is described. A total of 10 studies was performed in children with glycogen storage disease type I (GSD-I) and type III (GSD-III) and control subjects. A primed dose-constant nasogastric infusion of D-[U-13C]glucose or an infusion diluted with nonlabeled glucose solution was administered following different periods of fasting. Hepatic glucose carbon recycling was estimated from 13C NMR spectra. The values obtained for GSD-I patients coincided with the standard [U-13C]glucose dilution curve. These results indicate that the plasma glucose of GSD-I subjects comprises only a mixture of 99% 13C-enriched D-[U-13C]glucose and unlabeled glucose but lacks any recycled glucose. Significantly different glucose carbon recycling values were obtained for two GSD-III patients in comparison to GSD-I patients. The results eliminate a mechanism for glucose production in GSD-I children involving gluconeogenesis. However, glucose release by amylo-1,6-glucosidase activity would result in endogenous glucose production of non-13C-labeled and nonrecycled glucose carbon, as was found in this study. In GSD-III patients gluconeogenesis is suggested as the major route for endogenous glucose synthesis. The contribution of the triose-phosphate pathway in these patients has been determined

  1. Compartmentalised cerebral metabolism of [1,6-13C]glucose determined by in vivo 13C NMR spectroscopy at 14.1 T

    João M.N. Duarte

    2011-06-01

    Full Text Available Cerebral metabolism is compartmentalised between neurons and glia. Although glial glycolysis is thought to largely sustain the energetic requirements of neurotransmission while oxidative metabolism takes place mainly in neurons, this hypothesis is matter of debate. The compartmentalization of cerebral metabolic fluxes can be determined by 13C NMR spectroscopy upon infusion of 13C-enriched compounds, especially glucose. Rats under light α-chloralose anaesthesia were infused with [1,6-13C]glucose and 13C enrichment in the brain metabolites was measured by 13C NMR spectroscopy with high sensitivity and spectral resolution at 14.1 T. This allowed determining 13C enrichment curves of amino acid carbons with high reproducibility and to reliably estimate cerebral metabolic fluxes (mean error of 8%. We further found that TCA cycle intermediates are not required for flux determination in mathematical models of brain metabolism. Neuronal tricarboxylic acid cycle rate (VTCA and neurotransmission rate (VNT were 0.45±0.01 and 0.11±0.01 µmol/g/min, respectively. Glial VTCA was found to be for 38±3% of total cerebral oxidative metabolism, accounting for more than half of neuronal oxidative metabolism. Furthermore, glial anaplerotic pyruvate carboxylation rate (VPC was 0.069±0.004 µmol/g/min, i.e. 25±1% of the glial TCA cycle rate. These results support a role of glial cells as active partners of neurons during synaptic transmission beyond glycolytic metabolism.

  2. LOW DOSE CAPSULE BASED 13C-UREA BREATH TEST COMPARED WITH THE CONVENTIONAL 13C-UREA BREATH TEST AND INVASIVE TESTS

    Rejane MATTAR

    2014-04-01

    Full Text Available Context One of the limitations of 13C-urea breath test for Helicobacter pylori infection diagnosis in Brazil is the substrate acquisition in capsule presentation. Objectives The purpose of this study was to evaluate a capsule-based 13C-urea, manipulated by the Pharmacy Division, for the clinical practice. Methods Fifty patients underwent the conventional and the capsule breath test. Samples were collected at the baseline and after 10, 20 and 30 minutes of 13C-urea ingestion. Urease and histology were used as gold standard in 83 patients. Results In a total of 50 patients, 17 were positive with the conventional 13C-urea (75 mg breath test at 10, 20 and 30 minutes. When these patients repeated breath test with capsule (50 mg, 17 were positive at 20 minutes and 15 at 10 and 30 minutes. The relative sensitivity of 13C-urea with capsule was 100% at 20 minutes and 88.24% at 10 and at 30 minutes. The relative specificity was 100% at all time intervals. Among 83 patients that underwent capsule breath test and endoscopy the capsule breath test presented 100% of sensitivity and specificity. Conclusions Capsule based breath test with 50 mg 13C-urea at twenty minutes was found highly sensitive and specific for the clinical setting. HEADINGS- Helicobacter pylori. Breath Test. Urea, analysis.

  3. Synthesis of 2-(bromomethyl-13C)-fumaric acid (bromomesaconic acid)

    The fumarase inhibitor, bromomescaconic acid, has been synthesized with 13C labeling in the bromomethyl group. Di-t-butyl acetylenedicarboxylate was converted with Li (13CH3)2Cu to di-t-butyl (methyl-13C)citraconate. Photochemical isomerization of this di-t-butyl (methyl-13C)mesaconate, followed by deblocking with trifluoroacetic acid gave the title compound. (author)

  4. A large metabolic carbon contribution to the δ 13C record in marine aragonitic bivalve shells

    Gillikin, David P.; Lorrain, Anne; Meng, Li; Dehairs, Frank

    2007-06-01

    It is well known that the incorporation of isotopically light metabolic carbon (C M) significantly affects the stable carbon isotope (δ 13C) signal recorded in biogenic carbonates. This can obscure the record of δ 13C of seawater dissolved inorganic carbon (δ 13C DIC) potentially archived in the shell carbonate. To assess the C M contribution to Mercenaria mercenaria shells collected in North Carolina, USA, we sampled seawater δ 13C DIC, tissue, hemolymph and shell δ 13C. All shells showed an ontogenic decrease in shell δ 13C, with as much as a 4‰ decrease over the lifespan of the clam. There was no apparent ontogenic change in food source indicated by soft tissue δ 13C values, therefore a change in the respired δ 13C value cannot be the cause of this decrease. Hemolymph δ 13C, on the other hand, did exhibit a negative relationship with shell height indicating that respired CO 2 does influence the δ 13C value of internal fluids and that the amount of respired CO 2 is related to the size or age of the bivalve. The percent metabolic C incorporated into the shell (%C M) was significantly higher (up to 37%, with a range from 5% to 37%) than has been found in other bivalve shells, which usually contain less than 10%C M. Interestingly, the hemolymph did contain less than 10%C M, suggesting that complex fractionation might occur between hemolymph and calcifying fluids. Simple shell biometrics explained nearly 60% of the observed variability in %C M, however, this is not robust enough to predict %C M for fossil shells. Thus, the metabolic effect on shell δ 13C cannot easily be accounted for to allow reliable δ 13C DIC reconstructions. However, there does seem to be a common effect of size, as all sites had indistinguishable slopes between the %C M and shell height (+0.19% per mm of shell height).

  5. Radiation oxidation of polypropylene: A solid-state 13C NMR study using selective isotopic labeling

    Polypropylene samples, in which the three different carbon atoms along the chain were selectively labeled with carbon-13, were subjected to radiation under inert and air atmospheres, and to post-irradiation exposure in air at various temperatures. By using solid-state 13C NMR measurements at room temperature, we have been able to identify and quantify the oxidation products. The isotopic labeling provides insight into chemical reaction mechanisms, since oxidation products can be traced back to their positions of origin on the macromolecule. The major products include peroxides and alcohols, both formed at tertiary carbon sites along the chain. Other products include methyl ketones, acids, esters, peresters, and hemiketals formed from reaction at the tertiary carbon, together with in-chain ketones and esters from reaction at the secondary chain carbon. No evidence is found of products arising from reactions at the methyl side chain. Significant temperature-dependent differences are apparent; for example much higher yields of chain-end methyl ketones, which are the indicator product of chain scission, are generated for both elevated temperature irradiation and for post-irradiation treatment at elevated temperatures. Time-dependent plots of yields of the various oxidation products have been obtained under a wide range of conditions, including the post-irradiation oxidation of a sample at room temperature in air that has been monitored for 2 years. Radiation-oxidation products of polypropylene are contrasted to products measured for 13C-labeled polyethylene in an earlier investigation: the peroxides formed in irradiated polypropylene are remarkably longer lived, the non-peroxidic products are significantly different, and the overall ratios of oxidation products in polypropylene change relatively little as a function of the extent of oxidation

  6. Shifts in controls on the temporal coherence of throughfall chemical flux in Acadia National Park, Maine, USA

    Nelson, Sarah J.; Webster, Katherine E.; Loftin, Cynthia S.; Weathers, Kathleen C.

    2013-01-01

    Major ion and mercury (Hg) inputs to terrestrial ecosystems include both wet and dry deposition (total deposition). Estimating total deposition to sensitive receptor sites is hampered by limited information regarding its spatial heterogeneity and seasonality. We used measurements of throughfall flux, which includes atmospheric inputs to forests and the net effects of canopy leaching or uptake, for ten major ions and Hg collected during 35 time periods in 1999–2005 at over 70 sites within Acadia National Park, Maine to (1) quantify coherence in temporal dynamics of seasonal throughfall deposition and (2) examine controls on these patterns at multiple scales. We quantified temporal coherence as the correlation between all possible site pairs for each solute on a seasonal basis. In the summer growing season and autumn, coherence among pairs of sites with similar vegetation was stronger than for site-pairs that differed in vegetation suggesting that interaction with the canopy and leaching of solutes differed in coniferous, deciduous, mixed, and shrub or open canopy sites. The spatial pattern in throughfall hydrologic inputs across Acadia National Park was more variable during the winter snow season, suggesting that snow re-distribution affects net hydrologic input, which consequently affects chemical flux. Sea-salt corrected calcium concentrations identified a shift in air mass sources from maritime in winter to the continental industrial corridor in summer. Our results suggest that the spatial pattern of throughfall hydrologic flux, dominant seasonal air mass source, and relationship with vegetation in winter differ from the spatial pattern of throughfall flux in these solutes in summer and autumn. The coherence approach applied here made clear the strong influence of spatial heterogeneity in throughfall hydrologic inputs and a maritime air mass source on winter patterns of throughfall flux. By contrast, vegetation type was the most important influence on

  7. 13C- and 1H-ENDOR studies of a phenoxyl type radical

    13C- and 1H-ENDOR studies on a phenoxyl type radical in fluid solution are reported. The 13C-ENDOR resonance lines are comparable with those of the protons concerning amplitude, linewidth, and optimum experimental conditions. These findings are in contrast to previous ENDOR experiments on other 13C-labelled systems and can be explained by assuming similar hfs anisotropies for carbon-13 and protons in this radical. From saturation measurements the relaxation parameters were determined. The hyperfines couplings are discussed in terms of McLachlan and INDO calculations. For the first time natural abundance 13C-ENDOR measurement have been successful. (orig.) 891 WBU

  8. South American tree rings show declining [delta][sup 13]C trend

    Leavitt, S.W. (Univ. of Arizona, Tucson, AZ (United States). Lab. of Tree-Ring Research); Lara, A. (Univ. Austral de Chile, Valdivia (Chile). Inst. de Silvicultura)

    1994-04-01

    A composite, 290-year tree-ring [delta][sup 13]C chronology was developed from a site in Chile where 5 Fitzroya cupressoides (alerce) trees were sampled, 2 increment cores per tree, and the holocellulose component was analyzed in 5-year ring groups. This chronology shows a decreasing [delta][sup 13]C trend of approximately 1.2 per mille, primarily since the turn of this century. This [delta][sup 13]C decline is similar to that of major tree-ring studies in the Northern Hemisphere, but it is the only major Southern Hemisphere study which clearly exhibits such a [delta][sup 13]C trend. This is the first evidence for any interhemispheric reproducibility of tree-ring [delta][sup 13]C chronologies, and furthermore, the Fitzroya [delta][sup 13]C trend conforms well to that of [delta][sup 13]C of atmospheric CO[sub 2] determined from ice cores and direct measurements. This correspondence suggests the alerce [delta][sup 13]C trend has not been substantially influenced by systematic changes in environmental factors such as light, relative humidity and soil moisture or by changing atmospheric CO[sub 2] concentration, all of which are, in theory, capable of altering C[sub i]/C[sub a] ratios and obscuring the atmospheric [delta][sup 13]C record contained in the tree rings. 31 refs, 2 figs

  9. Effect of spectra recording conditions on the example of chemical shifts calculation in CMR spectra of 1-pentylbenzoylformate

    Mizyuk, Volodymyr; Shibanov, Volodymyr

    2011-01-01

    The concept of "compatible" and "incompatible" CMR spectra has been introduced. Application of compatibility increments (IC) allows to calculate the chemical shifts of C and C3 atoms of pentyloxyl fragment in 1-pentylbenzoylformate with a sufficiently good accuracy. Введено поняття "сумісних " і "несумісних " ЯМР спектрів. Застосування "інкрементів узгодження " дало можливість з достатньою точністю розрахувати хімічні зсуви атомів С2 і С пентилоксильного фрагменту в 1-пентилбензоїлформіаті....

  10. Cytoplasmic fat detection utilizing chemical shift gradient. Echo MR imaging in cases of clear cell renal cell carcinoma

    We investigated whether cytoplasmic fat in clear cell renal cell carcinoma (CCC) can be identified by chemical shift gradient-echo magnetic resonance imaging (CSI). CSI was performed for 22 cases of CCC and 30 cases of other renal tumors (including 16 cases of non-CCC), all of which were surgically proven. Signal reduction in out-of-phase images of these tumors was retrospectively evaluated and compared. The signal loss ratio (SLR) was defined and calculated. Fat staining of specimens from 16 tumors was performed and correlated with SLR. SLR was found to be significantly higher in CCC than in non-CCC (p<0.002). There was a significant correlation between the degree of fat staining positively of the specimens and SLR (p<0.01). When signal reduction in out-of-phase images suggested a diagnosis of CCC, a correct diagnosis of this entity was made in the resected renal tumors with a sensitivity, specificity, and accuracy of 82%, 93%, and 88%, respectively. CSI can demonstrate cytoplasmic fat in CCC, which helps to differentiate this entity from other renal tumors. (author)

  11. Quantitative evaluation of norcholesterol scintigraphy, CT attenuation value, and chemical-shift MR imaging for characterizing adrenal adenomas

    The objective of our study was to evaluate diagnostic ability and features of quantitative indices of three modalities: uptake rate on norcholesterol scintigraphy, computed tomography (CT) attenuation value, and fat suppression on chemical-shift magnetic resonance imaging (MRI) for characterizing adrenal adenomas. Image findings of norcholesterol scintigraphy, CT, and MRI were reviewed for 78 patients with functioning (n=48) or nonfunctioning (n=30) adrenal masses. The norcholesterol uptake rate, attenuation value on unenhanced CT, and suppression on in-phase to opposed-phase MRI were measured for adrenal masses. The norcholesterol uptake rate, CT attenuation value, and MR suppression index showed the sensitivity of 60%, 82%, and 100%, respectively, for functioning adenomas of <2.0 cm, and 96%, 79%, and 67%, respectively, for those of ≥2.0 cm. A statistically significant correlation was observed between size and norcholesterol uptake, and between CT attenuation value and MR suppression index. Regarding norcholesterol uptake, the adenoma-to-contralateral gland ratio was significantly higher in cortisol releasing than in aldosterone-releasing adenomas. The norcholesterol uptake rate was reliable for characterization of adenomas among adrenal masses of ≥2.0 cm. CT attenuation value and MR suppression index were well correlated with each other, and were useful regardless of mass size. (author)

  12. The study on temporal lobe epilepsy with single-voxel proton MR spectroscopy and chemical shift imaging

    Objective: To investigate the value of different proton MR spectroscopy techniques including single-voxel spectroscopy (SVS) and chemical shift imaging (CSI) in diagnosing patients with temporal lobe epilepsy. Methods: Sixty cases (40 normal, 20 temporal lobe epilepsy) experienced SVS and CSI. The volume of interest (VOI) of SVS was placed over the anterior hippocampus formation (HF) region, including part of the head and body of the HF. The VOI of CSI encompassed bilateral HF and the head, body and tail of HF. The VOI was divided into 5 voxels from anterior to posterior. The metabolite data of both SVS and CSI were obtained and the ratios of NAA/Cr and NAA/(Cho+Cr) were recorded or calculated. Results: The ipsilateral hippocampus to the seizure of TLE patients had lower ratios of NAA/(Cho+Cr) and NAA/Cr, and the differences compared with those of the normal group and contralateral subgroup were statistically significant (F=41.958, P1HMRS study improved the diagnostic yield of MR evaluation in TLE patients. There was a correlation between the ratio of NAA/(Cho+Cr) and the location of HF. Regional variation must be considered when interpreting proton spectra of the HF. (author)

  13. Solid state NMR chemical shift assignment and conformational analysis of a cellulose binding protein facilitated by optimized glycerol enrichment.

    Ivanir, Hadar; Goldbourt, Amir

    2014-07-01

    Magic-angle spinning solid-state NMR has been applied to study CBM3b-Cbh9A (CBM3b), a cellulose binding module protein belonging to family 3b. It is a 146-residue protein having a unique nine-stranded β-sandwich fold, in which 35% of the structure is in a β-sheet conformation and the remainder of the protein is composed of loops and unstructured regions. Yet, the protein can be crystalized and it forms elongated needles. Close to complete chemical shift assignment of the protein was obtained by combining two- and three-dimensional experiments using a fully labeled sample and a glycerol-labeled sample. The use of an optimized protocol for glycerol-based sparse labeling reduces sample preparation costs and facilitates the assignment of the large number of aromatic signals in this protein. Conformational analysis shows good correlation between the NMR-predicted secondary structure and the reported X-ray crystal structure, in particular in the structured regions. Residues which show high B-factor values are situated mainly in unstructured regions, and are missing in our spectra indicating conformational flexibility rather than heterogeneity. Interestingly, long-range contacts, which could be clearly detected for tyrosine residues, could not be observed for aromatic phenylalanine residues pointing into the hydrophobic core, suggesting possible high ring mobility. These studies will allow us to further investigate the cellulose-bound form of CBM proteins. PMID:24824437

  14. Molecular structure and vibrational and chemical shift assignments of 3‧-chloro-4-dimethylamino azobenzene by DFT calculations

    Toy, Mehmet; Tanak, Hasan

    2016-01-01

    In the present work, a combined experimental and theoretical study on ground state molecular structure, spectroscopic and nonlinear optical properties of azo compound 3‧-chloro-4-dimethlamino azobenzene are reported. The molecular geometry, vibrational wavenumbers and the first order hyperpolarizability of the title compound were calculated with the help of density functional theory computations. The optimized geometric parameters obtained by using DFT (B3LYP/6-311++G(d,p)) show good agreement with the experimental data. The vibrational transitions were identified based on the recorded FT-IR spectra in the range of 4000-400 cm-1 for solid state. The 1H isotropic chemical shifts with respect to TMS were also calculated using the gauge independent atomic orbital (GIAO) method and compared with the experimental data. Using the TD-DFT method, electronic absorption spectra of the title compound have been predicted, and good agreement is determined with the experimental ones. To investigate the NLO properties of the title compound, the polarizability and the first hyperpolarizability were calculated using the density functional B3LYP method with the 6-311++G(d,p) basis set. According to results, the title compound exhibits non-zero first hyperpolarizability value revealing second order NLO behavior. In addition, DFT calculations of the title compound, molecular electrostatic potential and frontier molecular orbitals were also performed at 6-311++G(d,p) level of theory.

  15. Site-specific 13C content by quantitative isotopic 13C Nuclear Magnetic Resonance spectrometry: A pilot inter-laboratory study

    Graphical abstract: -- Highlights: •First ring test on isotopic 13C NMR spectrometry. •Evaluation of the intra- and inter-variability of the NMR spectrometers used. •Definition of a protocol for qualification of the performance of the spectrometer. -- Abstract: Isotopic 13C NMR spectrometry, which is able to measure intra-molecular 13C composition, is of emerging demand because of the new information provided by the 13C site-specific content of a given molecule. A systematic evaluation of instrumental behaviour is of importance to envisage isotopic 13C NMR as a routine tool. This paper describes the first collaborative study of intra-molecular 13C composition by NMR. The main goals of the ring test were to establish intra- and inter-variability of the spectrometer response. Eight instruments with different configuration were retained for the exercise on the basis of a qualification test. Reproducibility at the natural abundance of isotopic 13C NMR was then assessed on vanillin from three different origins associated with specific δ13Ci profiles. The standard deviation was, on average, between 0.9 and 1.2‰ for intra-variability. The highest standard deviation for inter-variability was 2.1‰. This is significantly higher than the internal precision but could be considered good in respect of a first ring test on a new analytical method. The standard deviation of δ13Ci in vanillin was not homogeneous over the eight carbons, with no trend either for the carbon position or for the configuration of the spectrometer. However, since the repeatability for each instrument was satisfactory, correction factors for each carbon in vanillin could be calculated to harmonize the results

  16. Photobioreactor design for isotopic non-stationary 13C-metabolic flux analysis (INST 13C-MFA) under photoautotrophic conditions.

    Martzolff, Arnaud; Cahoreau, Edern; Cogne, Guillaume; Peyriga, Lindsay; Portais, Jean-Charles; Dechandol, Emmanuel; Le Grand, Fabienne; Massou, Stéphane; Gonçalves, Olivier; Pruvost, Jérémy; Legrand, Jack

    2012-12-01

    Adaptive metabolic behavior of photoautotrophic microorganisms toward genetic and environmental perturbations can be interpreted in a quantitative depiction of carbon flow through a biochemical reaction network using isotopic non-stationary (13) C-metabolic flux analysis (INST (13) C-MFA). To evaluate (13) C-metabolic flux maps for Chlamydomonas reinhardtii, an original experimental framework was designed allowing rapid, reliable collection of high-quality isotopomer data against time. It involved (i) a short-time (13) C labeling injection device based on mixing control in a torus-shaped photobioreactor with plug-flow hydrodynamics allowing a sudden step-change in the (13) C proportion in the substrate feed and (ii) a rapid sampling procedure using an automatic fast filtration method coupled to a manual rapid liquid nitrogen quenching step. (13) C-substrate labeling enrichment was controlled through the total dissolved inorganic carbon concentration in the pulsed solution. First results were obtained from steady-state continuous culture measurements allowing the characterization of the kinetics of label incorporation into light-limited growing cells cultivated in a photobioreactor operating at the maximal biomass productivity for an incident photon flux density of 200 µmol m(-2) s(-1). (13)C label incorporation was measured for 21 intracellular metabolites using IC-MS/MS in 58 samples collected across a labeling experiment duration of 7 min. The fastest labeling rate was observed for 2/3-phosphoglycerate with an apparent isotopic stationary state reached after 300 s. The labeling rate was consistent with the optimized mixing time of about 4.9 s inside the reactor and the shortest reliable sampling period assessed at 5 s. PMID:22688667

  17. A Large Metabolic Carbon Ccontribution to the δ13C Record in Marine Aragonitic Bivalve Shells

    Gillikin, D. P.; Lorrain, A.; Dehairs, F.

    2006-12-01

    The stable carbon isotopic signature archived in bivalve shells was originally thought to record the δ13C of seawater dissolved inorganic carbon (δ13C-DIC). However, more recent studies have shown that the incorporation of isotopically light metabolic carbon (M) significantly affects the δ13C signal recorded in biogenic carbonates. To assess the M contribution to Mercenaria mercenaria shells collected in North Carolina, USA, we sampled seawater δ13C-DIC, tissue, hemolymph and shell δ13C. We found up to a 4‰ decrease through ontogeny in shell δ13C in a 23 year old individual. There was no correlation between shell height or age and tissue δ13C. Thus, the ontogenic decrease observed in the shell δ13C could not be attributed to changes in food sources as the animal ages leading to more negative metabolic CO2, since this would require a negative relationship between tissue δ13C and shell height. Hemolymph δ13C, on the other hand, did exhibit a negative relationship with height, but the δ13C values were more positive than expected, indicating that hemolymph may not be a good proxy of extrapallial fluid δ13C. Nevertheless, the hemolymph data indicate that respired CO2 does influence the δ13C of internal fluids and that the amount of respired CO2 is related to the age of the bivalve. The percent metabolic C incorporated into the shell (%M) was significantly higher (up to 37%) than has been found in other bivalve shells, which usually contain less than 10 %M. Attempts to use shell biometrics to predict %M could not explain more than ~60% of the observed variability. Moreover, there were large differences in the %M between different sites. Thus, the metabolic effect on shell δ13C cannot easily be accounted for to allow reliable δ13C-DIC reconstructions. However, there does seem to be a common effect of size, as all sites had indistinguishable slopes between the %M and shell height (+0.19% per mm of shell height).

  18. Robust hyperpolarized (13)C metabolic imaging with selective non-excitation of pyruvate (SNEP).

    Chen, Way Cherng; Teo, Xing Qi; Lee, Man Ying; Radda, George K; Lee, Philip

    2015-08-01

    In vivo metabolic imaging using hyperpolarized [1-(13)C]pyruvate provides localized biochemical information and is particularly useful in detecting early disease changes, as well as monitoring disease progression and treatment response. However, a major limitation of hyperpolarized magnetization is its unrecoverable decay, due not only to T1 relaxation but also to radio-frequency (RF) excitation. RF excitation schemes used in metabolic imaging must therefore be able to utilize available hyperpolarized magnetization efficiently and robustly for the optimal detection of substrate and metabolite activities. In this work, a novel RF excitation scheme called selective non-excitation of pyruvate (SNEP) is presented. This excitation scheme involves the use of a spectral selective RF pulse to specifically exclude the excitation of [1-(13)C]pyruvate, while uniformly exciting the key metabolites of interest (namely [1-(13)C]lactate and [1-(13)C]alanine) and [1-(13)C]pyruvate-hydrate. By eliminating the loss of hyperpolarized [1-(13)C]pyruvate magnetization due to RF excitation, the signal from downstream metabolite pools is increased together with enhanced dynamic range. Simulation results, together with phantom measurements and in vivo experiments, demonstrated the improvement in signal-to-noise ratio (SNR) and the extension of the lifetime of the [1-(13)C]lactate and [1-(13)C]alanine pools when compared with conventional non-spectral selective (NS) excitation. SNEP has also been shown to perform comparably well with multi-band (MB) excitation, yet SNEP possesses distinct advantages, including ease of implementation, less stringent demands on gradient performance, increased robustness to frequency drifts and B0 inhomogeneity as well as easier quantification involving the use of [1-(13)C]pyruvate-hydrate as a proxy for the actual [1-(13)C] pyruvate signal. SNEP is therefore a promising alternative for robust hyperpolarized [1-(13)C]pyruvate metabolic imaging with high

  19. Improved 3D triple resonance experiments, HNN and HN(C)N, for HN and 15N sequential correlations in (13C, 15N) labeled proteins: Application to unfolded proteins

    Panchal, Sanjay C.; Bhavesh, Neel S.; Hosur, Ramakrishna V. [Tata Institute of Fundamental Research, Department of Chemical Sciences (India)

    2001-06-15

    Two triple resonance experiments, HNN and HN(C)N, are presented which correlate H{sup N} and {sup 15}N resonances sequentially along the polypeptide chain of a doubly ({sup 13}C, {sup 15}N) labeled protein. These incorporate several improvements over the previously published sequences for a similar purpose and have several novel features. The spectral characteristics enable direct identification of certain triplets of residues, which provide many starting points for the sequential assignment procedure. The experiments are sensitive and their utility has been demonstrated with a 22 kDa protein under unfolding conditions where most of the standard triple resonance experiments such as HNCA, CBCANH etc. have limited success because of poor amide, C{sup {alpha}} and C{sup {beta}} chemical shift dispersions.

  20. Improved 3D triple resonance experiments, HNN and HN(C)N, for HN and 15N sequential correlations in (13C, 15N) labeled proteins: Application to unfolded proteins

    Two triple resonance experiments, HNN and HN(C)N, are presented which correlate HN and 15N resonances sequentially along the polypeptide chain of a doubly (13C, 15N) labeled protein. These incorporate several improvements over the previously published sequences for a similar purpose and have several novel features. The spectral characteristics enable direct identification of certain triplets of residues, which provide many starting points for the sequential assignment procedure. The experiments are sensitive and their utility has been demonstrated with a 22 kDa protein under unfolding conditions where most of the standard triple resonance experiments such as HNCA, CBCANH etc. have limited success because of poor amide, Cα and Cβ chemical shift dispersions