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Sample records for 15n nmr spectroscopic

  1. UV-visible and (1)H-(15)N NMR spectroscopic studies of colorimetric thiosemicarbazide anion sensors.

    PubMed

    Farrugia, Kristina N; Makuc, Damjan; Podborska, Agnieszka; Szaciłowski, Konrad; Plavec, Janez; Magri, David C

    2015-02-14

    Four model thiosemicarbazide anion chemosensors containing three N-H bonds, substituted with phenyl and/or 4-nitrophenyl units, were synthesised and studied for their anion binding abilities with hydroxide, fluoride, acetate, dihydrogen phosphate and chloride. The anion binding properties were studied in DMSO and 9 : 1 DMSO-H2O by UV-visible absorption and (1)H/(13)C/(15)N NMR spectroscopic techniques and corroborated with DFT studies. Significant changes were observed in the UV-visible absorption spectra with all anions, except for chloride, accompanied by dramatic colour changes visible to the naked eye. These changes were determined to be due to the deprotonation of the central N-H proton and not due to hydrogen bonding based on (1)H/(15)N NMR titration studies with acetate in DMSO-d6-0.5% water. Direct evidence for deprotonation was confirmed by the disappearance of the central thiourea proton and the formation of acetic acid. DFT and charge distribution calculations suggest that for all four compounds the central N-H proton is the most acidic. Hence, the anion chemosensors operate by a deprotonation mechanism of the central N-H proton rather than by hydrogen bonding as is often reported. PMID:25451865

  2. QUANTITATIVE 15N NMR SPECTROSCOPY

    EPA Science Inventory

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

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

    PubMed

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

    2003-11-01

    A solution NMR spectroscopic study of the cyanide-inhibited, substrate-bound complex of uniformly (15)N-labeled human heme oxygenase, hHO, has led to characterization of the active site with respect to the nature and identity of strong hydrogen bonds and the occupation of ordered water molecules within both the hydrogen bonding network and an aromatic cluster on the distal side. [(1)H-(15)N]-HSQC spectra confirm the functionalities of several key donors in particularly robust H-bonds, and [(1)H-(15)N]HSQC-NOESY spectra lead to the identification of three additional robust H-bonds, as well as the detection of two more relatively strong H-bonds whose identities could not be established. The 3D NMR experiments provided only a modest, but important, extension of assignments because of the loss of key TOCSY cross-peaks due to the line broadening from a dynamic heterogeneity in the active site. Steady-state NOEs upon saturating the water signal locate nine ordered water molecules in the immediate vicinity of the H-bond donors, six of which are readily identified in the crystal structure. The additional three are positioned in available spaces to account for the observed NOEs. (15)N-filtered steady-state NOEs upon saturating the water resonances and (15)N-filtered NOESY spectra demonstrate significant negative NOEs between water molecules and the protons of five aromatic rings. Many of the NOEs can be rationalized by water molecules located in the crystal structure, but strong water NOEs, particularly to the rings of Phe47 and Trp96, demand the presence of at least an additional two immobilized water molecules near these rings. The H-bond network appears to function to order water molecules to provide stabilization for the hydroperoxy intermediate and to serve as a conduit to the active site for the nine protons required per HO turnover. PMID:14583035

  4. (15)N NMR studies of a nitrile-modified nucleoside.

    PubMed

    Gillies, Anne T; Gai, Xin Sonia; Buckwalter, Beth L; Fenlon, Edward E; Brewer, Scott H

    2010-12-30

    Nitrile-modified molecules have proven to be excellent probes of local environments in biomolecules via both vibrational and fluorescence spectroscopy. The utility of the nitrile group as a spectroscopic probe has been expanded here to (15)N NMR spectroscopy by selective (15)N incorporation. The (15)N NMR chemical shift (δ((15)N)) of the (15)N-labeled 5-cyano-2'-deoxyuridine (C(15)NdU, 1a) was found to change from 153.47 to 143.80 ppm in going from THF-d(8) to D(2)O. A 0.81 ppm downfield shift was measured upon formation of a hydrogen-bond-mediated heterodimer between 2,6-diheptanamidopyridine and a silyl ether analogue of 1a in chloroform, and the small intrinsic temperature dependence of δ((15)N) of C(15)NdU was measured as a 0.38 ppm downfield shift from 298 to 338 K. The experiments were complemented with density functional theory calculations exploring the effect of solvation on the (15)N NMR chemical shift. PMID:21126044

  5. Identification of novel hydrazine metabolites by 15N-NMR.

    PubMed

    Preece, N E; Nicholson, J K; Timbrell, J A

    1991-05-01

    15N-NMR has been used to study the metabolism of hydrazine in rats in vivo. Single doses of [15N2]hydrazine (2.0 mmol/kg: 98.6% g atom) were administered to rats and urine collected for 24 hr over ice. A number of metabolites were detected by 15N-NMR analysis of lyophilized urine. Ammonia was detected as a singlet at 0 ppm and unchanged [15N2]hydrazine was present in the urine detectable as a singlet at 32 ppm. Peaks were observed at 107 and 110 ppm which were identified as being due to the hydrazido nitrogen of acetylhydrazine and diacetylhydrazine, respectively. A resonance at 85 ppm was ascribed to carbazic acid, resulting from reaction of hydrazine with carbon dioxide. A singlet detected at 316 ppm was thought to be due to the hydrazono nitrogen of the pyruvate hydrazone. The resonance at 56 ppm was assigned to 15N-enriched urea, this together with the presence of ammonia indicates that the N-N bond of hydrazine is cleaved in vivo, possibly by N-oxidation, and the resultant ammonia is incorporated into urea. A doublet centred at 150 ppm and a singlet at 294 ppm were assigned to a metabolite which results from cyclization of the 2-oxoglutarate hydrazone. Therefore 15N-NMR spectroscopic analysis of urine has yielded significant new information on the metabolism of hydrazine. PMID:2018564

  6. Structure and reactivity of lithium amides. /sup 6/Li, /sup 13/C, and /sup 15/N NMR spectroscopic studies and colligative measurements of lithium diphenylamide and lithium diphenylamide-lithium bromide complex solvated by tetrahydrofuran

    SciTech Connect

    DePue, J.S.; Collum, D.B.

    1988-08-03

    /sup 6/Li, /sup 13/C, and /sup 15/N NMR spectroscopic studies of lithium diphenylamide in THF/hydrocarbon solutions (THF = tetrahydrofuran) detected two different species. /sup 6/Li and /sup 15/N NMR spectroscopic studies of (/sup 6/Li, /sup 15/N)lithium diphenylamide showed the species observed at low THF concentrations to be a cyclic oligomer. Structural analogies provided strong support for a dimer while colligative measurements at 0/degrees/C indicated the dimer to be di- or trisolvated. On the basis of the observed mass action effects, the species appearing at intermediate THF concentrations is assigned as a contact or solvent-separated ion-paired monomer. Lithium diphenylamide forms a 1:1 adduct with lithium bromide at low THF concentrations. A combination of /sup 6/Li-/sup 15/N double labeling studies and colligative measurements supports a trisolvated cyclic mixed dimer structure. Although detailed spectroscopic studies at elevated THF concentrations were precluded by high fluctionality, the similarity of the /sup 13/C chemical shifts of lithium diphenylamide in the presence and absence of lithium bromide provide indirect evidence that the mixed dimer undergoes a THF concentration dependent dissociation to the monomeric amide and free lithium bromide. 24 references, 9 figures, 2 tables.

  7. 15N and13C NMR investigation of hydroxylamine-derivatized humic substances

    USGS Publications Warehouse

    Thorn, K.A.; Arterburn, J.B.; Mikita, M.A.

    1992-01-01

    Five fulvic and humic acid samples of diverse origins were derivatized with 15N-labeled hydroxylamine and analyzed by liquid-phase 15N NMR spectrometry. The 15N NMR spectra indicated that hydroxylamine reacted similarly with all samples and could discriminate among carbonyl functional groups. Oximes were the major derivatives; resonances attributable to hydroxamic acids, the reaction products of hydroxylamine with esters, and resonances attributable to the tautomeric equilibrium position between the nitrosophenol and monoxime derivatives of quinones, the first direct spectroscopic evidence for quinones, also were evident. The 15N NMR spectra also suggested the presence of nitriles, oxazoles, oxazolines, isocyanides, amides, and lactams, which may all be explained in terms of Beckmann reactions of the initial oxime derivatives. INEPT and ACOUSTIC 15N NMR spectra provided complementary information on the derivatized samples. 13C NMR spectra of derivatized samples indicated that the ketone/quinone functionality is incompletely derivatized with hydroxylamine. ?? 1991 American Chemical Society.

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

    PubMed

    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

  9. 15N chemical shift referencing in solid state NMR.

    PubMed

    Bertani, Philippe; Raya, Jésus; Bechinger, Burkhard

    2014-01-01

    Solid-state NMR spectroscopy has much advanced during the last decade and provides a multitude of data that can be used for high-resolution structure determination of biomolecules, polymers, inorganic compounds or macromolecules. In some cases the chemical shift referencing has become a limiting factor to the precision of the structure calculations and we have therefore evaluated a number of methods used in proton-decoupled (15)N solid-state NMR spectroscopy. For (13)C solid-state NMR spectroscopy adamantane is generally accepted as an external standard, but to calibrate the (15)N chemical shift scale several standards are in use. As a consequence the published chemical shift values exhibit considerable differences (up to 22 ppm). In this paper we report the (15)N chemical shift of several commonly used references compounds in order to allow for comparison and recalibration of published data and future work. We show that (15)NH4Cl in its powdered form (at 39.3 ppm with respect to liquid NH3) is a suitable external reference as it produces narrow lines when compared to other reference compounds and at the same time allows for the set-up of cross-polarization NMR experiments. The compound is suitable to calibrate magic angle spinning and static NMR experiments. Finally the temperature variation of (15)NH4Cl chemical shift is reported. PMID:24746715

  10. Theoretical and experimental study of 15N NMR protonation shifts.

    PubMed

    Semenov, Valentin A; Samultsev, Dmitry O; Krivdin, Leonid B

    2015-06-01

    A combined theoretical and experimental study revealed that the nature of the upfield (shielding) protonation effect in 15N NMR originates in the change of the contribution of the sp(2)-hybridized nitrogen lone pair on protonation resulting in a marked shielding of nitrogen of about 100 ppm. On the contrary, for amine-type nitrogen, protonation of the nitrogen lone pair results in the deshielding protonation effect of about 25 ppm, so that the total deshielding protonation effect of about 10 ppm is due to the interplay of the contributions of adjacent natural bond orbitals. A versatile computational scheme for the calculation of 15N NMR chemical shifts of protonated nitrogen species and their neutral precursors is proposed at the density functional theory level taking into account solvent effects within the supermolecule solvation model. PMID:25891386

  11. 15N NMR chemical shifts in papaverine decomposition products

    NASA Astrophysics Data System (ADS)

    Czyrski, Andrzej; Girreser, Ulrich; Hermann, Tadeusz

    2013-03-01

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

  12. Backbone dynamics of barstar: a (15)N NMR relaxation study.

    PubMed

    Sahu, S C; Bhuyan, A K; Majumdar, A; Udgaonkar, J B

    2000-12-01

    Backbone dynamics of uniformly (15)N-labeled barstar have been studied at 32 degrees C, pH 6.7, by using (15)N relaxation data obtained from proton-detected 2D (1)H-(15)N NMR spectroscopy. (15)N spin-lattice relaxation rate constants (R(1)), spin-spin relaxation rate constants (R(2)), and steady-state heteronuclear (1)H-(15)N NOEs have been determined for 69 of the 86 (excluding two prolines and the N-terminal residue) backbone amide (15)N at a magnetic field strength of 14.1 Tesla. The primary relaxation data have been analyzed by using the model-free formalism of molecular dynamics, using both isotropic and axially symmetric diffusion of the molecule, to determine the overall rotational correlation time (tau(m)), the generalized order parameter (S(2)), the effective correlation time for internal motions (tau(e)), and NH exchange broadening contributions (R(ex)) for each residue. As per the axially symmetric diffusion, the ratio of diffusion rates about the unique and perpendicular axes (D( parallel)/D( perpendicular)) is 0.82 +/- 0.03. The two results have only marginal differences. The relaxation data have also been used to map reduced spectral densities for the NH vectors of these residues at three frequencies: 0, omega(H), and omega(N), where omega(H),(N) are proton and nitrogen Larmor frequencies. The value of tau(m) obtained from model-free analysis of the relaxation data is 5.2 ns. The reduced spectral density analysis, however, yields a value of 5.7 ns. The tau(m) determined here is different from that calculated previously from time-resolved fluorescence data (4.1 ns). The order parameter ranges from 0.68 to 0.98, with an average value of 0.85 +/- 0.02. A comparison of the order parameters with the X-ray B-factors for the backbone nitrogens of wild-type barstar does not show any considerable correlation. Model-free analysis of the relaxation data for seven residues required the inclusion of an exchange broadening term, the magnitude of which ranges from 2

  13. Covalent binding of reduced metabolites of [{sup 15}N{sub 3}]TNT to soil organic matter during a bioremediation process analyzed by {sup 15}N NMR spectroscopy

    SciTech Connect

    Achtnich, C.; Fernandes, E.; Bollag, J.M.; Knackmuss, H.J.; Lenke, H.

    1999-12-15

    Evidence is presented for the covalent binding of biologically reduced metabolites of 2,4,6-{sup 15}N{sub 3}-trinitrotoluene (TNT) to different soil fractions, using liquid {sup 15}N NMR spectroscopy. A silylation procedure was used to release soil organic matter from humin and whole soil for spectroscopic measurements. TNT-contaminated soil was spiked with 2,4,6-{sup 15}N{sub 3}-trinitrotoluene and {sup 14}C-ring labeled TNT, before treatment in a soil slurry reactor. During the anaerobic/aerobic incubation the amount of radioactivity detected in the fulvic and humic acid fractions did not change significantly whereas the radioactivity bound to humin increased to 71%. The {sup 15}N NMR spectra of the fulvic acid samples were dominated by a large peak that corresponded to aliphatic amines or ammonia. In the early stages of incubation, {sup 15}N NMR analysis of the humic acids indicated bound azoxy compounds. The signals arising from nitro and azoxy groups disappeared with further anaerobic treatment. At the end of incubation, the NMR shifts showed that nitrogen was covalently bound to humic acid as substituted amines and amides. The NMR spectra of the silylated humin suggest formation of azoxy compounds and imine linkages. Bound metabolites possessing nitro groups were also detected. Primary amines formed during the anaerobic incubation disappeared during the aerobic treatment. Simultaneously, the amount of amides and tertiary amines increased. Nitro and azoxy groups of bound molecules were still present in humin at the end of the incubation period. Formation of azoxy compounds from partially reduced TNT followed by binding and further reduction appears to be an important mechanism for the immobilization of metabolites of TNT to soil.

  14. Accessible NMR Experiments Studying the Hydrodynamics of [subscript 15]N-Enriched Ubiquitin at Low Fields

    ERIC Educational Resources Information Center

    Thompson, Laura E.; Rovnyak, David

    2007-01-01

    We have recently developed and implemented two experiments in biomolecular NMR for an undergraduate-level biophysical chemistry laboratory with commercially available [subscript 15]N-enriched human ubiquitin. These experiments take advantage of [subscript 15]N direct detection of the NMR signal. The first experiment develops skills in acquiring…

  15. Accessible NMR Experiments Studying the Hydrodynamics of [superscript 15]N-Enriched Ubiquitin at Low Fields

    ERIC Educational Resources Information Center

    Thompson, Laura E.; Rovnyak, David

    2007-01-01

    We have recently developed and implemented two experiments in biomolecular NMR for an undergraduate-level biophysical chemistry laboratory with commercially available [superscript 15]N-enriched human ubiquitin. These experiments take advantage of [superscript 15]N direct detection of the NMR signal. The first experiment develops skills in…

  16. Covalent binding of aniline to humic substances. 2. 15N NMR studies of nucleophilic addition reactions

    USGS Publications Warehouse

    Thorn, K.A.; Pettigrew, P.J.; Goldenberg, W.S.; Weber, E.J.

    1996-01-01

    Aromatic amines are known to undergo covalent binding with humic substances in the environment. Although previous studies have examined reaction conditions and proposed mechanisms, there has been no direct spectroscopic evidence for the covalent binding of the amines to the functional groups in humic substances. In order to further elucidate the reaction mechanisms, the Suwannee River and IHSS soil fulvic and humic acids were reacted with 15N-labeled aniline at pH 6 and analyzed using 15N NMR spectrometry. Aniline underwent nucleophilic addition reactions with the quinone and other carbonyl groups in the samples and became incorporated in the form of anilinohydroquinone, anilinoquinone, anilide, imine, and heterocyclic nitrogen, the latter comprising 50% or more of the bound amine. The anilide and anilinohydroquinone nitrogens were determined to be susceptible to chemical exchange by ammonia. In the case of Suwannee River fulvic acid, reaction under anoxic conditions and pretreatment with sodium borohydride or hydroxylamine prior to reaction under oxic conditions resulted in a decrease in the proportion of anilinohydroquinone nitrogen incorporated. The relative decrease in the incorporation of anilinohydroquinone nitrogen with respect to anilinoquinone nitrogen under anoxic conditions suggested that inter- or intramolecular redox reactions accompanied the nucleophilic addition reactions.

  17. 15N NMR investigation of the reduction and binding of TNT in an aerobic bench scale reactor simulating windrow composting

    USGS Publications Warehouse

    Thorn, K.A.; Pennington, J.C.; Hayes, C.A.

    2002-01-01

    T15NT was added to a soil of low organic carbon content and composted for 20 days in an aerobic bench scale reactor. The finished whole compost and fulvic acid, humic acid, humin, and lignocellulose fractions extracted from the compost were analyzed by solid-state CP/MAS and DP/MAS 15N NMR. 15N NMR spectra provided direct spectroscopic evidence for reduction of TNT followed by covalent binding of the reduced metabolites to organic matter of the composted soil, with the majority of metabolite found in the lignocellulose fraction, by mass also the major fraction of the compost. In general, the types of bonds formed between soil organic matter and reduced TNT amines in controlled laboratory reactions were observed in the spectra of the whole compost and fractions, confirming that during composting TNT is reduced to amines that form covalent bonds with organic matter through aminohydroquinone, aminoquinone, heterocyclic, and imine linkages, among others. Concentrations of imine nitrogens in the compost spectra suggestthat covalent binding bythe diamines 2,4DANT and 2,6DANT is a significant process in the transformation of TNT into bound residues. Liquid-phase 15N NMR spectra of the fulvic acid and humin fractions provided possible evidence for involvement of phenoloxidase enzymes in covalent bond formation.

  18. Hydrogen Bonds in Crystalline Imidazoles Studied by 15N NMR and ab initio MO Calculations

    NASA Astrophysics Data System (ADS)

    Ueda, Takahiro; Nagatomo, Shigenori; Masui, Hirotsugu; Nakamura, Nobuo; Hayashi, Shigenobu

    1999-07-01

    Intermolecular hydrogen bonds of the type N-H...N in crystals of imidazole and its 4-substituted and 4,5-disubstituted derivatives were studied by 15N CP/MAS NMR and an ab initio molecular orbital (MO) calculation. In the 15N CP/MAS NMR spectrum of each of the imidazole derivatives, two peaks due to the two different functional groups, >NH and =N-, were observed. The value of the 15N isotropic chemical shift for each nitrogen atom depends on both the length of the intermolecular hydrogen bond and the kind of the substituent or substituents. It was found that the difference between the experimen-tal chemical shifts of >NH and =N-varies predominantly with the hydrogen bond length but does not show any systematic dependence on the kind of substituent. The ab initio MO calculations suggest that the hydrogen bond formation influences the 15N isotropic chemical shift predominantly, and that the difference between the 15N isotropic chemical shift of >NH and =N-varies linearly with the hydrogen bond length.

  19. Synthesis and NMR of {sup 15}N-labeled DNA fragments

    SciTech Connect

    Jones, R.A.

    1994-12-01

    DNA fragments labeled with {sup 15}N at the ring nitrogens and at the exocyclic amino groups can be used to obtain novel insight into interactions such as base pairing, hydration, drug binding, and protein binding. A number of synthetic routes to {sup 15}N-labeled pyrimidine nucleosides, purines, and purine nucleosides have been reported. Moreover, many of these labeled bases or monomers have been incorporated into nucleic acids, either by chemical synthesis or by biosynthetic procedures. The focus of this chapter will be on the preparation of {sup 15}N-labeled purine 2{prime}-deoxynucleosides, their incorporation into DNA fragments by chemical synthesis, and the results of NMR studies using these labeled DNA fragments.

  20. 1H, 13C and 15N NMR assignments of phenazopyridine derivatives.

    PubMed

    Burgueño-Tapia, Eleuterio; Mora-Pérez, Yolanda; Morales-Ríos, Martha S; Joseph-Nathan, Pedro

    2005-03-01

    Phenazopyridine hydrochloride (1), a drug in clinical use for many decades, and some derivatives were studied by one- and two-dimensional (1)H, (13)C and (15)N NMR methodology. The assignments, combined with DFT calculations, reveal that the preferred protonation site of the drug is the pyridine ring nitrogen atom. The chemoselective acetylation of phenazopyridine (2) and its influence on the polarization of the azo nitrogen atoms were evidenced by the (15)N NMR spectra. Molecular calculations of the phenazopyridines 2-4 show that the pyridine and phenyl groups are oriented in an antiperiplanar conformation with intramolecular hydrogen bonding between the N-b atom and the C-2 amino group preserving the E-azo stereochemistry. PMID:15625718

  1. Natural abundance 14N and 15N solid-state NMR of pharmaceuticals and their polymorphs

    DOE PAGESBeta

    Veinberg, Stanislav L.; Johnston, Karen E.; Jaroszewicz, Michael J.; Kispal, Brianna M.; Mireault, Christopher R.; Kobayashi, Takeshi; Pruski, Marek; Schurko, Robert W.

    2016-06-08

    14N ultra-wideline (UW), 1H{15N} indirectly-detected HETCOR (idHETCOR) and 15N dynamic nuclear polarization (DNP) solid-state NMR (SSNMR) experiments, in combination with plane-wave density functional theory (DFT) calculations of 14N EFG tensors, were utilized to characterize a series of nitrogen-containing active pharmaceutical ingredients (APIs), including HCl salts of scopolamine, alprenolol, isoprenaline, acebutolol, dibucaine, nicardipine, and ranitidine. Here, a case study applying these methods for the differentiation of polymorphs of bupivacaine HCl is also presented. All experiments were conducted upon samples with naturally-abundant nitrogen isotopes. For most of the APIs, it was possible to acquire frequency-stepped UW 14N SSNMR spectra of stationarymore » samples, which display powder patterns corresponding to pseudo-tetrahedral (i.e., RR'R"NH+ and RR'NH2+) or other (i.e., RNH2 and RNO2) nitrogen environments.« less

  2. (13)C and (15)N solid-state NMR studies on albendazole and cyclodextrin albendazole complexes.

    PubMed

    Ferreira, M João G; García, A; Leonardi, D; Salomon, Claudio J; Lamas, M Celina; Nunes, Teresa G

    2015-06-01

    (13)C and (15)N solid-state nuclear magnetic resonance (NMR) spectra were recorded from albendazole (ABZ) and from ABZ:β-cyclodextrin, ABZ:methyl-β-cyclodextrin, ABZ:hydroxypropyl-β-cyclodextrin and ABZ:citrate-β-cyclodextrin, which were prepared by the spray-drying technique. ABZ signals were typical of a crystalline solid for the pure drug and of an amorphous compound obtained from ABZ:cyclodextrin samples. Relevant spectral differences were correlated with chemical interaction between ABZ and cyclodextrins. The number and type of complexes revealed a strong dependence on the cyclodextrin group substituent. Solid-state NMR data were consistent with the presence of stable inclusion complexes. PMID:25843843

  3. Natural abundance (14)N and (15)N solid-state NMR of pharmaceuticals and their polymorphs.

    PubMed

    Veinberg, Stanislav L; Johnston, Karen E; Jaroszewicz, Michael J; Kispal, Brianna M; Mireault, Christopher R; Kobayashi, Takeshi; Pruski, Marek; Schurko, Robert W

    2016-06-29

    (14)N ultra-wideline (UW), (1)H{(15)N} indirectly-detected HETCOR (idHETCOR) and (15)N dynamic nuclear polarization (DNP) solid-state NMR (SSNMR) experiments, in combination with plane-wave density functional theory (DFT) calculations of (14)N EFG tensors, were utilized to characterize a series of nitrogen-containing active pharmaceutical ingredients (APIs), including HCl salts of scopolamine, alprenolol, isoprenaline, acebutolol, dibucaine, nicardipine, and ranitidine. A case study applying these methods for the differentiation of polymorphs of bupivacaine HCl is also presented. All experiments were conducted upon samples with naturally-abundant nitrogen isotopes. For most of the APIs, it was possible to acquire frequency-stepped UW (14)N SSNMR spectra of stationary samples, which display powder patterns corresponding to pseudo-tetrahedral (i.e., RR'R''NH(+) and RR'NH2(+)) or other (i.e., RNH2 and RNO2) nitrogen environments. Directly-excited (14)N NMR spectra were acquired using the WURST-CPMG pulse sequence, which incorporates WURST (wideband, uniform rate, and smooth truncation) pulses and a CPMG (Carr-Purcell Meiboom-Gill) refocusing protocol. In certain cases, spectra were acquired using (1)H → (14)N broadband cross-polarization, via the BRAIN-CP (broadband adiabatic inversion - cross polarization) pulse sequence. These spectra provide (14)N electric field gradient (EFG) tensor parameters and orientations that are particularly sensitive to variations in local structure and intermolecular hydrogen-bonding interactions. The (1)H{(15)N} idHETCOR spectra, acquired under conditions of fast magic-angle spinning (MAS), used CP transfers to provide (1)H-(15)N chemical shift correlations for all nitrogen environments, except for two sites in acebutolol and nicardipine. One of these two sites (RR'NH2(+) in acebutolol) was successfully detected using the DNP-enhanced (15)N{(1)H} CP/MAS measurement, and one (RNO2 in nicardipine) remained elusive due to the absence of

  4. (15)N CSA tensors and (15)N-(1)H dipolar couplings of protein hydrophobic core residues investigated by static solid-state NMR.

    PubMed

    Vugmeyster, Liliya; Ostrovsky, Dmitry; Fu, Riqiang

    2015-10-01

    In this work, we assess the usefulness of static (15)N NMR techniques for the determination of the (15)N chemical shift anisotropy (CSA) tensor parameters and (15)N-(1)H dipolar splittings in powder protein samples. By using five single labeled samples of the villin headpiece subdomain protein in a hydrated lyophilized powder state, we determine the backbone (15)N CSA tensors at two temperatures, 22 and -35 °C, in order to get a snapshot of the variability across the residues and as a function of temperature. All sites probed belonged to the hydrophobic core and most of them were part of α-helical regions. The values of the anisotropy (which include the effect of the dynamics) varied between 130 and 156 ppm at 22 °C, while the values of the asymmetry were in the 0.32-0.082 range. The Leu-75 and Leu-61 backbone sites exhibited high mobility based on the values of their temperature-dependent anisotropy parameters. Under the assumption that most differences stem from dynamics, we obtained the values of the motional order parameters for the (15)N backbone sites. While a simple one-dimensional line shape experiment was used for the determination of the (15)N CSA parameters, a more advanced approach based on the "magic sandwich" SAMMY pulse sequence (Nevzorov and Opella, 2003) was employed for the determination of the (15)N-(1)H dipolar patterns, which yielded estimates of the dipolar couplings. Accordingly, the motional order parameters for the dipolar interaction were obtained. It was found that the order parameters from the CSA and dipolar measurements are highly correlated, validating that the variability between the residues is governed by the differences in dynamics. The values of the parameters obtained in this work can serve as reference values for developing more advanced magic-angle spinning recoupling techniques for multiple labeled samples. PMID:26367322

  5. Preparation of 13C and 15N labelled RNAs for heteronuclear multi-dimensional NMR studies.

    PubMed

    Nikonowicz, E P; Sirr, A; Legault, P; Jucker, F M; Baer, L M; Pardi, A

    1992-09-11

    A procedure is described for the efficient preparation of isotopically enriched RNAs of defined sequence. Uniformly labelled nucleotide 5'triphosphates (NTPs) were prepared from E.coli grown on 13C and/or 15N isotopically enriched media. These procedures routinely yield 180 mumoles of labelled NTPs per gram of 13C enriched glucose. The labelled NTPs were then used to synthesize RNA oligomers by in vitro transcription. Several 13C and/or 15N labelled RNAs have been synthesized for the sequence r(GGCGCUUGCGUC). Under conditions of high salt or low salt, this RNA forms either a symmetrical duplex with two U.U base pairs or a hairpin containing a CUUG loop respectively. These procedures were used to synthesize uniformly labelled RNAs and a RNA labelled only on the G and C residues. The ability to generate milligram quantities of isotopically labelled RNAs allows application of multi-dimensional heteronuclear magnetic resonance experiments that enormously simplify the resonance assignment and solution structure determination of RNAs. Examples of several such heteronuclear NMR experiments are shown. PMID:1383927

  6. Characterizing the Microstructure of Heparin and Heparan Sulfate using N-sulfoglucosamine 1H and 15N NMR Chemical Shift Analysis

    PubMed Central

    Langeslay, Derek J.; Beecher, Consuelo N.; Naggi, Annamaria; Guerrini, Marco; Torri, Giangiacomo; Larive, Cynthia K.

    2014-01-01

    Heparin and heparan sulfate (HS) are members of a biologically important group of highly anionic linear polysaccharides called glycosaminoglycans (GAGs). Because of their structural complexity, the molecular-level characterization of heparin and HS continues to be a challenge. The work presented herein describes an emerging approach for the analysis of unfractionated and low molecular weight heparins as well as porcine and human-derived HS. This approach utilizes the untapped potential of 15N NMR to characterize these preparations through detection of the NH resonances of N-sulfo-glucosamine residues. The sulfamate group 1H and 15N chemical shifts of six GAG microenvironments were assigned based on the critical comparison of selectively modified heparin derivatives, NMR measurements for a library of heparin-derived oligosaccharide standards, and an in-depth NMR analysis of the low molecular weight heparin enoxaparin through systematic investigation of the chemical exchange properties of NH resonances and residue-specific assignments using the [1H, 15N] HSQC-TOCSY experiment. The sulfamate microenvironments characterized in this study include GlcNS(6S)-UA(2S), ΔUA(2S)-GlcNS(6S), GlcNS(3S)(6S)-UA(2S), GlcNS-UA, GlcNS(6S)-redα, and 1,6-anhydro GlcNS demonstrate the utility of [1H, 15N] HSQC NMR spectra to provide a spectroscopic fingerprint reflecting the composition of intact GAGs and low molecular weight heparin preparations. PMID:23240897

  7. Chemoselective detection and discrimination of carbonyl-containing compounds in metabolite mixtures by 1H-detected 15N NMR

    PubMed Central

    Lane, Andrew N.; Arumugam, Sengodagounder; Lorkiewicz, Pawel K.; Higashi, Richard M.; Laulhé, Sébastien; Nantz, Michael H.; Moseley, Hunter N.B.; Fan, Teresa W.-M.

    2015-01-01

    NMR spectra of mixtures of metabolites extracted from cells or tissues are extremely complex, reflecting the large number of compounds that are present over a wide range of concentrations. Although multidimensional NMR can greatly improve resolution as well as improve reliability of compound assignments, lower abundance metabolites often remain hidden. We have developed a carbonyl selective aminooxy probe that specifically reacts with free keto and aldehyde functions, but not carboxylates. By incorporating 15N in the aminooxy functional group, 15N-edited NMR was used to select exclusively those metabolites that contain a free carbonyl function while all other metabolites are rejected. Here we demonstrate that the chemical shifts of the aminooxy adducts of ketones and aldehydes are very different, which can be used to discriminate between aldoses and ketoses for example. Utilizing the 2 or 3 bond 15N-1H couplings, the 15N-edited NMR analysis was optimized first with authentic standards and then applied to an extract of the lung adenocarcinoma cell line A549. More than 30 carbonyl containing compounds at NMR detectable levels, 6 of which we have assigned by reference to our database. As the aminooxy probe contains a permanently charged quaternary ammonium group, the adducts are also optimized for detection by mass spectrometry. Thus, this sample preparation technique provides a better link between the two structural determination tools, thereby paving the way to faster and more reliable identification of both known and unknown metabolites directly in crude biological extracts. PMID:25616249

  8. Backbone dynamics of the oligomerization domain of p53 determined from 15N NMR relaxation measurements.

    PubMed

    Clubb, R T; Omichinski, J G; Sakaguchi, K; Appella, E; Gronenborn, A M; Clore, G M

    1995-05-01

    The backbone dynamics of the tetrameric p53 oligomerization domain (residues 319-360) have been investigated by two-dimensional inverse detected heteronuclear 1H-15N NMR spectroscopy at 500 and 600 MHz. 15N T1, T2, and heteronuclear NOEs were measured for 39 of 40 non-proline backbone NH vectors at both field strengths. The overall correlation time for the tetramer, calculated from the T1/T2 ratios, was found to be 14.8 ns at 35 degrees C. The correlation times and amplitudes of the internal motions were extracted from the relaxation data using the model-free formalism (Lipari G, Szabo A, 1982, J Am Chem Soc 104:4546-4559). The internal dynamics of the structural core of the p53 oligomerization domain are uniform and fairly rigid, with residues 327-354 exhibiting an average generalized order parameter (S2) of 0.88 +/- 0.08. The N- and C-termini exhibit substantial mobility and are unstructured in the solution structure of p53. Residues located at the N- and C-termini, in the beta-sheet, in the turn between the alpha-helix and beta-sheet, and at the C-terminal end of the alpha-helix display two distinct internal motions that are faster than the overall correlation time. Fast internal motions (< or = 20 ps) are within the extreme narrowing limit and are of uniform amplitude. The slower motions (0.6-2.2 ns) are outside the extreme narrowing limit and vary in amplitude.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:7663341

  9. 15N NMR study of nitrate ion structure and dynamics in hydrotalcite-like compounds

    USGS Publications Warehouse

    Hou, X.; James, Kirkpatrick R.; Yu, P.; Moore, D.; Kim, Y.

    2000-01-01

    We report here the first nuclear magnetic resonance (NMR) spectroscopic study of the dynamical and structural behavior of nitrate on the surface and in the interlayer of hydrotalcite-like compounds (15NO3--HT). Spectroscopically resolvable surface-absorbed and interlayer NO3- have dramatically different dynamical characteristics. The interlayer nitrate shows a well defined, temperature independent uniaxial chemical shift anisotropy (CS A) powder pattern. It is rigidly held or perhaps undergoes rotation about its threefold axis at all temperatures between -100 ??C and +80 ??C and relative humidities (R.H.) from 0 to 100% at room temperature. For surface nitrate, however, the dynamical behavior depends substantially on temperature and relative humidity. Analysis of the temperature and R.H. dependences of the peak width yields reorieritational frequencies which increase from essentially 0 at -100 ??C to 2.6 ?? 105 Hz at 60 ??C and an activation energy of 12.6 kJ/mol. For example, for samples at R.H. = 33%, the surface nitrate is isotropically mobile at frequencies greater than 105 Hz at room temperature, but it becomes rigid or only rotates on its threefold axis at -100 ??C. For dry samples and samples heated at 200 ??C (R.H. near 0%), the surface nitrate is not isotropically averaged at room temperature. In contrast to our previous results for 35Cl--containing hydrotalcite (35Cl--HT), no NMR detectable structural phase transition is observed for 15NO3--HT. The mobility of interlayer nitrate in HT is intermediate between that of carbonate and chloride.

  10. A closer look at the nitrogen next door: 1H-15N NMR methods for glycosaminoglycan structural characterization

    NASA Astrophysics Data System (ADS)

    Langeslay, Derek J.; Beni, Szabolcs; Larive, Cynthia K.

    2012-03-01

    Recently, experimental conditions were presented for the detection of the N-sulfoglucosamine (GlcNS) NHSO3- or sulfamate 1H and 15N NMR resonances of the pharmaceutically and biologically important glycosaminoglycan (GAG) heparin in aqueous solution. In the present work, we explore further the applicability of nitrogen-bound proton detection to provide structural information for GAGs. Compared to the detection of 15N chemical shifts of aminosugars through long-range couplings using the IMPACT-HNMBC pulse sequence, the more sensitive two-dimensional 1H-15N HSQC-TOCSY experiments provided additional structural data. The IMPACT-HNMBC experiment remains a powerful tool as demonstrated by the spectrum measured for the unsubstituted amine of 3-O-sulfoglucosamine (GlcN(3S)), which cannot be observed with the 1H-15N HSQC-TOCSY experiment due to the fast exchange of the amino group protons with solvent. The 1H-15N HSQC-TOCSY NMR spectrum reported for the mixture of model compounds GlcNS and N-acetylglucosamine (GlcNAc) demonstrate the broad utility of this approach. Measurements for the synthetic pentasaccharide drug Arixtra® (Fondaparinux sodium) in aqueous solution illustrate the power of this NMR pulse sequence for structural characterization of highly similar N-sulfoglucosamine residues in GAG-derived oligosaccharides.

  11. (1)H, (13)C and (15)N NMR assignments of a calcium-binding protein from Entamoeba histolytica.

    PubMed

    Verma, Deepshikha; Bhattacharya, Alok; Chary, Kandala V R

    2016-04-01

    We report almost complete sequence specific (1)H, (13)C and (15)N NMR assignments of a 150-residue long calmodulin-like calcium-binding protein from Entamoeba histolytica (EhCaBP6), as a prelude to its structural and functional characterization. PMID:26377206

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

    NASA Astrophysics Data System (ADS)

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

    2003-11-01

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

  13. 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.

    PubMed

    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

  14. An NMR study of the interaction of 15N-labelled bradykinin with an antibody mimic of the bradykinin B2 receptor.

    PubMed

    Ottleben, H; Haasemann, M; Ramachandran, R; Görlach, M; Müller-Esterl, W; Brown, L R

    1997-03-01

    An isotope-edited NMR study of the peptide hormone bradykinin (RPPGFSPFR) bound to the Fab fragment of a monoclonal antibody against bradykinin (MBK3) is reported. MBK3 was previously shown to provide a binding site model of the B2 bradykinin receptor [Haasemann, M., Buschko, J., Faussner, A., Roscher, A. A., Hoebeke, J., Burch, R. M. & Muller-Esterl, W. (1991) Anti-idiotypic antibodies bearing the internal image of a bradykinin epitope, J. Immunol. 147, 3882-3892]. Bradykinin was obtained in a uniformly 15N-labelled form using recombinant expression of a fusion protein consisting of the glutathione-binding domain of glutathione S-transferase fused to residues 354-375 of the high-molecular-mass kininogen from which bradykinin was released by proteolytic digestion with its natural protease plasma kallikrein. Bradykinin forms a complex with the Fab fragment of MBK3 which exchanges slowly on the NMR time scale. The 15N and 1H resonances of the tightly bound residues of bradykinin show appreciable changes in chemical shift with respect to the free form, while the 15N and 1H linewidths indicate that the hydrodynamic behaviour of bound bradykinin is dominated by the high-molecular-mass Fab fragment. The NMR data indicate that essentially the entire nonapeptide is involved in binding. The kinetics of the ligand-exchange process, together with resonance assignments obtained via exchange spectroscopy. indicate that bradykinin binds to MBK3 only in the all-trans conformation at all three Xaa-Pro amide bonds. NH-NH NOE connectivities suggest that bradykinin is bound in an extended conformation. The spectroscopic data obtained from this study are compared to recently proposed computational models of the conformation of bradykinin bound to the B2 receptor. PMID:9119014

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

    NASA Astrophysics Data System (ADS)

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

    2014-11-01

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

  16. (13)C, (15)N CPMAS NMR and GIAO DFT calculations of stereoisomeric oxindole alkaloids from Cat's Claw (Uncaria tomentosa).

    PubMed

    Paradowska, Katarzyna; Wolniak, Michał; Pisklak, Maciej; Gliński, Jan A; Davey, Matthew H; Wawer, Iwona

    2008-11-01

    Oxindole alkaloids, isolated from the bark of Uncaria tomentosa [Willd. ex Schult.] Rubiaceae, are considered to be responsible for the biological activity of this herb. Five pentacyclic and two tetracyclic alkaloids were studied by solid-state NMR and theoretical GIAO DFT methods. The (13)C and (15)N CPMAS NMR spectra were recorded for mitraphylline, isomitraphylline, pteropodine (uncarine C), isopteropodine (uncarine E), speciophylline (uncarine D), rhynchophylline and isorhynchophylline. Theoretical GIAO DFT calculations of shielding constants provide arguments for identification of asymmetric centers and proper assignment of NMR spectra. These alkaloids are 7R/7S and 20R/20S stereoisomeric pairs. Based on the (13)C CP MAS chemical shifts the 7S alkaloids (delta C3 70-71ppm) can be easily and conveniently distinguished from 7R (deltaC3 74.5-74.9ppm), also 20R (deltaC20 41.3-41.7ppm) from the 20S (deltaC20 36.3-38.3ppm). The epiallo-type isomer (3R, 20S) of speciophylline is characterized by a larger (15)N MAS chemical shift of N4 (64.6ppm) than the allo-type (3S, 20S) of isopteropodine (deltaN4 53.3ppm). (15)N MAS chemical shifts of N1-H in pentacyclic alkaloids are within 131.9-140.4ppm. PMID:19019638

  17. A New Tool for NMR Crystallography: Complete (13)C/(15)N Assignment of Organic Molecules at Natural Isotopic Abundance Using DNP-Enhanced Solid-State NMR.

    PubMed

    Märker, Katharina; Pingret, Morgane; Mouesca, Jean-Marie; Gasparutto, Didier; Hediger, Sabine; De Paëpe, Gaël

    2015-11-01

    NMR crystallography of organic molecules at natural isotopic abundance (NA) strongly relies on the comparison of assigned experimental and computed NMR chemical shifts. However, a broad applicability of this approach is often hampered by the still limited (1)H resolution and/or difficulties in assigning (13)C and (15)N resonances without the use of structure-based chemical shift calculations. As shown here, such difficulties can be overcome by (13)C-(13)C and for the first time (15)N-(13)C correlation experiments, recorded with the help of dynamic nuclear polarization. We present the complete de novo (13)C and (15)N resonance assignment at NA of a self-assembled 2'-deoxyguanosine derivative presenting two different molecules in the asymmetric crystallographic unit cell. This de novo assignment method is exclusively based on aforementioned correlation spectra and is an important addition to the NMR crystallography approach, rendering firstly (1)H assignment straightforward, and being secondly a prerequisite for distance measurements with solid-state NMR. PMID:26485326

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

    PubMed Central

    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,15N-labeled DNA based on enzymatic synthesis using Taq DNA polymerase. The highly efficient protocol results in quantitative polymerization of the template and approximately 80% incorporation of the labeled dNTPs. Procedures for avoiding non-templated addition of nucleotides or for their removal are given. The method has been used to synthesize several DNA oligonucleotides, including two complementary 15 base strands, a 32 base DNA oligonucleotide that folds to form an intramolecular triplex and a 12 base oligonucleotide that dimerizes and folds to form a quadruplex. Heteronuclear NMR spectra of the samples illustrate the quality of the labeled DNA obtained by these procedures. PMID:9592146

  19. 15N NMR investigation of the covalent binding of reduced TNT amines to soil humic acid, model compounds, and lignocellulose.

    PubMed

    Thorn, K A; Kennedy, K R

    2002-09-01

    The five major reductive degradation products of TNT-4ADNT (4-amino-2,6-dinitrotoluene), 2ADNT (2-amino-4,6-dinitrotoluene), 2,4DANT (2,4-diamino-6-nitrotoluene), 2,6DANT (2,6-diamino-4-nitrotoluene), and TAT (2,4,6-triaminotoluene)-labeled with 15N in the amine positions, were reacted with the IHSS soil humic acid and analyzed by 15N NMR spectrometry. In the absence of catalysts, all five amines underwent nucleophilic addition reactions with quinone and other carbonyl groups in the soil humic acid to form both heterocyclic and nonheterocyclic condensation products. Imine formation via 1,2-addition of the amines to quinone groups in the soil humic acid was significant with the diamines and TAT but not the monoamines. Horseradish peroxidase (HRP) catalyzed an increase in the incorporation of all five amines into the humic acid. In the case of the diamines and TAT, HRP also shifted the binding away from heterocyclic condensation product toward imine formation. A comparison of quantitative liquid phase with solid-state CP/MAS 15N NMR indicated that the CP experiment underestimated imine and heterocyclic nitrogens in humic acid, even with contact times optimal for observation of these nitrogens. Covalent binding of the mono- and diamines to 4-methylcatechol, the HRP catalyzed condensation of 4ADNT and 2,4DANT to coniferyl alcohol, and the binding of 2,4DANT to lignocellulose with and without birnessite were also examined. PMID:12322752

  20. 15N NMR investigation of the covalent binding of reduced TNT amines to soil humic acid, model compounds, and lignocellulose

    USGS Publications Warehouse

    Thorn, K.A.; Kennedy, K.R.

    2002-01-01

    The five major reductive degradation products of TNT-4ADNT (4-amino-2,6-dinitrotoluene), 2ADNT (2-amino-4,6-dinitrotoluene), 2,4DANT (2,4-diamino-6-nitrotoluene), 2,6DANT (2,6-diamino-4-nitrotoluene), and TAT (2,4,6-triaminotoluene)-labeled with 15N in the amine positions, were reacted with the IHSS soil humic acid and analyzed by 15N NMR spectrometry. In the absence of catalysts, all five amines underwent nucleophilic addition reactions with quinone and other carbonyl groups in the soil humic acid to form both heterocyclic and nonheterocyclic condensation products. Imine formation via 1,2-addition of the amines to quinone groups in the soil humic acid was significant with the diamines and TAT but not the monoamines. Horseradish peroxidase (HRP) catalyzed an increase in the incorporation of all five amines into the humic acid. In the case of the diamines and TAT, HRP also shifted the binding away from heterocyclic condensation product toward imine formation. A comparison of quantitative liquid phase with solid-state CP/MAS 15N NMR indicated that the CP experiment underestimated imine and heterocyclic nitrogens in humic acid, even with contact times optimal for observation of these nitrogens. Covalent binding of the mono- and diamines to 4-methylcatechol, the HRP catalyzed condensation of 4ADNT and 2,4DANT to coniferyl alcohol, and the binding of 2,4DANT to lignocellulose with and without birnessite were also examined.

  1. Monitoring the refinement of crystal structures with (15)N solid-state NMR shift tensor data.

    PubMed

    Kalakewich, Keyton; Iuliucci, Robbie; Mueller, Karl T; Eloranta, Harriet; Harper, James K

    2015-11-21

    The (15)N chemical shift tensor is shown to be extremely sensitive to lattice structure and a powerful metric for monitoring density functional theory refinements of crystal structures. These refinements include lattice effects and are applied here to five crystal structures. All structures improve based on a better agreement between experimental and calculated (15)N tensors, with an average improvement of 47.0 ppm. Structural improvement is further indicated by a decrease in forces on the atoms by 2-3 orders of magnitude and a greater similarity in atom positions to neutron diffraction structures. These refinements change bond lengths by more than the diffraction errors including adjustments to X-Y and X-H bonds (X, Y = C, N, and O) of 0.028 ± 0.002 Å and 0.144 ± 0.036 Å, respectively. The acquisition of (15)N tensors at natural abundance is challenging and this limitation is overcome by improved (1)H decoupling in the FIREMAT method. This decoupling dramatically narrows linewidths, improves signal-to-noise by up to 317%, and significantly improves the accuracy of measured tensors. A total of 39 tensors are measured with shifts distributed over a range of more than 400 ppm. Overall, experimental (15)N tensors are at least 5 times more sensitive to crystal structure than (13)C tensors due to nitrogen's greater polarizability and larger range of chemical shifts. PMID:26590548

  2. 15N-Cholamine – A Smart Isotope Tag for Combining NMR- and MS-Based Metabolite Profiling

    PubMed Central

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

    2013-01-01

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

  3. Catalytic Roles of βLys87 in Tryptophan Synthase: 15N Solid State NMR Studies

    PubMed Central

    Caulkins, Bethany G.; Yang, Chen; Hilario, Eduardo; Fan, Li; Dunn, Michael F.; Mueller, Leonard J.

    2015-01-01

    The proposed mechanism for tryptophan synthase shows βLys87 playing multiple catalytic roles: it bonds to the PLP cofactor, activates C4′ for nucleophilic attack via a protonated Schiff base nitrogen, and abstracts and returns protons to PLP-bound substrates (i.e. acid-base catalysis). ε-15N-lysine TS was prepared to access the protonation state of βLys87 using 15N solid-state nuclear magnetic resonance (SSNMR) spectroscopy for three quasi-stable intermediates along the reaction pathway. These experiments establish that the protonation state of the ε-amino group switches between protonated and neutral states as the β-site undergoes conversion from one intermediate to the next during catalysis, corresponding to mechanistic steps where this lysine residue has been anticipated to play alternating acid and base catalytic roles that help steer reaction specificity in tryptophan synthase catalysis. PMID:25688830

  4. Mechanism of Solid-State Thermolysis of Ammonia Boraine: 15N NMR Study Using Fast Magic-Angle Spinning and Dynamic Nuclear Polarization

    SciTech Connect

    Kobayashi, Takeshi; Gupta, Shalabh; Caporini, Marc A; Pecharsky, Vitalij K; Pruski, Marek

    2014-08-28

    The solid-state thermolysis of ammonia borane (NH3BH3, AB) was explored using state-of-the-art 15N solid-state NMR spectroscopy, including 2D indirectly detected 1H{15N} heteronuclear correlation and dynamic nuclear polarization (DNP)-enhanced 15N{1H} cross-polarization experiments as well as 11B NMR. The complementary use of 15N and 11B NMR experiments, supported by density functional theory calculations of the chemical shift tensors, provided insights into the dehydrogenation mechanism of AB—insights that have not been available by 11B NMR alone. Specifically, highly branched polyaminoborane derivatives were shown to form from AB via oligomerization in the “head-to-tail” manner, which then transform directly into hexagonal boron nitride analog through the dehydrocyclization reaction, bypassing the formation of polyiminoborane.

  5. 15N and 1H NMR spectroscopy of the catalytic histidine in chloromethyl ketone-inhibited complexes of serine proteases.

    PubMed

    Tsilikounas, E; Rao, T; Gutheil, W G; Bachovchin, W W

    1996-02-20

    The hemiketal hydroxyl groups in chloromethyl ketone (cmk) complexes of trypsin and chymotrypsin have been reported to ionize to the oxyanion with pK(a) values 2-4 pK(a) units below expectations for such a functional group on the basis of the behavior of the hemiketal carbon atom in 13C NMR spectra [Finucane, M. D., & Malthouse, J. P. G. (1992) Biochem. J. 286, 889-900]. The low pK(a) indicates the enzymes selectively stabilize the oxyanion form of the bound inhibitor, and therefore that cmk complexes may be good models of enzyme-mediated transition-state stabilization. However, the 13C NMR studies could not rule out His57 as the titrating group. Here we report the behavior of the ring 15N atoms of His57 in the Ala-Ala-Pro-Val-cmk complex of alpha-lytic protease. Both N(delta 1) and N(epsilon 2) of His57 respond to an ionization with a pK(a) of approximately 7.5, but His57 itself does not titrate as N(epsilon 2) remains alkylated and N(delta 1) remains bonded to a proton over the entire pH range. The species titrating with a pK(a) of approximately 7.5 must therefore be the hemiketal hydroxyl. The results also show that the 1H NMR signal from the proton in the Asp-His hydrogen bond behaves in a characteristic manner in cmk complexes and can be used diagnostically to confirm that His57 does not titrate and to measure the pK(a) of the hemiketal hydroxyl in cmk-protease complexes without resorting to 15N-labeling. We have used the behavior of this signal to directly confirm that His57 does not titrate in the trypsin and chymotrypsin complexes that were the subjects of the original 13C NMR studies. PMID:8652587

  6. Differentiation of histidine tautomeric states using (15)N selectively filtered (13)C solid-state NMR spectroscopy.

    PubMed

    Miao, Yimin; Cross, Timothy A; Fu, Riqiang

    2014-08-01

    The histidine imidazole ring in proteins usually contains a mixture of three possible tautomeric states (two neutral - τ and π states and a charged state) at physiological pHs. Differentiating the tautomeric states is critical for understanding how the histidine residue participates in many structurally and functionally important proteins. In this work, one dimensional (15)N selectively filtered (13)C solid-state NMR spectroscopy is proposed to differentiate histidine tautomeric states and to identify all (13)C resonances of the individual imidazole rings in a mixture of tautomeric states. When (15)N selective 180° pulses are applied to the protonated or non-protonated nitrogen region, the (13)C sites that are bonded to the non-protonated or protonated nitrogen sites can be identified, respectively. A sample of (13)C, (15)N labeled histidine powder lyophilized from a solution at pH 6.3 has been used to illustrate the usefulness of this scheme by uniquely assigning resonances of the neutral τ and charged states from the mixture. PMID:25026459

  7. Differentiation of Histidine Tautomeric States using 15N Selectively Filtered 13C Solid-State NMR Spectroscopy

    PubMed Central

    Miao, Yimin; Cross, Timothy A.; Fu, Riqiang

    2014-01-01

    The histidine imidazole ring in proteins usually contains a mixture of three possible tautomeric states (two neutral - τ and π states and a charged state) at physiological pHs. Differentiating the tautomeric states is critical for understanding how the histidine residue participates in many structurally and functionally important proteins. In this work, one dimensional 15N selectively filtered 13C solid-state NMR spectroscopy is proposed to differentiate histidine tautomeric states and to identify all 13C resonances of the individual imidazole rings in a mixture of tautomeric states. When 15N selective 180° pulses are applied to the protonated or non-protonated nitrogen region, the 13C sites that are bonded to the non-protonated or protonated nitrogen sites can be identified, respectively. A sample of 13C,15N labeled histidine powder lyophilized from a solution at pH 6.3 has been used to illustrate the usefulness of this scheme by uniquely assigning resonances of the neutral τ and charged states from the mixture. PMID:25026459

  8. Differentiation of histidine tautomeric states using 15N selectively filtered 13C solid-state NMR spectroscopy

    NASA Astrophysics Data System (ADS)

    Miao, Yimin; Cross, Timothy A.; Fu, Riqiang

    2014-08-01

    The histidine imidazole ring in proteins usually contains a mixture of three possible tautomeric states (two neutral - τ and π states and a charged state) at physiological pHs. Differentiating the tautomeric states is critical for understanding how the histidine residue participates in many structurally and functionally important proteins. In this work, one dimensional 15N selectively filtered 13C solid-state NMR spectroscopy is proposed to differentiate histidine tautomeric states and to identify all 13C resonances of the individual imidazole rings in a mixture of tautomeric states. When 15N selective 180° pulses are applied to the protonated or non-protonated nitrogen region, the 13C sites that are bonded to the non-protonated or protonated nitrogen sites can be identified, respectively. A sample of 13C, 15N labeled histidine powder lyophilized from a solution at pH 6.3 has been used to illustrate the usefulness of this scheme by uniquely assigning resonances of the neutral τ and charged states from the mixture.

  9. Backbone dynamics of free barnase and its complex with barstar determined by 15N NMR relaxation study.

    PubMed

    Sahu, S C; Bhuyan, A K; Udgaonkar, J B; Hosur, R V

    2000-10-01

    Backbone dynamics of uniformly 15N-labeled free barnase and its complex with unlabelled barstar have been studied at 40 degrees C, pH 6.6, using 15N relaxation data obtained from proton-detected 2D [1H]-15N NMR spectroscopy. 15N spin-lattice relaxation rate constants (R1), spin-spin relaxation rate constants (R2), and steady-state heteronuclear [1H]-15N NOEs have been measured at a magnetic field strength of 14.1 Tesla for 91 residues of free barnase and for 90 residues out of a total of 106 in the complex (excluding three prolines and the N-terminal residue) backbone amide 15N sites of barnase. The primary relaxation data for both the cases have been analyzed in the framework of the model-free formalism using both isotropic and axially symmetric models of the rotational diffusion tensor. As per the latter, the overall rotational correlation times (tau(m)) are 5.0 and 9.5 ns for the free and complexed barnase, respectively. The average order parameter is found to be 0.80 for free barnase and 0.86 for the complex. However, the changes are not uniform along the backbone and for about 5 residues near the binding interface there is actually a significant decrease in the order parameters on complex formation. These residues are not involved in the actual binding. For the residues where the order parameter increases, the magnitudes vary significantly. It is observed that the complex has much less internal mobility, compared to free barnase. From the changes in the order parameters, the entropic contribution of NH bond vector motion to the free energy of complex formation has been calculated. It is apparent that these motion's cause significant unfavorable contributions and therefore must be compensated by many other favorable contributions to effect tight complex formation. The observed variations in the motion and their different locations with regard to the binding interface may have important implications for remote effects and regulation of the enzyme action. PMID

  10. /sup 15/N and /sup 13/C NMR determination of methionine metabolism in developing soybean cotyledons

    SciTech Connect

    Coker, G.T. III; Garbow, J.R.; Schaefer, J.

    1987-03-01

    The metabolism of D- and L-methionine by immature cotyledons of soybean (Glycine max, L. cv Elf) grown in culture has been investigated using solid-state /sup 13/C and /sup 15/N nuclear magnetic resonance. D-Methionine is taken up by the cotyledons and converted to an amide, most likely by N-malonylation. About 16% of the L-methionine taken up is incorporated intact into protein, and 25% remains as soluble methionine. Almost two-thirds of the L-methionine that enters the cotyledons is degraded. The largest percentage of this is used in transmethylation of the carboxyl groups of pectin. Methionine is not extensively converted to polyamines. The authors attribute the stimulation of growth of the cotyledons by exogenous methionine to the bypassing of a rate-limiting methyl-transfer step in the synthesis of methionine itself, and subsequently of pectins and proteins.

  11. 15N-labeled tRNA. Identification of 4-thiouridine in Escherichia coli tRNASer1 and tRNATyr2 by 1H-15N two-dimensional NMR spectroscopy.

    PubMed

    Griffey, R H; Davis, D R; Yamaizumi, Z; Nishimura, S; Hawkins, B L; Poulter, C D

    1986-09-15

    Uridine is uniquely conserved at position 8 in elongator tRNAs and binds to A14 to form a reversed Hoogsteen base pair which folds the dihydrouridine loop back into the core of the L-shaped molecule. On the basis of 1H NMR studies, Hurd and co-workers (Hurd, R. E., Robillard, G. T., and Reid, B. R. (1977) Biochemistry 16, 2095-2100) concluded that the interaction between positions 8 and 14 is absent in Escherichia coli tRNAs with only 3 base pairs in the dihydrouridine stem. We have taken advantage of the unique 15N chemical shift of N3 in thiouridine to identify 1H and 15N resonances for the imino units of S4U8 and s4U9 in E. coli tRNASer1 and tRNATyr2. Model studies with chloroform-soluble derivatives of uridine and 4-thiouridine show that the chemical shifts of the protons in the imino moieties move downfield from 7.9 to 14.4 ppm and from 9.1 to 15.7 ppm, respectively; whereas, the corresponding 15N chemical shifts move downfield from 157.5 to 162.5 ppm and from 175.5 to 180.1 ppm upon hydrogen bonding to 5'-O-acetyl-2',3'-isopropylidene adenosine. The large difference in 15N chemical shifts for U and s4U allows one to unambiguously identify s4U imino resonances by 15N NMR spectroscopy. E. coli tRNASer1 and tRNATyr2 were selectively enriched with 15N at N3 of all uridines and modified uridines. Two-dimensional 1H-15N chemical shift correlation NMR spectroscopy revealed that both tRNAs have resonances with 1H and 15N chemical shifts characteristic of s4UA pairs. The 1H shift is approximately 1 ppm upfield from the typical s4U8 resonance at 14.8 ppm, presumably as a result of local diamagnetic anisotropies. An additional s4U resonance with 1H and 15N shifts typical of interaction of a bound water or a sugar hydroxyl group with s4U9 was discovered in the spectrum of tRNATyr2. Our NMR results for tRNAs with 3-base pair dihydrouridine stems suggest that these molecules have an U8A14 tertiary interaction similar to that found in tRNAs with 4-base pair dihydrouridine

  12. Solution NMR Experiment for Measurement of (15)N-(1)H Residual Dipolar Couplings in Large Proteins and Supramolecular Complexes.

    PubMed

    Eletsky, Alexander; Pulavarti, Surya V S R K; Beaumont, Victor; Gollnick, Paul; Szyperski, Thomas

    2015-09-01

    NMR residual dipolar couplings (RDCs) are exquisite probes of protein structure and dynamics. A new solution NMR experiment named 2D SE2 J-TROSY is presented to measure N-H RDCs for proteins and supramolecular complexes in excess of 200 kDa. This enables validation and refinement of their X-ray crystal and solution NMR structures and the characterization of structural and dynamic changes occurring upon complex formation. Accurate N-H RDCs were measured at 750 MHz (1)H resonance frequency for 11-mer 93 kDa (2)H,(15)N-labeled Trp RNA-binding attenuator protein tumbling with a correlation time τc of 120 ns. This is about twice as long as that for the most slowly tumbling system, for which N-H RDCs could be measured, so far, and corresponds to molecular weights of ∼200 kDa at 25 °C. Furthermore, due to the robustness of SE2 J-TROSY with respect to residual (1)H density from exchangeable protons, increased sensitivity at (1)H resonance frequencies around 1 GHz promises to enable N-H RDC measurement for even larger systems. PMID:26293598

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

    PubMed

    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

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

    NASA Astrophysics Data System (ADS)

    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.

  15. Mapping membrane protein backbone dynamics: a comparison of site-directed spin labeling with NMR 15N-relaxation measurements.

    PubMed

    Lo, Ryan H; Kroncke, Brett M; Solomon, Tsega L; Columbus, Linda

    2014-10-01

    The ability to detect nanosecond backbone dynamics with site-directed spin labeling (SDSL) in soluble proteins has been well established. However, for membrane proteins, the nitroxide appears to have more interactions with the protein surface, potentially hindering the sensitivity to backbone motions. To determine whether membrane protein backbone dynamics could be mapped with SDSL, a nitroxide was introduced at 55 independent sites in a model polytopic membrane protein, TM0026. Electron paramagnetic resonance spectral parameters were compared with NMR (15)N-relaxation data. Sequential scans revealed backbone dynamics with the same trends observed for the R1 relaxation rate, suggesting that nitroxide dynamics remain coupled to the backbone on membrane proteins. PMID:25296323

  16. Alkaline Hydrolysis/Polymerization of 2,4,6-Trinitrotoluene: Characterization of Products by 13C and 15N NMR

    USGS Publications Warehouse

    Thorn, K.A.; Thorne, P.G.; Cox, L.G.

    2004-01-01

    Alkaline hydrolysis has been investigated as a nonbiological procedure for the destruction of 2,4,6-trinitrotoluene (TNT) in explosives contaminated soils and munitions scrap. Nucleophilic substitutions of the nitro and methyl groups of TNT by hydroxide ion are the initial steps in the alkaline degradation of TNT. Potential applications of the technique include both in situ surface liming and ex situ alkaline treatment of contaminated soils. A number of laboratory studies have reported the formation of an uncharacterized polymeric material upon prolonged treatment of TNT in base. As part of an overall assessment of alkaline hydrolysis as a remediation technique, and to gain a better understanding of the chemical reactions underlying the hydrolysis/polymerization process, the soluble and precipitate fractions of polymeric material produced from the calcium hydroxide hydrolysis of unlabeled and 15N-labeled TNT were analyzed by elemental analysis and 13C and 15N nuclear magnetic resonance spectroscopy. Spectra indicated that reactions leading to polymerization included nucleophilic displacement of nitro groups by hydroxide ion, formation of ketone, carboxyl, alcohol, ether, and other aliphatic carbons, conversion of methyl groups to diphenyl methylene carbons, and recondensation of aromatic amines and reduced forms of nitrite, including ammonia and possibly hydroxylamine, into the polymer. Compared to the distribution of carbons in TNT as 14% sp 3- and 86% sp2-hybridized, the precipitate fraction from hydrolysis of unlabeled TNT contained 33% sp3- and 67% sp 2-hybridized carbons. The concentration of nitrogen in the precipitate was 64% of that in TNT. The 15N NMR spectra showed that, in addition to residual nitro groups, forms of nitrogen present in the filtrate and precipitate fractions include aminohydroquinone, primary amide, indole, imine, and azoxy, among others. Unreacted nitrite was recovered in the filtrate fraction. The toxicities and susceptibilities to

  17. Interaction of yeast iso-1-cytochrome c with cytochrome c peroxidase investigated by [15N, 1H] heteronuclear NMR spectroscopy.

    PubMed

    Worrall, J A; Kolczak, U; Canters, G W; Ubbink, M

    2001-06-19

    The interaction of yeast iso-1-cytochrome c with its physiological redox partner cytochrome c peroxidase has been investigated using heteronuclear NMR techniques. Chemical shift perturbations for both 15N and 1H nuclei arising from the interaction of isotopically enriched 15N cytochrome c with cytochrome c peroxidase have been observed. For the diamagnetic, ferrous cytochrome c, 34 amides are affected by binding, corresponding to residues at the front face of the protein and in agreement with the interface observed in the 1:1 crystal structure of the complex. In contrast, for the paramagnetic, ferric protein, 56 amides are affected, corresponding to residues both at the front and toward the rear of the protein. In addition, the chemical shift perturbations were larger for the ferric protein. Using experimentally observed pseudocontact shifts the magnetic susceptibility tensor of yeast iso-1-cytochrome c in both the free and bound forms has been calculated with HN nuclei as inputs. In contrast to an earlier study, the results indicate that there is no change in the geometry of the magnetic axes for cytochrome c upon binding to cytochrome c peroxidase. This leads us to conclude that the additional effects observed for the ferric protein arise either from a difference in binding mode or from the more flexible overall structure causing a transmittance effect upon binding. PMID:11401551

  18. Mechanism of the bisphosphatase reaction of 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase probed by (1)H-(15)N NMR spectroscopy.

    PubMed

    Okar, D A; Live, D H; Devany, M H; Lange, A J

    2000-08-15

    The histidines in the bisphosphatase domain of rat liver 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase were labeled with (15)N, both specifically at N1' and globally, for use in heteronuclear single quantum correlation (HSQC) NMR spectroscopic analyses. The histidine-associated (15)N resonances were assigned by correlation to the C2' protons which had been assigned previously [Okar et al., Biochemistry 38, 1999, 4471-79]. Acquisition of the (1)H-(15)N HSQC from a phosphate-free sample demonstrated that the existence of His-258 in the rare N1' tautomeric state is dependent upon occupation of the phosphate binding site filled by the O2 phosphate of the substrate, fructose-2,6-bisphosphate, and subsequently, the phosphohistidine intermediate. The phosphohistidine intermediate is characterized by two hydrogen bonds involving the catalytic histidines, His-258 and His-392, which are directly observed at the N1' positions of the imidazole rings. The N1' of phospho-His-258 is protonated ((1)H chemical shift, 14.0 ppm) and hydrogen bonded to the backbone carbonyl of Gly-259. The N1' of cationic His-392 is hydrogen bonded ((1)H chemical shift, 13.5 ppm) to the phosphoryl moiety of the phosphohistidine. The existence of a protonated phospho-His-258 intermediate and the observation of a fairly strong hydrogen bond to the same phosphohistidine implies that hydrolysis of the covalent intermediate proceeds without any requirement for an "activated" water. Using the labeled histidines as probes of the catalytic site mutation of Glu-327 to alanine revealed that, in addition to its function as the proton donor to fructose-6-phosphate during formation of the transient phosphohistidine intermediate at the N3' of His-258, this residue has a significant role in maintaining the structural integrity of the catalytic site. The (1)H-(15)N HSQC data also provide clear evidence that despite being a surface residue, His-446 has a very acidic pK(a), much less than 6.0. On the basis of

  19. COVALENT BINDING OF REDUCED METABOLITES OF [15N3] TNT TO SOIL ORGANIC MATTER DURING A BIOREMEDIATION PROCESS ANALYZED BY 15N NMR SPECTROSCOPY. (R826646)

    EPA Science Inventory

    Evidence is presented for the covalent binding of
    biologically reduced metabolites of 2,4,6-15N3-trinitrotoluene
    (TNT) to different soil fractions (humic acids, fulvic
    acids, and humin) using liquid 15N NMR spectroscopy. A
    silylation p...

  20. sup 15 N NMR study on cyanide (C sup 15 N sup minus ) complex of cytochrome P-450 sub cam. Effects of d-camphor and putidaredoxin on the iron-ligand structure

    SciTech Connect

    Shiro, Yoshitsugu; Iizuka, Tetsutaro ); Makino, Ryu; Ishimura, Yuzuru ); Morishima, Isao )

    1989-11-27

    The cyanide (C{sup 15}N{sup {minus}}) complex of Pseudomonas putida cytochrome P-450 (P-450{sub cam}) exhibited well-resolved and hyperfine-shifted {sup 15}N NMR resonances arising from the iron-bound C{sup 15}N{sup {minus}} at 423 and 500 ppm in the absence and presence of the substrate, d-camphor, respectively. The values were smaller than those for cyanide complexes of myoglobin and hemoglobin ({approx} 1000 ppm) but fell into the same range as those for the cyanide complexes of peroxidases ({approx} 500 ppm). The {sup 15}N shift values of P-450{sub cam} were not incompatible with the existence of anionic ligand, such as cysteinyl thiolate anion, at the fifth coordination site of heme iron. The difference in the {sup 15}N chemical shift values between camphor-free and bound enzymes was inferred by the increase in the steric constraint to the Fe-C-N bond upon substrate binding.

  1. Theoretical and experimental (15)N NMR study of enamine-imine tautomerism of 4-trifluoromethyl[b]benzo-1,4-diazepine system.

    PubMed

    Semenov, Valentin A; Samultsev, Dmitry O; Rulev, Alexander Yu; Krivdin, Leonid B

    2015-12-01

    The tautomeric structure of 4-trifluoromethyl[b]benzo-1,4-diazepine system in solution has been evaluated by means of the calculation of (15)N NMR chemical shifts of individual tautomers in comparison with the averaged experimental shifts to show that the enamine-imine equilibrium is entirely shifted toward the imine form. The adequacy of the theoretical level used for the computation of (15)N NMR chemical shifts in this case has been verified based on the benchmark calculations in the series of the push-pull and captodative enamines together with related azomethynes, which demonstrated a good to excellent agreement with experiment. PMID:26290420

  2. Effects of ion binding on the backbone dynamics of calbindin D9k determined by 15N NMR relaxation.

    PubMed

    Akke, M; Skelton, N J; Kördel, J; Palmer, A G; Chazin, W J

    1993-09-21

    The backbone dynamics of apo- and (Cd2+)1-calbindin D9k have been characterized by 15N nuclear magnetic resonance spectroscopy. Spin-lattice and spin-spin relaxation rate constants and steady-state [1H]-15N nuclear Overhauser effects were measured at a magnetic field strength of 11.74 T by two-dimensional, proton-detected heteronuclear NMR experiments using 15N-enriched samples. The relaxation parameters were analyzed using a model-free formalism that characterizes the dynamics of the N-H bond vectors in terms of generalized order parameters and effective correlation times. The data for the apo and (Cd2+)1 states were compared to those for the (Ca2+)2 state [Kördel, J., Skelton, N. J., Akke, M., Palmer, A. G., & Chazin, W. J. (1992) Biochemistry 31, 4856-4866] to ascertain the effects on ion ligation on the backbone dynamics of calbindin D9k. The two binding loops respond differently to ligation by metal ions: high-frequency (10(9)-10(12) s-1) fluctuations of the N-terminal ion-binding loop are not affected by ion binding, whereas residues G57, D58, G59, and E60 in the C-terminal ion-binding loop have significantly lower order parameters in the apo state than in the metal-bound states. The dynamical responses of the four helices to binding of ions are much smaller than that for the C-terminal binding loop, with the strongest effect on helix III, which is located between the linker loop and binding site II. Significant fluctuations on slower time scales also were detected in the unoccupied N-terminal ion-binding loop of the apo and (Cd2+)1 states; the apparent rates were greater for the (Cd2+)1 state. These results on the dynamical response to ion binding in calbindin D9k provide insights into the molecular details of the binding process and qualitative evidence for entropic contributions to the cooperative phenomenon of calcium binding for the pathway in which the ion binds first in the C-terminal site. PMID:8373781

  3. Spectroscopic labeling of A, S/T in the 1H- 15N HSQC spectrum of uniformly ( 15N- 13C) labeled proteins

    NASA Astrophysics Data System (ADS)

    Chugh, Jeetender; Hosur, Ramakrishna V.

    2008-10-01

    A new triple resonance two-dimensional experiment, termed (HC)NH, has been described to generate specific labels on the peaks of alanines and serines/threonines, separately, in the 1H- 15N HSQC spectrum of a protein. The performance of the pulse sequence has been demonstrated with a 151 residue protein. The method permits the investigation of local environments around those specific residues without actually having to obtain complete resonance assignments for the entire protein. With this one can envisage use of the technique for studying large protein systems from different points of view.

  4. High Field Solid-State NMR Spectroscopy Investigation of (15)N-Labeled Rosette Nanotubes: Hydrogen Bond Network and Channel-Bound Water.

    PubMed

    Fenniri, Hicham; Tikhomirov, Grigory A; Brouwer, Darren H; Bouatra, Souhaila; El Bakkari, Mounir; Yan, Zhimin; Cho, Jae-Young; Yamazaki, Takeshi

    2016-05-18

    (15)N-labeled rosette nanotubes were synthesized and investigated using high-field solid-state NMR spectroscopy, X-ray diffraction, atomic force microscopy, and electron microscopy. The results established the H-bond network involved in the self-assembly of the nanostructure as well as bound water molecules in the nanotube's channel. PMID:27141817

  5. Exogenous proline relieves growth inhibition caused by NaCl in petunia cells: Metabolism of L-( sup 15 M)-proline followed by sup 15 N NMR

    SciTech Connect

    Heyser, J.W.; Chacon, M.J. )

    1989-04-01

    Exogenous proline stimulated the growth of Petunia hybrida cells on 195 mM NaCl 10-fold as compared with cells grown on 195 mM CaCl medium minus proline. L-({sup 15}N)-proline was fed to cells growing on 0 and 195 mM CaCl, and its metabolism was followed by {sup 15}N NMR analysis of cell extracts. Total proline and amino acids were determined by ninhydrin assay. Proline and primary amino acids were easily resolved in NMR spectra and the amount of {sup 15}N-label which remained in proline was determined. Reduced catabolism of proline in cells grown on NaCl was evident. The role of exogenous proline in conferring increased NaCl tolerance in this nonhalophyte will be discussed.

  6. Multinuclear 1H, 13C and 15N NMR study of some substituted 2-amino-4-nitropyridines and their N-oxides

    NASA Astrophysics Data System (ADS)

    Laihia, K.; Kolehmainen, E.; Kauppinen, R.; Lorenc, J.; Puszko, A.

    2002-05-01

    1H, 13C and 15N NMR chemical shift assignments based on pulsed field gradient selected PFG 1H,X (X= 13C and 15N) HMQC and HMBC experiments are reported for three 4-nitropyridine N-oxides and four 4-nitropyridines. It was found that an ortho effect of a methyl group inhibits the deshielding effect of the 4-nitro group and that this effect and the so-called back donation is influenced by electronegativity and position of substituents in the multisubstituted pyridine N-oxides. The shielding effect of N-oxide group is most pronounced in the 15N NMR chemical shifts of the studied compounds. This effect is further modified by methylamino, methylnitramino, 5- or 3-methyl and 4-nitro groups. Among them the 4-nitro group exerts the highest influence on the shielding effect of the N-oxide functionality. Experimental 1H, 13C and 15N NMR chemical shifts and GIAO/DFT theoretical calculations are consistent with each other and supported by the reactivity on nucleophilic substitution, the UV spectral and the dipole moment data.

  7. Characterization of the nitrate complexes of Pu(IV) using absorption spectroscopy, {sup 15}N NMR, and EXAFS

    SciTech Connect

    Veirs, D.K.; Smith, C.A.; Zwick, B.D.; Marsh, S.F.; Conradson, S.D.

    1993-12-01

    Nitrate complexes of Pu(IV) are studied in solutions containing nitrate up to 13 molar (M). Three major nitrato complexes are observed and identified using absorption spectroscopy, {sup 15}N nuclear magnetic resonance (NMR), and extended x-ray absorption fine structure (EXAFS) as Pu(NO{sub 3}){sub 2}{sup 2+}, Pu(NO{sub 3}){sub 4}, and Pu(NO{sub 3}){sub 6}{sup 2{minus}}. The possibility that Pu(NO{sub 3}){sub 1}{sup 3+}, Pu(NO{sub 3}){sub 3}{sup 1+} and Pu(NO{sub 3}){sub 5}{sup 1{minus}} are major species in solution is not consistent with these results and an upper limit of 0.10 can be set on the fraction for each of these three nitrate complexes in nitrate containing solutions. Fraction of the three major species in nitric acid over the 1--13 M range were calculated from absorption spectra data. The fraction of Pu(NO{sub 3}){sub 6}{sup 2{minus}} as a function of nitric acid concentration is in good agreement with the literature, whereas the fraction of Pu(NO{sub 3}){sub 2}{sup 2+} and Pu(NO{sub 3}){sub 4} species differ from previous studies. We have modeled the chemical equilibria up to moderate ionic strength ( < 6 molal) using the specific ion interaction theory (SM. Comparison of our experimental observations to literature stability constants that assume the presence of mononitrate species is poor. Stability constant at zero ionic strength for the dinitrato complex is determined to be log({beta}{sub 2}{sup 0})=3.77 {plus_minus} 0.14 (2{sigma}).

  8. 1H, 13C, 15N and 195Pt NMR studies of Au(III) and Pt(II) chloride organometallics with 2-phenylpyridine.

    PubMed

    Pazderski, Leszek; Pawlak, Tomasz; Sitkowski, Jerzy; Kozerski, Lech; Szłyk, Edward

    2009-11-01

    (1)H, (13)C, (15)N and (195)Pt NMR studies of gold(III) and platinum(II) chloride organometallics with N(1),C(2')-chelated, deprotonated 2-phenylpyridine (2ppy*) of the formulae [Au(2ppy*)Cl(2)], trans(N,N)-[Pt(2ppy*)(2ppy)Cl] and trans(S,N)-[Pt(2ppy*)(DMSO-d(6))Cl] (formed in situ upon dissolving [Pt(2ppy*)(micro-Cl)](2) in DMSO-d(6)) were performed. All signals were unambiguously assigned by HMBC/HSQC methods and the respective (1)H, (13)C and (15)N coordination shifts (i.e. differences between chemical shifts of the same atom in the complex and ligand molecules: Delta(1H)(coord) = delta(1H)(complex) - delta(1H)(ligand), Delta(13C)(coord) = delta(13C)(complex) - delta(13C)(ligand), Delta(15N)(coord) = delta(15N)(complex) - delta(15N)(ligand)), as well as (195)Pt chemical shifts and (1)H-(195)Pt coupling constants discussed in relation to the known molecular structures. Characteristic deshielding of nitrogen-adjacent H(6) protons and metallated C(2') atoms as well as significant shielding of coordinated N(1) nitrogens is discussed in respect to a large set of literature NMR data available for related cyclometallated compounds. PMID:19691018

  9. NMR-spectroscopic analysis of mixtures: from structure to function

    PubMed Central

    Forseth, Ry R.; Schroeder, Frank C.

    2010-01-01

    NMR spectroscopy as a particularly information-rich method offers unique opportunities for improving the structural and functional characterization of metabolomes, which will be essential for advancing the understanding of many biological processes. Whereas traditionally NMR spectroscopy was mostly relegated to the characterization of pure compounds, the last few years have seen a surge of interest in using NMR spectroscopic techniques for characterizing complex metabolite mixtures. Development of new methods was motivated partly by the realization that using NMR for the analysis of metabolite mixtures can help identify otherwise inaccessible small molecules, for example compounds that are prone to chemical decomposition and thus cannot be isolated. Furthermore, comparative metabolomics and statistical analyses of NMR-spectra have proven highly effective at identifying novel and known metabolites that correlate with changes in genotype or phenotype. In this review, we provide an overview of the range of NMR spectroscopic techniques recently developed for characterizing metabolite mixtures, including methods used in discovery-oriented natural product chemistry, in the study of metabolite biosynthesis and function, or for comparative analyses of entire metabolomes. PMID:21071261

  10. Simultaneous cross polarization to 13C and 15N with 1H detection at 60 kHz MAS solid-state NMR

    NASA Astrophysics Data System (ADS)

    Das, Bibhuti B.; Opella, Stanley J.

    2016-01-01

    We describe high resolution MAS solid-state NMR experiments that utilize 1H detection with 60 kHz magic angle spinning; simultaneous cross-polarization from 1H to 15N and 13C nuclei; bidirectional cross-polarization between 13C and 15N nuclei; detection of both amide nitrogen and aliphatic carbon 1H; and measurement of both 13C and 15N chemical shifts through multi-dimensional correlation experiments. Three-dimensional experiments correlate amide 1H and alpha 1H selectively with 13C or 15N nuclei in a polypeptide chain. Two separate three-dimensional spectra correlating 1Hα/13Cα/1HN and 1HN/15N/1Hα are recorded simultaneously in a single experiment, demonstrating that a twofold savings in experimental time is potentially achievable. Spectral editing using bidirectional coherence transfer pathways enables simultaneous magnetization transfers between 15N, 13Cα(i) and 13C‧(i-1), facilitating intra- and inter-residue correlations for sequential resonance assignment. Non-uniform sampling is integrated into the experiments, further reducing the length of experimental time.

  11. ¹H and (15)N NMR Analyses on Heparin, Heparan Sulfates and Related Monosaccharides Concerning the Chemical Exchange Regime of the N-Sulfo-Glucosamine Sulfamate Proton.

    PubMed

    Pomin, Vitor H

    2016-01-01

    Heparin and heparan sulfate are structurally related glycosaminoglycans (GAGs). Both GAGs present, although in different concentrations, N-sulfo-glucosamine (GlcNS) as one of their various composing units. The conditional fast exchange property of the GlcNS sulfamate proton in these GAGs has been pointed as the main barrier to its signal detection via NMR experiments, especially ¹H-(15)N HSQC. Here, a series of NMR spectra is collected on heparin, heparan sulfate and related monosaccharides. The N-acetyl glucosamine-linked uronic acid types of these GAGs were properly assigned in the ¹H-(15)N HSQC spectra. Dynamic nuclear polarization (DNP) was employed in order to facilitate 1D spectral acquisition of the sulfamate (15)N signal of free GlcNS. Analyses on the multiplet pattern of scalar couplings of GlcNS (15)N has helped to understand the chemical properties of the sulfamate proton in solution. The singlet peak observed for GlcNS happens due to fast chemical exchange of the GlcNS sulfamate proton in solution. Analyses on kinetics of alpha-beta anomeric mutarotation via ¹H NMR spectra have been performed in GlcNS as well as other glucose-based monosaccharides. 1D ¹H and 2D ¹H-(15)N HSQC spectra recorded at low temperature for free GlcNS dissolved in a proton-rich solution showed signals from all exchangeable protons, including those belonging to the sulfamate group. This work suits well to the current grand celebration of one-century-anniversary of the discovery of heparin. PMID:27618066

  12. Evidence of entropy-driven bistability through (15)N NMR analysis of a temperature- and solvent-induced, chiroptical switching polycarbodiimide.

    PubMed

    Reuther, James F; Novak, Bruce M

    2013-12-26

    The thermo- and solvo-driven chiroptical switching process observed in specific polycarbodiimides occurs in a concerted fashion with large deviations in specific optical rotation (OR) and CD Cotton effect as a consequence of varying populations of two distinct polymer conformations. These two conformations are clearly visible in the (15)N NMR and IR spectra of the (15)N-labeled poly((15)N-(1-naphthyl)-N'-octadecylcarbodiimide) (Poly-3) and poly((15)N-(1-naphthyl)-(15)N'-octadecylcarbodiimide) (Poly-5). Using van't Hoff analysis, the enthalpies and entropies of switching (ΔHswitching; ΔSswitching) were calculated for both Poly-3 and Poly-5 using the relative integrations of both peaks in the (15)N NMR spectra at different temperatures to measure the populations of each state. The chiroptical switching (i.e., transitioning from state A to state B) was found to be an endothermic process (positive ΔHswitching) for both Poly-3 and Poly-5 in all solvents studied, meaning the conformation correlating with the downfield chemical shift (ca. 148 ppm, state B) is the higher enthalpy state. The compensating factor behind this phenomenon has been determined to be the large increase in entropy in CHCl3 as a result of the switching. Herein, we propose that the increased entropy in the system is a direct consequence of increased disorder in the solvent as the switching occurs. Specifically, the chloroform solvent molecules are very ordered around the polymer chains due to favorable solvent-polymer interactions, but as the switching occurs, these interactions become less favorable and disorder results. The same level of solvent disorder is not achieved in toluene, causing the chiroptical switching process to occur at higher temperatures. PMID:24313274

  13. Quantitation of metabolic compartmentation in hyperammonemic brain by natural abundance 13C-NMR detection of 13C-15N coupling patterns and isotopic shifts.

    PubMed

    Lapidot, A; Gopher, A

    1997-02-01

    In the present study, the removal of cerebral ammonia by glutamine synthetase (GS) and by reductive amination of 2-oxoglutarate by glutamate dehydrogenase in the presence of an amino donor group, was determined in hyperammonemic rabbit brains. The 15N enrichments of brain metabolite alpha-amino and amide positions of glutamine, glutamate, and alanine were determined by the indirect detection of 15N-labeled compounds of the 13C-15N spin coupling patterns of natural abundance 13C-NMR spectra. The 13C-NMR spectra of brain extracts were obtained from rabbits infused with 15NH4Cl with or without intraperitoneal infusion of the GS inhibitor, L-methionine DL-sulfoximine, in a reasonable acquisition time period. When 15NH4Cl was infused, [5-15N]glutamine and [2-15N]glutamine concentrations reached 5.2 mumol/100 mg protein and 3.6 mumol/100 mg protein, respectively, which indicates the relatively high activity of reductive amination of 2-oxoglutarate in the glutamate dehydrogenase reaction. The low concentration of [2-15N]glutamate, which is about 30% of that of [2-15N]glutamine obtained in this study, suggests that very little glutamine serves as a precursor of neuronal glutamate. When GS was inhibited by L-methionine DL-sulfoximine, a flux of 15NH4+ via the residual activity of GS was accompanied by an apparent increase of [2-15N]glutamate and [15N]alanine concentrations (2.9 mumol/100 mg protein and 1.8 mumol/100 mg protein, respectively). These findings and those obtained from 13C-13C isotopomer analysis (Lapidot and Gopher, 1994b) suggest that astrocytic 2-oxoglutarate is partially utilized (together with an amino group donor) as a precursor for neuronal glutamate in the hyperammonemic brain when GS is inhibited. This process can partly replace GS activity in metabolizing ammonia in the hyperammonemic rabbit brain. PMID:9057821

  14. DFT calculations of 15N NMR shielding constants, chemical shifts and complexation shifts in complexes of rhodium(II) tetraformate with some nitrogenous organic ligands

    NASA Astrophysics Data System (ADS)

    Leniak, Arkadiusz; Jaźwiński, Jarosław

    2015-03-01

    Benchmark calculations of 15N NMR shielding constants for a set of model complexes of rhodium(II) tetraformate with nine organic ligands using the Density Functional Theory (DFT) methods have been carried out. The calculations were performed by means of several methods: the non-relativistic, relativistic scalar ZORA, and spin-orbit ZORA approaches at the CGA-PBE/QZ4P theory level, and the GIAO NMR method using the B3PW91 functional with the 6-311++G(2d,p) basis set for C, H, N, O atoms and the Stuttgart basis set for the Rh atom. The geometry of compounds was optimised either by the same basis set as for the NMR calculations or applying the B3LYP functional with the 6-31G(2d) basis set for C, H, N, O atoms and LANL2DZ for the Rh atom. Computed 15N NMR shielding constants σ were compatible with experimental 15N chemical shifts δ of complexes exhibiting similar structure and fulfil the linear equation δ = aσ + b. The a and b parameters for all data sets have been estimated by means of linear regression analysis. In contrast to the correlation method giving "scaled" chemical shifts, the conversion of shielding constants to chemical shifts with respect to the reference shielding of CH3NO2 provided very inaccurate "raw" δ values. The application of the former to the calculation of complexation shifts Δδ (Δδ = δcompl - δlig) reproduced experimental values qualitatively or semi-quantitatively. The non-relativistic B3PW91/[6-311++G(2d,p), Stuttgart] theory level reproduced the NMR parameters as good as the more expensive relativistic CGA-PBE//QZ4P ZORA approaches.

  15. A facile method for expression and purification of (15)N isotope-labeled human Alzheimer's β-amyloid peptides from E. coli for NMR-based structural analysis.

    PubMed

    Sharma, Sudhir C; Armand, Tara; Ball, K Aurelia; Chen, Anna; Pelton, Jeffrey G; Wemmer, David E; Head-Gordon, Teresa

    2015-12-01

    Alzheimer's disease (AD) is a progressive neurodegenerative disease affecting millions of people worldwide. AD is characterized by the presence of extracellular plaques composed of aggregated/oligomerized β-amyloid peptides with Aβ42 peptide representing a major isoform in the senile plaques. Given the pathological significance of Aβ42 in the progression of AD, there is considerable interest in understanding the structural ensembles for soluble monomer and oligomeric forms of Aβ42. This report describes an efficient method to express and purify high quality (15)N isotope-labeled Aβ42 for structural studies by NMR. The protocol involves utilization of an auto induction system with (15)N isotope labeled medium, for high-level expression of Aβ42 as a fusion with IFABP. After the over-expression of the (15)N isotope-labeled IFABP-Aβ42 fusion protein in the inclusion bodies, pure (15)N isotope-labeled Aβ42 peptide is obtained following a purification method that is streamlined and improved from the method originally developed for the isolation of unlabeled Aβ42 peptide (Garai et al., 2009). We obtain a final yield of ∼ 6 mg/L culture for (15)N isotope-labeled Aβ42 peptide. Mass spectrometry and (1)H-(15)N HSQC spectra of monomeric Aβ42 peptide validate the uniform incorporation of the isotopic label. The method described here is equally applicable for the uniform isotope labeling with (15)N and (13)C in Aβ42 peptide as well as its other variants including any Aβ42 peptide mutants. PMID:26231074

  16. Cerebral glutamine metabolism under hyperammonemia determined in vivo by localized 1H and 15N NMR spectroscopy

    PubMed Central

    Cudalbu, Cristina; Lanz, Bernard; Duarte, João MN; Morgenthaler, Florence D; Pilloud, Yves; Mlynárik, Vladimir; Gruetter, Rolf

    2012-01-01

    Brain glutamine synthetase (GS) is an integral part of the glutamate–glutamine cycle and occurs in the glial compartment. In vivo Magnetic Resonance Spectroscopy (MRS) allows noninvasive measurements of the concentrations and synthesis rates of metabolites. 15N MRS is an alternative approach to 13C MRS. Incorporation of labeled 15N from ammonia in cerebral glutamine allows to measure several metabolic reactions related to nitrogen metabolism, including the glutamate–glutamine cycle. To measure 15N incorporation into the position 5N of glutamine and position 2N of glutamate and glutamine, we developed a novel 15N pulse sequence to simultaneously detect, for the first time, [5-15N]Gln and [2-15N]Gln+Glu in vivo in the rat brain. In addition, we also measured for the first time in the same experiment localized 1H spectra for a direct measurement of the net glutamine accumulation. Mathematical modeling of 1H and 15N MRS data allowed to reduce the number of assumptions and provided reliable determination of GS (0.30±0.050 μmol/g per minute), apparent neurotransmission (0.26±0.030 μmol/g per minute), glutamate dehydrogenase (0.029±0.002 μmol/g per minute), and net glutamine accumulation (0.033±0.001 μmol/g per minute). These results showed an increase of GS and net glutamine accumulation under hyperammonemia, supporting the concept of their implication in cerebral ammonia detoxification. PMID:22167234

  17. Monitoring the refinement of crystal structures with {sup 15}N solid-state NMR shift tensor data

    SciTech Connect

    Kalakewich, Keyton; Eloranta, Harriet; Harper, James K.; Iuliucci, Robbie; Mueller, Karl T.

    2015-11-21

    The {sup 15}N chemical shift tensor is shown to be extremely sensitive to lattice structure and a powerful metric for monitoring density functional theory refinements of crystal structures. These refinements include lattice effects and are applied here to five crystal structures. All structures improve based on a better agreement between experimental and calculated {sup 15}N tensors, with an average improvement of 47.0 ppm. Structural improvement is further indicated by a decrease in forces on the atoms by 2–3 orders of magnitude and a greater similarity in atom positions to neutron diffraction structures. These refinements change bond lengths by more than the diffraction errors including adjustments to X–Y and X–H bonds (X, Y = C, N, and O) of 0.028 ± 0.002 Å and 0.144 ± 0.036 Å, respectively. The acquisition of {sup 15}N tensors at natural abundance is challenging and this limitation is overcome by improved {sup 1}H decoupling in the FIREMAT method. This decoupling dramatically narrows linewidths, improves signal-to-noise by up to 317%, and significantly improves the accuracy of measured tensors. A total of 39 tensors are measured with shifts distributed over a range of more than 400 ppm. Overall, experimental {sup 15}N tensors are at least 5 times more sensitive to crystal structure than {sup 13}C tensors due to nitrogen’s greater polarizability and larger range of chemical shifts.

  18. Properties of bridgehead-substituted polycycloalkanes. Synthesis and NMR analysis of /sup 15/N-labeled 1-aminobicycloalkanes and their hydrochlorides

    SciTech Connect

    Della, E.W.; Kasum, B.; Kirkbride, K.P.

    1987-04-29

    NMR analysis of adamantane and four bicycloalkanes substituted at the bridgehead with /sup 15/N-labeled amino and ammonio groups is described. It is found that where most of the one-bond carbon-nitrogen coupling constants are relatively large, those in 1-aminobicyclo (1.1.1)pentane and its hydrochloride are significantly reduced; in fact, in the latter compound one-bond /sup 13/C-/sup 15/N coupling could not even be detected. Values of experimentally determined vicinal couplings were in accord with those expected on the basis of the number of three-bond pathways available for transmission of spin-spin information; INDO calculations, however, suggest that in the more highly strained systems there is a substantial contribution to /sup 3/J(CN) arising from through-space interactions and that these oppose through-bond effects. Large four-bond /sup 15/N-/sup 1/H couplings were found to occur in 1-aminobicyclo(1.1.1)pentane and its hydrochloride; MO calculations indicate that through-space interactions constitute the predominant mechanism contributing to /sup 4/J(/sup 15/N-/sup 1/H), although in this case through-bond and through-space effects reinforce each other. The nitrogen-15 chemical shifts of the amine hydrochlorides were determined, and they appear to occur in random fashion.

  19. 2D NMR-spectroscopic screening reveals polyketides in ladybugs

    PubMed Central

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

    2011-01-01

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

  20. 2D NMR-spectroscopic screening reveals polyketides in ladybugs.

    PubMed

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

    2011-06-14

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

  1. HCN, a triple-resonance NMR technique for selective observation of histidine and tryptophan side chains in 13C/15N-labeled proteins.

    PubMed

    Sudmeier, J L; Ash, E L; Günther, U L; Luo, X; Bullock, P A; Bachovchin, W W

    1996-12-01

    HCN, a new 3D NMR technique for stepwise coherence transfer from 1H to 13C to 15N and reverse through direct spin couplings 1JCH and 1JCN, is presented as a method for detection and assignment of histidine and tryptophan side-chain 1H, 13C, and 15N resonances in uniformly 13C/15N-labeled proteins. Product-operator calculations of cross-peak volumes vs adjustable delay tau 3 were employed for determination of optimal tau 3. For the phosphatidylinositol 3-kinase (PI3K SH3 domain, MW = 9.6 kD) at pH 6, H(C)N, the 1H/15N projection, produced observable cross peaks within 20 min. and was completely selective for the single tryptophan and single histidine. The 3D HCN experiment yielded well-defined cross peaks in 20 h for the 13C/15N-labeled origin-specific DNA binding domain from simian virus 40 T-antigen (T-ag-OBD131-259, MW = 15.4 kD) at pH 5.5. Resonances from all six histidines in T-ag-OBD were observed, and 11 of the 12 1H and 13C chemical shifts and 10 of the 12 15N chemical shifts were determined. The 13C dimension proved essential in assignment of the multiply overlapping 1H and 15N resonances. From the spectra recorded at a single pH, three of the imidazoles were essentially neutral and the other three were partially protonated (22-37%). HCN yielded strong cross peaks after 18 h on a 2.0 mM sample of phenylmethanesulfonyl fluoride (PMSF)-inhibited alpha-lytic protease (MW = 19.8 kD) at pH 4.4. No spectra have been obtained, however, of native or boronic acid-inhibited alpha-lytic protease after 18 h at various temperatures ranging from 5 to 55 degrees C, probably due to efficient relaxation of active-site imidazole 1H and/or 15N nuclei. PMID:8995843

  2. Oligomeric complexes of some heteroaromatic ligands and aromatic diamines with rhodium and molybdenum tetracarboxylates: 13C and 15N CPMAS NMR and density functional theory studies.

    PubMed

    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

  3. Assignment of the sup 1 H and sup 15 N NMR spectra of Rhodobacter capsulatus ferrocytochrome c sub 2

    SciTech Connect

    Gooley, P.R.; Caffrey, M.S.; Cusanovich, M.A.; MacKenzie, N.E. )

    1990-03-06

    The peptide resonances of the {sup 1}H and {sup 15}N nuclear magnetic resonance spectra of ferrocytochrome c{sub 2} from Rhodobacter capsulatus are sequentially assigned by a combination of 2D {sup 1}H-{sup 1}H and {sup 1}H-{sup 15}N spectroscopy, the latter performed on {sup 15}N-enriched protein. Short-range nuclear Overhauser effect (NOE) data show {alpha}-helices from residues 3-17, 55-65, 69-88, and 103-115. Within the latter two {alpha}-helices, there are three single 3{sub 10} turns, 70-72, 76-78, and 107-109. In addition {alpha}H-NH{sub i+1} and {alpha}H-NH{sub i+2} NOEs indicate that the N-terminal helix (3-17) is distorted. Compared to horse or tuna cytochrome c and cytochrome c{sub 2} of Rhodospirillium rubrum, there is a 6-residue insertion at residues 23-29 in R. capsulatus cytochrome c{sub 2}. The NOE data show that this insertion forms a loop, probably an {Omega} loop. {sup 1}H-{sup 15}N heteronuclear multiple quantum correlation experiments are used to follow NH exchange over a period of 40 h. As the 2D spectra are acquired in short time periods (30 min), rates for intermediate exchanging protons can be measured. Comparison of the NH exchange data for the N-terminal helix of cytochrome c{sub 2} of R. capsulatus with the highly homologous horse heart cytochrome c shows that this helix is less stable in cytochrome c{sub 2}.

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

    PubMed Central

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

    2014-01-01

    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 liposomes. 13C MAS NMR spectra were recorded without sensitivity enhancement for direct comparison of Cα, Cβ, and C=O bands of superimposed resonances with predictions from protein structures generated by MD. The experimental NMR spectra matched the calculated spectra reasonably well indicating agreement of the global fold of the protein between experiment and simulations. In particular, the 13C chemical shift distribution of Cα resonances was shown to be very sensitive to both the primary amino acid sequence and the secondary structure of CB2. Thus the shape of the Cα band can be used as an indicator of CB2 global fold. The prediction from MD simulations indicated that upon receptor activation a rather limited number of amino acid residues, mainly located in the extracellular loop 2 and the second half of intracellular loop 3, change their chemical shifts significantly (≥1.5 ppm for carbons and ≥5.0 ppm for nitrogens). Simulated two-dimensional 13Cα(i)-13C=O(i) and 13C=O(i)-15NH(i+1) dipolar-interaction correlation spectra provide guidance for selective amino-acid labeling and signal assignment schemes to study the molecular mechanism of activation of CB2 by solid-state MAS NMR. PMID:23999926

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

    NASA Astrophysics Data System (ADS)

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

    1996-12-01

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

  6. The theoretical investigation of solvent effects on the relative stability and 15N NMR shielding of antidepressant heterocyclic drug

    NASA Astrophysics Data System (ADS)

    Tahan, Arezoo; Khojandi, Mahya; Salari, Ali Akbar

    2016-01-01

    The density functional theory (DFT) and Tomasi's polarized continuum model (PCM) were used for the investigation of solvent polarity and its dielectric constant effects on the relative stability and NMR shielding tensors of antidepressant mirtazapine (MIR). The obtained results indicated that the relative stability in the polar solvents is higher than that in non-polar solvents and the most stable structure was observed in the water at the B3LYP/6-311++G ( d, p) level of theory. Also, natural bond orbital (NBO) interpretation demonstrated that by increase of solvent dielectric constant, negative charge on nitrogen atoms of heterocycles and resonance energy for LP(N10) → σ* and π* delocalization of the structure's azepine ring increase and the highest values of them were observed in water. On the other hand, NMR calculations showed that with an increase in negative charge of nitrogen atoms, isotropic chemical shielding (σiso) around them increase and nitrogen of piperazine ring (N19) has the highest values of negative charge and σiso among nitrogen atoms. NMR calculations also represented that direct solvent effect on nitrogen of pyridine ring (N15) is more than other nitrogens, while its effect on N19 is less than other ones. Based on NMR data and NBO interpretation, it can be deduced that with a decrease in the negative charge on nitrogen atoms, the intramolecular effects on them decrease, while direct solvent effect increases.

  7. Time resolved spectroscopic NMR imaging using hyperpolarized 129Xe.

    PubMed

    Han, S; Kühn, H; Häsing, F W; Münnemann, K; Blümich, B; Appelt, S

    2004-04-01

    We have visualized the melting and dissolution processes of xenon (Xe) ice into different solvents using the methods of nuclear magnetic resonance (NMR) spectroscopy, imaging, and time resolved spectroscopic imaging by means of hyperpolarized 129Xe. Starting from the initial condition of a hyperpolarized solid Xe layer frozen on top of an ethanol (ethanol/water) ice block we measured the Xe phase transitions as a function of time and temperature. In the pure ethanol sample, pieces of Xe ice first fall through the viscous ethanol to the bottom of the sample tube and then form a thin layer of liquid Xe/ethanol. The xenon atoms are trapped in this liquid layer up to room temperature and keep their magnetization over a time period of 11 min. In the ethanol/water mixture (80 vol%/20%), most of the polarized Xe liquid first stays on top of the ethanol/water ice block and then starts to penetrate into the pores and cracks of the ethanol/water ice block. In the final stage, nearly all the Xe polarization is in the gas phase above the liquid and trapped inside the pores. NMR spectra of homogeneous samples of pure ethanol containing thermally polarized Xe and the spectroscopic images of the melting process show that very high concentrations of hyperpolarized Xe (about half of the density of liquid Xe) can be stored or delivered in pure ethanol. PMID:15040986

  8. 2D 1H and 3D 1H-15N NMR of zinc-rubredoxins: contributions of the beta-sheet to thermostability.

    PubMed Central

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

    1996-01-01

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

  9. High Resolution 15N NMR of the 225 K Phase Transition of Ammonia Borane (NH3BH3): Mixed Order-Disorder and Displacive Behavior

    SciTech Connect

    Gunaydin-Sen, Ozge; Achey, Randall; Dalal, Nar S.; Stowe, Ashley C.; Autrey, Thomas

    2007-02-01

    We report high resolution 15N NMR probing of the solid-solid phase transition of 15N-labeled ammonia borane (NH3BH3) around 225 K. Both the 15N isotropic chemical shift, δiso, and the spin-lattice relaxation rate (T1-1) exhibited strong anomalies around 225 K. The analysis of T1-1 using the Bloembergen-Purcell and Pound model showed that the motional correlation time, τ, increased from about 1 ps to 100 ps while the corresponding Arrhenius activation energy increased from 6 to 13.4 kJ/mol on going through the transition. The observed strong temperature dependence of δiso was interpreted by an extension of the Bayer model. The time scale of the underlying motion was found to be in a reasonable agreement with the T1-1 data. These results imply that the NH3 rotor motion plays a pivotal role in the transition mechanism, and that the transition is of both order-disorder and displacive type. This work was supported by the Office of Basic Energy Sciences of the U. S. Department of Energy Chemical Sciences program. Pacific Northwest National Laboratory is operated by Battelle for the U. S. Department of Energy.

  10. Evidence for tautomerism in nucleic acid base pairs. 1H NMR study of 15N labeled tRNA.

    PubMed Central

    Rüterjans, H; Kaun, E; Hull, W E; Limbach, H H

    1982-01-01

    The imino proton resonances of 15N labeled tRNA appear as asymmetric doublet signals, the asymmetry being dependent on the applied magnetic field strength. Assuming a tautomerism of the type N-H...N not equal to N...H-N in the base pairs the line shapes can be simulated. The most important parameters fitted in the simulation are the rate constants of the proton transfer and the mole fractions of either tautomeric state. The rate constants are of the order of 100s-1 and the mole fractions of the non dominant tautomer about 0.1 depending on the temperature and on the nature of the base pairing. The observations are attributed to a double proton transfer in the base pairs. The unexpectedly slow rates of the double proton transfer process may be connected with a concomitant conformational change of the duplex structure. PMID:7177856

  11. NMR spectroscopic study of organic phosphate esters coprecipitated with calcite

    NASA Astrophysics Data System (ADS)

    Phillips, Brian L.; Zhang, Zelong; Kubista, Laura; Frisia, Silvia; Borsato, Andrea

    2016-06-01

    Organic phosphorus incorporated in calcite during laboratory precipitation experiments and in natural cave deposits was investigated by solid-state NMR spectroscopy. For calcite precipitated in the presence of organic phosphoesters of varying size and functionality, solid-state 31P{1H} CP/MAS NMR shows that the phosphoesters were incorporated intact into the solid. Systematic changes in the 31P NMR chemical shift of the phosphate group were observed between the solid phosphoester and that incorporated in the solid precipitate, yielding 31P NMR chemical shifts of the coprecipitates in the range of +1.8 to -2.2 ppm. These chemical shifts are distinct from that of similarly prepared calcite coprecipitated with inorganic phosphate, 3.5 ppm. Only minor changes were noted in the phosphoester 31P chemical shift anisotropy (CSA) which suggests no significant change in the local structure of the phosphate group, which is dominated by C-O-P bonding. Close spatial proximity of the organic phosphate group to calcite structural components was revealed by 31P/13C rotational echo double resonance (REDOR) experiments for coprecipitates prepared with 13C-labeled carbonate. All coprecipitates showed significant 31P dephasing effects upon 13C-irradiation, signaling atomic-scale proximity to carbonate carbon. The dephasing rate for smaller organophosphate molecules is similar to that observed for inorganic phosphate, whereas much slower dephasing was observed for larger molecules having long and/or bulky side-chains. This result suggests that small organic molecules can be tightly enclosed within the calcite structure, whereas significant structural disruption required to accommodate the larger organic molecules leads to longer phosphate-carbonate distances. Comparison of 31P NMR spectroscopic data from the synthetic coprecipitates with those from calcite moonmilk speleothems indicates that phosphorus occurs mainly as inorganic orthophosphate in the natural deposits, although small

  12. (15)N NMR spectroscopy unambiguously establishes the coordination mode of the diimine linker 2-(2'-pyridyl)pyrimidine-4-carboxylic acid (cppH) in Ru(ii) complexes.

    PubMed

    Battistin, Federica; Balducci, Gabriele; Demitri, Nicola; Iengo, Elisabetta; Milani, Barbara; Alessio, Enzo

    2015-09-21

    We investigated the reactivity of three Ru(ii) precursors -trans,cis,cis-[RuCl2(CO)2(dmso-O)2], cis,fac-[RuCl2(dmso-O)(dmso-S)3], and trans-[RuCl2(dmso-S)4] - towards the diimine linker 2-(2'-pyridyl)pyrimidine-4-carboxylic acid (cppH) or its parent compound 4-methyl-2-(2'-pyridyl)pyrimidine ligand (mpp), in which a methyl group replaces the carboxylic group on the pyrimidine ring. In principle, both cppH and mpp can originate linkage isomers, depending on how the pyrimidine ring binds to ruthenium through the nitrogen atom ortho (N(o)) or para (N(p)) to the group in position 4. The principal aim of this work was to establish a spectroscopic fingerprint for distinguishing the coordination mode of cppH/mpp also in the absence of an X-ray structural characterization. By virtue of the new complexes described here, together with the others previously reported by us, we successfully recorded {(1)H,(15)N}-HMBC NMR spectra at natural abundance of the (15)N isotope on a consistent number of fully characterized Ru(ii)-cppH/mpp compounds, most of them being stereoisomers and/or linkage isomers. Thus, we found that (15)N NMR chemical shifts unambiguously establish the binding mode of cppH and mpp - either through N(o) or N(p)- and can be conveniently applied also in the absence of the X-ray structure. In fact, coordination of cppH to Ru(ii) induces a marked upfield shift for the resonance of the N atoms directly bound to the metal, with coordination induced shifts (CIS) ranging from ca.-45 to -75 ppm, depending on the complex, whereas the unbound N atom resonates at a frequency similar to that of the free ligand. Similar results were found for the complexes of mpp. This work confirmed our previous finding that cppH has no binding preference, whereas mpp binds exclusively through N(p). Interestingly, the two cppH linkage isomers trans,cis-[RuCl2(CO)2(cppH-κN(p))] (5) and trans,cis-[RuCl2(CO)2(cppH-κN(o))] (6) were easily obtained in pure form by exploiting their different

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

    NASA Astrophysics Data System (ADS)

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

    2015-02-01

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

  14. Binding of oxytocin and 8-arginine-vasopressin to neurophysin studied by /sup 15/N NMR using magnetization transfer and indirect detection via protons

    SciTech Connect

    Live, D.H.; Cowburn, D.

    1987-10-06

    NMR was used to monitor the binding to neurophysin of oxytocin and 8-arginine-vasopressin, /sup 15/N labeling being used to identify specific backbone /sup 15/N and /sup 1/H signals. The most significant effects of binding were large downfield shifts in the amino nitrogen resonance of Phe-3 of vasopressin and in its associated proton, providing evidence that the peptide bond between residues 2 and 3 of the hormones is hydrogen-bonded to the protein within hormone-neurophysin complexes. Suggestive evidence for hydrogen bonding of the amino nitrogen of Tyr-2 was also obtained in the form of decreased proton exchange rates on binding; however, the chemical shift changes of this nitrogen and its associated proton indicated that such hydrogen bonding, if present, is probably weak. Shifts in the amino nitrogen of Asn-5 and in the -NH protons of both Asn-5 and Cys-6 demonstrated that these residues are significantly perturbed by binding, suggesting conformational changes of the ring on binding and/or the presence of binding sites on the hormone outside the 1-3 region. No support was obtained for the thesis that there is a significant second binding site for vasopressin on each neutrophysin chain. The behavior of both oxytocin and vasopressin on binding was consistent with formation of 1:1 complexes in slow exchange with the free state under most pH conditions. At low pH there was evidence of an increased exchange rate. Additionally, broadening of /sup 15/N resonances in the bound state at low pH occurred without a corresponding change in the resonances of equilibrating free hormone. The results suggest significant conformational alteration in neurophysin-hormone complexes at low pH possibly associated with protonation of the carboxyl group of the hormone-protein salt bridge.

  15. Carbon-13, sup 15 N, and sup 31 P NMR studies on 6-hydroxy-L-nicotine oxidase from Arthrobacter oxidans

    SciTech Connect

    Pust, S.; Vervoort, J.; Decker, K.; Bacher, A.; Mueller, F. )

    1989-01-24

    The interaction between the apoprotein of 6-hydroxy-L-nicotine oxidase from Arthrobacter oxidans and the prosthetic group FAD has been investigated by {sup 13}C, {sup 15}N and {sup 31}P NMR techniques. The FAD prosthetic group was selectively enriched in {sup 13}C and {sup 15}N isotopes by adding isotopically labeled riboflavin derivatives to the growth medium of riboflavin-requiring mutant cells. In the oxidized state the chemical shift of the C(7) and C(8) atoms indicates that the xylene moiety of the isoalloxazine ring is embedded in a hydrophobic environment. The binding of the competitive inhibitor, 6-hydroxy-D-nicotine, influences the resonances of the C(4a) and the N(5) atom strongly. It is suggested that these shifts are due to a strong hydrogen-bonding interaction between the N(5) atom and the inhibitor. On reduction all resonances, except those of the C(10a) and the N(1) atoms, shift upfield, indicating the increased electron density in the ring system. It can unambiguously be concluded from the chemical shift of the N(1) atom that the reduced flavin is anionic. The doublet character of the N(3) and N(5) resonances suggests that bulk water has no access to the active center. The strong downfield shift of the N(1) position indicates that this atom is embedded in a polar environment, but it does not indicate the presence of a positively charged residue. The {sup 31}P NMR spectra show that the resonances of the pyrophosphate group of the bound FAD differ slightly from those of free FAD. Besides the {sup 31}P resonances from FAD, four peaks around 0 ppm are observed that belongs to bound phosphorus residues. The residues are not located close to the isoalloxazine ring.

  16. Analysis of internal motions of interleukin-13 variant associated with severe bronchial asthma using {sup 15}N NMR relaxation measurements

    SciTech Connect

    Yoshida, Yuichiro; Ohkuri, Takatoshi; Takeda, Chika; Kuroki, Ryota; Izuhara, Kenji; Imoto, Taiji; Ueda, Tadashi . E-mail: ueda@phar.kyushu-u.ac.jp

    2007-06-22

    The single nucleotide polymorphism interleukin-13 (IL-13) R110Q is associated with severe bronchial asthma because its lower affinity leads to the augmentation of local IL-13 concentration, resulting in an increase in the signal transduction via IL-13R. Since the mutation site does not directly bind to IL-13R{alpha}2, we carried out NMR relaxation analyses of the wild-type IL-13 and IL-13-R110Q in order to examine whether the R110Q mutation affects the internal motions in IL-13 molecules. The results showed that the internal motion in the micro- to millisecond time scale on helix D, which is suggested to be important for the interaction between IL-13 and IL-13R{alpha}2, is increased in IL-13-R110Q compared with that in the wild-type IL-13. It therefore appears that the difference in the internal motions on helix D between the wild-type IL-13 and IL-13-R110Q may be involved in their affinity differences with IL-13R{alpha}2.

  17. 1H, 15N and 13C assignment of the amyloidogenic protein medin using fast-pulsing NMR techniques.

    PubMed

    Davies, H A; Phelan, M M; Madine, J

    2016-04-01

    Thirty-one proteins are known to form extracellular fibrillar amyloid in humans. Molecular information about many of these proteins in their monomeric, intermediate or fibrillar form and how they aggregate and interact to form the insoluble fibrils is sparse. This is because amyloid proteins are notoriously difficult to study in their soluble forms, due to their inherent propensity to aggregate. Using recent developments in fast NMR techniques, band-selective excitation short transient and band-selective optimized flip-angle short-transient heteronuclear multiple quantum coherence we have been able to assign a 5 kDa full-length amyloidogenic protein called medin. Medin is the key protein component of the most common form of localised amyloid with a proposed role in aortic aneurysm and dissection. This assignment will now enable the study of the early interactions that could influence initiation and progression of medin aggregation. The chemical shifts have been deposited in the BioMagRes-Bank accession Nos. 25399 and 26576. PMID:26377205

  18. (1)H NMR assignment corrections and (1)H, (13)C, (15)N NMR coordination shifts structural correlations in Fe(II), Ru(II) and Os(II) cationic complexes with 2,2'-bipyridine and 1,10-phenanthroline.

    PubMed

    Pazderski, Leszek; Pawlak, Tomasz; Sitkowski, Jerzy; Kozerski, Lech; Szłyk, Edward

    2010-06-01

    (1)H, (13)C and (15)N NMR studies of iron(II), ruthenium(II) and osmium(II) tris-chelated cationic complexes with 2,2'-bipyridine and 1,10-phenanthroline of the general formula [M(LL)(3)](2+) (M = Fe, Ru, Os; LL = bpy, phen) were performed. Inconsistent literature (1)H signal assignments were corrected. Significant shielding of nitrogen-adjacent protons [H(6) in bpy, H(2) in phen] and metal-bonded nitrogens was observed, being enhanced in the series Ru(II) --> Os(II) --> Fe(II) for (1)H, Fe(II) --> Ru(II) --> Os(II) for (15)N and bpy --> phen for both nuclei. The carbons are deshielded, the effect increasing in the order Ru(II) --> Os(II) --> Fe(II). PMID:20474023

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

    SciTech Connect

    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.

  20. Complete thermodynamic characterization of the multiple protonation equilibria of the aminoglycoside antibiotic paromomycin: a calorimetric and natural abundance 15N NMR study.

    PubMed

    Barbieri, Christopher M; Pilch, Daniel S

    2006-02-15

    The binding of aminoglycoside antibiotics to a broad range of macromolecular targets is coupled to protonation of one or more of the amino groups that typify this class of drugs. Determining how and to what extent this linkage influences the energetics of the aminoglycoside-macromolecule binding reaction requires a detailed understanding of the thermodynamics associated with the protonation equilibria of the aminoglycoside amino groups. In recognition of this need, a calorimetric- and NMR-based approach for obtaining the requisite thermodynamic information is presented using paromomycin as the model aminoglycoside. Temperature- and pH-dependent 15N NMR studies provide pK(a) values for the five paromomycin amino groups, as well as the temperature dependence of these pK(a) values. These studies also indicate that the observed pK(a) values associated with the free base form of paromomycin are lower in magnitude than the corresponding values associated with the sulfate salt form of the drug. This difference in pK(a) is due to drug interactions with the sulfate counterions at the high drug concentrations (> or = 812 mM) used in the 15N NMR studies. Isothermal titration calorimetry studies conducted at drug concentrations < or = 45 microM reveal that the extent of paromomycin protonation linked to the binding of the drug to its pharmacologically relevant target, the 16 S rRNA A-site, is consistent with the pK(a) values of the free base and not the sulfate salt form of the drug. Temperature- and pH-dependent isothermal titration calorimetry studies yield exothermic enthalpy changes (deltaH) for protonation of the five paromomycin amino groups, as well as positive heat capacity changes (deltaC(p)) for three of the five amino groups. Regarded as a whole, the results presented here represent an important first step toward establishing a thermodynamic database that can be used to predict how aminoglycoside-macromolecule binding energetics will be influenced by conditions such

  1. 1H/15N HSQC NMR studies of ligand carboxylate group interactions with arginine residues in complexes of brodimoprim analogues and Lactobacillus casei dihydrofolate reductase.

    PubMed

    Morgan, W D; Birdsall, B; Nieto, P M; Gargaro, A R; Feeney, J

    1999-02-16

    1H and 15N NMR studies have been undertaken on complexes of Lactobacillus casei dihydrofolate reductase (DHFR) formed with analogues of the antibacterial drug brodimoprim (2,4-diamino-5-(3', 5'-dimethoxy-4'-bromobenzyl)pyrimidine) in order to monitor interactions between carboxylate groups on the ligands and basic residues in the protein. These analogues had been designed by computer modeling with carboxylated alkyl chains introduced at the 3'-O position in order to improve their binding properties by making additional interactions with basic groups in the protein. Specific interactions between ligand carboxylate groups and the conserved Arg57 residue have been detected in studies of 1H/15N HSQC spectra of complexes of DHFR with both the 4-carboxylate and the 4, 6-dicarboxylate brodimoprim analogues. The spectra from both complexes showed four resolved signals for the four NHeta protons of the guanidino group of Arg57, and this is consistent with hindered rotation in the guanidino group resulting from interactions with the 4-carboxylate group in each analogue. In the spectra of each complex, one of the protons from each of the two NH2 groups and both nitrogens are considerably deshielded compared to the shielding values normally observed for such nuclei. This pattern of deshielding is that expected for a symmetrical end-on interaction of the carboxylate oxygens with the NHeta12 and NHeta22 guanidino protons. The differences in the degree of deshielding between the complexes of the two structurally similar brodimoprim analogues and the methotrexate indicates that the shielding is very sensitive to geometry, most probably to hydrogen bond lengths. The 1H/15N HSQC spectrum of the DHFR complex with the brodimoprim-6-carboxylate analogue does not feature any deshielded Arg NHeta protons and this argues against a similar interaction with the Arg57 in this case. It has not proved possible to determine whether the 6-carboxylate in this analogue is interacting directly with

  2. Aggregation of [Au(CN)4]- anions: examination by crystallography and 15N CP-MAS NMR and the structural factors influencing intermolecular Au···N interactions.

    PubMed

    Geisheimer, Andrew R; Wren, John E C; Michaelis, Vladimir K; Kobayashi, Masayuki; Sakai, Ken; Kroeker, Scott; Leznoff, Daniel B

    2011-02-21

    intensity of the observed bands), (15)N{(1)H} CP-MAS NMR reveals well-defined, ordered cyanide groups in the six diamagnetic compounds with chemical shifts between 250 and 275 ppm; the resonances between 260 and 275 ppm can be assigned to C-bound terminal ligands, while those subject to CN···H-N bonding resonate lower, around 250-257 ppm. The (15)N chemical shift also correlates with the intermolecular Au···N distances: the shortest Au-N distances also shift the (15)N peak to lower frequency. This provides a real, spectroscopically measurable electronic effect associated with the crystallographic observation of intermolecular Au···NC interactions, thereby lending support for their viability. PMID:21268652

  3. 15N NMR spectroscopy of hydrogen-bonding interactions in the active site of serine proteases: evidence for a moving histidine mechanism.

    PubMed

    Bachovchin, W W

    1986-11-18

    Nitrogen-15 NMR spectroscopy has been used to study the hydrogen-bonding interactions involving the histidyl residue in the catalytic triad of alpha-lytic protease in the resting enzyme and in the transition-state or tetrahedral intermediate analogue complexes formed with phenylmethanesulfonyl fluoride and diisopropyl fluorophosphate. The 15N shifts indicate that a strong hydrogen bond links the active site histidine and serine residues in the resting enzyme in solution. This result is at odds with interpretations of the X-ray diffraction data of alpha-lytic protease and of other serine proteases, which indicate that the serine and histidine residues are too far apart and not properly aligned for the formation of a hydrogen bond. In addition, the nitrogen-15 shifts demonstrate that protonation of the histidine imidazole ring at low pH in the transition-state or tetrahedral intermediate analogue complexes formed with phenylmethanesulfonyl fluoride and diisopropyl fluorophosphate triggers the disruption of the aspartate-histidine hydrogen bond. These results suggest a catalytic mechanism involving directed movement of the imidazole ring of the active site histidyl residue. PMID:3542033

  4. Main chain and side chain dynamics of a heme protein: 15N and 2H NMR relaxation studies of R. capsulatus ferrocytochrome c2.

    PubMed

    Flynn, P F; Bieber Urbauer, R J; Zhang, H; Lee, A L; Wand, A J

    2001-06-01

    A detailed characterization of the main chain and side chain dynamics in R. capsulatus ferrocytochrome c(2) derived from (2)H NMR relaxation of methyl group resonances is presented. (15)N relaxation measurements confirm earlier results indicating that R. capsulatus ferrocytochrome c(2) exhibits minor rotational anisotropy in solution. The current study is focused on the use of deuterium relaxation in side chain methyl groups, which has been shown to provide a detailed and accurate measure of internal dynamics. Results obtained indicate that the side chains of ferrocytochrome c(2) exhibit a wide range of motional amplitudes, but are more rigid than generally found in the interior of nonprosthetic group bearing globular proteins. This unusual rigidity is ascribed to the interactions of the protein with the large heme prosthetic group. This observation has significant implications for the potential of the heme-protein interface to modulate the redox properties of the protein and also points to the need for great precision in the design and engineering of heme proteins. PMID:11380250

  5. Amino-acid selective experiments on uniformly 13C and 15N labeled proteins by MAS NMR: Filtering of lysines and arginines

    NASA Astrophysics Data System (ADS)

    Jehle, Stefan; Rehbein, Kristina; Diehl, Anne; van Rossum, Barth-Jan

    2006-12-01

    Amino-acid selective magic-angle spinning (MAS) NMR experiments can aid the assignment of ambiguous cross-peaks in crowded spectra of solid proteins. In particular for larger proteins, data analysis can be hindered by severe resonance overlap. In such cases, filtering techniques may provide a good alternative to site-specific spin-labeling to obtain unambiguous assignments that can serve as starting points in the assignment procedure. In this paper we present a simple pulse sequence that allows selective excitation of arginine and lysine residues. To achieve this, we make use of a combination of specific cross-polarization for selective excitation [M. Baldus, A.T. Petkova, J. Herzfeld, R.G. Griffin, Cross polarization in the tilted frame: assignment and spectral simplification in heteronuclear spin systems, Mol. Phys. 95 (1998) 1197-1207.] and spin diffusion for transfer along the amino-acid side-chain. The selectivity of the filter is demonstrated with the excitation of lysine and arginine side-chain resonances in a uniformly 13C and 15N labeled protein preparation of the α-spectrin SH3 domain. It is shown that the filter can be applied as a building block in a 13C- 13C lysine-only correlation experiment.

  6. Experimental and quantum-chemical studies of 15N NMR coordination shifts in palladium and platinum chloride complexes with pyridine, 2,2'-bipyridine and 1,10-phenanthroline.

    PubMed

    Pazderski, Leszek; Szłyk, Edward; Sitkowski, Jerzy; Kamieński, Bohdan; Kozerski, Lech; Tousek, Jaromír; Marek, Radek

    2006-02-01

    A series of Pd and Pt chloride complexes with pyridine (py), 2,2'-bipyridine (bpy) and 1,10-phenanthroline (phen), of general formulae trans-/cis-[M(py)2Cl2], [M(py)4]Cl2, trans-/cis-[M(py)2Cl4], [M(bpy)Cl2], [M(bpy)Cl4], [M(phen)Cl2], [M(phen)Cl4], where M = Pd, Pt, was studied by 1H, 195Pt, and 15N NMR. The 90-140 ppm low-frequency 15N coordination shifts are discussed in terms of such structural features of the complexes as the type of platinide metal, oxidation state, coordination sphere geometry and the type of ligand. The results of quantum-chemical NMR calculations were compared with the experimental 15N coordination shifts, well reproducing their magnitude and correlation with the molecular structure. PMID:16392105

  7. NMR, MRI, and spectroscopic MRI in inhomogeneous fields

    DOEpatents

    Demas, Vasiliki; Pines, Alexander; Martin, Rachel W; Franck, John; Reimer, Jeffrey A

    2013-12-24

    A method for locally creating effectively homogeneous or "clean" magnetic field gradients (of high uniformity) for imaging (with NMR, MRI, or spectroscopic MRI) both in in-situ and ex-situ systems with high degrees of inhomogeneous field strength. THe method of imaging comprises: a) providing a functional approximation of an inhomogeneous static magnetic field strength B.sub.0({right arrow over (r)}) at a spatial position {right arrow over (r)}; b) providing a temporal functional approximation of {right arrow over (G)}.sub.shim(t) with i basis functions and j variables for each basis function, resulting in v.sub.ij variables; c) providing a measured value .OMEGA., which is an temporally accumulated dephasing due to the inhomogeneities of B.sub.0({right arrow over(r)}); and d) minimizing a difference in the local dephasing angle .phi.({right arrow over (r)},t)=.gamma..intg..sub.0.sup.t{square root over (|{right arrow over (B)}.sub.1({right arrow over (r)},t')|.sup.2+({right arrow over (r)}{right arrow over (G)}.sub.shimG.sub.shim(t')+.parallel.{right arrow over (B)}.sub.0({right arrow over (r)}).parallel..DELTA..omega.({right arrow over (r)},t'/.gamma/).sup.2)}dt'-.OMEGA. by varying the v.sub.ij variables to form a set of minimized v.sub.ij variables. The method requires calibration of the static fields prior to minimization, but may thereafter be implemented without such calibration, may be used in open or closed systems, and potentially portable systems.

  8. Secondary Structure, Backbone Dynamics, and Structural Topology of Phospholamban and Its Phosphorylated and Arg9Cys-Mutated Forms in Phospholipid Bilayers Utilizing 13C and 15N Solid-State NMR Spectroscopy

    PubMed Central

    2015-01-01

    Phospholamban (PLB) is a membrane protein that regulates heart muscle relaxation rates via interactions with the sarcoplasmic reticulum Ca2+ ATPase (SERCA). When PLB is phosphorylated or Arg9Cys (R9C) is mutated, inhibition of SERCA is relieved. 13C and 15N solid-state NMR spectroscopy is utilized to investigate conformational changes of PLB upon phosphorylation and R9C mutation. 13C=O NMR spectra of the cytoplasmic domain reveal two α-helical structural components with population changes upon phosphorylation and R9C mutation. The appearance of an unstructured component is observed on domain Ib. 15N NMR spectra indicate an increase in backbone dynamics of the cytoplasmic domain. Wild-type PLB (WT-PLB), Ser16-phosphorylated PLB (P-PLB), and R9C-mutated PLB (R9C-PLB) all have a very dynamic domain Ib, and the transmembrane domain has an immobile component. 15N NMR spectra indicate that the cytoplasmic domain of R9C-PLB adopts an orientation similar to P-PLB and shifts away from the membrane surface. Domain Ib (Leu28) of P-PLB and R9C-PLB loses the alignment. The R9C-PLB adopts a conformation similar to P-PLB with a population shift to a more extended and disordered state. The NMR data suggest the more extended and disordered forms of PLB may relate to inhibition relief. PMID:24511878

  9. Effect of phosphorylation on hydrogen-bonding interactions of the active site histidine of the phosphocarrier protein HPr of the phosphoenolpyruvate-dependent phosphotransferase system determined by sup 15 N NMR spectroscopy

    SciTech Connect

    van Dijk, A.A.; de Lange, L.C.M.; Robillard, G.T. ); Bachovchin, W.W. )

    1990-09-04

    The phosphocarrier protein HPr of the phosphoenolpyruvate-dependent sugar transport system of Escherichia coli can exist in a phosphorylated and a nonphosphorylated form. During phosphorylation, the phosphoryl group is carried on a histidine residue, His15. The hydrogen-bonding state of this histidine was examined with {sup 15}N NMR. For this purpose we selectively enriched the histidine imidazole nitrogens with {sup 15}N by supplying an E. coli histidine auxotroph with the amino acid labeled either at the N{delta}1 and N{epsilon}2 positions or at only the N{delta}1 position. {sup 15}N NMR spectra of two synthesized model compound, phosphoimidazole and phosphomethylimidazole, were also recorded. The authors show that, prior to phosphorylation, the protonated His15 N{epsilon}2 is strongly hydrogen bonded, most probably to a carboxylate moiety. The H-bond should strengthen the nucleophilic character of the deprotonated N{delta}1, resulting in a good acceptor for the phosphoryl group. The hydrogen bond to the His15 N{delta}1 breaks upon phosphorylation of the residue. Implications of the H-bond structure for the mechanism of phosphorylation of HPr are discussed.

  10. Effect of phosphorylation on hydrogen-bonding interactions of the active site histidine of the phosphocarrier protein HPr of the phosphoenolpyruvate-dependent phosphotransferase system determined by 15N NMR spectroscopy.

    PubMed

    van Dijk, A A; de Lange, L C; Bachovchin, W W; Robillard, G T

    1990-09-01

    The phosphocarrier protein HPr of the phosphoenolpyruvate-dependent sugar transport system of Escherichia coli can exist in a phosphorylated and a nonphosphorylated form. During phosphorylation, the phosphoryl group is carried on a histidine residue, His15. The hydrogen-bonding state of this histidine was examined with 15N NMR. For this purpose we selectively enriched the histidine imidazole nitrogens with 15N by supplying an E. coli histidine auxotroph with the amino acid labeled either at the N delta 1 and N epsilon 2 positions or at only the N delta 1 position. 15N NMR spectra of two synthesized model compounds, phosphoimidazole and phosphomethylimidazole, were also recorded. We show that, prior to phosphorylation, the protonated His15 N epsilon 2 is strongly hydrogen bonded, most probably to a carboxylate moiety. The H-bond should strengthen the nucleophilic character of the deprotonated N delta 1, resulting in a good acceptor for the phosphoryl group. The hydrogen bond to the His15 N delta 1 breaks upon phosphorylation of the residue. Implications of the H-bond structure for the mechanism of phosphorylation of HPr are discussed. PMID:2261470

  11. Restraints on backbone conformations in solid state NMR studies of uniformly labeled proteins from quantitative amide 15N–15N and carbonyl 13C–13C dipolar recoupling data

    PubMed Central

    Hu, Kan-Nian; Qiang, Wei; Bermejo, Guillermo A.; Schwieters, Charles D.; Tycko, Robert

    2013-01-01

    Recent structural studies of uniformly 15N, 13C-labeled proteins by solid state nuclear magnetic resonance (NMR) rely principally on two sources of structural restraints: (i) restraints on backbone conformation from isotropic 15N and 13C chemical shifts, based on empirical correlations between chemical shifts and backbone torsion angles; (ii) restraints on inter-residue proximities from qualitative measurements of internuclear dipole–dipole couplings, detected as the presence or absence of inter-residue crosspeaks in multidimensional spectra. We show that site-specific dipole–dipole couplings among 15N-labeled backbone amide sites and among 13C-labeled backbone carbonyl sites can be measured quantitatively in uniformly-labeled proteins, using dipolar recoupling techniques that we call 15N-BARE and 13C-BARE (BAckbone REcoupling), and that the resulting data represent a new source of restraints on backbone conformation. 15N-BARE and 13C-BARE data can be incorporated into structural modeling calculations as potential energy surfaces, which are derived from comparisons between experimental 15N and 13C signal decay curves, extracted from crosspeak intensities in series of two-dimensional spectra, with numerical simulations of the 15N-BARE and 13C-BARE measurements. We demonstrate this approach through experiments on microcrystalline, uniformly 15N, 13C-labeled protein GB1. Results for GB1 show that 15N-BARE and 13C-BARE restraints are complementary to restraints from chemical shifts and inter-residue crosspeaks, improving both the precision and the accuracy of calculated structures. PMID:22449573

  12. Mixed Aggregates of the Dilithiated Koga Tetraamine: NMR Spectroscopic and Computational Studies.

    PubMed

    Ma, Yun; Mack, Kyle A; Liang, Jun; Keresztes, Ivan; Collum, David B; Zakarian, Armen

    2016-08-16

    A combination of (1) H, (6) Li, (13) C, and (15) N NMR spectroscopies and density functional theory computations explores the formation of mixed aggregates by a dilithium salt of a C2 -symmetric chiral tetraamine (Koga's base). Lithium halides, acetylides, alkoxides, and monoalkylamides form isostructural trilithiated mixed aggregates with few exceptions. (6) Li-(13) C and (6) Li-(15) N couplings reveal heretofore undetected transannular contacts (laddering) with lithium acetylides and lithium monoalkylamides. Marked temperature-dependent (15) N chemical shifts seem to be associated with this laddering. Computational studies shed light on the general structures of the aggregates, their penchant for laddering, and the stereochemical consequences of aggregation. PMID:27435147

  13. Experimental and quantum-chemical studies of 1H, 13C and 15N NMR coordination shifts in Au(III), Pd(II) and Pt(II) chloride complexes with picolines.

    PubMed

    Pazderski, Leszek; Tousek, Jaromír; Sitkowski, Jerzy; Malináková, Katerina; Kozerski, Lech; Szłyk, Edward

    2009-03-01

    (1)H, (13)C and (15)N NMR studies of gold(III), palladium(II) and platinum(II) chloride complexes with picolines, [Au(PIC)Cl(3)], trans-[Pd(PIC)(2)Cl(2)], trans/cis-[Pt(PIC)(2)Cl(2)] and [Pt(PIC)(4)]Cl(2), were performed. After complexation, the (1)H and (13)C signals were shifted to higher frequency, whereas the (15)N ones to lower (by ca 80-110 ppm), with respect to the free ligands. The (15)N shielding phenomenon was enhanced in the series [Au(PIC)Cl(3)] < trans-[Pd(PIC)(2)Cl(2)] < cis-[Pt(PIC)(2)Cl(2)] < trans-[Pt(PIC)(2)Cl(2)]; it increased following the Pd(II) --> Pt(II) replacement, but decreased upon the trans --> cis-transition. Experimental (1)H, (13)C and (15)N NMR chemical shifts were compared to those quantum-chemically calculated by B3LYP/LanL2DZ + 6-31G**//B3LYP/LanL2DZ + 6-31G*. PMID:19097135

  14. Structural correlations for (1)H, (13)C and (15)N NMR coordination shifts in Au(III), Pd(II) and Pt(II) chloride complexes with lutidines and collidine.

    PubMed

    Pazderski, Leszek; Pawlak, Tomasz; Sitkowski, Jerzy; Kozerski, Lech; Szłyk, Edward

    2010-06-01

    (1)H, (13)C and (15)N NMR studies of gold(III), palladium(II) and platinum(II) chloride complexes with dimethylpyridines (lutidines: 2,3-lutidine, 2,3lut; 2,4-lutidine, 2,4lut; 3,5-lutidine, 3,5lut; 2,6-lutidine, 2,6lut) and 2,4,6-trimethylpyridine (2,4,6-collidine, 2,4,6col) having general formulae [AuLCl(3)], trans-[PdL(2)Cl(2)] and trans-/cis-[PtL(2)Cl(2)] were performed and the respective chemical shifts (delta(1H), delta(13C), delta(15N)) reported. The deshielding of protons and carbons, as well as the shielding of nitrogens was observed. The (1)H, (13)C and (15)N NMR coordination shifts (Delta(1H) (coord), Delta(13C) (coord), Delta(15N) (coord); Delta(coord) = delta(complex) - delta(ligand)) were discussed in relation to some structural features of the title complexes, such as the type of the central atom [Au(III), Pd(II), Pt(II)], geometry (trans- or cis-), metal-nitrogen bond lengths and the position of both methyl groups in the pyridine ring system. PMID:20474019

  15. NMR spectroscopic examination of shocked sandstone from meteor crater, Arizona

    SciTech Connect

    Cygan, R.T.; Boslough, M.B. ); Kirkpatrick, R.J. )

    1994-07-10

    Solid state silicon-29 nuclear magnetic resonance (NMR) spectroscopy has been used to characterize the formation of high pressure silica polymorphs and amorphous material associated with the shocked Coconino Sandstone from Meteor Crater, Arizona. Five samples of the sandstone were obtained from several locations at the crater to represent a range of shock conditions associated with the hypervelocity impact of a 30 m-diameter meteorite. The NMR spectra for these powdered materials exhibit peaks assigned to quartz, coesite, stishovite, and glass. A new resonance in two of the moderately shocked samples is also observed. This resonance has been identified as a densified form of amorphous silica with silicon in tetrahedra with one hydroxyl group. Such a phase is evidence for a shock-induced reaction between quartz and steam under high pressure conditions. [copyright] 1994 American Institute of Physics

  16. NMR spectroscopic examination of shocked sandstone from Meteor Crater, Arizona

    SciTech Connect

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

    1993-08-01

    Solid state silicon-29 nuclear magnetic resonance (NMR) spectroscopy has been used to characterize the formation of high pressure silica polymorphs and amorphous material associated with the shocked Coconino Sandstone from Meteor Crater, Arizona. Five samples of the sandstone were obtained from several locations at the crater to represent a range of shock conditions associated with the hypervelocity impact of a 30 m-diameter meteorite. The NMR spectra for these powdered materials exhibit peaks assigned to quartz, coesite, stishovite, and glass. A new resonance in two of the moderately shocked samples is also observed. This resonance has been identified as a densified form of amorphous silica with silicon in tetrahedra with one hydroxyl group. Such a phase is evidence for a shock-induced reaction between quartz and steam under high pressure conditions.

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

    PubMed Central

    Mahrous, Engy A.; Farag, Mohamed A.

    2014-01-01

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

  18. Combined ligand-observe 19F and protein-observe 15N,1H-HSQC NMR suggests phenylalanine as the key Δ-somatostatin residue recognized by human protein disulfide isomerase

    PubMed Central

    Richards, Kirsty L.; Rowe, Michelle L.; Hudson, Paul B.; Williamson, Richard A.; Howard, Mark J.

    2016-01-01

    Human protein disulphide isomerase (hPDI) is an endoplasmic reticulum (ER) based isomerase and folding chaperone. Molecular detail of ligand recognition and specificity of hPDI are poorly understood despite the importance of the hPDI for folding secreted proteins and its implication in diseases including cancer and lateral sclerosis. We report a detailed study of specificity, interaction and dissociation constants (Kd) of the peptide-ligand Δ-somatostatin (AGSKNFFWKTFTSS) binding to hPDI using 19F ligand-observe and 15N,1H-HSQC protein-observe NMR methods. Phe residues in Δ-somatostatin are hypothesised as important for recognition by hPDI therefore, step-wise peptide Phe-to-Ala changes were progressively introduced and shown to raise the Kd from 103 + 47 μM until the point where binding was abolished when all Phe residues were modified to Ala. The largest step-changes in Kd involved the F11A peptide modification which implies the C-terminus of Δ-somatostatin is a prime recognition region. Furthermore, this study also validated the combined use of 19F ligand-observe and complimentary 15N,1H-HSQC titrations to monitor interactions from the protein’s perspective. 19F ligand-observe NMR was ratified as mirroring 15N protein-observe but highlighted the advantage that 19F offers improved Kd precision due to higher spectrum resolution and greater chemical environment sensitivity. PMID:26786784

  19. E-2-Benzylidenebenzocycloalkanones. Stereostructure and NMR spectroscopic investigation

    NASA Astrophysics Data System (ADS)

    Perjési, P.; Nusser, T.; Tarczay, Gy.; Sohár, P.

    1999-04-01

    Series of E-2-benzylideneindanones ( a), -tetralones ( b) and -benzosuberones ( c) with OCH 3 ( 2- 4), NO 2 ( 5- 7) and F ( 8- 10) substitutions ( ortho, meta and para) on their benzylidene moiety were synthesized by aldol condensation of the appropriate aldehydes and benzocyclanones. The stereostructure (configuration and conformation) and the electronic properties (conjugation of the enone moiety with the aromatic rings) of the compounds were studied by IR, 1H and 13C NMR spectroscopy including also 2D-HSC, DNOE and DEPT measurements. Ab initio calculations were carried out to corroborate the experimental findings.

  20. 1H, 13C and 15N NMR assignments of the E. coli peptide deformylase in complex with a natural inhibitor called actinonin.

    PubMed

    Larue, Valéry; Seijo, Bili; Tisne, Carine; Dardel, Frédéric

    2009-06-01

    In eubacteria, the formyl group of nascent polypeptides is removed by peptide deformylase protein (PDF). This is the reason why PDF has received special attention in the course of the search for new antibacterial agents. We observed by NMR that actinonin, a natural inhibitor, induced drastic changes in the HSQC spectrum of E. coli PDF. We report here the complete NMR chemical shift assignments of PDF resonances bound to actinonin. PMID:19636969

  1. NMR spectroscopic observation of a metal-free acetylide anion.

    PubMed

    Tanaka, Yoshiyuki; Arakawa, Makoto; Yamaguchi, Yohei; Hori, Chieko; Ueno, Masahiro; Tanaka, Takeyuki; Imahori, Tatsushi; Kondo, Yoshinori

    2006-10-20

    A metal-free acetylide was observed by using NMR spectroscopy. Metal-free acetylides are closely related to reactive intermediates (carbanions) in solution; therefore, they have been regarded as unobservable species. However, we generated this highly reactive and unstable species through the deprotonation of phenylacetylene by using the strong nonmetallic phosphazene base tBu-P4. In the presence of tBu-P4, the J coupling between the ethynyl carbon and hydrogen nuclei (1J(C,H)) of phenylacetylene disappeared; this indicates the deprotonation of the alkyne terminal. Furthermore, a large low-field shift (approximately 90 ppm) of the alkyne carbon resonance was observed. We concluded that we have observed a metal-free carbanion with a formal charge on an sp-hybridized carbon atom for the first time. PMID:17441096

  2. Phosphorus-31, sup 15 N, and sup 13 C NMR of glyphosate: Comparison of pH titrations to the herbicidal dead-end complex with 5-enolpyruvoylshikimate-3-phosphate synthase

    SciTech Connect

    Castellino, S.; Leo, G.C.; Sammons, R.D.; Sikorski, J.A. )

    1989-05-02

    The herbicidal dead-end ternary complex (E{sup S3P}{sub Glyph}) of glyphosate (N-(phosphonomethyl)glycine) with 5-enolpyruvoylshikimate-3-phosphate synthase (EPSPS) and the substrate shikimate 3-phosphate (S3P) has been characterized by {sup 31}P, {sup 15}N, and {sup 13}C NMR. The NMR spectra of EPSPS-bound glyphosate show unique chemical shifts ({delta}) for each of the three nuclei. By {sup 31}P NMR, glyphosate in the dead-end complex is a distinct species 3.5 ppm downfield from free glyphosate. The {sup 13}C signal of glyphosate in the dead-end complex is shifted 4 ppm downfield from that of free glyphosate. The {sup 15}N 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 {sup 31}P {delta} and the C-P-O bond angle, and the {sup 13}C and {sup 15}N {delta} values are postulated to be related to C-C-O and C-N-C bond angles, respectively. The downfield {sup 31}P 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 {sup 31}P {delta} vs pH titration curve specifies predominantly the dianion of the 3-phosphate in the E{sup S3P} binary complex, while the E{sup S3P}{sub Glyph} 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.

  3. Experimental and quantum-chemical studies of 1H, 13C and 15N NMR coordination shifts in Pd(II) and Pt(II) chloride complexes with quinoline, isoquinoline, and 2,2'-biquinoline.

    PubMed

    Pazderski, Leszek; Tousek, Jaromír; Sitkowski, Jerzy; Kozerski, Lech; Szłyk, Edward

    2007-12-01

    1H, 13C, and 15N NMR studies of platinide(II) (M=Pd, Pt) chloride complexes with quinolines (L=quinoline-quin, or isoquinoline-isoquin; LL=2,2'-biquinoline-bquin), having the general formulae trans-/cis-[ML2Cl2] and [M(LL)Cl2], were performed and the respective chemical shifts (delta1H, delta13C, delta15N) reported. 1H coordination shifts of various signs and magnitudes (Delta1Hcoord=delta1Hcomplex-delta1Hligand) are discussed in relation to the changes of diamagnetic contribution to the relevant 1H shielding constants. The comparison to the literature data for similar complexes containing auxiliary ligands other than chlorides exhibited a large dependence of delta1H parameters on electron density variations and ring-current effects (inductive and anisotropic phenomena). The influence of deviations from planarity, concerning either MN2Cl2 chromophores or azine ring systems, revealed by the known X-ray structures of [Pd(bquin)Cl2] and [Pt(bquin)Cl2], is discussed in respect to 1H NMR spectra. 15N coordination shifts (Delta15Ncoord=delta15Ncomplex-delta15Nligand) of ca. 78-100 ppm (to lower frequency) are attributed mainly to the decrease of the absolute value of paramagnetic contribution in the relevant 15N shielding constants, this phenomenon being noticeably dependent on the type of a platinide metal and coordination sphere geometry. The absolute magnitude of Delta15Ncoord parameter increased by ca 15 ppm upon Pd(II)-->Pt(II) replacement but decreased by ca. 15 ppm following trans-->cis transition. Experimental 1H, 13C, 15N NMR chemical shifts are compared to those quantum-chemically calculated by B3LYP/LanL2DZ+6-31G**//B3LYP/LanL2DZ+6-31G*, both in vacuo and in CHCl3 or DMF solution. PMID:18044805

  4. 1H, 13C, 195Pt and 15N NMR structural correlations in Pd(II) and Pt(II) chloride complexes with various alkyl and aryl derivatives of 2,2'-bipyridine and 1,10-phenanthroline.

    PubMed

    Pawlak, Tomasz; Pazderski, Leszek; Sitkowski, Jerzy; Kozerski, Lech; Szłyk, Edward

    2011-02-01

    (1)H, (13)C, (195)Pt and (15)N NMR studies of platinide(II) (M = Pd, Pt) chloride complexes with such alkyl and aryl derivatives of 2,2'-bipyridine and 1,10-phenanthroline as LL = 6,6'-dimethyl-bpy, 5,5'-dimethyl-bpy, 4,4'-di-tert-butyl-bpy, 2,9-dimethyl-phen, 2,9-dimethyl-4,7-diphenyl-phen, 3,4,7,8-tetramethyl-phen, having the general [M(LL)Cl(2)] formula were performed and the respective chemical shifts (δ(1H), δ(13C), δ(195Pt), δ(15N)) reported. (1)H high-frequency coordination shifts (Δ(coord)(1H) = δ(complex)(1H)-δ(ligand)(1H)) mostly pronounced for nitrogen-adjacent protons and methyl groups in the nearest adjacency of nitrogen, as well as (15)N low-frequency coordination shifts (Δ(coord)(15H) = δ(complex)(15H)-δ(ligand)(15H)) were discussed in relation to the molecular structures. PMID:21254225

  5. 1H, 13C and 15N NMR coordination shifts in gold(III), cobalt(III), rhodium(III) chloride complexes with pyridine, 2,2'-bipyridine and 1,10-phenanthroline.

    PubMed

    Pazderski, Leszek; Tousek, Jaromír; Sitkowski, Jerzy; Kozerski, Lech; Marek, Radek; Szłyk, Edward

    2007-01-01

    Au(III), Co(III) and Rh(III) chloride complexes with pyridine (py), 2,2'-bipyridine (bpy) and 1,10-phenanthroline (phen) of the general formulae [M1LCl3], trans-[M2L4Cl2]+, mer-[M2L3Cl3], [M1(LL)Cl2]+, cis-[M2(LL)2Cl2]+, where M1=Au; M2=Co, Rh; L=py; LL=bpy, phen, were studied by 1H--13C HMBC and 1H--15N HMQC/HSQC. The 1H, 13C and 15N coordination shifts (the latter from ca-78 to ca-107 ppm) are discussed in relation to the type of metal, electron configuration, coordination sphere geometry and the type of ligand. The 13C and 15N chemical shifts were also calculated by quantum-chemical NMR methods, which reproduced well the experimental tendencies concerning the coordination sphere geometry and the ligand type. PMID:17048265

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

    SciTech Connect

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

    2014-01-03

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

  7. Layered structure of room-temperature ionic liquids in microemulsions by multinuclear NMR spectroscopic studies.

    PubMed

    Falcone, R Dario; Baruah, Bharat; Gaidamauskas, Ernestas; Rithner, Christopher D; Correa, N Mariano; Silber, Juana J; Crans, Debbie C; Levinger, Nancy E

    2011-06-01

    Microemulsions form in mixtures of polar, nonpolar, and amphiphilic molecules. Typical microemulsions employ water as the polar phase. However, microemulsions can form with a polar phase other than water, which hold promise to diversify the range of properties, and hence utility, of microemulsions. Here microemulsions formed by using a room-temperature ionic liquid (RTIL) as the polar phase were created and characterized by using multinuclear NMR spectroscopy. (1)H, (11)B, and (19)F NMR spectroscopy was applied to explore differences between microemulsions formed by using 1-butyl-3-methylimidazolium tetrafluoroborate ([bmim][BF(4)]) as the polar phase with a cationic surfactant, benzylhexadecyldimethylammonium chloride (BHDC), and a nonionic surfactant, Triton X-100 (TX-100). NMR spectroscopy showed distinct differences in the behavior of the RTIL as the charge of the surfactant head group varies in the different microemulsion environments. Minor changes in the chemical shifts were observed for [bmim](+) and [BF(4)](-) in the presence of TX-100 suggesting that the surfactant and the ionic liquid are separated in the microemulsion. The large changes in spectroscopic parameters observed are consistent with microstructure formation with layering of [bmim](+) and [BF(4)](-) and migration of Cl(-) within the BHDC microemulsions. Comparisons with NMR results for related ionic compounds in organic and aqueous environments as well as literature studies assisted the development of a simple organizational model for these microstructures. PMID:21547960

  8. 1H, 13C, 15N NMR coordination shifts in Fe(II), Ru(II) and Os(II) cationic complexes with 2,2':6',2″-terpyridine.

    PubMed

    Pazderski, Leszek; Pawlak, Tomasz; Sitkowski, Jerzy; Kozerski, Lech; Szlyk, Edward

    2011-05-01

    (1)H, (13)C and (15)N NMR studies of iron(II), ruthenium(II) and osmium(II) bis-chelated cationic complexes with 2,2':6',2″-terpyridine ([M(terpy)(2) ](2+) ; M = Fe, Ru, Os) were performed. Significant shielding of nitrogen-adjacent H(6) and deshielding of H(3'), H(4') protons were observed, both effects being mostly expressed for Fe(II) compounds. The metal-bonded nitrogens were shielded, this effect being much larger for the outer N(1), N(1″) than the inner N(1') atoms, and enhanced in the Fe(II) → Ru(II) → Os(II) series. PMID:21491480

  9. Study of stereospecificity of 1H, 13C, 15N and 77Se shielding constants in the configurational isomers of the selenophene-2-carbaldehyde azine by NMR spectroscopy and MP2-GIAO calculations.

    PubMed

    Afonin, Andrei V; Pavlov, Dmitry V; Albanov, Alexander I; Levanova, Ekaterina P; Levkovskaya, Galina G

    2011-11-01

    In the (1)H and (13)C NMR spectra of selenophene-2-carbaldehyde azine, the (1)H-5, (13)C-3 and (13)C-5 signals of the selenophene ring are shifted to higher frequencies, whereas those of the (1)H-1, (13)C-1, (13)C-2 and (13)C-4 are shifted to lower frequencies on going from the EE to ZZ isomer or from the E moiety to the Z moiety of EZ isomer. The (15)N chemical shift is significantly larger in the EE isomer relative to the ZZ isomer and in the E moiety relative to the Z moiety of EZ isomer. A very pronounced difference (60-65 mg/g) between the (77)Se resonance positions is revealed in the studied azine isomers, the (77)Se peak being shifted to higher frequencies in the ZZ isomer and in the Z moiety of EZ isomer. The trends in the changes of the measured chemical shifts are reasonably reproduced by the GIAO calculations at the MP2 level of the (1)H, (13)C, (15)N and (77)Se shielding constants in the energy-favorable conformation with the syn orientation of both selenophene rings relative to the C = N groups. The NBO analysis suggests that such an arrangement of the selenophene rings may take place because of a higher energy of some intramolecular interactions. PMID:22002712

  10. (1)H-, (13)C- and (15)N-NMR assignment of the N-terminal domain of human cerebral dopamine neurotrophic factor (CDNF).

    PubMed

    Latgé, Cristiane; Cabral, Kátia M S; Almeida, Marcius S; Foguel, Débora

    2013-04-01

    Parkinson's disease (PD) is a neurodegenerative disorder that is caused by the death of midbrain dopaminergic neurons. Current therapies for PD do not halt the neurodegeneration nor repair the affected neurons. Therefore, search for novel neurotrophic factors (NTF) for midbrain dopaminergic neurons, which could be used in novel therapeutic approaches, is highly wanted. In 2007, a potent NTF for dopaminergic neurons was described as the conserved dopamine neurotrophic factor (CDNF). Single doses of this protein protect and restore dopaminergic neurons in experimental models of PD. CDNF has two domains; an N-terminal saposin-like domain, which may bind to membranes; and a presumably intrinsically unstructured C-terminal which contains an internal cysteine bridge in a CXXC motif similar to that of thiol/disulphide oxidoreductases and isomerases, and may thus reduce the endoplasmic reticulum stress caused by incorrectly folded proteins. We show for the first time the nuclear magnetic resonance assignment of N-terminal domain of recombinant CDNF (residues 1-105) by solution 2D and 3D NMR spectroscopy. We were able to obtain a nearly complete resonance assignment, which is the first step toward the solution structure determination of this neurotrophic factor. PMID:22528768

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

    PubMed

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

    2015-05-01

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

  12. Low temperature FTIR, Raman, NMR spectroscopic and theoretical study of hydroxyethylammonium picrate

    NASA Astrophysics Data System (ADS)

    Sudharsana, N.; Sharma, A.; Kuş, N.; Fausto, R.; Luísa Ramos, M.; Krishnakumar, V.; Pal, R.; Guru Row, T. N.; Nagalakshmi, R.

    2016-01-01

    A combined experimental (infrared, Raman and NMR) and theoretical quantum chemical study is performed on the charge-transfer complex hydroxyethylammonium picrate (HEAP). The infrared (IR) spectra for HEAP were recorded at various temperatures, ranging from 16 K to 299 K, and the Raman spectrum was recorded at room temperature. A comparison of the experimental IR and Raman spectra with the corresponding calculated spectra was done, in order to facilitate interpretation of the experimental data. Formation of the HEAP complex is evidenced by the presence of the most prominent characteristic bands of the constituting groups of the charge-transfer complex [e.g., NH3+, CO- and NO2]. Vibrational spectroscopic analysis, together with natural bond orbital (NBO) and theoretical charge density analysis in the crystalline phase, was used to shed light on relevant structural details of HEAP resulting from deprotonation of picric acid followed by formation of a hydrogen bond of the N-H⋯OC type between the hydroxyethylammonium cation and the picrate. 13C and 1H NMR spectroscopic analysis are also presented for the DMSO-d6 solution of the compound revealing that in that medium the HEAP crystal dissolves forming the free picrate and hydroxyethylammonium ions. Finally, the electron excitation analysis of HEAP was performed in an attempt to determine the nature of the most important excited states responsible for the NLO properties exhibited by the compound.

  13. 15N NMR coordination shifts in Pd(II), Pt(II), Au(III), Co(III), Rh(III), Ir(III), Pd(IV), and Pt(IV) complexes with pyridine, 2,2'-bipyridine, 1,10-phenanthroline, quinoline, isoquinoline, 2,2'-biquinoline, 2,2':6', 2'-terpyridine and their alkyl or aryl derivatives.

    PubMed

    Pazderski, Leszek

    2008-01-01

    The 15N NMR data for 105 complexes of Pd(II), Pt(II), Au(III), Co(III), Rh(III), Ir(III), Pd(IV), and Pt(IV) complexes with simple azines such as pyridine, 2,2'-bipyridine, 1,10-phenanthroline, quinoline, isoquinoline, 2,2'-biquinoline, 2,2':6', 2''-terpyridine and their alkyl or aryl derivatives have been reviewed. The 15N NMR coordination shifts, i.e. the differences between the 15N chemical shifts of the same nitrogen in the molecules of the complex and the ligand (Delta(15N) (coord) = delta(15N) (compl)--delta(15N) (lig)), have been related to some structural features of the reviewed coordination compounds, like the type of the central ion and the character of auxiliary ligands (mainly in trans position). These Delta(15N) (coord) parameters are negative, their absolute magnitudes (ca 30-150 ppm) generally increasing in the metal order Au(III) < Pd(II) < Pt(II) and Rh(III) < Co(III) < Pt(IV) < Ir(III), as well as with the enhanced trans influence of the other donor atoms (H, C < Cl < N). PMID:18855335

  14. Synthesis, spectroscopic (UV-vis and GIAO NMR), crystallographic and theoretical studies of triazine heterocyclic derivatives

    NASA Astrophysics Data System (ADS)

    Khan, Salman A.; Obaid, Abdullah Y.; Al-Harbi, Laila M.; Arshad, Muhammad Nadeem; Şahin, Onur; Ersanlı, Cem Cüneyt; Abdel-Rehman, R. M.; Asiri, Abdullah M.; Hursthouse, Michael B.

    2015-09-01

    This work presents the synthesis and characterization of triazine heterocyclic derivatives. The spectroscopic properties like nuclear magnetic resonance [NMR, (1H and 13C)] were recorded in CDCl3 solution and Ultraviolet-Visible (UV-vis) absorption spectrums of compounds, 5,6-diphenyl-[1,2,4]triazin-3-ylamine (1), (5,6-diphenyl-[1,2,4]triazin-3-yl)-hydrazine (2) and 5,6-diphenyl-4H-[1,2,4] triazine-3-thione (3), were recorded in the range of 200-800 nm, using chloroform as base solvent. Molecular geometry of compounds with triazine heterocyclic derivative in the ground state have been calculated using the density functional theory (DFT) with 6-31G(d,p) basis set and compared with the X-ray experimental data. The calculated results show that the optimized geometry can well reproduce the crystal structures. Total static dipole moment (μ), the average linear polarizability (α) and the first hyperpolarizability (β) values of the investigated molecules have been computed using the same methods. The energetic behavior of compounds in solvent media has been examined using B3LYP method with the 6-31G(d,p) basis set by applying the polarizable continuum model (PCM). The total energy of compounds decreases with increasing polarity of the solvent. Frontier molecular orbitals and the molecular electrostatic potential (MEP), 1H NMR, and 13C NMR of three triazine derivatives were investigated using theoretical calculations. The linear polarizabilities and first hyperpolarizabilities of the studied molecules indicate that the compounds 1-3 can be used as a good nonlinear optical material (NLO). Isotropic chemical shifts were calculated using the gauge-invariant atomic orbital (GIAO) method. Comparison of the NMR chemical shifts, absorption wavelengths with the experimental values revealed that DFT and time dependent-density functional theory (TD-DFT) method produce generally closer to good results.

  15. Occurrence of non-hydrolysable amides in the macromolecular constituent of Scenedesmus quadricauda cell wall as revealed by 15N NMR: Origin of n-alkylnitriles in pyrolysates of ultralaminae-containing kerogens

    NASA Astrophysics Data System (ADS)

    Derenne, S.; Largeau, C.; Taulelle, F.

    1993-02-01

    New structures, termed ultralaminae, were recently shown to occur in kerogens from numerous oil shales and source rocks. Morphological and chemical studies revealed that ultralaminae originate from the selective preservation of the non-hydrolysable biomacromolecules (algaenans) building up the thin outer walls of several Chlorophyceae (green microalgae) including the cosmopolitan genera Scenedesmus and Chlorella. The chemical correlation between such algaenans and fossil ultralaminae was mainly based on the production, on pyrolysis, of nitrogen compounds, n-alkylnitriles, with specific distributions depending on the lacustrine or marine origin of the considered samples. In addition, these bioand geopolymers were characterized by quite high N levels. Solid-state 15N NMR was carried out on 15N-enriched algaenan (isolated from Scenesdesmus quadricauda grown with 15NO 3- as sole nitrogen source) and revealed that amides are the most abundant nitrogen groups in this material. Minor amounts of two other nitrogen groups, amines and probably Nalkyl substituted pyrroles (indoles, carbazoles), are also observed. Amines are unlikely to contribute to the macromolecular structure but could simply correspond to trapped compounds. A part of the tentatively identified N-alkyl substituted pyrroles is released during pyrolysis, but a large fraction of these moieties is retained in the insoluble residue while their N-alkyl substituents are eliminated. The predominant amide groups associated with long polymethylenic chains, occurring in S. quadricauda algaenan, are eliminated during pyrolysis and lead, after a fast dehydration, to the formation of n-alkylnitriles. This study provides, to our knowledge, the first example of non-hydrolysable amide moieties in a biomacromolecule. This unusual resistance is probably due to steric protection within the macromolecular network. Such a protection also allows amide groups in chlorophycean algaenans to survive diagenesis and accounts for the

  16. Dynamics of a truncated prion protein, PrP(113-231), from (15)N NMR relaxation: order parameters calculated and slow conformational fluctuations localized to a distinct region.

    PubMed

    O'Sullivan, Denis B D; Jones, Christopher E; Abdelraheim, Salama R; Brazier, Marcus W; Toms, Harold; Brown, David R; Viles, John H

    2009-02-01

    Prion diseases are associated with the misfolding of the prion protein (PrP(C)) from a largely alpha-helical isoform to a beta-sheet rich oligomer (PrP(Sc)). Flexibility of the polypeptide could contribute to the ability of PrP(C) to undergo the conformational rearrangement during PrP(C)-PrP(Sc) interactions, which then leads to the misfolded isoform. We have therefore examined the molecular motions of mouse PrP(C), residues 113-231, in solution, using (15)N NMR relaxation measurements. A truncated fragment has been used to eliminate the effect of the 90-residue unstructured tail of PrP(C) so the dynamics of the structured domain can be studied in isolation. (15)N longitudinal (T(1)) and transverse relaxation (T(2)) times as well as the proton-nitrogen nuclear Overhauser effects have been used to calculate the spectral density at three frequencies, 0, omega(N,) and 0.87omega(H). Spectral densities at each residue indicate various time-scale motions of the main-chain. Even within the structured domain of PrP(C), a diverse range of motions are observed. We find that removal of the tail increases T(2) relaxation times significantly indicating that the tail is responsible for shortening of T(2) times in full-length PrP(C). The truncated fragment of PrP has facilitated the determination of meaningful order parameters (S(2)) from the relaxation data and shows for the first time that all three helices in PrP(C) have similar rigidity. Slow conformational fluctuations of mouse PrP(C) are localized to a distinct region that involves residues 171 and 172. Interestingly, residues 170-175 have been identified as a segment within PrP that will form a steric zipper, believed to be the fundamental amyloid unit. The flexibility within these residues could facilitate the PrP(C)-PrP(Sc) recognition process during fibril elongation. PMID:19173221

  17. Spectroscopic separation of (13) C NMR spectra of complex isomeric mixtures by the CSSF-TOCSY-INEPT experiment.

    PubMed

    Yang, Lu; Moreno, Aitor; Fieber, Wolfgang; Brauchli, Robert; Sommer, Horst

    2015-04-01

    Isomeric mixtures from synthetic or natural origins can pose fundamental challenges for their chromatographic separation and spectroscopic identification. A novel 1D selective NMR experiment, chemical shift selective filter (CSSF)-TOCSY-INEPT, is presented that allows the extraction of (13) C NMR subspectra of discrete isomers in complex mixtures without physical separation. This is achieved via CSS excitation of proton signals in the (1) H NMR mixture spectrum, propagation of the selectivity by polarization transfer within coupled (1) H spins, and subsequent relaying of the magnetization from (1) H to (13) C by direct INEPT transfer to generate (13) C NMR subspectra. Simple consolidation of the subspectra yields (13) C NMR spectra for individual isomers. Alternatively, CSSF-INEPT with heteronuclear long-range transfer can correlate the isolated networks of coupled spins and therefore facilitate the reconstruction of the (13) C NMR spectra for isomers containing multiple spin systems. A proof-of-principle validation of the CSSF-TOCSY-INEPT experiment is demonstrated on three mixtures with different spectral and structural complexities. The results show that CSSF-TOCSY-INEPT is a versatile, powerful tool for deconvoluting isomeric mixtures within the NMR tube with unprecedented resolution and offers unique, unambiguous spectral information for structure elucidation. PMID:25616134

  18. Polarization propagators: A powerful theoretical tool for a deeper understanding of NMR spectroscopic parameters

    NASA Astrophysics Data System (ADS)

    Aucar, Gustavo A.; Romero, Rodolfo H.; Maldonado, Alejandro F.

    Magnetic molecular spectroscopic properties, like NMR J-coupling and magnetic shielding σ, have been studied by non-relativistic quantum methods since their discovery. When they were found to depend strongly on relativistic effects in molecules containing heavy atoms, this started a new area of intensive research into the development of methods that include such effects. In most cases non-relativistic concepts were extended to the new field though keeping the previous non-relativistic point of view. Quantum mechanics can be formulated by two different formal approaches. Molecular physics and quantum chemistry were developed mostly within the Schrödinger or Heisenberg approaches. The path integral formalism of Feynman is less well known. This may be the reason why propagators are not broadly known in this field of research. Polarization propagators were developed in the early 1970s. Since that time they have been successfully applied to calculate NMR spectroscopic parameters. They are special theoretical devices from which one can do a deep analysis of the electronic mechanisms that underly any molecular response property from basic theoretical elements, like molecular orbitals, electronic excitation energies, coupling pathways, entanglement, contributions within different levels of theory, etc. All this is obtained in a natural way in both regimes: relativistic and non-relativistic. Its relativistic generalization in the early 1990s and the finding of a quantum electrodynamic (QED)-based theory for them, has given us the opportunity to improve our understanding of the physics behind such parameters. In this paper we give a presentation of polarization propagators that start in non-relativistic quantum physics and end up with the introduction of QED effects. The same and powerful basic quantum ideas are applied throughout this review, so that coherence and beauty arise in a natural way. We will give a new understanding that comes from the three levels of theory

  19. 1H, 13C, 15N backbone and side chain NMR resonance assignments for the N-terminal RNA recognition motif of the HvGR-RBP1 protein involved in the regulation of barley (Hordeum vulgare L.) senescence

    PubMed Central

    Mason, Katelyn E.; Tripet, Brian P.; Parrott, David; Fischer, Andreas M.; Copié, Valérie

    2013-01-01

    Leaf senescence is an important process in the developmental life of all plant species. Senescence efficiency influences important agricultural traits such as grain protein content and plant growth, which are often limited by nitrogen use. Little is known about the molecular mechanisms regulating this highly orchestrated process. To enhance our understanding of leaf senescence and its regulation, we have undertaken the structural and functional characterization of previously unknown proteins that are involved in the control of senescence in barley (Hordeum vulgare L.). Previous microarray analysis highlighted several barley genes whose transcripts are differentially expressed during senescence, including a specific gene which is greater than 40 fold up-regulated in the flag leaves of early- as compared to late-senescing near-isogenic barley lines at 14 and 21 days past flowering (anthesis). From inspection of its amino acid sequence, this gene is predicted to encode a glycine-rich RNA-binding protein herein referred to as HvGR-RBP1. HvGR-RBP1 has been expressed as a recombinant protein in E. coli, and preliminary NMR data analysis has revealed that its glycine-rich C-terminal region [residues: 93–162] is structurally disordered whereas its N-terminal region [residues: 1–92] forms a well-folded domain. Herein, we report the complete 1H, 13C, and 15N resonance assignments of backbone and sidechain atoms, and the secondary structural topology of the N-terminal RNA Recognition Motif (RRM) domain of HvGR-RBP1, as a first step to unraveling its structural and functional role in the regulation of barley leaf senescence. PMID:23417794

  20. Study of conformations and hydrogen bonds in the configurational isomers of pyrrole-2-carbaldehyde oxime by 1H, 13C and 15N NMR spectroscopy combined with MP2 and DFT calculations and NBO analysis.

    PubMed

    Afonin, Andrei V; Ushakov, Igor A; Pavlov, Dmitry V; Ivanov, Andrei V; Mikhaleva, Al'bina I

    2010-09-01

    The (1)H, (13)C and (15)N NMR studies have shown that the E and Z isomers of pyrrole-2-carbaldehyde oxime adopt preferable conformation with the syn orientation of the oxime group with respect to the pyrrole ring. The syn conformation of E and Z isomers of pyrrole-2-carbaldehyde oxime is stabilized by the N-H...N and N-H...O intramolecular hydrogen bonds, respectively. The N-H...N hydrogen bond in the E isomer causes the high-frequency shift of the bridge proton signal by about 1 ppm and increase the (1)J(N, H) coupling by approximately 3 Hz. The bridge proton shows further deshielding and higher increase of the (1)J(N, H) coupling constant due to the strengthening of the N-H...O hydrogen bond in the Z isomer. The MP2 calculations indicate that the syn conformation of E and Z isomers is by approximately 3.5 kcal/mol energetically less favorable than the anti conformation. The calculations of (1)H shielding and (1)J(N, H) coupling in the syn and anti conformations allow the contribution to these constants from the N-H...N and N-H...O hydrogen bondings to be estimated. The NBO analysis suggests that the N-H...N hydrogen bond in the E isomer is a pure electrostatic interaction while the charge transfer from the oxygen lone pair to the antibonding orbital of the N-H bond through the N-H...O hydrogen bond occurs in the Z isomer. PMID:20623827

  1. Electronic structure and solvatochromism of merocyanines NMR spectroscopic point of view.

    PubMed

    Kulinich, Andrii V; Ishchenko, Alexander A; Groth, Ulrich M

    2007-09-01

    (1)H and (13)C NMR spectra of two series of malononitrile-based merocyanines, which possess positive and negative solvatochromism have been in detail investigated in low polar chloroform and polar dimethyl sulfoxide (DMSO). Careful attribution of signals in spectra has been made with the help of two-dimensional NMR experiments (COSY, NOESY, HMBC, and HMQC). Hence, the dependence of merocyanines electronic structure on their chemical structure and solvent nature has been studied by this powerful method. It has been shown that there exists a good correlation between the calculated charges on carbon atoms of a polymethine chain and their chemical shifts in (13)C NMR spectra. The influence of solvent polarity on bond orders for dyes with positive and negative solvatochromism is also observed. The comparison of (13)C NMR spectra of merocyanines and corresponding parent ionic dyes allows to determine their sign of solvatochromism irrespectively of electronic spectra, and also to find the key atoms of chromophore whose signals in (13)C NMR spectra are most informative. PMID:17188560

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

    PubMed

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

    2004-12-01

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

  3. A newly synthesized thiazole derivative as a fluoride ion chemosensor: Naked-eye, spectroscopic, electrochemical and NMR studies

    NASA Astrophysics Data System (ADS)

    Sarıgüney, Ahmet Burak; Saf, Ahmet Özgür; Coşkun, Ahmet

    2014-07-01

    2,3-Indoledione 3-thiosemicarbazone (TSCI) and a novel compound 3-(2-(4-(4-phenoxyphenyl)thiazol-2-yl)hydrazono)indolin-2-one (FTHI) were synthesized with high yield and characterized by spectroscopic techniques. The complexation behaviors of TSCI and FTHI for various anionic species (F-, Cl-, Br-, I-, NO2-, NO3-, BzO-, HSO4-, ClO4-) in CH3CN were investigated and compared by UV-vis spectroscopy, cyclic voltammetry and 1H NMR titration techniques. FTHI showed high degree of selectivity for fluoride over other anions. This selectivity could be easily observed by the naked eye, indicating that FTHI is potential colorimetric sensor for fluoride anion.

  4. Experimental and quantum-chemical studies of 1H, 13C and 15N NMR coordination shifts in Pd(II) and Pt(II) chloride complexes with methyl and phenyl derivatives of 2,2'-bipyridine and 1,10-phenanthroline.

    PubMed

    Pazderski, Leszek; Tousek, Jaromír; Sitkowski, Jerzy; Kozerski, Lech; Szłyk, Edward

    2007-12-01

    1H, 13C and 15N NMR studies of platinide(II) (M=Pd, Pt) chloride complexes with methyl and phenyl derivatives of 2,2'-bipyridine and 1,10-phenanthroline [LL=4,4'-dimethyl-2,2'-bipyridine (dmbpy); 4,4'-diphenyl-2,2'-bipyridine (dpbpy); 4,7-dimethyl-1,10-phenanthroline (dmphen); 4,7-diphenyl-1,10-phenanthroline (dpphen)] having a general [M(LL)Cl2] formula were performed and the respective chemical shifts (delta1H, delta13C, delta15N) reported. 1H high-frequency coordination shifts (Delta1Hcoord=delta1Hcomplex-delta1Hligand) were discussed in relation to the changes of diamagnetic contribution in the relevant 1H shielding constants. The comparison to literature data for similar [M(LL)(XX)], [M(LL)X2] and [M(LL)XY] coordination or organometallic compounds containing various auxiliary ligands revealed a large dependence of delta1H parameters on inductive and anisotropic effects. 15N low-frequency coordination shifts (Delta15Ncoord=delta 15Ncomplex-delta15Nligand) of ca 88-96 ppm for M=Pd and ca 103-111 ppm for M=Pt were attributed to both the decrease of the absolute value of paramagnetic contribution and the increase of the diamagnetic term in the expression for 15N shielding constants. The absolute magnitude of Delta15Ncoord parameter increased by ca 15 ppm upon Pd(II)-->Pt(II) transition and by ca 6-7 ppm following dmbpy-->dmphen or dpbpy-->dpphen ligand replacement; variations between analogous complexes containing methyl and phenyl ligands (dmbpy vs dpbpy; dmphen vs dpphen) did not exceed+/-1.5 ppm. Experimental 1H, 13C, 15N NMR chemical shifts were compared to those quantum-chemically calculated by B3LYP/LanL2DZ+6-31G**//B3LYP/LanL2DZ+6-31G*, both in vacuo and in DMSO or DMF solution. PMID:18044804

  5. Operando NMR spectroscopic analysis of proton transfer in heterogeneous photocatalytic reactions

    PubMed Central

    Wang, Xue Lu; Liu, Wenqing; Yu, Yan-Yan; Song, Yanhong; Fang, Wen Qi; Wei, Daxiu; Gong, Xue-Qing; Yao, Ye-Feng; Yang, Hua Gui

    2016-01-01

    Proton transfer (PT) processes in solid–liquid phases play central roles throughout chemistry, biology and materials science. Identification of PT routes deep into the realistic catalytic process is experimentally challenging, thus leaving a gap in our understanding. Here we demonstrate an approach using operando nuclear magnetic resonance (NMR) spectroscopy that allows to quantitatively describe the complex species dynamics of generated H2/HD gases and liquid intermediates in pmol resolution during photocatalytic hydrogen evolution reaction (HER). In this system, the effective protons for HER are mainly from H2O, and CH3OH evidently serves as an outstanding sacrificial agent reacting with holes, further supported by our density functional theory calculations. This results rule out controversy about the complicated proton sources for HER. The operando NMR method provides a direct molecular-level insight with the methodology offering exciting possibilities for the quantitative studies of mechanisms of proton-involved catalytic reactions in solid–liquid phases. PMID:27311326

  6. Operando NMR spectroscopic analysis of proton transfer in heterogeneous photocatalytic reactions.

    PubMed

    Wang, Xue Lu; Liu, Wenqing; Yu, Yan-Yan; Song, Yanhong; Fang, Wen Qi; Wei, Daxiu; Gong, Xue-Qing; Yao, Ye-Feng; Yang, Hua Gui

    2016-01-01

    Proton transfer (PT) processes in solid-liquid phases play central roles throughout chemistry, biology and materials science. Identification of PT routes deep into the realistic catalytic process is experimentally challenging, thus leaving a gap in our understanding. Here we demonstrate an approach using operando nuclear magnetic resonance (NMR) spectroscopy that allows to quantitatively describe the complex species dynamics of generated H2/HD gases and liquid intermediates in pmol resolution during photocatalytic hydrogen evolution reaction (HER). In this system, the effective protons for HER are mainly from H2O, and CH3OH evidently serves as an outstanding sacrificial agent reacting with holes, further supported by our density functional theory calculations. This results rule out controversy about the complicated proton sources for HER. The operando NMR method provides a direct molecular-level insight with the methodology offering exciting possibilities for the quantitative studies of mechanisms of proton-involved catalytic reactions in solid-liquid phases. PMID:27311326

  7. 15N Hyperpolarization by Reversible Exchange Using SABRE-SHEATH

    PubMed Central

    2016-01-01

    NMR signal amplification by reversible exchange (SABRE) is a NMR hyperpolarization technique that enables nuclear spin polarization enhancement of molecules via concurrent chemical exchange of a target substrate and parahydrogen (the source of spin order) on an iridium catalyst. Recently, we demonstrated that conducting SABRE in microtesla fields provided by a magnetic shield enables up to 10% 15N-polarization (Theis, T.; et al. J. Am. Chem. Soc.2015, 137, 1404). Hyperpolarization on 15N (and heteronuclei in general) may be advantageous because of the long-lived nature of the hyperpolarization on 15N relative to the short-lived hyperpolarization of protons conventionally hyperpolarized by SABRE, in addition to wider chemical shift dispersion and absence of background signal. Here we show that these unprecedented polarization levels enable 15N magnetic resonance imaging. We also present a theoretical model for the hyperpolarization transfer to heteronuclei, and detail key parameters that should be optimized for efficient 15N-hyperpolarization. The effects of parahydrogen pressure, flow rate, sample temperature, catalyst-to-substrate ratio, relaxation time (T1), and reversible oxygen quenching are studied on a test system of 15N-pyridine in methanol-d4. Moreover, we demonstrate the first proof-of-principle 13C-hyperpolarization using this method. This simple hyperpolarization scheme only requires access to parahydrogen and a magnetic shield, and it provides large enough signal gains to enable one of the first 15N images (2 × 2 mm2 resolution). Importantly, this method enables hyperpolarization of molecular sites with NMR T1 relaxation times suitable for biomedical imaging and spectroscopy. PMID:25960823

  8. Optimization of amino acid type-specific 13C and 15N labeling for the backbone assignment of membrane proteins by solution- and solid-state NMR with the UPLABEL algorithm.

    PubMed

    Hefke, Frederik; Bagaria, Anurag; Reckel, Sina; Ullrich, Sandra Johanna; Dötsch, Volker; Glaubitz, Clemens; Güntert, Peter

    2011-02-01

    We present a computational method for finding optimal labeling patterns for the backbone assignment of membrane proteins and other large proteins that cannot be assigned by conventional strategies. Following the approach of Kainosho and Tsuji (Biochemistry 21:6273-6279 (1982)), types of amino acids are labeled with (13)C or/and (15)N such that cross peaks between (13)CO(i - 1) and (15)NH(i) result only for pairs of sequentially adjacent amino acids of which the first is labeled with (13)C and the second with (15)N. In this way, unambiguous sequence-specific assignments can be obtained for unique pairs of amino acids that occur exactly once in the sequence of the protein. To be practical, it is crucial to limit the number of differently labeled protein samples that have to be prepared while obtaining an optimal extent of labeled unique amino acid pairs. Our computer algorithm UPLABEL for optimal unique pair labeling, implemented in the program CYANA and in a standalone program, and also available through a web portal, uses combinatorial optimization to find for a given amino acid sequence labeling patterns that maximize the number of unique pair assignments with a minimal number of differently labeled protein samples. Various auxiliary conditions, including labeled amino acid availability and price, previously known partial assignments, and sequence regions of particular interest can be taken into account when determining optimal amino acid type-specific labeling patterns. The method is illustrated for the assignment of the human G-protein coupled receptor bradykinin B2 (B(2)R) and applied as a starting point for the backbone assignment of the membrane protein proteorhodopsin. PMID:21170670

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

    NASA Astrophysics Data System (ADS)

    Singh, Girija S.; Pheko, Tshepo

    2008-08-01

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

  10. Structural peculiarities of configurational isomers of 1-styrylpyrroles according to 1Н, 13С and 15N NMR spectroscopy and density functional theory calculations: electronic and steric hindrance for planar structure.

    PubMed

    Afonin, Andrei V; Ushakov, Igor A; Pavlov, Dmitry V; Schmidt, Elena Yu; Dvorko, Marina Yu

    2013-06-01

    Comparative analysis of the (1)Н and (13)С NMR data for a series of the E and Z-1-styrylpyrroles, E and Z-1-(1-propenyl)pyrroles, 1-vinylpyrroles and styrene suggests that the conjugation between the unsaturated fragments in the former compounds is reduced. This is the result of the mutual influence of the donor p-π and π-π conjugation having opposite directions. According to the NMR data combined with the density functional theory calculations, the Z isomer of 1-styrylpyrrole has essentially a nonplanar structure because of the steric hindrance. However, the E isomer of 1-styrylpyrrole is also an out-of-plane structure despite the absence of a sterical barrier for the planar one. Deviation of the E isomer from the planar structure seems to be caused by an electronic hindrance produced by a mutual influence of the p-π and π-π conjugation. The structure of the E isomer of the 2-substituted 1-styrylpyrroles is similar to that of the 2-substituted 1-vinylpyrroles. The steric effects in the Z isomer of the 2-substituted 1-styrylpyrroles result in the large increase of the dihedral angle between planes of the pyrrole ring and double bond. PMID:23558848

  11. Evaluation of transformer insulating oil quality using NIR, fluorescence, and NMR spectroscopic data fusion.

    PubMed

    Godinho, Mariana S; Blanco, Marcos R; Gambarra Neto, Francisco F; Lião, Luciano M; Sena, Marcelo M; Tauler, Romà; de Oliveira, Anselmo E

    2014-11-01

    Power transformers are essential components in electrical energy distribution. One of their most important parts is the insulation system, consisting of Kraft paper immersed in insulating oil. Interfacial tension and color are major parameters used for assessing oil quality and the system׳s degradation. This work proposes the use of near infrared (NIR), molecular fluorescence, and (1)H nuclear magnetic resonance (NMR) spectroscopy methods combined with chemometric multivariate calibration methods (Partial Least Squares - PLS) to predict interfacial tension and color in insulating mineral oil samples. Interfacial tension and color were also determined using tensiometry and colorimetry as standard reference methods, respectively. The best PLS model was obtained when NIR, fluorescence, and NMR data were combined (data fusion), demonstrating synergy among them. An optimal PLS model was calculated using the selected group of variables according to their importance on PLS projections (VIP). The root mean square errors of prediction (RMSEP) values of 2.9 mN m(-1) and 0.3 were estimated for interfacial tension and color, respectively. Mean relative standard deviations of 1.5% for interfacial tension and 6% for color were registered, meeting quality control requirements set by electrical energy companies. The methods proposed in this work are rapid and simple, showing great advantages over traditional approaches, which are slow and environmentally unfriendly due to chemical waste generation. PMID:25127577

  12. Determination of methyl 13C-15N dipolar couplings in peptides and proteins by three-dimensional and four-dimensional magic-angle spinning solid-state NMR spectroscopy

    NASA Astrophysics Data System (ADS)

    Helmus, Jonathan J.; Nadaud, Philippe S.; Höfer, Nicole; Jaroniec, Christopher P.

    2008-02-01

    We describe three- and four-dimensional semiconstant-time transferred echo double resonance (SCT-TEDOR) magic-angle spinning solid-state nuclear magnetic resonance (NMR) experiments for the simultaneous measurement of multiple long-range N15-Cmethyl13 dipolar couplings in uniformly C13, N15-enriched peptides and proteins with high resolution and sensitivity. The methods take advantage of C13 spin topologies characteristic of the side-chain methyl groups in amino acids alanine, isoleucine, leucine, methionine, threonine, and valine to encode up to three distinct frequencies (N15-Cmethyl13 dipolar coupling, N15 chemical shift, and Cmethyl13 chemical shift) within a single SCT evolution period of initial duration ˜1/JCC1 (where JCC1≈35Hz, is the one-bond Cmethyl13-C13 J-coupling) while concurrently suppressing the modulation of NMR coherences due to C13-C13 and N15-C13 J-couplings and transverse relaxation. The SCT-TEDOR schemes offer several important advantages over previous methods of this type. First, significant (approximately twofold to threefold) gains in experimental sensitivity can be realized for weak N15-Cmethyl13 dipolar couplings (corresponding to structurally interesting, ˜3.5Å or longer, distances) and typical Cmethyl13 transverse relaxation rates. Second, the entire SCT evolution period can be used for Cmethyl13 and/or N15 frequency encoding, leading to increased spectral resolution with minimal additional coherence decay. Third, the experiments are inherently "methyl selective," which results in simplified NMR spectra and obviates the use of frequency-selective pulses or other spectral filtering techniques. Finally, the N15-C13 cross-peak buildup trajectories are purely dipolar in nature (i.e., not influenced by J-couplings or relaxation), which enables the straightforward extraction of N15-Cmethyl13 distances using an analytical model. The SCT-TEDOR experiments are demonstrated on a uniformly C13, N15-labeled peptide, N-acetyl-valine, and a 56

  13. Spectroscopic (vibrational, NMR and UV-vis.) and quantum chemical investigations on 4-hexyloxy-3-methoxybenzaldehyde

    NASA Astrophysics Data System (ADS)

    Abbas, Ashgar; Gökce, Halil; Bahçeli, Semiha

    2016-01-01

    In this study, the 4-hexyloxy-3-methoxybenzaldehyde compound as one of the derivatives of vanillin which is a well known flavoring agent, C14H20O3, has been investigated by experimentally and extensively utilizing density functional theory (DFT) at the B3LYP/6-311++G(d,p) level. In this context, the optimized geometry, vibrational frequencies, 1H and 13C NMR chemical shifts, UV-vis. (in gas phase and in methanol solvent) spectra, HOMO-LUMO analysis, molecular electrostatic potential (MEP), thermodynamic parameters and atomic charges of 4-hexyloxy-3-methoxybenzaldehyde have been calculated. In addition, theoretically predicted IR, Raman and UV-vis. (in gas phase and in methanol solvent) spectra of the mentioned molecule have been constructed. The results calculated were compared with the experimental data.

  14. NMR spectroscopic characterization of β-cyclodextrin inclusion complex with vanillin

    NASA Astrophysics Data System (ADS)

    Pîrnau, Adrian; Bogdan, Mircea; Floare, Calin G.

    2009-08-01

    The inclusion of vanillin by β-cyclodextrin was investigated by 1H NMR. The continuous variation technique was used to evidence the formation of soluble 1:1 complex in aqueous solution. The association constant of vanillin with β-cyclodextrin has been obtained at 298 K by fitting the experimental chemical shifts differences, Δδobs = δfree - δobs of the observed guest and host protons, with a non-linear regression method. Besides the effective association constant, the fitting procedure allows a precise determination of all chemical shift parameters characterizing the pure complex. They can by used for an analysis of the geometry of the molecular complex in solution.

  15. Spectroscopic (vibrational, NMR and UV-vis.) and quantum chemical investigations on 4-hexyloxy-3-methoxybenzaldehyde.

    PubMed

    Abbas, Ashgar; Gökce, Halil; Bahçeli, Semiha

    2016-01-01

    In this study, the 4-hexyloxy-3-methoxybenzaldehyde compound as one of the derivatives of vanillin which is a well known flavoring agent, C14H20O3, has been investigated by experimentally and extensively utilizing density functional theory (DFT) at the B3LYP/6-311++G(d,p) level. In this context, the optimized geometry, vibrational frequencies, (1)H and (13)C NMR chemical shifts, UV-vis. (in gas phase and in methanol solvent) spectra, HOMO-LUMO analysis, molecular electrostatic potential (MEP), thermodynamic parameters and atomic charges of 4-hexyloxy-3-methoxybenzaldehyde have been calculated. In addition, theoretically predicted IR, Raman and UV-vis. (in gas phase and in methanol solvent) spectra of the mentioned molecule have been constructed. The results calculated were compared with the experimental data. PMID:25736185

  16. Spectroscopic (FT-IR, FT-Raman and NMR) and computational studies on 3-methoxyaniline

    NASA Astrophysics Data System (ADS)

    Sivaranjini, T.; Periandy, S.; Govindarajan, M.; Karabacak, M.; Asiri, A. M.

    2014-01-01

    In this work, the molecular structure, vibrational, UV and NMR spectra of 3-methoxyaniline (abbreviated as 3MOA, C7H9NO) were studied. The FT-IR and FT-Raman spectra were recorded. The ground-state molecular geometry and vibrational frequencies were calculated by using the Hartree-Fock (HF) and density functional theory (DFT)/B3LYP methods and 6-311++G(d, p) as a basis set. The fundamental vibrations were assigned on the basis of the total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method and PQS program. Comparison of the observed fundamental vibrational frequencies of 3MOA with calculated results by HF and DFT methods indicates that B3LYP is superior to HF method for molecular vibrational problems. The difference between the observed and scaled wavenumber values is very small. The theoretically predicted FT-IR and FT-Raman spectra of the title molecule have been constructed. A study on the Mulliken atomic charges, the electronic properties were performed by time-dependent DFT (TD-DFT) approach, Frontier molecular orbitals (FMO), molecular electrostatic potential (MEP) and thermodynamic properties were performed and compared with methoxybenzene and aniline. The electric dipole moment (μ) and the first hyperpolarizability (β) values of the investigated molecule were computed using ab initio quantum mechanical calculations. The calculated results also show that the 3MOA molecule might have microscopic nonlinear optical (NLO) behavior with non-zero values. The 13C nuclear magnetic resonance (NMR) chemical shifts of the molecule were calculated by the gauge independent atomic orbital (GIAO) method and compared with experimental results.

  17. {sup 1}H and {sup 15}N dynamic nuclear polarization studies of carbazole

    SciTech Connect

    Hu, J.Z.; Solum, M.S.; Wind, R.A.; Nilsson, B.L.; Peterson, M.A.; Pugmire, R.J.; Grant, D.M.

    2000-05-18

    {sup 15}N NMR experiments, combined with dynamic nuclear polarization (DNP), are reported on carbazole doped with the stable free radical 1,3-bisdiphenylene-2-phenylallyl (BDPA). Doping shortens the nuclear relaxation times and provides paramagnetic centers that can be used to enhance the nuclear signal by means of DNP so that {sup 15}N NMR experiments can be done in minutes. The factors were measured in a 1.4 T external field, using both unlabeled and 98% {sup 15}N labeled carbazole with doping levels varying between 0.65 and 5.0 wt {degree} BDPA. A doping level of approximately 1 wt {degree} produced optimal results. DNP enhancement factors of 35 and 930 were obtained for {sup 1}H and {sup 15}N, respectively, making it possible to perform {sup 15}N DNP NMR experiments at the natural abundance level.

  18. 1H and 15N Dynamic Nuclear Polarization Studies of Carbazole

    SciTech Connect

    Hu, Jian Zhi; Solum, Mark S.; Wind, Robert A.; Nilsson, Brad L.; Peterson, Matt A.; Pugmire, Ronald J.; Grant, David M.

    2000-01-01

    15N NMR experiments, combined with dynamic nuclear polarization (DNP), are reported on carbazole doped with the stable free radical 1,3 bisdiphenylene-2 phenylally1 (BDPA). Doping shortens the nuclear relaxation times and provides paramagnetic centers that can be used to enhance the nuclear signal by means of DNP so that 15 N NMR experiments can be done in minutes. The factors were measured in a 1.4 T external field, using both unlabeled and 98% 15N labeled carbazole with doping levels varying between 0.65 and 5.0 wt % BDPA. A doping level of approximately 1 wt % produced optimal results. DNP enhancement factors of 35 and 930 were obtained for 1H and 15N, respectively making it possible to perform 15N DNP NMR experiments at the natural abundance level.

  19. Synthesis of Radiation Curable Palm Oil-Based Epoxy Acrylate: NMR and FTIR Spectroscopic Investigations.

    PubMed

    Salih, Ashraf M; Ahmad, Mansor Bin; Ibrahim, Nor Azowa; Dahlan, Khairul Zaman Hj Mohd; Tajau, Rida; Mahmood, Mohd Hilmi; Yunus, Wan Md Zin Wan

    2015-01-01

    Over the past few decades, there has been an increasing demand for bio-based polymers and resins in industrial applications, due to their potential lower cost and environmental impact compared with petroleum-based counterparts. The present research concerns the synthesis of epoxidized palm oil acrylate (EPOLA) from an epoxidized palm oil product (EPOP) as environmentally friendly material. EPOP was acrylated by acrylic acid via a ring opening reaction. The kinetics of the acrylation reaction were monitored throughout the reaction course and the acid value of the reaction mixture reached 10 mg KOH/g after 16 h, indicating the consumption of the acrylic acid. The obtained epoxy acrylate was investigated intensively by means of FTIR and NMR spectroscopy, and the results revealed that the ring opening reaction was completed successfully with an acrylation yield about 82%. The UV free radical polymerization of EPOLA was carried out using two types of photoinitiators. The radiation curing behavior was determined by following the conversion of the acrylate groups. The cross-linking density and the hardness of the cured EPOLA films were measured to evaluate the effect of the photoinitiator on the solid film characteristics, besides, the thermal and mechanical properties were also evaluated. PMID:26248072

  20. Computational Chemistry Meets Experiments for Explaining the Behavior of Bibenzyl: A Thermochemical and Spectroscopic (Infrared, Raman, and NMR) Investigation.

    PubMed

    Latouche, Camille; Barone, Vincenzo

    2014-12-01

    The structure, conformational behavior, and spectroscopic parameters of bibenzyl have been investigated by a computational protocol including proper treatment of anharmonic and hindered rotor contributions. Conventional hybrid functionals overstabilize the anti conformer while low-order post-Hartree-Fock (MP2) approaches strongly favor the gauche conformer. However, inclusion of semiempirical dispersion effects in density functionals or coupled cluster post-Hartree-Fock models agree in forecasting the simultaneous presence of both conformers in the gas phase with a slightly larger stability (0.7 kcal·mol(-1)) of the gauche conformer. Addition of thermal and entropic effects finally leads to very close Gibbs free energies for both conformers and, thus, to a slight preference for the gauche form due to statistical factors (2 vs 1). The situation remains essentially the same in solution. On these grounds, perturbative vibrational computations including both electrical and mechanical anharmonicities lead to IR and Raman spectra in remarkable agreement with experiment. Full assignment of the IR spectra explains the presence of peaks from gauche or anti conformers. Comparison between computed and experimental Raman spectra confirms that both conformers are present in liquid phase, whereas the anti conformer seems to be preponderant in the solid state. Also computed NMR parameters are in good agreement with experiment. PMID:26583241

  1. Niobium-93 MQMAS NMR spectroscopic study of alkali and lead niobates.

    PubMed

    Prasad, S; Zhao, P; Huang, J; Fitzgerald, J J; Shore, J S

    2001-01-01

    93Nb (I = 9/2) multiple-quantum magic-angle spinning (MQMAS) NMR spectra of a series of inorganic niobates have been measured. 93Nb MQMAS spectroscopy yields spectra with typically an order of magnitude higher resolution than that obtainable with 93Nb MAS spectroscopy and 93Nb dynamic-angle spinning (DAS) spectroscopy. For example, the full-width at half-maximums of the 93Nb resonances of LiNbO3 were 9 (MAS), 5.8 (DAS), and 0.7 kHz (MQMAS). Broadening of the 93Nb MAS and DAS spectra is due to the second-order quadrupolar and homonuclear dipolar interactions, respectively. The quadrupolar products (P(O)) and isotropic chemical shifts (delta(iso)) of the 93Nb resonances of LiNbO3, NaNbO3, PbNb2O6, Pb2Nb2O7, Pb3Nb2O8, Pb3Nb4O15, Pb3Nb4O13, and Pb1.83Nb1.71Mg0.29O6.39 were determined from MQMAS spectra and range from 13.6 to 26.8 MHz and from -951 to -1113 ppm, respectively. Resonances with relatively large quadrupolar coupling constants (> 30 MHz) were not observed using MQMAS spectroscopy, but were detected using nutation spectroscopy. The applicability and limitations of MQMAS spectroscopy in studying inorganic niobates containing multiple 93Nb resonances are addressed and compared with those of MAS, nutation, and DAS spectroscopies. PMID:11407602

  2. a Combined Molecular Dynamics and NMR Spectroscopic Protocol for the Conformational Analysis of Oligosaccharides.

    NASA Astrophysics Data System (ADS)

    Varma, Vikram

    A combined experimental and theoretical protocol for the conformational analysis of oligosaccharides is presented. Three disaccharides, methyl alpha - scD-mannopyranosyl-(1 to 3)-alpha- scD-mannopyranoside, methyl beta- scD-galactopyranosyl-(1 to 4)-beta- scD-glucopyranoside, and propyl beta- scD-2-acetamido -2-deoxy glucopyranosyl-(1 to 3)- alpha- scL-rhamnopyranoside, are used to evaluate a protocol for conformational analysis that makes use of molecular dynamics calculations with the CHARMM force field. Dynamics trajectories computed in vacuo and in water are used to calculate time-averaged NMR parameters such as spin-lattice relaxation times (T_1 ), Nuclear Overhauser Enhancements (NOE), and heteronuclear spin-spin coupling constants (^3J _{rm CH}). The calculated NMR parameters are then compared to experimental values and used to evaluate the computational procedure. The energetically accessible conformations are effectively sampled by the simulations. The method has been extended to the conformational analysis of higher-order oligosaccharides corresponding to the cell-wall polysaccharide of the Streptococcus Group A, and the Shigella flexneri Y O-antigen. The Streptococcus Group A cell-wall polysaccharide is comprised of a backbone of rhamnopyranosyl units connected by alternating alpha- scL-(1 to 3) and alpha- scL -(1 to 2) linkages, to which are attached N-acetyl-beta- scD-glucosamine ( beta- scD-GlcpNAc) residues at the 3 positions of the rhamnose backbone.rm A&rm B^'qquad A^'& rm Bqquad Acr[{-alpha}{-}L{-}Rha {it p}{-}(1to2){-alpha }{-}L{-}Rha{it p} {-}(1to3){-alpha}{ -}L{-}Rha{it p}-(1to2) -alpha-L-Rha{it p}{-}(1 to3){-alpha}{-}L{- }Rha{it p}{-}cr&uparrow(1 to3)&uparrow(1to3)crbeta {-}D{-}&rm Glc{it p }NAcqquadbeta{-}D{-}& rm Glc{it p}NAccr&rm C ^'&rm C] A branched trisaccharide (A^' -(C)B), a tetrasaccharide (A^' -(C)B-A), a pentasaccharide (C^' -B^'-A ^'-(C)B), and two hexasaccharides (C^'-B^ '-A^' -(C)B-A) and (A-(C^')B ^'-A^' -(C)B), have been chosen

  3. REDOR NMR of stable-isotope-labeled protein binding sites

    SciTech Connect

    Schaefer, J.

    1994-12-01

    Rotational-echo, double resonance (REDOR) NMR, a new analytical spectroscopic technique for solids spinning at the magic angle, has been developed over the last 5 years. REDOR provides a direct measure of heteronuclear dipolar coupling between isolated pairs of labeled nuclei. In a solid with a {sup 13}C-{sup 15}N labeled pair, for example, the {sup 13}C rotational echoes that form each rotor period following a{sup 1}H-{sup 13}C cross-polarization transfer can be prevented from reaching full intensity by insertion of a {sup 15}N {pi} pulse each half rotor period. The REDOR difference (the difference between a {sup 13}C NMR spectrum obtained under these conditions and one obtained with no {sup 15}N {pi} pulses) has a strong dependence on the {sup 13}C-{sup 15}N dipolar coupling, and hence, the {sup 13}C-{sup 15}N internuclear distance. REDOR is described as double-resonance even though three radio frequencies (typically {sup 1}H, {sup 13}C, and {sup 15}N) are used because the protons are removed from the important evolution part of the experiment by resonant decoupling. The dephasing of magnetization in REDOR arises from a local dipolar {sup 13}C-{sup 15}N field gradient and involves no polarization transfer. REDOR has no dependence on {sup 13}C or {sup 15}N chemical-shift tensors and does not require resolution of a {sup 13}C-{sup 15}N coupling in the chemical-shift dimension.

  4. Electrochemical and NMR spectroscopic studies of distal pocket mutants of nitrophorin 2: Stability, structure, and dynamics of axial ligand complexes

    PubMed Central

    Shokhireva, Tatjana Kh.; Berry, Robert E.; Uno, Elizabeth; Balfour, Celia A.; Zhang, Hongjun; Walker, F. Ann

    2003-01-01

    WT and leucine → valine distal pocket mutants of nitrophorin 2 (NP2) and their NO complexes have been investigated by spectroelectrochemistry. NO complexes of two of the mutants exhibit more positive reduction potential shifts than does the WT protein, thus indicating stabilization of the Fe(II)–NO state. This more positive reduction potential for NP2-L132V and the double mutant is consistent with the hypothesis that smaller valine residues may allow the heme to regain planarity instead of being significantly ruffled, as in WT NP2. Thus, ruffling may stabilize the Fe(III)–NO state, which is required for facile NO dissociation. NMR spectroscopic investigations show that the sterically demanding 2-methylimidazole ligand readily binds to all three distal pocket mutants to create low-spin Fe(III) complexes having axial ligands in nearly perpendicular planes; it also binds to the WT protein in the presence of higher concentrations of 2-methylimidazole, but yields a different ligand plane orientation than is present in any of the three distal pocket mutants. NOESY spectra of NP2–ImH mutants exhibit chemical exchange cross peaks, whereas WT NP2–ImH shows no chemical exchange. Chemical exchange in the case of the distal leucine → valine mutants is caused by ImH ligand orientational dynamics. The two angular orientations of the ImH ligand could be determined from the 1H chemical shifts of the heme methyls, and the rate of interconversion of the two forms could be estimated from the NOESY diagonal and cross peak intensities. Keq is 100 or larger and favors an orientation similar to that found for the WT NP2–ImH complex. PMID:12642672

  5. Through-space (19) F-(15) N couplings for the assignment of stereochemistry in flubenzimine.

    PubMed

    Ghiviriga, Ion; Rubinski, Miles A; Dolbier, William R

    2016-07-01

    Through-space (19) F-(15) N couplings revealed the configuration of flubenzimine, with the CF3 group on N4 pointing towards the lone pair of N5. The (19) F-(15) N coupling constants were measured at natural abundance using a spin-state selective indirect-detection pulse sequence. As (15) N-labelled proteins are routinely synthesized for NMR studies, through-space (19) F-(15) N couplings have the potential to probe the stereochemistry of these proteins by (19) F labelling of some amino acids or can reveal the site of docking of fluorine-containing drugs. Copyright © 2016 John Wiley & Sons, Ltd. PMID:27059012

  6. Binding of thiocyanate to lactoperoxidase: 1H and 15N nuclear magnetic resonance studies

    SciTech Connect

    Modi, S.; Behere, D.V.; Mitra, S. )

    1989-05-30

    The binding of thiocyanate to lactoperoxidase (LPO) has been investigated by 1H and 15N NMR spectroscopy. 1H NMR of LPO shows that the major broad heme methyl proton resonance at about 61 ppm is shifted upfield by addition of the thiocyanate, indicating binding of the thiocyanate to the enzyme. The pH dependence of line width of 15N resonance of SC15N- in the presence of the enzyme has revealed that the binding of the thiocyanate to the enzyme is facilitated by protonation of an ionizable group (with pKa of 6.4), which is presumably distal histidine. Dissociation constants (KD) of SC15N-/LPO, SC15N-/LPO/I-, and SC15N-/LPO/CN- equilibria have been determined by 15N T1 measurements and found to be 90 +/- 5, 173 +/- 20, and 83 +/- 6 mM, respectively. On the basis of these values of KD, it is suggested that the iodide ion inhibits the binding of the thiocyanate but cyanide ion does not. The thiocyanate is shown to bind at the same site of LPO as iodide does, but the binding is considerably weaker and is away from the ferric ion. The distance of 15N of the bound thiocyanate ion from the iron is determined to be 7.2 +/- 0.2 A from the 15N T1 measurements.

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

    NASA Astrophysics Data System (ADS)

    Alver, Özgür; Dikmen, Gökhan

    2016-03-01

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

  8. A comparative study of selected disperse azo dye derivatives based on spectroscopic (FT-IR, NMR and UV-Vis) and nonlinear optical behaviors.

    PubMed

    Cinar, Mehmet; Coruh, Ali; Karabacak, Mehmet

    2014-03-25

    In the present work, a combined experimental and quantum chemical study on ground state equilibrium structure, spectroscopic and nonlinear optical properties of selected disperse azo dye molecules are reported. The vibrational transitions were identified based on the recorded FT-IR spectra in the range of 4000-400 cm(-1) for solid state, simulated IR spectra and total energy distribution (TED) of vibrational modes. The chemical shifts were determined from the results of observed (1)H and (13)C NMR spectra in chloroform and dimethylsulfoxide solution. The DFT/gauge-invariant atomic orbital (GIAO) methodology was applied to predict the magnetic properties. Electronic properties were carried out by UV-Vis spectroscopy and TD-DFT/CIS approach. The nonlinear optical (NLO) features were addressed theoretically. A detailed description of spectroscopic and NLO behaviors of studied disperse azo dyes was reported with the help of comparison of experimental measurements and theoretical calculations. PMID:24345608

  9. A comparative study of selected disperse azo dye derivatives based on spectroscopic (FT-IR, NMR and UV-Vis) and nonlinear optical behaviors

    NASA Astrophysics Data System (ADS)

    Cinar, Mehmet; Coruh, Ali; Karabacak, Mehmet

    2014-03-01

    In the present work, a combined experimental and quantum chemical study on ground state equilibrium structure, spectroscopic and nonlinear optical properties of selected disperse azo dye molecules are reported. The vibrational transitions were identified based on the recorded FT-IR spectra in the range of 4000-400 cm-1 for solid state, simulated IR spectra and total energy distribution (TED) of vibrational modes. The chemical shifts were determined from the results of observed 1H and 13C NMR spectra in chloroform and dimethylsulfoxide solution. The DFT/gauge-invariant atomic orbital (GIAO) methodology was applied to predict the magnetic properties. Electronic properties were carried out by UV-Vis spectroscopy and TD-DFT/CIS approach. The nonlinear optical (NLO) features were addressed theoretically. A detailed description of spectroscopic and NLO behaviors of studied disperse azo dyes was reported with the help of comparison of experimental measurements and theoretical calculations.

  10. Interaction of Lipopolysaccharide and Phospholipid in Mixed Membranes: Solid-State 31P-NMR Spectroscopic and Microscopic Investigations

    PubMed Central

    Nomura, Kaoru; Inaba, Takehiko; Morigaki, Kenichi; Brandenburg, Klaus; Seydel, Ulrich; Kusumoto, Shoichi

    2008-01-01

    Lipopolysaccharide (LPS), which constitutes the outermost layer of Gram-negative bacterial cells as a typical component essential for their life, induces the first line defense system of innate immunity of higher animals. To understand the basic mode of interaction between bacterial LPS and phospholipid cell membranes, distribution patterns were studied by various physical methods of deep rough mutant LPS (ReLPS) of Escherichia coli incorporated in phospholipid bilayers as simple models of cell membranes. Solid-state 31P-NMR spectroscopic analysis suggested that a substantial part of ReLPS is incorporated into 1,2-dimyristoyl-sn-glycero-3-phosphocholine lipid bilayers when multilamellar vesicles were prepared from mixtures of these. In egg L-α-phosphatidylcholine (egg-PC)-rich membranes, ReLPS undergoes micellization. In phosphatidylethanolamine-rich membranes, however, micellization was not observed. We studied by microscopic techniques the location of ReLPS in membranes of ReLPS/egg-PC (1:10 M/M) and ReLPS/egg-PC/1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol (POPG) (1:9:1 M/M/M). The influence of ReLPS on the physicochemical properties of the membranes was studied as well. Microscopic images of both giant unilamellar vesicles and supported planar lipid bilayers showed that LPS was uniformly incorporated in the egg-PC lipid bilayers. In the egg-PC/POPG (9:1 M/M) lipid bilayers, however, ReLPS is only partially incorporated and becomes a part of the membrane in a form of aggregates (or as mixed aggregates with the lipids) on the bilayer surface. The lipid lateral diffusion coefficient measurements at various molar ratios of ReLPS/egg-PC/POPG indicated that the incorporated ReLPS reduces the diffusion coefficients of the phospholipids in the membrane. The retardation of diffusion became more significant with increasing POPG concentrations in the membrane at high ReLPS/phospholipid ratios. This work demonstrated that the phospholipid composition has critical

  11. Palladium(II) complex with S-allyl- L-cysteine: New solid-state NMR spectroscopic measurements, molecular modeling and antibacterial assays

    NASA Astrophysics Data System (ADS)

    Spera, Marcelle B. M.; Quintão, Frederico A.; Ferraresi, Diego K. D.; Lustri, Wilton R.; Magalhães, Alviclér; Formiga, André L. B.; Corbi, Pedro P.

    2011-01-01

    Nuclear magnetic resonance studies, molecular modeling and antibacterial assays of the palladium(II) complex with S-allyl- L-cysteine (deoxyalliin) are presented. Studies based on solid and solution 13C and 15N nuclear magnetic resonance (NMR) spectroscopy confirmed that the palladium(II) complex preserved the same structural arrangement in both states, with no modifications on coordination sphere when dissolved in water. Density functional theory (DFT) studies stated that the trans isomer is the most stable one. Antibacterial activities of S-allyl- L-cysteine and its palladium(II) complex were evaluated by antibiogram assays using the disc diffusion method. The palladium(II) complex showed an effective antibacterial activity against S taphylococcus aureus (Gram-positive), Escherichia coli and Pseudomonas aeruginosa (Gram-negative) bacterial cells.

  12. A high-resolution phosphorus-31 nuclear magnetic resonance (NMR) spectroscopic method for the non-phosphorus markers of chemical warfare agents.

    PubMed

    Mazumder, Avik; Kumar, Ajeet; Purohit, Ajay K; Dubey, Devendra K

    2012-02-01

    A high-resolution phosphorus-31 nuclear magnetic resonance (NMR) spectroscopic method has been developed for detection, identification and quantification of non-phosphorus markers of toxic nerve agents (soman and V-class), vesicants (HD, HN-2, HN-3), and incapacitating agent (Bz). These analytes were converted to phosphorus-containing derivatives via phosphitylation reaction of their hydroxyl and sulfhydryl functions (using 2-chloro-4,4,5,5-tetramethyl-1,3,2-dioxaphospholane). This was followed by (31)P{(1)H} and (31)P NMR analysis of these derivatives. The chemical shifts (δ) and coupling constants ((3)J(P-H)) of derivatives were used for their specific detection and identification. The method allowed clear distinction between the alcohols and thiols. The lower limits of detection of these analytes were found to be between 12 and 28 μg obtained from 128 transients of (31)P{(1)H} quantitative NMR experiments. Utility of the method was ensured by the detection and identification of triethanolamine present (at an original concentration of 5 μg/mL) in an aqueous sample from 28th OPCW Official Proficiency Tests. PMID:22160203

  13. Proton and nitrogen-15 NMR spectroscopic studies of hydrogen ion-dependent pseudo-halide ion binding to chloroperoxidase

    SciTech Connect

    Lukat, G.S.; Goff, H.M.

    1986-12-15

    The proton nuclear magnetic resonance spectra of several chloroperoxidase-inhibitor complexes have been investigated. Titrations of chloroperoxidase with azide, thiocyanate, cyanate, or nitrite ions indicate that only the chloroperoxidase-thiocyanate complex exhibits slow ligand exchange on the 360-MHz NMR time scale. The temperature dependence of the proton NMR spectra of the complexes suggests that, although the complexes are predominantly low-spin ferric heme iron, a spin equilibrium is present presumably between S = 1/2 and S = 5/2 states. The pH dependence of the proton NMR spectra of the psuedo-halide-chloroperoxidase complexes was examined at 360 and 90 MHz. Chloroperoxidase complexes with azide and cyanate show similar behavior; 360-MHz proton spectra are readily observed at low pH (less than 5.0) but not at high pH. At high pH, the ligand exchange rate falls in an intermediate time range. When the complexes are examined at 90 MHz, however, spectra consisting of averaged signals are observed. The chloroperoxidase-thiocyanate complex does not form at high pH values; the proton NMR spectrum observed is that of native chloroperoxidase. The pKa for the chloroperoxidase-thiocyanate heme-linked ionizable amino acid residue falls between 4.2 and 5.0. Only an averaged azide signal was observed in the nitrogen-15 NMR spectra for solutions that contained the azide complex of chloroperoxidase, horseradish peroxidase, and myoglobin.

  14. Proton and nitrogen-15 NMR spectroscopic studies of hydrogen ion-dependent pseudo-halide ion binding to chloroperoxidase.

    PubMed

    Lukat, G S; Goff, H M

    1986-12-15

    The proton nuclear magnetic resonance spectra of several chloroperoxidase-inhibitor complexes have been investigated. Titrations of chloroperoxidase with azide, thiocyanate, cyanate, or nitrite ions indicate that only the chloroperoxidase-thiocyanate complex exhibits slow ligand exchange on the 360-MHz NMR time scale. The temperature dependence of the proton NMR spectra of the complexes suggests that, although the complexes are predominantly low-spin ferric heme iron, a spin equilibrium is present presumably between S = 1/2 and S = 5/2 states. The pH dependence of the proton NMR spectra of the psuedo-halide-chloroperoxidase complexes was examined at 360 and 90 MHz. Chloroperoxidase complexes with azide and cyanate show similar behavior; 360-MHz proton spectra are readily observed at low pH (less than 5.0) but not at high pH. At high pH, the ligand exchange rate falls in an intermediate time range. When the complexes are examined at 90 MHz, however, spectra consisting of averaged signals are observed. The chloroperoxidase-thiocyanate complex does not form at high pH values; the proton NMR spectrum observed is that of native chloroperoxidase. The pKa for the chloroperoxidase-thiocyanate heme-linked ionizable amino acid residue falls between 4.2 and 5.0. Only an averaged azide signal was observed in the nitrogen-15 NMR spectra for solutions that contained the azide complex of chloroperoxidase, horseradish peroxidase, and myoglobin. PMID:3023353

  15. UV-vis, IR and 1H NMR spectroscopic studies and characterization of ionic-pair crystal violet-oxytetracycline

    NASA Astrophysics Data System (ADS)

    Orellana, Sandra; Soto, César; Toral, M. Inés

    2010-01-01

    The present study shows the formation and characterization of the ionic-pair between the antibiotic oxytetracycline and the dye crystal violet in ammonia solution pH 9.0 ± 0.2 extracted into chloroform. The characterization was demonstrated using UV-vis spectrophotometry, 1H NMR, measurement of relaxation times T1 and IR spectroscopy, using a comparison between the signals of individual pure compounds with the signals with the mixture CV-OTC in different alkaline media. The formation of ionic-pair was also corroborated by new signals and chemical shifts. (2D) NMR spectroscopy experiments show that the interaction is electrostatic.

  16. A multinuclear solid state NMR spectroscopic study of the structural evolution of disordered calcium silicate sol-gel biomaterials.

    PubMed

    Lin, Zhongjie; Jones, Julian R; Hanna, John V; Smith, Mark E

    2015-01-28

    Disordered sol-gel prepared calcium silicate biomaterials show significant, composition dependent ability to bond with bone. Bone bonding is attributed to rapid hydroxycarbonate apatite (HCA) formation on the glass surface after immersion in body fluid (or implantation). Atomic scale details of the development of the structure of (CaO)x(SiO2)1-x (x = 0.2, 0.3 and 0.5) under heat treatment and subsequent dissolution in simulated body fluid (SBF) are revealed through a multinuclear solid state NMR approach using one-dimensional (17)O, (29)Si, (31)P and (1)H. Central to this study is the combination of conventional static and magic angle spinning (MAS) and two-dimensional (2D) triple quantum (3Q) (17)O NMR experiments that can readily distinguish and quantify the bridging (BOs) and non-bridging (NBOs) oxygens in the silicate network. Although soluble calcium is present in the sol, the (17)O NMR results reveal that the sol-gel produced network structure is initially dominated by BOs after gelation, aging and drying (e.g. at 120 °C), indicating a nanoscale mixture of the calcium salt and a predominantly silicate network. Only once the calcium salt is decomposed at elevated temperatures do the Ca(2+) ions become available to break BO. Apatite forming ability in SBF depends strongly on the surface OH and calcium content. The presence of calcium aids HCA formation via promotion of surface hydration and the ready availability of Ca(2+) ions. (17)O NMR shows the rapid loss of NBOs charge balanced by calcium as it is leached into the SBF. The formation of nanocrystalline, partially ordered HCA can be detected via(31)P NMR. This data indicates the importance of achieving the right balance of BO/NBO for optimal biochemical response and network properties. PMID:25494341

  17. Fast structure-based assignment of 15N HSQC spectra of selectively 15N-labeled paramagnetic proteins.

    PubMed

    Pintacuda, Guido; Keniry, Max A; Huber, Thomas; Park, Ah Young; Dixon, Nicholas E; Otting, Gottfried

    2004-03-10

    A novel strategy for fast NMR resonance assignment of (15)N HSQC spectra of proteins is presented. It requires the structure coordinates of the protein, a paramagnetic center, and one or more residue-selectively (15)N-labeled samples. Comparison of sensitive undecoupled (15)N HSQC spectra recorded of paramagnetic and diamagnetic samples yields data for every cross-peak on pseudocontact shift, paramagnetic relaxation enhancement, cross-correlation between Curie-spin and dipole-dipole relaxation, and residual dipolar coupling. Comparison of these four different paramagnetic quantities with predictions from the three-dimensional structure simultaneously yields the resonance assignment and the anisotropy of the susceptibility tensor of the paramagnetic center. The method is demonstrated with the 30 kDa complex between the N-terminal domain of the epsilon subunit and the theta subunit of Escherichia coli DNA polymerase III. The program PLATYPUS was developed to perform the assignment, provide a measure of reliability of the assignment, and determine the susceptibility tensor anisotropy. PMID:14995214

  18. Over 20% (15)N Hyperpolarization in Under One Minute for Metronidazole, an Antibiotic and Hypoxia Probe.

    PubMed

    Barskiy, Danila A; Shchepin, Roman V; Coffey, Aaron M; Theis, Thomas; Warren, Warren S; Goodson, Boyd M; Chekmenev, Eduard Y

    2016-07-01

    Direct NMR hyperpolarization of naturally abundant (15)N sites in metronidazole is demonstrated using SABRE-SHEATH (Signal Amplification by Reversible Exchange in SHield Enables Alignment Transfer to Heteronuclei). In only a few tens of seconds, nuclear spin polarization P(15)N of up to ∼24% is achieved using parahydrogen with 80% para fraction corresponding to P(15)N ≈ 32% if ∼100% parahydrogen were employed (which would translate to a signal enhancement of ∼0.1-million-fold at 9.4 T). In addition to this demonstration on the directly binding (15)N site (using J(2)H-(15)N), we also hyperpolarized more distant (15)N sites in metronidazole using longer-range spin-spin couplings (J(4)H-(15)N and J(5)H-(15)N). Taken together, these results significantly expand the range of molecular structures and sites amenable to hyperpolarization via low-cost parahydrogen-based methods. In particular, hyperpolarized nitroimidazole and its derivatives have powerful potential applications such as direct in vivo imaging of mechanisms of action or hypoxia sensing. PMID:27321159

  19. FT-IR and FT-Raman, NMR and UV spectroscopic investigation and hybrid computational (HF and DFT) analysis on the molecular structure of mesitylene.

    PubMed

    Kose, E; Atac, A; Karabacak, M; Nagabalasubramanian, P B; Asiri, A M; Periandy, S

    2013-12-01

    The spectroscopic properties of mesitylene were investigated by FT-IR, FT-Raman, UV, (1)H and (13)C NMR techniques. The geometrical parameters and energies have been obtained from density functional theory (DFT) B3LYP method and Hartree-Fock (HF) method with 6-311++G(d,p) and 6-311G(d,p) basis sets calculations. The geometry of the molecule was fully optimized, vibrational spectra were calculated and fundamental vibrations were assigned on the basis of the total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method and PQS program. Total and partial density of state (TDOS and PDOS) and also overlap population density of state (OPDOS) diagrams analysis were presented. (13)C and (1)H NMR chemical shifts were calculated by using the gauge-invariant atomic orbital (GIAO) method. The electronic properties, such as excitation energies, oscillator strength, wavelengths, HOMO and LUMO energies, were performed by time-dependent density functional theory (TD-DFT) results complements with the experimental findings. The results of the calculations were applied to simulate spectra of the title compound, which show excellent agreement with observed spectra. Besides, frontier molecular orbitals (FMO), molecular electrostatic potential (MEP) and thermodynamic properties were performed. Reduced density gradient (RDG) of the mesitylene was also given to investigate interactions of the molecule. PMID:23978748

  20. FT-IR and FT-Raman, NMR and UV spectroscopic investigation and hybrid computational (HF and DFT) analysis on the molecular structure of mesitylene

    NASA Astrophysics Data System (ADS)

    Kose, E.; Atac, A.; Karabacak, M.; Nagabalasubramanian, P. B.; Asiri, A. M.; Periandy, S.

    2013-12-01

    The spectroscopic properties of mesitylene were investigated by FT-IR, FT-Raman, UV, 1H and 13C NMR techniques. The geometrical parameters and energies have been obtained from density functional theory (DFT) B3LYP method and Hartree-Fock (HF) method with 6-311++G(d,p) and 6-311G(d,p) basis sets calculations. The geometry of the molecule was fully optimized, vibrational spectra were calculated and fundamental vibrations were assigned on the basis of the total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method and PQS program. Total and partial density of state (TDOS and PDOS) and also overlap population density of state (OPDOS) diagrams analysis were presented. 13C and 1H NMR chemical shifts were calculated by using the gauge-invariant atomic orbital (GIAO) method. The electronic properties, such as excitation energies, oscillator strength, wavelengths, HOMO and LUMO energies, were performed by time-dependent density functional theory (TD-DFT) results complements with the experimental findings. The results of the calculations were applied to simulate spectra of the title compound, which show excellent agreement with observed spectra. Besides, frontier molecular orbitals (FMO), molecular electrostatic potential (MEP) and thermodynamic properties were performed. Reduced density gradient (RDG) of the mesitylene was also given to investigate interactions of the molecule.

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

    PubMed

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

    2016-08-01

    Three experiments were conducted in developing a low resolution proton nuclear magnetic resonance ((1)H NMR) spectroscopic technique to study matrix mobility in fresh and freeze-thawed gelled yolk. The Carr-Purcell-Meiboom-Gill (CPMG) sequence was used to measure spin-spin relaxation times of proton pools representing major yolk constituents. A component identification test distinguished 3-4 pools. The least mobile pool was assigned to proteins, protein-lipid and protein-water interactions, and the most mobile to unbound water. The remaining pools were assigned to lipids, lipid-protein and lipid-water interactions. A stability test indicated that yolk had varied matrix mobility within the same sample across five days of refrigeration storage. A reproducibility test demonstrated high repeatability of fresh yolk measurements, but significant differences (p<0.05) were found within gelled yolk samples. This research determined that (1)H NMR spectroscopy, a non-destructive technique, can identify yolk components and detect changes in the matrix. PMID:26988489

  2. NMR, FT-IR, FT-Raman, UV spectroscopic, HOMO-LUMO and NBO analysis of cumene by quantum computational methods

    NASA Astrophysics Data System (ADS)

    Sivaranjani, T.; Xavier, S.; Periandy, S.

    2015-03-01

    This work presents the investigation of cumene using the FT-IR, FT-Raman, NMR and UV spectra obtained through various spectroscopic techniques. The theoretical vibrational frequencies and optimized geometric parameters have been calculated by using HF and density functional theory with the hybrid methods B3LYP, B3PW91 and 6-311+G(d,p)/6-311++G(d,p) basis sets. The theoretical vibrational frequencies have been scaled and compared with the corresponding experimental data. 1H and 13C NMR spectra were recorded and chemical shifts of the molecule were compared to TMS by using the Gauge-Independent Atomic Orbital (GIAO) method. A study on the electronic and optical properties, absorption wavelengths, excitation energy, dipole moment and frontier molecular orbital energies, and potential energy surface (PES) is performed using HF and DFT methods. The thermodynamic properties (heat capacity, entropy and enthalpy) at different temperatures are also calculated. NBO analysis is carried out to picture the charge transfer between the localized bonds and lone pairs. NLO properties related to polarizability and hyperpolarizability are also discussed.

  3. Characterization of fine particulate matter in ambient air by combining TEM and multiple spectroscopic techniques--NMR, FTIR and Raman spectroscopy.

    PubMed

    Ji, Zhurun; Dai, Rucheng; Zhang, Zengming

    2015-03-01

    This paper reports a systematic study of the microstructures and spectroscopic characteristics of PM2.5 and its potential sources in Beijing by combining transmission electron microscopy and multiple spectroscopic techniques: nuclear magnetic resonance, Fourier transform infrared and Raman spectroscopy. TEM images showed that dominant components of PM2.5 are airborne organic substances with many trace metal elements which are associated with combustion sources. NMR spectra precisely determined the percentage of carbonaceous speciation in both PM2.5 (with spatial and temporal distribution) and its potential sources, and distinguished the similarities and differences among them. In FTIR spectra, a remarkable peak at 1390 cm(-1) that appeared only in PM2.5 samples was attributed to NH4NO3, representing the occurrence of secondary processes. Raman spectra revealed certain inorganic compounds including sulfate and nitrate ions. Based on the analysis of the decomposition of Raman spectra, spectral parameters provided structural information and helped to find potential sources of PM2.5. In the space of carbon aromaticity index and ID1/IG, PM2.5 points followed a linear distribution which may also be useful in source tracing. The result shows that the combined non-destructive methods are efficient to trace the sources of PM2.5. PMID:25597896

  4. Molecular structure and spectroscopic analysis of homovanillic acid and its sodium salt - NMR, FT-IR and DFT studies

    NASA Astrophysics Data System (ADS)

    Samsonowicz, M.; Kowczyk-Sadowy, M.; Regulska, E.; Lewandowski, W.

    2014-01-01

    The estimation of the electronic charge distribution in metal complex or salt allows to predict what kind of deformation of the electronic system of ligand would undergo during complexation. It also permits to make more precise interpretation of mechanism by which metals affect the biochemical properties of ligands. The influence of sodium cation on the electronic system of homovanillic acid was studied in this paper. Optimized geometrical structures of studied compounds were calculated by B3LYP/6-311++G** method. Mulliken, MK and ChelpG atomic charges were analyzed. The theoretical NMR and IR spectra were obtained. 1H and 13C NMR as well as FT-IR and FT-Raman spectra of studied compounds were also recorded and analyzed. The calculated parameters are compared with experimental characteristics of these molecules.

  5. NMR spectroscopic study of the carbon and nitrogen dynamics of grass-derived pyrogenic organic material during 2.3 years of incubation in soil

    NASA Astrophysics Data System (ADS)

    Hilscher, André; Knicker, Heike

    2010-05-01

    Incomplete combustion of vegetation results in pyrogenic organic material (PyOM) which occurs ubiquitously in soils and sediments. To understand the C sequestration potential of PyOM in environmental systems knowledge is required about the respective degradation and humification mechanisms and the stability of the different chemical PyOM structures. The present study focuses on the microbial recalcitrance of PyOM on molecular scale. Therefore, microcosms incubation experiments were performed using PyOM produced from highly isotopically enriched 13C and 15N rye grass (Lolium perenne) at 350°C under oxic conditions for one (1M) and four minutes (4M). Solid-state CPMAS 13C and 15N NMR studies were accomplished to obtain insights into the involved humification mechanisms at different stages the PyOM degradation. In total up to 38% of the bulk PyOM C was mineralised during the 28 months of incubation. The O/N-alkyl C and alkyl C residues which survived the charring process were effectively decomposed. At the end of the incubation up to 73% and 57% of the initial O/N-alkyl C and alkyl C amount were mineralised or converted to other C groups, respectively. The total aryl C group recovery of the PyOM decreased significantly during the 28 months of incubation (P ≤ 0.001). After 20 months of incubation between 26% and 40% of the initial aryl C amount was lost. For this group, relative short half time periods in the range of 3.0 and 3.8 years were obtained. The observed loss of aromatic C structures may be attributed to two simultaneous processes, the mineralisation to CO2 and the conversion to other C groups by partial oxidation. The presence of a readily decomposable co-substrate showed no significant changes in the degradation pattern of the different PyOM, possibly because decomposable sources were already available in the starting PyOM. Most of the organic bound N of the fresh PyOM was assignable to heterocyclic aromatic compounds such as pyrrole and indole

  6. /sup 13/C and /sup 17/O NMR and IR spectroscopic study of a series of carbonyl(4-substituted pyridine)(meso-tetraphenylporphinato)iron(II) complexes. Correlations between NMR chemical shifts and IR stretching frequencies of the carbonyl ligand and Taft parameters of the pyridine substituent

    SciTech Connect

    Box, J.W.; Gray, G.M.

    1987-08-26

    The results of a /sup 13/C and /sup 17/O NMR and IR spectroscopic study of a series of carbonyl(4 substituted pyridine)(meso-tetraphenylporphinato)iron(II) (Fe(TPP)(CO)(py-4-X)) complexes are presented. Good to excellent linear correlations between the /sup 13/ and /sup 17/O NMR chemical shifts and the IR stretching frequencies of the carbonyl ligand are observed as the pyridine substituent is varied. Good to excellent linear correlations are also observed between these NMR chemical shifts and IR stretching frequencies and the NMR chemical shifts and IR stretching force constants for the trans carbonyls of a series of cis-Mo(CO)/sub 4/(py-4-X)/sub 2/ complexes as the pyridine substituent is varied. The relationship between the donor ability of the pyridine ligands and the /sup 13/C and /sup 17/O NMR chemical shifts and the IR stretching frequencies of the carbonyl ligands in the Fe(TPP)(CO)(py-4-X) complexes has been quantitated by fitting the spectroscopic data to the single and the dual Taft substituent parameters of the pyridine substituent. Good to excellent correlations are observed. The upfield shift in the /sup 13/C NMR resonance of the carbonyl ligand as the electron-donor ability of the pyridine increases is unique. This has been rationalized by using the Buchner and Schenk description of metal carbonyl /sup 13/C NMR chemical shifts. 49 references, 3 figures, 6 tables.

  7. CARBON-13 NMR OR SOLID STATE HYDROCARBONS AND RELATED SUBSTANCES-FINAL REPORT

    SciTech Connect

    Grant, David M.

    2007-08-16

    CARBON-13 NMR OR SOLID STATE HYDROCARBONS AND RELATED SUBSTANCES-FINAL REPORT Abstract: During recent years we have been engaged in SSNMR (Solid State NMR) structural studies of unusual tetracyanoethylene compounds with unusually long bonds between four carbons centered on two electrons. The chemical shift tensors reflect these unusual atomic arrangements. Quantum chemistry predicts the strange tensor shifts. The three dimensional molecular structure may be determined in this manner. Despite significant advances in structural determination from powder diffraction data, NMR shift tensors argument the structural accuracy and also suggest initial trial structures. Mixtures of polymorphs are difficult to analyze with diffraction methods whereas the SSNMR methods are able to characterize such mixtures in one another’s presence. Spectroscopic developments in our laboratory include SSNMR INADEQUATE and FIREMAT methods. We have used these methods to study the 13C and 15N NMR explosive CL-20.

  8. Insilico molecular modeling, docking and spectroscopic [FT-IR/FT-Raman/UV/NMR] analysis of Chlorfenson using computational calculations

    NASA Astrophysics Data System (ADS)

    Ramalingam, S.; Periandy, S.; Sugunakala, S.; Prabhu, T.; Bououdina, M.

    2013-11-01

    In the present work, the recorded FT-IR/FT-Raman spectra of the Chlorfenson (4-Chorophenyl-4-chlorobenzenesulfonate) are analysed. The observed vibrational frequencies are assigned and the computational calculations are carried out by DFT (LSDA, B3LYP and B3PW91) methods with 6-31++G(d,p) and 6-311++G(d,p) basis sets and the corresponding results are investigated with the UV/NMR data. The fluctuation of structure of Chlorobenzenesulfonate due to the substitution of C6H4Cl is investigated. The vibrational sequence pattern of the molecule related to the substitutions is intensely analysed. Moreover, 13C NMR and 1H NMR chemical shifts are calculated by using the gage independent atomic orbital (GIAO) technique with HF/B3LYP/B3PW91 methods on same basis set. A study on the electronic properties; absorption wavelengths, excitation energy, dipole moment and frontier molecular orbital energies, are performed by HF and DFT methods. The calculated energy of Kubo gap (HOMO and LUMO) ensures that the charge transfer occurs within the molecule. Besides frontier molecular orbitals (FMOs), molecular electrostatic potential (MEP) is executed. NLO properties and Mulliken charges of the Chlorfenson is also calculated and interpreted. Biological properties like the target receptor identification, and Identification of interacting residues, of this compound is identified and analysed by using SWISSMODEL, Castp, Hex and Pdb Sum. By using these properties, the mechanism of action of this compound on ATP Synthase of Tetranychus urticae is found and it is very much useful to develop efficient pesticides having less toxic to the environment.

  9. Phase behavior and 13C NMR spectroscopic analysis of the mixed methane + ethane + propane hydrates in mesoporous silica gels.

    PubMed

    Lee, Seungmin; Cha, Inuk; Seo, Yongwon

    2010-11-25

    In this study, the phase behavior and quantitative determination of hydrate composition and cage occupancy for the mixed CH(4) + C(2)H(6) + C(3)H(8) hydrates were closely investigated through the experimental measurement of three-phase hydrate (H)-water-rich liquid (L(W))-vapor (V) equilibria and (13)C NMR spectra. To examine the effect of pore size and salinity, we measured hydrate phase equilibria for the quaternary CH(4) (90%) + C(2)H(6) (7%) + C(3)H(8) (3%) + water mixtures in silica gel pores of nominal diameters of 6.0, 15.0, and 30.0 nm and for the quinary CH(4) (90%) + C(2)H(6) (7%) + C(3)H(8) (3%) + NaCl + water mixtures of two different NaCl concentrations (3 and 10 wt %) in silica gel pores of a nominal 30.0 nm diameter. The value of hydrate-water interfacial tension for the CH(4) (90%) + C(2)H(6) (7%) + C(3)H(8) (3%) hydrate was found to be 47 ± 4 mJ/m(2) from the relation of the dissociation temperature depression with the pore size of silica gels at a given pressure. At a specified temperature, three-phase H-L(W)-V equilibrium curves of pore hydrates were shifted to higher pressure regions depending on pore sizes and NaCl concentrations. From the cage-dependent (13)C NMR chemical shifts of enclathrated guest molecules, the mixed CH(4) (90%) + C(2)H(6) (7%) + C(3)H(8) (3%) gas hydrate was confirmed to be structure II. The cage occupancies of each guest molecule and the hydration number of the mixed gas hydrates were also estimated from the (13)C NMR spectra. PMID:20964277

  10. Gene synthesis, bacterial expression, and 1H NMR spectroscopic studies of the rat outer mitochondrial membrane cytochrome b5.

    PubMed

    Rivera, M; Barillas-Mury, C; Christensen, K A; Little, J W; Wells, M A; Walker, F A

    1992-12-01

    The gene coding for the water-soluble domain of the outer mitochondrial membrane cytochrome b5 (OM cytochrome b5) from rat liver has been synthetized and expressed in Escherichia coli. The DNA sequence was obtained by back-translating the known amino acid sequence [Lederer, F., Ghrir, R., Guiard, B., Cortial, S., & Ito, A. (1983) Eur. J. Biochem. 132, 95-102]. The recombinant OM cytochrome b5 was characterized by UV-visible, EPR, and 1H NMR spectroscopy. The UV-visible and EPR spectra of the OM cytochrome b5 are almost identical to the ones obtained from the overexpressed rat microsomal cytochrome b5 [Bodman, S. B. V., Schyler, M. A., Jollie, D. R., & Sligar, S. G. (1986) Proc. Natl. Acad. Sci. U.S.A. 83, 9443-9447]. The one-dimensional 1H NMR spectrum of the OM cytochrome b5 indicates that the rhombic perturbation of the ferric center is essentially identical to that in the microsomal beef, rabbit, chicken, and rat cytochromes b5. Two-dimensional 1H NMR spectroscopy (NOESY) and one-dimensional NOE difference spectroscopy were used to assign the contact-shifted resonances that correspond to each of the two isomers that result from the rotation of the heme around its alpha-gamma-meso axis. The assignment of the resonances allowed the determination of the heme orientation ratio in the OM cytochrome b5, which was found to be 1.0 +/- 0.1. It is noteworthy that the two cytochromes b5 that have similar populations of the two heme isomers (large heme disorder) originate from the rat liver. PMID:1333795

  11. Acetylation of raw cotton for oil spill cleanup application: an FTIR and 13C MAS NMR spectroscopic investigation.

    PubMed

    Adebajo, Moses O; Frost, Ray L

    2004-08-01

    Fourier transform infrared (FTIR) and 13C MAS NMR spectroscopy have been used to investigate the acetylation of raw cotton samples with acetic anhydride without solvents in the presence of different amounts of 4-dimethylaminopyridine (DMAP) catalyst. This is a continuation of our previous investigation of acetylation of commercial cotton in an effort to develop hydrophobic, biodegradable, cellulosic sorbent materials for cleaning up oil spills. The FTIR data have again provided a clear evidence for successful acetylation. The NMR results further confirm the successful acetylation. The extent of acetylation was quantitatively determined using the weight percent gain (WPG) due to acetylation and by calculating the ratio R between the intensity of the acetyl C=O stretching band at 1740-1745 cm(-1) and the intensity of C-O stretching vibration of the cellulose backbone at about 1020-1040 cm(-1). The FTIR technique was found to be highly sensitive and reliable for the determination of the extent of acetylation. The level of acetylation of the raw cotton samples was found to be much higher than that of cotton fabrics and the previously studied commercial cotton. The variation of the R and WPG with reaction time, amount of DMAP catalyst and different samples of raw cotton is discussed. PMID:15249021

  12. FTIR and {sup 31}P-NMR spectroscopic analyses of surface species in phosphate-catalyzed lactic acid conversion

    SciTech Connect

    Gunter, G.C.; Tam, M.S.; Miller, D.J.

    1996-11-01

    The surface species present on silica/alumina-supported sodium phosphates, active catalysts for the conversion of lactic acid to acrylic acid and 2,3-pentanedione, are examined by pre- and postreaction MAS {sup 31}P-NMR and FTIR spectroscopies. Species present following lactic acid conversion are identified by transmission FTIR of phosphates supported on silicon disks (as a model catalyst system) and verified by {sup 31}P-NMR and diffuse reflectance IR spectroscopy of actual catalysts used in reaction. Monosodium phosphate (NaH{sub 2}PO{sub 4}) condenses to a mixture of sodium polyphosphate (NaPO{sub 3}){sub n} and sodium trimetaphosphate (Na{sub 3}P{sub 3}O{sub 9}), which exhibit little catalytic activity for converting lactic acid to desired products. Disodium phosphate (Na{sub 2}HPO{sub 4}) condenses to tetrasodium pyrophosphate (Na{sub 4}P{sub 2}O{sub 7}), and proton transfer from lactic acid to pyrophosphate results in the formation of sodium lactate. Trisodium phosphate (Na{sub 3}PO{sub 4}) accepts a proton from lactic acid to form sodium lactate and disodium phosphate, which condenses to pyrophosphate. The presence of pyrophosphate and sodium lactate on supported disodium and trisodium phosphates explains their similar catalytic properties; the larger quantity of sodium lactate present on trisodium phosphate leads to higher conversions at lower temperatures. 40 refs., 14 figs., 2 tabs.

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

    PubMed

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

    2008-09-23

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

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

    PubMed Central

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

    2008-01-01

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

  15. Structural, NMR Spectroscopic, and Computational Investigation of Hemin Loading in the Hemophore HasAp from Pseudomonas aeruginosa

    SciTech Connect

    Jepkorir, Grace; Rodrguez, Juan Carlos; Rui, Huan; Im, Wonpil; Lovell, Scott; Battaile, Kevin P.; Alontaga, Aileen Y.; Yukl, Erik T.; Monne-Loccoz, Pierre; Rivera, Mario

    2010-08-16

    When challenged by low-iron conditions several Gram-negative pathogens secrete a hemophore (HasA) to scavenge hemin from its host and deliver it to a receptor (HasR) on their outer membrane for internalization. Here we report results from studies aimed at probing the structural and dynamic processes at play in the loading of the apo-hemophore secreted by P. aeruginosa (apo-HasAp) with hemin. The structure of apo-HasAp shows a large conformational change in the loop harboring axial ligand His32 relative to the structure of holo-HasAp, whereas the loop bearing the other axial ligand, Tyr75, remains intact. To investigate the role played by the axial ligand-bearing loops in the process of hemin capture we investigated the H32A mutant, which was found to exist as a monomer in its apo-form and as a mixture of monomers and dimers in its holo-form. We obtained an X-ray structure of dimeric H32A holo-HasAp, which revealed that the two subunits are linked by cofacial interactions of two hemin molecules and that the conformation of the Ala32 loop in the dimer is identical to that exhibited by the His32 loop in wild type apo-HasAp. Additional data suggest that the conformation of the Ala32 loop in the dimer is mainly a consequence of dimerization. Hence, to investigate the effect of hemin loading on the topology of the His32 loop we also obtained the crystal structure of monomeric H32A holo-HasAp coordinated by imidazole (H32A-imidazole) and investigated the monomeric H32A HasAp and H32A-imidazole species in solution by NMR spectroscopy. The structure of H32A-imidazole revealed that the Ala32 loop attains a 'closed' conformation nearly identical to that observed in wild type holo-HasAp, and the NMR investigations indicated that this conformation is maintained in solution. The NMR studies also highlighted conformational heterogeneity at the H32 loop hinges and in other key sections of the structure. Targeted molecular dynamics simulations allowed us to propose a possible path

  16. The spectroscopic (FT-IR, FT-Raman, dispersive Raman and NMR) study of ethyl-6-chloronicotinate molecule by combined density functional theory.

    PubMed

    Karabacak, Mehmet; Calisir, Zuhre; Kurt, Mustafa; Kose, Etem; Atac, Ahmet

    2016-01-15

    In this study, ethyl-6-chloronicotinate (E-6-ClN) molecule is recorded in the region 4000-400 cm(-1) and 3500-100 cm(-1) (FT-IR, FT-Raman and dispersive Raman, respectively) in the solid phase. ((1))H and ((13))C nuclear magnetic resonance (NMR) spectra are recorded in DMSO solution. The structural and spectroscopic data of the molecule are obtained for two possible isomers (S1 and S2) from DFT (B3LYP) with 6-311++G(d,p) basis set calculations. The geometry of the molecule is fully optimized, vibrational spectra are calculated and fundamental vibrations are assigned on the basis of the potential energy distribution (PED) of the vibrational modes. ((1))H and ((13))C NMR chemical shifts are calculated by using the gauge-invariant atomic orbital (GIAO) method. The electronic properties, such as excitation energies, oscillator strengths, wavelengths, HOMO and LUMO energies, are performed by time-dependent density functional theory (TD-DFT). Total and partial density of state and overlap population density of state diagrams analysis are presented for E-6-ClN molecule. Furthermore, frontier molecular orbitals (FMO), molecular electrostatic potential, and thermodynamic features are performed. In addition to these, reduced density gradient of the molecule is performed and discussed. As a conclusion, the calculated results are compared with the experimental spectra of the title compound. The results of the calculations are applied to simulate the vibrational spectra of the molecule, which show excellent agreement with the observed ones. The theoretical and tentative results will give us a detailed description of the structural and physicochemical properties of the molecule. Natural bond orbital analysis is done to have more information stability of the molecule arising from charge delocalization, and to reveal the information regarding charge transfer within the molecules. PMID:26483317

  17. The spectroscopic (FT-IR, FT-Raman, dispersive Raman and NMR) study of ethyl-6-chloronicotinate molecule by combined density functional theory

    NASA Astrophysics Data System (ADS)

    Karabacak, Mehmet; Calisir, Zuhre; Kurt, Mustafa; Kose, Etem; Atac, Ahmet

    2016-01-01

    In this study, ethyl-6-chloronicotinate (E-6-ClN) molecule is recorded in the region 4000-400 cm- 1 and 3500-100 cm- 1 (FT-IR, FT-Raman and dispersive Raman, respectively) in the solid phase. 1H and 13C nuclear magnetic resonance (NMR) spectra are recorded in DMSO solution. The structural and spectroscopic data of the molecule are obtained for two possible isomers (S1 and S2) from DFT (B3LYP) with 6-311++G(d,p) basis set calculations. The geometry of the molecule is fully optimized, vibrational spectra are calculated and fundamental vibrations are assigned on the basis of the potential energy distribution (PED) of the vibrational modes. 1H and 13C NMR chemical shifts are calculated by using the gauge-invariant atomic orbital (GIAO) method. The electronic properties, such as excitation energies, oscillator strengths, wavelengths, HOMO and LUMO energies, are performed by time-dependent density functional theory (TD-DFT). Total and partial density of state and overlap population density of state diagrams analysis are presented for E-6-ClN molecule. Furthermore, frontier molecular orbitals (FMO), molecular electrostatic potential, and thermodynamic features are performed. In addition to these, reduced density gradient of the molecule is performed and discussed. As a conclusion, the calculated results are compared with the experimental spectra of the title compound. The results of the calculations are applied to simulate the vibrational spectra of the molecule, which show excellent agreement with the observed ones. The theoretical and tentative results will give us a detailed description of the structural and physicochemical properties of the molecule. Natural bond orbital analysis is done to have more information stability of the molecule arising from charge delocalization, and to reveal the information regarding charge transfer within the molecules.

  18. Silver and Gold NMR

    PubMed Central

    Zangger, Klaus

    1999-01-01

    Silver and gold, together with copper, form the transition metal group IB elements in the periodic table and possess very different nuclear magnetic resonance (NMR) spectroscopic properties. While there is only one gold isotope (197Au), which has a spin of 3/2 and therefore a quadrupole moment, silver occurs in two isotopic forms (109Ag and 109Au), both of which have a spin 1/2 and similar NMR spectroscopic properties. The unfavorable properties of gold have prevented its NMR spectroscopic investigation thus far. On the other hand, there are several reports of silver NMR. However, the low sensitivity of silver, combined with its long relaxation times have rendered the direct detection of silver possible only with concentrations greater than a few tenth molar. Reviewed here are the general limitations of silver NMR and some techniques to partially overcome these limitations, as well as a summary of currently available chemical shift and scalar coupling data on 109Ag. PMID:18475898

  19. Spectroscopic (FT-IR, FT-Raman, UV, NMR, NBO) investigation and molecular docking study of (R)-2-Amino-1-PhenylEthanol

    NASA Astrophysics Data System (ADS)

    Subashini, K.; Periandy, S.

    2016-08-01

    A systematic spectroscopic study of (R)-2-Amino-1-Phenylethanol was carried out using FT-IR, FT-Raman, NMR and UV analysis. FT-IR (4000-400 cm-1) and FT-Raman (4000-100 cm-1) spectrum of the title molecule were recorded in solid phase, the 1H and 13C NMR spectra were recorded in CDCl3 (deuterated chloroform) solution phase and the UV-Vis (200-800 nm) spectrum was recorded in gas phase and ethanol solution phase. Potential energy surface (PES) scan was performed using B3LYP functional with 6-311++G (d, p) basis set. The geometrical parameters (such as bond length, bond angle, dihedral angles) and theoretical frequencies of the title compound were studied from density functional theory (DFT) using B3LYP and B3PW91 functionals with 6-311++G (d, p) basis sets. The computed frequencies were scaled and compared with the experimental values and potential energy distribution (PED) has been tabulated. A comparative study of atomic charges was made by calculating Mulliken, Natural Population Analysis (NPA) and Electrostatic Potential (ESP) simultaneously, with B3LYP/6-311++G (d, p) basis set. 1H and 13C NMR spectra were recorded and chemical shifts were compared to TMS by Gauge-Independent Atomic Orbital (GIAO) method. Electronic properties such as excitation energy, energy gap between HOMO and LUMO was calculated using time dependent DFT technique. NBO analysis, which predicts the different possibilities of electronic transition in the molecule, was computed using B3PW91 functional with 6-311++G (d, p) basis set. The thermodynamic properties such as heat capacity, entropy and enthalpy at different temperatures were computed and analyzed. Molecular docking study shows that the secondary hydroxyl group and the primary amino group in the aliphatic chain attached to the benzene ring are crucial for binding and the title compound might exhibit inhibitory activity against Bacteroides fragilis (3P24) and may act as anti-bacterial agent.

  20. Effect of steric hindrance on carbon dioxide absorption into new amine solutions: thermodynamic and spectroscopic verification through solubility and NMR analysis.

    PubMed

    Park, Jung-Yeon; Yoon, Sang Jun; Lee, Huen

    2003-04-15

    Acid gas absorption technology is of great importance in these days for the prevention of global warming and the resulting worldwide climate change. More efficient process design and development for the removal of acid gases has become important, together with the development of new absorbents as one of urgent areas of research in addressing global-warming problems. In the present work, aqueous solutions of 2-amino-2-hydroxymethyl-1,3-propanediol (AHPD), a sterically hindered amine, has been examined as a potential CO2 absorbent and compared with the most commonly used absorbent, monoethanolamine (MEA) solution, through equilibrium solubility measurements and 13C NMR spectroscopic analyses. The solubilities of CO2 in aqueous 10 mass % AHPD solutions were higher than those in aqueous 10 mass % MEA solutions above 4 kPa at 298.15 K, but below 4 kPa, the solubility behavior appeared to be the opposite. The solubility difference between these two solutions increased with the CO2 partial pressures above the crossover pressure. Equilibrated CO2-MEA-H2O and CO2-AHPD-H2O solutions at various CO2 partal pressures ranging from 0.01 to 3000 kPa were analyzed by 13C NMR spectroscopy to provide a more microscopic understanding of the reaction mechanisms in the two solutions. In the CO2-amine-H2O solutions, amine reacted with CO2 to form mainly the protonated amine (AMH+), bicarbonate ion (HCO3-), and carbamate anion (AMCO2-), where the quantitative ratio of bicarbonate ion to carbamate anion strongly influenced the CO2 loading in the amine solutions. A profusion of bicarbonate ions, but a very small amount of carbamate anions, was identified in the CO2-AHPD-H2O solution, whereas a considerable amount of carbamate anions was formed in the CO2-MEA-H2O solution. AHPD contains more hydroxyl groups than nonhindered MEA, and hence, the chemical shifts in its 13C NMR spectra were strongly influenced by the solution pH values. In contrast, MEA appeared to be insensitive to pH. The

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

    NASA Astrophysics Data System (ADS)

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

    2010-05-01

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

  2. Spectroscopic (FT-IR, FT-Raman, UV and NMR) investigation on 1-phenyl-2-nitropropene by quantum computational calculations.

    PubMed

    Xavier, S; Periandy, S

    2015-10-01

    In this paper, the spectral analysis of 1-phenyl-2-nitropropene is carried out using the FTIR, FT Raman, FT NMR and UV-Vis spectra of the compound with the help of quantum mechanical computations using ab-initio and density functional theories. The FT-IR (4000-400 cm(-1)) and FT-Raman (4000-100 cm(-1)) spectra were recorded in solid phase, the (1)H and (13)C NMR spectra were recorded in CDCl3 solution phase and the UV-Vis (200-800 nm) spectrum was recorded in ethanol solution phase. The different conformers of the compound and their minimum energies are studied using B3LYP functional with 6-311+G(d,p) basis set and two stable conformers with lowest energy were identified and the same was used for further computations. The computed wavenumbers from different methods are scaled so as to agree with the experimental values and the scaling factors are reported. All the modes of vibrations are assigned and the structure the molecule is analyzed in terms of parameters like bond length, bond angle and dihedral angle predicted by both B3LYP and B3PW91 methods with 6-311+G(d,p) and 6-311++G(d,p) basis sets. The values of dipole moment (μ), polarizability (α) and hyperpolarizability (β) of the molecule are reported, using which the non-linear property of the molecule is discussed. The HOMO-LUMO mappings are reported which reveals the different charge transfer possibilities within the molecule. The isotropic chemical shifts predicted for (1)H and (13)C atoms using gauge invariant atomic orbital (GIAO) theory show good agreement with experimental shifts. NBO analysis is carried out to picture the charge transfer between the localized bonds and lone pairs. The local reactivity of the molecule has been studied using the Fukui function. The thermodynamic properties (heat capacity, entropy and enthalpy) at different temperatures are also calculated. PMID:25965169

  3. Spectroscopic (FT-IR, FT-Raman, UV and NMR) investigation on 1-phenyl-2-nitropropene by quantum computational calculations

    NASA Astrophysics Data System (ADS)

    Xavier, S.; Periandy, S.

    2015-10-01

    In this paper, the spectral analysis of 1-phenyl-2-nitropropene is carried out using the FTIR, FT Raman, FT NMR and UV-Vis spectra of the compound with the help of quantum mechanical computations using ab-initio and density functional theories. The FT-IR (4000-400 cm-1) and FT-Raman (4000-100 cm-1) spectra were recorded in solid phase, the 1H and 13C NMR spectra were recorded in CDCl3 solution phase and the UV-Vis (200-800 nm) spectrum was recorded in ethanol solution phase. The different conformers of the compound and their minimum energies are studied using B3LYP functional with 6-311+G(d,p) basis set and two stable conformers with lowest energy were identified and the same was used for further computations. The computed wavenumbers from different methods are scaled so as to agree with the experimental values and the scaling factors are reported. All the modes of vibrations are assigned and the structure the molecule is analyzed in terms of parameters like bond length, bond angle and dihedral angle predicted by both B3LYP and B3PW91 methods with 6-311+G(d,p) and 6-311++G(d,p) basis sets. The values of dipole moment (μ), polarizability (α) and hyperpolarizability (β) of the molecule are reported, using which the non-linear property of the molecule is discussed. The HOMO-LUMO mappings are reported which reveals the different charge transfer possibilities within the molecule. The isotropic chemical shifts predicted for 1H and 13C atoms using gauge invariant atomic orbital (GIAO) theory show good agreement with experimental shifts. NBO analysis is carried out to picture the charge transfer between the localized bonds and lone pairs. The local reactivity of the molecule has been studied using the Fukui function. The thermodynamic properties (heat capacity, entropy and enthalpy) at different temperatures are also calculated.

  4. Complete fusion of 15N+27Al

    NASA Astrophysics Data System (ADS)

    Prosser, F. W., Jr.; Racca, R. A.; Daneshvar, K.; Geesaman, D. F.; Henning, W.; Kovar, D. G.; Rehm, K. E.; Tabor, S. L.

    1980-05-01

    The total fusion cross section for the system 15N + 27Al has been measured over an energy range 27 MeV<=Elab<=70 MeV by detection of the fusion-evaporation residues. In addition elastic scattering was measured at six energies and fitted by optical model calculations. The fusion cross section for the system saturates at 1150+/-50 mb. The data can be well described by the model of Glas and Mosel, using a reasonable set of parameters. The model of Horn and Ferguson also describes the data well if an appropriate charge radius is used. Comparison is made between these results and the fusion cross sections for 16O + 26Mg and 18O + 24Mg, which lead to the same compound nucleus. The results for 15N + 27Al are quite similar to those for 18O + 24Mg, and the differences between the fusion cross sections for these two systems and those for 16O + 26Mg may be evidence for an entrance channel effect. NUCLEAR REACTIONS 15N+27Al, Elab=27-70 MeV; measured σfusion(E) measured dσdΩ elastic scattering; data fitted with Glas and Mosel model, Horn and Ferguson model.

  5. Vibrational, NMR and UV-visible spectroscopic investigation and NLO studies on benzaldehyde thiosemicarbazone using computational calculations

    NASA Astrophysics Data System (ADS)

    Moorthy, N.; Prabakar, P. C. Jobe; Ramalingam, S.; Pandian, G. V.; Anbusrinivasan, P.

    2016-04-01

    In order to investigate the vibrational, electronic and NLO characteristics of the compound; benzaldehyde thiosemicarbazone (BTSC), the XRD, FT-IR, FT-Raman, NMR and UV-visible spectra were recorded and were analysed with the calculated spectra by using HF and B3LYP methods with 6-311++G(d,p) basis set. The XRD results revealed that the stabilized molecular systems were confined in orthorhombic unit cell system. The cause for the change of chemical and physical properties behind the compound has been discussed makes use of Mulliken charge levels and NBO in detail. The shift of molecular vibrational pattern by the fusing of ligand; thiosemicarbazone group with benzaldehyde has been keenly observed. The occurrence of in phase and out of phase molecular interaction over the frontier molecular orbitals was determined to evaluate the degeneracy of the electronic energy levels. The thermodynamical studies of the temperature region 100-1000 K to detect the thermal stabilization of the crystal phase of the compound were investigated. The NLO properties were evaluated by the determination of the polarizability and hyperpolarizability of the compound in crystal phase. The physical stabilization of the geometry of the compound has been explained by geometry deformation analysis.

  6. NMR spectroscopic analysis reveals extensive binding interactions of complex xyloglucan oligosaccharides with the Cellvibrio japonicus glycoside hydrolase family 31 α-xylosidase.

    PubMed

    Silipo, Alba; Larsbrink, Johan; Marchetti, Roberta; Lanzetta, Rosa; Brumer, Harry; Molinaro, Antonio

    2012-10-15

    The study of the interaction of glycoside hydrolases with their substrates is fundamental to diverse applications in medicine, food and feed production, and biomass-resource utilization. Recent molecular modeling of the α-xylosidase CjXyl31A from the soil saprophyte Cellvibrio japonicus, together with protein crystallography and enzyme-kinetic analysis, has suggested that an appended PA14 protein domain, unique among glycoside hydrolase family 31 members, may confer specificity for large oligosaccharide fragments of the ubiquitous plant polysaccharide xyloglucan (J. Larsbrink, A. Izumi, F.M. Ibatullin, A. Nakhai, H.J. Gilbert, G.J. Davies, H. Brumer, Biochem. J. 2011, 436, 567-580). In the present study, a combination of NMR spectroscopic techniques, including saturation transfer difference (STD) and transfer NOE (TR-NOE) spectroscopy, was used to reveal extensive interactions between CjXyl31A active-site variants and xyloglucan hexa- and heptasaccharides. The data specifically indicate that the enzyme recognizes the entire cello-tetraosyl backbone of the substrate and product in positive enzyme subsites and makes further significant interactions with internal pendant α-(1→6)-linked xylosyl units. As such, the present analysis provides an important rationalization of previous kinetic data on CjXyl31A and unique insight into the role of the PA14 domain, which was not otherwise obtainable by protein crystallography. PMID:22961810

  7. Spectroscopic (FT-IR and FT-Raman) studies, NBO, HOMO-LUMO, NMR analyses and thermodynamics functions of 5-bromo-2-methoxybenzaldehyde

    NASA Astrophysics Data System (ADS)

    Balachandran, V.; Santhi, G.; Karpagam, V.

    2013-04-01

    The (FT-IR and FT-Raman) spectral properties of 5-bromo-2-methoxybenzaldehyde (BMB) are studied using density functional theory (DFT) employing B3LYP/6-311++G (d) and B3LYP/6-311++G (d, p) levels of theory. There are four conformers, C1, C2, C3, and C4 for this molecule. The computational results diagnose the most stable conformer of BMB as the C1 form. The optimized geometrical parameters obtained by B3LYP/6-311++G (d, p) method show good agreement with experimental X-ray data. A study on the electronic properties, such as HOMO and LUMO energies, is performed. The isotropic chemical shift computed by 1H and 13C nuclear magnetic resonance (NMR) chemical shifts of the BMB calculated using the gauge invariant atomic orbital (GIAO) method also shows good agreement with experimental observations. The MEP surface reflects the chemical reactivity of a molecule. The thermodynamic functions (heat capacity, internal heat energy, Gibbs energy and entropy) from spectroscopic data by statistical methods were obtained for the range of temperature 100-1000 K. The energetic behavior of the compound in different solvent medium (water, ethanol, and methanol) was examined by applying polarizable continuum model (PCM). The complete molecular orbital simulations and theoretical UV-visible spectra carried out in this study yield better understanding of charge delocalization pattern and stability of the title molecules to a greater extent.

  8. UV-Vis, fluorescence and NMR spectroscopic investigations on inclusion properties of a designed tetrahomocalix[8]arene with fullerenes C 60 and C 70 in solution

    NASA Astrophysics Data System (ADS)

    Halder, Amal; Bhatt, Suchitra; Nayak, Sandip K.; Chattopadhyay, Subrata; Bhattacharya, Sumanta

    2011-12-01

    The present article reports the spectroscopic investigations on non-covalent interaction of fullerenes C 60 and C 70 with a macrocyclic receptor molecule, namely, 1,3,5,7-tetrahomo- p- tert-butylcalix[8]arene ( 1) in toluene. Jobs method of continuous variation reveals 1:1 stoichiometry for the fullerene complexes of 1. The most fascinating feature of the present study is that 1 binds selectively C 60 compared to C 70 as obtained from binding constant ( K) data of C 60- 1 ( KC60- 1) and C 70- 1 ( KC70- 1) complexes which are enumerated to be 265,000 dm 3 mol -1 and 63,430 dm 3 mol -1, respectively, and selectivity in binding ( KC60- 1/K C70- 1) is estimated to be 4.18 as obtained from UV-Vis study. Steady state fluorescence studies reveal quenching of fluorescence of 1 in presence of fullerenes and the K value of the C 60- 1 and C 70- 1 complexes are estimated to be 80,760 and 68,780 dm 3 mol -1, respectively, with selectivity in binding (K C60- 1/K C70- 1) ˜1.18. 1H NMR analysis provides very good support in favor of strong binding between C 60 and 1. The high value of K value for C 60- 1 complex indicates that 1 forms an inclusion complex with C 60.

  9. The spectroscopic properties of anticancer drug Apigenin investigated by using DFT calculations, FT-IR, FT-Raman and NMR analysis.

    PubMed

    Mariappan, G; Sundaraganesan, N; Manoharan, S

    2012-09-01

    The FT-Raman and FT-Infrared spectra of solid Apigenin sample were measured in order to elucidate the spectroscopic properties of title molecule in the spectral range of 3500-50 cm(-1) and 4000-400 cm(-1), respectively. The recorded FT-IR and FT-Raman spectral measurements favor the calculated (by B3LYP/6-31G(d,p) method) structural parameters which are further supported by spectral simulation. Additional support is given by the collected (1)H and (13)C NMR spectra recorded with the sample dissolved in DMSO. The predicted chemical shifts at the B3LYP/6-31G(d) level obtained using the Gauge-Invariant Atomic Orbitals (GIAO) method with and without inclusion of solvent using the Polarizable Continuum Model (PCM). By using TD-DFT method, electronic absorption spectra of the title compound have been predicted and a good agreement with the TD-DFT method and the experimental one is determined. The UV-visible absorption spectra of the compound that dissolved in Ethanol, Methanol and DMSO were recorded in the range of 800-200 nm. The formation of hydrogen bond and the most possible interaction are explained using natural bond orbital (NBO) analysis. In addition, the molecular electrostatic potential (MEP), frontier molecular orbitals (FMO) analysis and atomic charges of the title compound were investigated using theoretical calculations. The results are discussed herein and compared with similar molecules whenever appropriate. PMID:22617215

  10. The spectroscopic properties of anticancer drug Apigenin investigated by using DFT calculations, FT-IR, FT-Raman and NMR analysis

    NASA Astrophysics Data System (ADS)

    Mariappan, G.; Sundaraganesan, N.; Manoharan, S.

    2012-09-01

    The FT-Raman and FT-Infrared spectra of solid Apigenin sample were measured in order to elucidate the spectroscopic properties of title molecule in the spectral range of 3500-50 cm-1 and 4000-400 cm-1, respectively. The recorded FT-IR and FT-Raman spectral measurements favor the calculated (by B3LYP/6-31G(d,p) method) structural parameters which are further supported by spectral simulation. Additional support is given by the collected 1H and 13C NMR spectra recorded with the sample dissolved in DMSO. The predicted chemical shifts at the B3LYP/6-31G(d) level obtained using the Gauge-Invariant Atomic Orbitals (GIAO) method with and without inclusion of solvent using the Polarizable Continuum Model (PCM). By using TD-DFT method, electronic absorption spectra of the title compound have been predicted and a good agreement with the TD-DFT method and the experimental one is determined. The UV-visible absorption spectra of the compound that dissolved in Ethanol, Methanol and DMSO were recorded in the range of 800-200 nm. The formation of hydrogen bond and the most possible interaction are explained using natural bond orbital (NBO) analysis. In addition, the molecular electrostatic potential (MEP), frontier molecular orbitals (FMO) analysis and atomic charges of the title compound were investigated using theoretical calculations. The results are discussed herein and compared with similar molecules whenever appropriate.

  11. Cotton-mouton effects, magnetic hyperpolarizabilities, and magnetic anisotropies of the methyl halides. Comparison with molecular Zeeman and high-field NMR spectroscopic results

    SciTech Connect

    Coonan, M.H.; Ritchie, G.L.D. )

    1991-02-07

    Measurements of the vapor-phase Cotton-Mouton effects of methyl fluoride, methyl bromide, and methyl iodide are reported. Analysis of the results, in conjunction with those of an earlier study of methane and methyl chloride, shows that in the series CH{sub 3}X (X = H, F, Cl, Br, I) the magnetic hyperpolarizabiity anisotropy, which is related to the quadratic response of the molecular polarizability to a magnetic field, is positive in sign and roughly proportional in magnitude to the mean polarizability. The magnetic anisotropies (10{sup 29}{Delta}{sub {chi}}/J T{sup {minus}2}) found for methyl chloride,methyl bromide, and methyl iodide (CH{sub 3}Cl, {minus}15.0 {plus minus} 1.3; CH{sub 3}Br, -15.1 {plus minus} 0.8; CH{sub 3}I, {minus}18.0 {plus minus} 1.5) are compared with values obtained by the molecular Zeeman and high-field {sup 2}H NMR spectroscopic methods.

  12. Spectroscopic characteristic (FT-IR, FT-Raman, UV, 1H and 13C NMR), theoretical calculations and biological activity of alkali metal homovanillates

    NASA Astrophysics Data System (ADS)

    Samsonowicz, M.; Kowczyk-Sadowy, M.; Piekut, J.; Regulska, E.; Lewandowski, W.

    2016-04-01

    The structural and vibrational properties of lithium, sodium, potassium, rubidium and cesium homovanillates were investigated in this paper. Supplementary molecular spectroscopic methods such as: FT-IR, FT-Raman in the solid phase, UV and NMR were applied. The geometrical parameters and energies were obtained from density functional theory (DFT) B3LYP method with 6-311++G** basis set calculations. The geometry of the molecule was fully optimized, vibrational spectra were calculated and fundamental vibrations were assigned. Geometric and magnetic aromaticity indices, atomic charges, dipole moments, HOMO and LUMO energies were also calculated. The microbial activity of investigated compounds was tested against Bacillus subtilis (BS), Pseudomonas aeruginosa (PA), Escherichia coli (EC), Staphylococcus aureus (SA) and Candida albicans (CA). The relationship between the molecular structure of tested compounds and their antimicrobial activity was studied. The principal component analysis (PCA) was applied in order to attempt to distinguish the biological activities of these compounds according to selected band wavenumbers. Obtained data show that the FT-IR spectra can be a rapid and reliable analytical tool and a good source of information for the quantitative analysis of the relationship between the molecular structure of the compound and its biological activity.

  13. Genetically unstable CXG repeats are structurally dynamic and have a high propensity for folding. An NMR and UV spectroscopic study.

    PubMed

    Zheng, M; Huang, X; Smith, G K; Yang, X; Gao, X

    1996-11-29

    Recent molecular genetics studies have revealed a correlation between spontaneous, progressive expansion of several DNA trinucleotide repeats and certain hereditary neurodegenerative diseases. Triplet repeat (TR) sequences may be present in structured forms that can mediate the processes interrupting normal cellular replication, transcription, or repair activities, eventually leading to gene mutation. Using high resolution NMR spectroscopy and other biophysical methods, we probed the solution structures and properties of single-stranded TR sequences. These studies have led to the discovery of a new duplex motif (e-motif), present in CCG repeats, and to the elucidation of the structure of the (CTG)3 duplex. In this paper we provide a global picture of the solution behavior of the human disease-related CXG (X = A, C, G, or T) and the comparison GXC (X = A, or T) TR sequences. All six triplet repeats form antiparallel duplexes. The mismatched bases in CAG and CGG repeat duplexes are rather flexible and they do not appear to form stable, paired conformations. By comparison, GAC repeat duplexes and their mismatched A residues are well-structured. Most interestingly, the structures of the disease-related CXG repeats exhibit a propensity for folding at chain lengths as short as 12 residues. Furthermore, the energy barrier for the formation of homo-duplexes from the corresponding complementary hetero-duplexes are much lower for the CXG TR sequences than for the GAC or GTC TR sequences. These results provide insights into the conformation and physiochemical properties of TR sequences. Thus, a basis is provided for further studies of the behavior of long TR sequences in an effort to elucidate the molecular mechanisms of in vivo expansion and function of TR sequences. PMID:8951379

  14. Water proton spin saturation affects measured protein backbone 15 N spin relaxation rates

    NASA Astrophysics Data System (ADS)

    Chen, Kang; Tjandra, Nico

    2011-12-01

    Protein backbone 15N NMR spin relaxation rates are useful in characterizing the protein dynamics and structures. To observe the protein nuclear-spin resonances a pulse sequence has to include a water suppression scheme. There are two commonly employed methods, saturating or dephasing the water spins with pulse field gradients and keeping them unperturbed with flip-back pulses. Here different water suppression methods were incorporated into pulse sequences to measure 15N longitudinal T1 and transversal rotating-frame T1ρ spin relaxation. Unexpectedly the 15N T1 relaxation time constants varied significantly with the choice of water suppression method. For a 25-kDa Escherichiacoli. glutamine binding protein (GlnBP) the T1 values acquired with the pulse sequence containing a water dephasing gradient are on average 20% longer than the ones obtained using a pulse sequence containing the water flip-back pulse. In contrast the two T1ρ data sets are correlated without an apparent offset. The average T1 difference was reduced to 12% when the experimental recycle delay was doubled, while the average T1 values from the flip-back measurements were nearly unchanged. Analysis of spectral signal to noise ratios ( s/ n) showed the apparent slower 15N relaxation obtained with the water dephasing experiment originated from the differences in 1H N recovery for each relaxation time point. This in turn offset signal reduction from 15N relaxation decay. The artifact becomes noticeable when the measured 15N relaxation time constant is comparable to recycle delay, e.g., the 15N T1 of medium to large proteins. The 15N relaxation rates measured with either water suppression schemes yield reasonable fits to the structure. However, data from the saturated scheme results in significantly lower Model-Free order parameters (< S2> = 0.81) than the non-saturated ones (< S2> = 0.88), indicating such order parameters may be previously underestimated.

  15. Enzymatic synthesis of guanine nucleotides labeled with 15N at the 2-amino group of the purine ring.

    PubMed

    Bouhss, A; Sakamoto, H; Palibroda, N; Chiriac, M; Sarfati, R; Smith, J M; Craescu, C T; Bârzu, O

    1995-02-10

    GMP and dGMP labeled with 15N at the 2-amino group of the purine ring was obtained enzymatically from NH4Cl (> 99 at.% 15N) and from IMP or dIMP, respectively, by several reactions involving IMP-dehydrogenase, GMP-synthetase, adenylate kinase, and creatine kinase. The first three enzymes were obtained by overexpression in Escherichia coli of the corresponding genes. The isotope content of the primary amino group of guanine determined by mass spectrometry after acid hydrolysis of nucleotides was found higher than 98 at.% 15N. The proton NMR spectrum of [15N]GMP in solution in the absence of nitrogen decoupling showed a doublet with a coupling constant of 92 Hz. When nitrogen decoupling was used during the acquisition time, the doublet was replaced by a single peak at 6.47 ppm, indicating that the corresponding proton is bound to 15N. PMID:7778777

  16. Application of 15N nuclear magnetic resonance spectroscopy to the determination of the stability of aryl nitrogen mustards.

    PubMed

    Wilman, D E; Palmer, B D; Denny, W A

    1995-06-01

    An excellent correlation has been shown to exist between the 15N NMR chemical shifts of a series of aryl nitrogen mustards and the Hammett constant, sigma, which is much improved by the use of sigma-. These chemical shifts also correlate well with the hydrolysis rates of the compounds in 50% aqueous acetone at 66 degrees C and their alkylation of 4-(4'-nitrobenzyl)pyridine under similar conditions. Thus 15N NMR is a straightforward and material-conserving method for estimating the relative stabilities of aryl nitrogen mustards. PMID:7783158

  17. Synthesis, spectroscopic (FT-IR, FT-Raman, UV and NMR) and computational studies on 3t-pentyl-2r,6c-diphenylpiperidin-4-one semicarbazone

    NASA Astrophysics Data System (ADS)

    Arockia doss, M.; Savithiri, S.; Rajarajan, G.; Thanikachalam, V.; Saleem, H.

    2015-09-01

    The structural and spectroscopic studies of 3t-pentyl-2r,6c-diphenylpiperidin-4-one semicarbazone (PDPOSC) were made by adopting B3LYP/HF levels theory using 6-311++G(d,p) basis set. The FT-IR and Raman spectra were recorded in solid phase, the fundamental vibrations were assigned on the basis of the total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method and PQS program. DFT method indicates that B3LYP is superior to HF method for molecular vibrational analysis. UV-vis spectrum of the compound was recorded in different solvents in the region of 200-800 nm and the electronic properties such as excitation energies, oscillator strength, wavelengths, HOMO and LUMO energies were evaluated by time-dependent DFT (TD-DFT) approach. The polarizability and first order hyperpolarizability of the title molecule were calculated and interpreted. The hyperconjugative interaction energy (E(2)) and electron densities of donor (i) and acceptor (j) bonds were calculated using NBO analysis. In addition, MEP and atomic charges of carbon, nitrogen and oxygen were calculated using B3LYP/6-311++G(d,p) level theory. Moreover, thermodynamic properties of the title compound were calculated by B3LYP/HF, levels using 6-311++G(d,p) basis set. The 1H and 13C nuclear magnetic resonance (NMR) chemical shifts of the molecule were calculated by the gauge independent atomic orbital (GIAO) method and compared with experimental results.

  18. Effect of protein restriction on (15)N transfer from dietary [(15)N]alanine and [(15)N]Spirulina platensis into urea.

    PubMed

    Hamadeh, M J; Hoffer, L J

    2001-08-01

    Six normal men consumed a mixed test meal while adapted to high (1.5 g. kg(-1) x day(-1)) and low (0.3 g. kg(-1) x day(-1)) protein intakes. They completed this protocol twice: when the test meals included 3 mg/kg of [(15)N]alanine ([(15)N]Ala) and when they included 30 mg/kg of intrinsically labeled [(15)N]Spirulina platensis ([(15)N]SPI). Six subjects with insulin-dependent diabetes mellitus (IDDM) receiving conventional insulin therapy consumed the test meal with added [(15)N]Ala while adapted to their customary high-protein diet. Protein restriction increased serum alanine, glycine, glutamine, and methionine concentrations and reduced those of leucine. Whether the previous diet was high or low in protein, there was a similar increase in serum alanine, methionine, and branched-chain amino acid concentrations after the test meal and a similar pattern of (15)N enrichment in serum amino acids for a given tracer. When [(15)N]Ala was included in the test meal, (15)N appeared rapidly in serum alanine and glutamine, to a minor degree in leucine and isoleucine, and not at all in other circulating amino acids. With [(15)N]SPI, there was a slow appearance of the label in all serum amino acids analyzed. Despite the different serum amino acid labeling, protein restriction reduced the postmeal transfer of dietary (15)N in [(15)N]Ala or [(15)N]SPI into [(15)N]urea by similar amounts (38 and 43%, respectively, not significant). The response of the subjects with IDDM was similar to that of the normal subjects. Information about adaptive reductions in dietary amino acid catabolism obtained by adding [(15)N]Ala to a test meal appears to be equivalent to that obtained using an intrinsically labeled protein tracer. PMID:11440912

  19. Continuous field measurement of N2O isotopologues using FTIR spectroscopy following 15N addition

    NASA Astrophysics Data System (ADS)

    Phillips, R. L.; Griffith, D. W.; Dijkstra, F. A.; Lugg, G.; Lawrie, R.; Macdonald, B.

    2012-12-01

    15N applied was emitted as N2O. Average fractions of 15N recovered in soil, root, shoot, and microbial biomass pools varied between trials but were approximately 0.4, 0.08, 0.1 and 0.03, respectively. The results indicate that the portable FTIR spectroscopic technique can effectively trace transfer of 15N to the atmosphere as N2O after 15N addition, allowing for powerful quantification of N2O emissions under field conditions.

  20. Push-through Direction Injectin NMR Automation

    EPA Science Inventory

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

  1. High-Resolution NMR Determination of the Dynamic Structure of Membrane Proteins.

    PubMed

    Jaremko, Mariusz; Jaremko, Łukasz; Villinger, Saskia; Schmidt, Christian D; Griesinger, Christian; Becker, Stefan; Zweckstetter, Markus

    2016-08-22

    (15) N spin-relaxation rates are demonstrated to provide critical information about the long-range structure and internal motions of membrane proteins. Combined with an improved calculation method, the relaxation-rate-derived structure of the 283-residue human voltage-dependent anion channel revealed an anisotropically shaped barrel with a rigidly attached N-terminal helix. Our study thus establishes an NMR spectroscopic approach to determine the structure and dynamics of mammalian membrane proteins at high accuracy and resolution. PMID:27461260

  2. Synergistic effect of the simultaneous chemometric analysis of ¹H NMR spectroscopic and stable isotope (SNIF-NMR, ¹⁸O, ¹³C) data: application to wine analysis.

    PubMed

    Monakhova, Yulia B; Godelmann, Rolf; Hermann, Armin; Kuballa, Thomas; Cannet, Claire; Schäfer, Hartmut; Spraul, Manfred; Rutledge, Douglas N

    2014-06-23

    It is known that (1)H NMR spectroscopy represents a good tool for predicting the grape variety, the geographical origin, and the year of vintage of wine. In the present study we have shown that classification models can be improved when (1)H NMR profiles are fused with stable isotope (SNIF-NMR, (18)O, (13)C) data. Variable selection based on clustering of latent variables was performed on (1)H NMR data. Afterwards, the combined data of 718 wine samples from Germany were analyzed using linear discriminant analysis (LDA), partial least squares-discriminant analysis (PLS-DA), factorial discriminant analysis (FDA) and independent components analysis (ICA). Moreover, several specialized multiblock methods (common components and specific weights analysis (ComDim), consensus PCA and consensus PLS-DA) were applied to the data. The best improvement in comparison with (1)H NMR data was obtained for prediction of the geographical origin (up to 100% for the fused data, whereas stable isotope data resulted only in 60-70% correct prediction and (1)H NMR data alone in 82-89% respectively). Certain enhancement was obtained also for the year of vintage (from 88 to 97% for (1)H NMR to 99% for the fused data), whereas in case of grape varieties improved models were not obtained. The combination of (1)H NMR data with stable isotope data improves efficiency of classification models for geographical origin and vintage of wine and can be potentially used for other food products as well. PMID:24909771

  3. Lineshape-based polarimetry of dynamically-polarized 15N2O in solid-state mixtures

    NASA Astrophysics Data System (ADS)

    Kuzma, N. N.; Håkansson, P.; Pourfathi, M.; Ghosh, R. K.; Kara, H.; Kadlecek, S. J.; Pileio, G.; Levitt, M. H.; Rizi, R. R.

    2013-09-01

    Dynamic nuclear polarization (DNP) of 15N2O, known for its long-lived singlet-state order at low magnetic field, is demonstrated in organic solvent/trityl mixtures at ∼1.5 K and 5 T. Both 15N polarization and intermolecular dipolar broadening are strongly affected by the sample's thermal history, indicating spontaneous formation of N2O clusters. In situ 15N NMR reveals four distinct powder-pattern spectra, attributed to the chemical-shift anisotropy (CSA) tensors of the two 15N nuclei, further split by the intramolecular dipolar coupling between their magnetic moments. 15N polarization is estimated by fitting the free-induction decay (FID) signals to the analytical model of four single-quantum transitions. This analysis implies (10.2±2.2)% polarization after 37 h of DNP, and provides a direct, instantaneous probe of the absolute 15N polarization, without a need for time-consuming referencing to a thermal-equilibrium NMR signal.

  4. Retrieving nitrogen isotopic signatures from fresh leaf reflectance spectra: disentangling δ15N from biochemical and structural leaf properties

    PubMed Central

    Hellmann, Christine; Große-Stoltenberg, André; Lauströ, Verena; Oldeland, Jens; Werner, Christiane

    2015-01-01

    Linking remote sensing methodology to stable isotope ecology provides a promising approach to study ecological processes from small to large spatial scales. Here, we show that δ15N can be detected in fresh leaf reflectance spectra of field samples along a spatial gradient of increasing nitrogen input from an N2-fixing invasive species. However, in field data it is unclear whether δ15N directly influences leaf reflectance spectra or if the relationship is based on covariation between δ15N and foliar nitrogen content or other leaf properties. Using a 15N-labeling approach, we experimentally varied δ15N independently of any other leaf properties in three plant species across different leaf developmental and physiological states. δ15N could successfully be modeled by means of partial least squares (PLSs) regressions, using leaf reflectance spectra as predictor variables. PLS models explained 53–73% of the variation in δ15N within species. Several wavelength regions important for predicting δ15N were consistent across species and could furthermore be related to known absorption features of N-containing molecular bonds. By eliminating covariation with other leaf properties as an explanation for the relationship between reflectance and δ15N, our results demonstrate that 15N itself has an inherent effect on leaf reflectance spectra. Thus, our study substantiates the use of spectroscopic measurements to retrieve isotopic signatures for ecological studies and encourages future development. Furthermore, our results highlight the great potential of optical measurements for up-scaling isotope ecology to larger spatial scales. PMID:25983740

  5. HN-NCA heteronuclear TOCSY-NH experiment for (1)H(N) and (15)N sequential correlations in ((13)C, (15)N) labelled intrinsically disordered proteins.

    PubMed

    Wiedemann, Christoph; Goradia, Nishit; Häfner, Sabine; Herbst, Christian; Görlach, Matthias; Ohlenschläger, Oliver; Ramachandran, Ramadurai

    2015-10-01

    A simple triple resonance NMR experiment that leads to the correlation of the backbone amide resonances of each amino acid residue 'i' with that of residues 'i-1' and 'i+1' in ((13)C, (15)N) labelled intrinsically disordered proteins (IDPs) is presented. The experimental scheme, {HN-NCA heteronuclear TOCSY-NH}, exploits the favourable relaxation properties of IDPs and the presence of (1) J CαN and (2) J CαN couplings to transfer the (15)N x magnetisation from amino acid residue 'i' to adjacent residues via the application of a band-selective (15)N-(13)C(α) heteronuclear cross-polarisation sequence of ~100 ms duration. Employing non-uniform sampling in the indirect dimensions, the efficacy of the approach has been demonstrated by the acquisition of 3D HNN chemical shift correlation spectra of α-synuclein. The experimental performance of the RF pulse sequence has been compared with that of the conventional INEPT-based HN(CA)NH pulse scheme. As the availability of data from both the HCCNH and HNN experiments will make it possible to use the information extracted from one experiment to simplify the analysis of the data of the other and lead to a robust approach for unambiguous backbone and side-chain resonance assignments, a time-saving strategy for the simultaneous collection of HCCNH and HNN data is also described. PMID:26282620

  6. Insights into the molecular architecture of a peptide nanotube using FTIR and solid-state NMR spectroscopic measurements on an aligned sample.

    PubMed

    Middleton, David A; Madine, Jillian; Castelletto, Valeria; Hamley, Ian W

    2013-09-27

    Queuing up: Molecular orientation within macroscopically aligned nanotubes of the peptide AAAAAAK can be studied by solid-state NMR and IR spectroscopy. Line shape analysis of the NMR spectra indicates that the peptide N-H bonds are tilted 65-70° relative to the nanotube long axis. Re-evaluation of earlier X-ray fiber diffraction data suggests that the peptide molecules are hydrogen-bonded in a helical arrangement along the nanotube axis. PMID:23955926

  7. 1H, 13C and 15N resonance assignments of URNdesign, a computationally redesigned RRM protein

    SciTech Connect

    Dobson, Neil; Dantas, Gautam; Varani, Gabriele

    2005-10-01

    Protein design represents one of the great challenges of computational structural biology. The ability to successfully design new proteins would allow us to generate new reagents and enzymes, while at the same time providing us with an understanding of the principles of protein stability. Here we report 1H, 15N and 13C resonance assignments of a redesigned U1A protein, URNdesign. U1A has been studied extensively by our group and hence was chosen as a design target. For the assignments we sued 2D and 3D heteronuclearNMR experiments with uniformly 13C, 15N-labeled URNdesign. The assignments for the backbone NH, CO,Ca and Cb nuclei are 94%complete. Sidechain 1Hand13C, aromatic andQ/NNH2 resonances are essentially complete with guanidinium and K NH3 residues unassigned. BMRB deposit with accession number 6493

  8. Chemical, spectroscopic characterization, DFT studies and antibacterial activities in vitro of a new gold(I) complex with rimantadine.

    PubMed

    Sucena, Suelen F; Paiva, Raphael E F; Abbehausen, Camilla; Mattos, Ives B; Lancellotti, Marcelo; Formiga, André L B; Corbi, Pedro P

    2012-04-01

    A novel gold(I) complex with rimantadine (RTD) was obtained and structurally characterized by a set of chemical and spectroscopic analysis. 1H, 13C and 15N nuclear magnetic resonance (NMR) and infrared (IR) spectroscopic measurements suggest coordination of the ligand to Au(I) through the N atom of the ethanamine group. Theoretical (DFT) calculations confirmed the IR assignments and permit proposing an optimized geometry for the complex. The gold(I)-rimantadine complex (Au-RTD) is soluble in methanol, ethanol, dimethylsulfoxide, acetone and acetonitrile. The preliminary kinetic studies based on UV-vis spectroscopic measurements indicate the stability of the compound in solution. Antibacterial activities of the complex were evaluated by an antibiogram assay. The Au-RTD complex showed an effective in vitro antibacterial activity against the Pseudomonas aeruginosa, Escherichia coli (Gram-negative), and Staphylococcus aureus (Gram-positive) bacterial strains. PMID:22257715

  9. Quantum Chemical Calculations of Amide-15N Chemical Shift Anisotropy Tensors for a Membrane-Bound Cytochrome b5

    PubMed Central

    Pandey, Manoj Kumar; Ramamoorthy, Ayyalusamy

    2013-01-01

    There is considerable interest in determining amide-15N chemical shift anisotropy (CSA) tensors from biomolecules and understanding their variation for structural and dynamics studies using solution and solid-state NMR spectroscopy and also by quantum chemical calculations. Due to the difficulties associated with the measurement of CSA tensors from membrane proteins, NMR-based structural studies heavily relied on the CSA tensors determined from model systems, typically single crystals of model peptides. In the present study, the principal components of backbone amide-15N CSA tensor have been determined using density functional theory for a 16.7-kDa membrane-bound paramagnetic heme containing protein, cytochrome b5 (cytb5). All the calculations were performed by taking residues within 5Å distance from the backbone amide-15N nucleus of interest. The calculated amide-15N CSA spans agree less well with our solution NMR data determined for an effective internuclear distance rN-H = 1.023 Å and a constant angle β = 18° that the least shielded component (δ11) makes with the N-H bond. The variation of amide-15N CSA span obtained using quantum chemical calculations is found to be smaller than that obtained from solution NMR measurements, whereas the trends of the variations are found to be in close agreement. We believe that the results reported in this study will be useful in studying the structure and dynamics of membrane proteins and heme-containing proteins, and also membrane-bound protein-protein complexes such as cytochromes-b5-P450. PMID:23268659

  10. Box-modeling of 15N/14N in mammals.

    PubMed

    Balter, Vincent; Simon, Laurent; Fouillet, Hélène; Lécuyer, Christophe

    2006-03-01

    The 15N/14N signature of animal proteins is now commonly used to understand their physiology and quantify the flows of nutrient in trophic webs. These studies assume that animals are predictably 15N-enriched relative to their food, but the isotopic mechanism which accounts for this enrichment remains unknown. We developed a box model of the nitrogen isotope cycle in mammals in order to predict the 15N/14N ratios of body reservoirs as a function of time, N intake and body mass. Results of modeling show that a combination of kinetic isotope fractionation during the N transfer between amines and equilibrium fractionation related to the reversible conversion of N-amine into ammonia is required to account for the well-established approximately 4 per thousand 15N-enrichment of body proteins relative to the diet. This isotopic enrichment observed in proteins is due to the partial recycling of 15N-enriched urea and the urinary excretion of a fraction of the strongly 15N-depleted ammonia reservoir. For a given body mass and diet delta15N, the isotopic compositions are mainly controlled by the N intake. Increase of the urea turnover combined with a decrease of the N intake lead to calculate a delta15N increase of the proteins, in agreement with the observed increase of collagen delta15N of herbivorous animals with aridity. We further show that the low delta15N collagen values of cave bears cannot be attributed to the dormancy periods as it is commonly thought, but inversely to the hyperphagia behavior. This model highlights the need for experimental investigations performed with large mammals in order to improve our understanding of natural variations of delta15N collagen. PMID:16328553

  11. Synthesis of 7-15N-Oroidin and Evaluation of Utility for Biosynthetic Studies of Pyrrole-Imidazole Alkaloids by Microscale1H-15N HSQC and FTMS†

    PubMed Central

    Wang, Yong-Gang; Morinaka, Brandon I.; Reyes, Jeremy Chris P.; Wolff, Jeremy H.; Romo, Daniel; Molinski, Tadeusz F.

    2010-01-01

    Numerous marine-derived pyrrole-imidazole alkaloids (PIAs), ostensibly derived from the simple precursor oroidin, 1a, have been reported and have garnered intense synthetic interest due to their complex structures and in some cases biological activity; however very little is known regarding their biosynthesis. We describe a concise synthesis of 7-15N-oroidin (1d) from urocanic acid and a direct method for measurement of 15N incorporation by pulse labeling and analysis by 1D 1H-15N HSQC NMR and FTMS. Using a mock pulse labeling experiment, we estimate the limit of detection (LOD) for incorporation of newly biosynthesized PIA by 1D 1H-15N HSQC to be 0.96 μg equivalent of 15N oroidin (2.4 nmole) in a background of 1500 μg unlabeled oroidin (about 1 part per 1600). 7-15N-Oroidin will find utility in biosynthetic feeding experiments with live sponges to provide direct information to clarify the pathways leading to more complex pyrrole-imidazole alkaloids. PMID:20095632

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

    NASA Astrophysics Data System (ADS)

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

    2016-03-01

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

  13. Site-Selective Synthesis of (15)N- and (13)C-Enriched Flavin Mononucleotide Coenzyme Isotopologues.

    PubMed

    Neti, Syam Sundar; Poulter, C Dale

    2016-06-17

    Flavin mononucleotide (FMN) is a coenzyme for numerous proteins involved in key cellular and physiological processes. Isotopically labeled flavin is a powerful tool for studying the structure and mechanism of flavoenzyme-catalyzed reactions by a variety of techniques, including NMR, IR, Raman, and mass spectrometry. In this report, we describe the preparation of labeled FMN isotopologues enriched with (15)N and (13)C isotopes at various sites in the pyrazine and pyrimidine rings of the isoalloxazine core of the cofactor from readily available precursors by a five-step chemo-enzymatic synthesis. PMID:27176708

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

    NASA Astrophysics Data System (ADS)

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

    2014-01-01

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

  15. Mechanochemical and solution synthesis, X-ray structure and IR and 31P solid state NMR spectroscopic studies of copper(I) thiocyanate adducts with bulky monodentate tertiary phosphine ligands.

    PubMed

    Bowmaker, Graham A; Hanna, John V; Hart, Robert D; Healy, Peter C; King, Scott P; Marchetti, Fabio; Pettinari, Claudio; Skelton, Brian W; Tabacaru, Aurel; White, Allan H

    2012-07-01

    A number of adducts of copper(I) thiocyanate with bulky tertiary phosphine ligands, and some nitrogen-base solvates, were synthesized and structurally and spectroscopically characterised. CuSCN:PCy3 (1:2), as crystallized from pyridine, is shown by a single crystal X-ray study to be a one-dimensional polymer ...(Cy3P)2CuSCN(Cy3P)2CuSCN... (1) with the four-coordinate copper atoms linked end-on by S-SCN-N bridging thiocyanate groups. A second form (2), obtained from acetonitrile, was also identified and shown by IR and 31P CPMAS NMR spectroscopy to be mononuclear, with the magnitude of the dν(Cu) parameter measured from the 31P CPMAS and the ν(CN) value from the IR clearly establishing this compound as three-coordinate [(Cy3P)2CuNCS]. Two further CuSCN/PCy3 compounds CuSCN:PCy3 (1:1) (3), and CuSCN:PCy3:py (1:1:1) (4) were also characterized spectroscopically, with the dν(Cu) parameters indicating three- and four-coordinate copper sites, respectively. Attempts to obtain a 1:2 adduct with tri-t-butylphosphine have yielded, from pyridine, the 1:1 adduct as a dimer [(Bu(t)3P)((SCN)(NCS))Cu(PBu(t)3)] (5), while similar attempts with tri-o-tolylphosphine (from acetonitrile and pyridine (= L)) resulted in solvated 1:1:1 CuSCN:P(o-tol)3:L forms as dimeric [{(o-tol)3P}LCu((SCN)(NCS))CuL{P(o-tol)3}] (6 and 8). The solvent-free 1:1 CuSCN:P(o-tol)3 adduct (7), obtained by desolvation of 6, was characterized spectroscopically and dν(Cu) measurements from the 31P CPMAS NMR data are consistent with the decrease in coordination number of the copper atom from four (for 6) (P,N(MeCN)Cu,S,N) to three (for 7) (PCuS,N) upon loss of the acetonitrile of solvation. These results are compared with those previously reported for mononuclear and binuclear PPh3 adducts which demonstrate a clear tendency for the copper centre to remain four-coordinate. The IR spectroscopic measurements on these compounds show that bands in the far-IR spectra provide a much more definitive criterion for

  16. Synthesis, structural, and spectroscopic (FT-IR, NMR, and UV) Characterization of 1-(Cyclohexylmethyl)-2-(pyridin-2-yl)-1 H-benzo[ d]imidazole by experimental techniques and quantum chemical calculations

    NASA Astrophysics Data System (ADS)

    Özdemir, Namık; Dayan, Osman; Demirmen, Selin

    2016-05-01

    The title compound ( II), 1-(cyclohexylmethyl)-2-(pyridin-2-yl)-1 H-benzo[ d]imidazole (C19H21N3), was synthesized via N-alkylation of 2-(pyridin-2-yl)-1 H-benzo[ d]imidazole ( I). Both compounds I and II were characterized by IR, NMR and UV-vis spectroscopy. Solid-state structure of compound II was determined by single-crystal X-ray diffraction technique. Furthermore, quantum chemical calculations employing density functional theory (DFT/B3LYP) method with the 6-311++ G( d, p) basis set were performed for the theoretical characterization of the molecular and spectroscopic features of the compounds. Using the TD-DFT method, electronic absorption spectra of the compounds have been predicted at same level. When the obtained results were compared with the experimental findings, it is seen that theoretical results support the experimental data and a good agreement exists between them.

  17. Spectroscopic (FT-IR, FT-Raman, 1H, 13C NMR, UV/VIS), thermogravimetric and antimicrobial studies of Ca(II), Mn(II), Cu(II), Zn(II) and Cd(II) complexes of ferulic acid

    NASA Astrophysics Data System (ADS)

    Kalinowska, M.; Piekut, J.; Bruss, A.; Follet, C.; Sienkiewicz-Gromiuk, J.; Świsłocka, R.; Rzączyńska, Z.; Lewandowski, W.

    2014-03-01

    The molecular structure of Mn(II), Cu(II), Zn(II), Cd(II) and Ca(II) ferulates (4-hydroxy-3-methoxycinnamates) was studied. The selected metal ferulates were synthesized. Their composition was established by means of elementary and thermogravimetric analysis. The following spectroscopic methods were used: infrared (FT-IR), Raman (FT-Raman), nuclear magnetic resonance (13C, 1H NMR) and ultraviolet-visible (UV/VIS). On the basis of obtained results the electronic charge distribution in studied metal complexes in comparison with ferulic acid molecule was discussed. The microbiological study of ferulic acid and ferulates toward Escherichia coli, Bacillus subtilis, Candida albicans, Pseudomonas aeruginosa, Staphylococcus aureus and Proteus vulgaris was done.

  18. Microscale Syntheses, Reactions, and 1H NMR Spectroscopic Investigations of Square Planar Macrocyclic Tetraamido-N Cu(III) Complexes Relevant to Green Chemistry

    ERIC Educational Resources Information Center

    Uffelman, Erich S.; Doherty, Jonathan R.; Schulze, Carl; Burke, Amy L.; Bonnema, Kristen R.; Watson, Tanya T.; Lee, Daniel W., III

    2004-01-01

    Microscale fusions, description, and spectroscopic analysis of the reactivity of a square planar Cu(III) complex significant to green chemistry, are presented. The experiment also includes nine focal points on which pre-lab and post-lab questions are based, and the final exams reflect the students' comprehension of these and other features of…

  19. Stereospecific assignments of glycine in proteins by stereospecific deuteration and {sup 15}N labeling

    SciTech Connect

    Hansen, A.P.; Curley, R.W. Jr.; Panigot, M.J.; Fesik, S.W.

    1994-12-01

    Stereospecific assignments are important for accurately determining the three-dimensional structures of proteins through the use of multidimensional NMR techniques. It is especially important to stereospecifically assign the glycine {alpha}-protons in proteins because of the potential for different backbone conformations of this residue. These stereospecific assignments are critical for interpreting the {sup 3}J{sub NH,{alpha}H} coupling constants and NOEs involving the glycine {alpha}-protons that determine the conformation of this part of the protein. However, it is often difficult to unambiguously obtain the stereospecific assignments for glycine residues by using only NOE data. In this poster, we present a method for unambiguous, stereospecific assignment of the {alpha}-protons of glycine residues. This method involves synthesis of stereo-specifically deuterated and {sup 15}N-labeled Gly using a slightly modified procedure originally described by Woodard and coworkers for the stereoselective deuteration of glycine. The stereospecifically deuterated and {sup 15}N-labeled Gy has been incorporated into recombinant proteins expressed in both bacterial systems (FKBP) and mammalian cells (u-PA). Two- and three-dimensional isotope-filtered and isotope-edited NMR experiments were used to obtain the stereospecific assignments of the glycine {alpha}-protons for these proteins.

  20. One pot synthesis, molecular structure and spectroscopic studies (X-ray, IR, NMR, UV-Vis) of novel 2-(4,6-dimethoxy-1,3,5-triazin-2-yl) amino acid ester derivatives.

    PubMed

    El-Faham, Ayman; Soliman, Saied M; Osman, Sameh M; Ghabbour, Hazem A; Siddiqui, Mohammed R H; Fun, Hoong-Kun; Albericio, Fernando

    2016-04-15

    Novel series of 2-(4,6-dimethoxy,1,3,5-triazin-2-yl) amino acid ester derivatives were synthesized using simple one pot method in methanol. The products were obtained in high yields and purities as observed from their spectral data, elemental analyses, GC-MS and X-ray crystallographic analysis. The B3LYP/6-311G(d,p) calculated molecular structures are well correlated with the geometrical parameters obtained from the X-ray analyses. The spectroscopic properties such as IR vibrational modes, NMR chemical shifts and UV-Vis electronic transitions were discussed both experimentally and theoretically. The IR vibrational frequencies showed good correlations with the experimental data (R(2)=0.9961-0.9995). The electronic spectra were assigned based on the TD-DFT results. Intense electronic transition band is calculated at 198.1 nm (f=0.1389), 204.2 nm (f=0.2053), 205.0 (f=0.1704) and 205.7 (0.2971) for compounds 6a-i, respectively. The molecular orbital energy levels contributed in the longest wavelength transition band were explained. For all compounds, the experimental wavelengths showed red shifts compared to the calculations due to the solvent effect. The NMR chemical shifts were calculated using GIAO method. The NBO analyses were performed to predict the stabilization energies due to the electron delocalization processes occur in the studied systems. PMID:26845586

  1. One pot synthesis, molecular structure and spectroscopic studies (X-ray, IR, NMR, UV-Vis) of novel 2-(4,6-dimethoxy-1,3,5-triazin-2-yl) amino acid ester derivatives

    NASA Astrophysics Data System (ADS)

    El-Faham, Ayman; Soliman, Saied M.; Osman, Sameh M.; Ghabbour, Hazem A.; Siddiqui, Mohammed R. H.; Fun, Hoong-Kun; Albericio, Fernando

    2016-04-01

    Novel series of 2-(4,6-dimethoxy,1,3,5-triazin-2-yl) amino acid ester derivatives were synthesized using simple one pot method in methanol. The products were obtained in high yields and purities as observed from their spectral data, elemental analyses, GC-MS and X-ray crystallographic analysis. The B3LYP/6-311G(d,p) calculated molecular structures are well correlated with the geometrical parameters obtained from the X-ray analyses. The spectroscopic properties such as IR vibrational modes, NMR chemical shifts and UV-Vis electronic transitions were discussed both experimentally and theoretically. The IR vibrational frequencies showed good correlations with the experimental data (R2 = 0.9961-0.9995). The electronic spectra were assigned based on the TD-DFT results. Intense electronic transition band is calculated at 198.1 nm (f = 0.1389), 204.2 nm (f = 0.2053), 205.0 (f = 0.1704) and 205.7 (0.2971) for compounds 6a-i, respectively. The molecular orbital energy levels contributed in the longest wavelength transition band were explained. For all compounds, the experimental wavelengths showed red shifts compared to the calculations due to the solvent effect. The NMR chemical shifts were calculated using GIAO method. The NBO analyses were performed to predict the stabilization energies due to the electron delocalization processes occur in the studied systems.

  2. Isolation and measurement of 15N2 from respiratory gases of animals administered 15N-labeled substances.

    PubMed

    Springer, D L; Reed, D J; Dost, F N

    1981-01-01

    A method is described for collection of metabolic 15N2 from in vitro preparations or intact rats administered 15N-containing compounds. The methods enables routine collection and mass spectrometric measurement of as little as 10 mumol 15N2 respired by a rat over a 24-h period. A device is described that includes either an animal chamber or a tissue reaction vessel in a closed recycling atmosphere, with automatic O2 replenishment and removal of CO2 and water. It is capable of sustaining moderate vacuum and is coupled to a high-vacuum manifold designed to process the contained atmosphere and respiratory gases. The starting atmosphere is an 80:20 mix of sulfur hexafluoride and O2. Recovery of 15N2 gas from the system without an animal present was 101.3 +/- 5.75%. When 15N2 gas was very slowly infused iv into an animal, recovery was 89.1 +/- 5.38%. Use of the method in studies of the fate of [15N]hydrazine in rats indicated that about 15% of the administered hydrazine is rapidly converted to 15N2, followed by slower conversion of an additional 7-10% over the next several hours. PMID:7328697

  3. Synthesis and biosynthesis of {sup 13}C-, {sup 15}N-labeled deoxynucleosides useful for biomolecular structural determinations

    SciTech Connect

    Ashburn, D.A.; Garcia, K.; Hanners, J.L.; Silks, L.A. III; Unkefer, C.J.

    1994-12-01

    Currently, there is a great emphasis on elucidating the structure, function, and dynamics of DNA. Much of the research involved in this study uses nuclear magnetic resonance (NMR) spectroscopy. Effective use of NMR spectroscopy for DNA molecules with mw > 10,000 requires stable isotope enrichment. We present strategies for site-specific isotopic labeling of the purine bases adenosine and guanosine and the biosynthesis of (U-{sup 13}C, {sup 15}N) DNA from methylotropic bacteria. With commercially available 6-chloropurine, an effective two-step route leads to 2{prime}-deoxy-(amino-{sup 15}N)adenosine (dA). The resulting d(amino-{sup 15}N)A is used in a series of reactions to synthesize 2{prime}-deoxy-(2-{sup 13}C,1,amino-{sup 15}N{sub 2})guanosine or any combination thereof. An improved biosynthesis of labeled DNA has been accomplished using Methylobacterium extorquens AS1. Each liter of growth medium contains 4 g of methanol to yield 1 g of lyophilized cells. As much as 200 mg of RNA per liter of culture has been obtained. We are currently developing large-scale isolation protocols. General synthetic pathways to oligomeric DNA will be presented.

  4. Spectroscopic (FT-IR, Raman, NMR and UV-vis.) and quantum chemical investigations of (E)-3-[4-(pentyloxy)phenyl]-1-phenylprop-2-en-1-one

    NASA Astrophysics Data System (ADS)

    Abbas, Asghar; Gökce, Halil; Bahçeli, Semiha; Naseer, Muhammad Moazzam

    2014-10-01

    In this study, the molecular structure and vibrational and electronic transition spectra and 1H and 13C NMR chemical shift values (gas phase and in chloroform solvent), HOMO-LUMO analysis, molecular electrostatic potential (MEP), thermodynamic properties and Mulliken atomic charges of (E)-3-[4-(pentyloxy)phenyl]-1-phenylprop-2-en-1-one molecule, C20H22O2, which has many biological activities have been calculated using the DFT/B3LYP method with 6-311++G(d,p) basis set in the ground state. The obtained results indicate a good harmony among the calculated and the experimental FT-IR, Raman, UV-vis. (in methanol solvent) and 1H and 13C NMR (in chloroform-d solvent) spectra of the mentioned compound.

  5. Spectroscopic [FT-IR and FT-Raman] and theoretical [UV-Visible and NMR] analysis on α-Methylstyrene by DFT calculations

    NASA Astrophysics Data System (ADS)

    Karthikeyan, N.; Joseph Prince, J.; Ramalingam, S.; Periandy, S.

    2015-05-01

    In the present research work, the FT-IR, FT-Raman and 13C and 1H NMR spectra of the α-Methylstyrene were recorded. The observed fundamental frequencies in finger print as well as functional group regions were assigned according to their uniqueness region. The Gaussian computational calculations are carried out by HF and DFT (B3LYP and B3PW91) methods with 6-31++G(d,p) and 6-311++G(d,p) basis sets and the corresponding results were tabulated. The impact of the presence of vinyl group in phenyl structure of the compound is investigated. The modified vibrational pattern of the molecule associated vinyl group was analyzed. Moreover, 13C NMR and 1H NMR were calculated by using the gauge independent atomic orbital (GIAO) method with B3LYP methods and the 6-311++G(d,p) basis set and their spectra were simulated and the chemical shifts linked to TMS were compared. A study on the electronic and optical properties; absorption wavelengths, excitation energy, dipole moment and frontier molecular orbital energies were carried out. The kubo gap of the present compound was calculated related to HOMO and LUMO energies which confirm the occurring of charge transformation between the base and ligand. Besides frontier molecular orbitals (FMO), molecular electrostatic potential (MEP) was performed. The NLO properties related to Polarizability and hyperpolarizability based on the finite-field approach were also discussed.

  6. δ15N Value Does Not Reflect Fasting in Mysticetes

    PubMed Central

    Aguilar, Alex; Giménez, Joan; Gómez–Campos, Encarna; Cardona, Luís; Borrell, Asunción

    2014-01-01

    The finding that tissue δ15N values increase with protein catabolism has led researchers to apply this value to gauge nutritive condition in vertebrates. However, its application to marine mammals has in most occasions failed. We investigated the relationship between δ15N values and the fattening/fasting cycle in a model species, the fin whale, a migratory capital breeder that experiences severe seasonal variation in body condition. We analyzed two tissues providing complementary insights: one with isotopic turnover (muscle) and one that keeps a permanent record of variations in isotopic values (baleen plates). In both tissues δ15N values increased with intensive feeding but decreased with fasting, thus contradicting the pattern previously anticipated. The apparent inconsistency during fasting is explained by the fact that a) individuals migrate between different isotopic isoscapes, b) starvation may not trigger significant negative nitrogen balance, and c) excretion drops and elimination of 15N-depleted urine is minimized. Conversely, when intensive feeding is resumed in the northern grounds, protein anabolism and excretion start again, triggering 15N enrichment. It can be concluded that in whales and other mammals that accrue massive depots of lipids as energetic reserves and which have limited access to drinking water, the δ15N value is not affected by fasting and therefore cannot be used as an indicatior of nutritive condition. PMID:24651388

  7. Probing the Carbonyl Functionality of a Petroleum Resin and Asphaltene through Oximation and Schiff Base Formation in Conjunction with N-15 NMR.

    PubMed

    Thorn, Kevin A; Cox, Larry G

    2015-01-01

    Despite recent advances in spectroscopic techniques, there is uncertainty regarding the nature of the carbonyl groups in the asphaltene and resin fractions of crude oil, information necessary for an understanding of the physical properties and environmental fate of these materials. Carbonyl and hydroxyl group functionalities are not observed in natural abundance 13C nuclear magnetic resonance (NMR) spectra of asphaltenes and resins and therefore require spin labeling techniques for detection. In this study, the carbonyl functionalities of the resin and asphaltene fractions from a light aliphatic crude oil that is the source of groundwater contamination at the long term USGS study site near Bemidji, Minnesota, have been examined through reaction with 15N-labeled hydroxylamine and aniline in conjunction with analysis by solid and liquid state 15N NMR. Ketone groups were revealed through 15N NMR detection of their oxime and Schiff base derivatives, and esters through their hydroxamic acid derivatives. Anilinohydroquinone adducts provided evidence for quinones. Some possible configurations of the ketone groups in the resin and asphaltene fractions can be inferred from a consideration of the likely reactions that lead to heterocyclic condensation products with aniline and to the Beckmann reaction products from the initially formed oximes. These include aromatic ketones and ketones adjacent to quaternary carbon centers, β-hydroxyketones, β-diketones, and β-ketoesters. In a solid state cross polarization/magic angle spinning (CP/MAS) 15N NMR spectrum recorded on the underivatized asphaltene as a control, carbazole and pyrrole-like nitrogens were the major naturally abundant nitrogens detected. PMID:26556054

  8. Probing the carbonyl functionality of a petroleum resin and asphaltene through oximation and schiff base formation in conjunction with N-15 NMR

    USGS Publications Warehouse

    Thorn, Kevin A.; Cox, Larry G.

    2015-01-01

    Despite recent advances in spectroscopic techniques, there is uncertainty regarding the nature of the carbonyl groups in the asphaltene and resin fractions of crude oil, information necessary for an understanding of the physical properties and environmental fate of these materials. Carbonyl and hydroxyl group functionalities are not observed in natural abundance 13C nuclear magnetic resonance (NMR) spectra of asphaltenes and resins and therefore require spin labeling techniques for detection. In this study, the carbonyl functionalities of the resin and asphaltene fractions from a light aliphatic crude oil that is the source of groundwater contamination at the long term USGS study site near Bemidji, Minnesota, have been examined through reaction with 15N-labeled hydroxylamine and aniline in conjunction with analysis by solid and liquid state 15N NMR. Ketone groups were revealed through 15N NMR detection of their oxime and Schiff base derivatives, and esters through their hydroxamic acid derivatives. Anilinohydroquinone adducts provided evidence for quinones. Some possible configurations of the ketone groups in the resin and asphaltene fractions can be inferred from a consideration of the likely reactions that lead to heterocyclic condensation products with aniline and to the Beckmann reaction products from the initially formed oximes. These include aromatic ketones and ketones adjacent to quaternary carbon centers, β-hydroxyketones, β-diketones, and β-ketoesters. In a solid state cross polarization/magic angle spinning (CP/MAS) 15N NMR spectrum recorded on the underivatized asphaltene as a control, carbazole and pyrrole-like nitrogens were the major naturally abundant nitrogens detected.

  9. Probing the Carbonyl Functionality of a Petroleum Resin and Asphaltene through Oximation and Schiff Base Formation in Conjunction with N-15 NMR

    PubMed Central

    Thorn, Kevin A.; Cox, Larry G.

    2015-01-01

    Despite recent advances in spectroscopic techniques, there is uncertainty regarding the nature of the carbonyl groups in the asphaltene and resin fractions of crude oil, information necessary for an understanding of the physical properties and environmental fate of these materials. Carbonyl and hydroxyl group functionalities are not observed in natural abundance 13C nuclear magnetic resonance (NMR) spectra of asphaltenes and resins and therefore require spin labeling techniques for detection. In this study, the carbonyl functionalities of the resin and asphaltene fractions from a light aliphatic crude oil that is the source of groundwater contamination at the long term USGS study site near Bemidji, Minnesota, have been examined through reaction with 15N-labeled hydroxylamine and aniline in conjunction with analysis by solid and liquid state 15N NMR. Ketone groups were revealed through 15N NMR detection of their oxime and Schiff base derivatives, and esters through their hydroxamic acid derivatives. Anilinohydroquinone adducts provided evidence for quinones. Some possible configurations of the ketone groups in the resin and asphaltene fractions can be inferred from a consideration of the likely reactions that lead to heterocyclic condensation products with aniline and to the Beckmann reaction products from the initially formed oximes. These include aromatic ketones and ketones adjacent to quaternary carbon centers, β-hydroxyketones, β-diketones, and β-ketoesters. In a solid state cross polarization/magic angle spinning (CP/MAS) 15N NMR spectrum recorded on the underivatized asphaltene as a control, carbazole and pyrrole-like nitrogens were the major naturally abundant nitrogens detected. PMID:26556054

  10. Asymptotic Normalization Coefficients from the {sup 15}N({sup 3}He,d){sup 16}O Reaction and the Astrophysical Factor for the {sup 15}N(p,{gamma}){sup 16}O Capture

    SciTech Connect

    Burjan, V.; Bem, P.; Hons, Z.; Kroha, V.; Mrazek, J.; Novak, J.; Piskor, S.; Simeckova, E.; Vincour, J.; Cherubini, S.; La Cognata, M.; Pizzone, R. G.; Romano, S.; Spitaleri, C.; Tumino, A.; Gagliardi, C. A.; Mukhamedzhanov, A. M.; Plunkett, A.; Trache, L.; Tribble, R. E.

    2008-05-12

    The angular distributions of the {sup 15}N({sup 3}He,d){sup 16}O reaction were measured with the aim to determine the direct capture rate of the astrophysical reaction {sup 15}N(p, {gamma}){sup 16}O by deducing asymptotic normalization coefficients (ANC). The {sup 15}N(p,{gamma}){sup 16}O reaction is a part of the CNO cycle having importance in the nucleosynthesis of the N and O isotopes. The measurement was carried out on the cyclotron U120M of NPI CAS at the energy 25.74 MeV of {sup 3}He ions in a gas chamber containing the high purity {sup 15}N isotope. The preliminary results of corresponding spectroscopic factors and ANC's were used for the estimation of the S-factor for the direct capture {sup 15}N(p,{gamma}){sup 16}O. Using the widths of the resonances E{sub R} = 312 and 962 keV, the total S-factor was determined within the framework of the R-matrix approach.

  11. Chromatographic, NMR and vibrational spectroscopic investigations of astaxanthin esters: application to "Astaxanthin-rich shrimp oil" obtained from processing of Nordic shrimps.

    PubMed

    Subramanian, B; Thibault, M-H; Djaoued, Y; Pelletier, C; Touaibia, M; Tchoukanova, N

    2015-11-01

    Astaxanthin (ASTX) is a keto carotenoid, which possesses a non-polar linear central conjugated chain and polar β-ionone rings with ketone and hydroxyl groups at the extreme ends. It is well known as a super anti-oxidant, and recent clinical studies have established its nutritional benefits. Although it occurs in several forms, including free molecule, crystalline, aggregates and various geometrical isomers, in nature it exists primarily in the form of esters. Marine animals accumulate ASTX from primary sources such as algae. Nordic shrimps (P. borealis), which are harvested widely in the Atlantic Ocean, form a major source of astaxanthin esters. "Astaxanthin-rich shrimp oil" was developed as a novel product in a shrimp processing plant in Eastern Canada. A compositional analysis of the shrimp oil was performed, with a view to possibly use it as a nutraceutical product for humans and animals. Astaxanthin-rich shrimp oil contains 50% MUFAs and 22% PUFAs, of which 20% are omega-3. In addition, the shrimp oil contains interesting amounts of EPA and DHA, with 10%/w and 8%/w, respectively. Astaxanthin concentrations varied between 400 and 1000 ppm, depending on the harvesting season of the shrimp. Astaxanthin and its esters were isolated from the oil and analysed by NMR, FTIR and Micro-Raman spectroscopy. Astaxanthin mono- and diesters were synthesized and used as standards for the analysis of astaxanthin-rich shrimp oil. NMR and vibrational spectroscopy techniques were successfully used for the rapid characterization of monoesters and diesters of astaxanthin. Raman spectroscopy provided important intermolecular interactions present in the esterified forms of astaxanthin molecules. Also discussed in this paper is the use of NMR, FTIR and Micro-Raman spectroscopy for the detection of astaxanthin esters in shrimp oil. PMID:26393239

  12. Conformational analysis, spectroscopic study (FT-IR, FT-Raman, UV, 1H and 13C NMR), molecular orbital energy and NLO properties of 5-iodosalicylic acid

    NASA Astrophysics Data System (ADS)

    Karaca, Caglar; Atac, Ahmet; Karabacak, Mehmet

    2015-02-01

    In this study, 5-iodosalicylic acid (5-ISA, C7H5IO3) is structurally characterized by FT-IR, FT-Raman, NMR and UV spectroscopies. There are eight conformers, Cn, n = 1-8 for this molecule therefore the molecular geometry for these eight conformers in the ground state are calculated by using the ab-initio density functional theory (DFT) B3LYP method approach with the aug-cc-pVDZ-PP basis set for iodine and the aug-cc-pVDZ basis set for the other elements. The computational results identified that the most stable conformer of 5-ISA is the C1 form. The vibrational spectra are calculated DFT method invoking the same basis sets and fundamental vibrations are assigned on the basis of the total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method with PQS program. Total density of state (TDOS) and partial density of state (PDOS) and also overlap population density of state (COOP or OPDOS) diagrams analysis for C1 conformer were calculated using the same method. The energy and oscillator strength are calculated by time-dependent density functional theory (TD-DFT) results complement with the experimental findings. Besides, charge transfer occurring in the molecule between HOMO and LUMO energies, frontier energy gap, molecular electrostatic potential (MEP) are calculated and presented. The NMR chemical shifts (1H and 13C) spectra are recorded and calculated using the gauge independent atomic orbital (GIAO) method. Mulliken atomic charges of the title molecule are also calculated, interpreted and compared with salicylic acid. The optimized bond lengths, bond angles and calculated NMR and UV, vibrational wavenumbers showed the best agreement with the experimental results.

  13. (1)H NMR spectroscopic elucidation in solution of the kinetics and thermodynamics of spin crossover for an exceptionally robust Fe(2+) complex.

    PubMed

    Petzold, Holm; Djomgoue, Paul; Hörner, Gerald; Speck, J Matthäus; Rüffer, Tobias; Schaarschmidt, Dieter

    2016-09-21

    A series of Fe(2+) spin crossover (SCO) complexes [Fe(5/6)](2+) employing hexadentate ligands (5/6) with cis/trans-1,2-diamino cyclohexanes (4) as central building blocks were synthesised. The ligands were obtained by reductive amination of 4 with 2,2'-bipyridyl-6-carbaldehyde or 1,10-phenanthroline-2-carbaldehyde 3. The chelating effect and the rigid structure of the ligands 5/6 lead to exceptionally robust Fe(2+) and Zn(2+) complexes conserving their structure even in coordinating solvents like dmso at high temperatures. Their solution behavior was investigated using variable temperature (VT) (1)H NMR spectroscopy and VT Vis spectroscopy. SCO behavior was found for all Fe(2+) complexes in this series centred around and far above room temperature. For the first time we have demonstrated that the thermodynamics as well as kinetics for SCO can be deduced by using VT (1)H NMR spectroscopy. An alternative scheme using a linear correction term C(1) to model chemical shifts for Fe(2+) SCO complexes is presented. The rate constant for the SCO of [Fe(rac-trans-5)](2+) obtained by VT (1)H NMR was validated by Laser Flash Photolysis (LFP), with excellent agreement (1/(kHL + kLH) = 33.7/35.8 ns for NMR/LFP). The solvent dependence of the transition temperature T1/2 and the solvatochromism of complex [Fe(rac-trans-5)](2+) were ascribed to hydrogen bond formation of the secondary amine to the solvent. Enantiomerically pure complexes can be prepared starting with R,R- or S,S-1,2-diaminocyclohexane (R,R-trans-4 or S,S-trans-4). The high robustness of the complexes reduces a possible ligand scrambling and allows preparation of quasiracemic crystals of [Zn(R,R-5)][Fe(S,S-5)](ClO4)4·(CH3CN) composed of a 1 : 1 mixture of the Zn and Fe complexes with inverse chirality. PMID:27506162

  14. Metal Carbonation of Forsterite in Supercritical CO2 and H2O Using Solid State 29Si, 13C NMR Spectroscop

    SciTech Connect

    Kwak, Ja Hun; Hu, Jian Z.; Hoyt, David W.; Sears, Jesse A.; Wang, Chong M.; Rosso, Kevin M.; Felmy, Andrew R.

    2010-03-11

    Ex situ solid state NMR was used for the first time to study fundamental mineral carbonation processes and reaction extent relevant to geologic carbon sequestration (GCS) using a model silicate mineral forsterite (Mg2SiO4)+supercriticalCO2 with and without H2O. Run conditions were 80 C and 96 atm. 29Si NMR clearly shows that in the absence of CO2, the role of H2O is to hydrolyze surface Mg-O-Si bonds to produce dissolved Mg2+, and mono- and oligomeric hydroxylated silica species. Surface hydrolysis products contain only Q0 (Si(OH)4) and Q1(Si(OH)3OSi) species. An equilibrium between Q0, Q1 and Mg2+ with a saturated concentration equivalent to less than 3.2% of the Mg2SiO4 conversion is obtained at a reaction time of up to 7 days. Using scCO2 without H2O, no reaction is observed within 7 days. Using both scCO2 and H2O, the surface reaction products for silica are mainly Q3 (SiOH(OSi)3) species accompanied by a lesser amount of Q2 (Si(OH)2(OSi)2) and Q4 (Si(OSi)4). However, no Q0 and Q1 were detected, indicating the carbonic acid formation/deprotonation and magnesite (MgCO3) precipitation reactions are faster than the forsterite hydrolysis process. Thus it can be concluded that the Mg2SiO4 hydrolysis process is the rate limiting step of the overall mineral carbonation process. 29Si NMR combined with XRD, TEM, SAED and EDX further reveal that the reaction is a surface reaction with the Mg2SiO4 crystallite in the core and with condensed Q2-Q4 species forming amorphous surface layers. 13C MAS NMR identified a possible reaction intermediate as (MgCO3)4-Mg(OH)2-5H2O. However, at long reaction times only crystallite magnesite MgCO3 products are observed.

  15. The structural properties of the transmembrane segment of the integral membrane protein phospholamban utilizing (13)C CPMAS, (2)H, and REDOR solid-state NMR spectroscopy.

    PubMed

    Karp, Ethan S; Tiburu, Elvis K; Abu-Baker, Shadi; Lorigan, Gary A

    2006-06-01

    Solid-state NMR spectroscopic techniques were used to investigate the secondary structure of the transmembrane peptide phospholamban (TM-PLB), a sarcoplasmic Ca(2+) regulator. (13)C cross-polarization magic angle spinning spectra of (13)C carbonyl-labeled Leu39 of TM-PLB exhibited two peaks in a pure 1-palmitoyl-2-oleoyl-phosphocholine (POPC) bilayer, each due to a different structural conformation of phospholamban as characterized by the corresponding (13)C chemical shift. The addition of a negatively charged phospholipid (1-palmitoyl-2-oleoylphosphatidylglycerol (POPG)) to the POPC bilayer stabilized TM-PLB to an alpha-helical conformation as monitored by an enhancement of the alpha-helical carbonyl (13)C resonance in the corresponding NMR spectrum. (13)C-(15)N REDOR solid-state NMR spectroscopic experiments revealed the distance between the (13)C carbonyl carbon of Leu39 and the (15)N amide nitrogen of Leu42 to be 4.2+/-0.2A indicating an alpha-helical conformation of TM-PLB with a slight deviation from an ideal 3.6 amino acid per turn helix. Finally, the quadrupolar splittings of three (2)H labeled leucines (Leu28, Leu39, and Leu51) incorporated in mechanically aligned DOPE/DOPC bilayers yielded an 11 degrees +/-5 degrees tilt of TM-PLB with respect to the bilayer normal. In addition to elucidating valuable TM-PLB secondary structure information, the solid-state NMR spectroscopic data indicates that the type of phospholipids and the water content play a crucial role in the secondary structure and folding of TM-PLB in a phospholipid bilayer. PMID:16839519

  16. QM/MM methodology, docking and spectroscopic (FT-IR/FT-Raman, NMR, UV) and Fukui function analysis on adrenergic agonist.

    PubMed

    Uma Maheswari, J; Muthu, S; Sundius, Tom

    2015-02-25

    The Fourier transform infrared, FT-Raman, UV and NMR spectra of Ternelin have been recorded and analyzed. Harmonic vibrational frequencies have been investigated with the help of HF with 6-31G (d,p) and B3LYP with 6-31G (d,p) and LANL2DZ basis sets. The (1)H and (13)C nuclear magnetic resonance (NMR) chemical shifts of the molecule were calculated by GIAO method. The polarizability (α) and the first hyperpolarizability (β) values of the investigated molecule have been computed using DFT quantum mechanical calculations. Stability of the molecule arising from hyper conjugative interactions, and charge delocalization has been analyzed using natural bond orbital (NBO) analysis. The electron density-based local reactivity descriptors such as Fukui functions were calculated to explain the chemical selectivity or reactivity site in Ternelin. Finally the calculated results were compared to simulated infrared and Raman spectra of the title compound which show good agreement with observed spectra. Molecular docking studies have been carried out in the active site of Ternelin and reactivity with ONIOM was also investigated. PMID:25277632

  17. QM/MM methodology, docking and spectroscopic (FT-IR/FT-Raman, NMR, UV) and Fukui function analysis on adrenergic agonist

    NASA Astrophysics Data System (ADS)

    Uma Maheswari, J.; Muthu, S.; Sundius, Tom

    2015-02-01

    The Fourier transform infrared, FT-Raman, UV and NMR spectra of Ternelin have been recorded and analyzed. Harmonic vibrational frequencies have been investigated with the help of HF with 6-31G (d,p) and B3LYP with 6-31G (d,p) and LANL2DZ basis sets. The 1H and 13C nuclear magnetic resonance (NMR) chemical shifts of the molecule were calculated by GIAO method. The polarizability (α) and the first hyperpolarizability (β) values of the investigated molecule have been computed using DFT quantum mechanical calculations. Stability of the molecule arising from hyper conjugative interactions, and charge delocalization has been analyzed using natural bond orbital (NBO) analysis. The electron density-based local reactivity descriptors such as Fukui functions were calculated to explain the chemical selectivity or reactivity site in Ternelin. Finally the calculated results were compared to simulated infrared and Raman spectra of the title compound which show good agreement with observed spectra. Molecular docking studies have been carried out in the active site of Ternelin and reactivity with ONIOM was also investigated.

  18. X-ray and 1H-NMR spectroscopic studies of the structures and conformations of the new nootropic agents RU-35929, RU-47010 and RU-35965

    NASA Astrophysics Data System (ADS)

    Amato, Maria E.; Bandoli, Giuliano; Casellato, Umberto; Pappalardo, Giuseppe C.; Toja, Emilio

    1990-10-01

    The crystal and molecular structures of the nootropics (±)1-benzenesulphonyl-2-oxo-5-ethoxypyrrolidine ( 1), (±)1-(3-pyridinylsulphonyl)-2-oxo-5-ethoxypyrrolidine ( 2) and (±)1-benzenesulphonyl-2-oxo-5-isopropyloxypyrrolidine ( 3) have been determined by X-ray analysis. The solution conformation of 1, 2 and 3 has been investigated by 1H NMR spectroscopy. In the solid state, the main feature consists of the similar structural parameters and conformations, with the exception of the conformation adopted by the 5-ethoxy moiety which changes on passing from 1 to 2. The solid state overall enveloped conformation of the 2-pyrrolidinone ring for the three nootropics is found to be retained in solution on the basis of NMR evidence. Comparison between calculated and experimental coupling constant values shows that one of the two possible puckered opposite conformational isomers (half-chair shapes) occurs in solution. The relative pharmacological potencies of 1, 2 and 3 cannot therefore be interpreted in terms of the different conformation features presently detectable by available experimental methods.

  19. Elemental and structural analysis of silicon forms in herbal drugs using silicon-29 MAS NMR and WD-XRF spectroscopic methods.

    PubMed

    Pajchel, L; Nykiel, P; Kolodziejski, W

    2011-12-01

    The objective of this work was to study concentration of silicon and its structural forms present in herbal drugs. Equisetum arvense and Urtica dioica L. from teapot bags, dietary supplements (tablets and capsules) containing those herbs, dry extract obtained from a teapot bag of E. arvense, and samples of the latter herb harvested in wild habitat over four months were studied using wavelength dispersive X-ray spectroscopy (WD-XRF) and high-resolution solid-state (29)Si NMR. The highest concentration of Si, ca. 27mg/g, was found in the herbal material from the teapot bags containing E. arvense. The Si content in natural E. arvense (whole plants) increased from May to August by ca. 7mg/g, reaching value 26mg/g. Three different silicon forms were detected in the studied herbal samples: Si(OSi)4 (Q(4)), Si(OH)(OSi)3 (Q(3)) and Si(OH)2(OSi)2 (Q(2)). Those sites were populated in E. arvense in the following order: Q(4)≫Q(3)>Q(2). A dramatic, ca. 50-fold decrease of the Si concentration during the infusion process was observed. The infusion process and the subsequent drying procedure augmented population of the Q(4) sites at the cost of the Q(2) sites. The WD-XRF and (29)Si NMR methods occurred useful and complementary in the study of herbal materials. PMID:21813258

  20. Combined experimental and quantum chemical studies on spectroscopic (FT-IR, FT-Raman, UV-Vis, and NMR) and structural characteristics of quinoline-5-carboxaldehyde

    NASA Astrophysics Data System (ADS)

    Kumru, Mustafa; Altun, Ahmet; Kocademir, Mustafa; Küçük, Vesile; Bardakçı, Tayyibe; Şaşmaz, İbrahim

    2016-12-01

    Comparative experimental and theoretical studies have been performed on the structure and spectral (FT-IR, FT-Raman, UV-Vis and NMR) features of quinoline-5-carboxaldehyde. Quantum chemical calculations have been carried out at Hartree-Fock and density functional B3LYP levels with the triple-zeta 6-311++G** basis set. Two stable conformers of quinoline-5-carboxaldehyde arising from the orientation of the carboxaldehyde moiety have been located at the room temperature. The energetic separation of these conformers is as small as 2.5 kcal/mol with a low transition barrier (around 9 kcal/mol). Therefore, these conformers are expected to coexist at the room temperature. Several molecular characteristics of quinoline-5-carboxaldehyde obtained through B3LYP and time-dependent B3LYP calculations, such as conformational stability, key geometry parameters, vibrational frequencies, IR and Raman intensities, UV-Vis vertical excitation energies and the corresponding oscillator strengths have been analyzed. The 1H and 13C NMR chemical shifts of quinoline-5-carboxaldehyde were also investigated.

  1. In vivo activity of glutaminase in the brain of hyperammonaemic rats measured by 15N nuclear magnetic resonance.

    PubMed Central

    Kanamori, K; Ross, B D

    1995-01-01

    The in vivo activity of phosphate-activated glutaminase (PAG) was measured in the brain of hyperammonaemic rat by 15N n.m.r. Brain glutamine was 15N-enriched by intravenous infusion of 15NH4+ until the concentration of [5-15N]glutamine reached 6.1 mumol/g. Further glutamine synthesis was inhibited by intraperitoneal injection of methionine-DL-sulphoximine, an inhibitor of glutamine synthetase, and the infusate was changed to 14NH4+ during observation of decrease in brain [5-15N]glutamine due to PAG and other glutamine utilization pathways. Progressive decrease in brain [5-15N]glutamine, PAG-catalysed production of 15NH4+ and its subsequent assimilation into glutamate by glutamate dehydrogenase were monitored in vivo by 15N n.m.r. Brain [5-15N]glutamine (15N enrichment of 0.35-0.50) decreased at a rate of 1.2 mumol/h per g of brain. The in vivo PAG activity, determined from the observed rate and the quantity of 15NH4+ produced and subsequently assimilated into glutamate and aspartate, was 0.9-1.3 mumol/h per g. This activity is less than 1.1% of the reported activity in vitro measured in rat brain homogenate at a 10 mM concentration of the activator Pi. Inhibition by ammonia (brain level 1.4 mumol/g) alone does not account for the observed low activity in vivo. The result strongly suggests that, in intact brain, PAG activity is maintained at a low level by a suboptimal in situ concentration of Pi and the strong inhibitory effect of glutamate. The observed PAG activity in vivo is lower than the reported in vivo activity of glutamate decarboxylase which converts glutamate into gamma-aminobutyrate (GABA). The result suggests that PAG-catalysed hydrolysis of glutamine is not the sole provider of glutamate used for GABA synthesis. PMID:7826349

  2. NMR studies of isotopically labeled RNA

    SciTech Connect

    Pardi, A.

    1994-12-01

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

  3. Solution NMR of large molecules and assemblies†

    PubMed Central

    Foster, Mark P.; McElroy, Craig A.; Amero, Carlos D.

    2008-01-01

    Solution NMR spectroscopy represents a powerful tool for examining the structure and function of biological macromolecules. The advent of multidimensional (2D–4D) NMR, together with the widespread use of uniform isotopic labeling of proteins and RNA with the NMR-active isotopes, 15N and 13C, opened the door to detailed analyses of macromolecular structure, dynamics and interactions of smaller macromolecules (< ~25 kDa). Over the past 10 years, advances in NMR and isotope labeling methods have expanded the range of NMR-tractable targets by at least an order of magnitude. Here we briefly describe the methodological advances that allow NMR spectroscopy of large macromolecules and their complexes, and provide a perspective on the wide range of applications of NMR to biochemical problems. PMID:17209543

  4. Moving NMR

    NASA Astrophysics Data System (ADS)

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

    2008-12-01

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

  5. Synthesis, spectroscopic characterization and molecular modeling of a tetranuclear platinum(II) complex with thiazolidine-4-carboxylic acid

    NASA Astrophysics Data System (ADS)

    Corbi, Pedro P.; Formiga, André L. B.; Bonk, Fábio A.; Quintão, Frederico A.; Ferraresi, Diego K. D.; Lustri, Wilton R.; Massabni, Antonio C.

    2012-07-01

    The synthesis, spectroscopic characterization and molecular modeling of a novel tetranuclear platinum(II) complex with thiazolidine-4-carboxylic acid (THC) are described. Elemental analysis is consistent with the composition PtCl2C4H7NO2S·H2O. Infrared (IR) spectroscopic results and solid-state 13C and 15N nuclear magnetic resonance (NMR) data indicate coordination of the ligand to Pt(II) through the nitrogen and sulfur atoms. The square planar geometry of the platinum(II) complex is completed by chlorine atoms. Density functional theory (DFT) suggests the formation of a tetrameric cluster as the most probable structure, where each THC molecule bridges between two metal centers. The compound is insoluble in water.

  6. Refining cotton-wick method for 15N plant labelling.

    NASA Astrophysics Data System (ADS)

    Fustec, Joëlle; Mahieu, Stéphanie

    2010-05-01

    The symbiosis Fabaceae/Rhizobiaceae plays a critical role in the nitrogen cycle. It gives the plant the ability to fix high amounts of atmospheric N. A part of this N can be transferred to the soil via rhizodeposition. The contribution of Fabaceae to the soil N pool is difficult to measure, since it is necessary for assessing N benefits for other crops, for soil biological activity, and for reducing water pollution in sustainable agriculture (Fustec, 2009). The aim of this study was to test and improve the reliability of the 15N cotton-wick method for measuring the soil N derived from plant rhizodeposition (Mahieu et al., 2007). The effects of the concentration of the 15N-urea labelling solution and of the feeding frequency (continuous or pulses) on the assessment of nitrogen rhizodeposition were studied in two greenhouse experiments using the field pea (Pisum sativum L.) and the non-nodulating isoline P2. The plant parts and the soil were prepared for 15N:14N measurements for assessing N rhizodeposition (Mahieu et al., 2009). The fraction of plants' belowground nitrogen allocated to rhizodeposition in both Frisson pea and P2 was 20 to more than 50% higher when plants were labelled continuously than when they were labelled using fortnightly pulses. Our results suggested that when 15N root enrichment was high, nitrogen rhizodeposition was underestimated only for plants that were 15N-fed by fortnightly pulses, and not in plants 15N-fed continuously. This phenomenon was especially observed for plants relying on symbiotic N fixation for N acquisition; it may be linked to the concentration of the labelling solution. In conclusion, N rhizodeposition assessment was strongly influenced by the 15N-feeding frequency and the concentration of the labelling solution. The estimation of N rhizodeposition was more reliable when plants were labelled continuously with a dilute solution of 15N urea. Fustec et al. 2009. Agron. Sustain. Dev., DOI 10.1051/agro/2009003, in press. Mahieu

  7. New organic single crystal of (benzylthio)acetic acid: Synthesis, crystal structure, spectroscopic (ATR-FTIR, 1H and 13C NMR) and thermal characterization

    NASA Astrophysics Data System (ADS)

    Sienkiewicz-Gromiuk, Justyna; Tarasiuk, Bogdan; Mazur, Liliana

    2016-04-01

    (Benzylthio)acetic acid (Hbta) was synthesized with 78% yield from benzyl chloride and thiourea as substrates. Well-shaped crystals of Hbta were grown by slow solvent evaporation technique from pure methanol. The compound was investigated by single-crystal X-ray and powder diffraction techniques and was also characterized by other analytical methods, like ATR-FTIR, 1H and 13C NMR and TG/DSC. The acid molecule adopts bent conformation in the solid state. The crystal structure of Hbta is stabilized by numerous intermolecular interactions, including O-H···O, C-H···O, C-H···S and C-H···π contacts. Thermal decomposition of the obtained material takes place above 150 °C.

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

    NASA Astrophysics Data System (ADS)

    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.

  9. Quantum mechanical and spectroscopic (FT-IR, FT-Raman, 1H NMR and UV) investigations of 5-nitro-2-phenylbenzoxazole

    NASA Astrophysics Data System (ADS)

    Bhagyasree, J. B.; Varghese, Hema Tresa; Panicker, C. Yohannan; Samuel, Jadu; Van Alsenoy, Christian; Ertan-Bolelli, Tugba; Yildiz, Ilkay

    2014-04-01

    The optimized molecular structure, vibrational wavenumbers, corresponding vibrational assignments of 5-nitro-2-phenylbenzoxazole have been investigated experimentally and theoretically. The energy and oscillator strength calculated by Time Dependent Density Functional Theory results almost compliments with experimental findings. Gauge-including atomic orbital 1H-NMR chemical shifts calculations were carried out and compared with experimental data. The HOMO and LUMO analysis is used to determine the charge transfer with in the molecule. The stability of the molecule arising from hyper-conjugative interaction and charge delocalization has been analyzed using NBO analysis. molecular electrostatic potential was performed by the DFT method and the infrared intensities and Raman activities are also been reported. Fist hyperpolarizability is calculated in order to find its role in nonlinear optics. Antimicrobial properties indicated that the title compound possessed a broad spectrum activity against the tested Gram-positive, Gram-negative bacteria.

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

    SciTech Connect

    Lukevits, E.; Erchak, N.P.; Castro, I.; Popelis, Yu.Yu.; Kozyrev, A.K.; Anoshkin, V.I.; Kovalev, I.F.

    1986-03-10

    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.

  11. Spectroscopic (FT-IR, FT-Raman, FT-NMR and UV-Vis) investigation on benzil dioxime using quantum computational methods

    NASA Astrophysics Data System (ADS)

    Bakkiyaraj, D.; Periandy, S.; Xavier, S.

    2016-03-01

    The spectral analysis of benzil dioxime is carried out using the FTIR, FT Raman, FT NMR and UV-Vis spectra of the compound with the help of quantum computations by density functional theories. The FT-IR (4000 - 400 cm-1) and FT-Raman (4000-100 cm-1) spectra are recorded in solid phase, the 1H and 13C NMR spectra in DMSO phase and the UV spectrum (200-400 nm) in ethanol phase. The different conformers of the compound and their minimum energies are studied by potential energy surface scan, using semi-empirical method PM6. The computed wavenumbers from different methods are scaled so as to agree with the experimental values and the scaling factors are reported. All the fundamental modes have been assigned based on the potential energy distribution (PED) values and the structure the molecule is analyzed interms of parameters like bond length, bond angle and dihedral angles predicted byB3LYP and CAM-B3LYP methods with cc-pVDZ basis sets. The values of dipole moment (μ), polarizability (α) and hyperpolarizability (β) of the molecule are reported, using which the non -linear optical property of the molecule is discussed. The HOMO-LUMO mappings are reported which reveals the different charge transfer possibilities within the molecule. The isotropic chemical shifts predicted for 1H and 13C atoms using gauge invariant atomic orbital (GIAO) theory show good agreement with experimental shifts and the same is discussed in comparison with atomic charges, predicted by Mullikan and APT charge analysis. NBO analysis is carried out to picture the probable electronic transitions in the molecule.

  12. EPR and 1H-NMR spectroscopic studies on the paramagnetic iron at the active site of phenylalanine hydroxylase and its interaction with substrates and inhibitors.

    PubMed

    Martínez, A; Andersson, K K; Haavik, J; Flatmark, T

    1991-06-15

    The paramagnetic iron at the active site of highly purified, catalytically active phenylalanine hydroxylase was studied by EPR at 3.6 K and one-dimensional 1H-NMR spectroscopy at 293 K. The EPR-detectable iron of the bovine enzyme was found to be present as a high-spin form (S = 5/2) in different ligand field symmetries depending on medium conditions (buffer ions) and the presence of ligands known to bind at the active site. At 3.6 K and in phosphate buffer, the paramagnetic iron is coordinated in an environment of rhombic symmetry (g = 4.3), whereas Tris buffer favours an environment of axial ligand field symmetry (g = 6.7, 5.3 and 2.0). The latter axial type of signals resembles those observed at g = 7.0, 5.2 and 1.9 for the enzyme in phosphate buffer when L-noradrenaline is added as an active-site ligand (inhibitor). The same proportion of iron that coordinates to L-noradrenaline seems to be reduced by the pterin cofactor and participate in catalysis. Experimental evidence is presented that Tris inhibits the enzyme by interacting with the enzyme-bound ferric iron and decreases its rate of reduction by the tetrahydropterin cofactor. Preincubation with dithiothreitol also inhibits the enzyme activity and prevents the reduction of its catalytically active ferric iron by pterin cofactors as well as binding of catecholamines to the enzyme. 1H-NMR spectroscopy revealed that the substrate (L-phenylalanine) and L-noradrenaline bind close to the paramagnetic iron, and that the catecholamine displaces the substrate from its binding at the active site. The results support our recently proposed model for the cooperative binding of inhibitor and substrate at the active site [Martínez, A. et al. (1990) Eur. J. Biochem. 193, 211-219]. PMID:1646718

  13. Molecular structure, spectroscopic characterization (FT-IR, FT-Raman, UV and NMR), HOMO and LUMO analysis of 3-ethynylthiophene with DFT quantum chemical calculations.

    PubMed

    Karabacak, Mehmet; Bilgili, Sibel; Mavis, Tugba; Eskici, Mustafa; Atac, Ahmet

    2013-11-01

    In this work, FT-IR, FT-Raman, UV and NMR spectra of 3-ethynylthiophene (3-ETP, C6H4S) were carried out by using density functional theory DFT/B3LYP method with the 6-311++G(d,p), 6-311+G(d,p), 6-311G(d,p), 6-31++G(d,p), 6-31+G(d,p), 6-31G(d,p) basis sets. FT-IR and FT-Raman spectra were recorded in the regions of 3500-400cm(-1) and 3500-50cm(-1), respectively. The geometrical parameters, energies and wavenumbers were obtained and the complete assignments of fundamental vibrations were performed on the basis of the total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method and PQS program. The (1)H, (13)C and HMQC ((1)H-(13)C correlation) NMR spectra in chloroform (CDCl3) were recorded and calculated. The UV spectrum of investigated compound were recorded in the region of 200-400nm in ethanol solution. The electronic properties, such as excitation energies, absorption wavelengths, HOMO and LUMO energies were performed by DFT/B3LYP approach and the results were compared with experimental observations. The thermodynamic properties such zero-point vibrational energy, thermal energy, specific heat capacity, rotational constants, entropy, and dipole moment of the studied compound were calculated. As a result, the calculated results were compared with the observed data and found to be in good agreement. PMID:23886506

  14. Spectroscopic (FT-IR, FT-Raman, UV, NMR, NBO, NLO) investigation and molecular docking study of (R)-2-Methylamino-1-Phenylethanol (Halostachine)

    NASA Astrophysics Data System (ADS)

    Subashini, K.; Govindarajan, R.; Surendran, R.; Mukund, K.; Periandy, S.

    2016-12-01

    FT-IR (4000-400 cm-1) and FT-Raman (4000-100 cm-1) spectra of (R)-2-Methylamino-1-Phenylethanol have been recorded in solid phase, 1H and 13C NMR in deuterated chloroform (CDCl3) phase and UV spectrum (200-400 nm) in solid phase and in ethanol solution. The different conformers of the compound and their minimum energies were studied by potential energy surface scan, using semi-empirical method PM6. The computed wavenumbers obtained from B3LYP and B3PW91 functionals along with 6-311++G (d, p) basis sets were scaled so as to agree with the experimental values and the scaling factors have been reported. All the fundamental modes have been assigned based on the potential energy distribution (PED) values and the structure of the molecule was analyzed in parameters like bond length, bond angle and dihedral angles through B3LYP and B3PW91 functionals along with 6-311++G(d,p) basis set. The values of dipole moment (μ), polarizability (α) and hyper polarizability (β) of the molecule were calculated using which, the non-linear optical property of the molecule has been discussed. The observed HOMO-LUMO mappings reveals the different charge transfer possibilities within the molecule. Natural Bond Orbital analysis was computed and possible transitions were correlated with the electronic transitions. Mulliken charges, electrostatic potential charges and natural charges are also predicted. The theoretical 1H and 13C NMR chemical shifts were computed using B3LYP functionals using 6-311++G (2d, p) basis sets. The temperature dependence of the thermodynamic properties; heat capacity, entropy and enthalpy for the title compound were also determined by B3LYP functionals with 6-311++G (d, p) basis set. Molecular docking study shows that the title compound might exhibit inhibitory activity against Bacillus anthracis (3V5O).

  15. Molecular structure, spectroscopic characterization (FT-IR, FT-Raman, UV and NMR), HOMO and LUMO analysis of 3-ethynylthiophene with DFT quantum chemical calculations

    NASA Astrophysics Data System (ADS)

    Karabacak, Mehmet; Bilgili, Sibel; Mavis, Tugba; Eskici, Mustafa; Atac, Ahmet

    2013-11-01

    In this work, FT-IR, FT-Raman, UV and NMR spectra of 3-ethynylthiophene (3-ETP, C6H4S) were carried out by using density functional theory DFT/B3LYP method with the 6-311++G(d,p), 6-311+G(d,p), 6-311G(d,p), 6-31++G(d,p), 6-31+G(d,p), 6-31G(d,p) basis sets. FT-IR and FT-Raman spectra were recorded in the regions of 3500-400 cm-1 and 3500-50 cm-1, respectively. The geometrical parameters, energies and wavenumbers were obtained and the complete assignments of fundamental vibrations were performed on the basis of the total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method and PQS program. The 1H, 13C and HMQC (1H-13C correlation) NMR spectra in chloroform (CDCl3) were recorded and calculated. The UV spectrum of investigated compound were recorded in the region of 200-400 nm in ethanol solution. The electronic properties, such as excitation energies, absorption wavelengths, HOMO and LUMO energies were performed by DFT/B3LYP approach and the results were compared with experimental observations. The thermodynamic properties such zero-point vibrational energy, thermal energy, specific heat capacity, rotational constants, entropy, and dipole moment of the studied compound were calculated. As a result, the calculated results were compared with the observed data and found to be in good agreement.

  16. Electronic [UV-Visible] and vibrational [FT-IR, FT-Raman] investigation and NMR-mass spectroscopic analysis of terephthalic acid using quantum Gaussian calculations

    NASA Astrophysics Data System (ADS)

    Karthikeyan, N.; Joseph Prince, J.; Ramalingam, S.; Periandy, S.

    2015-03-01

    In this research work, the vibrational IR, polarization Raman, NMR and mass spectra of terephthalic acid (TA) were recorded. The observed fundamental peaks (IR, Raman) were assigned according to their distinctiveness region. The hybrid computational calculations were carried out for calculating geometrical and vibrational parameters by DFT (B3LYP and B3PW91) methods with 6-31++G(d,p) and 6-311++G(d,p) basis sets and the corresponding results were tabulated. The molecular mass spectral data related to base molecule and substitutional group of the compound was analyzed. The modification of the chemical property by the reaction mechanism of the injection of dicarboxylic group in the base molecule was investigated. The 13C and 1H NMR spectra were simulated by using the gauge independent atomic orbital (GIAO) method and the absolute chemical shifts related to TMS were compared with experimental spectra. The study on the electronic and optical properties; absorption wavelengths, excitation energy, dipole moment and frontier molecular orbital energies, were performed by hybrid Gaussian calculation methods. The orbital energies of different levels of HOMO and LUMO were calculated and the molecular orbital lobe overlapping showed the inter charge transformation between the base molecule and ligand group. From the frontier molecular orbitals (FMO), the possibility of electrophilic and nucleophilic hit also analyzed. The NLO activity of the title compound related to Polarizability and hyperpolarizability were also discussed. The present molecule was fragmented with respect to atomic mass and the mass variation depends on the substitutions have also been studied.

  17. Catalytic roles of βLys87 in tryptophan synthase: (15)N solid state NMR studies.

    PubMed

    Caulkins, Bethany G; Yang, Chen; Hilario, Eduardo; Fan, Li; Dunn, Michael F; Mueller, Leonard J

    2015-09-01

    The proposed mechanism for tryptophan synthase shows βLys87 playing multiple catalytic roles: it bonds to the PLP cofactor, activates C4' for nucleophilic attack via a protonated Schiff base nitrogen, and abstracts and returns protons to PLP-bound substrates (i.e. acid-base catalysis). ε-¹⁵N-lysine TS was prepared to access the protonation state of βLys87 using ¹⁵N solid-state nuclear magnetic resonance (SSNMR) spectroscopy for three quasi-stable intermediates along the reaction pathway. These experiments establish that the protonation state of the ε-amino group switches between protonated and neutral states as the β-site undergoes conversion from one intermediate to the next during catalysis, corresponding to mechanistic steps where this lysine residue has been anticipated to play alternating acid and base catalytic roles that help steer reaction specificity in tryptophan synthase catalysis. This article is part of a Special Issue entitled: Cofactor-dependent proteins: evolution, chemical diversity and bio-applications. Guest Editors: Andrea Mozzarelli and Loredano Pollegioni. PMID:25688830

  18. Modeling (15)N NMR chemical shift changes in protein backbone with pressure.

    PubMed

    La Penna, Giovanni; Mori, Yoshiharu; Kitahara, Ryo; Akasaka, Kazuyuki; Okamoto, Yuko

    2016-08-28

    Nitrogen chemical shift is a useful parameter for determining the backbone three-dimensional structure of proteins. Empirical models for fast calculation of N chemical shift are improving their reliability, but there are subtle effects that cannot be easily interpreted. Among these, the effects of slight changes in hydrogen bonds, both intramolecular and with water molecules in the solvent, are particularly difficult to predict. On the other hand, these hydrogen bonds are sensitive to changes in protein environment. In this work, the change of N chemical shift with pressure for backbone segments in the protein ubiquitin is correlated with the change in the population of hydrogen bonds involving the backbone amide group. The different extent of interaction of protein backbone with the water molecules in the solvent is put in evidence. PMID:27586953

  19. **1**5N-NMR INVESTIGATION OF HYDROXYLAMINE DERIVATIZED HUMIC SUBSTANCES.

    USGS Publications Warehouse

    Thorn, Kevin A.; Arterburn, Jeffrey B.; Mikita, Michael A.

    1986-01-01

    Humic substances are the most abundant naturally occurring refactory organic compounds in soils and water. They have a broad range of physical, chemical and physiological properties. In soils, humic substances contribute to the cation exchange capacity, help maintain the physical structure, and play a role in plant growth and nutrition. In aquatic systems, humic substances serve to regulate the levels of inorganic constituents, yield trihalomethanes upon chlorination, and transport or concentrate organic and inorganic pollutants. The oxygen containing functional groups of humic and fulvic acids are believed to play a key role in the chemical properties of humic substances. This study was undertaken to gain additional information on the specific types of oxygen functionalities in humic substances. Since the analysis of hydroxyl moieties had been earlier established, we focused our attention on the analysis of ketone and aldehyde functional groups in humic substances.

  20. Chimeric Avidin – NMR Structure and Dynamics of a 56 kDa Homotetrameric Thermostable Protein

    PubMed Central

    Tossavainen, Helena; Kukkurainen, Sampo; Määttä, Juha A. E.; Kähkönen, Niklas; Pihlajamaa, Tero; Hytönen, Vesa P.; Kulomaa, Markku S.; Permi, Perttu

    2014-01-01

    Chimeric avidin (ChiAVD) is a product of rational protein engineering remarkably resistant to heat and harsh conditions. In quest of the fundamentals behind factors affecting stability we have elucidated the solution NMR spectroscopic structure of the biotin–bound form of ChiAVD and characterized the protein dynamics through 15N relaxation and hydrogen/deuterium (H/D) exchange of this and the biotin–free form. To surmount the challenges arising from the very large size of the protein for NMR spectroscopy, we took advantage of its high thermostability. Conventional triple resonance experiments for fully protonated proteins combined with methyl–detection optimized experiments acquired at 58°C were adequate for the structure determination of this 56 kDa protein. The model–free parameters derived from the 15N relaxation data reveal a remarkably rigid protein at 58°C in both the biotin–bound and the free forms. The H/D exchange experiments indicate a notable increase in hydrogen protection upon biotin binding. PMID:24959850

  1. Understanding the directed ortho lithiation of (R)-Ph₂P(=NCO₂Me)NHCH(Me)Ph. NMR spectroscopic and computational study of the structure of the N-lithiated species.

    PubMed

    Casimiro, M; García-López, J; Iglesias, M J; López-Ortiz, F

    2014-10-14

    A multinuclear magnetic resonance ((1)H, (7)Li, (13)C, (15)N, (31)P) and DFT computational study at the M06-2X(SMD,THF)/6-311+G(d,p)//B3LYP/6-31G(d) level of the structure of a N-lithiated phosphinimidic amide (R)-Ph2P(=NCO2Me)NHCH(Me)Ph 13 has been performed. In THF solution it exists as an equilibrium mixture of monomers and dimers. The monomers consist of a six-membered ring formed by coordination of the lithium atom with the deprotonated nitrogen and the oxygen atom of the carbonyl group. This coordination mode is in contrast to the standard N,N-chelation observed in N-lithiated N,N'-bis(trimethylsilyl)phosphinimidic amides. The calculations showed that the metallacycle adopts a twist-boat conformation and that the lithium atom is in a tetrahedral environment involving O,N-chelation by the ligand and coordination to two/one THF molecules in the monomer/dimer. Dimerization takes place through O-Li bridges. For all species two series of isomers have been identified, which originated by restricted rotation of the methoxy group and ring inversion. The twist-boat conformational interconversion seems to be operating for explaining the pattern of signals observed in the (7)Li and (31)P NMR spectra. The structure found for the most stable dimer is analogous to the molecular structure reported for a related C(α)-lithiated phosphazene 20. The structural study revealed that the chiral side-arm of the N-lithiated species is oriented to the outer face of the pro-S P-phenyl ring, which shows one ortho-proton very close to the nitrogen atom of the carbamate moiety. In this conformation, proton abstraction by a base is highly favoured, in agreement with the experimental results. PMID:24849316

  2. NMR and EPR spectroscopic and structural studies of low-spin, (d(xz),d(y)(z))(4)(d(x)(y))(1) ground state Fe(III) bis-tert-butylisocyanide complexes of dodecasubstituted porphyrins.

    PubMed

    Yatsunyk, Liliya A; Walker, F Ann

    2004-07-12

    The bis-(1,1-dimethylethylisocyanide) (tert-butylisocyanide) complexes of three iron porphyrinates (2,3,7,8,12,13,17,18-octaethyl-5,10,15,20-tetraphenylporphyrin, OETPP; 2,3,7,8,12,13,17,18-octamethyl-5,10,15,20-tetraphenylporphyrin, OMTPP; and 2,3,7,8,12,13,17,18-tetra-beta,beta'-tetramethylene-5,10,15,20-tetraphenylporphyrin, TC(6)TPP) have been prepared and studied by EPR and (1)H NMR spectroscopy. From EPR and NMR spectroscopic results it has been found that the ground states of the bis-(t-BuNC) complexes of OETPP, OMTPP, and TC(6)TPP are represented mainly (99.1-99.4%) as (d(xz,)d(yz))(4)(d(xy))(1) electron configurations, with an excited state lying 700 cm(-)(1) to higher energy for the OMTPP complex, and probably at lower and higher energies, respectively, for the OETPP and TC(6)TPP complexes. In the (1)H NMR spectra the (d(xz,)d(yz))(4)(d(xy))(1) electron configurations of all three complexes are indicated by the large and positive meso-phenyl-H shift differences, delta(m)-delta(o) and delta(m)-delta(p), and close to the diamagnetic shifts of groups (CH(3) or CH(2)) directly attached to the beta-carbons. However, in comparison to meso-only substituted porphyrinates such as [FeTPP(t-BuNC)(2)]ClO(4), the meso-phenyl shift differences are much smaller, especially for the OETPP complex. 2D NOESY spectra show that the flexibility of the porphyrin core decreases with increasing nonplanar distortion in the order TC(6)TPP > OMTPP > OETPP and in the same order the stability of the binding to t-BuNC ligands decreases. In addition, the structures of two crystalline forms of [FeOMTPP(t-BuNC)(2)]ClO(4) have been determined by X-ray crystallography. Both structures showed purely saddled porphyrin cores and somewhat off-axis binding of the isocyanide ligands. To our knowledge, this is the first example of a porphyrin complex with a purely saddled conformation that adopts the (d(xz,)d(yz))(4)(d(xy))(1) ground state. All structurally-characterized complexes of this electron

  3. The contamination of commercial 15N2 gas stocks with 15N-labeled nitrate and ammonium and consequences for nitrogen fixation measurements.

    PubMed

    Dabundo, Richard; Lehmann, Moritz F; Treibergs, Lija; Tobias, Craig R; Altabet, Mark A; Moisander, Pia H; Granger, Julie

    2014-01-01

    We report on the contamination of commercial 15-nitrogen (15N) N2 gas stocks with 15N-enriched ammonium, nitrate and/or nitrite, and nitrous oxide. 15N2 gas is used to estimate N2 fixation rates from incubations of environmental samples by monitoring the incorporation of isotopically labeled 15N2 into organic matter. However, the microbial assimilation of bioavailable 15N-labeled N2 gas contaminants, nitrate, nitrite, and ammonium, is liable to lead to the inflation or false detection of N2 fixation rates. 15N2 gas procured from three major suppliers was analyzed for the presence of these 15N-contaminants. Substantial concentrations of 15N-contaminants were detected in four Sigma-Aldrich 15N2 lecture bottles from two discrete batch syntheses. Per mole of 15N2 gas, 34 to 1900 µmoles of 15N-ammonium, 1.8 to 420 µmoles of 15N-nitrate/nitrite, and ≥21 µmoles of 15N-nitrous oxide were detected. One 15N2 lecture bottle from Campro Scientific contained ≥11 µmoles of 15N-nitrous oxide per mole of 15N2 gas, and no detected 15N-nitrate/nitrite at the given experimental 15N2 tracer dilutions. Two Cambridge Isotopes lecture bottles from discrete batch syntheses contained ≥0.81 µmoles 15N-nitrous oxide per mole 15N2, and trace concentrations of 15N-ammonium and 15N-nitrate/nitrite. 15N2 gas equilibrated cultures of the green algae Dunaliella tertiolecta confirmed that the 15N-contaminants are assimilable. A finite-differencing model parameterized using oceanic field conditions typical of N2 fixation assays suggests that the degree of detected 15N-ammonium contamination could yield inferred N2 fixation rates ranging from undetectable, <0.01 nmoles N L(-1) d(-1), to 530 nmoles N L(-1) d(-1), contingent on experimental conditions. These rates are comparable to, or greater than, N2 fixation rates commonly detected in field assays. These results indicate that past reports of N2 fixation should be interpreted with caution, and demonstrate that the purity of commercial 15N2

  4. Quantum mechanical, spectroscopic studies (FT-IR, FT-Raman, NMR, UV) and normal coordinates analysis on 3-([2-(diaminomethyleneamino) thiazol-4-yl] methylthio)-N'-sulfamoylpropanimidamide

    NASA Astrophysics Data System (ADS)

    Muthu, S.; Uma Maheswari, J.; Sundius, Tom

    2013-05-01

    Famotidine (3-([2-(diaminomethyleneamino) thiazol-4-yl] methylthio)-N'-sulfamoylpropanimidamide) is a histamine H2-receptor antagonist that inhibits stomach acid production, and it is commonly used in the treatment of peptic ulcer disease (PUD) and gastroesophageal reflux disease (GERD/GORD). Quantum chemical calculations of the equilibrium geometry of famotidine in the ground state were carried out using density functional theory (DFT/B3LYP) with the 6-311G(d,p) basis set. In addition, harmonic vibrational frequencies, infrared intensities and Raman activities were calculated at the same level of theory. A detailed interpretation of the infrared and Raman spectrum of the drug is also reported. Theoretical simulations of the FT-IR, and FT-Raman spectra of the title compound have been calculated. Good correlations between the experimental 1H and 13C NMR chemical shifts and calculated GIAO shielding tensors were found. The results of the energy and oscillator strength calculations by time-dependent density functional theory (TD-DFT) supplement the experimental findings. Total and partial density of state (TDOS and PDOS) and also overlap population density of state (COOP or OPDOS) diagrams analysis were presented. The dipole moment, linear polarizability and first order hyperpolarizability values were also computed. The linear polarizability and first order hyperpolarizabilities of the studied molecule indicate that the compound is a good candidate for nonlinear optical materials.

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

    NASA Astrophysics Data System (ADS)

    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.

  6. Oligodeoxyribonucleoside methylphosphonates. NMR and UV spectroscopic studies of Rp-Rp and Sp-Sp methylphosphonate (Me) modified duplexes of (d[GGAATTCC])2.

    PubMed Central

    Bower, M; Summers, M F; Powell, C; Shinozuka, K; Regan, J B; Zon, G; Wilson, W D

    1987-01-01

    1H NMR chemical shift assignments for the title compounds were made for most of the 1H signals using two-dimensional nuclear Overhauser effect (2D-NOE) data, which were also used to establish the absolute configuration at the modified phosphorus. The chemical shifts were similar to those reported [Broido, M.S., et al. (1985) Eur. J. Biochem. 150, 117-128] for the unmodified, parent, B-type duplex [d(GGAATTCC)]2. Differences in chemical shifts were mostly localized to the nucleotides on the 5'- and 3'-sides of the modified phosphorus. The Rp-Rp isomers exhibited UV-derived Tm values similar to that of the parent duplex. On the other hand, the Sp-Sp isomers generally exhibited lower Tm values which correlated with P-CH3--H3' (n-1 nucleotide) cross peak intensities and 31P spectral parameters. The combined data argue for increased steric interactions with the Sp-P-Me methyl group as the modification position is moved toward the center of the oligomer. All of the Tm results can be explained in terms of three factors which result from replacement of a phosphate by a methylphosphonate group: reduction of oligomer charge; electronic and other substituent effects; steric interactions. PMID:3601658

  7. Vibrational [FT-IR, FT-Raman] analysis, NMR and mass - Spectroscopic investigation on 3,6-Dimethylphenanthrene using computational calculation

    NASA Astrophysics Data System (ADS)

    Manzoor Ali, M.; George, Gene; Ramalingam, S.; Periandy, S.; Gokulakrishnan, V.

    2015-11-01

    In this research work, in order to the vibrational, physical and chemical properties, a thorough investigation has been made by recording FT-IR, FT-Raman, Mass and 13C and 1H NMR spectra of pharmaceutically important compound; 3,6-Dimethylphenanthrene. The altered geometrical parameters of Phenanthrene due to the addition of methyl groups have been calculated using HF and DFT (B3LYP and B3PW91) methods with 6-31++G(d,p) and 6-311++G(d,p) basis sets and the discussion are made on their corresponding results. The alternation of the vibrational pattern of the molecule due to the injection of the substitutions; CH3 is investigated. The keen observation is made over the excitations between the electronic energy levels of the molecule which lead to the study of electronic properties. The alternation of distribution of Mulliken charges after the formation of present molecule has been correlated with the vibrational pattern of the molecular bonds. The charge transformation over the frontier molecular orbitals between the ligand and rings has been studied. The cause of the linear and non linear optical activity of the molecule is interpreted in detail from the average Polarizability first order diagonal hyperpolarizability calculations. The variation of thermodynamic properties; heat capacity, entropy, and enthalpy of the present compound at different temperatures are calculated using NIST thermodynamical function program and interpreted.

  8. Combination of spectroscopic methods: in situ NMR and UV/Vis measurements to understand the formation of group 4 metallacyclopentanes from the corresponding metallacyclopropenes.

    PubMed

    Beweries, Torsten; Fischer, Christian; Peitz, Stephan; Burlakov, Vladimir V; Arndt, Perdita; Baumann, Wolfgang; Spannenberg, Anke; Heller, Detlef; Rosenthal, Uwe

    2009-04-01

    By reaction of the dichloride rac-(ebthi)HfCl(2) [ebthi = 1,2-ethylene-1,1'-bis(eta(5)-tetrahydroindenyl)] with lithium in the presence of bis(trimethylsilyl)acetylene, the hafnacyclopropene rac-(ebthi)Hf(eta(2)-Me(3)SiC(2)SiMe(3)) (1-Hf) was obtained. The reaction of the blue-green complex 1-Hf with an excess of ethylene at room temperature leads by insertion of the olefin to the yellow-green hafnacyclopentene 2-Hf which is only stable in solution and eliminates the alkyne at 100 degrees C under ethylene to form the corresponding yellow hafnacyclopentane 3-Hf, which was characterized by X-ray crystal structure analysis. The reaction of 1-Hf to give stepwise via 2-Hf the complex 3-Hf was investigated in detail and compared to the formation and stability of the corresponding zirconacyclopropene 1-Zr, zirconacyclopentene 2-Zr, and zirconacyclopentane 3-Zr. Moreover, the reaction of the titanocene alkyne complex 1-Ti with ethylene was studied. For investigating the reaction behavior of the alkyne complexes 1-M, NMR spectroscopy was used and the results were compared with UV/vis spectroscopy, suggesting the existence of a bis-pi-complex prior to the formation of the hafnacyclopentene 2-Hf. PMID:19275148

  9. 8-Amino-BODIPYs: structural variation, solvent-dependent emission, and VT NMR spectroscopic properties of 8-R2N-BODIPY.

    PubMed

    Roacho, Robinson I; Metta-Magaña, Alejandro; Portillo, Michelle M; Peña-Cabrera, Eduardo; Pannell, Keith H

    2013-05-01

    New 8-NR2-BODIPYs, R2 = H(i)Pr (3a), H(i)Bu (3b), and Et2 (4), are reported. Restricted rotation about the C8-N bond in such molecules has been observed for the first time (3a and 3b) and evaluated using VT NMR. The fluorophores 3a and 3b are blue emitters, and the efficiency of the emission is closely related to the polarity of the solvent, e.g., hexane > toluene > DCM > THF > MeOH > H2O, an effect also noted by emission variation in alcohol solvents H(CH2)nOH, n = 1-6. In mixed-solvent systems, addition of 10-15% of the more polar solvent results in transformation of the emission properties to those of the bulk polar solvent. Compound 4 has zero emission in all solvents. The crystal structures of 3a, 3b, and 4 are reported, along with that of the parent 8-NH2-BODIPY (2). Compounds 2, 3a, and 3b exhibit trigonal planar N atoms which are coplanar with the BODIPY core; 4 exhibits a very significant distortion that breaks the planarity of the extended BODIPY π system due to the steric impact of the two ethyl groups, an observation that explains the lack of emission for 4. PMID:23544482

  10. Hyperpolarized 89Y NMR spectroscopic detection of yttrium ion and DOTA macrocyclic ligand complexation: pH dependence and Y-DOTA intermediates

    NASA Astrophysics Data System (ADS)

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

    Dissolution dynamic nuclear polarization (DNP) is a rapidly emerging physics technique used to enhance the signal strength in nuclear magnetic resonance (NMR) and imaging (MRI) experiments for nuclear spins such as yttrium-89 by >10,000-fold. One of the most common and stable MRI contrast agents used in the clinic is Gd-DOTA. In this work, we have investigated the binding of the yttrium and DOTA ligand as a model for complexation of Gd ion and DOTA ligand. The macrocyclic ligand DOTA is special because its complexation with lanthanide ions such as Gd3+ or Y3+ is highly pH dependent. Using this physics technology, we have tracked the complexation kinetics of hyperpolarized Y-triflate and DOTA ligand in real-time and detected the Y-DOTA intermediates. Different kinds of buffers were used (lactate, acetate, citrate, oxalate) and the pseudo-first order complexation kinetic calculations will be discussed. The authors would like to acknowledge the support by US Dept of Defense Award No. W81XWH-14-1-0048 and Robert A. Welch Foundation Grant No. AT-1877.

  11. Spectroscopic (FT-IR, FT-Raman, 1H- and 13C-NMR), theoretical and microbiological study of trans o-coumaric acid and alkali metal o-coumarates.

    PubMed

    Kowczyk-Sadowy, Małgorzata; Świsłocka, Renata; Lewandowska, Hanna; Piekut, Jolanta; Lewandowski, Włodzimierz

    2015-01-01

    This work is a continuation of research on a correlation between the molecular structure and electronic charge distribution of phenolic compounds and their biological activity. The influence of lithium, sodium, potassium, rubidium and cesium cations on the electronic system of trans o-coumaric (2-hydroxy-cinnamic) acid was studied. We investigated the relationship between the molecular structure of the tested compounds and their antimicrobial activity. Complementary molecular spectroscopic techniques such as infrared (FT-IR), Raman (FT-Raman), ultraviolet-visible (UV-VIS) and nuclear magnetic resonance (1H- and 13C-NMR) were applied. Structures of the molecules were optimized and their structural characteristics were calculated by the density functional theory (DFT) using the B3LYP method with 6-311++G** as a basis set. Geometric and magnetic aromaticity indices, atomic charges, dipole moments and energies were also calculated. Theoretical parameters were compared to the experimental characteristics of investigated compounds. Correlations between certain vibrational bands and some metal parameters, such as electronegativity, ionization energy, atomic and ionic radius, were found. The microbial activity of studied compounds was tested against Escherichia coli, Bacillus subtilis, Pseudomonas aeruginosa, Staphylococcus aureus, Proteus vulgaris and Candida albicans. PMID:25689641

  12. Stepwise enrichment of 15N along food chains: Further evidence and the relation between δ 15N and animal age

    NASA Astrophysics Data System (ADS)

    Minagawa, Masao; Wada, Eitaro

    1984-05-01

    The isotopic composition of nitrogen was measured in marine and fresh-water animals from the East China Sea, The Bering Sea, Lake Ashinoko and Usujiri intertidal zone. Primary producers, showed average δ15Nversus atmospheric nitrogen of +5.0%. (+3.4 to +7.5) in the Bering Sea and Lake Ashinoko, and +6.8%. (+6.0 to +7.6) in Usujiri intertidal zone. Blue green algae from the East China Sea show an average -0.55%. (-0.8 to +1.2). All consumers, Zooplankton, fish and bird exhibited Stepwise enrichment of 15N with increasing trophic level. The 15N enrichment at a single feeding process ranged from +1.3 to +5.3 averaging +3.4 ± 1.1%.. This isotopic fractionation seems to be independent of habitat. The effect of age in animals was obtained by analyzing two marine mussels. The soft tissue nitrogen showed +2.0%. enrichment relative to that of primary producers, and the magnitude was almost constant with shell ages ranging from 0 to 8 years. A similar 15N enrichment occurs in all Molluscs, Crustaceans, Insecta, Amphibia, Fish, Ave and Mammal species regardless of the difference in the form of excreted nitrogen and in laboratory cultured fish, brine shrimp and mice (+2.9 to +4.9%.). The excreted ammonia from guppy was sufficiently light to balance the concentration of 15N to animal body.

  13. Spectroscopic (FT-IR, FT-Raman, UV and NMR) investigation and NLO, HOMO-LUMO, NBO analysis of organic 2,4,5-trichloroaniline

    NASA Astrophysics Data System (ADS)

    Govindarajan, M.; Karabacak, M.; Periandy, S.; Tanuja, D.

    2012-11-01

    In this work, the experimental and theoretical study on the molecular structure and vibrational spectra of 2,4,5-trichloroaniline (C6H4NCl3, abbreviated as 2,4,5-TClA) were studied. The FT-IR and FT-Raman spectra were recorded. The molecular geometry and vibrational frequencies in the ground state were calculated by using the Hartree-Fock (HF) and density functional theory (DFT) methods (B3LYP) with 6-311++G(d,p) basis set. Comparison of the observed fundamental vibrational frequencies of 2,4,5-TClA with calculated results by HF and DFT indicates that B3LYP is superior to HF method for molecular vibrational problems. The difference between the observed and scaled wavenumber values of most of the fundamentals is very small. The theoretically predicted FT-IR and FT-Raman spectra of the title molecule have been constructed. A study on the electronic properties, such as HOMO and LUMO energies, were performed by time-dependent DFT (TD-DFT) approach. Besides, molecular electrostatic potential (MEP) and thermodynamic properties were performed. The electric dipole moment (μ) and the first hyperpolarizability (β) values of the investigated molecule were computed using ab initio quantum mechanical calculations. The calculated results also show that the 2,4,5-TClA molecule may have microscopic nonlinear optical (NLO) behavior with non-zero values. Mulliken atomic charges of 2,4,5-TClA was calculated and compared with aniline and chlorobenzene molecules. The 13C nuclear magnetic resonance (NMR) chemical shifts of the molecule were calculated by the gauge independent atomic orbital (GIAO) method and compared with experimental results.

  14. Spectroscopic (FT-IR, FT-Raman, UV and NMR) investigation and NLO, HOMO-LUMO, NBO analysis of organic 2,4,5-trichloroaniline.

    PubMed

    Govindarajan, M; Karabacak, M; Periandy, S; Tanuja, D

    2012-11-01

    In this work, the experimental and theoretical study on the molecular structure and vibrational spectra of 2,4,5-trichloroaniline (C(6)H(4)NCl(3), abbreviated as 2,4,5-TClA) were studied. The FT-IR and FT-Raman spectra were recorded. The molecular geometry and vibrational frequencies in the ground state were calculated by using the Hartree-Fock (HF) and density functional theory (DFT) methods (B3LYP) with 6-311++G(d,p) basis set. Comparison of the observed fundamental vibrational frequencies of 2,4,5-TClA with calculated results by HF and DFT indicates that B3LYP is superior to HF method for molecular vibrational problems. The difference between the observed and scaled wavenumber values of most of the fundamentals is very small. The theoretically predicted FT-IR and FT-Raman spectra of the title molecule have been constructed. A study on the electronic properties, such as HOMO and LUMO energies, were performed by time-dependent DFT (TD-DFT) approach. Besides, molecular electrostatic potential (MEP) and thermodynamic properties were performed. The electric dipole moment (μ) and the first hyperpolarizability (β) values of the investigated molecule were computed using ab initio quantum mechanical calculations. The calculated results also show that the 2,4,5-TClA molecule may have microscopic nonlinear optical (NLO) behavior with non-zero values. Mulliken atomic charges of 2,4,5-TClA was calculated and compared with aniline and chlorobenzene molecules. The (13)C nuclear magnetic resonance (NMR) chemical shifts of the molecule were calculated by the gauge independent atomic orbital (GIAO) method and compared with experimental results. PMID:22765942

  15. Ba3Pt4Al4-Structure, Properties, and Theoretical and NMR Spectroscopic Investigations of a Complex Platinide Featuring Heterocubane [Pt4Al4] Units.

    PubMed

    Stegemann, Frank; Benndorf, Christopher; Bartsch, Timo; Touzani, Rachid St; Bartsch, Manfred; Zacharias, Helmut; Fokwa, Boniface P T; Eckert, Hellmut; Janka, Oliver

    2015-11-16

    Ba3Pt4Al4 was prepared from the elements in niobium ampules and crystallizes in an orthorhombic structure, space group Cmcm (oP44, a = 1073.07(3), b = 812.30(3), c = 1182.69(3) pm) isopointal to the Zintl phase A2Zn5As4 (A = K, Rb). The structure features strands of distorted [Pt4Al4] heterocubane-like units connected by condensation over Pt/Al edges. These are arranged in a hexagonal rod packing by further condensation over Pt and Al atoms with the barium atoms located inside cavities of the [Pt4Al4](δ-) framework. Structural relaxation confirmed the electronic stability of the new phase, while band structure calculations indicate metallic behavior. Crystal orbital Hamilton bonding analysis coupled with Bader effective charge analysis suggest a polar intermetallic phase in which strong Al-Pt covalent bonds are present, while a significant electron transfer from Ba to the [Pt4Al4](δ-) network is found. By X-ray photoelectron spectroscopy measurements the Pt 4f5/2 and 4f7/2 energies for Ba3Pt4Al4 were found in the range of those of elemental Pt due to the electron transfer of Ba, while PtAl and PtAl2 show a pronounced shift toward a more cationic platinum state. (27)Al magic-angle spinning NMR investigations verified the two independent crystallographic Al sites with differently distorted tetrahedrally coordinated [AlPt4] units. Peak assignments could be made based on both geometrical considerations and in relation to electric field gradient calculations. PMID:26536164

  16. In Vitro Monitoring of Total Choline Levels in a Bioartificial Pancreas: 1H NMR Spectroscopic Studies of the Effects of Oxygen Level

    NASA Astrophysics Data System (ADS)

    Long, Robert C.; Papas, Klearchos K.; Sambanis, Athanassios; Constantinidis, Ioannis

    2000-09-01

    This investigation implements specifically designed solvent-suppressed adiabatic pulses whose properties make possible the long-term monitoring of 1H NMR detectable metabolites from alginate/poly-l-lysine/alginate (APA)-encapsulated βTC3 cells. Our encapsulated preparations were maintained in a perfusion bioreactor for periods exceeding 30 days. During this prolonged cultivation period, the cells were exposed to repetitive hypoxic episodes of 4 and 24 h. The ratio of the total choline signal (3.20 ppm) to the reference signal (observed at 0.94 ppm assigned to isoleucine, leucine, and valine) decreased by 8-10% for the 4-h and by 20-32% for the 24-h episodes and returned to its prehypoxic level upon reoxygenation. The decrease in the mean value of total choline to reference signal ratio for three 4-h and two 24-h episodes in two different cultures was highly significant (P < 0.01). The rate of recovery by this ratio was slower than the rates of recovery by oxygen consumption, lactate production, or glucose consumption. A step-up in oxygen level led to a new, higher value for the total choline to reference ratio. From spectra of extracts at 400 MHz, it was determined that 63.6% of the total choline signal is due to intracellular phosphorylcholine. Therefore, it is inferred that the observed changes in total choline signal are linked to an oxygen level dependence of the intracellular phosphorylcholine. Several possible mechanisms in which oxygen may influence phosphorylcholine metabolism are suggested. In addition, the implications of these findings to the development of a noninvasive monitoring method for tissue-engineered constructs composed of encapsulated cells are discussed.

  17. N.m.r. spectroscopic studies of fucose-containing oligosaccharides derived from keratanase digestion of articular cartilage keratan sulphates. Influence of fucose residues on keratanase cleavage.

    PubMed Central

    Tai, G H; Huckerby, T N; Nieduszynski, I A

    1993-01-01

    Keratan sulphate chains from bovine articular cartilage were fully digested with keratanase from Pseudomonas sp. and the products were reduced with alkaline borohydride. The resultant fragments were fractionated on a Nucleosil 5SB column and the earliest eluting fucose-containing oligosaccharides were isolated. Structural analysis using 1H n.m.r. spectroscopy (600 MHz) showed the two least-charged species to have the following structure: GlcNAc(6S) beta 1-3Gal beta 1-4(Fuc alpha 1-3)GlcNAc(6S) beta 1- 3Gal beta 1-4GlcNAc(6S) beta 1-3Gal-ol and GlcNAc(6S) beta 1-3Gal beta 1- 4(Fuc alpha 1-3)GlcNAc(6S) beta 1-3Gal beta 1-4GlcNAc(6S) beta 1-6(Gal beta 1- 3)GalNAc-ol. Both galactoses adjacent to the fucosylated N-acetylglucosamine residue are unsulphated. Therefore, it can be deduced from these structures that the presence of fucose on N-acetylglucosamine residues in keratan sulphates protects both of the adjacent unsulphated galactose residues from keratanase cleavage. This result has implications for the interpretation of keratanase fingerprints, because in articular cartilage keratan sulphates the keratanase-resistant blocks are not solely those with fully sulphated galactose residues, but also include the fucosylated sequences, which have unsulphated galactoses. It is, therefore, not possible to estimate their galactose sulphation or the size of the fully sulphated disaccharide-repeat sequences from keratan sulphates that contain fucose. PMID:8489515

  18. Nitrogen input 15N-signatures are reflected in plant 15N natural abundances of N-rich tropical forest in China

    NASA Astrophysics Data System (ADS)

    Abdisa Gurmesa, Geshere; Lu, Xiankai; Gundersen, Per; Yunting, Fang; Mo, Jiangming

    2016-04-01

    In this study, we tested the measurement of natural abundance of 15N15N) for its ability to assess changes in N cycling due to increased N deposition in two forest types; namely, an old-growth broadleaved forest and a pine forest, in southern China. We measured δ15N values of inorganic N in input and output fluxes under ambient N deposition, and N concentration and δ15N of major ecosystem compartments under ambient and increased N deposition. Our results showed that N deposition to the forests was 15N-depleted, and was dominated by NH4-N. Plants were 15N-depleted due to imprint from the 15N-depleted atmospheric N deposition. The old-growth forest had larger N concentration and was more 15N-enriched than the pine forest. Nitrogen addition did not significantly affect N concentration, but it significantly increased δ15N values of plants, and slightly more so in the pine forest, toward the 15N signature of the added N in both forests. The result indicates that the pine forest may rely more on the 15N-depleted deposition N. Soil δ15N values were slightly decreased by the N addition. Our result suggests that ecosystem δ15N is more sensitive to the changes in ecosystem N status and N cycling than N concentration in N-saturated sub-tropical forests.

  19. Cytochrome-P450-Cytochrome-b5 Interaction in a Membrane Environment Changes 15N Chemical Shift Anisotropy Tensors

    PubMed Central

    Pandey, Manoj Kumar; Vivekanandan, Subramanian; Ahuja, Shivani; Huang, Rui; Im, Sang-Choul; Waskell, Lucy; Ramamoorthy, Ayyalusamy

    2013-01-01

    It has been well realized that the dependence of chemical shift anisotropy (CSA) tensors on the amino acid sequence, secondary structure, dynamics and electrostatic interactions can be utilized in the structural and dynamic studies of proteins by NMR spectroscopy. In addition, CSA tensors could also be utilized to measure the structural interactions between proteins in a protein-protein complex. To this end, here we report the experimentally measured backbone amide-15N CSA tensors for a membrane-bound 16.7-kDa full-length rabbit cytochrome-b5 (cytb5), in complexation with a 55.8-kDa microsomal rabbit cytochrome P450 2B4 (cytP4502B4). The 15N-CSAs, determined using the 15N CSA/15N-1H dipolar coupling transverse cross-correlated rates, for free cytb5 are compared with that for the cytb5 bound to cytP4502B4. An overall increase in backbone amide-15N transverse cross-correlated rates for the cytb5 residues in the cytb5-cytP450 complex was observed as compared to the free cytb5 residues. Due to fast spin-spin relaxation (T2) and subsequent broadening of the signals in the complex, we were able to measure amide-15N CSAs only for 48 residues of cytb5 as compared to 84 residues of free cytb5. We observed a change in 15N CSA for most residues of cytb5 in the complex, when compared to free cytb5, suggesting a dynamic interaction between the oppositely charged surfaces of anionic cytb5 and cationic cytP450. The mean values of 15N CSA determined for residues in helical, sheet and turn regions of cytb5 in the complex are −184.5, −146.8, and −146.2 ppm, respectively, with an overall average value of −165.5 ppm (excluding the values from residues in more flexible termini). The measured CSA value for residues in helical conformation is slightly larger as compared to previously reported values. This may be attributed to the paramagnetic effect from Fe(III) of the heme in cytb5, which is similar to our previously reported values for the free cytb5. PMID:24107224

  20. Marking Drosophila suzukii (Diptera: Drosophilidae) With Rubidium or 15N.

    PubMed

    Klick, J; Yang, W Q; Bruck, D J

    2015-06-01

    Drosophila suzukii Matsumura (Diptera: Drosophilidae) has caused significant economic damage to berry and stone fruit production regions. Markers that are systemic in plants and easily transferred to target organisms are needed to track D. suzukii exploitation of host resources and trophic interactions. High and low concentrations of the trace element, rubidium (Rb), and the stable isotope, 15N, were tested to mark D. suzukii larvae feeding on fruits of enriched strawberry plants grown in containers under greenhouse conditions. Fly marker content and proportion of flies marked 1, 7, and 14 d after emergence from enriched fruits and fly dry mass were analyzed. Nearly 100% of the flies analyzed 14 d after emerging from 15N-enriched plants were marked, whereas only 30-75% and 0-3% were marked 14 d after emerging from high and low Rb concentration plants, respectively. Rapid Rb decay, strong 15N persistence, and the economics of using these markers in the field to elucidate D. suzukii pest ecology are discussed. PMID:26470275

  1. Isotope labeling for NMR studies of macromolecular structure and interactions

    SciTech Connect

    Wright, P.E.

    1994-12-01

    Implementation of biosynthetic methods for uniform or specific isotope labeling of proteins, coupled with the recent development of powerful heteronuclear multidimensional NMR methods, has led to a dramatic increase in the size and complexity of macromolecular systems that are now amenable to NMR structural analysis. In recent years, a new technology has emerged that combines uniform {sup 13}C, {sup 15}N labeling with heteronuclear multidimensional NMR methods to allow NMR structural studies of systems approaching 25 to 30 kDa in molecular weight. In addition, with the introduction of specific {sup 13}C and {sup 15}N labels into ligands, meaningful NMR studies of complexes of even higher molecular weight have become feasible. These advances usher in a new era in which the earlier, rather stringent molecular weight limitations have been greatly surpassed and NMR can begin to address many central biological problems that involve macromolecular structure, dynamics, and interactions.

  2. Characterization of the Vibrio cholerae Extracellular Matrix: A Top-Down Solid-State NMR Approach

    PubMed Central

    Reichhardt, Courtney; Fong, Jiunn C.N.; Yildiz, Fitnat; Cegelski, Lynette

    2015-01-01

    Bacterial biofilms are communities of bacterial cells surrounded by a self-secreted extracellular matrix. Biofilm formation by Vibrio cholerae, the human pathogen responsible for cholera, contributes to its environmental survival and infectivity. Important genetic and molecular requirements have been identified for V. cholerae biofilm formation, yet a compositional accounting of these parts in the intact biofilm or extracellular matrix has not been described. As insoluble and non-crystalline assemblies, determinations of biofilm composition pose a challenge to conventional biochemical and biophysical analysis. The V. cholerae extracellular matrix composition is particularly complex with several proteins, complex polysaccharides, and other biomolecules having been identified as matrix parts. We developed a new top-down solid-state NMR approach to spectroscopically assign and quantify the carbon pools of the intact V. cholerae extracellular matrix using 13C CPMAS and 13C{15N}, 15N{31P}, and 13C{31P}REDOR. General sugar, lipid, and amino acid pools were first profiled and then further annotated and quantified as specific carbon types, including carbonyls, amides, glycyl carbons, and anomerics. In addition, 15N profiling revealed a large amine pool relative to amide contributions, reflecting the prevalence of molecular modifications with free amine groups. Our top-down approach could be implemented immediately to examine the extracellular matrix from mutant strains that might alter polysaccharide production or lipid release beyond the cell surface; or to monitor changes that may accompany environmental variations and stressors such as altered nutrient composition, oxidative stress or antibiotics. More generally, our analysis has demonstrated that solid-state NMR is a valuable tool to characterize complex biofilm systems. PMID:24911407

  3. Superoxygenated Water as an Experimental Sample for NMR Relaxometry

    ERIC Educational Resources Information Center

    Nestle, Nikolaus; Dakkouri, Marwan; Rauscher, Hubert

    2004-01-01

    The increase in NMR relaxation rates as a result of dissolved paramagnetic species on the sample of superoxygenated drinking water is demonstrated. It is concluded that oxygen content in NMR samples is an important issue and can give rise to various problems in the interpretation of both spectroscopic and NMR imaging or relaxation experiments.

  4. Whole body nitric oxide synthesis in healthy men determined from [15N] arginine-to-[15N]citrulline labeling.

    PubMed Central

    Castillo, L; Beaumier, L; Ajami, A M; Young, V R

    1996-01-01

    The rates of whole body nitric oxide (NO) synthesis, plasma arginine flux, and de novo arginine synthesis and their relationships to urea production, were examined in a total of seven healthy adults receiving an L-amino acid diet for 6 days. NO synthesis was estimated by the rate of conversion of the [15N] guanidino nitrogen of arginine to plasma [15N] ureido citrulline and compared with that based on urinary nitrite (NO2-)/nitrate (NO3-) excretion. Six subjects received on dietary day 7, a 24-hr (12-hr fed/12-hr fasted) primed, constant, intravenous infusion of L-[guanidino-15N2]arginine and [13C]urea. A similar investigation was repeated with three of these subjects, plus an additional subject, in which they received L-[ureido-13C]citrulline, to determine plasma citrulline fluxes. The estimated rates (mean +/- SD) of NO synthesis over a period of 24 hr averaged 0.96 +/- 0.1 mumol .kg-1.hr-1 and 0.95 +/- 0.1 mumol.kg-1.hr-1, for the [15N]citrulline and the nitrite/nitrate methods, respectively. About 15% of the plasma arginine turnover was associated with urea formation and 1.2% with NO formation. De novo arginine synthesis averaged 9.2 +/- 1.4 mumol. kg-1.hr-1, indicating that approximately 11% of the plasma arginine flux originates via conversion of plasma citrulline to arginine. Thus, the fraction of the plasma arginine flux associated with NO and also urea synthesis in healthy humans is small, although the plasma arginine compartment serves as a significant precursor pool (54%) for whole body NO formation. This tracer model should be useful for exploring these metabolic relationships in vivo, under specific pathophysiologic states where the L-arginine-NO pathway might be altered. Images Fig. 4 PMID:8876157

  5. Spectroscopic study of low-lying {sup 16}N levels

    SciTech Connect

    Bardayan, D. W.; Nesaraja, C. D.; Pain, S. D.; Smith, M. S.; O'Malley, P. D.; Cizewski, J. A.; Hatarik, R.; Peters, W. A.; Blackmon, J. C.; Chae, K. Y.; Jones, K. L.; Moazen, B. H.; Paulauskas, S.; Pittman, S. T.; Schmitt, K. T.; Chipps, K. A.; Kozub, R. L.; Shriner, J. F. Jr.; Matei, C.

    2008-11-15

    The magnitude of the {sup 15}N(n,{gamma}){sup 16}N reaction rate in asymptotic giant branch stars depends directly on the neutron spectroscopic factors of low-lying {sup 16}N levels. A new study of the {sup 15}N(d,p){sup 16}N reaction is reported populating the ground and first three excited states in {sup 16}N. The measured spectroscopic factors are near unity as expected from shell model calculations, resolving a long-standing discrepancy with earlier measurements that had never been confirmed or understood. Updated {sup 15}N(n,{gamma}){sup 16}N reaction rates are presented.

  6. Measuring (13)C/(15)N chemical shift anisotropy in [(13)C,(15)N] uniformly enriched proteins using CSA amplification.

    PubMed

    Hung, Ivan; Ge, Yuwei; Liu, Xiaoli; Liu, Mali; Li, Conggang; Gan, Zhehong

    2015-11-01

    Extended chemical shift anisotropy amplification (xCSA) is applied for measuring (13)C/(15)N chemical shift anisotropy (CSA) of uniformly labeled proteins under magic-angle spinning (MAS). The amplification sequence consists of a sequence of π-pulses that repetitively interrupt MAS averaging of the CSA interaction. The timing of the pulses is designed to generate amplified spinning sideband manifolds which can be fitted to extract CSA parameters. The (13)C/(13)C homonuclear dipolar interactions are not affected by the π-pulses due to the bilinear nature of the spin operators and are averaged by MAS in the xCSA experiment. These features make the constant evolution-time experiment suitable for measuring CSA of uniformly labeled samples. The incorporation of xCSA with multi-dimensional (13)C/(15)N correlation is demonstrated with a GB1 protein sample as a model system for measuring (13)C/(15)N CSA of all backbone (15)NH, (13)CA and (13)CO sites. PMID:26404770

  7. Climbing up the vibrational ladder of HC15N: High-temperature near-infrared emission measurements

    NASA Astrophysics Data System (ADS)

    Predoi-Cross, A.; Johnson, E.; Hemsing, D.; Rozario, H.; Mellau, Georg Ch.

    2013-11-01

    The near-infrared (NIR) emission spectrum of H12C15N was measured in the 6050-6500 cm-1 range at a resolution of 0.044 cm-1 using an emission setup available at the Justus-Liebig Universität, Giessen, Germany. The rich emission spectrum showing numerous overlapped spectral profiles was analyzed with the spectrum analysis software SyMath running using Mathematica as a platform. This approach allowed us to retrieve the vibrational-rotational constants for 32 bands. Many spectroscopic transitions have been observed for the first time in a lab environment. We quantified four newly observed Coriolis resonances.

  8. Sequence-specific sup 1 H and sup 15 N resonance assignments for human dihydrofolate reductase in solution

    SciTech Connect

    Stockman, B.J.; Nirmala, N.R.; Wagner, G. ); Delcamp, T.J.; DeYarman, M.T.; Freisheim, J.H. )

    1992-01-14

    Dihydrofolate reductase is an intracellular target enzyme for folate antagonists, including the anticancer drug methotrexate. In order to design novel drugs with altered binding properties, a detailed description of protein-drug interactions in solution is desirable to understand the specificity of drug binding. As a first step in this process, heteronuclear three-dimensional NMR spectroscopy has been used to make sequential resonance assignments for more than 90% of the residues in human dihydrofolate reductase complexed with methotrexate. Uniform enrichment of the 21.5-kDa protein with {sup 15}N was required to obtain the resonance assignments via heteronuclear 3D NMR spectroscopy since homonuclear 2D spectra did not provide sufficient {sup 1}H resonance dispersion. Medium- and long-range NOE's have been used to characterize the secondary structure of the binary ligand-enzyme complex in solution.

  9. THz Dynamic Nuclear Polarization NMR

    PubMed Central

    Nanni, Emilio A.; Barnes, Alexander B.; Griffin, Robert G.; Temkin, Richard J.

    2013-01-01

    Dynamic nuclear polarization (DNP) increases the sensitivity of nuclear magnetic resonance (NMR) spectroscopy by using high frequency microwaves to transfer the polarization of the electrons to the nuclear spins. The enhancement in NMR sensitivity can amount to a factor of well above 100, enabling faster data acquisition and greatly improved NMR measurements. With the increasing magnetic fields (up to 23 T) used in NMR research, the required frequency for DNP falls into the THz band (140–600 GHz). Gyrotrons have been developed to meet the demanding specifications for DNP NMR, including power levels of tens of watts; frequency stability of a few megahertz; and power stability of 1% over runs that last for several days to weeks. Continuous gyrotron frequency tuning of over 1 GHz has also been demonstrated. The complete DNP NMR system must include a low loss transmission line; an optimized antenna; and a holder for efficient coupling of the THz radiation to the sample. This paper describes the DNP NMR process and illustrates the THz systems needed for this demanding spectroscopic application. THz DNP NMR is a rapidly developing, exciting area of THz science and technology. PMID:24639915

  10. THz Dynamic Nuclear Polarization NMR.

    PubMed

    Nanni, Emilio A; Barnes, Alexander B; Griffin, Robert G; Temkin, Richard J

    2011-08-29

    Dynamic nuclear polarization (DNP) increases the sensitivity of nuclear magnetic resonance (NMR) spectroscopy by using high frequency microwaves to transfer the polarization of the electrons to the nuclear spins. The enhancement in NMR sensitivity can amount to a factor of well above 100, enabling faster data acquisition and greatly improved NMR measurements. With the increasing magnetic fields (up to 23 T) used in NMR research, the required frequency for DNP falls into the THz band (140-600 GHz). Gyrotrons have been developed to meet the demanding specifications for DNP NMR, including power levels of tens of watts; frequency stability of a few megahertz; and power stability of 1% over runs that last for several days to weeks. Continuous gyrotron frequency tuning of over 1 GHz has also been demonstrated. The complete DNP NMR system must include a low loss transmission line; an optimized antenna; and a holder for efficient coupling of the THz radiation to the sample. This paper describes the DNP NMR process and illustrates the THz systems needed for this demanding spectroscopic application. THz DNP NMR is a rapidly developing, exciting area of THz science and technology. PMID:24639915

  11. The vibrational spectra of [ 15N 2]-succinonitrile

    NASA Astrophysics Data System (ADS)

    Fengler, O. I.

    2001-07-01

    For the first time, the infrared and Raman spectra of [ 15N 2]-succinonitrile are presented and discussed in detail. Assignments of the vibrational bands of its two rotational conformers gauche and trans, respectively, have been made for both infrared and Raman spectra. The assignments were based on a recent ab-initio force field calculation for succinonitrile, taking into account the vibrational frequencies of other succinonitrile isotopomers. There are differences in the frequencies of the vibrational bands due to the mass increase in the cyanide groups, which have been analysed in depth.

  12. The vibrational spectra of [15N2]-succinonitrile.

    PubMed

    Fengler, O I

    2001-07-01

    For the first time, the infrared and Raman spectra of [15N2]-succinonitrile are presented and discussed in detail. Assignments of the vibrational bands of its two rotational conformers gauche and trans, respectively, have been made for both infrared and Raman spectra. The assignments were based on a recent ab-initio force field calculation for succinonitrile, taking into account the vibrational frequencies of other succinonitrile isotopomers. There are differences in the frequencies of the vibrational bands due to the mass increase in the cyanide groups, which have been analysed in depth. PMID:11471715

  13. Experimental plant for simultaneous production of (14)N and (15)N by (15)N/(14)N exchange in NO, NO(2)-HNO(3) system under pressure.

    PubMed

    Axente, Damian; Marcu, Cristina; Muresan, Ancuţa; Kaucsar, Martin; Misan, Ioan; Popeneciu, Gabriel; Gligan, Nicolae; Cristea, Gabriela

    2010-06-01

    An experimental study on (14)N and (15)N simultaneous separation using the chemical exchange in NO, NO(2)-HNO(3) system under pressure is presented. The influence of the pressure and of the interstage 10 M HNO(3) flow rate on the separation of (14)N and (15)N was measured on a packed column with product and waste refluxers. At steady state and 1.8 atm (absolute), the isotopic concentration at the bottom of the separation column was 0.563 at% (15)N, and in the top of the column was 0.159 at% (15)N. The height equivalent to a theoretical plate and interstage 10 M HNO(3) flow rate values, obtained in these experimental conditions, allows the separation of (14)N highly depleted of (15)N and of (15)N at 99 at% (15)N concentration. PMID:20582793

  14. HN(α/β-COCA-J) Experiment for Measurement of 1JC‧Cα Couplings from Two-Dimensional [15N, 1H] Correlation Spectrum

    NASA Astrophysics Data System (ADS)

    Permi, Perttu; Sorsa, Tia; Kilpeläinen, Ilkka; Annila, Arto

    1999-11-01

    Anew method for measurement of one-bond 13C‧-13Cα scalar and dipolar couplings from a two-dimensional [15N, 1H] correlation spectrum is presented. The experiment is based on multiple-quantum coherence, which is created between nitrogen and carbonyl carbon for simultaneous evolution of 15N chemical shift and coupling between 13C‧ and 13Cα. Optional subspectral editing is provided by the spin-state-selective filters. The residual dipolar dipolar contribution to the 13C‧-13Cα coupling can be measured from these simplified [15N, 1H]-HSQC-like spectra. In this way, without explicit knowledge of carbon assignments, conformational changes of proteins dissolved in dilute liquid crystals can be probed conveniently, e.g., in structure activity relationship by NMR studies. The method is demonstrated with human cardiac troponin C.

  15. Chromatographic NMR in NMR solvents

    NASA Astrophysics Data System (ADS)

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

    2008-10-01

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

  16. Rapid and accurate calculation of protein 1H, 13C and 15N chemical shifts.

    PubMed

    Neal, Stephen; Nip, Alex M; Zhang, Haiyan; Wishart, David S

    2003-07-01

    A computer program (SHIFTX) is described which rapidly and accurately calculates the diamagnetic 1H, 13C and 15N chemical shifts of both backbone and sidechain atoms in proteins. The program uses a hybrid predictive approach that employs pre-calculated, empirically derived chemical shift hypersurfaces in combination with classical or semi-classical equations (for ring current, electric field, hydrogen bond and solvent effects) to calculate 1H, 13C and 15N chemical shifts from atomic coordinates. The chemical shift hypersurfaces capture dihedral angle, sidechain orientation, secondary structure and nearest neighbor effects that cannot easily be translated to analytical formulae or predicted via classical means. The chemical shift hypersurfaces were generated using a database of IUPAC-referenced protein chemical shifts--RefDB (Zhang et al., 2003), and a corresponding set of high resolution (<2.1 A) X-ray structures. Data mining techniques were used to extract the largest pairwise contributors (from a list of approximately 20 derived geometric, sequential and structural parameters) to generate the necessary hypersurfaces. SHIFTX is rapid (<1 CPU second for a complete shift calculation of 100 residues) and accurate. Overall, the program was able to attain a correlation coefficient (r) between observed and calculated shifts of 0.911 (1Halpha), 0.980 (13Calpha), 0.996 (13Cbeta), 0.863 (13CO), 0.909 (15N), 0.741 (1HN), and 0.907 (sidechain 1H) with RMS errors of 0.23, 0.98, 1.10, 1.16, 2.43, 0.49, and 0.30 ppm, respectively on test data sets. We further show that the agreement between observed and SHIFTX calculated chemical shifts can be an extremely sensitive measure of the quality of protein structures. Our results suggest that if NMR-derived structures could be refined using heteronuclear chemical shifts calculated by SHIFTX, their precision could approach that of the highest resolution X-ray structures. SHIFTX is freely available as a web server at http

  17. 15N solid-state nuclear magnetic resonance study of pyrolyzed metal-polyaniline cathode catalysts for oxygen reduction in fuel cells

    NASA Astrophysics Data System (ADS)

    Kuroki, Shigeki; Hosaka, Yo; Yamauchi, Chiharu; Nagata, Shinsuke; Sonoda, Mayu

    2015-09-01

    The oxygen reduction reaction (ORR) activity of pyrolyzed metal-free and metal (Mn, Fe, Co, Ni and Cu)-containing polyaniline (PANI) in polymer electrolyte fuel cell (PEFC) was studied. The metal-free PANI800 shows quite poor ORR catalytic activity, whilst the metal-containing PANIMe800 display a better ORR activity. The 15N CP/MAS NMR spectra of PANINi800 and PANICu800 show one weak peak at 118 ppm and there is no peak observed in PANIFe800, against that of PANI800, PANIMn800, PANICo800 and PANINi800 show two peaks at 273 and 118 ppm assigned to the pyridinic and pyridinium nitrogens. It is because of the paramagnetic effect of metal ions. The 15N spin-echo NMR spectra of PANIMe800 with fast recycle delay show the peaks at 140 and 270 ppm assigned to the graphitic and pyridinic nitrogens, against that of PANI800 shows no peak. The spectra of PANIMn800, PANICo800, PANINi800 and PANICu600 also contain a very broaden peak at 430 ppm assigned to the nitrogen with Fermi-contact effect from metal ions. The spectra of PANIFe800 show some spinning side bands and the average Fe3+-15N distance can be calculated. The some amount of iron ion are relieved and average Fe3+-15N distance increase after acid washing and the ORR activity decreases.

  18. Robust, integrated computational control of NMR experiments to achieve optimal assignment by ADAPT-NMR.

    PubMed

    Bahrami, Arash; Tonelli, Marco; Sahu, Sarata C; Singarapu, Kiran K; Eghbalnia, Hamid R; Markley, John L

    2012-01-01

    ADAPT-NMR (Assignment-directed Data collection Algorithm utilizing a Probabilistic Toolkit in NMR) represents a groundbreaking prototype for automated protein structure determination by nuclear magnetic resonance (NMR) spectroscopy. With a [(13)C,(15)N]-labeled protein sample loaded into the NMR spectrometer, ADAPT-NMR delivers complete backbone resonance assignments and secondary structure in an optimal fashion without human intervention. ADAPT-NMR achieves this by implementing a strategy in which the goal of optimal assignment in each step determines the subsequent step by analyzing the current sum of available data. ADAPT-NMR is the first iterative and fully automated approach designed specifically for the optimal assignment of proteins with fast data collection as a byproduct of this goal. ADAPT-NMR evaluates the current spectral information, and uses a goal-directed objective function to select the optimal next data collection step(s) and then directs the NMR spectrometer to collect the selected data set. ADAPT-NMR extracts peak positions from the newly collected data and uses this information in updating the analysis resonance assignments and secondary structure. The goal-directed objective function then defines the next data collection step. The procedure continues until the collected data support comprehensive peak identification, resonance assignments at the desired level of completeness, and protein secondary structure. We present test cases in which ADAPT-NMR achieved results in two days or less that would have taken two months or more by manual approaches. PMID:22427982

  19. Use of protein trans-splicing to produce active and segmentally 2H, 15N labeled mannuronan C5-epimerase AlgE4

    PubMed Central

    Buchinger, Edith; Aachmann, Finn L; Aranko, A Sesilja; Valla, Svein; Skjåk-BræK, Gudmund; Iwaï, Hideo; Wimmer, Reinhard

    2010-01-01

    Alginate epimerases are large multidomain proteins capable of epimerising C5 on β-d-mannuronic acid (M) turning it into α-l-guluronic acid (G) in a polymeric alginate. Azotobacter vinelandii secretes a family of seven epimerases, each of which is capable of producing alginates with characteristic G distribution patterns. All seven epimerases consist of two types of modules, denoted A and R, in varying numbers. Attempts to study these enzymes with solution-state NMR are hampered by their size—the smallest epimerase, AlgE4, consisting of one A- and one R-module, is 58 kDa, resulting in heavy signal overlap impairing the interpretation of NMR spectra. Thus we obtained segmentally 2H, 15N labeled AlgE4 isotopomeres (A-[2H, 15N]-R and [2H, 15N]-A-R) by protein trans-splicing using the naturally split intein of Nostoc punctiforme. The NMR spectra of native AlgE4 and the ligated versions coincide well proving the conservation of protein structure. The activity of the ligated AlgE4 was verified by two different enzyme activity assays, demonstrating that ligated AlgE4 displays the same catalytic activity as wild-type AlgE4. PMID:20552686

  20. The effect of noncollinearity of 15N-1H dipolar and 15N CSA tensors and rotational anisotropy on 15N relaxation, CSA/dipolar cross correlation, and TROSY.

    PubMed

    Fushman, D; Cowburn, D

    1999-02-01

    Current approaches to 15N relaxation in proteins assume that the 15N-1H dipolar and 15N CSA tensors are collinear. We show theoretically that, when there is significant anisotropy of molecular rotation, different orientations of the two tensors, experimentally observed in proteins, nucleic acids, and small peptides, will result in differences in site-specific correlation functions and spectral densities. The standard treatments of the rates of longitudinal and transverse relaxation of amide 15N nuclei, of the 15N CSA/15N-1H dipolar cross correlation, and of the TROSY experiment are extended to account for the effect of noncollinearity of the 15N-1H dipolar and 15N CSA (chemical shift anisotropy) tensors. This effect, proportional to the degree of anisotropy of the overall motion, (D parallel/D perpendicular - 1), is sensitive to the relative orientation of the two tensors and to the orientation of the peptide plane with respect to the diffusion coordinate frame. The effect is negligible at small degrees of anisotropy, but is predicted to become significant for D parallel/D perpendicular > or = 1.5, and at high magnetic fields. The effect of noncollinearity of 15N CSA and 15N-1H dipolar interaction is sensitive to both gross (hydrodynamic) properties and atomic-level details of protein structure. Incorporation of this effect into relaxation data analysis is likely to improve both precision and accuracy of the derived characteristics of protein dynamics, especially at high magnetic fields and for molecules with a high degree of anisotropy of the overall motion. The effect will also make TROSY efficiency dependent on local orientation in moderately anisotropic systems. PMID:10070755

  1. Tracking the incorporation of 15N from labeled beech litter into mineral-organic associations

    NASA Astrophysics Data System (ADS)

    Kleber, M.; Hatton, P.; Derrien, D.; Lajtha, K.; Zeller, B.

    2008-12-01

    Nitrogen containing organic compounds are thought to have a role in the complex web of processes that control the turnover time of soil organic matter. The sequential density fractionation technique is increasingly used for the purpose of investigating the association of organic materials with the mineral matrix. Organic materials in the denser fractions (>2.0 kg L-1) typically show 13C NMR signals indicative of carbohydrate and aliphatic structures, an absence of lignin and tannin structures and a narrow C:N ratio, suggesting a microbial origin of organic matter in these fractions. Here we take advantage of a labeling experiment conducted at two different sites in Germany and in France to investigate the incorporation of organic nitrogen into physical fractions of increasing density, representing a proximity gradient to mineral surfaces. 15N labeled beech litter was applied to two acidic forest topsoils 8 and 12 years ago. Although there are differences in the distribution patterns between the two soils, and the majority of the organic nitrogen was recovered in fractions representing organic matter of plant origin and not bound to the mineral matrix, our data clearly show that after a decade, significant amounts of the nitrogen had been incorporated in mineral-organic fractions of supposedly slow turnover. It remains to be shown to which extent the N in the densest fractions was incorporated by soil microbiota and associated with mineral surfaces in organic form or adsorbed to mineral surfaces in inorganic form (NH4+).

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

    SciTech Connect

    Osbakken, M.; Haselgrove, J.

    1987-01-01

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

  3. New flaxseed orbitides: Detection, sequencing, and (15)N incorporation.

    PubMed

    Okinyo-Owiti, Denis P; Young, Lester; Burnett, Peta-Gaye G; Reaney, Martin J T

    2014-03-01

    Three new orbitides (cyclolinopeptides 17, 18, and 19) were identified in flaxseed (Linum usitatissimum L.) extracts without any form of purification. Their structures were elucidated by a combination of (15) N-labeling experiments and extensive tandem mass spectrometry (MS/MS) with electrospray ionization (ESI). Putative linear peptide sequences of the new orbitides were used as the query in the Basic Local Alignment Search Tool (BLAST) searches of flax genome database. These searches returned linear sequences for the putative precursors of cyclolinopeptides 17 and 19 among others. Cyclolinopeptide 18 contains MetO (O) and is not directly encoded, but is a product of post-translation modification of the Met present in 17. The identification of precursor proteins in flax mRNA transcripts and DNA sequences confirmed the occurrence and amino acid sequences of these orbitides as [1-9-NαC]-MLKPFFFWI, [1-9-NαC]-OLKPFFFWI, and [1-9-NαC]-GIPPFWLTL for cyclolinopeptides 17, 18, and 19, respectively. PMID:24408479

  4. Native Corrinoids from Clostridium cochlearium Are Adeninylcobamides: Spectroscopic Analysis and Identification of Pseudovitamin B12 and Factor A

    PubMed Central

    Hoffmann, Bernd; Oberhuber, Michael; Stupperich, Erhard; Bothe, Harald; Buckel, Wolfgang; Konrat, Robert; Kräutler, Bernhard

    2000-01-01

    The corrinoids from the obligate anaerobe Clostridium cochlearium were extracted as a mixture of Coβ-cyano derivatives. From 50 g of frozen cells, approximately 2 mg (1.5 μmol) of B12 derivatives was obtained as a crystalline sample. Analysis of the corrinoid sample of C. cochlearium by a combination of high-pressure liquid chromatography and UV-Vis absorbance spectroscopy revealed the presence of three cyano corrinoids in a ratio of about 3:1:1. The spectroscopic data acquired for the sample indicated the main components to be pseudovitamin B12 (Coβ-cyano-7"-adeninylcobamide) (60%) and factor A (Coβ-cyano-7"-[2-methyl]adeninylcobamide) (20%). Authentic pseudovitamin B12 was prepared by guided biosynthesis from cobinamide and adenine. Both pseudovitamin B12 and its homologue, factor A, were subjected to complete spectroscopic analysis by UV-Vis, circular dichroism, mass spectrometry, and by one- and two-dimensional 1H, 13C-, and 15N nuclear magnetic resonance (NMR) spectroscopy. The third component was indicated by the mass spectra to be an isomer of factor A and is likely (according to NMR) to be 7"-[N6-methyl]-adeninylcobamide, a previously unknown corrinoid. C. cochlearium thus biosynthesizes as its native “complete” B12 cofactors the 7"-adeninylcobamides and two homologous corrinoids, in which the nucleotide base is a methylated adenine. PMID:10940017

  5. 15N2 formation and fast oxygen isotope exchange during pulsed 15N18O exposure of MnOx/CeO2

    SciTech Connect

    Kwak, Ja Hun; Szanyi, Janos

    2014-12-23

    Pulsing 15N18O onto an annealed 1% Mn16Ox/Ce16O2 catalyst resulted in very fast oxygen isotope exchange and 15N2 formation at 295 K. In the 1st 15N18O pulse, due to the presence of large number of surface oxygen defects, extensive 15N218O and 15N2 formations were observed. In subsequent pulses oxygen isotope exchange dominated as a result of highly labile oxygen in the oxide. We gratefully acknowledge the US Department of Energy (DOE), Office of Energy Efficiency and Renewable Energy/Vehicle Technologies Program for the support of this work. The research described in this paper was performed at the Environmental Molecular Sciences Laboratory (EMSL), a national scientific user facility sponsored by the DOE’s Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory (PNNL). PNNL is operated for the US DOE by Battelle.

  6. Fermentation and Cost-Effective 13C/15N Labeling of the Nonribosomal Peptide Gramicidin S for Nuclear Magnetic Resonance Structure Analysis.

    PubMed

    Berditsch, Marina; Afonin, Sergii; Steineker, Anna; Orel, Nataliia; Jakovkin, Igor; Weber, Christian; Ulrich, Anne S

    2015-06-01

    Gramicidin S (GS) is a nonribosomally synthesized decapeptide from Aneurinibacillus migulanus. Its pronounced antibiotic activity is attributed to amphiphilic structure and enables GS interaction with bacterial membranes. Despite its medical use for over 70 years, the peptide-lipid interactions of GS and its molecular mechanism of action are still not fully understood. Therefore, a comprehensive structural analysis of isotope-labeled GS needs to be performed in its biologically relevant membrane-bound state, using advanced solid-state nuclear magnetic resonance (NMR) spectroscopy. Here, we describe an efficient method for producing the uniformly (13)C/(15)N-labeled peptide in a minimal medium supplemented by selected amino acids. As GS is an intracellular product of A. migulanus, we characterized the producer strain DSM 5759 (rough-convex phenotype) and examined its biosynthetic activity in terms of absolute and biomass-dependent peptide accumulation. We found that the addition of either arginine or ornithine increases the yield only at very high supplementing concentrations (1% and 0.4%, respectively) of these expensive (13)C/(15)N-labeled amino acids. The most cost-effective production of (13)C/(15)N-GS, giving up to 90 mg per gram of dry cell weight, was achieved in a minimal medium containing 1% (13)C-glycerol and 0.5% (15)N-ammonium sulfate, supplemented with only 0.025% of (13)C/(15)N-phenylalanine. The 100% efficiency of labeling is corroborated by mass spectrometry and preliminary solid-state NMR structure analysis of the labeled peptide in the membrane-bound state. PMID:25795666

  7. Fermentation and Cost-Effective 13C/15N Labeling of the Nonribosomal Peptide Gramicidin S for Nuclear Magnetic Resonance Structure Analysis

    PubMed Central

    Berditsch, Marina; Afonin, Sergii; Steineker, Anna; Orel, Nataliia; Jakovkin, Igor; Weber, Christian

    2015-01-01

    Gramicidin S (GS) is a nonribosomally synthesized decapeptide from Aneurinibacillus migulanus. Its pronounced antibiotic activity is attributed to amphiphilic structure and enables GS interaction with bacterial membranes. Despite its medical use for over 70 years, the peptide-lipid interactions of GS and its molecular mechanism of action are still not fully understood. Therefore, a comprehensive structural analysis of isotope-labeled GS needs to be performed in its biologically relevant membrane-bound state, using advanced solid-state nuclear magnetic resonance (NMR) spectroscopy. Here, we describe an efficient method for producing the uniformly 13C/15N-labeled peptide in a minimal medium supplemented by selected amino acids. As GS is an intracellular product of A. migulanus, we characterized the producer strain DSM 5759 (rough-convex phenotype) and examined its biosynthetic activity in terms of absolute and biomass-dependent peptide accumulation. We found that the addition of either arginine or ornithine increases the yield only at very high supplementing concentrations (1% and 0.4%, respectively) of these expensive 13C/15N-labeled amino acids. The most cost-effective production of 13C/15N-GS, giving up to 90 mg per gram of dry cell weight, was achieved in a minimal medium containing 1% 13C-glycerol and 0.5% 15N-ammonium sulfate, supplemented with only 0.025% of 13C/15N-phenylalanine. The 100% efficiency of labeling is corroborated by mass spectrometry and preliminary solid-state NMR structure analysis of the labeled peptide in the membrane-bound state. PMID:25795666

  8. Spectral Snapshots of Bacterial Cell-Wall Composition and the Influence of Antibiotics by Whole-Cell NMR

    PubMed Central

    Nygaard, Rie; Romaniuk, Joseph A.H.; Rice, David M.; Cegelski, Lynette

    2015-01-01

    Gram-positive bacteria surround themselves with a thick cell wall that is essential to cell survival and is a major target of antibiotics. Quantifying alterations in cell-wall composition are crucial to evaluating drug modes of action, particularly important for human pathogens that are now resistant to multiple antibiotics such as Staphylococcus aureus. Macromolecular and whole-cell NMR spectroscopy allowed us to observe the full panel of carbon and nitrogen pools in S. aureus cell walls and intact whole cells. We discovered that one-dimensional 13C and 15N NMR spectra, together with spectroscopic selections based on dipolar couplings as well as two-dimensional spin-diffusion measurements, revealed the dramatic compositional differences between intact cells and cell walls and allowed the identification of cell-wall signatures in whole-cell samples. Furthermore, the whole-cell NMR approach exhibited the sensitivity to detect distinct compositional changes due to treatment with the antibiotics fosfomycin (a cell-wall biosynthesis inhibitor) and chloramphenicol (a protein synthesis inhibitor). Whole cells treated with fosfomycin exhibited decreased peptidoglycan contributions while those treated with chloramphenicol contained a higher percentage of peptidoglycan as cytoplasmic protein content was reduced. Thus, general antibiotic modes of action can be identified by profiling the total carbon pools in intact whole cells. PMID:25809251

  9. Studies with 15N-labeled ammonia and urea in the malnourished child

    PubMed Central

    Read, W. W. C.; McLaren, D. S.; Tchalian, Marie; Nassar, Siham

    1969-01-01

    Investigations using ammonium citrate-15N and urea-15N showed that children in the acute stage of kwashiorkor and marasmus receiving a diet of adequate protein content retained a considerable percentage of the label from both compounds. Excretion of both total 15N and urea-15N was subnormal and elimination was virtually completed 36 hr after administration of the isotope. During recovery from kwashiorkor total 15N excretion had approached normal a month after commencement of rehabilitation. Urea-15N excretion was still slightly subnormal after 3 months. In marasmus urea-15N formed a normal proportion of total 15N excretion after 1 month, although total 15N excretion then was still low. Ammonia nitrogen was retained to a greater extent than urea nitrogen in all cases. As it is known that a considerable amount of urea is degraded to ammonia in the gastrointestinal tract, it seems probable that urea nitrogen became available for use after this degradation. Examination of blood from one marasmic child after feeding ammonia-15N and from another after intravenous injection of urea-15N showed incorporation of the label into blood cells and plasma proteins. This did not occur in well nourished controls. It is concluded that ammonia and urea as sources of nonessential nitrogen may play an important part in protein metabolism in the malnourished child. PMID:5771193

  10. High-resolution NMR characterization of a spider-silk mimetic composed of 15 tandem repeats and a CRGD motif

    PubMed Central

    McLachlan, Glendon D; Slocik, Joseph; Mantz, Robert; Kaplan, David; Cahill, Sean; Girvin, Mark; Greenbaum, Steve

    2009-01-01

    Multidimensional solution NMR spectroscopic techniques have been used to obtain atomic level information about a recombinant spider silk construct in hexafluoro-isopropanol (HFIP). The synthetic 49 kDa silk-like protein mimics authentic silk from Nephila clavipes, with the inclusion of an extracellular matrix recognition motif. 2D 1H-15N HSQC NMR spectroscopy reveals 33 cross peaks, which were assigned to amino acid residues in the semicrystalline repeat units. Signals from the amorphous segments in the primary sequence were weak and broad, suggesting that this region is highly dynamic and undergoing conformational exchange. An analysis of the deviations of the 13Cα, 13Cβ, and 13CO chemical shifts relative to the expected random coil values reveals two highly α-helical regions from amino acid 12–19 and 26–32, which comprise the polyalanine track and a GGLGSQ sequence. This finding is further supported by φ-value analysis and sequential and medium-range NOE interactions. Pulsed field gradient NMR measurements indicate that the topology of the silk mimetic in HFIP is nonglobular. Moreover, the 3D 15N-NOESY HSQC spectrum exhibits few long-range NOEs. Similar spectral features have been observed for repeat modules in other polypeptides and are characteristic of an elongated conformation. The results provide a residue-specific description of a silk sequence in nonaqueous solution and may be insightful for understanding the fold and topology of highly concentrated, stable silk before spinning. Additionally, the insights obtained may find application in future design and large-scale production and storage of synthetic silks in organic solvents. PMID:19177364

  11. 1H NMR relaxation in urea

    NASA Astrophysics Data System (ADS)

    Taylor, R. E.; Bacher, Alfred D.; Dybowski, C.

    2007-11-01

    Proton NMR spin-lattice relaxation times T1 were measured for urea as a function of temperature. An activation energy of 46.3 ± 4.7 kJ/mol was extracted and compared with the range of 38-65 kJ/mol previously reported in the literature as measured by different magnetic resonance techniques. In addition, proton NMR spin-lattice relaxation times in the rotating frame T1 ρ were measured as a function of temperature. These measurements provide acquisition conditions for the 13C and 15N CP/MAS spectra of pure urea in the crystalline phase.

  12. Synthesis of 5-aryl-4-(2-acetylaminobenzoyl)-1,2,3-triazoles with the /sup 15/N isotope at the terminal positions of the triazole rings and the tautomeric composition

    SciTech Connect

    Kurkovskaya, L.N.; Velezheva, V.S.; Sorokina, I.K.; Dmitrevskaya, L.I.; Zhil'nikov, V.G.

    1988-12-20

    A mixture of 4-(2-acetylaminobenzoyl)-5-phenyl(p-cumenyl)-1-/sup 15/N,2,3- and 4-(2-acetylaminobenzoyl)-5-phenyl(p-cumenyl)-1,2,3-/sup 15/N-triazoles was obtained from 1-acetyl-2-arylmethylene-3-indolinones and Na/sup 15/N/sub 3/ with the label at the terminal position. The tautomeric composition of the mixture, which corresponds to a state of equilibrium between the 2H and 3H forms of the triazole ring, was established by /sup 1/H (at low temperatures) and /sup 15/N NMR spectroscopy. The 4-(2-acetylaminobenzoyl)-5-aryl-1,2,3-triazoles are acylated at the sterically less hindered position 2 of the triazole ring.

  13. LEGO-NMR spectroscopy: a method to visualize individual subunits in large heteromeric complexes.

    PubMed

    Mund, Markus; Overbeck, Jan H; Ullmann, Janina; Sprangers, Remco

    2013-10-18

    Seeing the big picture: Asymmetric macromolecular complexes that are NMR active in only a subset of their subunits can be prepared, thus decreasing NMR spectral complexity. For the hetero heptameric LSm1-7 and LSm2-8 rings NMR spectra of the individual subunits of the complete complex are obtained, showing a conserved RNA binding site. This LEGO-NMR technique makes large asymmetric complexes accessible to detailed NMR spectroscopic studies. PMID:23946163

  14. Isolation and measurement of /sup 15/N/sub 2/ from respiratory gases of animals administered /sup 15/N-labeled substances

    SciTech Connect

    Springer, D.L.; Reed, D.J.; Dost, F.N.

    1981-07-01

    A method is described for collection of metabolic /sup 15/N/sub 2/ from in vitro preparations or intact rats administered /sup 15/N-containing compounds. The method enables routine collection and mass spectrometric measurement of as little as 10 ..mu..mol /sup 15/N/sub 2/ respired by a rat over a 24-h period. A device is described that includes either an animal chamber or a tissue reaction vessel in a closed recycling atmosphere, with automatic O/sub 2/ replenishment and removal of CO/sub 2/ and water. It is capable of sustaining moderate vacuum and is coupled to a high-vacuum manifold designed to process the contained atmosphere and respiratory gases. The starting atmosphere is an 80:20 mix of sulfur hexafluoride and O/sub 2/. Recovery of /sup 15/N/sub 2/ gas from the system without an animal present was 101.3 +/- 5.75%. When /sup 15/N/sub 2/ gas was very slowly infused iv into an animal, recovery was 89.1 +/- 5.38%. Use of the method in studies of the fate of (/sup 15/N)hydrazine in rats indicated that about 15% of the administered hydrazine is rapidly converted to /sup 15/N/sub 2/, followed by slower conversion of an additional 7-10% over the next several hours.

  15. Numerical evaluation of subsoil diffusion of (15) N labelled denitrification products during employment of the (15) N gas flux method in the field

    NASA Astrophysics Data System (ADS)

    Well, Reinhard; Buchen, Caroline; Lewicka-Szczebak, Dominika; Ruoss, Nicolas

    2016-04-01

    Common methods for measuring soil denitrification in situ include monitoring the accumulation of 15N labelled N2 and N2O evolved from 15N labelled soil nitrate pool in soil surface chambers. Gas diffusion is considered to be the main accumulation process. Because accumulation of the gases decreases concentration gradients between soil and chamber over time, gas production rates are underestimated if calculated from chamber concentrations. Moreover, concentration gradients to the non-labelled subsoil exist, inevitably causing downward diffusion of 15N labelled denitrification products. A numerical model for simulating gas diffusion in soil was used in order to determine the significance of this source of error. Results show that subsoil diffusion of 15N labelled N2 and N2O - and thus potential underestimation of denitrification derived from chamber fluxes - increases with cover closure time as well as with increasing diffusivity. Simulations based on the range of typical gas diffusivities of unsaturated soils show that the fraction of subsoil diffusion after chamber closure for 1 hour is always significant with values up to >30 % of total production of 15N labelled N2 and N2O. Field experiments for measuring denitrification with the 15N gas flux method were conducted. The ability of the model to predict the time pattern of gas accumulation was evaluated by comparing measured 15N2 concentrations and simulated values.

  16. Platinum(II) complexes with 5,7-disubstituted-1,2,4-triazolo [1,5-a]pyrimidines: Spectroscopical characterization and cytotoxic activity in vitro

    NASA Astrophysics Data System (ADS)

    Łakomska, Iwona; Fandzloch, Marzena; Popławska, Beata; Sitkowski, Jerzy

    2012-06-01

    Complexes of the types: cis-[PtI2(dptp)2] (1), cis-[PtI2(NH3)(dptp)] (2), trans-[PtI2(dptp)(dmso)] (3) and trans-[PtI2(dbtp)(dmso)] (4), where dptp = 5,7-diphenyl-1,2,4-triazolo[1,5-a]pyrimidine (dptp), dbtp = 5,7-ditertbutyl-1,2,4-triazolo[1,5-a]pyrimidine have been synthesized and characterized by infrared and multinuclear magnetic resonance spectroscopic techniques (1H, 13C, 15N, 195Pt). In 195Pt NMR, the cis-diiodo complexes were observed between -2601 ppm and -3261 ppm, while the trans coordination compounds were found at higher field (ca. -4389 ppm). In all cases significant 15N NMR shielding (92-95 ppm) were observed for N(3) atom indicating this nitrogen atom as a coordination site. The cis complexes have been assayed for antitumor activity in vitro against two human cell lines: A549 (non-small cell lung carcinoma) and T47D (breast cancer). The results indicate a moderate antiproliferative activity of (2) against human cancer lines.

  17. (1)H, (13)C and (15)N backbone assignment of the EC-1 domain of human E-cadherin.

    PubMed

    Prasasty, Vivitri D; Krause, Mary E; Tambunan, Usman S F; Anbanandam, Asokan; Laurence, Jennifer S; Siahaan, Teruna J

    2015-04-01

    The Extracellular 1 (EC1) domain of E-cadherin has been shown to be important for cadherin-cadherin homophilic interactions. Cadherins are responsible for calcium-mediated cell-cell adhesion located at the adherens junction of the biological barriers (i.e., intestinal mucosa and the blood-brain barrier (BBB)). Cadherin peptides can modulate cadherin interactions to improve drug delivery through the BBB. However, the mechanism of modulating the E-cadherin interactions by cadherin peptides has not been fully elucidated. To provide a basis for subsequent examination of the structure and peptide-binding properties of the EC1 domain of human E-cadherin using solution NMR spectroscopy, the (1)H, (13)C and (15)N backbone resonance of the uniformly labeled-EC1 were assigned and the secondary structure was determined based on the chemical shift values. These resonance assignments are essential for assessing protein-ligand interactions and are reported here. PMID:24510398

  18. Benchmark fragment-based (1)H, (13)C, (15)N and (17)O chemical shift predictions in molecular crystals.

    PubMed

    Hartman, Joshua D; Kudla, Ryan A; Day, Graeme M; Mueller, Leonard J; Beran, Gregory J O

    2016-08-21

    The performance of fragment-based ab initio(1)H, (13)C, (15)N and (17)O chemical shift predictions is assessed against experimental NMR chemical shift data in four benchmark sets of molecular crystals. Employing a variety of commonly used density functionals (PBE0, B3LYP, TPSSh, OPBE, PBE, TPSS), we explore the relative performance of cluster, two-body fragment, and combined cluster/fragment models. The hybrid density functionals (PBE0, B3LYP and TPSSh) generally out-perform their generalized gradient approximation (GGA)-based counterparts. (1)H, (13)C, (15)N, and (17)O isotropic chemical shifts can be predicted with root-mean-square errors of 0.3, 1.5, 4.2, and 9.8 ppm, respectively, using a computationally inexpensive electrostatically embedded two-body PBE0 fragment model. Oxygen chemical shieldings prove particularly sensitive to local many-body effects, and using a combined cluster/fragment model instead of the simple two-body fragment model decreases the root-mean-square errors to 7.6 ppm. These fragment-based model errors compare favorably with GIPAW PBE ones of 0.4, 2.2, 5.4, and 7.2 ppm for the same (1)H, (13)C, (15)N, and (17)O test sets. Using these benchmark calculations, a set of recommended linear regression parameters for mapping between calculated chemical shieldings and observed chemical shifts are provided and their robustness assessed using statistical cross-validation. We demonstrate the utility of these approaches and the reported scaling parameters on applications to 9-tert-butyl anthracene, several histidine co-crystals, benzoic acid and the C-nitrosoarene SnCl2(CH3)2(NODMA)2. PMID:27431490

  19. Lactoperoxidase-catalyzed oxidation of thiocyanate by hydrogen peroxide: sup 15 N nuclear magnetic resonance and optical spectral studies

    SciTech Connect

    Modi, S.; Deodhar, S.S.; Behere, D.V.; Mitra, S. )

    1991-01-01

    To establish the agent(s) responsible for the activity of the lactoperoxidase (LPO)/SCN{sup {minus}}/H{sub 2}O{sub 2} system, the oxidation of thiocyanate with hydrogen peroxide, catalyzed by lactoperoxidase, has been studied by {sup 15}N NMR and optical spectroscopy at different concentrations of thiocyanate and hydrogen peroxide and at different pHs. The formation of hypothiocyanite ion (OSCN{sup {minus}}) as one of the oxidation products correlated well with activity of the LPO/SCN{sup {minus}}/H{sub 2}O{sub 2} system and was maximum when the concentrations of the H{sub 2}O{sub 2} and SCN{sup {minus}} were nearly the same and the pH was <6.0. At (H{sub 2}O{sub 2})/(SCN{sup {minus}}) = 1, OSCN{sup {minus}} decomposed very slowly back to thiocyanate. When the ratio (H{sub 2}O{sub 2})/(SCN{sup {minus}}) was above 2, formation of CN{sup {minus}} was observed, which was confirmed by {sup 15}N NMR and also by changes in the optical spectrum of LPO. The oxidation of thiocyanate by H{sub 2}O{sub 2} in the presence of LPO does not take place at pH >8.0. Since thiocyanate does not bind to LPO above this pH, the binding of thiocyanate to LPO is considered to be prerequisite for the oxidation of thiocyanate. Maximum inhibition of oxygen uptake by Streptococcus cremoris 972 bacteria was observed when hydrogen peroxide and thiocyanate were present in equimolar amounts and the pH was below 6.0.

  20. Ner protein of phage Mu: Assignments using {sup 13}C/{sup 15}N-labeled protein

    SciTech Connect

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

    1994-12-01

    The Ner protein is a small (74-amino acid) DNA-binding protein that regulates a switch between the lysogenic and lytic stages of phage Mu. It inhibits expression of the C repressor gene and down-regulates its own expression. Two-dimensional NMR experiments on uniformly {sup 15}N-labeled protein provided most of the backbone and some of the sidechain proton assignments. The secondary structure determination using two-dimensional NOESY experiments showed that Ner consists of five {alpha}-helices. However, because most of the sidechain protons could not be assigned, the full structure was not determined. Using uniformly {sup 13}C/{sup 15}N-labeled Ner and a set of three-dimensional experiments, we were able to assign all of the backbone and 98% of the sidechain protons. In particular, the CBCANH and CBCA(CO)NH experiments were used to sequentially assign the C{alpha} and C{beta} resonances; the HCCH-CTOCSY and HCCH-COSY were used to assign sidechain carbon and proton resonances.

  1. Probing Cancer Cell Metabolism Using NMR Spectroscopy.

    PubMed

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

    2016-01-01

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

  2. 13C and 15N fractionation of CH4/N2 mixtures during photochemical aerosol formation: Relevance to Titan

    NASA Astrophysics Data System (ADS)

    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.

  3. Soil processes drive seasonal variation in retention of 15N tracers in a deciduous forest catchment.

    PubMed

    Goodale, Christine L; Fredriksen, Guinevere; Weiss, Marissa S; McCalley, K; Sparks, Jed P; Thomas, Steven A

    2015-10-01

    Seasonal patterns of stream nitrate concentration have long been interpreted as demonstrating the central role of plant uptake in regulating stream nitrogen loss from forested catchments. Soil processes are rarely considered as important drivers of these patterns. We examined seasonal variation in N retention in a deciduous forest using three whole-ecosystem 15N tracer additions: in late April (post-snowmelt, pre-leaf-out), late July (mid-growing- season), and late October (end of leaf-fall). We expected that plant 15N uptake would peak in late spring and midsummer, that immobilization in surface litter and soil would peak the following autumn leaf-fall, and that leaching losses would vary inversely with 15N retention. Similar to most other 15N tracer studies, we found that litter and soils dominated ecosystem retention of added 15N. However, 15N recovery in detrital pools varied tremendously by season, with > 90% retention in spring and autumn and sharply reduced 15N retention in late summer. During spring, over half of the 15N retained in soil occurred within one day in the heavy (mineral-associated) soil fraction. During summer, a large decrease in 15N retention one week after addition coincided with increased losses of 15NO3- to soil leachate and seasonal increases in soil and stream NO3- concentrations, although leaching accounted for only a small fraction of the lost 15N (< 0.2%). Uptake of 15N into roots did not vary by season and accounted for < 4% of each tracer addition. Denitrification or other processes that lead to N gas loss may have consumed the rest. These measurements of 15N movement provide strong evidence for the dominant role of soil processes in regulating seasonal N retention and losses in this catchment and perhaps others with similar soils. PMID:26649387

  4. Thiol-thione tautomeric analysis, spectroscopic (FT-IR, Laser-Raman, NMR and UV-vis) properties and DFT computations of 5-(3-pyridyl)-4H-1,2,4-triazole-3-thiol molecule

    NASA Astrophysics Data System (ADS)

    Gökce, Halil; Öztürk, Nuri; Ceylan, Ümit; Alpaslan, Yelda Bingöl; Alpaslan, Gökhan

    2016-06-01

    In this study, the 5-(3-pyridyl)-4H-1,2,4-triazole-3-thiol molecule (C7H6N4S) molecule has been characterized by using FT-IR, Laser-Raman, NMR and UV-vis spectroscopies. Quantum chemical calculations have been performed to investigate the molecular structure (thione-thiol tautomerism), vibrational wavenumbers, electronic transition absorption wavelengths in DMSO solvent and vacuum, proton and carbon-13 NMR chemical shifts and HOMOs-LUMOs energies at DFT/B3LYP/6-311 ++G(d,p) level for all five tautomers of the title molecule. The obtained results show that the calculated vibrational wavenumbers, NMR chemical shifts and UV-vis wavelengths are in a good agreement with experimental data.

  5. Thiol-thione tautomeric analysis, spectroscopic (FT-IR, Laser-Raman, NMR and UV-vis) properties and DFT computations of 5-(3-pyridyl)-4H-1,2,4-triazole-3-thiol molecule.

    PubMed

    Gökce, Halil; Öztürk, Nuri; Ceylan, Ümit; Alpaslan, Yelda Bingöl; Alpaslan, Gökhan

    2016-06-15

    In this study, the 5-(3-pyridyl)-4H-1,2,4-triazole-3-thiol molecule (C7H6N4S) molecule has been characterized by using FT-IR, Laser-Raman, NMR and UV-vis spectroscopies. Quantum chemical calculations have been performed to investigate the molecular structure (thione-thiol tautomerism), vibrational wavenumbers, electronic transition absorption wavelengths in DMSO solvent and vacuum, proton and carbon-13 NMR chemical shifts and HOMOs-LUMOs energies at DFT/B3LYP/6-311++G(d,p) level for all five tautomers of the title molecule. The obtained results show that the calculated vibrational wavenumbers, NMR chemical shifts and UV-vis wavelengths are in a good agreement with experimental data. PMID:27054702

  6. A Primer of Fourier Transform NMR.

    ERIC Educational Resources Information Center

    Macomber, Roger S.

    1985-01-01

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

  7. NMR Studies of the Li-Mg-N-H Phases.

    NASA Astrophysics Data System (ADS)

    Bowman, Robert; Reiter, J. W.; Kulleck, J. G.; Hwang, S.-J.; Luo, Weifang

    2007-03-01

    Solid state NMR including magic-angle-spinning (MAS) and cross-polarization (CP) MAS experiments have been used to characterize various amide and imide phases containing Li and/or Mg. MAS-NMR spectra for the ^1H, ^6Li, ^7Li, and ^15N nuclei have been obtained to improve understanding on formation, processing, and degradation behavior. Only limited information could be obtained from the proton and ^7Li MAS-NMR spectra to due large dipolar interactions and small chemical shifts. However, more success was obtained from the ^6Li and ^15N nuclei although their very long spin-lattice relaxation times did impact signal acquisition times. For example, three distinct ^6Li peaks were resolved from LiNH2 phases that were clearly separated from the LiH secondary phase in these samples. While the ^15N spectra for LiNH2 phase in isotopically enriched samples exhibited only a single peak at least three distinct ^15N peaks were observed from the similarly enriched Mg amide samples. These differences will be related to crystal structures. The NMR spectra also revealed very little motion in these hydrides upon to nearly 500 K.

  8. NMR Imaging: Instrumentation and Techniques

    NASA Astrophysics Data System (ADS)

    Tingle, Jeremy Mark

    Available from UMI in association with The British Library. This thesis presents three original contributions to the field of Nuclear Magnetic Resonance (NMR): the experimental framework and analysis for the measurement of a new imaging parameter to describe perfusion; the measurement and analysis of magnetic field inhomogeneity and a practical correction system for their reduction; a novel system for the synchronous control of NMR experiments based on the microprogrammed concept. The thesis begins with an introduction to the theory of NMR. The application of NMR to imaging is also introduced with emphasis on the techniques which developed into those in common use today. Inaccurate determination of the traditional NMR parameters (T_1 and T_2 and the molecular diffusion coefficient) can be caused by non-diffusive fluid movement within the sample. The experimental basis for determining a new imaging parameter --the Perfusion coefficient--is presented. This provides a measure of forced isotropic fluid motion through an organ or tissue. The instrumentation required for conducting NMR experiments is described in order to introduce the contribution made in this area during this research: A sequence controller. The controller is based on the concept of microprogramming and enables completely synchronous output of 128 bits of data. The software for the generation and storage of control data and the regulation of the data to provide experimental control is microcomputer based. It affords precise and accurate regulation of the magnetic field gradients, the rf synthesizer and the spectrometer for spectroscopic and imaging applications. Fundamental to the science of NMR is the presence of a magnetic field. A detailed study of the analysis of magnetic field inhomogeneity in terms of spherical harmonics is presented. The field of a whole body imaging system with poor inhomogeneity was measured and analyzed to determine and describe the components of the inhomogeneity. Finally a

  9. Factors Controlling the Stable Nitrogen Isotopic Composition (δ15N) of Lipids in Marine Animals.

    PubMed

    Svensson, Elisabeth; Schouten, Stefan; Hopmans, Ellen C; Middelburg, Jack J; Sinninghe Damsté, Jaap S

    2016-01-01

    Lipid extraction of biomass prior to stable isotope analysis is known to cause variable changes in the stable nitrogen isotopic composition (δ15N) of residual biomass. However, the underlying factors causing these changes are not yet clear. Here we address this issue by comparing the δ15N of bulk and residual biomass of several marine animal tissues (fish, crab, cockle, oyster, and polychaete), as well as the δ15N of the extracted lipids. As observed previously, lipid extraction led to a variable offset in δ15N of biomass (differences ranging from -2.3 to +1.8 ‰). Importantly, the total lipid extract (TLE) was highly depleted in 15N compared to bulk biomass, and also highly variable (differences ranging from -14 to +0.7 ‰). The TLE consisted mainly of phosphatidylcholines, a group of lipids with one nitrogen atom in the headgroup. To elucidate the cause for the 15N-depletion in the TLE, the δ15N of amino acids was determined, including serine because it is one of the main sources of nitrogen to N-containing lipids. Serine δ15N values differed by -7 to +2 ‰ from bulk biomass δ15N, and correlated well with the 15N depletion in TLEs. On average, serine was less depleted (-3‰) than the TLE (-7 ‰), possibly due to fractionation during biosynthesis of N-containing headgroups, or that other nitrogen-containing compounds, such as urea and choline, or recycled nitrogen contribute to the nitrogen isotopic composition of the TLE. The depletion in 15N of the TLE relative to biomass increased with the trophic level of the organisms. PMID:26731720

  10. Factors Controlling the Stable Nitrogen Isotopic Composition (δ15N) of Lipids in Marine Animals

    PubMed Central

    Svensson, Elisabeth; Schouten, Stefan; Hopmans, Ellen C.; Middelburg, Jack J.; Sinninghe Damsté, Jaap S.

    2016-01-01

    Lipid extraction of biomass prior to stable isotope analysis is known to cause variable changes in the stable nitrogen isotopic composition (δ15N) of residual biomass. However, the underlying factors causing these changes are not yet clear. Here we address this issue by comparing the δ15N of bulk and residual biomass of several marine animal tissues (fish, crab, cockle, oyster, and polychaete), as well as the δ15N of the extracted lipids. As observed previously, lipid extraction led to a variable offset in δ15N of biomass (differences ranging from -2.3 to +1.8 ‰). Importantly, the total lipid extract (TLE) was highly depleted in 15N compared to bulk biomass, and also highly variable (differences ranging from -14 to +0.7 ‰). The TLE consisted mainly of phosphatidylcholines, a group of lipids with one nitrogen atom in the headgroup. To elucidate the cause for the 15N-depletion in the TLE, the δ15N of amino acids was determined, including serine because it is one of the main sources of nitrogen to N-containing lipids. Serine δ15N values differed by -7 to +2 ‰ from bulk biomass δ15N, and correlated well with the 15N depletion in TLEs. On average, serine was less depleted (-3‰) than the TLE (-7 ‰), possibly due to fractionation during biosynthesis of N-containing headgroups, or that other nitrogen-containing compounds, such as urea and choline, or recycled nitrogen contribute to the nitrogen isotopic composition of the TLE. The depletion in 15N of the TLE relative to biomass increased with the trophic level of the organisms. PMID:26731720

  11. Study on molecular structure, spectroscopic investigation (IR, Raman and NMR), vibrational assignments and HOMO-LUMO analysis of L-sodium folinate using DFT: a combined experimental and quantum chemical approach.

    PubMed

    Li, Linwei; Cai, Tiancheng; Wang, Zhiqiang; Zhou, Zhixu; Geng, Yiding; Sun, Tiemin

    2014-01-01

    In the present work, an exhaustive conformational search of N-[4-[[(2-amino-5-formyl-(6S)-3,4,5,6,7,8-hexahydro-4-oxo-6-pteridinyl)methyl]amino]benzoyl]-L-glutamic acid disodium salt (L-SF) has been preformed. The optimized structure of the molecule, vibrational frequencies and NMR spectra studies have been calculated by density functional theory (DFT) using B3LYP method with the 6-311++G (d, p) basis set. IR and FT-Raman spectra for L-SF have been recorded in the region of 400-4000 cm(-1) and 100-3500 cm(-1), respectively. 13C and 1H NMR spectra were recorded and 13C and 1H nuclear magnetic resonance chemical shifts of the molecule were calculated based on the gauge-independent atomic orbital (GIAO) method. Finally all of the calculation results were applied to simulate IR, Raman, 1H NMR and 13C NMR spectrum of the title compound which showed excellent agreement with observed spectrum. Furthermore, reliable vibrational assignments which have been made on the basis of potential energy distribution (PED) and characteristic vibratinonal absorption bands of the title compound in IR and Raman have been figured out. HOMO-LUMO energy and Mulliken atomic charges have been evaluated, either. PMID:24177877

  12. Synthesis, spectroscopic characterization, DFT studies, and antibacterial and antitumor activities of a novel water soluble Pd(II) complex with L-alliin

    NASA Astrophysics Data System (ADS)

    Abbehausen, Camilla; Sucena, Suelen F.; Lancellotti, Marcelo; Heinrich, Tassiele A.; Abrão, Emiliana P.; Costa-Neto, Claudio M.; Formiga, André L. B.; Corbi, Pedro P.

    2013-03-01

    A new water soluble Pd(II) complex with L-alliin (S-allyl-L-cysteine sulfoxide) was obtained and characterized by a set of chemical and spectroscopic measurements. Elemental and mass spectrometric data are consistent with the formula [Pd(C6H10NO3S)2]. The 1H and 13C nuclear magnetic resonance (NMR) data, [1H-15N] two dimensional (2D) NMR and infrared spectroscopic measurements indicate coordination of the ligand to Pd(II) through N and O atoms. DFT studies showed that the trans isomer is the most stable and preferred geometry for the complex. The complex is soluble in water and dimethylsulfoxide. An antibiogram assay revealed that the complex possess antibacterial activity against Escherichia coli, Pseudomonas aeruginosa and Staphylococcus aureus bacterial strains in the range 125-500 μg mL-1. Antitumor assays revealed that the complex presents cytotoxic activity over HeLa cells with an estimated IC50 of 20 μmol L-1.

  13. Sources and transformations of N in reclaimed coastal tidelands: evidence from soil δ15N data

    NASA Astrophysics Data System (ADS)

    Kwak, Jin-Hyeob; Choi, Woo-Jung; Lim, Sang-Sun; Lee, Seung-Heon; Lee, Sang-Mo; Chang, Scott X.; Jung, Jae-Woon; Yoon, Kwang-Sik; Choi, Soo-Myung

    2008-01-01

    Electrical conductivity of saturated soil extracts (ECe) in three reclaimed tideland (RTL) soils on the west coast of Korea decreased with time since reclamation, indicating natural desalinization through leaching of salts by precipitation water. Soil N concentration increased with decreasing ECe. With the increase in soil N concentration, the δ15N decreased, likely caused by the input of 15N-depleted N sources. As N2-fixing plant species were found in the oldest RTL, atmospheric N2 fixation likely contributed to the increase in soil N concentration in the oldest RTL. Negative δ15N (-7.1 to -2.0‰) of total inorganic N (NH4 ++NO3 -) and published data on N deposition near the study area indicate that atmospheric N deposition might be another source of N in the RTLs. Meanwhile, the consistently negative δ15N of soil NO3 - excluded N input from chemical fertilizer through groundwater flow as a potential N source, since NO3 - in groundwater generally have a positive δ15N. The patterns of δ15N of NH4 + (+2.3 to +5.1‰) and NO3 - (-9.2 to -5.0‰) suggested that nitrification was an active process that caused 15N enrichment in NH4 + but denitrification was probably minimal which would otherwise have caused 15N enrichment in NO3 -. A quantitative approach on N budget would provide a better understanding of soil N dynamics in the studied RTLs.

  14. Increased Plant Uptake of Nitrogen from 15N Depleted Fertilizer Using Plant Growth-Promoting Rhizobacteria

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The techniques of 15N isotope have been very useful for determining the behavior and fate of N in soil, including the use efficiency of applied N fertilizers by plants. Our objective in this study was to use 15N isotope techniques to demonstrate that a model plant growth-promoting rhizobacteria (PGP...

  15. Disturbance and topography shape nitrogen availability and δ15N over long-term forest succession

    EPA Science Inventory

    Forest disturbance and long-term succession can promote open N cycling that increases N loss and soil δ15N values. We examined soil and foliar patterns in N and δ15N, and soil N mineralization, across a topographically complex montane forest landscape influenced by human logging ...

  16. δ 15 N constraints on long-term nitrogen balances in temperate forests

    EPA Science Inventory

    Natural abundance δ15N of ecosystems integrates nitrogen (N) inputs and losses, and thus reflects factors that control the long-term development of ecosystem N balances. We here report N and carbon (C) content of forest vegetation and soils, and associated δ15N, across nine Doug...

  17. The 15N isotope effect in Escherichia coli: a neutron can make the difference.

    PubMed

    Filiou, Michaela D; Varadarajulu, Jeeva; Teplytska, Larysa; Reckow, Stefan; Maccarrone, Giuseppina; Turck, Christoph W

    2012-11-01

    Several techniques based on stable isotope labeling are used for quantitative MS. These include stable isotope metabolic labeling methods for cells in culture as well as live organisms with the assumption that the stable isotope has no effect on the proteome. Here, we investigate the (15) N isotope effect on Escherichia coli cultures that were grown in either unlabeled ((14) N) or (15) N-labeled media by LC-ESI-MS/MS-based relative protein quantification. Consistent protein expression level differences and altered growth rates were observed between (14) N and (15) N-labeled cultures. Furthermore, targeted metabolite analyses revealed altered metabolite levels between (14) N and (15) N-labeled bacteria. Our data demonstrate for the first time that the introduction of the (15) N isotope affects protein and metabolite levels in E. coli and underline the importance of implementing controls for unbiased protein quantification using stable isotope labeling techniques. PMID:22887715

  18. Symbiotic nitrogen fixation in an arid ecosystem measured by sup 15 N natural abundance

    SciTech Connect

    Johnson, G.V. )

    1990-05-01

    Plants dependent on nitrogen fixation have an {sup 15}N abundance similar to the atmosphere, while non-nitrogen fixing plants usually are enriched in {sup 15}N and are similar to soil nitrogen values. The natural abundance of {sup 15}N in leaf tissues and soils was determined to evaluate symbiotic nitrogen fixation by several legumes and actinorhizal species in the Sevilleta Long-term Ecological Research area in central New Mexico. Comparison of {delta}{sup 15}N values for the legume Prosopis glandulosa (mesquite) to adjacent Atriplex canascens (fourwing saltbush) indicated that P. glandulosa obtained 66% of its nitrogen by fixation. The legume Hoffmanseggia jamesii was found to be utilizing soil nitrogen. The {delta}{sup 15}N values for the actinorhizal plants, Elaeagnus angustifolia and Cercocarpus montanus, while below values for soil nitrogen, did not differ from associated non-fixing plants.

  19. Flexible Stoichiometry and Asymmetry of the PIDDosome Core Complex by Heteronuclear NMR Spectroscopy and Mass Spectrometry

    PubMed Central

    Nematollahi, Lily A.; Garza-Garcia, Acely; Bechara, Chérine; Esposito, Diego; Morgner, Nina; Robinson, Carol V.; Driscoll, Paul C.

    2015-01-01

    Homotypic death domain (DD)–DD interactions are important in the assembly of oligomeric signaling complexes such as the PIDDosome that acts as a platform for activation of caspase-2-dependent apoptotic signaling. The structure of the PIDDosome core complex exhibits an asymmetric three-layered arrangement containing five PIDD-DDs in one layer, five RAIDD-DDs in a second layer and an additional two RAIDD-DDs. We addressed complex formation between PIDD-DD and RAIDD-DD in solution using heteronuclear nuclear magnetic resonance (NMR) spectroscopy, nanoflow electrospray ionization mass spectrometry and size-exclusion chromatography with multi-angle light scattering. The DDs assemble into complexes displaying molecular masses in the range 130–158 kDa and RAIDD-DD:PIDD-DD stoichiometries of 5:5, 6:5 and 7:5. These data suggest that the crystal structure is representative of only the heaviest species in solution and that two RAIDD-DDs are loosely attached to the 5:5 core. Two-dimensional 1H,15N-NMR experiments exhibited signal loss upon complexation consistent with the formation of high-molecular-weight species. 13C-Methyl-transverse relaxation optimized spectroscopy measurements of the PIDDosome core exhibit signs of differential line broadening, cross-peak splitting and chemical shift heterogeneity that reflect the presence of non-equivalent sites at interfaces within an asymmetric complex. Experiments using a mutant RAIDD-DD that forms a monodisperse 5:5 complex with PIDD-DD show that the spectroscopic signature derives from the quasi- but non-exact equivalent environments of each DD. Since this characteristic was previously demonstrated for the complex between the DDs of CD95 and FADD, the NMR data for this system are consistent with the formation of a structure homologous to the PIDDosome core. PMID:25528640

  20. Flexible stoichiometry and asymmetry of the PIDDosome core complex by heteronuclear NMR spectroscopy and mass spectrometry.

    PubMed

    Nematollahi, Lily A; Garza-Garcia, Acely; Bechara, Chérine; Esposito, Diego; Morgner, Nina; Robinson, Carol V; Driscoll, Paul C

    2015-02-27

    Homotypic death domain (DD)-DD interactions are important in the assembly of oligomeric signaling complexes such as the PIDDosome that acts as a platform for activation of caspase-2-dependent apoptotic signaling. The structure of the PIDDosome core complex exhibits an asymmetric three-layered arrangement containing five PIDD-DDs in one layer, five RAIDD-DDs in a second layer and an additional two RAIDD-DDs. We addressed complex formation between PIDD-DD and RAIDD-DD in solution using heteronuclear nuclear magnetic resonance (NMR) spectroscopy, nanoflow electrospray ionization mass spectrometry and size-exclusion chromatography with multi-angle light scattering. The DDs assemble into complexes displaying molecular masses in the range 130-158kDa and RAIDD-DD:PIDD-DD stoichiometries of 5:5, 6:5 and 7:5. These data suggest that the crystal structure is representative of only the heaviest species in solution and that two RAIDD-DDs are loosely attached to the 5:5 core. Two-dimensional (1)H,(15)N-NMR experiments exhibited signal loss upon complexation consistent with the formation of high-molecular-weight species. (13)C-Methyl-transverse relaxation optimized spectroscopy measurements of the PIDDosome core exhibit signs of differential line broadening, cross-peak splitting and chemical shift heterogeneity that reflect the presence of non-equivalent sites at interfaces within an asymmetric complex. Experiments using a mutant RAIDD-DD that forms a monodisperse 5:5 complex with PIDD-DD show that the spectroscopic signature derives from the quasi- but non-exact equivalent environments of each DD. Since this characteristic was previously demonstrated for the complex between the DDs of CD95 and FADD, the NMR data for this system are consistent with the formation of a structure homologous to the PIDDosome core. PMID:25528640

  1. Disturbance and topography shape nitrogen availability and δ15 N over long-term forest succession

    USGS Publications Warehouse

    Perakis, Steven; Tepley, Alan J.; Compton, Jana

    2015-01-01

    Forest disturbance and long-term succession towards old-growth are thought to increase nitrogen (N) availability and N loss, which should increase soil δ15N values. We examined soil and foliar patterns in N and δ15N, and soil N mineralization, across 800 years of forest succession in a topographically complex montane landscape influenced by human logging and wildfire. In contrast to expectations, we found that disturbance caused declines in surface mineral soil δ15N values, both in logged forests measured 40–50 years after disturbance, and in unlogged forests disturbed by severe wildfire within the last 200 years. Both symbiotic N fixation and N transfers from disturbed vegetation and detritus could lower soil δ15N values after disturbance. A more important role for symbiotic N fixation is suggested by lower soil δ15N values in slow-successional sites with slow canopy closure, which favors early-successional N fixers. Soil δ15N values increased only marginally throughout 800 years of succession, reflecting soil N uptake by vegetation and strong overall N retention. Although post-disturbance N inputs lowered surface soil δ15N values, steady-state mass balance calculations suggest that wildfire combustion of vegetation and detritus can dominate long-term N loss and increase whole-ecosystem δ15N. On steeper topography, declining soil δ15N values highlight erosion and accelerated soil turnover as an additional abiotic control on N balances. We conclude for N-limited montane forests that soil δ15N and N availability are less influenced by nitrate leaching and denitrification loss than by interactions between disturbance, N fixation, and erosion.

  2. Structure effects in the 15N(n ,γ )16N radiative capture reaction from the Coulomb dissociation of 16N

    NASA Astrophysics Data System (ADS)

    Neelam, Shubhchintak, Chatterjee, R.

    2015-10-01

    Background: The 15N(n ,γ )16N reaction plays an important role in red giant stars and also in inhomogeneous big bang nucleosynthesis. However, there are controversies regarding spectroscopic factors of the four low-lying states of 16N, which have direct bearing on the total direct capture cross section and also on the reaction rate. Direct measurements of the capture cross section at low energies are scarce and available only at three energies below 500 keV. Purpose: The aim of this paper is to calculate the 15N(n ,γ )16N radiative capture cross section and its subsequent reaction rate by an indirect method and in that process investigate the effects of spectroscopic factors of different levels of 16N to the cross section. Method: A fully quantum mechanical Coulomb breakup theory under the aegis of post-form distorted wave Born approximation is used to calculate the Coulomb breakup of 16N on Pb at 100 MeV/u . This is then related to the photodisintegration cross section of 16N(γ ,n )15N and subsequently invoking the principle of detailed balance, the 15N(n ,γ )16N capture cross section is calculated. Results: The nonresonant capture cross section is calculated with spectroscopic factors from the shell model and those extracted (including uncertainties) from two recent experiments. The data seem to favor a more single particle nature for the low-lying states of 16N. The total neutron capture rate is also calculated by summing up nonresonant and resonant (significant only at temperatures greater than 1 GK) contributions and comparison is made with other charged particle capture rates. In the typical temperature range of 0.1 -1.2 GK, almost all the contributions to the reaction rate come from capture cross sections below 0.25 MeV. Conclusion: We have attempted to resolve the discrepancy in the spectroscopic factors of low-lying 16N levels and conclude that it would certainly be useful to perform a Coulomb dissociation experiment to find the low energy capture

  3. Compound-specific 15N analysis of amino acids in 15N tracer experiments provide an estimate of newly synthesised soil protein from inorganic and organic substrates

    NASA Astrophysics Data System (ADS)

    Charteris, Alice; Michaelides, Katerina; Evershed, Richard

    2015-04-01

    Organic N concentrations far exceed those of inorganic N in most soils and despite much investigation, the composition and cycling of this complex pool of SOM remains poorly understood. A particular problem has been separating more recalcitrant soil organic N from that actively cycling through the soil system; an important consideration in N cycling studies and for the soil's nutrient supplying capacity. The use of 15N-labelled substrates as stable isotope tracers has contributed much to our understanding of the soil system, but the complexity and heterogeneity of soil organic N prevents thorough compound-specific 15N analyses of organic N compounds and makes it difficult to examine any 15N-labelled organic products in any detail. As a result, a significant proportion of previous work has either simply assumed that since the majority of soil N is organic, all of the 15N retained in the soil is organic N (e.g. Sebilo et al., 2013) or subtracted 15N-labelled inorganic compounds from bulk values (e.g. Pilbeam et al., 1997). While the latter approach is more accurate, these methods only provide an estimate of the bulk 15N value of an extremely complex and non-uniformly labelled organic pool. A more detailed approach has been to use microbial biomass extraction (Brookes et al., 1985) and subsequent N isotopic analysis to determine the 15N value of biomass-N, representing the fraction of 15N assimilated by microbes or the 15N cycling through the 'living' or 'active' portion of soil organic N. However, this extraction method can only generate estimates and some lack of confidence in its validity and reliability remains. Here, we present an alternative technique to obtain a measure of the assimilation of an applied 15N substrate by the soil microbial biomass and an estimate of the newly synthesized soil protein, which is representative of the magnitude of the active soil microbial biomass. The technique uses a stable isotope tracer and compound-specific 15N analysis, but

  4. Quantum mechanical and spectroscopic (FT-IR, 13C, 1H NMR and UV) investigations of 2-(5-(4-Chlorophenyl)-3-(pyridin-2-yl)-4,5-dihydropyrazol-1-yl)benzo[d]thiazole by DFT method

    NASA Astrophysics Data System (ADS)

    Diwaker

    2014-07-01

    The electronic, NMR, vibrational, structural properties of a new pyrazoline derivative: 2-(5-(4-Chlorophenyl)-3-(pyridine-2-yl)-4,5-dihydropyrazol-1-yl)benzo[d]thiazole has been studied using Gaussian 09 software package. Using VEDA 4 program we have reported the PED potential energy distribution of normal mode of vibrations of the title compound. We have also reported the 1H and 13C NMR chemical shifts of the title compound using B3LYP level of theory with 6-311++G(2d,2p) basis set. Using time dependent (TD-DFT) approach electronic properties such as HOMO and LUMO energies, electronic spectrum of the title compound has been studied and reported. NBO analysis and MEP surface mapping has also been calculated and reported using ab initio methods.

  5. Indirect Measurement of {sup 15}N(p,{alpha}){sup 12}C and {sup 18}O(p,{alpha}){sup 15}N. Applications to the AGB Star Nucleosynthesis

    SciTech Connect

    La Cognata, M.; Spitaleri, C.; Cherubini, S.; Crucilla, V.; Gulino, M.; Lamia, L.; Pizzone, R. G.; Puglia, S. M. R.; Rapisarda, G. G.; Romano, S.; Sergi, M. L.; Tumino, A.; Tribble, R.; Al-Abdullah, T.; Banu, A.; Fu, C.; Goldberg, V.; Mukhamedzhanov, A.; Tabacaru, G.; Trache, L.

    2008-04-06

    The Trojan Horse Method has been recently applied to the study of reactions involved in fluorine nucleosynthesis inside AGB stars. Fluorine abundance is important since it allows to constrain mixing models from the comparison of the observed fluorine abundances with the ones predicted by models. Anyway direct measurements of the cross section do not extend down to the Gamow peak, which is the astrophysically relevant energy region. In particular the study focuses on the {sup 15}N(p,{alpha}){sup 12}C and the {sup 18}O(p,{alpha}){sup 15}N reactions which can influence fluorine yield as they are part of {sup 19}F production/destruction network.

  6. 15N Content Reflects Development of Mycorrhizae and Nitrogen Dynamics During Primary Succession

    NASA Astrophysics Data System (ADS)

    Hobbie, E. A.; Jumpponen, A.

    2004-05-01

    Mycorrhizal fungi are ubiquitous symbionts on terrestrial plants that are particularly important for plant nitrogen nutrition. 15N content appears to be a useful marker of the mycorrhizal role in plant nitrogen supply because of an apparent fractionation against 15N during transfer of nitrogen from mycorrhizal fungi to host plants. Because plants developing during primary succession are gradually colonized by mycorrhizal fungi, such situations provide good opportunities to study interactions between mycorrhizal colonization and plant 15N content. Here, we present results of a study of nitrogen isotope patterns in ecosystem components during the first 100 years of ecosystem development after glacial retreat, and compare those patterns with those on adjacent mature terrain. Soils in primary succession were depleted in 15N relative to nitrogen-fixing plants. Nonmycorrhizal plants and plants generally colonized by ectomycorrhizal, ericoid, or arbuscular fungi showed similar 15N content very early in succession (-4 to -6‰ ), corresponding to low colonization levels of all plant species. Subsequent colonization of evergreen plants by ectomycorrhizal and ericoid fungi led to a 5-6‰ decline in 15N content, indicating transfer of 15N-depleted N from fungi to plants. The values recorded (-10 to -14‰ ) are among the lowest yet observed in vascular plants. Nonmycorrhizal plants and plants colonized by arbuscular mycorrhizal fungi did not decline in 15N content. Most ectomycorrhizal and saprotrophic fungi were similar in 15N content in early succession (-1 to -3‰ ), with the notable exception of ectomycorrhizal fungi suspected of proteolytic capabilities, which were 15N enriched relative to all other fungi. 15N contents in both plants and soil from the mature site were 5‰ greater than in recently exposed sites. We conclude that 1) the primary nitrogen source to this ecosystem must be atmospheric deposition, 2) low plant 15N content generally corresponds with greater

  7. Climate-Dependence of Plant-Soil 15N/14N Interactions Across Tropical Rainforests

    NASA Astrophysics Data System (ADS)

    Houlton, B. Z.; Sigman, D. M.; Hedin, L. O.

    2005-12-01

    In most areas of the world, the 15N/14N of bulk soils is higher than that of plant leaves, and the isotopic signatures of these two ecosystem N pools progressively diverge with increasing rainfall. However, both the cause for this isotopic trend and its implications for understanding interactions between climate and N cycles are largely unknown. We report 15N/14N measurements of nitrate, ammonium, and total dissolved N in soil extracts from a highly constrained rainfall sequence in Hawaii, across which this trend in ecosystem 15N/14N is captured, to examine the competing explanations for plant-soil 15N/14N uncouplings. While the isotopic influences of microbial transfers of N between nitrate and ammonium pools and plant-mycorrhizae interactions have been posited in plant-soil 15N/14N relationships, our data did not support an important role for either of these mechanisms. Instead, preferential regeneration of 14N during the breakdown of DON to ammonium explains why the 15N/14N of plants is lower than that of bulk soils. Fractionation at this step leads to two isotopically distinct N subcycles in each forest, a lower-15N/14N subcycle composed of ammonium, nitrate, and bulk plant biomass N that `spins' rapidly and a higher-15N/14N subcycle composed of bulk soil N and DON that is much less dynamic. The increased difference between soil and plant 15N/14N is due to changes in the impacts of nitrification and denitrification on the 15N/14N of ammonium and nitrate, coupled with a switch from nitrate to ammonium uptake by plants under the wettest conditions. For instance, the particularly large (~6 per mil) 15N/14N difference between plants and soils in the wettest sites is due to the lack of 15N-enrichment of ammonium by nitrification coupled with plant dependence on ammonium uptake only. Our results highlight the importance of interactions between DON breakdown, ecosystem N recycling, and gaseous N losses in the explaining the interactions between the 15N signatures of

  8. Characterization of a buried neutral histidine residue in Bacillus circulans xylanase: NMR assignments, pH titration, and hydrogen exchange.

    PubMed Central

    Plesniak, L. A.; Connelly, G. P.; Wakarchuk, W. W.; McIntosh, L. P.

    1996-01-01

    Bacillus circulans xylanase contains two histidines, one of which (His 156) is solvent exposed, whereas the other (His 149) is buried within its hydrophobic core. His 149 is involved in a network of hydrogen bonds with an internal water and Ser 130, as well as a potential weak aromatic-aromatic interaction with Tyr 105. These three residues, and their network of interactions with the bound water, are conserved in four homologous xylanases. To probe the structural role played by His 149, NMR spectroscopy was used to characterize the histidines in BCX. Complete assignments of the 1H, 13C, and 15N resonances and tautomeric forms of the imidazole rings were obtained from two-dimensional heteronuclear correlation experiments. An unusual spectroscopic feature of BCX is a peak near 12 ppm arising from the nitrogen bonded 1H epsilon 2 of His 149. Due to its solvent inaccessibility and hydrogen bonding to an internal water molecule, the exchange rate of this proton (4.0 x 10(-5) s-1 at pH*7.04 and 30 degrees C) is retarded by > 10(6)-fold relative to an exposed histidine. The pKa of His 156 is unperturbed at approximately 6.5, as measured from the pH dependence of the 15N- and 1H-NMR spectra of BCX. In contrast, His 149 has a pKa < 2.3, existing in the neutral N epsilon 2H tautomeric state under all conditions examined. BCX unfolds at low pH and 30 degrees C, and thus His 149 is never protonated significantly in the context of the native enzyme. The structural importance of this buried histidine is confirmed by the destablizing effect of substituting a phenylalanine or glutamine at position 149 in BCX. PMID:8931150

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

    PubMed

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

    2010-07-01

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

  10. The spectroscopic (FT-IR, FT-Raman, (l3)C, (1)H NMR and UV) and NBO analyses of 4-bromo-1-(ethoxycarbonyl)piperidine-4-carboxylic acid.

    PubMed

    Vitnik, Vesna D; Vitnik, Željko J

    2015-03-01

    In this work, we will report a combined experimental and theoretical study on molecular and vibrational structure of 4-bromo-1-(ethoxycarbonyl)piperidine-4-carboxylic acid (BEPA). BEPA has been characterized by FT-IR, FT-Raman, (1)H NMR, (13)C NMR and UV spectroscopy. The FT-IR and FT-Raman spectra of BEPA were recorded in the solid phase. The optimized geometry was calculated by B3LYP and M06-2X methods using 6-311G(d,p) basis set. The FT-IR and FT-Raman spectra of BEPA were calculated at the same level and were interpreted in terms of Potential Energy Distribution (PED) analysis. The scaled theoretical wavenumber showed very good agreement with the experimental values. The (1)H and (l3)C nuclear magnetic resonance (NMR) chemical shifts of the molecule were calculated by the Gauge-Independent Atomic Orbital (GIAO) method. Stability of the molecule arising from hyperconjugative interactions and charge delocalization has been analyzed using Natural Bond Orbital (NBO) analysis. Density plots over the highest occupied molecular orbitals (HOMO) and lowest unoccupied molecular orbitals (LUMO) energy surface directly identifies the donor and acceptor atoms in the molecule. It also provides information about the charge transfer within the molecule. To obtain chemical reactivity of the molecule, the molecular electrostatic potential (MEP) surface map is plotted over the optimized geometry of the molecule. PMID:25434858

  11. NMR Methods to Study Dynamic Allostery

    PubMed Central

    Grutsch, Sarina; Brüschweiler, Sven; Tollinger, Martin

    2016-01-01

    Nuclear magnetic resonance (NMR) spectroscopy provides a unique toolbox of experimental probes for studying dynamic processes on a wide range of timescales, ranging from picoseconds to milliseconds and beyond. Along with NMR hardware developments, recent methodological advancements have enabled the characterization of allosteric proteins at unprecedented detail, revealing intriguing aspects of allosteric mechanisms and increasing the proportion of the conformational ensemble that can be observed by experiment. Here, we present an overview of NMR spectroscopic methods for characterizing equilibrium fluctuations in free and bound states of allosteric proteins that have been most influential in the field. By combining NMR experimental approaches with molecular simulations, atomistic-level descriptions of the mechanisms by which allosteric phenomena take place are now within reach. PMID:26964042

  12. Investigation of the reaction of 1,3-dimethylurea with formaldehyde by quantitative on-line NMR spectroscopy: a model for the urea-formaldehyde system.

    PubMed

    Steinhof, Oliver; Scherr, Günter; Hasse, Hans

    2016-06-01

    Quantitative on-line NMR spectroscopy is applied to study equilibria and reaction kinetics of the reaction of formaldehyde with 1,3-dimethylurea. This reaction system serves as a model system for the much more complex but industrially relevant urea-formaldehyde system. The aim is to study individual reactions and intermediates. The 1,3-dimethylurea-formaldehyde system undergoes only four reactions and, unlike urea-formaldehyde, does not form polymers. The following reactions are studied in detail: (1) the hydroxymethylation, (2) the formation of hemiformals of the hydroxymethylated intermediate, and (3) two condensation reactions of which the first leads to methylene bridges, the other to ether bridges. NMR spectroscopic chemical shift data of the reacting species are provided for the (1) H, (13) C, and (15) N domains. Equilibrium data of reactions (1), (2), and (3) are determined by quantitative (1) H and (13) C NMR spectroscopy at molar ratios of formaldehyde to 1,3-dimethylurea between 1:2 and 16:1 at a pH value of 8.5. Reaction kinetic experiments using an NMR spectrometer coupled to a batch reactor led to a reaction kinetic model parametrized with true species concentrations. The model takes into account reactions (1), (2), and (3). It describes the reaction system well for molar ratios of 1:1, 2:1, and 4:1, temperatures of 303 to 333K, and pH values from 5.0 to 9.5. Dilution experiments with a micro mixer coupled to the NMR spectrometer are conducted to estimate the time to equilibrium of reaction (2) of which the time constant is significantly lower than those of reactions (1) and (3). Copyright © 2015 John Wiley & Sons, Ltd. PMID:26095823

  13. Nitrogen stable isotope composition (δ15N) of vehicle-emitted NOx.

    PubMed

    Walters, Wendell W; Goodwin, Stanford R; Michalski, Greg

    2015-02-17

    The nitrogen stable isotope ratio of NOx (δ(15)N-NOx) has been proposed as a regional indicator for NOx source partitioning; however, knowledge of δ(15)N values from various NOx emission sources is limited. This study presents a detailed analysis of δ(15)N-NOx emitted from vehicle exhaust, the largest source of anthropogenic NOx. To accomplish this, NOx was collected from 26 different vehicles, including gasoline and diesel-powered engines, using a modification of a NOx collection method used by the United States Environmental Protection Agency, and δ(15)N-NOx was analyzed. The vehicles sampled in this study emitted δ(15)N-NOx values ranging from -19.1 to 9.8‰ that negatively correlated with the emitted NOx concentrations (8.5 to 286 ppm) and vehicle run time because of kinetic isotope fractionation effects associated with the catalytic reduction of NOx. A model for determining the mass-weighted δ(15)N-NOx from vehicle exhaust was constructed on the basis of average commute times, and the model estimates an average value of -2.5 ± 1.5‰, with slight regional variations. As technology improvements in catalytic converters reduce cold-start emissions in the future, it is likely to increase current δ(15)N-NOx values emitted from vehicles. PMID:25621737

  14. Steroselective synthesis and application of L-( sup 15 N) amino acids

    SciTech Connect

    Unkefer, C.J. ); Lodwig, S.N. . Div. of Science)

    1991-01-01

    We have developed two general approaches to the stereoselective synthesis of {sup 15}N- and {sup 13}C-labeled amino acids. First, labeled serine, biosynthesized using the methylotrophic bacterium M. extorquens AM1, serves as a chiral precursor for the synthesis of other amino acids. For example, pyridoxal phosphate enzymes can be used for the conversion of L-({alpha}-{sup 15}N)serine to L-({alpha}-{sup 15}N)tyrosine, L-({alpha}-{sup 15}N)tryptophan, and L-({alpha}-{sup 15}N)cysteine. In the second approach, developed by Oppolzer and Tamura, an electrophilic amination'' reagent, 1-chloro-1-nitrosocyclohexane, was used to convert chiral enolates into L-{alpha}-amino acids. We prepared 1-chloro-1-({sup 15}N) nitrosocyclohexane and used it to aminate chiral enolates to produce L-({alpha}-{sup 15}N)amino acids. The stereoselectivity of this scheme using the Oppolzer sultam chiral auxiliary is remarkable, producing enantiomer ratios of 200 to 1. 22 refs., 4 figs.

  15. Production of 15N-depleted biomass during cyanobacterial N2-fixation at high Fe concentrations

    NASA Astrophysics Data System (ADS)

    Zerkle, Aubrey L.; Junium, Christopher K.; Canfield, Donald E.; House, Christopher H.

    2008-09-01

    In this study we examine the effects of varying Fe, Mo, and P concentrations on δ15N fractionation during N2 fixation in the cyanobacterium Anabaena variabilis. We show that when grown in Fe-enriched media ([Fe] ≥ 50 nM), this organism produces biomass up to 3‰ lower in δ15N than when grown in Fe-limited media ([Fe] < 50 nM). A compilation of our data with previous measurements of δ15N in N2-fixing cyanobacteria reveals a general trend toward the production of more 15N-depleted biomass at higher Fe concentrations. We discuss our results in the context of negative δ15N values preserved in Archean and some Phanerozoic sediments, generally attributed to the production of marine organic matter with low δ15N by N2 fixation (and potentially NH4+ regeneration) during periods of fluctuating nutrient dynamics. We suggest that enhanced Fe availability during periods of widespread ocean anoxia can further stimulate the production of 15N-depleted biomass by N2-fixing organisms, contributing to the isotopic record.

  16. Light-mediated 15N fractionation in Caribbean gorgonian octocorals: implications for pollution monitoring

    NASA Astrophysics Data System (ADS)

    Baker, D. M.; Kim, K.; Andras, J. P.; Sparks, J. P.

    2011-09-01

    The stable nitrogen isotope ratio ( δ 15N) of coral tissue is a useful recorder of anthropogenic pollution in tropical marine ecosystems. However, little is known of the natural environmentally induced fractionations that affect our interpretation of coral δ 15N values. In symbiotic scleractinians, light affects metabolic fractionation of N during photosynthesis, which may confound the identification of N pollution between sites of varied depth or turbidity. Given the superiority of octocorals for δ 15N studies, our goal was to quantify the effect of light on gorgonian δ 15N in the context of monitoring N pollution sources. Using field collections, we show that δ 15N declined by 1.4‰ over 20 m depth in two species of gorgonians, the common sea fan, Gorgonia ventalina, and the slimy sea plume, Pseudopterogorgia americana. An 8-week laboratory experiment with P. americana showed that light, not temperature causes this variation, whereby the lowest fractionation of the N source was observed in the highest light treatment. Finally, we used a yearlong reciprocal depth transplant experiment to quantify the time frame over which δ 15N changes in G. ventalina as a function of light regime . Over the year, δ 15N was unchanged and increased slightly in the deep control colonies and shallow colonies transplanted to the deep site, respectively. Within 6 months, colonies transplanted from deep to shallow became enriched by 0.8‰, mirroring the enrichment observed in the shallow controls, which was likely due to the combined effect of an increase in the source δ 15N and reduced fractionation. We conclude that light affects gorgonian δ 15N fractionation and should be considered in sampling designs for N pollution monitoring. However, these fractionations are small relative to differences observed between natural and anthropogenic N sources.

  17. Fate and metabolism of [15N]2,4,6-trinitrotoluene in soil.

    PubMed

    Weiss, Martin; Geyer, Roland; Russow, Rolf; Richnow, Hans H; Kästner, Matthias

    2004-08-01

    The fates of the labels from [14C] and [15N] trinitrotoluene were analyzed in bioreactors under aerobic conditions in soil treated by a fungal bioremediation process with Stropharia rugosoannulata and in control soil. Up to 17.5% of the 15N label had a different fate than the 14C label. Three N-mineralization processes were identified in detailed experiments with [15N]TNT. About 2% of the 15N label was found as NO3- and NH4+, showing simultaneous processes of direct TNT denitration (I) and reduction with cleavage of the amino groups (II). The enrichment of NO2-/NO3- (up to 7.5 atom% 15N abundance) indicates the formation of Meisenheimer complexes with a denitration of [15N]TNT. A 1.4% of the label was found distributed between N2O and N2. However, the 15N enrichment of the N2O (up to 38 atom%) demonstrated that both N atoms were generated from the labeled TNT and clearly indicates a novel formation process (III). We propose, as an explanation, the generation of N2O by cleavage from condensed azoxy metabolites. In addition, 1.7% of the 15N label was detected as biogenic amino acids in the wheat straw containing the fungus. Overall, 60 to 85% of the applied [15N]TNT was degraded and 52 to 64% was found as nonextractable residues in the soil matrix. Three percent was detected as 2-amino-4,6-dinitrotoluene and 4-amino-2,6-dinitrotoluene. PMID:15352472

  18. Chemical and spectroscopic characterizations, ESI-QTOF mass spectrometric measurements and DFT studies of new complexes of palladium(II) with tryptamine and mefenamic acid

    NASA Astrophysics Data System (ADS)

    Carvalho, Marcos A.; Arruda, Eduardo G. R.; Profirio, Daniel M.; Gomes, Alexandre F.; Gozzo, Fábio C.; Formiga, André L. B.; Corbi, Pedro P.

    2015-11-01

    New palladium(II) complexes with tryptamine (Pd-tra) and mefenamic acid (Pd-mef) were prepared and characterized by chemical and spectroscopic methods. Elemental, ESI-QTOF mass spectrometric and thermogravimetric analyses of the compounds confirm the composition [PdCl2(tra)2] for Pd-tra and [Pd(mef)2(bipy)] for Pd-mef. Infrared data indicate the coordination of tryptamine to Pd(II) by the nitrogen atom of the amino group, while for mefenamic acid coordination occurs by the oxygen atom of carboxylate group in a monodentate form. The 1H, 13C and {15N,1H} NMR spectroscopic data confirm the nitrogen coordination of the NH2 group of trypatmine to Pd(II) in the Pd-tra complex and also the oxygen coordination of the carboxylate group of mefenamic acid to Pd(II) in the Pd-mef complex. Density functional theory (DFT) studies were applied to determine the difference in energy between the geometric isomers (cis/trans) of Pd-tra and to optimize the structure of the Pd-mef complex. Raman spectroscopic measurements reinforce the nitrogen coordination of tryptamine to Pd(II) in the Pd-tra complex and confirms the presence of the cis-[PdCl2(tra)2] isomer in the solid state. The complexes are insoluble in water.

  19. Radiative p 15N Capture in the Region of Astrophysical Energies

    NASA Astrophysics Data System (ADS)

    Dubovichenko, S. B.; Burtebaev, N.; Dzhazairov-Kakhramanov, A. V.; Alimov, D. K.

    2016-06-01

    Within the framework of the modified potential cluster model with classification of orbital states according to the Young schemes, the possibility of describing experimental data for the astrophysical S-factor of p 15N radiative capture at energies from 50 to 1500 keV is considered. It is shown that on the basis of M1 and E1 transitions from various p 15N scattering states to the ground state of the 16O nucleus in the p 15N channel it is entirely possible to successfully explain the overall behavior of the S-factor in the considered energy region in the presence of two resonances.

  20. Inhibition of alanine racemase by alanine phosphonate: detection of an imine linkage to pyridoxal 5'-phosphate in the enzyme-inhibitor complex by solid-state /sup 15/N nuclear magnetic resonance

    SciTech Connect

    Copie, V.; Faraci, W.S.; Walsh, C.T.; Griffin, R.G.

    1988-07-12

    Inhibition of alanine racemase from the Gram-positive bacterium Bacillus stearothermophilus by (1-aminoethyl)phosphonic acid (Ala-P) proceeds via a two-step reaction pathway in which reactivation occurs very slowly. In order to determine the mechanism of inhibition, the authors have recorded low-temperature, solid-state /sup 15/N NMR spectra from microcrystals of the (/sup 15/N)Ala-P-enzyme complex, together with spectra of a series of model compounds that provide the requisite database for the interpretation of the /sup 15/N chemical shifts. Proton-decoupled spectra of the microcrystals exhibit a line at approx. 150 ppm, which conclusively demonstrates the presence of a protonated Ala-P-PLP aldimine and thus clarifies the structure of the enzyme-inhibitor complex. They also report the pH dependence of Ala-P binding to alanine racemase.

  1. Nitrogen dynamics in a Western Boundary Upwelling System (Cabo Frio, Brazil) based on δ15N-nitrate and δ15N of sinking particle signals

    NASA Astrophysics Data System (ADS)

    Fontana, L.; Belem, A. L.; Venancio, I.; Duarte, C.; Chiara, S. D.; Albuquerque, A. L.

    2014-12-01

    To improve the efficiency of upwelling to control nitrogen dynamic in the ocean, better understanding of the occurring processes is necessary. This research explores δ15N of nitrate and sinking particles on a western boundary upwelling System (Cabo Frio, Brazil). The Continental Shelf of southeastern Brazil is dominated by the oligotrophic Brazil Current, whose instabilities promote the coastal upwelling of South Atlantic Central Water (SACW), and consequently increases of primary productivity. The coastal upwelling system plays an important role in the nitrogen dynamics on the Cabo Frio Upwelling System (CFUS). However, the interactions between biological induced processes, including biological N-fixation and nitrate inputs from upwelled waters in CFUS still have not been well explored. Then, this study aims clarify N-dynamics on CFUS based on a cross-shelf approach. δ15N-nitrate was characterized for each water masses present on the shelf (South Atlantic Central Water, Tropical Water and Coastal Water) and associated with physicochemical parameters (T/S, nutrients), as well as the δ15N of sinking particles at different depths (from surface to the bottom water). Samples were collected in a time interval of 1 month during ~4 years (2011 to 2014). Cross-shelf gradients of nitrogen species concentration (ammonium + nitrite + nitrate) and stable isotopes were observed. The δ15N of nitrate and sinking particles were interpreted according to the prevailing processes of the N-transformations. Considering the region as N-limited (N:P < 16), processes as biological N-fixation seems to be dominant on oligotrophic Tropical Waters. Coastal upwelled SACW showed δ15N-nitrate signature within the global average of deep ocean (5-6‰) characterizing the inner and mid-shelf conditions, where the input of new nitrate from upwelling is rapidly used by organisms in the euphotic zone without any fractionation. On the other hands, the dominance of N-limited Tropical Waters on the

  2. Silver sulfadoxinate: Synthesis, structural and spectroscopic characterizations, and preliminary antibacterial assays in vitro

    NASA Astrophysics Data System (ADS)

    Zanvettor, Nina T.; Abbehausen, Camilla; Lustri, Wilton R.; Cuin, Alexandre; Masciocchi, Norberto; Corbi, Pedro P.

    2015-02-01

    The sulfa drug sulfadoxine (SFX) reacted with Ag+ ions in aqueous solution, affording a new silver(I) complex (AgSFX), which was fully characterized by chemical, spectroscopic and structural methods. Elemental, ESI-TOF mass spectrometric and thermal analyses of AgSFX suggested a [Ag(C12H13N4O2S)] empirical formula. Infrared spectroscopic measurements indicated ligand coordination to Ag(I) through the nitrogen atoms of the (deprotonated) sulfonamide group and by the pyrimidine ring, as well as through oxygen atom(s) of the sulfonamide group. These hypotheses were corroborated by 13C and 15N SS-NMR spectroscopy and by an unconventional structural characterization based on X-ray powder diffraction data. The latter showed that AgSFX crystallizes as centrosymmetric dimers with a strong Ag⋯Ag interaction of 2.7435(6) Å, induced by the presence of exo-bidentate N,N‧ bridging ligands and the formation of an eight-membered ring of [AgNCN]2 sequence, nearly planar. Participation of oxygen atoms of the sulfonamide residues generates in the crystal a 1D coordination polymer, likely responsible for its very limited solubility in all common solvents. Besides the analytical, spectroscopic and structural description, the antibacterial properties of AgSFX were assayed using disc diffusion methods against Escherichia coli and Pseudomonas aeruginosa (Gram-negative), and Staphylococcus aureus (Gram-positive) bacterial strains. The AgSFX complex showed to be active against Gram-positive and Gram-negative bacterial strains, being comparable to the activities of silver sulfadiazine.

  3. Carbon-rich Presolar Grains from Massive Stars: Subsolar 12C/13C and 14N/15N Ratios and the Mystery of 15N

    NASA Astrophysics Data System (ADS)

    Pignatari, M.; Zinner, E.; Hoppe, P.; Jordan, C. J.; Gibson, B. K.; Trappitsch, R.; Herwig, F.; Fryer, C.; Hirschi, R.; Timmes, F. X.

    2015-08-01

    Carbon-rich grains with isotopic anomalies compared to the Sun are found in primitive meteorites. They were made by stars, and carry the original stellar nucleosynthesis signature. Silicon carbide grains of Type X and C and low-density (LD) graphites condensed in the ejecta of core-collapse supernovae. We present a new set of models for the explosive He shell and compare them with the grains showing 12C/13C and 14N/15N ratios lower than solar. In the stellar progenitor H was ingested into the He shell and not fully destroyed before the explosion. Different explosion energies and H concentrations are considered. If the supernova shock hits the He-shell region with some H still present, the models can reproduce the C and N isotopic signatures in C-rich grains. Hot-CNO cycle isotopic signatures are obtained, including a large production of 13C and 15N. The short-lived radionuclides 22Na and 26Al are increased by orders of magnitude. The production of radiogenic 22Ne from the decay of 22Na in the He shell might solve the puzzle of the Ne-E(L) component in LD graphite grains. This scenario is attractive for the SiC grains of type AB with 14N/15N ratios lower than solar, and provides an alternative solution for SiC grains originally classified as nova grains. Finally, this process may contribute to the production of 14N and 15N in the Galaxy, helping to produce the 14N/15N ratio in the solar system.

  4. New pyrolytic and spectroscopic data on Orgueil and Murchison insoluble organic matter: A different origin than soluble?

    NASA Astrophysics Data System (ADS)

    Remusat, Laurent; Derenne, Sylvie; Robert, François; Knicker, Heike

    2005-08-01

    Pyrolysis with and without tetramethylammonium hydroxide (TMAH), vacuum pyrolysis, and solid state 15N nuclear magnetic resonance (NMR) were used to examine the macromolecular insoluble organic matter (IOM) from the Orgueil and Murchison meteorites. Conventional pyrolysis reveals a set of poorly functionalized aromatic compounds, ranging from one to four rings and with random methyl substitutions. These compounds are in agreement with spectroscopic and pyrolytic results previously reported. For the first time, TMAH thermochemolysis was used to study extraterrestrial material. The detection of aromatics bearing methyl esters and methoxy groups reveals the occurrence of ester and ether bridges between aromatic units in the macromolecular network. No nitrogen-containing compounds were detected with TMAH thermochemolysis, although they are a common feature in terrestrial samples. Along with vacuum pyrolysis results, thermochemolysis shows that nitrogen is probably sequestered in condensed structures like heterocyclic aromatic rings, unlike oxygen, which is mainly located within linkages between aromatic units. This is confirmed by solid state 15N NMR performed on IOM from Orgueil, showing that nitrogen is present in pyrrole, indole, and carbazole moieties. These data show that amino acids are neither derived from the hydrolysis of IOM nor from a common precursor. In order to reconcile the literature isotopic data and the present molecular results, it is proposed that aldehydes and ketones (1) originated during irradiation of ice in space and (2) were then mobilized during the planetesimal hydrothermalism, yielding the formation of amino acids. If correct, prebiotic molecules are the products of the subsurface chemistry of planetesimals and are thus undetectable through astronomical probes.

  5. Acid treatment biasing to C/N, δ13C and δ15N of organic matter: A Molecular insight

    NASA Astrophysics Data System (ADS)

    Brodie, C.; Casford, J.; Leng, M. J.; Zong, Y.

    2011-12-01

    It is known that acid treatment methods employed to remove inorganic carbon (IC) from sample material prior to analysis for C/N, δ13C and δ15N cause non-linear, unpredictable biasing to the organic matter (OM) fraction [1, 2, 3]. Consequently, measured C/N, δ13C and δ15N have an uncertainty much greater than instrument precision with biases for C/N reported in the range of 1 - 100, for δ13C in the range of 0.2 - 6.8 % and for δ15N in the range of 0.2 - 1.5 % [1, 2, 3], in both modern and palaeo environmental materials. Brodie et al [3] extended this investigation to a down-core lake sedimentary archive (Lake Tianyang, South China) and noted the potential for this biasing to preclude "common" interpretations of the data (e.g., C/N values as an OM provenance tool; δ13C as a proxy for changes in C3 and C4 vegetation). It is evident that the size of biasing between sample horizons varies considerably implying a differential relative reaction to acid treatment down-core (i.e., as the type, relative amount and physical state of organic components changes. We now investigate this biasing at the molecular level by employing 13C-NMR and GC-IRMS techniques on a suite of modern and palaeo environmental materials and on a lake sedimentary archive. This will provide an important insight into the effect of acid treatment on organic compounds (i.e. removal from the sample, breakdown of compounds and partial removal) and associated isotopic fractionation. From an improved understanding of the type of compounds most susceptible to alteration/removal during the acid treatment processes it will be possible to consider refinements to the acid pre-treatment process and provide information on the relative down-core changes in those compounds susceptible to change (which we may be able to glean environmental information from). [1] Brodie, C.R., Leng, M.J., Casford, J.S.L., Kendrick, C.K., Lloyd, J.M., Zong, Y.Q., and Bird, M.I. (2011) Evidence for bias in C and N concentrations

  6. Fast automated protein NMR data collection and assignment by ADAPT-NMR on Bruker spectrometers

    NASA Astrophysics Data System (ADS)

    Lee, Woonghee; Hu, Kaifeng; Tonelli, Marco; Bahrami, Arash; Neuhardt, Elizabeth; Glass, Karen C.; Markley, John L.

    2013-11-01

    ADAPT-NMR (Assignment-directed Data collection Algorithm utilizing a Probabilistic Toolkit in NMR) supports automated NMR data collection and backbone and side chain assignment for [U-13C, U-15N]-labeled proteins. Given the sequence of the protein and data for the orthogonal 2D 1H-15N and 1H-13C planes, the algorithm automatically directs the collection of tilted plane data from a variety of triple-resonance experiments so as to follow an efficient pathway toward the probabilistic assignment of 1H, 13C, and 15N signals to specific atoms in the covalent structure of the protein. Data collection and assignment calculations continue until the addition of new data no longer improves the assignment score. ADAPT-NMR was first implemented on Varian (Agilent) spectrometers [A. Bahrami, M. Tonelli, S.C. Sahu, K.K. Singarapu, H.R. Eghbalnia, J.L. Markley, PLoS One 7 (2012) e33173]. Because of broader interest in the approach, we present here a version of ADAPT-NMR for Bruker spectrometers. We have developed two AU console programs (ADAPT_ORTHO_run and ADAPT_NMR_run) that run under TOPSPIN Versions 3.0 and higher. To illustrate the performance of the algorithm on a Bruker spectrometer, we tested one protein, chlorella ubiquitin (76 amino acid residues), that had been used with the Varian version: the Bruker and Varian versions achieved the same level of assignment completeness (98% in 20 h). As a more rigorous evaluation of the Bruker version, we tested a larger protein, BRPF1 bromodomain (114 amino acid residues), which yielded an automated assignment completeness of 86% in 55 h. Both experiments were carried out on a 500 MHz Bruker AVANCE III spectrometer equipped with a z-gradient 5 mm TCI probe. ADAPT-NMR is available at http://pine.nmrfam.wisc.edu/ADAPT-NMR in the form of pulse programs, the two AU programs, and instructions for installation and use.

  7. Fast automated protein NMR data collection and assignment by ADAPT-NMR on Bruker spectrometers.

    PubMed

    Lee, Woonghee; Hu, Kaifeng; Tonelli, Marco; Bahrami, Arash; Neuhardt, Elizabeth; Glass, Karen C; Markley, John L

    2013-11-01

    ADAPT-NMR (Assignment-directed Data collection Algorithm utilizing a Probabilistic Toolkit in NMR) supports automated NMR data collection and backbone and side chain assignment for [U-(13)C, U-(15)N]-labeled proteins. Given the sequence of the protein and data for the orthogonal 2D (1)H-(15)N and (1)H-(13)C planes, the algorithm automatically directs the collection of tilted plane data from a variety of triple-resonance experiments so as to follow an efficient pathway toward the probabilistic assignment of (1)H, (13)C, and (15)N signals to specific atoms in the covalent structure of the protein. Data collection and assignment calculations continue until the addition of new data no longer improves the assignment score. ADAPT-NMR was first implemented on Varian (Agilent) spectrometers [A. Bahrami, M. Tonelli, S.C. Sahu, K.K. Singarapu, H.R. Eghbalnia, J.L. Markley, PLoS One 7 (2012) e33173]. Because of broader interest in the approach, we present here a version of ADAPT-NMR for Bruker spectrometers. We have developed two AU console programs (ADAPT_ORTHO_run and ADAPT_NMR_run) that run under TOPSPIN Versions 3.0 and higher. To illustrate the performance of the algorithm on a Bruker spectrometer, we tested one protein, chlorella ubiquitin (76 amino acid residues), that had been used with the Varian version: the Bruker and Varian versions achieved the same level of assignment completeness (98% in 20 h). As a more rigorous evaluation of the Bruker version, we tested a larger protein, BRPF1 bromodomain (114 amino acid residues), which yielded an automated assignment completeness of 86% in 55 h. Both experiments were carried out on a 500 MHz Bruker AVANCE III spectrometer equipped with a z-gradient 5 mm TCI probe. ADAPT-NMR is available at http://pine.nmrfam.wisc.edu/ADAPT-NMR in the form of pulse programs, the two AU programs, and instructions for installation and use. PMID:24091140

  8. Increase of Natural 15N Enrichment of Soybean Nodules with Mean Nodule Mass 1

    PubMed Central

    Shearer, Georgia; Bryan, Barbara A.; Kohl, Daniel H.

    1984-01-01

    The 15N abundance of soybean (Glycine max L. Merrill var Harosoy) nodules is usually greater than it is for other tissues or for atmospheric N2. Results of experiments in which nodules were separated by size show that the magnitude of the 15N enrichment is correlated with nodule mass. The results support the hypothesis that 15N enrichment of nodules results from differential N isotopic fractionation for synthesis of nodule tissue versus synthesis of compounds for export from the nodule. The physiological significance of this hypothesis is that it requires that a substantial fraction of the N for nodule tissue synthesis in 15N-enriched nodules be N recently fixed within the same nodule. PMID:16663917

  9. Preparation of 13C/15N-labeled oligomers using the polymerase chain reaction

    DOEpatents

    Chen, Xian; Gupta, Goutam; Bradbury, E. Morton

    2001-01-01

    Preparation of .sup.13 C/.sup.15 N-labeled DNA oligomers using the polymerase chain reaction (PCR). A PCR based method for uniform (.sup.13 C/.sup.15 N)-labeling of DNA duplexes is described. Multiple copies of a blunt-ended duplex are cloned into a plasmid, each copy containing the sequence of interest and restriction Hinc II sequences at both the 5' and 3' ends. PCR using bi-directional primers and uniformly .sup.13 C/.sup.15 N-labeled dNTP precursors generates labeled DNA duplexes containing multiple copies of the sequence of interest. Twenty-four cycles of PCR, followed by restriction and purification, gave the uniformly .sup.13 C/.sup.15 N-labeled duplex sequence with a 30% yield. Such labeled duplexes find significant applications in multinuclear magnetic resonance spectroscopy.

  10. Eastern oyster (Crassostrea virginica) δ15N as a bioindicator of nitrogen sources: Observations and modeling

    PubMed Central

    Fertig, B.; Carruthers, T.J.B.; Dennison, W.C.; Fertig, E.J.; Altabet, M.A.

    2013-01-01

    Stable nitrogen isotopes (δ15N) in bioindicators are increasingly employed to identify nitrogen sources in many ecosystems and biological characteristics of the eastern oyster (Crassostrea virginica) make it an appropriate species for this purpose. To assess nitrogen isotopic fractionation associated with assimilation and baseline variations in oyster mantle, gill, and muscle tissue δ15N, manipulative fieldwork in Chesapeake Bay and corresponding modeling exercises were conducted. This study (1) determined that five individuals represented an optimal sample size; (2) verified that δ15N in oysters from two locations converged after shared deployment to a new location reflecting a change in nitrogen sources; (3) identified required exposure time and temporal integration (four months for muscle, two to three months for gill and mantle); and (4) demonstrated seasonal δ15N increases in seston (summer) and oysters (winter). As bioindicators, oysters can be deployed for spatial interpolation of nitrogen sources, even in areas lacking extant populations. PMID:20381097

  11. Synthesis, structural characterization, Hirshfeld surface analysis and spectroscopic studies of cadmium (II) chloride complex with 4-hydroxy-1-methylpiperidine

    NASA Astrophysics Data System (ADS)

    Soudani, S.; Ferretti, V.; Jelsch, C.; Lefebvre, F.; Nasr, C. Ben

    2016-05-01

    The chemical preparation, crystal structure, Hirshfeld surface analysis and spectroscopic characterization of the novel cadmium (II) 4-hydroxy-1-methylpiperidine complex, Cd4Cl10(C6H14NO)2·2H2O, have been reported. The atomic arrangement can be described as built up by an anionic framework, formed by edge sharing CdCl6 and CdCl5O octahedral linear chains spreading along the a-axis. These chains are interconnected by water molecules via O-H⋯Cl and O-H⋯O hydrogen bonds to form layers parallel to (011) plane. The organic cations are inserted between layers through C-H⋯Cl hydrogen bonds. Investigation of intermolecular interactions and crystal packing via Hirshfeld surface analysis reveals that the HC⋯Cl and HC⋯HC intermolecular interactions are the most abundant contacts of the organic cation in the crystal packing. The statistical analysis of crystal contacts reveals the driving forces in the packing formation. The 13C and 15N CP-MAS NMR spectra are in agreement with the X-ray structure. The vibrational absorption bands were identified by infrared spectroscopy. DFT calculations allowed the attribution of the NMR peaks and of the IR bands.

  12. Sources of δ15N variability in sinking particulate nitrogen in the Cariaco Basin, Venezuela

    NASA Astrophysics Data System (ADS)

    Montes, Enrique; Thunell, Robert; Muller-Karger, Frank E.; Lorenzoni, Laura; Tappa, Eric; Troccoli, Luis; Astor, Yrene; Varela, Ramón

    2013-09-01

    Ten years of monthly observations of the δ15N of sinking particulate nitrogen (δ15N-PN (in ‰ versus atmospheric N2)=[(15N/14N)sample/(15N/14N)standard)-1]1000) in the Cariaco Basin, Venezuela, confirm that the basin's bottom sediments store information about nitrogen dynamics related to seasonal and interannual variability in regional surface ocean processes. During the upwelling period of the southern Caribbean Sea (February-April), the δ15N-PN is similar to that of the thermocline nitrate (˜3.5‰). This nitrate is imported into the Cariaco Basin with Subtropical Underwater (SUW), which wells up near the coast. Thus, particles generated by phytoplankton photosynthesis during this productive period bear a sub-tropical North Atlantic isotopic imprint of N2 fixation (low compared to the global average of nitrate δ15N≈5‰). During the non-upwelling period when surface waters are stratified (September-November), the δ15N-PN is also 3.5-4.0‰, and reflects a mixture of local N2 fixation within the mixed layer, inputs of terrigenous organic matter and SUW nitrate consumption by phytoplankton below the mixed layer, which most likely exerts the strongest control on the δ15N-PN signal during this time. In the transition periods of May-July and December-January, the δ15N-PN increases to 4.5-6.5‰. This coincides with maxima of continental material fluxes (terrestrial PON δ15N is >6‰) into the Cariaco Basin. The δ15N signal in the sediments of the Cariaco Basin thus provides information about the relative strength of the local coastal upwelling, the relative input of continental material via river runoff, and local N2 fixation. The findings contribute to interpretations of the basin's paleoclimatic nitrogen cycle variations based on observations of the sedimentary δ15N record at this location.

  13. 15N fractionation in star-forming regions and Solar System objects

    NASA Astrophysics Data System (ADS)

    Wirström, Eva; Milam, Stefanie; Adande, Gilles; Charnley, Steven B.; Cordiner, Martin A.

    2015-08-01

    A central issue for understanding the formation and evolution of matter in the early Solar System is the relationship between the chemical composition of star-forming interstellar clouds and that of primitive Solar System materials. The pristine molecular content of comets, interplanetary dust particles and carbonaceous chondrites show significant bulk nitrogen isotopic fractionation relative to the solar value, 14N/15N ~ 440. In addition, high spatial resolution measurements in primitive materials locally show even more extreme enhancements of 14N/15N < 100.The coherent 15N enrichment in comets from different formation zones suggests that these isotopic enhancements are remnants of the interstellar chemistry in the natal molecular cloud core and the outer protosolar nebula. Indeed, early chemical models of gas-phase ion-molecule nitrogen fractionation showed that HCN and HNC (nitriles) can hold significant 15N enrichments in cold dark clouds where CO is depleted onto dust grains. In addition, 15N fractionation in nitriles and amines (NH2, NH3) follow different chemical pathways. More recently we have shown that once the spin-state dependence in rates of reactions with H2 is included in the models, amines can either be enhanced or depleted in 15N, depending on the core’s evolutionary stage. Observed 15N fractionation in amines and nitriles therefore cannot be expected to be the same, instead their ratio is a potential chemical clock.Observations of molecular isotope ratios in dark cores are challenging. Limited published results in general show higher 15N/14N ratios in HCN and HNC than ammonia, but more measurements are necessary to confirm these trends. We will present recent results from our ongoing observing campaign of 14N/15N isotopic ratios in HCN, HNC and NH3 in dense cores and protostars which seem consistent with significant fractionation in nitriles as compared to other molecules in each object. The few 14N/15N ratios observed in N2H+ are similar to

  14. 15N techniques and analytical procedures. Indo/U. S. science and technology initiative. Research report

    SciTech Connect

    Porter, L.K.; Mosier, A.R.

    1992-05-01

    (15)N technology is used to explore many agricultural research topics, including the movement of nitrates to groundwater, use of fertilizer nitrogen by plants, ways to increase nitrogen fixation, and effects of management practices on denitrification. The publication reviews (15)N procedures and methods for handling and collecting samples, introducing isotopes into plants and soils, and for performing Kjeldahl analyses, isotope dilutions, Rittenberg oxidation conversions for isotope-ration analyses, and automated Dumas isotope-ratio analyses.

  15. The First in Vivo Observation of 13C- 15N Coupling in Mammalian Brain

    NASA Astrophysics Data System (ADS)

    Kanamori, Keiko; Ross, Brian D.

    2001-12-01

    [5-13C,15N]Glutamine, with 1J(13C-15N) of 16 Hz, was observed in vivo in the brain of spontaneously breathing rats by 13C MRS at 4.7 T. The brain [5-13C]glutamine peak consisted of the doublet from [5-13C,15N]glutamine and the center [5-13C,14N]glutamine peak, resulting in an apparent triplet with a separation of 8 Hz. The time course of formation of brain [5-13C,15N]glutamine was monitored in vivo with a time resolution of 20-35 min. This [5-13C,15N]glutamine was formed by glial uptake of released neurotransmitter [5-13C]glutamate and its reaction with 15NH3 catalyzed by the glia-specific glutamine synthetase. The neurotransmitter glutamate C5 was selectively13C-enriched by intravenous [2,5-13C]glucose infusion to 13C-label whole-brain glutamate C5, followed by [12C]glucose infusion to chase 13C from the small and rapidly turning-over glial glutamate pool, leaving 13C mainly in the neurotransmitter [5-13C]glutamate pool, which is sequestered in vesicles until release. Hence, the observed [5-13C,15N]glutamine arises from a coupling between 13C of neuronal origin and 15N of glial origin. Measurement of the rate of brain [5-13C,15N]glutamine formation provides a novel noninvasive method of studying the kinetics of neurotransmitter uptake into glia in vivo, a process that is crucial for protecting the brain from glutamate excitotoxicity.

  16. Ecosystem N distribution and δ15N during a century of forest regrowth after agricultural abandonment

    USGS Publications Warehouse

    Compton, J.E.; Hooker, T.D.; Perakis, S.S.

    2007-01-01

    Stable isotope ratios of terrestrial ecosystem nitrogen (N) pools reflect internal processes and input–output balances. Disturbance generally increases N cycling and loss, yet few studies have examined ecosystem δ15N over a disturbance-recovery sequence. We used a chronosequence approach to examine N distribution and δ15N during forest regrowth after agricultural abandonment. Site ages ranged from 10 to 115 years, with similar soils, climate, land-use history, and overstory vegetation (white pine Pinus strobus). Foliar N and δ15N decreased as stands aged, consistent with a progressive tightening of the N cycle during forest regrowth on agricultural lands. Over time, foliar δ15N became more negative, indicating increased fractionation along the mineralization–mycorrhizal–plant uptake pathway. Total ecosystem N was constant across the chronosequence, but substantial internal N redistribution occurred from the mineral soil to plants and litter over 115 years (>25% of ecosystem N or 1,610 kg ha−1). Temporal trends in soil δ15N generally reflected a redistribution of depleted N from the mineral soil to the developing O horizon. Although plants and soil δ15N are coupled over millennial time scales of ecosystem development, our observed divergence between plants and soil suggests that they can be uncoupled during the disturbance-regrowth sequence. The approximate 2‰ decrease in ecosystem δ15N over the century scale suggests significant incorporation of atmospheric N, which was not detected by traditional ecosystem N accounting. Consideration of temporal trends and disturbance legacies can improve our understanding of the influence of broader factors such as climate or N deposition on ecosystem N balances and δ15N.

  17. NMR structural studies on antifreeze proteins.

    PubMed

    Sönnichsen, F D; Davies, P L; Sykes, B D

    1998-01-01

    Antifreeze proteins (AFPs) are a structurally diverse class of proteins that bind to ice and inhibit its growth in a noncolligative manner. This adsorption-inhibition mechanism operating at the ice surface results in a lowering of the (nonequilibrium) freezing point below the melting point. A lowering of approximately 1 degree C, which is sufficient to prevent fish from freezing in ice-laden seawater, requires millimolar AFP levels in the blood. The solubility of AFPs at these millimolar concentrations and the small size of the AFPs (typically 3-15 kDa) make them ideal subjects for NMR analysis. Although fish AFPs are naturally abundant, seasonal expression, restricted access to polar fishes, and difficulties in separating numerous similar isoforms have made protein expression the method of choice for producing AFPs for structural studies. Expression of recombinant AFPs has also facilitated NMR analysis by permitting isotopic labeling with 15N and 13C and has permitted mutations to be made to help with the interpretation of NMR data. NMR analysis has recently solved two AFP structures and provided valuable information about the disposition of ice-binding side chains in a third. The potential exists to solve other AFP structures, including the newly described insect AFPs, and to use solid-state NMR techniques to address fundamental questions about the nature of the interaction between AFPs and ice. PMID:9923697

  18. Elastic and inelastic scattering of 15N ions by 9Be at 84 MeV

    NASA Astrophysics Data System (ADS)

    Rudchik, A. T.; Chercas, K. A.; Kemper, K. W.; Rusek, K.; Rudchik, A. A.; Herashchenko, O. V.; Koshchy, E. I.; Pirnak, Val. M.; Piasecki, E.; Trzcińska, A.; Sakuta, S. B.; Siudak, R.; Strojek, I.; Stolarz, A.; Ilyin, A. P.; Ponkratenko, O. A.; Stepanenko, Yu. M.; Shyrma, Yu. O.; Szczurek, A.; Uleshchenko, V. V.

    2016-03-01

    Angular distributions of the 9Be + 15N elastic and inelastic scattering were measured at Elab(15N) = 84 MeV (Ec.m. = 31.5 MeV) for the 0-6.76 MeV states of 9Be and 0-6.32 MeV states of 15N. The data were analyzed within the optical model and coupled-reaction-channels method. The elastic and inelastic scattering, spin reorientations of 9Be in ground and excited states and 15N in excited states as well as the most important one- and two-step transfer reactions were included in the channels-coupling scheme. The parameters of the 9Be + 15N optical potential of Woods-Saxon form as well as deformation parameters of these nuclei were deduced. The analysis showed that the 9Be + 15N pure potential elastic scattering dominates at the forward angles whereas the ground state spin reorientation of 9Be gives a major contribution to the elastic scattering cross sections at the large angles. Contributions from particle transfers are found to be negligible for the present scattering system.

  19. Spectroscopic (FT-IR, FT-Raman, UV absorption, 1H and 13C NMR) and theoretical (in B3LYP/6-311++G** level) studies on alkali metal salts of caffeic acid

    NASA Astrophysics Data System (ADS)

    Świsłocka, Renata

    The effect of some metals on the electronic system of benzoic and nicotinic acids has recently been investigated by IR, Raman and UV spectroscopy [1-3]. Benzoic and nicotinic acids are regarded model systems representing a wide group of aromatic ligands which are incorporated into enzymes. In this work the FT-IR (in solid state and in solution), FT-Raman, UV absorption and 1H and 13C NMR spectra of caffeic acid (3,4-dihydroxycinnamic acid) and its salts with lithium, sodium, potassium, rubidium and caesium were registered, assigned and analyzed. The effect of alkali metals on the electronic system of ligands was discussed. Studies of differences in the number and position of bands from the IR, Raman, UV absorption spectra and chemical shifts from NMR spectra allowed to conclude on the distribution of electronic charge in the molecules, the delocalization energy of π electrons and the reactivity of ligands in metal complexes. Optimized geometrical structures of studied compounds were calculated by B3LYP method using 6-311++G** basis set. Bond lengths, angles and dipole moments for the optimized structures of caffeic acid and lithium, sodium, potassium caffeinates were also calculated. The theoretical wavenumbers and intensities of IR spectra were obtained. The calculated parameters were compared to the experimental characteristics of investigated compounds. Microbial activity of studied compounds was tested against Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus and Proteus vulgaris.

  20. Spectroscopic (FT-IR, FT-Raman, UV absorption, 1H and 13C NMR) and theoretical (in B3LYP/6-311++G** level) studies on alkali metal salts of caffeic acid.

    PubMed

    Świsłocka, Renata

    2013-01-01

    The effect of some metals on the electronic system of benzoic and nicotinic acids has recently been investigated by IR, Raman and UV spectroscopy [1-3]. Benzoic and nicotinic acids are regarded model systems representing a wide group of aromatic ligands which are incorporated into enzymes. In this work the FT-IR (in solid state and in solution), FT-Raman, UV absorption and (1)H and (13)C NMR spectra of caffeic acid (3,4-dihydroxycinnamic acid) and its salts with lithium, sodium, potassium, rubidium and caesium were registered, assigned and analyzed. The effect of alkali metals on the electronic system of ligands was discussed. Studies of differences in the number and position of bands from the IR, Raman, UV absorption spectra and chemical shifts from NMR spectra allowed to conclude on the distribution of electronic charge in the molecules, the delocalization energy of π electrons and the reactivity of ligands in metal complexes. Optimized geometrical structures of studied compounds were calculated by B3LYP method using 6-311++G** basis set. Bond lengths, angles and dipole moments for the optimized structures of caffeic acid and lithium, sodium, potassium caffeinates were also calculated. The theoretical wavenumbers and intensities of IR spectra were obtained. The calculated parameters were compared to the experimental characteristics of investigated compounds. Microbial activity of studied compounds was tested against Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus and Proteus vulgaris. PMID:22369898

  1. New NMR spectroscopic probe of the absolute stereoselectivity for metal-hydride and metal-alkyl additions to the carbon-carbon double bond. Demonstration with a single-component, isospecific Ziegler-Natta {alpha}-olefin polymerization catalyst

    SciTech Connect

    Gilchrist, J.H.; Bercaw, J.E.

    1996-12-04

    Optically active (98% ee) (R)-1,1,3,4,4,5,5,5-octadeutero-1-pentene (1) was prepared and used to evaluate the stereoselectivity of Y-H and Y-n-pentyl additions for the optically pure C{sub 2}-symmetric (R,S)-(BnBp)Y-R/(S,R)-(BnBp)Y-R and racemic ({+-})-(BnBp)Y-R isospecific polypropylene catalysts (BnBp = [(OC{sub 10}H{sub 6}C{sub 10}H{sub 6}O)Si(C{sub 5}H{sub 2}-2-SiMe{sub 3}-4-CMe{sub 3}){sub 2}]). Deuteration and deuterodimerization of 1 mediated by (R,S)-, (S,R)-, and ({+-})-(BnBp)Y-D provide alkanes whose {sup 1}H NMR spectra indicate the sense and magnitude of olefin facial selectivity for insertions into metal-hydride and metal-n-pentyl bonds. It is shown that useful information concerning the stereochemistry of olefin insertion can be deduced from the {sup 2}H NMR spectra of 1-pentene deuterodimers without the requirement of a stereochemically labeled pentene or a resolved catalyst. 26 refs., 4 figs.

  2. Highly 15N-Enriched Chondritic Clasts in the Isheyevo Meteorite

    SciTech Connect

    Bonal, L; Huss, G R; Krot, A N; Nagashima, K; Ishii, H A; Bradley, J P; Hutcheon, I D

    2009-01-14

    The metal-rich carbonaceous chondrites (CB and CH) have the highest whole-rock {sup 15}N enrichment ({delta}{sup 15}N up to +1500{per_thousand}), similar to {delta}{sup 15}N values reported in micron-sized regions (hotspots) of Interplanetary Dust Particles (IDPs) of possibly cometary origin and fine-grained matrices of unmetamorphosed chondrites. These {sup 15}N-rich hotspots are commonly attributed to low-temperature ion-molecule reactions in the protosolar molecular cloud or in the outer part of the protoplanetary disk. The nature of the whole-rock {sup 15}N enrichment of the metal-rich chondrites is not understood. We report a discovery of a unique type of primitive chondritic clasts in the CH/CB-like meteorite Isheyevo, which provides important constraints on the origin of {sup 15}N anomaly in metal-rich chondrites and nitrogen-isotope fractionation in the Solar System. These clasts contain tiny chondrules and refractory inclusions (5-15 {micro}m in size), and abundant ferromagnesian chondrule fragments (1-50 {micro}m in size) embedded in the partly hydrated, fine-grained matrix material composed of olivines, pyroxenes, poorly-organized aromatic organics, phyllosilicates and other hydrous phases. The mineralogy and oxygen isotope compositions of chondrules and refractory inclusions in the clasts are similar to those in the Isheyevo host, suggesting formation at similar heliocentric distances. In contrast to the previously known extraterrestrial samples, the fine-grained material in the clasts is highly and rather uniformly enriched in {sup 15}N, with bulk {delta}{sup 15}N values ranging between +1000 and +1300{per_thousand}; the {delta}{sup 15}N values in rare hotspots range from +1400 to +4000{per_thousand}. Since fine-grained matrices in the lithic clasts are the only component containing thermally unprocessed (during CAI and chondrule formation or during impact melting) materials that accreted into the metal rich chondrite parent body(ies), the {sup 15}N

  3. Effects of low-temperature catalytic pretreatments on coal structure and reactivity in liquefaction. Final technical report, Volume 2 - hydrogenative and hydrothermal pretreatments and spectroscopic characterization using pyrolysis-GC-MS, CPMAS {sup 13}C NMR and FT-IR

    SciTech Connect

    Chunshan Song; Hatcher, P.G.; Saini, A.K.; Wenzel, K.A.

    1998-01-01

    It has been indicated by DOE COLIRN panel that low-temperature catalytic pretreatment is a promising approach to the development of an improved liquefaction process. This work is a fundamental study on effects of pretreatments on coal structure and reactivity in liquefaction. The main objectives of this project are to study the coal structural changes induced by low-temperature catalytic and thermal pretreatments by using spectroscopic techniques; and to clarify the pretreatment-induced changes in reactivity or convertibility of coals. As the second volume of the final report, here we summarize our work on spectroscopic characterization of four raw coals including two subbituminous coals and two bituminous coals, tetrahydrofuran (THF)-extracted but unreacted coals, the coals (THF-insoluble parts) that have been thermally pretreated. in the absence of any solvents and in the presence of either a hydrogen-donor solvent or a non-donor solvent, and the coals (THF-insoluble parts) that have been catalytically pretreated in the presence of a dispersed Mo sulfide catalyst in the absence of any solvents and in the presence of either a hydrogen-donor solvent or a non-donor solvent.

  4. Automated protein fold determination using a minimal NMR constraint strategy

    PubMed Central

    Zheng, Deyou; Huang, Yuanpeng J.; Moseley, Hunter N.B.; Xiao, Rong; Aramini, James; Swapna, G.V.T.; Montelione, Gaetano T.

    2003-01-01

    Determination of precise and accurate protein structures by NMR generally requires weeks or even months to acquire and interpret all the necessary NMR data. However, even medium-accuracy fold information can often provide key clues about protein evolution and biochemical function(s). In this article we describe a largely automatic strategy for rapid determination of medium-accuracy protein backbone structures. Our strategy derives from ideas originally introduced by other groups for determining medium-accuracy NMR structures of large proteins using deuterated, 13C-, 15N-enriched protein samples with selective protonation of side-chain methyl groups (13CH3). Data collection includes acquiring NMR spectra for automatically determining assignments of backbone and side-chain 15N, HN resonances, and side-chain 13CH3 methyl resonances. These assignments are determined automatically by the program AutoAssign using backbone triple resonance NMR data, together with Spin System Type Assignment Constraints (STACs) derived from side-chain triple-resonance experiments. The program AutoStructure then derives conformational constraints using these chemical shifts, amide 1H/2H exchange, nuclear Overhauser effect spectroscopy (NOESY), and residual dipolar coupling data. The total time required for collecting such NMR data can potentially be as short as a few days. Here we demonstrate an integrated set of NMR software which can process these NMR spectra, carry out resonance assignments, interpret NOESY data, and generate medium-accuracy structures within a few days. The feasibility of this combined data collection and analysis strategy starting from raw NMR time domain data was illustrated by automatic analysis of a medium accuracy structure of the Z domain of Staphylococcal protein A. PMID:12761394

  5. Coherence selection in double CP MAS NMR spectroscopy

    NASA Astrophysics Data System (ADS)

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

    2008-11-01

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

  6. Mechanism of dilute-spin-exchange in solid-state NMR

    SciTech Connect

    Lu, George J.; Opella, Stanley J.

    2014-03-28

    In the stationary, aligned samples used in oriented sample (OS) solid-state NMR, {sup 1}H-{sup 1}H homonuclear dipolar couplings are not attenuated as they are in magic angle spinning solid-state NMR; consequently, they are available for participation in dipolar coupling-based spin-exchange processes. Here we describe analytically the pathways of {sup 15}N-{sup 15}N spin-exchange mediated by {sup 1}H-{sup 1}H homonuclear dipolar couplings. The mixed-order proton-relay mechanism can be differentiated from the third spin assisted recoupling mechanism by setting the {sup 1}H to an off-resonance frequency so that it is at the “magic angle” during the spin-exchange interval in the experiment, since the “magic angle” irradiation nearly quenches the former but only slightly attenuates the latter. Experimental spectra from a single crystal of N-acetyl leucine confirm that this proton-relay mechanism plays the dominant role in {sup 15}N-{sup 15}N dilute-spin-exchange in OS solid-state NMR in crystalline samples. Remarkably, the “forbidden” spin-exchange condition under “magic angle” irradiation results in {sup 15}N-{sup 15}N cross-peaks intensities that are comparable to those observed with on-resonance irradiation in applications to proteins. The mechanism of the proton relay in dilute-spin-exchange is crucial for the design of polarization transfer experiments.

  7. Acetylene inhibition of N2O reduction in laboratory soil and groundwater denitrification assays: evaluation by 15N tracer and 15N site preference of N2O

    NASA Astrophysics Data System (ADS)

    Weymann, Daniel; Well, Reinhard; Lewicka-Szczebak, Dominika; Lena, Rohe

    2013-04-01

    The measurement of denitrification in soils and aquifers is still challenging and often enough associated with considerable experimental effort and high costs. Against this background, the acetylene inhibition technique (AIT) applied in laboratory soil and groundwater denitrification assays is by far the most effective approach. However, this method has been largely criticized, as it is susceptible to underestimate denitrification rates and adds an additional carbon source to the substrates to be investigated. Here we provide evidence that the AIT is not necessarily an inappropriate approach to measure denitrification, that its reliability depends on the drivers governing the process, and that the 15N site preference of N2O (SP) may serve as a tool to assess this reliability. Two laboratory batch experiments were conducted, where sandy aquifer material and a peat soil were incubated as slurries. We established (i) a standard anaerobic treatment by adding KNO3 (10 mg N L-1), (ii) an oxygen treatment by adding KNO3 and O2 (5 mg L-1), and (iii) a glucose treatment by adding KNO3 supplemented with glucose (200 mg C L-1). Both experiments were run under 10 % (v/v) acetylene atmosphere and as 15N tracer treatments using labeled K15NO3 (60 atom % 15N). In the case of the standard anaerobic treatments, we found a very good agreement of denitrification potential obtained by the AIT and 15N tracer methods. SP of N2O of the AIT samples from this treatment ranged between -4.8 and 2.6 ‰ which is indicative for N2O production during bacterial denitrification but not for N2O reduction to N2. In contrast, we observed substantial underestimation of denitrification by AIT for the glucose treatments compared to the 15N method, i.e. denitrification was underestimated by 36 % (sandy aquifer material) and 47 % (peat soil). SP of N2O of the AIT samples from this treatment ranged between 4.5 and 9.6 ‰, which suggests occurrence of bacterial N2O reduction. In the case of the oxygen

  8. Compound-specific δ15N and chlorin preservation in surface sediments of the Peru Margin with implications for ancient bulk δ15N records

    NASA Astrophysics Data System (ADS)

    Junium, Christopher K.; Arthur, Michael A.; Freeman, Katherine H.

    2015-07-01

    Understanding the processes that control the preservation of paleoceanographic proxies is of clear importance. Surface sediments from the Peru Margin oxygen-minimum zone are subject to lateral and downslope transport by bottom currents that decrease organic matter (OM) quality. Indicators of bulk OM quality (pyrolysis hydrogen index, pyrolysis S1 + S2 and C/N) demonstrate significant degradation between 150 and 400 m water depth, within the oxygen-minimum zone. Concentrations of the three most abundant chlorins (chlorophyllone, pheophytin and pyropheophytin) decrease from 750 to 150 nmol g TOC-1 from 150 to 400 m water depth though the relative abundances of the chlorins in an individual sample do not change. This suggests that the three chlorins have similar reactivity over the ambient conditions. Values for δ15N of bulk sediments (δ15Nbulk) decrease by 3‰ from the inner shelf to the upper slope (1000 m) but co-occurring compound-specific δ15N values (δ15Nchlorin) do not decrease downslope. The low variability of δ15Nchlorin values supports a single source for the chlorins, and demonstrates the recalcitrance of δ15Nchlorin values despite degradation. This set of observation raises questions about which type of OM fraction best records 'primary' signatures. We assess two possible models to guide our interpretation of these disparate datasets (1) that decreasing δ15Nbulk values are the result of degradation of a 15N-enriched fraction during downslope transport, and that δ15Nchlorin values reflect primary values; (2) that δ15Nbulk values are primary and that chlorins are derived from material transported from upslope. These data reaffirm that in active sedimentary environments such as the Eastern Tropical Pacific, transport of OM can significantly alter bulk geochemical parameters of OM integrity, but the impacts on the δ15N record of bulk sediments and chlorins are less clear, and require more study to be thoroughly understood.

  9. A mutagenesis-free approach to assignment of (19)F NMR resonances in biosynthetically labeled proteins.

    PubMed

    Kitevski-LeBlanc, Julianne L; Al-Abdul-Wahid, M Sameer; Prosser, R Scott

    2009-02-18

    Solution NMR studies of protein structure and dynamics using fluorinated amino acid probes are a valuable addition to the repertoire of existing (13)C, (15)N, and (1)H experiments. Despite the numerous advantages of the (19)F nucleus in NMR, protein studies are complicated by the dependence of resonance assignments on site-directed mutagenesis methods which are laborious and often problematic. Here we report an NMR-based route to the assignment of fluorine resonances in (13)C,(15)N-3-fluoro-l-tyrosine labeled calmodulin. The assignment begins with the correlation of the fluorine nucleus to the delta proton in the novel (13)C,(15)N-enriched probe which is achieved using a CT-HCCF-COSY experiment. Connection to the backbone is made through two additional solution NMR experiments, namely the (H(beta))C(beta)(C(gamma)C(delta))H(delta) and HNCACB. Assignments are completed using either previously published backbone chemical shift data or obtained experimentally provided uniform (13)C,(15)N labeling procedures are employed during protein expression. Additional benefits of the (13)C,(15)N-3-fluoro-l-tyrosine probe include the reduction of spectral overlap through ((13)C(19)F) CT-HSQCs, as well as the ability to monitor side chain dynamics using (19)F T(1), T(2), and the (13)C-(19)F NOE. PMID:19173647

  10. Synthesis and valence Isomerization of delta-dimethylamino-. gamma. -chlorodienones to 2-dimethylamino-3chloro-2H-pyrans. /sup 1/H and /sup 13/C NMR and UV spectroscopic study

    SciTech Connect

    Zav'yalov, S.I.; Sitkareva, I.V.

    1985-11-01

    The authors continue their research in the development of synthetic methods for various types of sigma-dimethylamino-gamma-chlorodienones and investigate their valence isomerization: the compounds are subjected to a systematic study of their solvation, thermal, and photochromic properties. The starting materials used in this study were the previously unknown aminal (Ia) and aminoacetal (Ib) of alpha-chloro-beta-dimethylaminoacrolein; these compounds were obtained via the reaction of (2-chloro-3-dimethylamino-2-propenylidene) dimethylammonium perchlorate (II) with MeOK in C/sub 6/H/sub 6/. The C 13 NMR spectral parameters for the compounds are shown, and the rate constants and activation parameters for the photoisomerization of the CHC1/sub 3/ and heptane are presented.

  11. Spectroscopic analysis (FT-IR, FT-Raman and NMR) and molecular docking study of ethyl 2-(4-oxo-3-phenethyl-3,4-dihydroquinazolin-2-ylthio)-acetate

    NASA Astrophysics Data System (ADS)

    El-Azab, Adel S.; Jalaja, K.; Abdel-Aziz, Alaa A.-M.; Al-Obaid, Abdulrahman M.; Sheena Mary, Y.; Yohannan Panicker, C.; Van Alsenoy, C.

    2016-09-01

    The vibrational wavenumbers, molecular structure, MEP, NLO, NBO and HOMO, LUMO analysis of Ethyl 2-(4-oxo-3-phenethyl-3,4-dihydroquinazolin-2-ylthio)-acetate (EPDA) were reported. The change in electron density in the antibonding orbitals and stabilization energies have been calculated by NBO analysis to give clear evidence of stabilization in the hyperconjugation of hydrogen bonded interaction. The difference in HOMO and LUMO energy support the charge transfer interaction within the molecule. NMR studies and Fukui functions are also reported. From molecular electrostatic potential plot it is evident that the negative charge covers the carbonyl groups, phenyl rings and the positive region is over the CH2 groups with the acetate group. Molecular docking studies shows that the title compound forms a stable complex with pyrrole inhibitor and gives a binding affinity value of -8.3 kcal/mol and the results suggest that the compound might exhibit inhibitory activity against pyrrole inhibitor.

  12. Sewage derive [sup 15]N in the Baltic traced in fucus

    SciTech Connect

    Hobbie, J.E.; Fry, B. ); Larsson, U.; Elmgren, R. )

    1990-01-09

    Himmerfjarden, a fjord-like bay on the eastern shore of the Baltic, receives treated sewage from 250,000 inhabitants. Because the inorganic N in the effluent is enriched in [sup 15]N through denitrification, nitrification, and ammonia volatilization, an analysis of the distribution of [sup 15]N in the Bay tells how far from the source the sewage nitrogen moves. The attached macroalga Fucus vesiculosus was collected in early May from rocky shore at 0-0.5 m depth and the [sup 15]N content of the tips of the fronds analyzed. This N represents uptake and storage during the previous six months and growth during March and April. The [delta][sup 15]N was uniformly high (11-13[per thousand]) in the main body of the Bay within 15 km from the sewage source. Beyond 15 km values decreased with distance to a low of 4.6[per thousand] at 35 km, where the Bay ends and the coastal waters begin. Using the 11-13 and 4.6[per thousand] as endmembers, the percentage of sewage N making up the Fucus at any point may be calculated. The [delta][sub 15]N of particulate organic matter in the offshore Baltic waters was around 0[per thousand] and Fucus had an [delta][sup 15]N about 1.5[per thousand] higher than the POM. From this and other evidence we conclude that there is a belt of coastal water with an elevated [delta][sup 15]N lying along the east coast of the Baltic. This presumably derives from sewage and perhaps from agriculture and is potentially of use as a tracer of coastal zone/pelagic zone interactions.

  13. Why is Mineral-Associated Organic Matter Enriched in 15N? Evidence from Grazed Pasture Soil

    NASA Astrophysics Data System (ADS)

    Baisden, W. T.; Wells, N. S.; Mudge, P. L.; Clough, T. J.; Schipper, L. A.; Ghani, A.; Stevenson, B.

    2014-12-01

    Throughout the scientific literature, measurements across soil depth and density fractions suggest that, with few exceptions, mineral-associated organic matter (OM) has higher δ15N than non-mineral-associated OM. This implies that the δ15N difference between N inputs and mineral-stabilized OM may characterize the microbial processes involved in stabilization and mineral association. Yet current understanding of observed N isotope fractionation in terrestrial ecosystems suggests the large isotope effects are expressed during inorganic N transformations from NH4 to gaseous loss pathways of NH3 volatilization and denitrification. How can the relative importance of N isotope fractionation during OM stabilization versus loss pathways be resolved? We recently examined N isofluxes when a temporary nitrogen excess is created by urine deposition in a New Zealand dairy pasture. We found that the N isotopic composition of volatilized NH3, and NO3 available for leaching or denitrification could not be linked back to the added N using Rayleigh distillation models. Instead, the results imply that the added N was immobilized, and the N available for losses was increasingly derived from mineralization of organic matter during the course of the experiment. These results are consistent with recent evidence of enhanced OM mineralization in urine patches, understanding of N isotope mass balances and long-standing evidence that gross mineralization and immobilization fluxes greatly exceed net mineralization and nitrification, except at very high N saturation. These results suggest that where 15N enrichment occurs due to fractionating loss pathways, the isotope effects are primarily transmitted to immobilized N, forming 15N enriched stabilized OM. This further explains earlier findings that the δ15N of soil OM represents an integrated indicator of losses, reflecting the intensity and duration of pastoral agriculture. We suggest that development of an indicator based on δ15N in

  14. Nitrogen source tracking with delta(15)N content of coastal wetland plants in Hawaii.

    PubMed

    Bruland, Gregory L; MacKenzie, Richard A

    2010-01-01

    Inter- and intra-site comparisons of the nitrogen (N) stable isotope composition of wetland plant species have been used to identify sources of N in coastal areas. In this study, we compared delta(15)N values from different herbaceous wetland plants across 34 different coastal wetlands from the five main Hawaiian Islands and investigated relationships of delta(15)N with land use, human population density, and surface water quality parameters (i.e., nitrate, ammonium, and total dissolved N). The highest delta(15)N values were observed in plants from wetlands on the islands of Oahu (8.7-14.6 per thousand) and Maui (8.9-9.2 per thousand), whereas plants from wetlands on the islands of Kauai, Hawaii, and Molokai had delta(15)N values usually <4 per thousand. The enrichment in delta(15)N values in plant tissues from wetlands on Oahu and Maui was most likely a result of the more developed and densely populated watersheds on these two islands. Urban development within a 1000-m radius and population density were positively correlated to average delta(15)N vegetation values from each wetland site (r = 0.56 and 0.51, respectively; p < 0.001). This suggested that site mean delta(15)N values from mixed stands of wetland plants have potential as indices of N sources in coastal lowland wetlands in Hawaii and that certain sites on Oahu and Maui have experienced significant anthropogenic N loading. This information can be used to monitor future changes in N inputs to coastal wetlands throughout Hawaii and the Pacific. PMID:20048329

  15. (29)Si, (47)Ti, (49)Ti and (195)Pt solid state MAS NMR spectroscopic investigations of ternary silicides TPtSi, germanides TPtGe (T = Ti, Zr, Hf) and stannide TiPtSn.

    PubMed

    Benndorf, Christopher; Eckert, Hellmut; Pöttgen, Rainer

    2016-05-10

    Eight ternary tetrelides TPtX (T = Ti, Zr, Hf; X = Si, Ge, Sn) were synthesized from the elements by arc-melting and subsequent annealing. TiPtSi, ZrPtSi, ZrPtGe, HfPtSi and HfPtGe crystallize with the orthorhombic TiNiSi type structure, in the space group Pnma. The structures of HfPtSi (a = 654.44(9), b = 387.97(6), c = 750.0(1) pm, wR2 = 0.0592, 411 F(2) values, 20 variables) and HfPtGe (a = 660.36(7), b = 395.18(4), c = 763.05(8) pm, wR2 = 0.0495, 430 F(2) values, 20 variables) were refined from single crystal X-ray diffractometer data. TiPtSn adopts the cubic MgAgAs type. TiPtGe is dimorphic with a TiNiSi type high-temperature modification which transforms to cubic LT-TiPtGe (MgAgAs type). All phases were investigated by high resolution (29)Si, (47)Ti, (49)Ti and (195)Pt solid state MAS NMR spectroscopy. In the cubic compounds, the (47/49)Ti NMR signals are easily detected owing to the absence of quadrupolar broadening effects. The (195)Pt resonances of the orthorhombic compounds are characterized by strongly negative isotropic Knight shifts and large Knight shift anisotropies, whereas positive isotropic Knight shifts and no anisotropies are observed for the cubic compounds. These results indicate that the phase transition in TiPtGe is associated with dramatic changes in the electronic properties. Within each group of isotypic compounds the isotropic (29)Si, (47/49)Ti and (195)Pt Knight shifts show systematic dependences on the transition metal or tetrel atomic number, suggesting that the numerical values are influenced by the electronegativities of the metallic (or metalloid) neighbours. PMID:27097719

  16. High-level expression of biologically active glycoprotein hormones in Pichia pastoris strains—selection of strain GS115, and not X-33, for the production of biologically active N-glycosylated 15N-labeled phCG

    PubMed Central

    Blanchard, Véronique; Gadkari, Rupali A.; George, Albert V. E.; Roy, Satarupa; Gerwig, Gerrit J.; Leeflang, Bas R.; Dighe, Rajan R.; Boelens, Rolf

    2008-01-01

    The methylotrophic yeast Pichia pastoris is widely used for the production of recombinant glycoproteins. With the aim to generate biologically active 15N-labeled glycohormones for conformational studies focused on the unravelling of the NMR structures in solution, the P. pastoris strains GS115 and X-33 were explored for the expression of human chorionic gonadotropin (phCG) and human follicle-stimulating hormone (phFSH). In agreement with recent investigations on the N-glycosylation of phCG, produced in P. pastoris GS115, using ammonia/glycerol-methanol as nitrogen/carbon sources, the N-glycosylation pattern of phCG, synthesized using NH4Cl/glucose–glycerol–methanol, comprised neutral and charged, phosphorylated high-mannose-type N-glycans (Man8–15GlcNAc2). However, the changed culturing protocol led to much higher amounts of glycoprotein material, which is of importance for an economical realistic approach of the aimed NMR research. In the context of these studies, attention was also paid to the site specific N-glycosylation in phCG produced in P. pastoris GS115. In contrast to the rather simple N-glycosylation pattern of phCG expressed in the GS115 strain, phCG and phFSH expressed in the X-33 strain revealed, besides neutral high-mannose-type N-glycans, also high concentrations of neutral hypermannose-type N-glycans (Manup-to-30GlcNAc2). The latter finding made the X-33 strain not very suitable for generating 15N-labeled material. Therefore, 15N-phCG was expressed in the GS115 strain using the new optimized protocol. The 15N-enrichment was evaluated by 15N-HSQC NMR spectroscopy and GLC-EI/MS. Circular dichroism studies indicated that 15N-phCG/GS115 had the same folding as urinary hCG. Furthermore, 15N-phCG/GS115 was found to be similar to the unlabeled protein in every respect as judged by radioimmunoassay, radioreceptor assays, and in vitro bioassays. PMID:18274893

  17. Determination of Multimodal Isotopic Distributions: The Case of a (15)N Labeled Protein Produced into Hairy Roots.

    PubMed

    Trouillard, Romain; Hubert-Roux, Marie; Tognetti, Vincent; Guilhaudis, Laure; Plasson, Carole; Menu-Bouaouiche, Laurence; Coquet, Laurent; Guerineau, François; Hardouin, Julie; Ele Ekouna, Jean-Pierre; Cosette, Pascal; Lerouge, Patrice; Boitel-Conti, Michèle; Afonso, Carlos; Ségalas-Milazzo, Isabelle

    2015-06-16

    Isotopic labeling is widely used in various fields like proteomics, metabolomics, fluxomics, as well as in NMR structural studies, but it requires an efficient determination of the isotopic enrichment. Mass spectrometry is the method of choice for such analysis. However, when complex expression systems like hairy roots are used for production, multiple populations of labeled proteins may be obtained. If the isotopic incorporation determination is actually well-known for unimodal distributions, the multimodal distributions have scarcely been investigated. Actually, only a few approaches allow the determination of the different labeled population proportions from multimodal distributions. Furthermore, they cannot be used when the number of the populations and their respective isotope ratios are unknown. The present study implements a new strategy to measure the (15)N labeled populations inside a multimodal distribution knowing only the peptide sequence and peak intensities from mass spectrometry analyses. Noteworthy, it could be applied to other elements, like carbon and hydrogen, and extended to a larger range of biomolecules. PMID:25973921

  18. Distinguishing Protonation States of Histidine Ligands to the Oxidized Rieske Iron-Sulfur Cluster through (15) N Vibrational Frequency Shifts.

    PubMed

    Jagger, Benjamin R; Koval, Ashlyn M; Wheeler, Ralph A

    2016-01-18

    The Rieske [2Fe-2S] cluster is a vital component of many oxidoreductases, including mitochondrial cytochrome bc1; its chloroplast equivalent, cytochrome b6f; one class of dioxygenases; and arsenite oxidase. The Rieske cluster acts as an electron shuttle and its reduction is believed to couple with protonation of one of the cluster's His ligands. In cytochromes bc1 and b6f, for example, the Rieske cluster acts as the first electron acceptor in a modified Q cycle. The protonation states of the cluster's His ligands determine its ability to accept a proton and possibly an electron through a hydrogen bond to the electron carrier, ubiquinol. Experimental determination of the protonation states of a Rieske cluster's two His ligands by NMR spectroscopy is difficult, due to the close proximity of the two paramagnetic iron atoms of the cluster. Therefore, this work reports density functional calculations and proposes that difference vibrational spectroscopy with (15) N isotopic substitution may be used to assign the protonation states of the His ligands of the oxidized Rieske [2Fe-2S] complex. PMID:26603967

  19. 1H, 13C and 15N Backbone Assignment of the EC-1 Domain of Human E-Cadherin

    PubMed Central

    Prasasty, Vivitri D.; Krause, Mary E.; Tambunan, Usman S. F.; Anbanandam, Asokan; Laurence, Jennifer S.; Siahaan, Teruna J.

    2014-01-01

    The EC1 domain of E-cadherin has been shown to be important for cadherin-cadherin homophilic interactions. Cadherins are responsible for calcium-mediated cell-cell adhesion located at the adherens junction of the biological barriers (i.e., intestinal mucosa and the blood-brain barrier (BBB). Cadherin peptides can modulate cadherin interactions to improve drug delivery through the blood-brain barriers (BBB). However, the mechanism of modulating the E-cadherin interactions by cadherin peptides has not been fully elucidated. To provide a basis for subsequent examination of the structure and peptide-binding properties of the EC1 domain of human E-cadherin using solution NMR spectroscopy, the 1H, 13C and 15N backbone resonance of the uniformly labeled-EC1 were assigned and the secondary structure was determined based on the chemical shift values. These resonance assignments are essential for assessing protein-ligand interactions and are reported here. PMID:24510398

  20. Vibrational spectroscopic studies, NMR, HOMO-LUMO, NLO and NBO analysis of 1-(2-nitrobenzoyl)-3,5-diphenyl-4,5-dihydro-1H-pyrazole with use X-ray diffractions and DFT calculations

    NASA Astrophysics Data System (ADS)

    Demir, Sibel; Tinmaz, Feyza; Dege, Necmi; Ilhan, Ilhan Ozer

    2016-03-01

    The crystal and molecular structure of the title compound, 1-(2-nitrobenzoyl)-3,5-diphenyl-4,5-dihydro-1H-pyrazole, was reported and confirmed by single crystal X-ray diffraction and spectroscopic data. The structure, geometry optimization, vibrational frequencies and nuclear magnetic resonance were also investigated. Stability of the molecule arising from hyperconjugative interactions and charge delocalisation was analysed using natural bond orbital analysis. The results show that charge in electron density (ED) in the σ∗ and π∗ antibonding orbitals and second-order delocalisation energies E(2) confirms the occurrence of intramolecular charge transfer within the molecule. Satisfactory theoretical aspects were made for the stable conformer of the molecule using density functional theory DFT-B3LYP methods with the 6-311G++(d,p) basis set.

  1. On the Influence of Crosslinker on Template Complexation in Molecularly Imprinted Polymers: A Computational Study of Prepolymerization Mixture Events with Correlations to Template-Polymer Recognition Behavior and NMR Spectroscopic Studies

    PubMed Central

    Shoravi, Siamak; Olsson, Gustaf D.; Karlsson, Björn C. G.; Nicholls, Ian A.

    2014-01-01

    Aspects of the molecular-level basis for the function of ethylene glycol dimethacrylate and trimethylolproprane trimethacrylate crosslinked methacrylic acid copolymers molecularly imprinted with (S)-propranolol have been studied using a series of all-component and all-atom molecular dynamics studies of the corresponding prepolymerization systems. The crosslinking agents were observed to contribute to template complexation, and the results were contrasted with previously reported template-recognition behavior of the corresponding polymers. Differences in the extent to which the two crosslinkers interacted with the functional monomer were identified, and correlations were made to polymer-ligand recognition behavior and the results of nuclear magnetic resonance spectroscopic studies studies. This study demonstrates the importance of considering the functional monomer–crosslinker interaction when designing molecularly imprinted polymers, and highlights the often neglected general contribution of crosslinker to determining the nature of molecularly imprinted polymer-template selectivity. PMID:24927149

  2. Nitrate reductase 15N discrimination in Arabidopsis thaliana, Zea mays, Aspergillus niger, Pichea angusta, and Escherichia coli

    PubMed Central

    Carlisle, Eli; Yarnes, Chris; Toney, Michael D.; Bloom, Arnold J.

    2014-01-01

    Stable 15N isotopes have been used to examine movement of nitrogen (N) through various pools of the global N cycle. A central reaction in the cycle involves the reduction of nitrate (NO−3) to nitrite (NO−2) catalyzed by nitrate reductase (NR). Discrimination against 15N by NR is a major determinant of isotopic differences among N pools. Here, we measured in vitro 15N discrimination by several NRs purified from plants, fungi, and a bacterium to determine the intrinsic 15N discrimination by the enzyme and to evaluate the validity of measurements made using 15N-enriched NO−3. Observed NR isotope discrimination ranged from 22 to 32‰ (kinetic isotope effects of 1.022–1.032) among the different isozymes at natural abundance 15N (0.37%). As the fractional 15N content of substrate NO−3 increased from natural abundance, the product 15N fraction deviated significantly from that expected based on substrate enrichment and 15N discrimination measured at natural abundance. Additionally, isotopic discrimination by denitrifying bacteria used to reduce NO−3 and NO−2 in some protocols became a greater source of error as 15N enrichment increased. We briefly discuss potential causes of the experimental artifacts with enriched 15N and recommend against the use of highly enriched 15N tracers to study N discrimination in plants or soils. PMID:25071800

  3. Highly 15N-enriched chondritic clasts in the CB/CH-like meteorite Isheyevo

    NASA Astrophysics Data System (ADS)

    Bonal, L.; Huss, G. R.; Krot, A. N.; Nagashima, K.; Ishii, H. A.; Bradley, J. P.

    2010-11-01

    The metal-rich carbonaceous chondrites (CB and CH) have the highest whole-rock 15N-enrichments (δ 15N up to 1500‰) among planetary materials. They are also characterized by the absence of interchondrule fine-grained matrix. The only fine-grained material is present as lithic clasts, which experienced extensive aqueous alteration in contrast to the surrounding high-temperature components (chondrules, refractory inclusions, metal grains). Hence, the clasts are foreign objects that were incorporated at a late stage into the final parent body of Isheyevo. Their origin is poorly constrained. Based on mineralogy, petrography, and thermal processing of the aromatic carbonaceous component, different types of clasts have been previously identified in the CB/CH-like chondrite Isheyevo. Here, we focus on the rare lithic clasts characterized by the presence of anhydrous silicates (chondrules, chondrule fragments, and CAIs). Their mineralogy and oxygen isotopic compositions reveal them to be micro-chondrules, fragments of chondrules, and refractory inclusions related to those in the Isheyevo host, suggesting accretion in the same region. In contrast to previously studied IDPs or primitive chondritic matrices, the fine-grained material in the clasts we studied is highly and rather uniformly enriched in heavy nitrogen, with bulk δ 15N values ranging between 1000‰ and 1300‰. It is also characterized by the presence of numerous 15N hotspots (δ 15N ranging from 1400‰ to 4000‰). No bulk (δD <-240‰) or localized deuterium enrichments were observed. These clasts have the highest bulk enrichment in heavy nitrogen measured to date in a fine-grained material. They represent a unique material, of asteroidal or cometary origin, in our collection of cosmomaterials. We show that they were 15N-enriched before their incorporation in the final parent body of Isheyevo. They experienced an extensive aqueous alteration that most likely played a role in redistributing 15N over the

  4. Nitrogen Isotopic Ratios in Cometary NH2: Implication for 15N-fractionation in Ammonia

    NASA Astrophysics Data System (ADS)

    Shinnaka, Yoshiharu; Kawakita, Hideyo; Jehin, Emmanuël; Decock, Alice; Hutsemékers, Damien; Manfroid, Jean; Arai, Akira

    2015-11-01

    Isotopic ratios in cometary molecules are diagnostic for the physico-chemical conditions where molecules formed and are processed, from the interstellar medium to the solar nebula. Usually temperatures at the molecular formation control the fractionation of the heavier element in molecular species, e.g., D-fractionation in water.In cometary volatiles, the 14N/15N ratios in CN have been well observed (Manfroid et al. 2009, A&A, 503, 613, and reference therein) and is consistent with the ratio in HCN (a most probable parent of CN) measured in few comets (Bockelée-Morvan et al. 2008, ApJ, 679, L49). Those ratios are enriched compared to the proto-solar value by a factor of ~3. In contrast to those Nitriles, there are only few reports on 14N/15N ratios in Ammonia (as Amine) (Rousselot et al. 2014, ApJ, 780, L17; Shinnaka et al. 2014, ApJ, 782, L16). Ammonia (NH3) is usually the most abundant and HCN is the second most abundant N-bearing volatiles in cometary ice. Especially, recent observations of 15NH2 revealed the 14N/15N ratios in NH3 are comparable to those of CN. However, from the viewpoint of theoretical work, the enrichment of 15N in cometary NH3 cannot be reproduced by current chemical network models. Information about the diversity of the 14N/15N ratios in NH3 of individual comets is needed to understand the formation mechanisms/environments of NH3 in the early solar system.To clarify the diversity of the 14N/15N ratios in cometary NH3, we determine the 14N/15N ratios in NH3 for more than ten comets individually which include not only Oort cloud comets but also short period comets by using the high-resolution optical spectra of NH2. These spectra were obtained with both the UVES mounted on the VLT in Chile and the HDS on the Subaru Telescope in Hawaii.The derived 14N/15N ratios in NH3 for more than ten comets show high 15N-enrichment compared with the elemental abundances of nitrogen in the Sun by about factor of ~3 and has no large diversity depending on

  5. Rivermouth alteration of agricultural impacts on consumer tissue δ15N

    USGS Publications Warehouse

    Larson, James H.; Richardson, William B.; Vallazza, Jonathan M.; Nelson, J. C.

    2013-01-01

    Terrestrial agricultural activities strongly influence riverine nitrogen (N) dynamics, which is reflected in the δ15N of riverine consumer tissues. However, processes within aquatic ecosystems also influence consumer tissue δ15N. As aquatic processes become more important terrestrial inputs may become a weaker predictor of consumer tissue δ15N. In a previous study, this terrestrial-consumer tissue δ15N connection was very strong at river sites, but was disrupted by processes occurring in rivermouths (the ‘rivermouth effect’). This suggested that watershed indicators of N loading might be accurate in riverine settings, but could be inaccurate when considering N loading to the nearshore of large lakes and oceans. In this study, the rivermouth effect was examined on twenty-five sites spread across the Laurentian Great Lakes. Relationships between agriculture and consumer tissue δ15N occurred in both upstream rivers and at the outlets where rivermouths connect to the nearshore zone, but agriculture explained less variation and had a weaker effect at the outlet. These results suggest that rivermouths may sometimes be significant sources or sinks of N, which would cause N loading estimates to the nearshore zone that are typically made at discharge gages further upstream to be inaccurate. Identifying definitively the controls over the rivermouth effect on N loading (and other nutrients) will require integration of biogeochemical and hydrologic models.

  6. Multidimensional NMR spectroscopy in a single scan.

    PubMed

    Gal, Maayan; Frydman, Lucio

    2015-11-01

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

  7. NMR Studies of Ligand Binding to P450eryF Provides Insight into the Mechanism of Cooperativity

    SciTech Connect

    Roberts, Arthur G.; Diaz, Maria D.; Lampe, Jed N.; Shireman, Laura; Grinstead, Jeffrey S.; Dabrowski, Michael J.; Pearson, Josh T.; Bowman, Michael K.; Atkins, William M.; Campbell, Ann P.

    2006-02-14

    Cytochrome P450’s (P450’s) catalyze the oxidative metabolism of most drugs and toxins. Although extensive studies have proven that some P450’s demonstrate both homotropic and heterotropic cooperativity toward a number of substrates, the mechanistic and molecular details of P450 allostery are still not well-established. Here, we use UV/vis and heteronuclear nuclear magnetic resonance (NMR) spectroscopic techniques to study the mechanism and thermodynamics of the binding of two 9-aminophenanthrene (9-AP) and testosterone (TST) molecules to the erythromycin-metabolizing bacterial P450eryF. UV/vis absorbance spectra of P450eryF demonstrated that binding occurs with apparent negative homotropic cooperativity for TST and positive homotropic cooperativity for 9-AP with Hill-equation-derived dissociation constants of KS ) 4 and 200 íM, respectively. The broadening and shifting observed in the 2D-{1H,15N}-HSQC-monitored titrations of 15N-Phe-labeled P450eryF with 9-AP and TST indicated binding on intermediate and fast chemical exhange time scales, respectively, which was consistent with the Hillequation- derived KS values for these two ligands. Regardless of the type of spectral perturbation observed (broadening for 9-AP and shifting for TST), the 15N-Phe NMR resonances most affected were the same in each titration, suggesting that the two ligands “contact” the same phenylalanines within the active site of P450eryF. This finding is in agreement with X-ray crystal structures of bound P450eryF showing different ligands occupying similar active-site niches. Complex spectral behavior was additionally observed for a small collection of resonances in the TST titration, interpreted as multiple binding modes for the lowaffinity TST molecule or multiple TST-bound P450eryF conformational substates. A structural and energetic model is presented that combines the energetics and structural aspects of 9-AP and TST binding derived from these observations.

  8. Review of NMR characterization of pyrolysis oils

    DOE PAGESBeta

    Hao, Naijia; Ben, Haoxi; Yoo, Chang Geun; Adhikari, Sushil; Ragauskas, Arthur J.

    2016-08-24

    Here, pyrolysis of renewable biomass has been developed as a method to produce green fuels and chemicals in response to energy security concerns as well as to alleviate environmental issues incurred with fossil fuel usage. However, pyrolysis oils still have limited commercial application, mainly because unprocessed oils cannot be readily blended with current petroleum-based transportation fuels. To better understand these challenges, researchers have applied diverse characterization techniques in the development of bio-oil studies. In particular, nuclear magnetic resonance (NMR) is a key spectroscopic characterization method through analysis of bio-oil components. This review highlights the NMR strategies for pyrolysis oil characterizationmore » and critically discusses the applications of 1H, 13C, 31P, 19F, and two-dimensional (2-D NMR) analyses such as heteronuclear single quantum correlation (HSQC) in representative pyrolysis oil studies.« less

  9. NMR analysis on microfluidic devices by remote detection

    SciTech Connect

    McDonnell, Erin E.; Han, SongI; Hilty, Christian; Pierce,Kimberly; Pines, Alexander

    2005-08-15

    We present a novel approach to perform high-sensitivity NMR imaging and spectroscopic analysis on microfluidic devices. The application of NMR, the most information rich spectroscopic technique, to microfluidic devices remains a challenge because the inherently low sensitivity of NMR is aggravated by small fluid volumes leading to low NMR signal, and geometric constraints resulting in poor efficiency for inductive detection. We address the latter by physically separating signal detection from encoding of information with remote detection. Thereby, we use a commercial imaging probe with sufficiently large diameter to encompass the entire device, enabling encoding of NMR information at any location on the chip. Because large-diameter coils are too insensitive for detection, we store the encoded information as longitudinal magnetization and flow it into the outlet capillary. There, we detect the signal with optimal sensitivity using a solenoidal microcoil, and reconstruct the information encoded in the fluid. We present a generally applicable design for a detection-only microcoil probe that can be inserted into the bore of a commercial imaging probe. Using hyperpolarized 129Xe gas, we show that this probe enables sensitive reconstruction of NMR spectroscopic information encoded by the large imaging probe while keeping the flexibility of a large coil.

  10. Molecular structure, spectroscopic (FT-IR, FT-Raman, NMR, UV) studies and first-order molecular hyperpolarizabilities of 1,2-bis(3-methoxy-4-hydroxybenzylidene)hydrazine by density functional method

    NASA Astrophysics Data System (ADS)

    Subramanian, N.; Sundaraganesan, N.; Jayabharathi, J.

    2010-07-01

    Quantum chemical calculations of energies, geometrical structure and vibrational wavenumbers of 1,2-bis(3-methoxy-4-hydroxybenzylidene)hydrazine [vanillin azine (VA)] were carried out by using density functional (DFT/B3LYP) method with 6-31G(d) as basis set. The optimized geometrical parameters obtained by DFT calculations are in good agreement with single crystal XRD data. The vibrational spectral data obtained from solid phase FT-IR and FT-Raman spectra are assigned based on the results of the theoretical calculations. The observed spectra are found to be in good agreement with calculated values. The electric dipole moment ( μ) and the first hyperpolarizability ( β) values of the investigated molecule have been computed using ab initio quantum mechanical calculations. The calculation results also show that the VA molecule might have microscopic nonlinear optical (NLO) behavior with non-zero values. A detailed interpretation of the infrared and Raman spectra of VA was also reported. The energy and oscillator strength calculated by time-dependent density functional theory (TD-DFT) results complements with the experimental findings. The calculated HOMO and LUMO energies show that charge transfer occurs within the molecule. The theoretical NMR chemical shifts complement with experimentally measured ones.

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

    NASA Astrophysics Data System (ADS)

    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.

  12. Synthesis, X-ray crystallography, spectroscopic (FT-IR, 1H &13C NMR and UV), computational (DFT/B3LYP) and enzymes inhibitory studies of 7-hydroximinocholest-5-en-3-ol acetate

    NASA Astrophysics Data System (ADS)

    Ahmad, Faheem; Parveen, Mehtab; Alam, Mahboob; Azaz, Shaista; Malla, Ali Mohammed; Alam, Mohammad Jane; Lee, Dong-Ung; Ahmad, Shabbir

    2016-07-01

    The present study reports the synthesis of 7-Hydroximinocholest-5-en-3-ol acetate (syn. 3β-acetoxycholest-5-en-7-one oxime; in general, steroidal oxime). The identity of steroidal molecule was confirmed by NMR, FT-IR, MS, CHN microanalysis and X-ray crystallography. DFT calculations on the titled molecule have been performed. The molecular structure and spectra interpreted by Gaussian hybrid computational analysis theory (B3LYP) are found to be in good correlation with the experimental data obtained from the various spectrophotometric techniques. The vibrational bands appearing in the FTIR are assigned with great accuracy using harmonic frequencies along with intensities and animated modes. Molecular properties like HOMO-LUMO analysis, chemical reactivity descriptors, MEP mapping, dipole moment and natural atomic charges have been presented at the same level of theory. Moreover, the Hirshfeld analysis was carried out to ascertain the secondary interactions and associated 2D fingerprint plots. The percentages of various interactions are pictorialized by fingerprint plots of Hirshfeld surface. Steroidal oxime exhibited promising inhibitory activity against acetylcholinesterase (AChE) as compared to the reference drug, tacrine. Molecular docking was performed to introduce steroidal molecules into the X-ray crystal structures of acetylcholinesterase at the active site to find out the probable binding mode. The results of molecular docking admitted that steroidal oxime may exhibit enzyme inhibitor activity.

  13. Thermochromism in nickel(II) complexes: thermal, IR spectroscopic, solid-state 1H NMR and single crystal X-ray analysis of diaqua-bis(2,2-dimethyl-1,3-propanediamine) nickel(II) nitrate

    NASA Astrophysics Data System (ADS)

    Koner, Subratanath; Ghosh, Ashutosh; Pariya, Chandi; Das, Debasis; Kikuchi, Hikomitsu; Okamoto, Ken-Ichi; Ikeda, Ryuichi

    1995-02-01

    The newly synthesized complex [Ni(dmtn) 2(H 2O) 2](NO 3) 2 (dmtn = 2,2-dimethyl-1,3-propanediamine) undergoes a reversible thermochromic phase transition in the range of 180-202°C ( ΔH = 10.4kJ mol -1) on heating after dehydration (dehydration temperature range 43-102°C). The complex has been characterized by X-ray crystallography at room temperature. The crystals are monoclinic, space group {C2}/{m}, a = 20.385(2), b = 6.9004(4), c = 6.9552(3) Å, β = 102.60(5)°, V = 954.8(1) Å3, Z = 2 and R = 0.046. The geometry of the nickel atom in the complex is tetragonally distorted octahedral with two H 2O molecules coordinated at the trans position. The diamine chelate rings are in the trans chair-chair conformations. The broad-line 1H NMR of partially deuterated [Ni(dmtn- d4) 2(NO 3) 2] (deuterated amine protons) indicates the onset of dynamic disorder of the diamine chelate rings at the phase transition temperature. The high temperature IR spectral measurement shows the complex retains its trans configuration after dehydration and phase transition with NO -3 ions coordinated as a monodentate ligand.

  14. Spectroscopic (FTIR, FT-Raman, 13C and 1H NMR) investigation, molecular electrostatic potential, polarizability and first-order hyperpolarizability, FMO and NBO analysis of 1-methyl-2-imidazolethiol.

    PubMed

    Xavier, R John; Dinesh, P

    2014-01-24

    In this work, experimental and theoretical study on the molecular structure and vibrational spectra of 1-methyl-2-imidazolethiol (MIME) were presented. The vibrational frequencies of the title compound were obtained theoretically by ab initio HF and DFT (B3LYP/LSDA) employing 6-311G (d,p) and 6-311++G(d,p) basis sets and compared with experimental spectral bands (FTIR and FT-Raman). The thermodynamic properties of the studied compound have been computed at different temperatures. The atomic charges and charge delocalization of the molecule have been analyzed by natural bond orbital (NBO) analysis. The reactivity sites are identified by mapping the molecular electrostatic potential (MESP) surface. Electronic properties HOMO and LUMO energies were measured by time-dependent TD-DFT approach. Besides, (13)C and (1)H nuclear magnetic resonance (NMR) chemical shifts of the molecule in chloroform solvent calculated using the Gauge-Independent Atomic Orbital (GIAO) method are found to be in good agreement with experimental values. PMID:24184581

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

    PubMed

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

    2014-03-25

    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 (1)H and (13)C NMR chemical shifts of the molecule have been anlysed. PMID:24316546

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

    PubMed

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

    2015-01-25

    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 (1)H and (13)C NMR chemical shifts of the molecules have been analysed. PMID:25062058

  17. Spectroscopic (FT-IR, FT-Raman, UV, 1H and 13C NMR) profiling and theoretical calculations of (2E)-2-[3-(1H-imidazol-1-yl)-1-phenylpropylidene]hydrazinecarboxamide: An anticonvulsant agent

    NASA Astrophysics Data System (ADS)

    Haress, Nadia G.; Govindarajan, Munusamy; AL-Wabli, Reem I.; Almutairi, Maha S.; Al-Alshaikh, Monirah A.; Al-Saadi, Abdulaziz A.; Attia, Mohamed I.

    2016-08-01

    Vibrational characteristics of the anticonvulsant agent, (2E)-2-[3-(1H-imidazol-1-yl)-1-phenylpropylidene]hydrazinecarboxamide ((2E)-IPHC) have been investigated. The computational data are obtained by adopting ab initio Hartree-Fock (HF) and DFT/B3LYP/6-31 + G(d,p) methods. The most stable conformer is identified by a potential energy scan. The optimized geometrical parameters indicated that the overall symmetry of the most stable conformer is CS. Atoms in molecules (AIM) analysis is contained out and the chemical bondings between the atoms are as characterized. Mulliken atomic charges and simulated thermo-molecular (heat capacity and enthalpy) characteristics of the (2E)-IPHC molecule also have been analyzed. The magnitude of the molecular electrostatic potential (MEP) of oxygen, hydrogen, and nitrogen atoms as well as phenyl and imidazole rings in the title molecule were investigated along with their contribution to the biological activity. The energy gap between HOMO and LUMO orbitals has been found to be 5.1334 eV in the gaseous phase. Excitation energies, oscillator strength and wavelengths were computed by the time-dependent density function theory (TD-DFT) approach. Predicted wavenumbers have been assigned and they are consistent with the experimental values. The 1H and 13C nuclear magnetic resonance (NMR) chemical shifts of the (2E)-IPHC molecule were computed by the gauge independent atomic orbital (GIAO) method and were compared with the experimental results.

  18. Neutron capture cross section of {sup 15}N at stellar energies

    SciTech Connect

    Meissner, J.; Schatz, H.; Herndl, H.; Wiescher, M.; Beer, H.; Kaeppeler, F.

    1996-02-01

    The neutron capture rate on {sup 15}N may be of considerable importance for {ital s}-process nucleosynthesis in red giants as well as for the nucleosynthesis in inhomogeneous big bang scenarios. We measured the reaction cross section of {sup 15}N({ital n},{gamma}){sup 16}N at the Forschungszentrum Karlsruhe with a fast cyclic neutron activation technique at laboratory neutron energies of 25, 152, and 370 keV. Direct capture and shell model calculations were performed to interpret the results. The presented reaction rate is 30{endash}50{percent} smaller than the previously used theoretical rates. {copyright} {ital 1996 The American Physical Society.}

  19. 15N Fractionation in Star-Forming Regions and Solar System Objects

    NASA Technical Reports Server (NTRS)

    Wirstrom, Eva; Milam, Stefanie; Adande, GIlles; Charnley, Steven; Cordiner, Martin

    2015-01-01

    A central issue for understanding the formation and evolution of matter in the early Solar System is the relationship between the chemical composition of star-forming interstellar clouds and that of primitive Solar System materials. The pristinemolecular content of comets, interplanetary dust particles and carbonaceous chondrites show significant bulk nitrogen isotopic fractionation relative to the solar value, 14N15N 440. In addition, high spatial resolution measurements in primitive materials locally show even more extreme enhancements of 14N15N 100.

  20. First results on the incorporation and excretion of 15N from orally administered urea in lactating pony mares.

    PubMed

    Schubert, R; Zander, R; Gruhn, K; Hennig, A

    1991-05-01

    Two lactating pony mares were given oral offers of 20 g 15N urea [95 atom-% 15N-excess (15N')] on 6 subsequent days. About 80% of the consumed 15N' were excreted via urine and faeces, but only about 2% via milk. The 15N' secreted via milk-lysine only amounted to 0.04% of the 15N' intake. The recovery was about 90% in each case. Tissues with active metabolism had an unexpectedly high labelling (greater than 0.3 atom-% 15N'). The low extent of the conversion of oral urea N into milk-lysine speaks against an essential participation of the enteral synthesis in meeting the amino acid requirement of lactating mares. It was already concluded from this results that the determination of the amino acid requirement will be necessary for this group of performance. PMID:1888274

  1. Guiding automated NMR structure determination using a global optimization metric, the NMR DP score.

    PubMed

    Huang, Yuanpeng Janet; Mao, Binchen; Xu, Fei; Montelione, Gaetano T

    2015-08-01

    ASDP is an automated NMR NOE assignment program. It uses a distinct bottom-up topology-constrained network anchoring approach for NOE interpretation, with 2D, 3D and/or 4D NOESY peak lists and resonance assignments as input, and generates unambiguous NOE constraints for iterative structure calculations. ASDP is designed to function interactively with various structure determination programs that use distance restraints to generate molecular models. In the CASD-NMR project, ASDP was tested and further developed using blinded NMR data, including resonance assignments, either raw or manually-curated (refined) NOESY peak list data, and in some cases (15)N-(1)H residual dipolar coupling data. In these blinded tests, in which the reference structure was not available until after structures were generated, the fully-automated ASDP program performed very well on all targets using both the raw and refined NOESY peak list data. Improvements of ASDP relative to its predecessor program for automated NOESY peak assignments, AutoStructure, were driven by challenges provided by these CASD-NMR data. These algorithmic improvements include (1) using a global metric of structural accuracy, the discriminating power score, for guiding model selection during the iterative NOE interpretation process, and (2) identifying incorrect NOESY cross peak assignments caused by errors in the NMR resonance assignment list. These improvements provide a more robust automated NOESY analysis program, ASDP, with the unique capability of being utilized with alternative structure generation and refinement programs including CYANA, CNS, and/or Rosetta. PMID:26081575

  2. Nuclear magnetic resonance characterization of a paramagnetic DNA-drug complex with high spin cobalt; assignment of the 1H and 31P NMR spectra, and determination of electronic, spectroscopic and molecular properties.

    PubMed

    Gochin, M

    1998-08-01

    The proton NMR spectrum of the ternary complex between the octamer duplex d(TTGGCCAA)2, two molecules of the drug chromomycin-A3, and a divalent cobalt ion has been assigned. Assignment procedures used standard two-dimensional techniques and relied upon the expected NOE contacts observed in the equivalent diamagnetic complex containing zinc. The magnetic susceptibility tensor for the cobalt was determined and used to calculate shifts for all nuclei, aiding in the assignment process and verification. Relaxation, susceptibility, temperature and field dependence studies of the paramagnetic spectrum enabled determination of electronic properties of the octahedral cobalt complex. The electronic relaxation tau(s) was determined to be 2.5 +/- 1.5 ps; the effective isotropic g value was found to be 2.6 +/- 0.2, indicating strong spin-orbit coupling. The magnetic susceptibility tensor was determined to be chi(xx) = 8.9 x 10(-3) cm3/mol, chi(yy) = 9.5 x 10(-3) cm3/mol, chi(zz) = 12.8 * 10(-3) cm3/mol. A tentative rotational correlation time of 8 ns was obtained for the complex. Both macroscopic and microscopic susceptibility measurements revealed deviations from Curie behavior over the temperature range accessible in the study. Non-selective relaxation rates were found to be inaccurate for defining distances from the metal center. However, pseudocontact shifts could be calculated with high accuracy using the dipolar shift equation. Isotropic hyperfine shifts were factored into contact and dipolar terms, revealing that the dipolar shift predominates and that contact shifts are relatively small. PMID:9751997

  3. Compound-Specific δ15N Amino Acid Measurements in Littoral Mussels in the California Upwelling Ecosystem: A New Approach to Generating Baseline δ15N Isoscapes for Coastal Ecosystems

    PubMed Central

    Vokhshoori, Natasha L.; McCarthy, Matthew D.

    2014-01-01

    We explored δ15N compound-specific amino acid isotope data (CSI-AA) in filter-feeding intertidal mussels (Mytilus californianus) as a new approach to construct integrated isoscapes of coastal primary production. We examined spatial δ15N gradients in the California Upwelling Ecosystem (CUE), determining bulk δ15N values of mussel tissue from 28 sites between Port Orford, Oregon and La Jolla, California, and applying CSI-AA at selected sites to decouple trophic effects from isotopic values at the base of the food web. Bulk δ15N values showed a strong linear trend with latitude, increasing from North to South (from ∼7‰ to ∼12‰, R2 = 0.759). In contrast, CSI-AA trophic position estimates showed no correlation with latitude. The δ15N trend is therefore most consistent with a baseline δ15N gradient, likely due to the mixing of two source waters: low δ15N nitrate from the southward flowing surface California Current, and the northward transport of the California Undercurrent (CUC), with15N-enriched nitrate. This interpretation is strongly supported by a similar linear gradient in δ15N values of phenylalanine (δ15NPhe), the best AA proxy for baseline δ15N values. We hypothesize δ15NPhe values in intertidal mussels can approximate annual integrated δ15N values of coastal phytoplankton primary production. We therefore used δ15NPhe values to generate the first compound-specific nitrogen isoscape for the coastal Northeast Pacific, which indicates a remarkably linear gradient in coastal primary production δ15N values. We propose that δ15NPhe isoscapes derived from filter feeders can directly characterize baseline δ15N values across major biochemical provinces, with potential applications for understanding migratory and feeding patterns of top predators, monitoring effects of climate change, and study of paleo- archives. PMID:24887109

  4. Nitrate Removal in Two Relict Oxbow Urban Wetlands: A 15N Mass-balance Approach

    EPA Science Inventory

    A 15N-tracer method was used to quantify nitrogen (N) removal processes in two relict oxbow wetlands located adjacent to the Minebank Run restored stream reach in Baltimore County (Maryland, USA) during summer 2009 and early spring 2010. A mass-balance approach was used to determ...

  5. Using a Macroalgal δ15N Bioassay to Detect Cruise Ship Waste Water Effluent Inputs

    EPA Science Inventory

    Nitrogen stable isotopes are a powerful tool for tracking sources of N to marine ecosystems. I used green macroalgae as a bioassay organism to evaluate if the δ15N signature of cruise ship waste water effluent (CSWWE) could be detected in Skagway Harbor, AK. Opportunistic green...

  6. {sup 15}N(p,{alpha}{sub 0}){sup 12}C S factor

    SciTech Connect

    Barker, F. C.

    2008-10-15

    Experimental values of the astrophysical S factor for the {sup 15}N(p,{alpha}{sub 0}){sup 12}C reaction are available both from direct measurements and from the Trojan horse method. We here use R-matrix formulas to fit these values and to extrapolate to zero energy to obtain values of S(0)

  7. The use of delta(15)N in assessing sewage stress on coral reefs.

    PubMed

    Risk, Michael J; Lapointe, Brian E; Sherwood, Owen A; Bedford, Bradley J

    2009-06-01

    While coral reefs decline, scientists argue, and effective strategies to manage land-based pollution lag behind the extent of the problem. There is need for objective, cost-effective, assessment methods. The measurement of stable nitrogen isotope ratios, delta(15)N, in tissues of reef organisms shows promise as an indicator of sewage stress. The choice of target organism will depend upon study purpose, availability, and other considerations such as conservation. Algae are usually plentiful and have been shown faithfully to track sewage input. The organic matrix of bivalve shells can provide time series spanning, perhaps, decades. Gorgonians have been shown to track sewage, and can provide records potentially centuries-long. In areas where baseline data are lacking, which is almost everywhere, delta(15)N in gorgonians can provide information on status and trends. In coral tissue, delta(15)N combined with insoluble residue determination can provide information on both sewage and sediment stress in areas lacking baseline data. In the developed world, delta(15)N provides objective assessment in a field complicated by conflicting opinions. Sample handling and processing are simple and analysis costs are low. This is a method deserving widespread application. PMID:19286230

  8. δ15N as a proxy for historic anthropogenic nitrogen loading in Charleston Harbor, SC, USA

    NASA Astrophysics Data System (ADS)

    Payne, T. N.; Andrus, C. F. T.

    2015-12-01

    Bivalve shell geochemistry can serve as a useful indicator of changes in coastal environments. There is increasing interest in developing paleoenvironmental proxies from mollusk shell organic components. Numerous studies have focused on how the δ15N obtained from bivalve tissues can be used to trace present-day wastewater input into estuaries. However, comparatively little attention has been paid to tracing the impact of anthropogenic nitrogen loading into estuaries over time. By measuring historic levels of δ15N in the organic fraction of oyster shells (Crassostrea virginica) from archaeological sites around Charleston Harbor and comparing those levels to the δ15N content of modern shells, it is possible to assess how nitrogen has fluctuated historically in the area. Whole-shell samples from the Late Archaic Period (~3000-4000 BP, Late Woodland Period (~1400-800 BP), 18th and 19th centuries, and modern controls were measured for %N and d15N. Evidence of increased anthropogenic input of N is expected to begin in the early historic period based on similar analysis in Chesapeake Bay. More ancient samples may give insight into baseline conditions prior to recent population growth and industrialization. This information could help understand how large-scale anthropogenic nitrogen loading has affected coastal ecosystems over time and guide future remediation. Furthermore, this project will help refine and improve this novel proxy of past environmental conditions.

  9. Tracing Nitrogen through Landscapes to Coastal Wetlands using d15N of Larval Fish

    EPA Science Inventory

    Our objective was to evaluate the use of the nitrogen stable isotope value (d15N) of larval fish as an indicator of incipient anthropogenic nitrogen loading to coastal wetlands in the Great Lakes. We sampled coastal wetlands in five Lake Superior south shore tributaries that had ...

  10. Characterization of Two Distinct Amorphous Forms of Valsartan by Solid-State NMR.

    PubMed

    Skotnicki, Marcin; Apperley, David C; Aguilar, Juan A; Milanowski, Bartłomiej; Pyda, Marek; Hodgkinson, Paul

    2016-01-01

    Valsartan (VAL) is an antihypertensive drug marketed in an amorphous form. Amorphous materials can have different physicochemical properties depending on preparation method, thermal history, etc., but the nature of such materials is difficult to study by diffraction techniques. This study characterizes two different amorphous forms of valsartan (AR and AM) using solid-state NMR (SSNMR) as a primary investigation tool, supported by solution-state NMR, FT-IR, TMDSC, and dissolution tests. The two forms are found to be clearly distinct, with a significantly higher level of structural arrangement in the AR form, as observed in (13)C, (15)N, and (1)H SSNMR. (13)C and (15)N NMR indicates that the fully amorphous material (AM) contains an approximately equal ratio of cis-trans conformers about the amide bond, whereas the AR form exists mainly as one conformer, with minor conformational "defects". (1)H ultrafast MAS NMR shows significant differences in the hydrogen bonding involving the tetrazole and acid hydrogens between the two materials, while (15)N NMR shows that both forms exist as a 1,2,3,4-tetrazole tautomer. NMR relaxation times show subtle differences in local and bulk molecular mobility, which can be connected with the glass transition, the stability of the glassy material, and its response to aging. Counterintuitively the fully amorphous material is found to have a significantly lower dissolution rate than the apparently more ordered AR material. PMID:26602457

  11. Vertical δ13C and δ15N changes during pedogenesis

    NASA Astrophysics Data System (ADS)

    Brunn, Melanie; Spielvogel, Sandra; Wells, Andrew; Condron, Leo; Oelmann, Yvonne

    2015-04-01

    The natural abundance of soil organic matter (SOM) stable C and N isotope ratios are subjected to vertical changes throughout the soil profile. This vertical distribution is a widely reported phenomenon across varieties of ecosystems and constitutes important insights of soil carbon cycling. In most ecosystems, SOM becomes enriched in heavy isotopes by several per mill in the first few centimeters of the topsoil. The enrichment of 13C in SOM with soil depth is attributed to biological and physical-chemical processes in soil e.g., plant physiological impacts, microbial decomposition, sorption and transport processes. Such vertical trends in 13C and 15N abundance have rarely been related to SOM composition during pedogenesis. The aims of our study were to investigate short and long-term δ13C and δ15N depth changes and their interrelations under progressing pedogenesis and ecosystem development. We sampled soils across the well studied fordune progradation Haast-chronosequence, a dune ridge system under super-humid climate at the West Coast of New Zealand's South Island (43° 53' S, 169° 3' E). Soils from 11 sites with five replicates each covered a time span of around 2870 yr of soil development (from Arenosol to Podzol). Vertical changes of δ13C and δ15N values of SOM were investigated in the organic layers and in 1-cm depth intervals of the upper 10 cm of the mineral soil. With increasing soil depth SOM became enriched in δ13C by 1.9 ± SE 0.1 o and in δ15N by 6.0 ± 0.4 ‰˙Litter δ13C values slightly decreased with increasing soil age (r = -0.61; p = 0.00) likely due to less efficient assimilation linked to nutrient limitations. Fractionation processes during mycorrhizal transfer appeared to affect δ15N values in the litter. We found a strong decrease of δ15N in the early succession stages ≤ 300 yr B.P. (r = -0.95; p = 0.00). Positive relations of vertical 13C and 15N enrichment with soil age might be related to decomposition and appeared to be

  12. Variable δ15N Diet-Tissue Discrimination Factors among Sharks: Implications for Trophic Position, Diet and Food Web Models

    PubMed Central

    Olin, Jill A.; Hussey, Nigel E.; Grgicak-Mannion, Alice; Fritts, Mark W.; Wintner, Sabine P.; Fisk, Aaron T.

    2013-01-01

    The application of stable isotopes to characterize the complexities of a species foraging behavior and trophic relationships is dependent on assumptions of δ15N diet-tissue discrimination factors (∆15N). As ∆15N values have been experimentally shown to vary amongst consumers, tissues and diet composition, resolving appropriate species-specific ∆15N values can be complex. Given the logistical and ethical challenges of controlled feeding experiments for determining ∆15N values for large and/or endangered species, our objective was to conduct an assessment of a range of reported ∆15N values that can hypothetically serve as surrogates for describing the predator-prey relationships of four shark species that feed on prey from different trophic levels (i.e., different mean δ15N dietary values). Overall, the most suitable species-specific ∆15N values decreased with increasing dietary-δ15N values based on stable isotope Bayesian ellipse overlap estimates of shark and the principal prey functional groups contributing to the diet determined from stomach content analyses. Thus, a single ∆15N value was not supported for this speciose group of marine predatory fishes. For example, the ∆15N value of 3.7‰ provided the highest percent overlap between prey and predator isotope ellipses for the bonnethead shark (mean diet δ15N = 9‰) whereas a ∆15N value < 2.3‰ provided the highest percent overlap between prey and predator isotope ellipses for the white shark (mean diet δ15N = 15‰). These data corroborate the previously reported inverse ∆15N-dietary δ15N relationship when both isotope ellipses of principal prey functional groups and the broader identified diet of each species were considered supporting the adoption of different ∆15N values that reflect the predators’ δ15N-dietary value. These findings are critical for refining the application of stable isotope modeling approaches as inferences regarding a species’ ecological role in their

  13. Variable δ(15)N diet-tissue discrimination factors among sharks: implications for trophic position, diet and food web models.

    PubMed

    Olin, Jill A; Hussey, Nigel E; Grgicak-Mannion, Alice; Fritts, Mark W; Wintner, Sabine P; Fisk, Aaron T

    2013-01-01

    The application of stable isotopes to characterize the complexities of a species foraging behavior and trophic relationships is dependent on assumptions of δ(15)N diet-tissue discrimination factors (∆(15)N). As ∆(15)N values have been experimentally shown to vary amongst consumers, tissues and diet composition, resolving appropriate species-specific ∆(15)N values can be complex. Given the logistical and ethical challenges of controlled feeding experiments for determining ∆(15)N values for large and/or endangered species, our objective was to conduct an assessment of a range of reported ∆(15)N values that can hypothetically serve as surrogates for describing the predator-prey relationships of four shark species that feed on prey from different trophic levels (i.e., different mean δ(15)N dietary values). Overall, the most suitable species-specific ∆(15)N values decreased with increasing dietary-δ(15)N values based on stable isotope Bayesian ellipse overlap estimates of shark and the principal prey functional groups contributing to the diet determined from stomach content analyses. Thus, a single ∆(15)N value was not supported for this speciose group of marine predatory fishes. For example, the ∆(15)N value of 3.7‰ provided the highest percent overlap between prey and predator isotope ellipses for the bonnethead shark (mean diet δ(15)N = 9‰) whereas a ∆(15)N value < 2.3‰ provided the highest percent overlap between prey and predator isotope ellipses for the white shark (mean diet δ(15)N = 15‰). These data corroborate the previously reported inverse ∆(15)N-dietary δ(15)N relationship when both isotope ellipses of principal prey functional groups and the broader identified diet of each species were considered supporting the adoption of different ∆(15)N values that reflect the predators' δ(15)N-dietary value. These findings are critical for refining the application of stable isotope modeling approaches as inferences regarding a

  14. 1H, 13C, and 15N resonance assignments for the protein coded by gene locus BB0938 of Bordetella bronchiseptica

    SciTech Connect

    Rossi, Paolo; Ramelot, Theresa A.; Xiao, Rong; Ho, Chi K.; Ma, LiChung; Acton, Thomas; Kennedy, Michael A.; Montelione, Gaetano

    2005-11-01

    The product of gene locus BB0938 from Bordetella bronchiseptica (Swiss-Prot ID: Q7WNU7-BORBR; NESG target ID: BoR11; Wunderlich et al., 2004; Pfam ID: PF03476) is a 128-residue protein of unknown function. This broadly conserved protein family is found in eubacteria and eukaryotes. Using triple resonance NMR techniques, we have determined 98% of backbone and 94% of side chain 1H, 13C, and 15N resonance assignments. The chemical shift and 3J(HN?Ha) scalar coupling data reveal a b topology with a seven-residue helical insert, ??????????. BMRB deposit with accession number 6693. Reference: Wunderlich et al. (2004) Proteins, 56, 181?187.

  15. 1H, 13C, and 15N resonance assignments for Escherichia coli ytfP, a member of the broadly conserved UPF0131 protein domain family

    SciTech Connect

    Aramini, James M.; Swapna, G.V.T.; Huang, Yuanpeng; Rajan, Paranji K.; Xiao, Rong; Shastry, Ritu; Acton, Thomas; Cort, John R.; Kennedy, Michael A.; Montelione, Gaetano

    2005-11-01

    Protein ytfP from Escherichia coli (Swiss-Prot ID: YTFP-ECOLI; NESG target ID: ER111; Wunderlich et al., 2004) is a 113-residue member of the UPF0131 protein family (Pfam ID: PF03674) of unknown function. This domain family is found in organisms from all three kingdoms, archaea, eubacteria and eukaryotes. Using triple resonance NMR techniques, we have determined 97% of backbone and 91% of side chain 1H, 13C, and 15N resonance assignments. The chemical shift and 3J(HN?Ha) scalar coupling data reveal a mixed a/b topology,????????. BMRB deposit with Accession No. 6448. Reference: Wunderlich et al. (2004) Proteins, 56, 181?187.

  16. Efficient and accurate determination of the overall rotational diffusion tensor of a molecule from 15N relaxation data using computer program ROTDIF

    NASA Astrophysics Data System (ADS)

    Walker, Olivier; Varadan, Ranjani; Fushman, David

    2004-06-01

    We present a computer program ROTDIF for efficient determination of a complete rotational diffusion tensor of a molecule from NMR relaxation data. The derivation of the rotational diffusion tensor in the case of a fully anisotropic model is based on a six-dimensional search, which could be very time consuming, particularly if a grid search in the Euler angle space is involved. Here, we use an efficient Levenberg-Marquardt algorithm combined with Monte Carlo generation of initial guesses. The result is a dramatic, up to 50-fold improvement in the computational efficiency over the previous approaches [Biochemistry 38 (1999) 10225; J. Magn. Reson. 149 (2001) 214]. This method is demonstrated on a computer-generated and real protein systems. We also address the issue of sensitivity of the diffusion tensor determination from 15N relaxation measurements to experimental errors in the relaxation rates and discuss possible artifacts from applying higher-symmetry tensor model and how to recognize them.

  17. Do Low 15N Values in Paleozoic Epeiric Basins Indicate High Rates of N Fixation?

    NASA Astrophysics Data System (ADS)

    Tuite, M. L.; Macko, S. A.

    2011-12-01

    As a consequence of the high energetic requirements of dinitrogen (N2) fixation, organic N produced by diazotrophic microorganisms typically exhibits δ15N values similar to atmospheric N2 (approximately 0%). Because the δ15N of organic-rich Paleozoic epeiric basin sediments often has values in the vicinity of 0%, it is frequently asserted that N2 fixation was the primary source of new reactive N for productivity. There are two broad reasons why recourse to widespread and intensive N fixation as the primary source of the organic N is problematic. First, there are substantial physiological and ecological constraints on marine N fixation that limit its extent in modern oceans primarily to open ocean basins. Second, preservation of an unaltered isotopic signature of diazotrophy in underlying sediments is not a likely outcome of oxic and anoxic diagenetic alteration and repeated cycles of mineralization and assimilation. Constraining the sources of reactive N for primary productivity is critical to understanding the N cycle in Paleozoic epeiric seas. In this study we report δ15N values from high organic matter Middle Ordovician through Late Devonian dysoxic and euxinic basinal sediments. We propose a nitrogen isotope mass balance model that incorporates the microbial ecology of a stratified water column and the biochemical stoichiometry of primary production and organic matter diagenesis. Results from the model support our contention that high rates of N fixation over extended time periods were not the cause of depleted nitrogen isotope values in organic-rich Paleozoic basinal sediments. Rather, the depleted values were a consequence of a diminished role for nitrification and subsequent N loss via denitrification and anammox, and the preferential preservation of a substantially 15N-depleted chlorophyll-influenced lipid fraction. The model may be applicable to earlier and later geological periods where high organic matter sediments feature depleted δ15N values.

  18. Evaluating δ(15)N-body size relationships across taxonomic levels using hierarchical models.

    PubMed

    Reum, Jonathan C P; Marshall, Kristin N

    2013-12-01

    Ecologists routinely set out to estimate the trophic position of individuals, populations, and species composing food webs, and nitrogen stable isotopes (δ(15)N) are a widely used proxy for trophic position. Although δ(15)N values are often sampled at the level of individuals, estimates and confidence intervals are frequently sought for aggregations of individuals. If individual δ(15)N values are correlated as an artifact of sampling design (e.g., clustering of samples in space or time) or due to intrinsic groupings (e.g., life history stages, social groups, taxonomy), such estimates may be biased and exhibit overly optimistic confidence intervals. However, these issues can be accommodated using hierarchical modeling methods. Here, we demonstrate how hierarchical models offer an additional quantitative tool for investigating δ(15)N variability and we explicitly evaluate how δ(15)N varies with body size at successively higher levels of taxonomic aggregation in a diverse fish assemblage. The models take advantage of all available data, better account for uncertainty in parameters estimates, may improve inferences on coefficients corresponding to groups with small to moderate sample sizes, and partition variation across model levels, which provides convenient summaries of the 'importance' of each level in terms of unexplained heterogeneity in the data. These methods can easily be applied to diet-based studies of trophic position. Although hierarchical models are well-understood and established tools, their benefits have yet to be fully reaped by stable isotope and food web ecologists. We suggest that hierarchical models can provide a robust framework for conceptualizing and statistically modeling trophic position at multiple levels of aggregation. PMID:23812110

  19. NMR analysis of biodiesel

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Biodiesel is usually analyzed by the various methods called for in standards such as ASTM D6751 and EN 14214. Nuclear magnetic resonance (NMR) is not one of these methods. However, NMR, with 1H-NMR commonly applied, can be useful in a variety of applications related to biodiesel. These include monit...

  20. Influence of open ocean nitrogen supply on the skeletal δ15N of modern shallow-water scleractinian corals

    NASA Astrophysics Data System (ADS)

    Wang, Xingchen T.; Sigman, Daniel M.; Cohen, Anne L.; Sinclair, Daniel J.; Sherrell, Robert M.; Cobb, Kim M.; Erler, Dirk V.; Stolarski, Jarosław; Kitahara, Marcelo V.; Ren, Haojia

    2016-05-01

    The isotopic composition of skeleton-bound organic nitrogen in shallow-water scleractinian corals (hereafter, CS-δ15N) is an emerging tool for studying the marine nitrogen cycle in the past. The CS-δ15N has been shown to reflect the δ15N of nitrogen (N) sources to corals, with most applications to date focusing on the anthropogenic/terrestrial N inputs to reef environments. However, many coral reefs receive their primary N sources from the open ocean, and the CS-δ15N of these corals may provide information on past changes in the open ocean regional and global N cycle. Using a recently developed persulfate/denitrifier-based method, we measured CS-δ15N in modern shallow-water scleractinian corals from 8 sites proximal to the open ocean. At sites with low open ocean surface nitrate concentrations typical of the subtropics and tropics, measured CS-δ15N variation on seasonal and annual timescales is most often less than 2‰. In contrast, a broad range in CS-δ15N (of ∼10‰) is measured across these sites, with a strong correlation between CS-δ15N and the δ15N of the deep nitrate supply to the surface waters near the reefs. While CS-δ15N can be affected by other N sources as well and can vary in response to local reef conditions as well as coral/symbiont physiological changes, this survey indicates that, when considering corals proximal to the open ocean, the δ15N of the subsurface nitrate supply to surface waters drives most of the CS-δ15N variation across the global ocean. Thus, CS-δ15N is a promising proxy for reconstructing the open ocean N cycle in the past.

  1. Polymorphism and disorder in natural active ingredients. Low and high-temperature phases of anhydrous caffeine: Spectroscopic ((1)H-(14)N NMR-NQR/(14)N NQR) and solid-state computational modelling (DFT/QTAIM/RDS) study.

    PubMed

    Seliger, Janez; Žagar, Veselko; Apih, Tomaž; Gregorovič, Alan; Latosińska, Magdalena; Olejniczak, Grzegorz Andrzej; Latosińska, Jolanta Natalia

    2016-03-31

    The polymorphism of anhydrous caffeine (1,3,7-trimethylxanthine; 1,3,7-trimethyl-1H-purine-2,6-(3H,7H)-dione) has been studied by (1)H-(14)N NMR-NQR (Nuclear Magnetic Resonance-Nuclear Quadrupole Resonance) double resonance and pure (14)N NQR (Nuclear Quadrupole Resonance) followed by computational modelling (Density Functional Theory, supplemented Quantum Theory of Atoms in Molecules with Reduced Density Gradient) in solid state. For two stable (phase II, form β) and metastable (phase I, form α) polymorphs the complete NQR spectra consisting of 12 lines were recorded. The assignment of signals detected in experiment to particular nitrogen sites was verified with the help of DFT. The shifts of the NQR frequencies, quadrupole coupling constants and asymmetry parameters at each nitrogen site due to polymorphic transition were evaluated. The strongest shifts were observed at N(3) site, while the smallest at N(9) site. The commercial pharmaceutical sample was found to contain approximately 20-25% of phase I and 75-80% of phase II. The orientational disorder in phase II with a local molecular arrangement mimics that in phase I. Substantial differences in the intermolecular interaction phases I and II of caffeine were analysed using computational (DFT/QTAIM/RDS) approach. The analysis of local environment of each nitrogen nucleus permitted drawing some conclusions on the topology of interactions in both polymorphs. For the most stable orientations in phase I and phase II the maps of the principal component qz of EFG tensor and its asymmetry parameter at each point of the molecular system were calculated and visualized. The relevant maps calculated for both phases I and II indicates small variation in electrostatic potential upon phase change. Small differences between packings in phases slightly disturb the neighbourhood of the N(1) and N(7) nitrogens, thus are meaningless from the biological point of view. The composition of two phases in pharmaceutical material

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

    SciTech Connect

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

    2005-09-23

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

  3. Near-complete 1H, 13C, 15N resonance assignments of dimethylsulfoxide-denatured TGFBIp FAS1-4 A546T.

    PubMed

    Kulminskaya, Natalia V; Yoshimura, Yuichi; Runager, Kasper; Sørensen, Charlotte S; Bjerring, Morten; Andreasen, Maria; Otzen, Daniel E; Enghild, Jan J; Nielsen, Niels Chr; Mulder, Frans A A

    2016-04-01

    The transforming growth factor beta induced protein (TGFBIp) is a major protein component of the human cornea. Mutations occurring in TGFBIp may cause corneal dystrophies, which ultimately lead to loss of vision. The majority of the disease-causing mutations are located in the C-terminal domain of TGFBIp, referred as the fourth fascilin-1 (FAS1-4) domain. In the present study the FAS1-4 Ala546Thr, a mutation that causes lattice corneal dystrophy, was investigated in dimethylsulfoxide using liquid-state NMR spectroscopy, to enable H/D exchange strategies for identification of the core formed in mature fibrils. Isotope-labeled fibrillated FAS1-4 A546T was dissolved in a ternary mixture 95/4/1 v/v/v% dimethylsulfoxide/water/trifluoroacetic acid, to obtain and assign a reference 2D (1)H-(15)N HSQC spectrum for the H/D exchange analysis. Here, we report the near-complete assignments of backbone and aliphatic side chain (1)H, (13)C and (15)N resonances for unfolded FAS1-4 A546T at 25 °C. PMID:26275916

  4. 1H, 15N and 13C resonance assignments of light organ-associated fatty acid-binding protein of Taiwanese fireflies.

    PubMed

    Tseng, Kai-Li; Lee, Yi-Zong; Chen, Yun-Ru; Lyu, Ping-Chiang

    2016-04-01

    Fatty acid-binding proteins (FABPs) are a family of proteins that modulate the transfer of various fatty acids in the cytosol and constitute a significant portion in many energy-consuming cells. The ligand binding properties and specific functions of a particular type of FABP seem to be diverse and depend on the respective binding cavity as well as the cell type from which this protein is derived. Previously, a novel FABP (lcFABP; lc: Luciola cerata) was identified in the light organ of Taiwanese fireflies. The lcFABP was proved to possess fatty acids binding capabilities, especially for fatty acids of length C14-C18. However, the structural details are unknown, and the structure-function relationship has remained to be further investigated. In this study, we finished the (1)H, (15)N and (13)C chemical shift assignments of (15)N/(13)C-enriched lcFABP by solution NMR spectroscopy. In addition, the secondary structure distribution was revealed based on the backbone N, H, Cα, Hα, C and side chain Cβ assignments. These results can provide the basis for further structural exploration of lcFABP. PMID:26373428

  5. Regional patterns of 15N natural abundance in forest ecosystems along a large transect in eastern China

    NASA Astrophysics Data System (ADS)

    Sheng, Wenping; Yu, Guirui; Fang, Huajun; Liu, Yingchun; Wang, Qiufeng; Chen, Zhi; Zhang, Li

    2014-02-01

    The regional determining factors underlying inter- and intra-site variation of 15N natural abundance in foliage, O horizon and mineral soil were investigated in eastern China.15N natural abundance values for these forest ecosystems were in the middle of the range of values previously found for global forest ecosystems. In contrast to commonly reported global patterns, temperate forest ecosystems were significantly more15N-enriched than tropical forest ecosystems, and foliage δ15N was negatively correlated with increasing mean annual temperature and net soil N mineralisation in eastern China. Tight N cycling in forest ecosystems and the use of atmospheric N deposition by trees might underlie the δ15N distribution patterns in eastern China. The existence of mycorrhizal fungi and root distribution profiles in the soil may also influence the15N natural abundance patterns in forest ecosystems of eastern China.

  6. Nitrogen cycling in an extreme hyperarid environment inferred from δ15N analyses of plants, soils and herbivore diet

    NASA Astrophysics Data System (ADS)

    Díaz, Francisca P.; Frugone, Matías; Gutiérrez, Rodrigo A.; Latorre, Claudio

    2016-03-01

    Climate controls on the nitrogen cycle are suggested by the negative correlation between precipitation and δ15N values across different ecosystems. For arid ecosystems this is unclear, as water limitation among other factors can confound this relationship. We measured herbivore feces, foliar and soil δ15N and δ13C values and chemically characterized soils (pH an