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Sample records for 15n nmr spectra

  1. Experimental and calculated 1H, 13C, 15N NMR spectra of famotidine

    NASA Astrophysics Data System (ADS)

    Barańska, M.; Czarniecki, K.; Proniewicz, L. M.

    2001-05-01

    Famotidine, 3-[[[2-[(aminoiminomethyl)amino]-4-thiazolyl]methyl]thio]- N-(aminosulfonyl), is a histamine H 2-receptor blocker that has been used mainly for the treatment of peptic ulcers and the Zollinger-Ellison syndrome. Its NMR spectra in different solvents were reported earlier; however, detailed interpretation has not been done thus far. In this work, experimental 1H, 13C and 15N NMR spectra of famotidine dissolved in DMSO-d 6 are shown. The assignment of observed chemical shifts is based on quantum chemical calculation at the Hartree-Fock/6-31G ∗ level. The geometry optimization of the famotidine molecule with two internal hydrogen bonds, i.e. [N(3)-H(23)⋯N(9) and N(3)⋯H(34)-N(20)], is done by using the B3LYP method with the 6-31G ∗ basis set.

  2. 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}.

  3. 15N-15N Proton Assisted Recoupling in Magic Angle Spinning NMR

    PubMed Central

    Lewandowski, Józef R.; De Paëpe, Gaël; Eddy, Matthew T.; Griffin, Robert G.

    2009-01-01

    We describe a new magic angle spinning (MAS) NMR experiment for obtaining 15N-15N correlation spectra. The approach yields direct information about the secondary and tertiary structure of proteins, including identification of α-helical stretches and inter-strand connectivity in antiparallel β-sheets, which are of major interest for structural studies of membrane proteins and amyloid fibrils. The method, 15N-15N proton assisted recoupling (PAR), relies on a second order mechanism, third spin assisted recoupling (TSAR), used previously in the context of 15N-13C and 13C-13C polarization transfer schemes. In comparison to 15N-15N proton driven spin diffusion experiments, the PAR technique accelerates polarization transfer between 15N’s by a factor of ~102−103, and is furthermore applicable over the entire range of currently available MAS frequencies (10–70 kHz). PMID:19334788

  4. 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.

  5. 15N chemical shift tensors and conformation of solid polypeptides containing 15N-labeled glycine residue by 15N NMR

    NASA Astrophysics Data System (ADS)

    Shoji, Akira; Ozaki, Takuo; Fujito, Teruaki; Deguchi, Kenzo; Ando, Isao; Magoshi, Jun

    1998-01-01

    The correlation between the isotropic 15N chemical shift ( δiso) and 15N chemical shift tensor components ( δ11, δ22 and δ33) and the main-chain conformation such as the polyglycine I (PGI: β-sheet), II (PGII: 3 1-helix), α-helix and β-sheet forms of solid polypeptides [Gly∗,X] n consisting of 15N-labeled glycine (Gly∗) and other amino acids (X: natural abundance of 15N) has been studied by solid-state 15N NMR method. A series of polypeptides [Gly∗,X] n (X = glycine, L-alanine, L-leucine, L-valine, L-isoleucine, β-benzyl L-aspartate, γ-benzyl L-glutamate, ɛ-carbobenzoxy L-lysine, and sarcosine) were synthesized by the α-amino acid N-carboxy anhydride (NCA) method. Conformations of these polypeptides in the solid state were characterized on the basis of conformation-dependent 13C chemical shifts in the 13C cross-polarization-magic angle spinning (CP-MAS) NMR spectra and by the characteristic bands in the IR and far-IR spectra. The δiso, δ11, δ22 and δ33 of the polypetides were determined from the 15N CP-MAS and 15N CP-static (powder pattern) spectra. It was found that the δiso, δ11, δ22 and δ33 in the PGI form (δ 83.5, 185, 40.7 and 25 ppm, resp.) are upfield from those in the PGII form (88.5, 194, 42.1 and 29 ppm, resp.), which were reproduced by the calculated 15N shielding constants using the finite perturbation theory (FPT)-INDO method. It was also found that the δ22 of the Gly∗ of [Gly∗,X] n is closely related to the main-chain conformation and the neighboring amino acid sequence, although the δiso is almost independent of the glycine content and conformation. Consequently, the δ22 value of Gly∗ containing copolypeptides is useful for the structural (main-chain conformation and neighboring amino acid sequence) analysis in the solid state by 15N NMR, if the 15N-labeled copolypeptide or natural protein can be provided. In addition, it is shown that the δiso of the glycine residue is useful for the conformational study of some

  6. 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.

  7. 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

  8. 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.

  9. 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.

  10. Overcoming the overlap problem in the assignment of 1H NMR spectra of larger proteins by use of three-dimensional heteronuclear 1H-15N Hartmann-Hahn-multiple quantum coherence and nuclear Overhauser-multiple quantum coherence spectroscopy: application to interleukin 1 beta.

    PubMed

    Marion, D; Driscoll, P C; Kay, L E; Wingfield, P T; Bax, A; Gronenborn, A M; Clore, G M

    1989-07-25

    The application of three-dimensional (3D) heteronuclear NMR spectroscopy to the sequential assignment of the 1H NMR spectra of larger proteins is presented, using uniformly labeled (approximately 95%) [15N]interleukin 1 beta, a protein of 153 residues and molecular mass of 17.4 kDa, as an example. The two-dimensional (2D) 600-MHz spectra of interleukin 1 beta are too complex for complete analysis, owing to extensive cross-peak overlap and chemical shift degeneracy. We show that the combined use of 3D 1H-15N Hartmann-Hahn-multiple quantum coherence (HOHAHA-HMQC) and nuclear Overhauser-multiple quantum coherence (NOESY-HMQC) spectroscopy, designed to provide the necessary through-bond and through-space correlations for sequential assignment, provides a practical general-purpose method for resolving ambiguities which severely limit the analysis of conventional 2D NMR spectra. The absence of overlapping cross-peaks in these 3D spectra allows the unambiguous identification of C alpha H(i)-NH(i+1) and NH(i)-NH(i+1) through-space nuclear Overhauser connectivities necessary for connecting a particular C alpha H(i)-NH(i) through-bond correlation with its associated through-space sequential cross-peak The problem of amide NH chemical shift degeneracy in the 1H NMR spectrum is therefore effectively removed, and the assignment procedure simply involves inspecting a series of 2D 1H-1H slices edited by the chemical shift of the directly bonded 15N atom. Connections between residues can be identified almost without any knowledge of the spin system types involved, though this type of information is clearly required for the eventual placement of the connected residues within the primary sequence.

  11. 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

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

    DOE PAGES

    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

  13. 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

  14. Solid-state /sup 15/N NMR of oriented lipid bilayer bound gramicidin A'

    SciTech Connect

    Nicholson, L.K.; Moll, F.; Mixon, T.E.; LoGrasso, P.V.; Lay, J.C.; Cross, T.A.

    1987-10-20

    Highly oriented samples of lipid and gramicidin A' (8:1 molar ratio) have been prepared with the samples extensively hydrated (approximately 70% water v/w). These preparations have been shown to be completely in a bilayer phase with a transition temperature of 28/sup 0/C, and evidence is presented indicating that the gramicidin is in the channel conformation. An estimate of the disorder in the alignment of the bilayers parallel with the glass plates used to align the bilayers can be made from the asymmetry of the nuclear magnetic resonances (NMR). Such an analysis indicates a maximal range of disorder of +-3/sup 0/. Uniformly /sup 15/N-labeled gramicidin has been biosynthesized by Bacillus brevis grown in a media containing /sup 15/N-labeled Escherichia coli cells as the only nitrogen source. When prepared with labeled gramicidin, the oriented samples result in high-resolution /sup 15/N NMR spectra showing 12 resonances for the 20 nitrogen sites of the polypeptide. The frequency of the three major multiple resonance peaks has been interpreted to yield the approximate orientation of the N-H bonds in the peptide linkages with respect to the magnetic field. The bond orientations are only partially consistent with the extant structural models of gramicidin.

  15. 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…

  16. 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…

  17. 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

  18. A spectral correlation function for efficient sequential NMR assignments of uniformly (15)N-labeled proteins.

    PubMed

    Bartels, C; Wüthrich, K

    1994-11-01

    A new computer-based approach is described for efficient sequence-specific assignment of uniformly (15)N-labeled proteins. For this purpose three-dimensional (15)N-correlated [(1)H, (1)H]-NOESY spectra are divided up into two-dimensional (1)H-(1)H strips which extend over the entire spectral width along one dimension and have a width of ca. 100 Hz, centered about the amide proton chemical shifts along the other dimension. A spectral correlation function enables sorting of these strips according to proximity of the corresponding residues in the amino acid sequence. Thereby, starting from a given strip in the spectrum, the probability of its corresponding to the C-terminal neighboring residue is calculated for all other strips from the similarity of their peak patterns with a pattern predicted for the sequentially adjoining residue, as manifested in the scalar product of the vectors representing the predicted and measured peak patterns. Tests with five different proteins containing both α-helices and β-sheets, and ranging in size from 58 to 165 amino acid residues show that the discrimination achieved between the sequentially neighboring residue and all other residues compares well with that obtained with an unguided interactive search of pairs of sequentially neighboring strips, with important savings in the time needed for complete analysis of 3D (15)N-correlated [(1)H, (1)H]-NOESY spectra. The integration of this routine into the program package XEASY ensures that remaining ambiguities can be resolved by visual inspection of the strips, combined with reference to the amino acid sequence and information on spin-system types obtained from additional NMR spectra.

  19. 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.

  20. (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.

  1. 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.

  2. 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.

  3. Membrane orientation of the N-terminal segment of alamethicin determined by solid-state 15N NMR.

    PubMed Central

    North, C L; Barranger-Mathys, M; Cafiso, D S

    1995-01-01

    Alamethicin was synthesized with 15N incorporated into alanine at position 6 in the peptide sequence. In dispersions of hydrated dimyristoylphosphatidylcholine, solid-state 15N NMR yields an axially symmetric powder pattern indicating that the peptide is reorienting with a single axis of symmetry when associated with lamellar lipids. When incorporated into bilayers that are uniformly oriented with the bilayer normal parallel to the B(o) field, the position of the observed 15N chemical shift is 171 ppm. This is coincident with the sigma parallel to edge of the axially symmetric powder pattern for non-oriented hydrated samples. Thus the axis of motional averaging lies along the bilayer normal. Two-dimensional separated local field spectra were obtained that provide a measure of the N-H dipolar coupling in one dimension and the 15N chemical shift in the other. These data yield a dipolar coupling of 17 kHz corresponding to an average angle of 24 degrees for the N-H bond with respect to the B(o) field axis. An analysis of the possible structures and orientations that could produce the observed spectral parameters show that these values are consistent with an alpha-helical conformation inserted along the bilayer normal. Images FIGURE 1 FIGURE 6 PMID:8599645

  4. Incorporation of (15)N-TNT transformation products into humifying plant organic matter as revealed by one- and two-dimensional solid state NMR spectroscopy.

    PubMed

    Knicker, Heike

    2003-06-01

    Solid-state double cross polarization magic angle spinning (DCPMAS) 15N 13C nuclear magnetic resonance (NMR) spectroscopy was applied to study the incorporation of TNT transformation products into humifying plant organic matter. For this approach, 13C-enriched plant material (Lolium perenne) was mixed with quartz sand and aerobically incubated for 11 months after addition of 15N(3)-2,4,6-trinitrotoluene (TNT). After successive extraction of the incubate with water, methanol and ethyl acetate, approximately 60% of the 15N added as 15N(3)-TNT (15N(add)) remained in the solid organic residue (SOR-fraction). The acid insoluble fraction (AI) obtained after NaOH and HCl extractions contained approximately 20% of 15N(add). For both fractions, 15N NMR spectroscopy revealed an almost complete reduction of the TNT after 11 months of aerobic incubation. Most of the reduced nitrogen groups underwent further condensation. The corresponding DCPMAS NMR spectra allowed the identification of amides that are further substituted by alkyl groups that resist even acid hydrolysis. This assigns them to relatively stable compounds rather than to newly synthesized microbial peptides. The results of this study suggest further that the covalent binding of TNT transformation products to plant derived organic matter is mediated by alkylation and acetylation reactions, rather than by 1,4 addition of TNT-derived nitrogenous groups to quinones of the humic material.

  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. 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

  7. 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

    2016-09-07

    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.

  8. 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

  9. 1H and 15N NMR Analyses on Heparin, Heparan Sulfates and Related Monosaccharides Concerning the Chemical Exchange Regime of the N-Sulfo-Glucosamine Sulfamate Proton

    PubMed Central

    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-15N 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-15N HSQC spectra. Dynamic nuclear polarization (DNP) was employed in order to facilitate 1D spectral acquisition of the sulfamate 15N signal of free GlcNS. Analyses on the multiplet pattern of scalar couplings of GlcNS 15N 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-15N 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

  10. 15N solid-state NMR provides a sensitive probe of oxidized flavin reactive sites.

    PubMed

    Koder, Ronald L; Walsh, Joseph D; Pometun, Maxim S; Dutton, P Leslie; Wittebort, Richard J; Miller, Anne-Frances

    2006-11-29

    Flavins are central to the reactivity of a wide variety of enzymes and electron transport proteins. There is great interest in understanding the basis for the different reactivities displayed by flavins in different protein contexts. We propose solid-state nuclear magnetic resonance (SS-NMR) as a tool for directly observing reactive positions of the flavin ring and thereby obtaining information on their frontier orbitals. We now report the SS-NMR signals of the redox-active nitrogens N1 and N5, as well as that of N3. The chemical shift tensor of N5 is over 720 ppm wide, in accordance with the predictions of theory and our calculations. The signal of N3 can be distinguished on the basis of coupling to 1H absent for N1 and N5, as well as the shift tensor span of only 170 ppm, consistent with N3's lower aromaticity and lack of a nonbonding lone pair. The isotropic shifts and spans of N5 and N1 reflect two opposite extremes of the chemical shift range for "pyridine-type" N's, consistent with their electrophilic and nucleophilic chemical reactivities, respectively. Upon flavin reduction, N5's chemical shift tensor contracts dramatically to a span of less than 110 ppm, and the isotropic chemical shift changes by approximately 300 ppm. Both are consistent with loss of N5's nonbonding lone pair and decreased aromaticity, and illustrate the responsiveness of the 15N chemical shift principal values to electronic structure. Thus. 15N chemical shift principal values promise to be valuable tools for understanding electronic differences that underlie variations in flavin reactivity, as well as the reactivities of other heterocyclic cofactors. PMID:17117871

  11. 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.

  12. 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.

  13. 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

  14. Heteronuclear NMR studies of cobalamins. 11. sup 15 N NMR studies of the axial nucleotide and amide side chains of cyanocobalamin and dicyanocobamides

    SciTech Connect

    Brown, K.; Brooks, H.B.; Xiang, Zou ); Victor, M.; Ray, A. ); Timkovich, R. )

    1990-11-28

    Spectroscopic and thermodynamic evidence for the structure of cobalamines and dicyanocobalamin (CN){sub 2}Cbl have been previously reported. The structure indicated the occurrence of the so-called tuck-in species. Further observations and characterization of the tuck-in species of (CN){sub 2}Cbl by {sup 15}N NMR spectroscopy are presented herein. These results represent the first observation of the {sup 15}N NMR spectrum of benzimidazole nucleotide of cobalamins. The first NMR observation of the amide protons of cobalamins and their connectivity to the amide nitrogens are also reported. 50 refs., 2 figs., 2 tabs.

  15. 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.

  16. 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.

  17. Retrieving nitrogen isotopic signatures from fresh leaf reflectance spectra: disentangling δ(15)N from biochemical and structural leaf properties.

    PubMed

    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 δ(15)N 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 δ(15)N directly influences leaf reflectance spectra or if the relationship is based on covariation between δ(15)N and foliar nitrogen content or other leaf properties. Using a (15)N-labeling approach, we experimentally varied δ(15)N independently of any other leaf properties in three plant species across different leaf developmental and physiological states. δ(15)N 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 δ(15)N within species. Several wavelength regions important for predicting δ(15)N 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 δ(15)N, our results demonstrate that (15)N 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.

  18. 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

  19. NMR spectra of androstane analogs of brassinosteroids

    NASA Astrophysics Data System (ADS)

    Baranovskii, A. V.; Litvinovskaya, R. P.; Aver'kova, M. A.; Khripach, N. B.; Khripach, V. A.

    2007-09-01

    We have used two-dimensional NMR spectroscopy to make a complete assignment of signals from the nuclei of hydrogen and carbon atoms in the spectra of brassinosteroids in the androstane series. We have confirmed the stereochemistry of the chiral centers and the structure of the molecules. We have studied the effect of the configuration of the 2,3-diol groups in the A ring of the steroids on the chemical shift of adjacent atoms in the 13C and 1H NMR spectra.

  20. Detection of organic sulfur by {sup 15}N and {sup 19}F NMR via formation of iminosulfuranes

    SciTech Connect

    Franz, J.A.; Linehan, J.C.; Lamb, C.N.

    1992-08-01

    We have synthesized new iminosulfuranes from a variety of diaryl-and dialkyl sulfides and dibenzothiophene. The pattern of {sup 15}N chemical shifts indicates that functional groups attached to sulfur are not simply resolved into aryl and alkyl groups. Thus, resolution of sulfur functional groups using {sup 15}N NMR via iminosulfurane does not appear practicable. However, iminosulfurane formation, together with the N-haloamide reaction and the Pummerer rearrangement, provides pathways for chemical discrimination of different sulfur substituents using unique {sup 15}N- or, {sup 19}F-labelled fragments for different categories of sulfur functional groups. In efforts currently underway, we are applying these reactions to methylated extracts and conversion products of the high-organic-sulfur containing Yugoslavian Rasa and Spanish Mequinenza lignites. 1 tab, 14 refs.

  1. An sup 15 N NMR method for the characterization of organic sulfur in coal and coal products via iminosulfurane formation

    SciTech Connect

    Franz, J.A.; Lamb, C.N.; Linehan, J.C.

    1991-09-01

    The indirect of organic sulfur by {sup 15}N NMR spectroscopy in the solid state is feasible by facile reactions providing the iminosulfurane structures. Unfortunately, nitrogen chemical shifts appear to be insufficiently sensitive to the nature of the sulfur substituent to be useful for structural studies. Further work is underway to determine the {sup 15}N chemical shifts of iminosulfuranes formed from dibenzothiophene, 4-4{prime}-dimethoxydiphenyl sulfide, and a sulfur-containing, methylated asphaltene to determine the sensitivity of {sup 15}N shifts to a broader variation of aromatic structure. Although double cross-polarization experiments or rotational echo experiments could make use of iminosulfurane formation for detection of carbon in proximity to sulfur, the difficulties in quantitation using these methods are not encouraging for coal product mixtures. 6 refs., 1 fig., 1 tab.

  2. Detection of organic sulfur by [sup 15]N and [sup 19]F NMR via formation of iminosulfuranes

    SciTech Connect

    Franz, J.A.; Linehan, J.C.; Lamb, C.N.

    1992-08-01

    We have synthesized new iminosulfuranes from a variety of diaryl-and dialkyl sulfides and dibenzothiophene. The pattern of [sup 15]N chemical shifts indicates that functional groups attached to sulfur are not simply resolved into aryl and alkyl groups. Thus, resolution of sulfur functional groups using [sup 15]N NMR via iminosulfurane does not appear practicable. However, iminosulfurane formation, together with the N-haloamide reaction and the Pummerer rearrangement, provides pathways for chemical discrimination of different sulfur substituents using unique [sup 15]N- or, [sup 19]F-labelled fragments for different categories of sulfur functional groups. In efforts currently underway, we are applying these reactions to methylated extracts and conversion products of the high-organic-sulfur containing Yugoslavian Rasa and Spanish Mequinenza lignites. 1 tab, 14 refs.

  3. 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.

  4. Imaging of complex NMR spectra.

    PubMed

    Harrison, C G; Adams, D F; Kramer, P B

    1985-01-01

    The Point Spread Function (PSF) in NMR imaging is the result of both the line broadening due to magnet field inhomogeneity and the intrinsic spectrum of the nucleus at resonance. In the case of proton imaging, the line broadening dominates the small chemical shifts and the spectral lines are not resolved. This is not generally the case with other nuclei having strong chemical shifts and the PSF then has a complex structure. During imaging, the complex PSF is convolved with the spatial distribution of the nucleus at resonance and this leads to halo artifacts which are dependent on the imaging technique employed. The images due to the ensemble of spectral lines can be separated in principle by deconvolution of the data with the PSF before reconstruction. In the special case where the complex PSF is spatially independent, it can be obtained from the Free Induction Decay (FID) data produced in the absence of a spatially encoding gradient field. This technique has been successfully applied to in-vivo imaging of exogenous perfluorocarbon material. PMID:3988470

  5. NMR study of Met-1 human Angiogenin: (1)H, (13)C, (15)N backbone and side-chain resonance assignment.

    PubMed

    Tsika, Aikaterini C; Chatzileontiadou, Demetra S M; Leonidas, Demetres D; Spyroulias, Georgios A

    2016-10-01

    Here, we report the high yield expression and preliminary structural analysis via solution hetero-nuclear NMR spectroscopy of the recombinant Met-1 human Angiogenin. The analysis reveals a well folded as well as, a monomeric polypeptide. Τhe sequence-specific assignment of its (1)H, (15)N and (13)C resonances at high percentage was obtained. Also, using TALOS+ its secondary structure elements were determined.

  6. Natural-abundance 15N NMR studies of Turkey ovomucoid third domain. Assignment of peptide 15N resonances to the residues at the reactive site region via proton-detected multiple-quantum coherence

    NASA Astrophysics Data System (ADS)

    Ortiz-Polo, Gilberto; Krishnamoorthi, R.; Markley, John L.; Live, David H.; Davis, Donald G.; Cowburn, David

    Heteronuclear two-dimensional 1H{ 15N} multiple-quantum (MQ) spectroscopy has been applied to a protein sample at natural abundance: ovomucoid third domain from turkey ( Meleagris gallopavo), a serine proteinase inhibitor of 56 amino acid residues. Peptide amide 1H NMR assignments obtained by two-dimensional 1H{ 1H} NMR methods (R. Krishnamoorthi and J. L. Markley, unpublished data) led to identification of the corresponding 1H{ 15N} MQ coherence cross peaks. From these, 15N NMR chemical shifts were determined for several specific backbone amide groups of amino acid residues located around the reactive site region of the inhibitor. The results suggest that amide 15N chemical shifts, which are readily obtained in this way, may serve as sensitive probes for conformational studies of proteins.

  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. Acid-base interactions and secondary structures of poly-L-lysine probed by 15N and 13C solid state NMR and Ab initio model calculations.

    PubMed

    Dos, Alexandra; Schimming, Volkmar; Tosoni, Sergio; Limbach, Hans-Heinrich

    2008-12-11

    The interactions of the 15N-labeled amino groups of dry solid poly-L-lysine (PLL) with various halogen and oxygen acids HX and the relation to the secondary structure have been studied using solid-state 15N and 13C CPMAS NMR spectroscopy (CP = cross polarization and MAS = magic angle spinning). For comparison, 15N NMR spectra of an aqueous solution of PLL were measured as a function of pH. In order to understand the effects of protonation and hydration on the 15N chemical shifts of the amino groups, DFT and chemical shielding calculations were performed on isolated methylamine-acid complexes and on periodic halide clusters of the type (CH3NH3(+)X(-))n. The combined experimental and computational results reveal low-field shifts of the amino nitrogens upon interaction with the oxygen acids HX = HF, H2SO4, CH3COOH, (CH3)2POOH, H3PO4, HNO3, and internal carbamic acid formed by reaction of the amino groups with gaseous CO2. Evidence is obtained that only hydrogen-bonded species of the type (Lys-NH2***H-X)n are formed in the absence of water. 15N chemical shifts are maximum when H is located in the hydrogen bond center and then decrease again upon full protonation, as found for aqueous solution at low pH. By contrast, halogen acids interact in a different way. They form internal salts of the type (Lys-NH3(+)X(-))n via the interaction of many acid-base pairs. This salt formation is possible only in the beta-sheet conformation. By contrast, the formation of hydrogen-bonded complexes can occur both in beta-sheet domains as well as in alpha-helical domains. The 15N chemical shifts of the protonated ammonium groups increase when the size of the interacting halogen anions is increased from chloride to iodide and when the number of the interacting anions is increased. Thus, the observed high-field 15N shift of ammonium groups upon hydration is the consequence of replacing interacting halogen atoms by oxygen atoms.

  9. 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.

  10. 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.

  11. 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

  12. 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.

  13. 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.

  14. Site-specific protein backbone and side-chain NMR chemical shift and relaxation analysis of human vinexin SH3 domain using a genetically encoded {sup 15}N/{sup 19}F-labeled unnatural amino acid

    SciTech Connect

    Shi, Pan; Xi, Zhaoyong; Wang, Hu; Shi, Chaowei; Xiong, Ying; Tian, Changlin

    2010-11-19

    Research highlights: {yields} Chemical synthesis of {sup 15}N/{sup 19}F-trifluomethyl phenylalanine. {yields} Site-specific incorporation of {sup 15}N/{sup 19}F-trifluomethyl phenylalanine to SH3. {yields} Site-specific backbone and side chain chemical shift and relaxation analysis. {yields} Different internal motions at different sites of SH3 domain upon ligand binding. -- Abstract: SH3 is a ubiquitous domain mediating protein-protein interactions. Recent solution NMR structural studies have shown that a proline-rich peptide is capable of binding to the human vinexin SH3 domain. Here, an orthogonal amber tRNA/tRNA synthetase pair for {sup 15}N/{sup 19}F-trifluoromethyl-phenylalanine ({sup 15}N/{sup 19}F-tfmF) has been applied to achieve site-specific labeling of SH3 at three different sites. One-dimensional solution NMR spectra of backbone amide ({sup 15}N){sup 1}H and side-chain {sup 19}F were obtained for SH3 with three different site-specific labels. Site-specific backbone amide ({sup 15}N){sup 1}H and side-chain {sup 19}F chemical shift and relaxation analysis of SH3 in the absence or presence of a peptide ligand demonstrated different internal motions upon ligand binding at the three different sites. This site-specific NMR analysis might be very useful for studying large-sized proteins or protein complexes.

  15. 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

  16. 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

  17. 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.

  18. 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.

  19. Triple resonance experiments for aligned sample solid-state NMR of 13C and 15N labeled proteins

    PubMed Central

    Sinha, Neeraj; Grant, Christopher V.; Park, Sang Ho; Brown, Jonathan Miles; Opella, Stanley J.

    2013-01-01

    Initial steps in the development of a suite of triple-resonance 1H/13C/15N solid-state NMR experiments applicable to aligned samples of 13C and 15N labeled proteins are described. The experiments take advantage of the opportunities for 13C detection without the need for homonuclear 13C/13C decoupling presented by samples with two different patterns of isotopic labeling. In one type of sample, the proteins are ~20% randomly labeled with 13C in all backbone and side chain carbon sites and ~100% uniformly 15N labeled in all nitrogen sites; in the second type of sample, the peptides and proteins are 13C labeled at only the α-carbon and 15N labeled at the amide nitrogen of a few residues. The requirement for homonuclear 13C/13C decoupling while detecting 13C signals is avoided in the first case because of the low probability of any two 13C nuclei being bonded to each other; in the second case, the labeled 13Cα sites are separated by at least three bonds in the polypeptide chain. The experiments enable the measurement of the 13C chemical shift and 1H–13C and 15N–13C heteronuclear dipolar coupling frequencies associated with the 13Cα and 13C′ backbone sites, which provide orientation constraints complementary to those derived from the 15N labeled amide backbone sites. 13C/13C spin-exchange experiments identify proximate carbon sites. The ability to measure 13C–15N dipolar coupling frequencies and correlate 13C and 15N resonances provides a mechanism for making backbone resonance assignments. Three-dimensional combinations of these experiments ensure that the resolution, assignment, and measurement of orientationally dependent frequencies can be extended to larger proteins. Moreover, measurements of the 13C chemical shift and 1H–13C heteronuclear dipolar coupling frequencies for nearly all side chain sites enable the complete three-dimensional structures of proteins to be determined with this approach. PMID:17293139

  20. 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.

  1. Unraveling the complexity of protein backbone dynamics with combined (13)C and (15)N solid-state NMR relaxation measurements.

    PubMed

    Lamley, Jonathan M; Lougher, Matthew J; Sass, Hans Juergen; Rogowski, Marco; Grzesiek, Stephan; Lewandowski, Józef R

    2015-09-14

    Typically, protein dynamics involve a complex hierarchy of motions occurring on different time scales between conformations separated by a range of different energy barriers. NMR relaxation can in principle provide a site-specific picture of both the time scales and amplitudes of these motions, but independent relaxation rates sensitive to fluctuations in different time scale ranges are required to obtain a faithful representation of the underlying dynamic complexity. This is especially pertinent for relaxation measurements in the solid state, which report on dynamics in a broader window of time scales by more than 3 orders of magnitudes compared to solution NMR relaxation. To aid in unraveling the intricacies of biomolecular dynamics we introduce (13)C spin-lattice relaxation in the rotating frame (R1ρ) as a probe of backbone nanosecond-microsecond motions in proteins in the solid state. We present measurements of (13)C'R1ρ rates in fully protonated crystalline protein GB1 at 600 and 850 MHz (1)H Larmor frequencies and compare them to (13)C'R1, (15)N R1 and R1ρ measured under the same conditions. The addition of carbon relaxation data to the model free analysis of nitrogen relaxation data leads to greatly improved characterization of time scales of protein backbone motions, minimizing the occurrence of fitting artifacts that may be present when (15)N data is used alone. We also discuss how internal motions characterized by different time scales contribute to (15)N and (13)C relaxation rates in the solid state and solution state, leading to fundamental differences between them, as well as phenomena such as underestimation of picosecond-range motions in the solid state and nanosecond-range motions in solution.

  2. Post-grafting amination of alkyl halide-functionalized silica for applications in catalysis, adsorption, and 15N NMR spectroscopy.

    PubMed

    Moschetta, Eric G; Sakwa-Novak, Miles A; Greenfield, Jake L; Jones, Christopher W

    2015-02-24

    An anhydrous synthesis of aminosilica materials from alkyl halide-functionalized mesoporous SBA-15 silica by post-grafting amination is introduced for applications in CO2 adsorption, cooperative catalysis, and (15)N solid-state NMR spectroscopy. The synthesis is demonstrated to convert terminal alkyl halide-functionalized silica materials containing Cl, Br, and I to primary alkylamines using anhydrous ammonia in a high-pressure reactor. The benefits of the post-grafting amination procedure include (i) use of anhydrous isotopically labeled ammonia, (15)NH3, to create aminosilica materials that can be investigated using (15)N solid-state NMR to elucidate potential intermediates and surface species in CO2 adsorption processes and catalysis, (ii) similar CO2 uptake in experiments extracting CO2 from dry simulated air experiments, and (iii) improved activity in acid-base bifunctional catalysis compared to traditional amine-grafted materials. The effects of the type of halide, the initial halide loading, and the total reaction time on the conversion of the halides to primary amines are explored. Physical and chemical characterizations of the materials show that the textural properties of the silica are unaffected by the reaction conditions and that quantitative conversion to primary amines is achieved even at short reaction times and high initial alkyl halide loadings. Additionally, preliminary (15)N solid-state NMR experiments indicate formation of nitrogen-containing species and demonstrate that the synthesis can be used to create materials useful for investigating surface species by NMR spectroscopy. The differences between the materials prepared via post-grafting amination vs traditional aminosilane grafting are attributed to the slightly increased spacing of the amines synthesized by amination because the alkylhalosilanes are initially better spaced on the silica surface after grafting, whereas the aminosilanes likely cluster to a greater extent when grafted on the

  3. 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

  4. sup 15 N and sup 13 C NMR studies of ligands bound to the 280,000-dalton protein porphobilinogen synthase elucidate the structures of enzyme-bound product and a Schiff base intermediate

    SciTech Connect

    Jaffe, E.K.; Rajagopalan, J.S. ); Markham, G.D. )

    1990-09-11

    Porphobilinogen synthase (PBGS) catalyzes the asymmetric condensation of two molecules of 5-aminolevulinic acid (ALA). Despite the 280,000-dalton size of PBGS, much can be learned about the reaction mechanism through {sup 13}C and {sup 15}N NMR. The authors knowledge, these studies represent the largest protein complex for which individual nuclei have been characterized by {sup 13}C or {sup 15}N NMR. Here they extend their {sup 13}C NMR studies to PBGS complexes with (3,3-{sup 2}H{sub 2},3-{sup 13}C)ALA and report {sup 15}N NMR studies of ({sup 15}N)ALA bound to PBGS. As in their previous {sup 13}C NMR studies, observation of enzyme-bound {sup 15}N-labeled species was facilitated by deuteration at nitrogens that are attached to slowly exchanging hydrogens. For holo-PBGS at neutral pH, the NMR spectra reflect the structure of the enzyme-bound product porphobilinogen (PBG), whose chemical shifts are uniformly consistent with deprotonation of the amino group whose solution pK{sub a} is 11. Despite this local environment, the protons of the amino group are in rapid exchange with solvent. For methyl methanethiosulfonate (MMTS) modified PBGS, the NMR spectra reflect the chemistry of an enzyme-bound Schiff base intermediate that is formed between C{sub 4} of ALA and an active-site lysine. The {sup 13}C chemical shift of (3,3-{sup 2}H{sub 2},3-{sup 13}C)ALA confirms that the Schiff base is an imine of E stereochemistry. By comparison to model imines formed between ({sup 15}N)ALA and hydrazine or hydroxylamine, the {sup 15}N chemical shift of the enzyme-bound Schiff base suggests that the free amino group is an environment resembling partial deprotonation. Deprotonation of the amino group would facilitate formation of a Schiff base between the amino group of the enzyme-bound Schiff base and C{sub 4} of the second ALA substrate. This is the first evidence supporting carbon-nitrogen bond formation as the initial site of interaction between the two substrate molecules.

  5. A solution NMR study of the selectively 13C, 15N-labeled peptaibol chrysospermin C in methanol.

    PubMed

    Anders, R; Wenschuh, H; Soskic, V; Fischer-Frühholz, S; Ohlenschläger, O; Dornberger, K; Brown, L R

    1998-07-01

    The conformation of the 19-residue peptaibol chrysospermin C in methanol has been investigated by NMR spectroscopy using selective 15N and 13C labeling of the alpha-aminoisobutyric acid (Aib) residues. Complete 1H and 13C sequential assignments, including stereospecific assignments for the heavily overlapped resonances from the two Cbeta methyl groups of the eight Aib residues, are reported for a peptaibol for the first time. An Aib residue followed by a Pro is an exception to previous suggestions regarding stereospecific assignment of the two Cbeta methyl groups of Aib residues. Local nuclear Overhauser effects and 3J(HNC') and 3J(HNCbeta) scalar couplings indicate that the phi angles of the Aib residues are restricted sterically to local conformations consistent with right-handed helices. Despite these constraints on the eight Aib residues, the NMR data for chrysospermin C in methanol are generally most consistent with an ensemble of transient conformations, including backbone conformations inconsistent with helical structures. Initial NMR measurements for chrysospermin C bound to micelles suggest structural and dynamic differences relative to alamethicin bound to micelles which may be related to differences in gating voltages for formation of ion channels.

  6. 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.

  7. 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

  8. Accurate determination of order parameters from 1H,15N dipolar couplings in MAS solid-state NMR experiments.

    PubMed

    Chevelkov, Veniamin; Fink, Uwe; Reif, Bernd

    2009-10-01

    A reliable site-specific estimate of the individual N-H bond lengths in the protein backbone is the fundamental basis of any relaxation experiment in solution and in the solid-state NMR. The N-H bond length can in principle be influenced by hydrogen bonding, which would result in an increased N-H distance. At the same time, dynamics in the backbone induces a reduction of the experimental dipolar coupling due to motional averaging. We present a 3D dipolar recoupling experiment in which the (1)H,(15)N dipolar coupling is reintroduced in the indirect dimension using phase-inverted CP to eliminate effects from rf inhomogeneity. We find no variation of the N-H dipolar coupling as a function of hydrogen bonding. Instead, variations in the (1)H,(15)N dipolar coupling seem to be due to dynamics of the protein backbone. This is supported by the observed correlation between the H(N)-N dipolar coupling and the amide proton chemical shift. The experiment is demonstrated for a perdeuterated sample of the alpha-spectrin SH3 domain. Perdeuteration is a prerequisite to achieve high accuracy. The average error in the analysis of the H-N dipolar couplings is on the order of +/-370 Hz (+/-0.012 A) and can be as small as 150 Hz, corresponding to a variation of the bond length of +/-0.005 A.

  9. 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.

  10. 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...

  11. 1H- and 15N-NMR assignment and solution structure of the chemotactic Escherichia coli Che Y protein.

    PubMed

    Bruix, M; Pascual, J; Santoro, J; Prieto, J; Serrano, L; Rico, M

    1993-08-01

    Che Y is a 129-residue parallel alpha/beta protein involved in bacterial chemotaxis. We have used this protein as a model to study the folding reaction of parallel alpha/beta proteins. As a first step we carried out the complete assignment of the 1H and 15N spectra from Escherichia coli Che Y protein on the basis of two-dimensional 1H homonuclear and 1H-15N heteronuclear experiments by using sequence-specific methods. Our assignments differ from the preliminary assignments made by Kar et al. [Kar, L., Matsumura, P. & Johnson, M.E. (1992) Biochem. J. 287, 521-531] of aromatic residues obtained by comparison of NOEs with short proton-proton distances in the crystal structure of Che Y. The analysis of the extension of the secondary elements, as well as a preliminary calculation of the three-dimensional structure, indicate that the solution structure is closely coincident with the single crystal structure determined by X-ray diffraction.

  12. Screening enoxaparin tetrasaccharide SEC fractions for 3-O-sulfo-N-sulfoglucosamine residues using [(1)H,(15)N] HSQC NMR.

    PubMed

    Beecher, Consuelo N; Manighalam, Matthew S; Nwachuku, Adanma F; Larive, Cynthia K

    2016-02-01

    Heparin and heparan sulfate (HS) are important in mediating a variety of biological processes through binding to myriad different proteins. Specific structural elements along the polysaccharide chains are essential for high affinity protein binding, such as the 3-O-sulfated N-sulfoglucosamine (GlcNS3S) residue, a relatively rare modification essential for heparin's anticoagulant activity. The isolation of 3-O-sulfated oligosaccharides from complex mixtures is challenging because of their low abundance. Although methods such as affinity chromatography are useful in isolating oligosaccharides that bind specific proteins with high affinity, other important 3-O-sulfated oligosaccharides may easily be overlooked. Screening preparative-scale size-exclusion chromatography (SEC) fractions of heparin or HS digests using [(1)H,(15)N] HSQC NMR allows the identification of fractions containing 3-O-sulfated oligosaccharides through the unique (1)H and (15)N chemical shifts of the GlcNS3S residue. Those SEC fractions containing 3-O-sulfated oligosaccharides can then be isolated using strong anion-exchange (SAX)-HPLC. Compared with the results obtained by pooling the fractions comprising a given SEC peak, SAX-HPLC analysis of individual SEC fractions produces a less complicated chromatogram in which the 3-O-sulfated oligosaccharides are enriched relative to more abundant components. The utility of this approach is demonstrated for tetrasaccharide SEC fractions of the low molecular weight heparin drug enoxaparin facilitating the isolation and characterization of an unsaturated 3-O-sulfated tetrasaccharide containing a portion of the antithrombin-III binding sequence.

  13. Computational identification of a phospholipidosis toxicophore using (13)C and (15)N NMR-distance based fingerprints.

    PubMed

    Slavov, Svetoslav H; Wilkes, Jon G; Buzatu, Dan A; Kruhlak, Naomi L; Willard, James M; Hanig, Joseph P; Beger, Richard D

    2014-12-01

    Modified 3D-SDAR fingerprints combining (13)C and (15)N NMR chemical shifts augmented with inter-atomic distances were used to model the potential of chemicals to induce phospholipidosis (PLD). A curated dataset of 328 compounds (some of which were cationic amphiphilic drugs) was used to generate 3D-QSDAR models based on tessellations of the 3D-SDAR space with grids of different density. Composite PLS models averaging the aggregated predictions from 100 fully randomized individual models were generated. On each of the 100 runs, the activities of an external blind test set comprised of 294 proprietary chemicals were predicted and averaged to provide composite estimates of their PLD-inducing potentials (PLD+ if PLD is observed, otherwise PLD-). The best performing 3D-QSDAR model utilized a grid with a density of 8ppm×8ppm in the C-C region, 8ppm×20ppm in the C-N region and 20ppm×20ppm in the N-N region. The classification predictive performance parameters of this model evaluated on the basis of the external test set were as follows: accuracy=0.70, sensitivity=0.73 and specificity=0.66. A projection of the most frequently occurring bins on the standard coordinate space suggested a toxicophore composed of an aromatic ring with a centroid 3.5-7.5Å distant from an amino-group. The presence of a second aromatic ring separated by a 4-5Å spacer from the first ring and at a distance of between 5.5Å and 7Å from the amino-group was also associated with a PLD+ effect. These models provide comparable predictive performance to previously reported models for PLD with the added benefit of being based entirely on non-confidential, publicly available training data and with good predictive performance when tested in a rigorous, external validation exercise.

  14. Expression, purification, and mass spectrometric analysis of 15N, 13C-labeled RGD-hirudin, expressed in Pichia pastoris, for NMR studies.

    PubMed

    Huang, Yinong; Zhang, Yanling; Wu, Yi; Wang, Jue; Liu, Xingang; Dai, Linsen; Wang, Longsheng; Yu, Min; Mo, Wei

    2012-01-01

    A novel recombinant hirudin, RGD-hirudin, inhibits the activity of thrombin and the aggregation of platelets. Here, we successfully expressed (15)N, (13)C-labeled RGD-hirudin in Pichia pastoris in a fermenter. The protein was subsequently purified to yield sufficient quantities for structural and functional studies. The purified protein was characterized by HPLC and MALDI-TOF mass spectroscopy. Analysis revealed that the protein was pure and uniformly labeled with (15)N and (13)C. A bioassay showed that the anti-thrombin activity and the anti-platelet aggregation ability of the labeled protein were the same as those of unlabeled RGD-hirudin. Multidimensional heteronuclear NMR spectroscopy has been used to determine almost complete backbone (15)N, (13)C and (1)H resonance assignments of the r-RGD-Hirudin. The (15)N-(1)H HSQC spectrum of uniformly (15)N, (13)C-labeled RGD-hirudin allowed successful assignment of the signals. Examples of the quality of the data are provided for the (15)N-(l)H correlation spectrum, and by selected planes of the CBCA(CO)NH, CBCANH, and HNCO experiments. These results provide a basis for further studies on the structure-function relationship of RGD-hirudin with thrombin and platelets. PMID:22879918

  15. Solid-phase peptide synthesis and solid-state NMR spectroscopy of (Ala/sup 3/-/sup 15/N)(Val/sup 1/)gramicidin A

    SciTech Connect

    Fields, G.B.; Fields, C.G.; Petefish, J.; Van Wart, H.E.; Cross, T.A.

    1988-03-01

    (Ala/sup 3-15/N)(Val/sup 1/)Gramicidin A has been prepared by solid-phase peptide synthesis and studied by solid-state /sup 15/N nuclear magnetic resonance spectroscopy. The synthesis of desformyl(Ala/sup 3-15/N)(Val/sup 1/)gramicidin A employed N-hydroxysuccinimide esters of 9-fluorenylmethoxycarbonyl-N/sup ..cap alpha../-amino acids and completely avoided the use of acid. Since deblocking was done with piperidine and the peptide was removed from the resin by treatment with ethanolamine, this synthetic protocol prevented oxidation of the indole rings of this tryptophan-rich peptide and reduced truncations produced by acid hydrolysis. After formylation and purification by anion-exchange and high-pressure liquid chromatography, the peptide was obtained in an overall yield of 30%. Solid-state /sup 15/N nuclear magnetic resonance spectra of this peptide and uniformly labeled (/sup 15/N)gramicidin A' oriented in hydrated lipid bilayers have been obtained, allowing unambiguous assignment of the (/sup 15/N)Ala/sup 3/ resonance in the latter. The solid-state /sup 15/N nuclear magnetic resonance experiments provide evidence that (Val/sup 1/)gramicidin A is rotating about an axis that is perpendicular to the plane of the lipid bilayer and that the N-H axis is nearly parallel with the rotational axis. This study demonstrates that site-specifically labeled (/sup 15/N)gramicidin A analogs prepared by solid-phase peptide synthesis are valuable tools in the study of the solid-state nuclear magnetic resonance spectra of samples in oriented lipid bilayers.

  16. 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.

  17. Structure Determination of an Ag(I) -Mediated Cytosine-Cytosine Base Pair within DNA Duplex in Solution with (1) H/(15) N/(109) Ag NMR Spectroscopy.

    PubMed

    Dairaku, Takenori; Furuita, Kyoko; Sato, Hajime; Šebera, Jakub; Nakashima, Katsuyuki; Kondo, Jiro; Yamanaka, Daichi; Kondo, Yoshinori; Okamoto, Itaru; Ono, Akira; Sychrovský, Vladimír; Kojima, Chojiro; Tanaka, Yoshiyuki

    2016-09-01

    The structure of an Ag(I) -mediated cytosine-cytosine base pair, C-Ag(I) -C, was determined with NMR spectroscopy in solution. The observation of 1-bond (15) N-(109) Ag J-coupling ((1) J((15) N,(109) Ag): 83 and 84 Hz) recorded within the C-Ag(I) -C base pair evidenced the N3-Ag(I) -N3 linkage in C-Ag(I) -C. The triplet resonances of the N4 atoms in C-Ag(I) -C demonstrated that each exocyclic N4 atom exists as an amino group (-NH2 ), and any isomerization and/or N4-Ag(I) bonding can be excluded. The 3D structure of Ag(I) -DNA complex determined with NOEs was classified as a B-form conformation with a notable propeller twist of C-Ag(I) -C (-18.3±3.0°). The (109) Ag NMR chemical shift of C-Ag(I) -C was recorded for cytidine/Ag(I) complex (δ((109) Ag): 442 ppm) to completed full NMR characterization of the metal linkage. The structural interpretation of NMR data with quantum mechanical calculations corroborated the structure of the C-Ag(I) -C base pair. PMID:27505707

  18. Structure Determination of an Ag(I) -Mediated Cytosine-Cytosine Base Pair within DNA Duplex in Solution with (1) H/(15) N/(109) Ag NMR Spectroscopy.

    PubMed

    Dairaku, Takenori; Furuita, Kyoko; Sato, Hajime; Šebera, Jakub; Nakashima, Katsuyuki; Kondo, Jiro; Yamanaka, Daichi; Kondo, Yoshinori; Okamoto, Itaru; Ono, Akira; Sychrovský, Vladimír; Kojima, Chojiro; Tanaka, Yoshiyuki

    2016-09-01

    The structure of an Ag(I) -mediated cytosine-cytosine base pair, C-Ag(I) -C, was determined with NMR spectroscopy in solution. The observation of 1-bond (15) N-(109) Ag J-coupling ((1) J((15) N,(109) Ag): 83 and 84 Hz) recorded within the C-Ag(I) -C base pair evidenced the N3-Ag(I) -N3 linkage in C-Ag(I) -C. The triplet resonances of the N4 atoms in C-Ag(I) -C demonstrated that each exocyclic N4 atom exists as an amino group (-NH2 ), and any isomerization and/or N4-Ag(I) bonding can be excluded. The 3D structure of Ag(I) -DNA complex determined with NOEs was classified as a B-form conformation with a notable propeller twist of C-Ag(I) -C (-18.3±3.0°). The (109) Ag NMR chemical shift of C-Ag(I) -C was recorded for cytidine/Ag(I) complex (δ((109) Ag): 442 ppm) to completed full NMR characterization of the metal linkage. The structural interpretation of NMR data with quantum mechanical calculations corroborated the structure of the C-Ag(I) -C base pair.

  19. Assignment of congested NMR spectra: Carbonyl backbone enrichment via the Entner Doudoroff pathway

    NASA Astrophysics Data System (ADS)

    Goldbourt, Amir; Day, Loren A.; McDermott, Ann E.

    2007-12-01

    In NMR spectra of complex proteins, sparse isotope enrichment can be important, in that the removal of many 13C- 13C homonuclear J-couplings can narrow the lines and thereby facilitate the process of spectral assignment and structure elucidation. We present a simple scheme for selective yet extensive isotopic enrichment applicable for production of proteins in organisms utilizing the Entner-Doudoroff (ED) metabolic pathway. An enrichment scheme so derived is demonstrated in the context of a magic-angle spinning solid-state NMR (MAS SSNMR) study of Pf1 bacteriophage, the host of which is Pseudomonas aeruginosa, strain K (PAK), an organism that uses the ED pathway for glucose catabolism. The intact and infectious Pf1 phage in this study was produced by infected PAK cells grown on a minimal medium containing 1- 13C D-glucose ( 13C in position 1) as the sole carbon source, as well as 15NH 4Cl as the only nitrogen source. The 37 MDa Pf1 phage consists of about 93% major coat protein, 1% minor coat proteins, and 6% single-stranded, circular DNA. As a consequence of this composition and the enrichment scheme, the resonances in the MAS SSNMR spectra of the Pf1 sample were almost exclusively due to carbonyl carbons in the major coat protein. Moreover, 3D heteronuclear NCOCX correlation experiments also show that the amino acids leucine, serine, glycine, and tyrosine were not isotopically enriched in their carbonyl positions (although most other amino acids were), which is as expected based upon considerations of the ED metabolic pathway. 3D NCOCX NMR data and 2D 15N- 15N data provided strong verification of many previous assignments of 15N amide and 13C carbonyl shifts in this highly congested spectrum; both the semi-selective enrichment patterns and the narrowed linewidths allowed for greater certainty in the assignments as compared with use of uniformly enriched samples alone.

  20. 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.

  1. 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.

  2. The economical synthesis of [2'-(13)C, 1,3-(15)N2]uridine; preliminary conformational studies by solid state NMR.

    PubMed

    Patching, Simon G; Middleton, David A; Henderson, Peter J F; Herbert, Richard B

    2003-06-21

    The synthesis of [2'-(13)C, 1,3-(15)N2]uridine 11 was achieved as follows. An epimeric mixture of D-[1-(13)C]ribose 3 and D-[1-(13)C]arabinose 4 was obtained in excellent yield by condensation of K13CN with D-erythrose 2 using a modification of the Kiliani-Fischer synthesis. Efficient separation of the two aldose epimers was pivotally achieved by a novel ion-exchange (Sm3+) chromatography method. D-[2-(13)C]Ribose 5 was obtained from D-[1-(13)C]arabinose 4 using a Ni(II) diamine complex (nickel chloride plus TEMED). Combination of these procedures in a general cycling manner can lead to the very efficient preparation of specifically labelled 13C-monosaccharides of particular chirality. 15N-labelling was introduced in the preparation of [2'-(13)C, 1,3-(15)N2]uridine 11 via [15N2]urea. Cross polarisation magic angle spinning (CP-MAS) solid-state NMR experiments using rotational echo double resonance (REDOR) were carried out on crystals of the labelled uridine to show that the inter-atomic distance between C-2' and N-1 is closely similar to that calculated from X-ray crystallographic data. The REDOR method will be used now to determine the conformation of bound substrates in the bacterial nucleoside transporters NupC and NupG.

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

    PubMed Central

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

    2009-01-01

    DD K, a peptide first isolated from the skin secretion of the Phyllomedusa distincta frog, has been prepared by solid-phase chemical peptide synthesis and its conformation was studied in trifluoroethanol/water as well as in the presence of sodium dodecyl sulfate and dodecylphosphocholine micelles or small unilamellar vesicles. Multidimensional solution NMR spectroscopy indicates an α-helical conformation in membrane environments starting at residue 7 and extending to the C-terminal carboxyamide. Furthermore, DD K has been labeled with 15N at a single alanine position that is located within the helical core region of the sequence. When reconstituted into oriented phosphatidylcholine membranes the resulting 15N solid-state NMR spectrum shows a well-defined helix alignment parallel to the membrane surface in excellent agreement with the amphipathic character of DD K. Proton-decoupled 31P solid-state NMR spectroscopy indicates that the peptide creates a high level of disorder at the level of the phospholipid headgroup suggesting that DD K partitions into the bilayer where it severely disrupts membrane packing. PMID:19289046

  4. In vivo, large-scale preparation of uniformly (15)N- and site-specifically (13)C-labeled homogeneous, recombinant RNA for NMR studies.

    PubMed

    Le, My T; Brown, Rachel E; Simon, Anne E; Dayie, T Kwaku

    2015-01-01

    Knowledge of how ribonucleic acid (RNA) structures fold to form intricate, three-dimensional structures has provided fundamental insights into understanding the biological functions of RNA. Nuclear magnetic resonance (NMR) spectroscopy is a particularly useful high-resolution technique to investigate the dynamic structure of RNA. Effective study of RNA by NMR requires enrichment with isotopes of (13)C or (15)N or both. Here, we present a method to produce milligram quantities of uniformly (15)N- and site-specifically (13)C-labeled RNAs using wild-type K12 and mutant tktA Escherichia coli in combination with a tRNA-scaffold approach. The method includes a double selection protocol to obtain an E. coli clone with consistently high expression of the recombinant tRNA-scaffold. We also present protocols for the purification of the tRNA-scaffold from a total cellular RNA extract and the excision of the RNA of interest from the tRNA-scaffold using DNAzymes. Finally, we showcase NMR applications to demonstrate the benefit of using in vivo site-specifically (13)C-labeled RNA. PMID:26577743

  5. 1H, 15N, and 13C backbone chemical shift assignments, secondary structure, and magnesium-binding characteristics of the Bacillus subtilis response regulator, Spo0F, determined by heteronuclear high-resolution NMR.

    PubMed Central

    Feher, V. A.; Zapf, J. W.; Hoch, J. A.; Dahlquist, F. W.; Whiteley, J. M.; Cavanagh, J.

    1995-01-01

    Spo0F, sporulation stage 0 F protein, a 124-residue protein responsible, in part, for regulating the transition of Bacillus subtilis from a vegetative state to a dormant endospore, has been studied by high-resolution NMR. The 1H, 15N, and 13C chemical shift assignments for the backbone residues have been determined from analyses of 3D spectra, 15N TOCSY-HSQC, 15N NOESY-HSQC, HNCA, and HN(CO)CA. Assignments for many sidechain proton resonances are also reported. The secondary structure, inferred from short- and medium-range NOEs, 3JHN alpha coupling constants, and hydrogen exchange patterns, define a topology consistent with a doubly wound (alpha/beta)5 fold. Interestingly, comparison of the secondary structure of Spo0F to the structure of the Escherichia coli response regulator, chemotaxis Y protein (CheY) (Volz K, Matsumura P, 1991, J Biol Chem 266:15511-15519; Bruix M et al., 1993, Eur J Biochem 215:573-585), show differences in the relative length of secondary structure elements that map onto a single face of the tertiary structure of CheY. This surface may define a region of binding specificity for response regulators. Magnesium titration of Spo0F, followed by amide chemical shift changes, gives an equilibrium dissociation constant of 20 +/- 5 mM. Amide resonances most perturbed by magnesium binding are near the putative site of phosphorylation, Asp 54. PMID:8528078

  6. 1H, 13C, and 15N NMR assignments of StnII-Y111N, a highly impaired mutant of the sea anemone actinoporin Sticholysin II.

    PubMed

    Pardo-Cea, Miguel A; Alegre-Cebollada, Jorge; Martínez-del-Pozo, Alvaro; Gavilanes, José G; Bruix, Marta

    2010-04-01

    Sticholysin II is an actinoporin of 175 amino acids produced by the sea anemone Stichodactyla helianthus. Several studies with different mutants have been performed to characterize its molecular properties and activity. As a first step towards a 3D structural characterization and its interaction with membrane models at a residue level, herein we report the nearly complete NMR (15)N, (13)C and (1)H chemical shifts assignments of the Y111N variant at pH 4.0 and 25 degrees C (BMRB No. 16630). The assignment is complete for the biologically relevant residues, specially for those implicated in membrane interactions.

  7. Artifact suppression in electron paramagnetic resonance imaging of 14N- and 15N-labeled nitroxyl radicals with asymmetric absorption spectra

    NASA Astrophysics Data System (ADS)

    Takahashi, Wataru; Miyake, Yusuke; Hirata, Hiroshi

    2014-10-01

    This article describes an improved method for suppressing image artifacts in the visualization of 14N- and 15N-labeled nitroxyl radicals in a single image scan using electron paramagnetic resonance (EPR). The purpose of this work was to solve the problem of asymmetric EPR absorption spectra in spectral processing. A hybrid function of Gaussian and Lorentzian lineshapes was used to perform spectral line-fitting to successfully separate the two kinds of nitroxyl radicals. This approach can process the asymmetric EPR absorption spectra of the nitroxyl radicals being measured, and can suppress image artifacts due to spectral asymmetry. With this improved visualization method and a 750-MHz continuous-wave EPR imager, a temporal change in the distributions of a two-phase paraffin oil and water/glycerin solution system was visualized using lipophilic and hydrophilic nitroxyl radicals, i.e., 2-(14-carboxytetradecyl)-2-ethyl-4,4-dimethyl-3-oxazolidinyloxy (16-DOXYL stearic acid) and 4-hydroxyl-2,2,6,6-tetramethylpiperidine-d17-1-15N-1-oxyl (TEMPOL-d17-15N). The results of the two-phase separation experiment verified that reasonable artifact suppression could be achieved by the present method that deals with asymmetric absorption spectra in the EPR imaging of 14N- and 15N-labeled nitroxyl radicals.

  8. 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.

  9. 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

  10. Backbone 1H, 13C, and 15N NMR assignments for the Cyanothece 51142 protein cce_0567: a protein associated with nitrogen fixation in the DUF683 family

    SciTech Connect

    Buchko, Garry W.; Sofia, Heidi J.

    2008-06-01

    The recently sequenced genome of the diurnal cyanobacterium Cyanothece sp. PCC 51142 (contig 83.1_1_243_746) contains the sequence for an hypothetical protein that falls into the DUF683 family. As observed for the other 54 DUF683 proteins currently listed in the GenBank database, this 78-residue (9.0 kDa) protein in Cyanothece is also found in a nitrogen fixation gene cluster suggesting that it is involved in the process. To date no structural information exists for any of the proteins in the DUF683 family. In an effort to elucidate the biochemical role DUF683 may play in nitrogen fixation and to obtain structural information for a member of the DUF683 protein family, a construct containing DUF683 from Cyanothece 51142 was generated, expressed, purified, and the solution properties characterized. A total rotational correlation time (tc) of 17.1 ns was estimated by nuclear magnetic resonance (NMR) spectroscopy suggesting a molecular weight of ~ 40 kDa, an observation dictating that DUF683 is a tetramer in solution. Using triple-labeled (2H, 13C, 15N) and residue-specific 15N-labeled amino acids (L, K, V, and E/Q) samples, most of the backbone and side chain resonances for DUF683 were assigned. The 13C alpha chemical shifts and NOESY NMR data indicate that the protein is helical from K18-E75.

  11. Dependence of in vivo glutamine synthetase activity on ammonia concentration in rat brain studied by 1H - 15N heteronuclear multiple-quantum coherence-transfer NMR.

    PubMed Central

    Kanamori, K; Ross, B D; Kuo, E L

    1995-01-01

    The dependence of the in vivo rate of glutamine synthesis on the substrate ammonia concentration was studied in rat brain by 1H-15N heteronuclear multiple-quantum coherence-transfer NMR in combination with biochemical techniques. In vivo rates were measured at various steady-state blood and brain ammonia concentrations within the ranges 0.4-0.55 mumol/g and 0.86-0.98 mumol/g respectively, after low-rate intravenous 15NH4+ infusion (isotope chase). The rate of glutamine synthesis at steady state was determined from the change in brain [5-15N]glutamine levels during isotope chase, observed selectively through the amide proton by NMR, and 15N enrichments of brain glutamine and of blood and brain ammonia measured byN gas chromatography-MS. The in vivo rate (v) was 3.3-4.5 mumol/h per g of brain at blood ammonia concentrations (s) of 0.40-0.55 mumol/g. A linear increase of 1/v with 1/s permitted estimation of the in vivo glutamine synthetase (GS) activity at a physiological blood ammonia concentration to be 0.4-2.1 mumol/h per g. The observed ammonia-dependence strongly suggests that, under physiological conditions, in vivo GS activity is kinetically limited by sub-optimal in situ concentrations of ammonia as well as glutamate and ATP. Comparison of the observed in vivo GS activity with the reported in vivo rates of glutaminase and of gamma-aminobutyrate (GABA) synthesis suggests that, under mildly hyperammonaemic conditions, glutamine is synthesized at a sufficiently high rate to serve as a precursor of GABA, but glutaminase-catalysed hydrolysis of glutamine is too slow to be the sole provider of glutamate used for GABA synthesis. PMID:7487913

  12. Complete 15N and 1H NMR assignments for the amino-terminal domain of the phage 434 repressor in the urea-unfolded form

    PubMed Central

    Neri, Dario; Wider, Gerhard; Wüthrich, Kurt

    1992-01-01

    The amino-terminal domain of the phage 434 repressor consisting of residues 1-69 forms a globular structure of five tightly packed helices, with nearly identical molecular architectures in crystals and in solution. Upon addition of urea to an aqueous solution of this protein, the NMR spectrum of a second form of the protein appears in addition to the native form, and at a urea concentration of 7 M, this urea-unfolded form is the only species observed. At intermediate urea concentrations, the two forms of the protein inter-convert at a rate that allows the observation of the exchange process by NMR. Starting from the previous assignments for the native protein, we obtained nearly complete sequence-specific 1H and 15N NMR assignments for the unfolded form of the protein. For most amino acid residues, the 1H chemical shifts of the urea-unfolded protein are very similar to the random coil values, but some discrete regions of the polypeptide chain were identified that are likely to retain residual nonrandom spatial structure as evidenced by deviations of 1H chemical shifts and amide proton exchange rates from the expected random coil values. PMID:1584772

  13. NMR studies on /sup 15/N-labeled creatine (CR), creatinine (CRN), phosphocreatine (PCR), and phosphocreatinine (PCRN), and on barriers to rotation in creatine kinase-bound creatine in the enzymatic reaction

    SciTech Connect

    Kenyon, G.L.; Reddick, R.E.

    1986-05-01

    Recently, the authors have synthesized /sup 15/N-2-Cr, /sup 15/N-3-Crn, /sup 15/N-2-Crn, /sup 15/N-3-PCrn, /sup 15/N-3-PCr, and /sup 15/N-2-PCr. /sup 1/H, /sup 15/N, /sup 31/P NMR data show that Crn protonates exclusively at the non-methylated ring nitrogen, confirm that PCrn is phosphorylated at the exocyclic nitrogen, and demonstrate that the /sup 31/P-/sup 15/N one-bond coupling constant in /sup 15/N-3-PCr is 18 Hz, not 3 Hz as previously reported by Brindle, K.M., Porteous, R. and Radda, G.K.. The authors have found that creatine kinase is capable of catalyzing the /sup 14/N//sup 15/N positional isotope exchange of 3-/sup 15/N-PCr in the presence of MgADP, but not in its absence. Further, the exchange does not take place when labeled PCr is resynthesized exclusively from the ternary complex E X Cr X MgATP as opposed to either E X Cr or free Cr. This suggests that the enzyme both imparts an additional rotational barrier to creatine in the complex and catalyzes the transfer of phosphoryl group with essentially complete regiospecificity.

  14. 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

  15. 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.

  16. The HSP90 binding mode of a radicicol-like E-oxime from docking, binding free energy estimations, and NMR 15N chemical shifts

    PubMed Central

    Spichty, Martin; Taly, Antoine; Hagn, Franz; Kessler, Horst; Barluenga, Sofia; Winssinger, Nicolas; Karplus, Martin

    2009-01-01

    We determine the binding mode of a macrocyclic radicicol-like oxime to yeast HSP90 by combining computer simulations and experimental measurements. We sample the macrocyclic scaffold of the unbound ligand by parallel tempering simulations and dock the most populated conformations to yeast HSP90. Docking poses are then evaluated by the use of binding free energy estimations with the linear interaction energy method. Comparison of QM/MM-calculated NMR chemical shifts with experimental shift data for a selective subset of back-bone 15N provides an additional evaluation criteria. As a last test we check the binding modes against available structure-activity-relationships. We find that the most likely binding mode of the oxime to yeast HSP90 is very similar to the known structure of the radicicol-HSP90 complex. PMID:19482409

  17. Detection of closed influenza virus hemagglutinin fusion peptide structures in membranes by backbone (13)CO- (15)N rotational-echo double-resonance solid-state NMR.

    PubMed

    Ghosh, Ujjayini; Xie, Li; Weliky, David P

    2013-02-01

    The influenza virus fusion peptide is the N-terminal ~20 residues of the HA2 subunit of the hemagglutinin protein and this peptide plays a key role in the fusion of the viral and endosomal membranes during initial infection of a cell. The fusion peptide adopts N-helix/turn/C-helix structure in both detergent and membranes with reports of both open and closed interhelical topologies. In the present study, backbone (13)CO-(15)N REDOR solid-state NMR was applied to the membrane-associated fusion peptide to detect the distribution of interhelical distances. The data clearly showed a large fraction of closed and semi-closed topologies and were best-fitted to a mixture of two structures that do not exchange. One of the earlier open structural models may have incorrect G13 dihedral angles derived from TALOS analysis of experimentally correct (13)C shifts.

  18. 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.

  19. (15)N and (13)C group-selective techniques extend the scope of STD NMR detection of weak host-guest interactions and ligand screening.

    PubMed

    Kövér, Katalin E; Wéber, Edit; Martinek, Tamás A; Monostori, Eva; Batta, Gyula

    2010-10-18

    Saturation transfer difference (STD) is a valuable tool for studying the binding of small molecules to large biomolecules and for obtaining detailed information on the binding epitopes. Here, we demonstrate that the proposed (15)N/(13)C variants of group-selective, "GS-STD" experiments provide a powerful approach to mapping the binding epitope of a ligand even in the absence of efficient spin diffusion within the target protein. Therefore, these experimental variants broaden the scope of STD studies to smaller and/or more-dynamic targets. The STD spectra obtained in four different experimental setups (selective (1)H STD, (15)N GS-STD, (13)C(Ar) and (13)C(aliphatic) GS-STD approaches) revealed that the signal-intensity pattern of the difference spectra is affected by both the type and the spatial distribution of the excited "transmitter" atoms, as well as by the efficiency of the spin-diffusion-mediated magnetization transfer. The performance of the experiments is demonstrated on a system by using the lectin, galectin-1 and its carbohydrate ligand, lactose.

  20. Sorting signals from protein NMR spectra: SPI, a Bayesian protocol for uncovering spin systems.

    PubMed

    Grishaev, Alexander; Llinás, Miguel

    2002-11-01

    Grouping of spectral peaks into J-connected spin systems is essential in the analysis of macromolecular NMR data as it provides the basis for disentangling chemical shift degeneracies. It is a mandatory step before resonance and NOESY cross-peak identities can be established. We have developed SPI, a computational protocol that scrutinizes peak lists from homo- and hetero-nuclear multidimensional NMR spectra and progressively assembles sets of resonances into consensus J- and/or NOE-connected spin systems. SPI estimates the likelihood of nuclear spin resonances appearing at defined frequencies given sets of cross-peaks measured from multi-dimensional experiments. It quantifies spin system matching probabilities via Bayesian inference. The protocol takes advantage of redundancies in the number of connectivities revealed by suites of diverse NMR experiments, systematically tracking the adequacy of each grouping hypothesis. SPI was tested on 2D homonuclear and 2D/3D(15)N-edited data recorded from two protein modules, the col 2 domain of matrix metalloproteinase-2 (MMP-2) and the kringle 2 domain of plasminogen, of 60 and 83 amino acid residues, respectively. For these protein domains SPI identifies approximately 95% unambiguous resonance frequencies, a relatively good performance vis-à-vis the reported 'manual' (interactive) analyses. Abbreviations and Acronyms: SPI, SPin Identification; BMRB, BioMagResBank (Madison, WI).

  1. On the accuracy of the GIAO-DFT calculation of 15N NMR chemical shifts of the nitrogen-containing heterocycles--a gateway to better agreement with experiment at lower computational cost.

    PubMed

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

    2014-05-01

    The main factors affecting the accuracy and computational cost of the gauge-independent atomic orbital density functional theory (GIAO-DFT) calculation of (15)N NMR chemical shifts in the representative series of key nitrogen-containing heterocycles--azoles and azines--have been systematically analyzed. In the calculation of (15)N NMR chemical shifts, the best result has been achieved with the KT3 functional used in combination with Jensen's pcS-3 basis set (GIAO-DFT-KT3/pcS-3) resulting in the value of mean absolute error as small as 5 ppm for a range exceeding 270 ppm in a benchmark series of 23 compounds with an overall number of 41 different (15)N NMR chemical shifts. Another essential finding is that basically, the application of the locally dense basis set approach is justified in the calculation of (15)N NMR chemical shifts within the 3-4 ppm error that results in a dramatic decrease in computational cost. Based on the present data, we recommend GIAO-DFT-KT3/pcS-3//pc-2 as one of the most effective locally dense basis set schemes for the calculation of (15)N NMR chemical shifts.

  2. 13C NMR spectra of pyridine chalcone analogs

    NASA Astrophysics Data System (ADS)

    Jovanović, B. Ž.; Mišić-Vuković, M.; Marinković, A. D.; Csanádi, J.

    1999-05-01

    13C NMR spectra of two series of pyridine chalcone analogs were determined in deuterated dimethylsulphoxide (DMSO-d 6). It was established that these compounds were in more stable E-configurations except for the 4-pyridalacetophenone which was in Z-configuration. On the basis of the Hammett correlations of 13C NMR chemical shifts of the ethylenic bond carbon atoms and the σ values for the pyridine "aza" groups, the polarization of ethylenic bonds were discussed. It was established that the opposite effect of the pyridine substituents at the electronic density distribution in pyridalacetophenone and cinnamoylpyridines depends on its direct bonding to the ethylenic carbon or the transmission electronic effects via the carbonyl group, respectively.

  3. Three-Dimensional Solid-State NMR Spectroscopy Is Essential for Resolution of Resonances from In-Plane Residues in Uniformly 15N-Labeled Helical Membrane Proteins in Oriented Lipid Bilayers

    NASA Astrophysics Data System (ADS)

    Marassi, Francesca M.; Ma, Che; Gesell, Jennifer J.; Opella, Stanley J.

    2000-05-01

    Uniformly 15N-labeled samples of membrane proteins with helices aligned parallel to the membrane surface give two-dimensional PISEMA spectra that are highly overlapped due to limited dispersions of 1H-15N dipolar coupling and 15N chemical shift frequencies. However, resolution is greatly improved in three-dimensional 1H chemical shift/1H-15N dipolar coupling/15N chemical shift correlation spectra. The 23-residue antibiotic peptide magainin and a 54-residue polypeptide corresponding to the cytoplasmic domain of the HIV-1 accessory protein Vpu are used as examples. Both polypeptides consist almost entirely of α-helices, with their axes aligned parallel to the membrane surface. The measurement of three orientationally dependent frequencies for Val17 of magainin enabled the three-dimensional orientation of this helical peptide to be determined in the lipid bilayer.

  4. Formation of a noncovalent serpin-proteinase complex involves no conformational change in the serpin. Use of 1H-15N HSQC NMR as a sensitive nonperturbing monitor of conformation.

    PubMed

    Peterson, F C; Gordon, N C; Gettins, P G

    2000-10-01

    A structural understanding of the nature and scope of serpin inhibition mechanisms has been limited by the inability so far to crystallize any serpin-proteinase complex. We describe here the application of [(1)H-(15)N]-HSQC NMR on uniformly and residue-selectively (15)N-labeled serpin alpha(1)-proteinase inhibitor (Pittsburgh variant with stabilizing mutations) to provide a nonperturbing and exquisitely sensitive means of probing the conformation of the serpin alone and in a noncovalent complex with inactive, serine 195-modified, bovine trypsin. The latter should be a good model both for the few examples of reversible serpin-proteinase complexes and for the initial Michaelis-like complex formed en route to irreversible covalent inhibition. Cleavage of the reactive center loop, with subsequent insertion into beta-sheet A, caused dramatic perturbation of most of the NMR cross-peaks. This was true for both the uniformly labeled and alanine-specifically labeled samples. The spectra of uniformly or leucine- or alanine-specifically labeled alpha(1)-proteinase inhibitor in noncovalent complex with unlabeled inactive trypsin gave almost no detectable chemical shift changes of cross-peaks, but some general increase in line width. Residue-specific assignments of the four alanines in the reactive center loop, at P12, P11, P9, and P4, allowed specific examination of the behavior of the reactive center loop. All four alanines showed higher mobility than the body of the serpin, consistent with a flexible reactive center loop, which remained flexible even in the noncovalent complex with proteinase. The three alanines near the hinge point for insertion showed almost no chemical shift perturbation upon noncovalent complex formation, while the alanine at P4 was perturbed, presumably by interaction with the active site of bound trypsin. Reporters from both the body of the serpin and the reactive center loop therefore indicate that noncovalent complex formation involves no

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

    PubMed Central

    Gopinath, T.; Veglia, Gianluigi

    2013-01-01

    We propose a general method that enables the acquisition of multiple 2D and 3D solid-state NMR spectra for U-13C, 15N-labeled proteins. This method, called MEIOSIS (Multiple ExperIments via Orphan SpIn operatorS), makes it possible to detect four coherence transfer pathways simultaneously, utilizing orphan (i.e., neglected) spin operators of nuclear spin polarization generated during 15N-13C cross polarization (CP). In the MEIOSIS experiments, two phase-encoded free-induction decays are decoded into independent nuclear polarization pathways using Hadamard transformations. As a proof of principle, we show the acquisition of multiple 2D and 3D spectra of U-13C, 15N-labeled microcrystalline ubiquitin. Hadamard decoding of CP coherences into multiple independent spin operators is a new concept in solid-state NMR and is extendable to many other multidimensional experiments. The MEIOSIS method will increase the throughput of solid-state NMR techniques for microcrystalline proteins, membrane proteins, and protein fibrils. PMID:23676036

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

    NASA Astrophysics Data System (ADS)

    Gopinath, T.; Veglia, Gianluigi

    2013-05-01

    We propose a general method that enables the acquisition of multiple 2D and 3D solid-state NMR spectra for U-13C, 15N-labeled proteins. This method, called MEIOSIS (Multiple ExperIments via Orphan SpIn operatorS), makes it possible to detect four coherence transfer pathways simultaneously, utilizing orphan (i.e., neglected) spin operators of nuclear spin polarization generated during 15N-13C cross polarization (CP). In the MEIOSIS experiments, two phase-encoded free-induction decays are decoded into independent nuclear polarization pathways using Hadamard transformations. As a proof of principle, we show the acquisition of multiple 2D and 3D spectra of U-13C, 15N-labeled microcrystalline ubiquitin. Hadamard decoding of CP coherences into multiple independent spin operators is a new concept in solid-state NMR and is extendable to many other multidimensional experiments. The MEIOSIS method will increase the throughput of solid-state NMR techniques for microcrystalline proteins, membrane proteins, and protein fibrils.

  7. 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.

  8. N-15 NMR spectra of naturally abundant nitrogen in soil and aquatic natural organic matter samples of the International Humic Substances Society

    USGS Publications Warehouse

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

    2009-01-01

    The naturally abundant nitrogen in soil and aquatic NOM samples from the International Humic Substances Society has been characterized by solid state CP/MAS 15N NMR. Soil samples include humic and fulvic acids from the Elliot soil, Minnesota Waskish peat and Florida Pahokee peat, as well as the Summit Hill soil humic acid and the Leonardite humic acid. Aquatic samples include Suwannee River humic, fulvic and reverse osmosis isolates, Nordic humic and fulvic acids and Pony Lake fulvic acid. Additionally, Nordic and Suwannee River XAD-4 acids and Suwannee River hydrophobic neutral fractions were analyzed. Similar to literature reports, amide/aminoquinone nitrogens comprised the major peaks in the solid state spectra of the soil humic and fulvic acids, along with heterocyclic and amino sugar/terminal amino acid nitrogens. Spectra of aquatic samples, including the XAD-4 acids, contain resolved heterocyclic nitrogen peaks in addition to the amide nitrogens. The spectrum of the nitrogen enriched, microbially derived Pony Lake, Antarctica fulvic acid, appeared to contain resonances in the region of pyrazine, imine and/or pyridine nitrogens, which have not been observed previously in soil or aquatic humic substances by 15N NMR. Liquid state 15N NMR experiments were also recorded on the Elliot soil humic acid and Pony Lake fulvic acid, both to examine the feasibility of the techniques, and to determine whether improvements in resolution over the solid state could be realized. For both samples, polarization transfer (DEPT) and indirect detection (1H-15N gHSQC) spectra revealed greater resolution among nitrogens directly bonded to protons. The amide/aminoquinone nitrogens could also be observed by direct detection experiments.

  9. Total lineshape analysis of high-resolution NMR spectra powered by simulated annealing

    NASA Astrophysics Data System (ADS)

    Cheshkov, D. A.; Sinitsyn, D. O.; Sheberstov, K. F.; Chertkov, V. A.

    2016-11-01

    The novel algorithm for a total lineshape analysis of high-resolution NMR spectra has been developed. A global optimization by simulated annealing has been applied that has allowed to overcome the main trouble of common approaches which had frequently returned solutions for local minima rather than for global ones. The algorithm has been verified for the four-spin test systems ABCD, and has been successfully used for analysis of experimental NMR spectra of proline. The approach has allowed to avoid a sophisticated manual setup of initial parameters and to conduct the analysis of complicated high-resolution NMR spectra nearly automatically.

  10. Access to experimentally infeasible spectra by pure-shift NMR covariance

    NASA Astrophysics Data System (ADS)

    Fredi, André; Nolis, Pau; Cobas, Carlos; Parella, Teodor

    2016-09-01

    Covariance processing is a versatile processing tool to generate synthetic NMR spectral representations without the need to acquire time-consuming experimental datasets. Here we show that even experimentally prohibited NMR spectra can be reconstructed by introducing key features of a reference 1D CHn-edited spectrum into standard 2D spectra. This general procedure is illustrated with the calculation of experimentally infeasible multiplicity-edited pure-shift NMR spectra of some very popular homonuclear (ME-psCOSY and ME-psTOCSY) and heteronuclear (ME-psHSQC-TOCSY and ME-psHMBC) experiments.

  11. Access to experimentally infeasible spectra by pure-shift NMR covariance.

    PubMed

    Fredi, André; Nolis, Pau; Cobas, Carlos; Parella, Teodor

    2016-09-01

    Covariance processing is a versatile processing tool to generate synthetic NMR spectral representations without the need to acquire time-consuming experimental datasets. Here we show that even experimentally prohibited NMR spectra can be reconstructed by introducing key features of a reference 1D CHn-edited spectrum into standard 2D spectra. This general procedure is illustrated with the calculation of experimentally infeasible multiplicity-edited pure-shift NMR spectra of some very popular homonuclear (ME-psCOSY and ME-psTOCSY) and heteronuclear (ME-psHSQC-TOCSY and ME-psHMBC) experiments.

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

    PubMed Central

    Frydman, Lucio; Scherf, Tali; Lupulescu, Adonis

    2002-01-01

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

  13. Sensitivity Gains, Linearity, and Spectral Reproducibility in Nonuniformly Sampled Multidimensional MAS NMR Spectra of High Dynamic Range.

    SciTech Connect

    Suiter, Christopher L.; Paramasivam, Sivakumar; Hou, Guangjin; Sun, Shangjin; Rice, David M.; Hoch, Jeffrey C.; Rovnyak, David S.; Polenova, Tatyana E.

    2014-04-22

    Recently, we have demonstrated that considerable inherent sensitivity gains are attained in MAS NMR spectra acquired by nonuniform sampling (NUS) and introduced maximum entropy interpolation (MINT) processing that assures the linearity of transformation between the time and frequency domains. In this report, we examine the utility of the NUS/MINT approach in multidimensional datasets possessing high dynamic range, such as homonuclear 13C–13C correlation spectra. We demonstrate on model compounds and on 1–73-(U-13C,15N)/74–108-(U-15N) E. coli thioredoxin reassembly, that with appropriately constructed 50 % NUS schedules inherent sensitivity gains of 1.7–2.1-fold are readily reached in such datasets. We show that both linearity and line width are retained under these experimental conditions throughout the entire dynamic range of the signals. Furthermore, we demonstrate that the reproducibility of the peak intensities is excellent in the NUS/MINT approach when experiments are repeated multiple times and identical experimental and processing conditions are employed. Finally, we discuss the principles for design and implementation of random exponentially biased NUS sampling schedules for homonuclear 13C–13C MAS correlation experiments that yield high quality artifact-free datasets.

  14. Sensitivity gains, linearity, and spectral reproducibility in nonuniformly sampled multidimensional MAS NMR spectra of high dynamic range

    PubMed Central

    Suiter, Christopher L.; Paramasivam, Sivakumar; Hou, Guangjin; Sun, Shangjin; Rice, David; Hoch, Jeffrey C.; Rovnyak, David

    2014-01-01

    Recently, we have demonstrated that considerable inherent sensitivity gains are attained in MAS NMR spectra acquired by nonuniform sampling (NUS) and introduced maximum entropy interpolation (MINT) processing that assures the linearity of transformation between the time and frequency domains. In this report, we examine the utility of the NUS/MINT approach in multidimensional datasets possessing high dynamic range, such as homonuclear 13C–13C correlation spectra. We demonstrate on model compounds and on 1–73-(U-13C, 15N)/74–108-(U-15N) E. coli thioredoxin reassembly, that with appropriately constructed 50 % NUS schedules inherent sensitivity gains of 1.7–2.1-fold are readily reached in such datasets. We show that both linearity and line width are retained under these experimental conditions throughout the entire dynamic range of the signals. Furthermore, we demonstrate that the reproducibility of the peak intensities is excellent in the NUS/MINT approach when experiments are repeated multiple times and identical experimental and processing conditions are employed. Finally, we discuss the principles for design and implementation of random exponentially biased NUS sampling schedules for homonuclear 13C–13C MAS correlation experiments that yield high-quality artifact-free datasets. PMID:24752819

  15. Proton NMR Spectra: Deceptively Simple and Deceptively Complex Examples.

    ERIC Educational Resources Information Center

    Gurst, J. E.; And Others

    1985-01-01

    Describes relatively simple nuclear magnetic resonance (NMR) experiments that demonstrate unexpected results of the deceptively simple and deceptively complex types. Background information, experimental procedures, and typical results obtained are included. (JN)

  16. Paramagnetic 13C and 15N NMR analyses of the push and pull effects in cytochrome c peroxidase and Coprinus cinereus peroxidase variants: functional roles of highly conserved amino acids around heme.

    PubMed

    Nonaka, Daisuke; Wariishi, Hiroyuki; Welinder, Karen G; Fujii, Hiroshi

    2010-01-12

    Paramagnetic (13)C and (15)N nuclear magnetic resonance (NMR) spectroscopy of heme-bound cyanide ((13)C(15)N) was applied to 11 cytochrome c peroxidase (CcP) and Coprinus cinereus peroxidase (CIP) mutants to investigate contributions to the push and pull effects of conserved amino acids around heme. The (13)C and (15)N NMR data for the distal His and Arg mutants indicated that distal His is the key amino acid residue creating the strong pull effect and that distal Arg assists. The mutation of distal Trp of CcP to Phe, the amino acid at this position in CIP, changed the push and pull effects so they resembled those of CIP, whereas the mutation of distal Phe of CIP to Trp changed this mutant to become CcP-like. The (13)C NMR shifts for the proximal Asp mutants clearly showed that the proximal Asp-His hydrogen bonding strengthens the push effect. However, even in the absence of a hydrogen bond, the push effect of proximal His in peroxidase is significantly stronger than in globins. Comparison of these NMR data with the compound I formation rate constants and crystal structures of these mutants showed that (1) the base catalysis of the distal His is more critical for rapid compound I formation than its acid catalysis, (2) the primary function of the distal Arg is to maintain the distal heme pocket in favor of rapid compound I formation via hydrogen bonding, and (3) the push effect is the major contributor to the differential rates of compound I formation in wild-type peroxidases.

  17. Proton-detected 3D (15)N/(1)H/(1)H isotropic/anisotropic/isotropic chemical shift correlation solid-state NMR at 70kHz MAS.

    PubMed

    Pandey, Manoj Kumar; Yarava, Jayasubba Reddy; Zhang, Rongchun; Ramamoorthy, Ayyalusamy; Nishiyama, Yusuke

    2016-01-01

    Chemical shift anisotropy (CSA) tensors offer a wealth of information for structural and dynamics studies of a variety of chemical and biological systems. In particular, CSA of amide protons can provide piercing insights into hydrogen-bonding interactions that vary with the backbone conformation of a protein and dynamics. However, the narrow span of amide proton resonances makes it very difficult to measure (1)H CSAs of proteins even by using the recently proposed 2D (1)H/(1)H anisotropic/isotropic chemical shift (CSA/CS) correlation technique. Such difficulties due to overlapping proton resonances can in general be overcome by utilizing the broad span of isotropic chemical shifts of low-gamma nuclei like (15)N. In this context, we demonstrate a proton-detected 3D (15)N/(1)H/(1)H CS/CSA/CS correlation experiment at fast MAS frequency (70kHz) to measure (1)H CSA values of unresolved amide protons of N-acetyl-(15)N-l-valyl-(15)N-l-leucine (NAVL).

  18. Quantification of in vivo ³¹P NMR brain spectra using LCModel.

    PubMed

    Deelchand, Dinesh Kumar; Nguyen, Tra-My; Zhu, Xiao-Hong; Mochel, Fanny; Henry, Pierre-Gilles

    2015-06-01

    Quantification of (31)P NMR spectra is commonly performed using line-fitting techniques with prior knowledge. Currently available time- and frequency-domain analysis software includes AMARES (in jMRUI) and CFIT respectively. Another popular frequency-domain approach is LCModel, which has been successfully used to fit both (1)H and (13)C in vivo NMR spectra. To the best of our knowledge LCModel has not been used to fit (31)P spectra. This study demonstrates the feasibility of using LCModel to quantify in vivo (31)P MR spectra, provided that adequate prior knowledge and LCModel control parameters are used. Both single-voxel and MRSI data are presented, and similar results are obtained with LCModel and with AMARES. This provides a new method for automated, operator-independent analysis of (31)P NMR spectra. PMID:25871439

  19. 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

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

    NASA Astrophysics Data System (ADS)

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

    2014-04-01

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

  1. Beckmann rearrangement of 15N-cyclohexanone oxime on zeolites silicalite-1, H-ZSM-5, and H-[B]ZSM-5 studied by solid-state NMR spectroscopy.

    PubMed

    Marthala, V R Reddy; Jiang, Yijiao; Huang, Jun; Wang, Wei; Gläser, Roger; Hunger, Michael

    2006-11-22

    By means of solid-state 15N NMR spectroscopy, evidence for the formation of nitrilium ions as intermediates of the Beckmann rearrangement of 15N-cyclohexanone oxime to epsilon-caprolactam on silicalite-1, H-ZSM-5, and H-[B]ZSM-5 is reported. The zeolites under study are characterized by different acid strengths (silicalite-1 < H-[B]ZSM-5 < H-ZSM-5). Depending on the nature of catalytically active surface OH groups, reactant and product molecules exist in the nonprotonated or protonated state. In addition, formation of byproducts such as 5-cyano-1-pentene and epsilon-aminocapric acid as a result of dehydration and hydrolysis of the reactant and product molecules, respectively, were observed.

  2. Vibrational spectra, NMR and theoretical studies of the enantiomers and rotamers of alpha-cypermethrin.

    PubMed

    Jubert, Alicia H; Alegre, María L; Diez, Reinaldo Pis; Pomilio, Alicia B; Szewczuk, Víctor D

    2007-04-01

    NMR, infrared and Raman vibrational spectra of alpha-cypermethrin have been measured at room temperature. Infrared spectra were also recorded to low temperature. The spectra were analyzed by means of ab initio calculations. The conformational space of both enantiomers and some rotamers A, B and C of alpha-cypermethrin has been scanned using molecular dynamics and complemented with functional density calculations that optimize the geometry of the lowest-energy conformers of each species as obtained in the simulations. The vibrational frequencies and the 1H and 13C NMR chemical shifts were assigned using functional density calculations. The molecular electrostatic potential maps were obtained and analyzed.

  3. Vibrational spectra, NMR and theoretical studies of the enantiomers and rotamers of alpha-cypermethrin

    NASA Astrophysics Data System (ADS)

    Jubert, Alicia H.; Alegre, María L.; Diez, Reinaldo Pis; Pomilio, Alicia B.; Szewczuk, Víctor D.

    2007-04-01

    NMR, infrared and Raman vibrational spectra of alpha-cypermethrin have been measured at room temperature. Infrared spectra were also recorded to low temperature. The spectra were analyzed by means of ab initio calculations. The conformational space of both enantiomers and some rotamers A, B and C of alpha-cypermethrin has been scanned using molecular dynamics and complemented with functional density calculations that optimize the geometry of the lowest-energy conformers of each species as obtained in the simulations. The vibrational frequencies and the 1H and 13C NMR chemical shifts were assigned using functional density calculations. The molecular electrostatic potential maps were obtained and analyzed.

  4. Median Modified Wiener Filter for nonlinear adaptive spatial denoising of protein NMR multidimensional spectra

    PubMed Central

    Cannistraci, Carlo Vittorio; Abbas, Ahmed; Gao, Xin

    2015-01-01

    Denoising multidimensional NMR-spectra is a fundamental step in NMR protein structure determination. The state-of-the-art method uses wavelet-denoising, which may suffer when applied to non-stationary signals affected by Gaussian-white-noise mixed with strong impulsive artifacts, like those in multi-dimensional NMR-spectra. Regrettably, Wavelet's performance depends on a combinatorial search of wavelet shapes and parameters; and multi-dimensional extension of wavelet-denoising is highly non-trivial, which hampers its application to multidimensional NMR-spectra. Here, we endorse a diverse philosophy of denoising NMR-spectra: less is more! We consider spatial filters that have only one parameter to tune: the window-size. We propose, for the first time, the 3D extension of the median-modified-Wiener-filter (MMWF), an adaptive variant of the median-filter, and also its novel variation named MMWF*. We test the proposed filters and the Wiener-filter, an adaptive variant of the mean-filter, on a benchmark set that contains 16 two-dimensional and three-dimensional NMR-spectra extracted from eight proteins. Our results demonstrate that the adaptive spatial filters significantly outperform their non-adaptive versions. The performance of the new MMWF* on 2D/3D-spectra is even better than wavelet-denoising. Noticeably, MMWF* produces stable high performance almost invariant for diverse window-size settings: this signifies a consistent advantage in the implementation of automatic pipelines for protein NMR-spectra analysis. PMID:25619991

  5. NMR study of non-structural proteins--part I: (1)H, (13)C, (15)N backbone and side-chain resonance assignment of macro domain from Mayaro virus (MAYV).

    PubMed

    Melekis, Efstathios; Tsika, Aikaterini C; Lichière, Julie; Chasapis, Christos T; Margiolaki, Irene; Papageorgiou, Nicolas; Coutard, Bruno; Bentrop, Detlef; Spyroulias, Georgios A

    2015-04-01

    Macro domains are ADP-ribose-binding modules present in all eukaryotic organisms, bacteria and archaea. They are also found in non-structural proteins of several positive strand RNA viruses such as alphaviruses. Here, we report the high yield expression and preliminary structural analysis through solution NMR spectroscopy of the macro domain from New World Mayaro Alphavirus. The recombinant protein was well-folded and in a monomeric state. An almost complete sequence-specific assignment of its (1)H, (15)N and (13)C resonances was obtained and its secondary structure determined by TALOS+.

  6. Computer aided evaluation of two-dimensional NMR spectra of proteins.

    PubMed

    Neidig, K P; Bodenmueller, H; Kalbitzer, H R

    1984-12-28

    A computer program for the automatic evaluation of two-dimensional NMR spectra of peptides and proteins has been developed. The used strategy is described, the advantages and limits of this approach are discussed. The program was successfully tested on a COSY-spectrum of the neuropeptide Glp-Pro-Pro-Gly-Gly-Ser-Lys-Val-Ile-Leu-Phe from hydra, resulting in a drastic reduction of the time needed for the evaluation of two-dimensional NMR data.

  7. 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.

  8. 17O NMR and Raman spectra of water with different calcium salts

    NASA Astrophysics Data System (ADS)

    Yan, Ying; Ou, Xiao-xia; Zhang, Hui-ping

    2014-09-01

    17O NMR and Raman spectra of water with different calcium salts have been measured. Different water samples were prepared by adding nano-materials, calcium gluconate, calcium citrate and calcium chloride into distilled water. Both 17O NMR and Raman spectra of different water samples were recorded. The effects of temperature and time on 17O NMR line-width of different water samples were analyzed as well. The experimental results showed that Raman spectra of water with these four calcium salts were almost the same as those for distilled water when the temperature increased to 40 °C. The 17O NMR line-width of distilled water decreased from 76.8 Hz to 46.9 Hz and 65.8 Hz after nano-materials and calcium chloride were added, respectively. Besides, the 17O NMR line-width of distilled water increased from 76.8 Hz to 131.6 Hz after calcium citrate was added, while the 17O NMR line-width of distilled water increased from 76.8 Hz to 77.2 Hz after calcium gluconate was added. The 17O NMR line-width of water with calcium chloride increased while the other three water samples were nearly stable as the temperature increased from 30 °C to 85 °C. The 17O NMR line-width of water with nano-materials kept steady while the 17O NMR line-width of the other three water samples all increased in 42 days.

  9. RUBIDIUM, a program for computer-aided assignment of two-dimensional NMR spectra of polypeptides.

    PubMed

    Yu, C; Hwang, J F; Chen, T B; Soo, V W

    1992-01-01

    Taking advantage of the rule-based expert system technology, a program named RUBIDIUM (Rule-Based Identification In 2D NMR Spectrum) was developed to accomplish the automatic 1H NMR resonance assignments of polypeptides. Besides noise elimination and peak selection capabilities, RUBIDIUM detects the cross-peak patterns of amino acid residues in the COSY spectrum, assigning these patterns to amino acid types, performing sequential assignments using combined COSY/NOESY spectra, and finally, achieving the total assignment of the 1H NMR spectrum.

  10. An efficient spectra processing method for metabolite identification from 1H-NMR metabolomics data.

    PubMed

    Jacob, Daniel; Deborde, Catherine; Moing, Annick

    2013-06-01

    The spectra processing step is crucial in metabolomics approaches, especially for proton NMR metabolomics profiling. During this step, noise reduction, baseline correction, peak alignment and reduction of the 1D (1)H-NMR spectral data are required in order to allow biological information to be highlighted through further statistical analyses. Above all, data reduction (binning or bucketing) strongly impacts subsequent statistical data analysis and potential biomarker discovery. Here, we propose an efficient spectra processing method which also provides helpful support for compound identification using a new data reduction algorithm that produces relevant variables, called buckets. These buckets are the result of the extraction of all relevant peaks contained in the complex mixture spectra, rid of any non-significant signal. Taking advantage of the concentration variability of each compound in a series of samples and based on significant correlations that link these buckets together into clusters, the method further proposes automatic assignment of metabolites by matching these clusters with the spectra of reference compounds from the Human Metabolome Database or a home-made database. This new method is applied to a set of simulated (1)H-NMR spectra to determine the effect of some processing parameters and, as a proof of concept, to a tomato (1)H-NMR dataset to test its ability to recover the fruit extract compositions. The implementation code for both clustering and matching steps is available upon request to the corresponding author. PMID:23525538

  11. Bayesian deconvolution and quantification of metabolites in complex 1D NMR spectra using BATMAN.

    PubMed

    Hao, Jie; Liebeke, Manuel; Astle, William; De Iorio, Maria; Bundy, Jacob G; Ebbels, Timothy M D

    2014-01-01

    Data processing for 1D NMR spectra is a key bottleneck for metabolomic and other complex-mixture studies, particularly where quantitative data on individual metabolites are required. We present a protocol for automated metabolite deconvolution and quantification from complex NMR spectra by using the Bayesian automated metabolite analyzer for NMR (BATMAN) R package. BATMAN models resonances on the basis of a user-controllable set of templates, each of which specifies the chemical shifts, J-couplings and relative peak intensities for a single metabolite. Peaks are allowed to shift position slightly between spectra, and peak widths are allowed to vary by user-specified amounts. NMR signals not captured by the templates are modeled non-parametrically by using wavelets. The protocol covers setting up user template libraries, optimizing algorithmic input parameters, improving prior information on peak positions, quality control and evaluation of outputs. The outputs include relative concentration estimates for named metabolites together with associated Bayesian uncertainty estimates, as well as the fit of the remainder of the spectrum using wavelets. Graphical diagnostics allow the user to examine the quality of the fit for multiple spectra simultaneously. This approach offers a workflow to analyze large numbers of spectra and is expected to be useful in a wide range of metabolomics studies.

  12. 13C-NMR spectra and contact time experiment for Skjervatjern fulvic and humic acids

    USGS Publications Warehouse

    Malcolm, R.L.

    1992-01-01

    The T(CP) and T(1p) time constants for Skjervatjern fulvic and humic acids were determined to be short with T(CP) values ranging from 0.14 ms to 0.53 ms and T(1p) values ranging from 3.3 ms to 5.9 ms. T(CP) or T(1p) time constants at a contact time of 1 ms are favorable for quantification of 13C-NMR spectra. Because of the short T(CP) values, correction factors for signal intensity for various regions of the 13C-NMR spectra would be necessary at contact times greater than 1.1 ms or less than 0.9 ms. T(CP) and T(1p) values have a limited non-homogeneity within Skjervatjern fulvic and humic acids. A pulse delay or repeat time of 700 ms is more than adequate for quantification of these 13C-NMR spectra. Paramagnetic effects in these humic substances are precluded due to low inorganic ash contents, low contents of Fe, Mn, and Co, and low organic free-radical contents. The observed T(CP) values suggest that all the carbon types in Skjervatjern fulvic and humic acids are fully cross-polarized before significant proton relaxation occurs. The 13C-NMR spectra for Skjervatjern fulvic acid is similar to most aquatic fulvic acids as it is predominantly aliphatic, low in aromaticity (fa1 = 24), low in phenolic content, high in carboxyl content, and has no resolution of a methoxyl peak. The 13C-NMR spectra for Skjervatjern humic acid is also similar to most other aquatic humic acids in that it is also predominantly aliphatic, high in aromaticity (fa1 = 38), moderate in phenolic content, moderate in carboxyl content, and has a clear resolution of a methoxyl carbon region. After the consideration of the necessary 13C-NMR experimental conditions, these spectra are considered to be quantitative. With careful consideration of the previously determined 13C-NMR experimental conditions, quantitative spectra can be obtained for humic substances in the future from the HUMEX site. Possible changes in humic substances due to acidification should be determined from 13C-NMR data.

  13. In Vivo potassium-39 NMR spectra by the burg maximum-entropy method

    NASA Astrophysics Data System (ADS)

    Uchiyama, Takanori; Minamitani, Haruyuki

    The Burg maximum-entropy method was applied to estimate 39K NMR spectra of mung bean root tips. The maximum-entropy spectra have as good a linearity between peak areas and potassium concentrations as those obtained by fast Fourier transform and give a better estimation of intracellular potassium concentrations. Therefore potassium uptake and loss processes of mung bean root tips are shown to be more clearly traced by the maximum-entropy method.

  14. Bulk magnetization and 1H NMR spectra of magnetically heterogeneous model systems

    SciTech Connect

    Levin, E M; Bud' ko, S L

    2011-04-28

    Bulk magnetization and ¹H static and magic angle spinning (MAS) nuclear magnetic resonance (NMR) spectra of two magnetically heterogeneous model systems based on laponite (LAP) layered silicate or polystyrene (PS) with low and high proton concentration, respectively, and ferrimagnetic Fe₂O₃ nano- or micro-particles have been studied. In LAP+Fe₂O₃, a major contribution to the NMR signal broadening is due to the dipolar coupling between the magnetic moments of protons and magnetic particles. In PS+Fe₂O₃, due to the higher proton concentration in polystyrene and stronger proton–proton dipolar coupling, an additional broadening is observed, i.e. ¹H MAS NMR spectra of magnetically heterogeneous systems are sensitive to both proton–magnetic particles and proton–proton dipolar couplings. An increase of the volume magnetization by ~1 emu/cm³ affects the ¹H NMR signal width in a way that is similar to an increase of the proton concentration by ~2×10²²/cm³. ¹H MAS NMR spectra, along with bulk magnetization measurements, allow the accurate determination of the hydrogen concentration in magnetically heterogeneous systems.

  15. Molecular Structures from [superscript 1]H NMR Spectra: Education Aided by Internet Programs

    ERIC Educational Resources Information Center

    Debska, Barbara; Guzowska-Swider, Barbara

    2007-01-01

    The article presents the way in which freeware Internet programs can be applied to teach [superscript 1]H NMR spectroscopy. The computer programs described in this article are part of the educational curriculum that explores spectroscopy and spectra interpretation. (Contains 6 figures.)

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

    PubMed

    Bermel, Wolfgang; Bruix, Marta; Felli, Isabella C; Kumar M V, Vasantha; Pierattelli, Roberta; Serrano, Soraya

    2013-03-01

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

  17. Differential Analysis of 2D NMR Spectra: New Natural Products from a Pilot-Scale Fungal Extract Library

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Using a newly developed protocol for the differential analysis of arrays of 2D NMR spectra, we were able to rapidly identify two previously unreported indole alkaloids from a library of unfractionated fungal extracts. Differential analyses of NMR spectra thus constitute an effective tool for the non...

  18. NMR study of non-structural proteins--part II: (1)H, (13)C, (15)N backbone and side-chain resonance assignment of macro domain from Venezuelan equine encephalitis virus (VEEV).

    PubMed

    Makrynitsa, Garyfallia I; Ntonti, Dioni; Marousis, Konstantinos D; Tsika, Aikaterini C; Lichière, Julie; Papageorgiou, Nicolas; Coutard, Bruno; Bentrop, Detlef; Spyroulias, Georgios A

    2015-10-01

    Macro domains consist of 130-190 amino acid residues and appear to be highly conserved in all kingdoms of life. Intense research on this field has shown that macro domains bind ADP-ribose and other similar molecules, but their exact function still remains intangible. Macro domains are highly conserved in the Alphavirus genus and the Venezuelan equine encephalitis virus (VEEV) is a member of this genus that causes fatal encephalitis to equines and humans. In this study we report the high yield recombinant expression and preliminary solution NMR study of the macro domain of VEEV. An almost complete sequence-specific assignment of its (1)H, (15)N and (13)C resonances was obtained and its secondary structure predicted by TALOS+. The protein shows a unique mixed α/β-fold.

  19. HyperBIRD: a sensitivity-enhanced approach to collecting homonuclear-decoupled proton NMR spectra.

    PubMed

    Donovan, Kevin J; Frydman, Lucio

    2015-01-01

    Samples prepared following dissolution dynamic nuclear polarization (DNP) enable the detection of NMR spectra from low-γ nuclei with outstanding sensitivity, yet have limited use for the enhancement of abundant species like (1)H nuclei. Small- and intermediate-sized molecules, however, show strong heteronuclear cross-relaxation effects: spontaneous processes with an inherent isotopic selectivity, whereby only the (13)C-bonded protons receive a polarization enhancement. These effects are here combined with a recently developed method that delivers homonuclear-decoupled (1)H spectra in natural abundance samples based on heteronuclear couplings to these same, (13)C-bonded nuclei. This results in the HyperBIRD methodology; a single-shot combination of these two effects that can simultaneously simplify and resolve complex, congested (1)H NMR spectra with many overlapping spin multiplets, while achieving 50-100 times sensitivity enhancements over conventional thermal counterparts. PMID:25256418

  20. (15)N NMR Spectroscopy, X-ray and Neutron Diffraction, Quantum-Chemical Calculations, and UV/vis-Spectrophotometric Titrations as Complementary Techniques for the Analysis of Pyridine-Supported Bicyclic Guanidine Superbases.

    PubMed

    Schwamm, Ryan J; Vianello, Robert; Maršavelski, Aleksandra; García, M Ángeles; Claramunt, Rosa M; Alkorta, Ibon; Saame, Jaan; Leito, Ivo; Fitchett, Christopher M; Edwards, Alison J; Coles, Martyn P

    2016-09-01

    Pyridine substituted with one and two bicyclic guanidine groups has been studied as a potential source of superbases. 2-{hpp}C5H4N (I) and 2,6-{hpp}2C5H3N (II) (hppH = 1,3,4,6,7,8-hexahydro-2H-pyrimido[1,2-a]pyrimidine) were protonated using [HNEt3][BPh4] to afford [I-H][BPh4] (1a), [II-H][BPh4] (2), and [II-H2][BPh4]2 (3). Solution-state (1)H and (15)N NMR spectroscopy shows a symmetrical cation in 2, indicating a facile proton-exchange process in solution. Solid-state (15)N NMR data differentiates between the two groups, indicating a mixed guanidine/guanidinium. X-ray diffraction data are consistent with protonation at the imine nitrogen, confirmed for 1a by single-crystal neutron diffraction. The crystal structure of 1a shows association of two [I-H](+) cations within a cage of [BPh4](-) anions. Computational analysis performed in the gas phase and in MeCN solution shows that the free energy barrier to transfer a proton between imino centers in [II-H](+) is 1 order of magnitude lower in MeCN than in the gas phase. The results provide evidence that linking hpp groups with the pyridyl group stabilizes the protonation center, thereby increasing the intrinsic basicity in the gas phase, while the bulk prevents efficient cation solvation, resulting in diminished pKa(MeCN) values. Spectrophotometrically measured pKa values are in excellent agreement with calculated values and confirm that I and II are superbases in solution.

  1. (15)N NMR Spectroscopy, X-ray and Neutron Diffraction, Quantum-Chemical Calculations, and UV/vis-Spectrophotometric Titrations as Complementary Techniques for the Analysis of Pyridine-Supported Bicyclic Guanidine Superbases.

    PubMed

    Schwamm, Ryan J; Vianello, Robert; Maršavelski, Aleksandra; García, M Ángeles; Claramunt, Rosa M; Alkorta, Ibon; Saame, Jaan; Leito, Ivo; Fitchett, Christopher M; Edwards, Alison J; Coles, Martyn P

    2016-09-01

    Pyridine substituted with one and two bicyclic guanidine groups has been studied as a potential source of superbases. 2-{hpp}C5H4N (I) and 2,6-{hpp}2C5H3N (II) (hppH = 1,3,4,6,7,8-hexahydro-2H-pyrimido[1,2-a]pyrimidine) were protonated using [HNEt3][BPh4] to afford [I-H][BPh4] (1a), [II-H][BPh4] (2), and [II-H2][BPh4]2 (3). Solution-state (1)H and (15)N NMR spectroscopy shows a symmetrical cation in 2, indicating a facile proton-exchange process in solution. Solid-state (15)N NMR data differentiates between the two groups, indicating a mixed guanidine/guanidinium. X-ray diffraction data are consistent with protonation at the imine nitrogen, confirmed for 1a by single-crystal neutron diffraction. The crystal structure of 1a shows association of two [I-H](+) cations within a cage of [BPh4](-) anions. Computational analysis performed in the gas phase and in MeCN solution shows that the free energy barrier to transfer a proton between imino centers in [II-H](+) is 1 order of magnitude lower in MeCN than in the gas phase. The results provide evidence that linking hpp groups with the pyridyl group stabilizes the protonation center, thereby increasing the intrinsic basicity in the gas phase, while the bulk prevents efficient cation solvation, resulting in diminished pKa(MeCN) values. Spectrophotometrically measured pKa values are in excellent agreement with calculated values and confirm that I and II are superbases in solution. PMID:27494395

  2. Solid-state NMR spectra of lipid-anchored proteins under magic angle spinning.

    PubMed

    Nomura, Kaoru; Harada, Erisa; Sugase, Kenji; Shimamoto, Keiko

    2014-03-01

    Solid-state NMR is a promising tool for elucidating membrane-related biological phenomena. We achieved the measurement of high-resolution solid-state NMR spectra for a lipid-anchored protein embedded in lipid bilayers under magic angle spinning (MAS). To date, solid-state NMR measurements of lipid-anchored proteins have not been accomplished due to the difficulty in supplying sufficient amount of stable isotope labeled samples in the overexpression of lipid-anchored proteins requiring complex posttranslational modification. We designed a pseudo lipid-anchored protein in which the protein component was expressed in E. coli and attached to a chemically synthesized lipid-anchor mimic. Using two types of membranes, liposomes and bicelles, we demonstrated different types of insertion procedures for lipid-anchored protein into membranes. In the liposome sample, we were able to observe the cross-polarization and the (13)C-(13)C chemical shift correlation spectra under MAS, indicating that the liposome sample can be used to analyze molecular interactions using dipolar-based NMR experiments. In contrast, the bicelle sample showed sufficient quality of spectra through scalar-based experiments. The relaxation times and protein-membrane interaction were capable of being analyzed in the bicelle sample. These results demonstrated the applicability of two types of sample system to elucidate the roles of lipid-anchors in regulating diverse biological phenomena.

  3. 29Si and 27Al MAS NMR spectra of mullites from different kaolinites.

    PubMed

    He, Hongping; Guo, Jiugao; Zhu, Jianxi; Yuan, Peng; Hu, Cheng

    2004-04-01

    Mullites synthesized from four kaolinites with different random defect densities have been studied by 27Al and 29Si magic angle spinning nuclear magnetic resonance spectroscopy (MAS NMR) and X-ray diffraction (XRD). All these mullites show the same XRD pattern. However, 29Si and 27Al MAS NMR spectra reveal that the mullites derived from kaolinites with high defect densities, have a sillimanite-type Al/Si ordering scheme and are low in silica, whereas those mullites derived from kaolinites with low defect densities, consist of both sillimanite- and mullite-type Al/Si ordering schemes and are rich in silica. PMID:15084323

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

    NASA Astrophysics Data System (ADS)

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

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

  5. Rapid assignment of solution 31P NMR spectra of large proteins by solid-state spectroscopy.

    PubMed

    Iuga, Adriana; Spoerner, Michael; Ader, Christian; Brunner, Eike; Kalbitzer, Hans Robert

    2006-07-21

    The application of the (31)P NMR spectroscopy to large proteins or protein complexes in solution is hampered by a relatively low intrinsic sensitivity coupled with large line widths. Therefore, the assignment of the phosphorus signals by two-dimensional NMR methods in solution is often extremely time consuming. In contrast, the quality of solid-state NMR spectra is not dependent on the molecular mass and the solubility of the protein. For the complex of Ras with the GTP-analogue GppCH(2)p we show solid-state (31)P NMR methods to be more sensitive by almost one order of magnitude than liquid-state NMR. Thus, solid-state NMR seems to be the method of choice for obtaining the resonance assignment of the phosphorus signals of protein complexes in solution. Experiments on Ras.GDP complexes show that the microcrystalline sample can be substituted by a precipitate of the sample and that unexpectedly the two structural states observed earlier in solution are present in crystals as well.

  6. N,N-Di- n-octyl- N,N-dimethyl and N,N-di- n-nonyl- N,N-dimethyl ammonium cholates: 13C and 15N CPMAS NMR, powder X-ray diffraction and thermoanalytical characterization

    NASA Astrophysics Data System (ADS)

    Kolehmainen, Erkki; Lahtinen, Manu; Valkonen, Arto; Behera, Babita; Kauppinen, Reijo

    2009-07-01

    N,N-Di- n-octyl- N,N-dimethyl cholate ( 1) and N,N-di- n-nonyl- N,N-dimethyl ammonium cholate ( 2) have been prepared by crystallization from equimolar mixtures of sodium cholate and quaternary N,N-di- n-alkyl- N,N-dimethyl ( n-octyl or n-nonyl) ammonium bromides. The formed crystalline materials have been structurally characterized by 13C and 15N cross polarization magic angle spinning (CPMAS) NMR, powder X-ray diffraction (PXRD) and thermoanalytical (TGA/DTA and DSC) methods and compared with each other. Powder X-ray diffraction patterns of 1 and 2 reveal clear similarities. Combined with the thermoanalytical data of these structures an existence of two hydrated polymorphs (most probably mono- and dihydrates) can be proposed. This presumption is further supported by 13C CPMAS NMR showing clearly double resonances for the carboxylic and majority of other carbons in these quaternary ammonium cholates. Owing to the endogenous character of cholate anion these ionic structures possess great potential in many pharmaceutical applications such as controlled drug delivery.

  7. Disentangling Complex Mixtures of Compounds with Near-Identical (1) H and (13) C NMR Spectra using Pure Shift NMR Spectroscopy.

    PubMed

    Castañar, Laura; Roldán, Raquel; Clapés, Pere; Virgili, Albert; Parella, Teodor

    2015-05-18

    The thorough analysis of highly complex NMR spectra using pure shift NMR experiments is described. The enhanced spectral resolution obtained from modern 2D HOBS experiments incorporating spectral aliasing in the (13) C indirect dimension enables the distinction of similar compounds exhibiting near-identical (1) H and (13) C NMR spectra. It is shown that a complete set of extremely small Δδ((1) H) and Δδ((13) C) values, even below the natural line width (1 and 5 ppb, respectively), can be simultaneously determined and assigned.

  8. Measurement of longitudinal relaxation times in crowded 1H NMR spectra using one- and two-dimensional maximum quantum (MAXY) NMR spectroscopy

    NASA Astrophysics Data System (ADS)

    Liu, Maili; Ye, Chaohui; Farrant, R. Duncan; Nicholson, Jeremy K.; Lindon, John C.

    Methods for measuring longitudinal relaxation times of protons in heavily overlapped 1H NMR spectra are introduced and exemplified using a solution of cholesteryl acetate. The methods are based on 1-dimensional and 2-dimensional maximum quantum NMR spectroscopy (MAXY), which makes possible the selective detection of CH, CH2 and CH31H NMR resonances. A modification of the BIRD pulse sequence to achieve selective inversion of protons bonded to either 12C or 13C is given. The approach should find application in studies of molecular dynamics where isotopic enrichment is not possible and the level of available sample dictates the use of 1H NMR spectroscopy.

  9. TCA Cycle Turnover And Serum Glucose Sources By Automated Bayesian Analysis Of NMR Spectra

    SciTech Connect

    Merritt, Matthew E.; Burgess, Shawn; Jeffrey, F. Mark; Sherry, A. Dean; Malloy, Craig; Bretthorst, G. Larry

    2004-04-21

    Changes in sources of serum glucose are indicative of a variety of pathological metabolic states. It is possible to measure the sources of serum glucose by the administration of deuterated water to a subject followed by analysis of the 2H enrichment levels in glucose extracted from plasma from a single blood draw by 2H NMR. Markov Chain Monte Carlo simulations of the posterior probability densities may then be used to evaluate the contribution of glycogenolysis, glycerol, and the Kreb's cycle to serum glucose. Experiments with simulated NMR spectra show that in spectra with a S/N of 20 to 1, the resulting metabolic information may be evaluated with an accuracy of about 4 percent.

  10. TCA Cycle Turnover And Serum Glucose Sources By Automated Bayesian Analysis Of NMR Spectra

    NASA Astrophysics Data System (ADS)

    Merritt, Matthew E.; Burgess, Shawn; Jeffrey, F. Mark; Sherry, A. Dean; Malloy, Craig; Bretthorst, G. Larry

    2004-04-01

    Changes in sources of serum glucose are indicative of a variety of pathological metabolic states. It is possible to measure the sources of serum glucose by the administration of deuterated water to a subject followed by analysis of the 2H enrichment levels in glucose extracted from plasma from a single blood draw by 2H NMR. Markov Chain Monte Carlo simulations of the posterior probability densities may then be used to evaluate the contribution of glycogenolysis, glycerol, and the Kreb's cycle to serum glucose. Experiments with simulated NMR spectra show that in spectra with a S/N of 20 to 1, the resulting metabolic information may be evaluated with an accuracy of about 4 percent.

  11. Interpreting C-13 NMR spectra of technical lignins based on ionization chemical shifts

    SciTech Connect

    Akim, L.G.; Fedulina, T.G.; Shevchenko, S.M.

    1996-10-01

    Newly developed technique of C-13 NMR spectroscopy of ionized lignins in aqueous alkali has been applied to analysis of the chemical structure of technical lignins. Ionization of phenolic and carboxylic hydroxyl groups has a strong effect on the electronic structure of lignin and leads to significant changes in C-13 NMR spectra of the polymer. Comparative analysis of the spectra of organosolv and alkali lignins in neutral organic and aqueous alkaline media based on the data obtained for lignin model compounds demonstrated the usefulness and scope of applicability of the method. This method was especially useful when applied to a highly degraded alkaline lignin, enhancing our ability to analyze the poorly resolved spectrum. A technique is developed that permits the user to analyze a lignin spectrum in an aqueous alkaline solution without the accompanying spectrum in an organic solution. The research described was made possible by Grant No. NWFOOO from the International Science Foundation.

  12. Sensitivity enhancement of MQMAS NMR spectra of spin 3/2 nuclei using hyperbolic secant pulses

    NASA Astrophysics Data System (ADS)

    Siegel, Renée; Nakashima, Thomas T.; Wasylishen, Roderick E.

    2005-02-01

    The use of hyperbolic secant (HS) pulses to enhance the intensity of the central transition in MQMAS experiments for spin 3/2 quadrupolar nuclei is investigated by examining 87Rb NMR spectra of a powder sample of RbNO 3. The application of HS pulses prior to the triple-quantum (3Q) excitation provides sensitivity enhancements in MQMAS spectra that are superior to those previously reported. For the conversion of 3Q to single-quantum (1Q) observables, the HS pulses have an efficiency similar to that reported for double frequency sweeps (DFS) but greater than that of the fast amplitude modulation (FAM) technique.

  13. Deuteron and triton magnetic moments from NMR spectra of the hydrogen molecule

    NASA Astrophysics Data System (ADS)

    Puchalski, Mariusz; Komasa, Jacek; Pachucki, Krzysztof

    2015-08-01

    We present a theory and calculations of the nuclear magnetic shielding with finite nuclear mass effects and determine the magnetic moments of deuteron and triton using the known NMR spectra of HD and HT molecules. The results μd=0.857 438 234 6 (53 ) μN and μt=2.978 962 471 (10 ) μN are more accurate and in good agreement with the currently accepted values.

  14. NMR studies of active-site properties of human carbonic anhydrase II by using (15) N-labeled 4-methylimidazole as a local probe and histidine hydrogen-bond correlations.

    PubMed

    Shenderovich, Ilya G; Lesnichin, Stepan B; Tu, Chingkuang; Silverman, David N; Tolstoy, Peter M; Denisov, Gleb S; Limbach, Hans-Heinrich

    2015-02-01

    By using a combination of liquid and solid-state NMR spectroscopy, (15) N-labeled 4-methylimidazole (4-MI) as a local probe of the environment has been studied: 1) in the polar, wet Freon CDF3 /CDF2 Cl down to 130 K, 2) in water at pH 12, and 3) in solid samples of the mutant H64A of human carbonic anhydrase II (HCA II). In the latter, the active-site His64 residue is replaced by alanine; the catalytic activity is, however, rescued by the presence of 4-MI. For the Freon solution, it is demonstrated that addition of water molecules not only catalyzes proton tautomerism but also lifts its quasidegeneracy. The possible hydrogen-bond clusters formed and the mechanism of the tautomerism are discussed. Information about the imidazole hydrogen-bond geometries is obtained by establishing a correlation between published (1) H and (15) N chemical shifts of the imidazole rings of histidines in proteins. This correlation is useful to distinguish histidines embedded in the interior of proteins and those at the surface, embedded in water. Moreover, evidence is obtained that the hydrogen-bond geometries of His64 in the active site of HCA II and of 4-MI in H64A HCA II are similar. Finally, the degeneracy of the rapid tautomerism of the neutral imidazole ring His64 reported by Shimahara et al. (J. Biol. Chem.- 2007, 282, 9646) can be explained with a wet, polar, nonaqueous active-site conformation in the inward conformation, similar to the properties of 4-MI in the Freon solution. The biological implications for the enzyme mechanism are discussed. PMID:25521423

  15. NMR studies of active-site properties of human carbonic anhydrase II by using (15) N-labeled 4-methylimidazole as a local probe and histidine hydrogen-bond correlations.

    PubMed

    Shenderovich, Ilya G; Lesnichin, Stepan B; Tu, Chingkuang; Silverman, David N; Tolstoy, Peter M; Denisov, Gleb S; Limbach, Hans-Heinrich

    2015-02-01

    By using a combination of liquid and solid-state NMR spectroscopy, (15) N-labeled 4-methylimidazole (4-MI) as a local probe of the environment has been studied: 1) in the polar, wet Freon CDF3 /CDF2 Cl down to 130 K, 2) in water at pH 12, and 3) in solid samples of the mutant H64A of human carbonic anhydrase II (HCA II). In the latter, the active-site His64 residue is replaced by alanine; the catalytic activity is, however, rescued by the presence of 4-MI. For the Freon solution, it is demonstrated that addition of water molecules not only catalyzes proton tautomerism but also lifts its quasidegeneracy. The possible hydrogen-bond clusters formed and the mechanism of the tautomerism are discussed. Information about the imidazole hydrogen-bond geometries is obtained by establishing a correlation between published (1) H and (15) N chemical shifts of the imidazole rings of histidines in proteins. This correlation is useful to distinguish histidines embedded in the interior of proteins and those at the surface, embedded in water. Moreover, evidence is obtained that the hydrogen-bond geometries of His64 in the active site of HCA II and of 4-MI in H64A HCA II are similar. Finally, the degeneracy of the rapid tautomerism of the neutral imidazole ring His64 reported by Shimahara et al. (J. Biol. Chem.- 2007, 282, 9646) can be explained with a wet, polar, nonaqueous active-site conformation in the inward conformation, similar to the properties of 4-MI in the Freon solution. The biological implications for the enzyme mechanism are discussed.

  16. Post-translational heterocyclic backbone modifications in the 43-peptide antibiotic microcin B17. Structure elucidation and NMR study of a 13C,15N-labelled gyrase inhibitor.

    PubMed

    Bayer, A; Freund, S; Jung, G

    1995-12-01

    Microcin B17 (McB17), the first known gyrase inhibitor of peptidic nature, is produced by ribosomal synthesis and post-translational modification of the 69-residue precursor protein by an Escherichia coli strain. To elucidate the chemical structure of the mature 43-residue peptide antibiotic, fermentation and purification protocols were established and optimized which allowed the isolation and purification of substantial amounts of highly pure McB17 (non-labelled, 15N-labelled and 13C/15N-labelled peptide. By ultraviolet-absorption spectroscopy. HPLC-electrospray mass spectrometry and GC-mass spectrometry, amino acid analysis, protein sequencing, and, in particular, multidimensional NMR, we could demonstrate and unequivocally prove that the enzymic modification of the precursor backbone at Gly-Cys and Gly-Ser segments leads to the formation of 2-aminomethylthiazole-4-carboxylic acid and 2-aminomethyloxazole-4-carboxylic acid, respectively. In addition, two bicyclic modifications 2-(2-aminomethyloxazolyl)thiazole-4-carboxylic acid and 2-(2-aminomethylthiazolyl)oxazole-4-carboxylic acid were found that consist of directly linked thiazole and oxazole rings derived from one Gly-Ser-Cys and one Gly-Cys-Ser segment. Analogous to the thiazole and oxazole rings found in antitumor peptides of microbial and marine origin, these heteroaromatic ring systems of McB17 presumably play an important role in its gyrase-inhibiting activity, e.g. interacting with the DNA to trap the covalent protein-DNA intermediate of the breakage-reunion reaction of the gyrase.

  17. Fast acquisition of multidimensional NMR spectra of solids and mesophases using alternative sampling methods.

    PubMed

    Lesot, Philippe; Kazimierczuk, Krzysztof; Trébosc, Julien; Amoureux, Jean-Paul; Lafon, Olivier

    2015-11-01

    Unique information about the atom-level structure and dynamics of solids and mesophases can be obtained by the use of multidimensional nuclear magnetic resonance (NMR) experiments. Nevertheless, the acquisition of these experiments often requires long acquisition times. We review here alternative sampling methods, which have been proposed to circumvent this issue in the case of solids and mesophases. Compared to the spectra of solutions, those of solids and mesophases present some specificities because they usually display lower signal-to-noise ratios, non-Lorentzian line shapes, lower spectral resolutions and wider spectral widths. We highlight herein the advantages and limitations of these alternative sampling methods. A first route to accelerate the acquisition time of multidimensional NMR spectra consists in the use of sparse sampling schemes, such as truncated, radial or random sampling ones. These sparsely sampled datasets are generally processed by reconstruction methods differing from the Discrete Fourier Transform (DFT). A host of non-DFT methods have been applied for solids and mesophases, including the G-matrix Fourier transform, the linear least-square procedures, the covariance transform, the maximum entropy and the compressed sensing. A second class of alternative sampling consists in departing from the Jeener paradigm for multidimensional NMR experiments. These non-Jeener methods include Hadamard spectroscopy as well as spatial or orientational encoding of the evolution frequencies. The increasing number of high field NMR magnets and the development of techniques to enhance NMR sensitivity will contribute to widen the use of these alternative sampling methods for the study of solids and mesophases in the coming years.

  18. Distinguishing Vaccinium species by chemical fingerprinting based on NMR spectra, validated with spectra collected in different laboratories.

    PubMed

    Markus, Michelle A; Ferrier, Jonathan; Luchsinger, Sarah M; Yuk, Jimmy; Cuerrier, Alain; Balick, Michael J; Hicks, Joshua M; Killday, K Brian; Kirby, Christopher W; Berrue, Fabrice; Kerr, Russell G; Knagge, Kevin; Gödecke, Tanja; Ramirez, Benjamin E; Lankin, David C; Pauli, Guido F; Burton, Ian; Karakach, Tobias K; Arnason, John T; Colson, Kimberly L

    2014-06-01

    A method was developed to distinguish Vaccinium species based on leaf extracts using nuclear magnetic resonance spectroscopy. Reference spectra were measured on leaf extracts from several species, including lowbush blueberry (Vaccinium angustifolium), oval leaf huckleberry (Vaccinium ovalifolium), and cranberry (Vaccinium macrocarpon). Using principal component analysis, these leaf extracts were resolved in the scores plot. Analysis of variance statistical tests demonstrated that the three groups differ significantly on PC2, establishing that the three species can be distinguished by nuclear magnetic resonance. Soft independent modeling of class analogies models for each species also showed discrimination between species. To demonstrate the robustness of nuclear magnetic resonance spectroscopy for botanical identification, spectra of a sample of lowbush blueberry leaf extract were measured at five different sites, with different field strengths (600 versus 700 MHz), different probe types (cryogenic versus room temperature probes), different sample diameters (1.7 mm versus 5 mm), and different consoles (Avance I versus Avance III). Each laboratory independently demonstrated the linearity of their NMR measurements by acquiring a standard curve for chlorogenic acid (R(2) = 0.9782 to 0.9998). Spectra acquired on different spectrometers at different sites classifed into the expected group for the Vaccinium spp., confirming the utility of the method to distinguish Vaccinium species and demonstrating nuclear magnetic resonance fingerprinting for material validation of a natural health product. PMID:24963620

  19. Distinguishing Vaccinium species by chemical fingerprinting based on NMR spectra, validated with spectra collected in different laboratories.

    PubMed

    Markus, Michelle A; Ferrier, Jonathan; Luchsinger, Sarah M; Yuk, Jimmy; Cuerrier, Alain; Balick, Michael J; Hicks, Joshua M; Killday, K Brian; Kirby, Christopher W; Berrue, Fabrice; Kerr, Russell G; Knagge, Kevin; Gödecke, Tanja; Ramirez, Benjamin E; Lankin, David C; Pauli, Guido F; Burton, Ian; Karakach, Tobias K; Arnason, John T; Colson, Kimberly L

    2014-06-01

    A method was developed to distinguish Vaccinium species based on leaf extracts using nuclear magnetic resonance spectroscopy. Reference spectra were measured on leaf extracts from several species, including lowbush blueberry (Vaccinium angustifolium), oval leaf huckleberry (Vaccinium ovalifolium), and cranberry (Vaccinium macrocarpon). Using principal component analysis, these leaf extracts were resolved in the scores plot. Analysis of variance statistical tests demonstrated that the three groups differ significantly on PC2, establishing that the three species can be distinguished by nuclear magnetic resonance. Soft independent modeling of class analogies models for each species also showed discrimination between species. To demonstrate the robustness of nuclear magnetic resonance spectroscopy for botanical identification, spectra of a sample of lowbush blueberry leaf extract were measured at five different sites, with different field strengths (600 versus 700 MHz), different probe types (cryogenic versus room temperature probes), different sample diameters (1.7 mm versus 5 mm), and different consoles (Avance I versus Avance III). Each laboratory independently demonstrated the linearity of their NMR measurements by acquiring a standard curve for chlorogenic acid (R(2) = 0.9782 to 0.9998). Spectra acquired on different spectrometers at different sites classifed into the expected group for the Vaccinium spp., confirming the utility of the method to distinguish Vaccinium species and demonstrating nuclear magnetic resonance fingerprinting for material validation of a natural health product.

  20. Distinguishing Vaccinium Species by Chemical Fingerprinting Based on NMR Spectra, Validated with Spectra Collected in Different Laboratories

    PubMed Central

    Markus, Michelle A.; Ferrier, Jonathan; Luchsinger, Sarah M.; Yuk, Jimmy; Cuerrier, Alain; Balick, Michael J.; Hicks, Joshua M.; Killday, K. Brian; Kirby, Christopher W.; Berrue, Fabrice; Kerr, Russell G.; Knagge, Kevin; Gödecke, Tanja; Ramirez, Benjamin E.; Lankin, David C.; Pauli, Guido F.; Burton, Ian; Karakach, Tobias K.; Arnason, John T.; Colson, Kimberly L.

    2014-01-01

    A method was developed to distinguish Vaccinium species based on leaf extracts using nuclear magnetic resonance spectroscopy. Reference spectra were measured on leaf extracts from several species, including lowbush blueberry (Vaccinium angustifolium), oval leaf huckleberry (Vaccinium ovalifolium), and cranberry (Vaccinium macrocarpon). Using principal component analysis, these leaf extracts were resolved in the scores plot. Analysis of variance statistical tests demonstrated that the three groups differ significantly on PC2, establishing that the three species can be distinguished by nuclear magnetic resonance. Soft independent modeling of class analogies models for each species also showed discrimination between species. To demonstrate the robustness of nuclear magnetic resonance spectroscopy for botanical identification, spectra of a sample of lowbush blueberry leaf extract were measured at five different sites, with different field strengths (600 versus 700 MHz), different probe types (cryogenic versus room temperature probes), different sample diameters (1.7 mm versus 5 mm), and different consoles (Avance I versus Avance III). Each laboratory independently demonstrated the linearity of their NMR measurements by acquiring a standard curve for chlorogenic acid (R2 = 0.9782 to 0.9998). Spectra acquired on different spectrometers at different sites classifed into the expected group for the Vaccinium spp., confirming the utility of the method to distinguish Vaccinium species and demonstrating nuclear magnetic resonance fingerprinting for material validation of a natural health product. PMID:24963620

  1. Frequency-Selective Heteronuclear Dephasing and Selective Carbonyl Labeling to Deconvolute Crowded Spectra of Membrane Proteins By Magic Angle Spinning NMR

    PubMed Central

    Traaseth, Nathaniel J.; Veglia, Gianluigi

    2011-01-01

    We present a new method that combines carbonyl-selective labeling with frequency-selective heteronuclear recoupling to resolve the spectral overlap of magic angle spinning (MAS) NMR spectra of membrane proteins in fluid lipid membranes with broad lines and high redundancy in the primary sequence. We implemented this approach in both heteronuclear 15N-13Cα and homonuclear 13C-13C dipolar assisted rotational resonance (DARR) correlation experiments. We demonstrate its efficacy for the membrane protein phospholamban reconstituted in fluid PC/PE/PA lipid bilayers. The main advantage of this method is to discriminate overlapped 13Cα resonances by strategically labeling the preceding residue. This method is highly complementary to 13C′i-1-15Ni-13Cαi and 13Cαi-1-15Ni-1-13C′i experiments to discriminate inter-residue spin systems at a minimal cost to signal-to-noise. PMID:21482162

  2. Exploring the use of Generalized Indirect Covariance to reconstruct pure shift NMR spectra: Current Pros and Cons.

    PubMed

    Fredi, André; Nolis, Pau; Cobas, Carlos; Martin, Gary E; Parella, Teodor

    2016-05-01

    The current Pros and Cons of a processing protocol to generate pure chemical shift NMR spectra using Generalized Indirect Covariance are presented and discussed. The transformation of any standard 2D homonuclear and heteronuclear spectrum to its pure shift counterpart by using a reference DIAG spectrum is described. Reconstructed pure shift NMR spectra of NOESY, HSQC, HSQC-TOCSY and HSQMBC experiments are reported for the target molecule strychnine.

  3. Investigation of structure, vibrational and NMR spectra of oxycodone and naltrexone: A combined experimental and theoretical study

    NASA Astrophysics Data System (ADS)

    Tavakol, Hossein; Esfandyari, Maryam; Taheri, Salman; Heydari, Akbar

    2011-08-01

    In this work, two important opioid antagonists, naltrexone and oxycodone, were prepared from thebaine and were characterized by IR, 1H NMR and 13C NMR spectroscopy. Moreover, computational NMR and IR parameters were obtained using density functional theory (DFT) at B3LYP/6-311++G** level of theory. Complete NMR and vibrational assignment were carried out using the observed and calculated spectra. The IR frequencies and NMR chemical shifts, determined experimentally, were compared with those obtained theoretically from DFT calculations, showed good agreements. The RMS errors observed between experimental and calculated data for the IR absorptions are 85 and 105 cm -1, for the 1H NMR peaks are 0.87 and 0.17 ppm and for those of 13C NMR are 5.6 and 5.3 ppm, respectively for naltrexone and oxycodone.

  4. (129) Xe and (131) Xe nuclear magnetic dipole moments from gas phase NMR spectra.

    PubMed

    Makulski, Włodzimierz

    2015-04-01

    (3) He, (129) Xe and (131) Xe NMR measurements of resonance frequencies in the magnetic field B0=11.7586 T in different gas phase mixtures have been reported. Precise radiofrequency values were extrapolated to the zero gas pressure limit. These results combined with new quantum chemical values of helium and xenon nuclear magnetic shielding constants were used to determine new accurate nuclear magnetic moments of (129) Xe and (131) Xe in terms of that of the (3) He nucleus. They are as follows: μ((129) Xe) = -0.7779607(158)μN and μ((131) Xe) = +0.6918451(70)μN . By this means, the new 'helium method' for estimations of nuclear dipole moments was successfully tested. Gas phase NMR spectra demonstrate the weak intermolecular interactions observed on the (3) He and (129) Xe and (131) Xe shielding in the gaseous mixtures with Xe, CO2 and SF6 .

  5. Predicting the spin state of paramagnetic iron complexes by DFT calculation of proton NMR spectra.

    PubMed

    Borgogno, Andrea; Rastrelli, Federico; Bagno, Alessandro

    2014-07-01

    Many transition-metal complexes easily change their spin state S in response to external perturbations (spin crossover). Determining such states and their dynamics can play a central role in the understanding of useful properties such as molecular magnetism or catalytic behavior, but is often far from straightforward. In this work we demonstrate that, at a moderate computational cost, density functional calculations can predict the correct ground spin state of Fe(ii) and Fe(iii) complexes and can then be used to determine the (1)H NMR spectra of all spin states. Since the spectral features are remarkably different according to the spin state, calculated (1)H NMR resonances can be used to infer the correct spin state, along with supporting the structure elucidation of numerous paramagnetic complexes.

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

    PubMed

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

    2016-08-01

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

  7. Disentangling crystallographic inequivalence and crystallographic forms of L-arginine by one- and two-dimensional solid-state NMR spectroscopy.

    PubMed

    Herbert-Pucheta, Jose-Enrique; Colaux, Henri; Bodenhausen, Geoffrey; Tekely, Piotr

    2011-12-29

    Overlapping (13)C or (15)N solid-state NMR spectra from crystallographically different forms of L-arginine hydrochloride can be separated by exploiting differential proton T(1) relaxation in conjunction with cross-polarization. Dipolar (13)C-(13)C and (15)N-(15)N two-dimensional correlation experiments reveal resonances belonging to crystallographically and magnetically inequivalent molecules.

  8. Gas phase NMR spectra of N,N-dimethylnitrosamine. Environmental effects on kinetic parameters

    NASA Astrophysics Data System (ADS)

    Chauvel, J. Paul; Leung, Doris Y.; True, Nancy S.

    1984-04-01

    Gas phase 1H NMR spectra of N,N-dimethylnitrosamine are consistent with first order chemical exchange rate constants which are ca. 25 times faster than those observed in neat liquids at corresponding temperatures. The associated kinetic parameters: Eact(∞), 20.5(1.1) kcal mol -1, Δ H‡, 19.7(1.0) kcal mol -1 and Δ G‡, 21.1(0.4) kcal mol -1 are approximately 2.5 kcal mol -1 lower than the most recently reported values for the neat liquid. The observed phase dependence is consistent with a process proceeding via a freely rotating transition state.

  9. Determination of orientational order parameters from 2H NMR spectra of magnetically partially oriented lipid bilayers.

    PubMed Central

    Schäfer, H; Mädler, B; Sternin, E

    1998-01-01

    The partial orientation of multilamellar vesicles (MLVs) in high magnetic fields is known to affect the shape of 2H NMR spectra. There are numerical methods for extracting either the orientational order parameters of lipid molecules for a random distribution of domain orientations in the sample, or the distribution of orientations for a known set of spectral anisotropies. A first attempt at determining the orientational order parameters in the presence of an unknown nonrandom distribution of orientations is presented. The numerical method is based on the Tikhonov regularization algorithm. It is tested using simulated partially oriented spectra. An experimental spectrum of a phospholipid-ether mixture in water is analyzed as an example. The experimental spectrum is consistent with an ellipsoidal shape of MLVs with a ratio of semiaxes of approximately 3.4. PMID:9533713

  10. Spectral investigations of 2,5-difluoroaniline by using mass, electronic absorption, NMR, and vibrational spectra

    NASA Astrophysics Data System (ADS)

    Kose, Etem; Karabacak, Mehmet; Bardak, Fehmi; Atac, Ahmet

    2016-11-01

    One of the most significant aromatic amines is aniline, a primary aromatic amine replacing one hydrogen atom of a benzene molecule with an amino group (NH2). This study reports experimental and theoretical investigation of 2,5-difluoroaniline molecule (2,5-DFA) by using mass, ultraviolet-visible (UV-vis), 1H and 13C nuclear magnetic resonance (NMR), Fourier transform infrared and Raman (FT-IR and FT-Raman) spectra, and supported with theoretical calculations. Mass spectrum (MS) of 2,5-DFA is presented with their stabilities. The UV-vis spectra of the molecule are recorded in the range of 190-400 nm in water and ethanol solvents. The 1H and 13C NMR chemical shifts are recorded in CDCl3 solution. The vibrational spectra are recorded in the region 4000-400 cm-1 (FT-IR) and 4000-10 cm-1 (FT-Raman), respectively. Theoretical studies are underpinned the experimental results as described below; 2,5-DFA molecule is optimized by using B3LYP/6-311++G(d,p) basis set. The mass spectrum is evaluated and possible fragmentations are proposed based on the stable structure. The electronic properties, such as excitation energies, oscillator strengths, wavelengths, frontier molecular orbitals (FMO), HOMO and LUMO energies, are determined by time-dependent density functional theory (TD-DFT). The electrostatic potential surface (ESPs), density of state (DOS) diagrams are also prepared and evaluated. In addition to these, reduced density gradient (RDG) analysis is performed, and thermodynamic features are carried out theoretically. The NMR spectra (1H and 13C) are calculated by using the gauge-invariant atomic orbital (GIAO) method. The vibrational spectra of 2,5-DFA molecule are obtained by using DFT/B3LYP method with 6-311++G(d,p) basis set. Fundamental vibrations are assigned based on the potential energy distribution (PED) of the vibrational modes. The nonlinear optical properties (NLO) are also investigated. The theoretical and experimental results give a detailed description of

  11. Structures of Si-Carbohydrate Aqueous Complexes: Comparison of NMR Spectra and Molecular Orbital Results

    NASA Astrophysics Data System (ADS)

    Kubicki, J. D.; Heaney, P. J.

    2002-12-01

    Researchers recently have made the discovery that hypercoordinate Si-sorbitol complexes will readily form in biologically relevant fluids, and they have reported the first evidence for a transient organosilicon complex generated within the life cycle of an organism. These interpretations are based upon peak assignments of Si-29 NMR spectra that invoke Si-polyol complexes with Si in five- and six-fold coordination states. However, ab initio analyses of the proposed organosilicon structures do not reproduce the experimentally observed chemical shifts. We have successfully modeled one of the observed Si-29 chemical shifts with a 5-fold Si-disorbitol complex involving 5-membered ring configurations (i.e., Si-O-C-C-O), which yielded Si-29 chemical shifts that closely matched the observed values in the -100 to -102 ppm range. Likewise, Si-29 NMR peaks near -144 ppm were well fit by a model in which a 6-fold Si was complexed to three sorbitol molecules in a 5-membered ring configuration. The ability to simulate observed NMR signals using molecular orbital calculations provides strong support for the controversial role of hypercoordinate organosilicon species in the uptake and transport of silica by biological systems. The existence of such complexes in turn may explain other puzzles in Si biogeochemistry, such as the persistence of monomeric silica in concentrated biological fluids and the biofractionation of Si isotopes and Ge.

  12. Quantification of Human Brain Metabolites from in Vivo1H NMR Magnitude Spectra Using Automated Artificial Neural Network Analysis

    NASA Astrophysics Data System (ADS)

    Hiltunen, Yrjö; Kaartinen, Jouni; Pulkkinen, Juhani; Häkkinen, Anna-Maija; Lundbom, Nina; Kauppinen, Risto A.

    2002-01-01

    Long echo time (TE=270 ms) in vivo proton NMR spectra resembling human brain metabolite patterns were simulated for lineshape fitting (LF) and quantitative artificial neural network (ANN) analyses. A set of experimental in vivo1H NMR spectra were first analyzed by the LF method to match the signal-to-noise ratios and linewidths of simulated spectra to those in the experimental data. The performance of constructed ANNs was compared for the peak area determinations of choline-containing compounds (Cho), total creatine (Cr), and N-acetyl aspartate (NAA) signals using both manually phase-corrected and magnitude spectra as inputs. The peak area data from ANN and LF analyses for simulated spectra yielded high correlation coefficients demonstrating that the peak areas quantified with ANN gave similar results as LF analysis. Thus, a fully automated ANN method based on magnitude spectra has demonstrated potential for quantification of in vivo metabolites from long echo time spectroscopic imaging.

  13. 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

  14. Quantum Mechanical Calculations to Interpret Vibrational and NMR Spectra of Organic Compounds Adsorbed onto Mineral Surfaces

    NASA Astrophysics Data System (ADS)

    Kubicki, J. D.

    2008-12-01

    Vibrational (e.g., ATR FTIR and Raman) and nuclear magnetic resonance (NMR) spectroscopies provide excellent information on the bonding and atomic environment of adsorbed organic compounds. However, interpretation of observed spectra collected for organic compounds adsorbed onto mineral surfaces can be complicated by the lack of comparable analogs of known structure and uncertainties about the mineral surface structure. Quantum mechanical calculations provide a method for testing interpretations of observed spectra because models can be built to mimic predicted structures, and the results are independent of experimental parameters (i.e., no fitting to data is necessary). In this talk, methodologies for modeling vibrational frequencies and NMR chemical shifts of adsorbed organic compounds are discussed. Examples included salicylic acid (as an analog for important binding functional groups in humic acids) adsorbed onto aluminum oxides, organic phosphoryl compounds that represent herbicides and bacterial extracellular polymeric substances (EPS), and ofloxacin (a common agricultural antibiotic). The combination of the ability of quantum mechanical calculations to predict structures, spectroscopic parameters and energetics of adsorption with experimental data on these same properties allows for more definitive construction of surface complex models.

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

    NASA Astrophysics Data System (ADS)

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

    2011-04-01

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

  16. Cu-NMR spectra in UCu4Ni uncover site disorder

    NASA Astrophysics Data System (ADS)

    Bernal, O. O.; Rose, D. A.; Wu, Hsin-Ju; Chiang, M.; MacLaughlin, D. E.; Stewart, G. R.; Kim, J. S.

    2012-12-01

    Cu-NMR measurements in a random powder of UCu4Ni reveal two types of spectral lines for each of the two isotopes of naturally abundant Cu in the material. These lines, which we label L1 and L2, point to the existence of two inequivalent Cu sites in the sample. We present a study of the NMR line shape in UCu4Ni at three different frequencies (in the range from 40-70 MHz) and two temperature values (10 K and 150 K), that allow us to assign the lines to particular Cu sites. L1 is strongly broadened as the frequency decreases, but changes less with increasing temperature. In contrast, the width of L2 grows in proportion to frequency and decreases noticeably with increasing temperature. This behavior indicates that the crystallographic site corresponding to L1 is exposed to electric field gradients and has lower point symmetry than the site corresponding to L2, which displays some anisotropy but no discernible quadrupole effects. By comparison with the Cu-NMR spectra in UCu4Pd, where only one type of Cu-NMR line has been observed clearly, we can associate L1 with Cu(16e) nuclei: Cu nuclei sitting at the 16e site (Wyckoff notation) in the AuBe5 structure of the parent compound UCu5. This leaves L2 as originating from Cu(4c) nuclei; i.e., those sitting at the 4c site of the same structure. Unlike in UCu4Pd, the appearance of signal from Cu(4c) nuclei in the Ni compound is clear evidence of site disorder in UCu4Ni.

  17. Automated data evaluation and modelling of simultaneous (19) F-(1) H medium-resolution NMR spectra for online reaction monitoring.

    PubMed

    Zientek, Nicolai; Laurain, Clément; Meyer, Klas; Paul, Andrea; Engel, Dirk; Guthausen, Gisela; Kraume, Matthias; Maiwald, Michael

    2016-06-01

    Medium-resolution nuclear magnetic resonance spectroscopy (MR-NMR) currently develops to an important analytical tool for both quality control and process monitoring. In contrast to high-resolution online NMR (HR-NMR), MR-NMR can be operated under rough environmental conditions. A continuous re-circulating stream of reaction mixture from the reaction vessel to the NMR spectrometer enables a non-invasive, volume integrating online analysis of reactants and products. Here, we investigate the esterification of 2,2,2-trifluoroethanol with acetic acid to 2,2,2-trifluoroethyl acetate both by (1) H HR-NMR (500 MHz) and (1) H and (19) F MR-NMR (43 MHz) as a model system. The parallel online measurement is realised by splitting the flow, which allows the adjustment of quantitative and independent flow rates, both in the HR-NMR probe as well as in the MR-NMR probe, in addition to a fast bypass line back to the reactor. One of the fundamental acceptance criteria for online MR-MNR spectroscopy is a robust data treatment and evaluation strategy with the potential for automation. The MR-NMR spectra are treated by an automated baseline and phase correction using the minimum entropy method. The evaluation strategies comprise (i) direct integration, (ii) automated line fitting, (iii) indirect hard modelling (IHM) and (iv) partial least squares regression (PLS-R). To assess the potential of these evaluation strategies for MR-NMR, prediction results are compared with the line fitting data derived from the quantitative HR-NMR spectroscopy. Although, superior results are obtained from both IHM and PLS-R for (1) H MR-NMR, especially the latter demands for elaborate data pretreatment, whereas IHM models needed no previous alignment. Copyright © 2015 John Wiley & Sons, Ltd.

  18. 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

  19. Spatially encoded pulse sequences for the acquisition of high resolution NMR spectra in inhomogeneous fields

    NASA Astrophysics Data System (ADS)

    Shapira, Boaz; Frydman, Lucio

    2006-09-01

    We have recently proposed a protocol for retrieving nuclear magnetic resonance (NMR) spectra based on a spatially-dependent encoding of the MR interactions. It has also been shown that the spatial selectivity with which spins are manipulated during such encoding opens up new avenues towards the removal of magnetic field inhomogeneities; not by demanding extreme Bo field uniformities, but rather by compensating for the dephasing effects introduced by the field distribution at a radiofrequency excitation and/or refocusing level. The present study discusses in further detail a number of strategies deriving from this principle, geared at acquiring both uni- as well as multi-dimensional spectroscopic data at high resolution conditions. Different variants are presented, tailored according to the relative sensitivity and chemical nature of the spin system being explored. In particular a simple multi-scan experiment is discussed capable of affording substantial improvements in the spectral resolution, at nearly no sensitivity or scaling penalties. This new compensation scheme is therefore well-suited for the collection of high-resolution data in low-field systems possessing limited signal-to-noise ratios, where magnetic field heterogeneities might present a serious obstacle. Potential areas of applications of these techniques include high-field in vivo NMR studies in regions near tissue/air interfaces, clinical low field MR spectroscopy on relatively large off-center volumes difficult to shim, and ex situ NMR. The principles of the different compensation methods are reviewed and experimentally demonstrated for one-dimensional inhomogeneities; further improvements and extensions are briefly discussed.

  20. Characterization of Paramagnetic Reactive Intermediates: Predicting the NMR Spectra of Iron(IV)-Oxo Complexes by DFT.

    PubMed

    Borgogno, Andrea; Rastrelli, Federico; Bagno, Alessandro

    2015-09-01

    The relative energies of spin states of several iron(IV)-oxo complexes and related species have been calculated with DFT methods by employing the B3LYP* functional. We show that such calculations can predict the correct ground spin state of Fe(IV) complexes and can then be used to determine the (1) H NMR spectra of all spin states; the spectral features are remarkably different, hence calculated paramagnetic (1) H NMR spectra can be used to support the structure elucidation of numerous paramagnetic complexes. Applications to a number of stable and reactive iron(IV)-oxo species are described.

  1. Investigation of broad resonances in 31P NMR spectra of the human brain in vivo.

    PubMed

    McNamara, R; Arias-Mendoza, F; Brown, T R

    1994-08-01

    Broad resonances that lie underneath the familiar small molecule profile of in vivo 31P NMR spectra can make accurate spectral integration of these mobile phosphates difficult. The two major broad components are the phosphate contained in the hydroxyapatite in cranial bone and the phosphodiester moiety in partially mobile membrane phospholipids. They can be removed with post-acquisition processing but this results in distortion of lineshapes and intensities and interferes with accurate quantitation. We have employed an off-resonance saturation procedure to eliminate the bone resonance and isolate the signal from the membrane phospholipids by subtraction. Selective saturation of the phospholipid resonance increases the clarity of the sharp peaks downfield from the phosphocreatine peak. Selective saturation 3-D chemical shift imaging techniques were used to create a localized phospholipid profile of the entire brain simultaneously. Monitoring localized phospholipid concentration may be important in studying demyelinating diseases. PMID:7848814

  2. An analytical derivation of a popular approximation of the Voigt function for quantification of NMR spectra.

    PubMed

    Bruce, S D; Higinbotham, J; Marshall, I; Beswick, P H

    2000-01-01

    The approximation of the Voigt line shape by the linear summation of Lorentzian and Gaussian line shapes of equal width is well documented and has proved to be a useful function for modeling in vivo (1)H NMR spectra. We show that the error in determining peak areas is less than 0.72% over a range of simulated Voigt line shapes. Previous work has concentrated on empirical analysis of the Voigt function, yielding accurate expressions for recovering the intrinsic Lorentzian component of simulated line shapes. In this work, an analytical approach to the approximation is presented which is valid for the range of Voigt line shapes in which either the Lorentzian or Gaussian component is dominant. With an empirical analysis of the approximation, the direct recovery of T(2) values from simulated line shapes is also discussed. PMID:10617435

  3. Fractional volume integration in two-dimensional NMR spectra: CAKE, a Monte Carlo approach.

    PubMed

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

    2008-06-01

    Quantitative information from multi-dimensional NMR experiments can be obtained by peak volume integration. The standard procedure (selection of a region around the chosen peak and addition of all values) is often biased by poor peak definition because of peak overlap. Here we describe a simple method, called CAKE, for volume integration of (partially) overlapping peaks. Assuming the axial symmetry of two-dimensional NMR peaks, as it occurs in NOESY and TOCSY when Lorentz-Gauss transformation of the signals is carried out, CAKE estimates the peak volume by multiplying a volume fraction by a factor R. It represents a proportionality ratio between the total and the fractional volume, which is identified as a slice in an exposed region of the overlapping peaks. The volume fraction is obtained via Monte Carlo Hit-or-Miss technique, which proved to be the most efficient because of the small region and the limited number of points within the selected area. Tests on simulated and experimental peaks, with different degrees of overlap and signal-to-noise ratios, show that CAKE results in improved volume estimates. A main advantage of CAKE is that the volume fraction can be flexibly chosen so as to minimize the effect of overlap, frequently observed in two-dimensional spectra. PMID:18396078

  4. Fractional volume integration in two-dimensional NMR spectra: CAKE, a Monte Carlo approach

    NASA Astrophysics Data System (ADS)

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

    2008-06-01

    Quantitative information from multi-dimensional NMR experiments can be obtained by peak volume integration. The standard procedure (selection of a region around the chosen peak and addition of all values) is often biased by poor peak definition because of peak overlap. Here we describe a simple method, called CAKE, for volume integration of (partially) overlapping peaks. Assuming the axial symmetry of two-dimensional NMR peaks, as it occurs in NOESY and TOCSY when Lorentz-Gauss transformation of the signals is carried out, CAKE estimates the peak volume by multiplying a volume fraction by a factor R. It represents a proportionality ratio between the total and the fractional volume, which is identified as a slice in an exposed region of the overlapping peaks. The volume fraction is obtained via Monte Carlo Hit-or-Miss technique, which proved to be the most efficient because of the small region and the limited number of points within the selected area. Tests on simulated and experimental peaks, with different degrees of overlap and signal-to-noise ratios, show that CAKE results in improved volume estimates. A main advantage of CAKE is that the volume fraction can be flexibly chosen so as to minimize the effect of overlap, frequently observed in two-dimensional spectra.

  5. Fractional volume integration in two-dimensional NMR spectra: CAKE, a Monte Carlo approach

    NASA Astrophysics Data System (ADS)

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

    2009-03-01

    Quantitative information from multidimensional NMR experiments can be obtained by peak volume integration. The standard procedure (selection of a region around the chosen peak and addition of all values) is often biased by poor peak definition because of peak overlap. Here we describe a simple method, called CAKE, for volume integration of (partially) overlapping peaks. Assuming the axial symmetry of two-dimensional NMR peaks, as it occurs in NOESY and TOCSY when Lorentz-Gauss transformation of the signals is carried out, CAKE estimates the peak volume by multiplying a volume fraction by a factor R. It represents a proportionality ratio between the total and the fractional volume, which is identified as a slice in an exposed region of the overlapping peaks. The volume fraction is obtained via Monte Carlo Hit-or-Miss technique, which proved to be the most efficient because of the small region and the limited number of points within the selected area. Tests on simulated and experimental peaks, with different degrees of overlap and signal-to-noise ratios, show that CAKE results in improved volume estimates. A main advantage of CAKE is that the volume fraction can be flexibly chosen so as to minimize the effect of overlap, frequently observed in two-dimensional spectra.

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

    PubMed Central

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

    2013-01-01

    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. PMID:23851025

  7. Spatially localized sup 1 H NMR spectra of metabolites in the human brain

    SciTech Connect

    Hanstock, C.C. ); Rothman, D.L.; Jue, T.; Shulman, R.G. ); Prichard, J.W. )

    1988-03-01

    Using a surface coil, the authors have obtained {sup 1}H NMR spectra from metabolites in the human brain. Localization was achieved by combining depth pulses with image-selected in vivo spectroscopy magnetic field gradient methods. {sup 1}H spectra in which total creatine (3.03 ppm) has a signal/noise ratio of 95:1 were obtained in 4 min from 14 ml of brain. A resonance at 2.02 ppm consisting predominantly of N-acetylaspartate was measured relative to the creatine peak in gray and white matter, and the ratio was lower in the white matter. The spin-spin relaxation times of N-acetylaspartate and creatine were measured in white and gray matter and while creatine relaxation times were the same in both, the N-acetylaspartate relaxation time was longer in white matter. Lactate was detected in the normoxic brain and the average of three measurements was {approx}0.5 mM from comparison with the creatine plus phosphocreatine peak, which was assumed to be 10.5 mM.

  8. 1H NMR spectra of humic and fulvic acids and their peracetic oxidation products

    NASA Astrophysics Data System (ADS)

    Ruggiero, P.; Interesse, F. S.; Cassidei, L.; Sciacovelli, O.

    1980-04-01

    1H NMR spectra of humic (HA) and fulvic (FA) acids and their oxidative degradation products are reported. The HA shows the presence of -( CH2) n - CH3 ( n > 6) chemical fragments belonging to n-alkanes and/or n-fatty acids physically adsorbed onto the macromolecule structure. These fragments are absent in the FA fraction. Both humic fractions reveal the presence of similar amounts of aromatic protons which partly undergo exchange phenomena. The importance of this experimental observation is discussed. Oxidative degradation seems to cause partial cleavage of aromatic rings, more pronounced in the FA than in the HA. The degraded FA shows a higher total acidity and a higher phenolic OH content than the degraded HA. Both degraded fractions display some sharp singlet signals at 1.9 and 3.9 ppm arising from protons belonging to repetitive chemical fragments probably formed during the oxidation reaction. Tentative assignments of these signals are given. A general analysis of the HA and FA degraded spectra seems to indicate that the chemical fragments which undergo peracetic oxidation are substantially similar. The extent of oxidation of the two humic fractions is different. The HA degradation products reveal the presence of oligomeric structures, whereas the degraded FA appears less resistant to the oxidizing agent.

  9. Separation and complete analyses of the overlapped and unresolved 1H NMR spectra of enantiomers by spin selected correlation experiments.

    PubMed

    Prabhu, Uday Ramesh; Baishya, Bikash; Suryaprakash, N

    2008-06-26

    NMR spectroscopic discrimination of optical enantiomers is most often carried out using (2)H and (13)C spectra of chiral molecules aligned in a chiral liquid crystalline solvent. The use of proton NMR for such a purpose is severely hindered due to the spectral complexity and the significant loss of resolution arising from numerous short- and long-distance couplings and the indistinguishable overlap of spectra from both R and S enantiomers. The determination of all the spectral parameters by the analyses of such intricate NMR spectra poses challenges, such as, unraveling of the resonances for each enantiomer, spectral resolution, and simplification of the multiplet pattern. The present study exploits the spin state selection achieved by the two-dimensional (1)H NMR correlation of selectively excited isolated coupled spins (Soft-COSY) of the molecules to overcome these problems. The experiment provides the relative signs and magnitudes of all of the proton-proton couplings, which are otherwise not possible to determine from the broad and featureless one-dimensional (1)H spectra. The utilization of the method for quantification of enantiomeric excess has been demonstrated. The studies on different chiral molecules, each having a chiral center, whose spectral complexity increases with the increasing number of interacting spins, and the advantages and limitations of the method over SERF and DQ-SERF experiments have been reported in this work.

  10. Complete assignment of (1)H and (13)C NMR spectra of standard neo-iota-carrabiose oligosaccharides.

    PubMed

    Jouanneau, Diane; Boulenguer, Patrick; Mazoyer, Jacques; Helbert, William

    2010-02-26

    Standard Eucheuma denticulatum iota-carrageenan was degraded with the Alteromonas fortis iota-carrageenase. The most abundant products, the neo-iota-carratetraose and neo-iota-carrahexaose were purified by permeation gel chromatography, and their corresponding (1)H and (13)C NMR spectra were fully assigned. PMID:20038459

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

    PubMed

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

    2007-12-15

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

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

    PubMed

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

    2007-12-15

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

  13. 13C NMR spectra of 1,3-dipyridyl- and pyridylphenylthioureas. Chemical shift assignments and conformational implications

    NASA Astrophysics Data System (ADS)

    Sudha, L. V.; Sathyanarayana, D. N.; Manogaran, S.

    The 13C NMR spectra of a series of 1,3-dipyridyl- and pyridylphenylthioureas have been obtained. Complete analyses of the experimental spectra have provided the chemical shifts and coupling constants. The spectra of dipyridylthioureas over a temperature range showed important changes which could be attributed to an intramolecular conversion between the two equivalent E,Z and Z,E conformations. The coalescence temperature of the 13C signals leads to a Δ G* of ˜ 58.0 kJ mol -1 for the dynamic process involved. The results show that pyridylphenyl thioureas exist in a single conformation at ambient temperature.

  14. Vibrational and multinuclear NMR spectra of anionic mercuriomethanes [CH 4-n(HgX) n] n-

    NASA Astrophysics Data System (ADS)

    Breitinger, D. K.; Krumphanzl, U.; Moll, M.

    1990-03-01

    Vibrational spectra of solid sodium sulfitomercuriomethanates Na n[CH 4-n(HgSO 3) n]·nH 2O (2 ≤ and ≤ 4) exhibit high frequencies of the valence vibrations ν as(SO 3) > ν s(SO 3) (average 1057 cm -1) with big differences ν as - ν s (mean 104 cm -1), and ν(HgS) vibrations in the 200 to 230 cm -1 range, thus indicating S-coordinated sulfite ligands. Force field calculations for the ion [C(HgSO 3) 4] 4- yield high force constants K(S-O) = 605 N/m, K(Hg-S) = 258 N/m, and even K(C-Hg) = 181 N/m.- For thiosulfatomercuriomethanates [CH 4-n(HgS 2O 3] n- (1 ≤ n ≤ 4) in aqueous solutions Raman spectra suggest S-coordination with high ν as(SO 3) and ν s(SO 3) (average 1130 cm -1), and low ν(S-S) (˜420 cm -1) frequencies, and strong ν(Hg-S) bands (˜250 cm -1). From 1H, 13C and 199Hg NMR data is concluded that the CHg bond strengths in the series decrease on a lower level than in other mercuriomethanes.- On the whole, the electronic properties of the peripheral ligands X in the mercuriomethanes CH 4-n(HgX) n seem to be more important for the CHg bond strengths than the total charge.

  15. Studies of nitrogen metabolism using /sup 13/C NMR spectroscopy. 3. Synthesis of DL-(3-/sup 13/C,2-/sup 15/N)Lysine and its incorporation into streptothricin F/sup 1/

    SciTech Connect

    Gould, S.J.; Thiruvengadam, T.K.

    1981-11-04

    A scheme for the synthesis of DL-(3-/sup 13/C, 2-/sup 15/N)Lysine, I, is presented. Data are also reported to show that the mutase reaction occurring in the biosynthesis of I occurs with an intramolecular migration of nitrogen from C-2 to C-3. (BLM)

  16. Resolution Improvements in in Vivo1H NMR Spectra with Increased Magnetic Field Strength

    NASA Astrophysics Data System (ADS)

    Gruetter, Rolf; Weisdorf, Sally A.; Rajanayagan, Vasantham; Terpstra, Melissa; Merkle, Hellmut; Truwit, Charles L.; Garwood, Michael; Nyberg, Scott L.; Ugurbil, Kâmil

    1998-11-01

    The measurement of cerebral metabolites using highly homologous localization techniques and similar shimming methods was performed in the human brain at 1.5 and 4 T as well as in the dog and rat brain at 9.4 T. In rat brain, improved resolution was achieved by shimming all first- and second-order shim coils using a fully adiabatic FASTMAP sequence. The spectra showed a clear improvement in spectral resolution for all metabolite resonances with increased field strength. Changes in cerebral glutamine content were clearly observed at 4 T compared to 1.5 T in patients with hepatic encephalopathy. At 9.4 T, glutamine H4 at 2.46 ppm was fully resolved from glutamate H4 at 2.37 ppm, as was the potential resonance from γ-amino-butyric acid at 2.30 ppm and N-acetyl-aspartyl-glutamate at 2.05 ppm. Singlet linewidths were found to be as low as 6 Hz (0.015 ppm) at 9.4 T, indicating a substantial decrease in ppm linewidth with field strength. Furthermore, the methylene peak of creatine was partially resolved from phosphocreatine, indicating a close to 1:1 relationship in gray matter. We conclude that increasing the magnetic field strength increases spectral resolution also for1H NMR, which can lead to more than linear sensitivity gains.

  17. Atomic structure of icosahedral B4C boron carbide from a first principles analysis of NMR spectra.

    PubMed

    Mauri, F; Vast, N; Pickard, C J

    2001-08-20

    Density functional theory is demonstrated to reproduce the 13C and 11B NMR chemical shifts of icosahedral boron carbides with sufficient accuracy to extract previously unresolved structural information from experimental NMR spectra. B4C can be viewed as an arrangement of 3-atom linear chains and 12-atom icosahedra. According to our results, all the chains have a CBC structure. Most of the icosahedra have a B11C structure with the C atom placed in a polar site, and a few percent have a B (12) structure or a B10C2 structure with the two C atoms placed in two antipodal polar sites.

  18. Variations of pH as an additional tool in the analysis of crowded NMR spectra of fucosylated chondroitin sulfates.

    PubMed

    Ustyuzhanina, Nadezhda E; Dmitrenok, Andrey S; Bilan, Maria I; Shashkov, Alexander S; Gerbst, Alexey G; Usov, Anatolii I; Nifantiev, Nikolay E

    2016-03-24

    The influence of pH variation on chemical shift values in NMR spectra of fucosylated chondroitin sulfates was studied using polysaccharides isolated from three sea cucumber species Apostichopus japonicus, Actinopyga mauritiana and Cucumaria japonica. The signals of glucuronic acid residues were found to be the most sensitive to pH changes in comparison to the chemical shifts of the sulfated galactosamine and fucosyl units, most of which were altered insignificantly. It was shown that in the presence of imidazole-HCl buffer (pH 7.2) NMR spectra of the polysaccharides from A. japonicus and A. mauritiana were sufficiently resolved, whereas under acidic conditions their (1)H NMR spectra were complicated by overlapping of H-1 signals of GlcA and GalNAc. In the case of polysaccharide from C. japonica bearing 3-O-fucosylated and 3-O-sulfated glucuronic acid residues in the backbone, acidification of the medium led to separation of H-1 signals of GlcA3S and GalNAc. Therefore, the combination of data obtained at different pH values may be useful for interpretation of overcrowded spectra of fucosylated chondroitin sulfates. PMID:26895544

  19. Variations of pH as an additional tool in the analysis of crowded NMR spectra of fucosylated chondroitin sulfates.

    PubMed

    Ustyuzhanina, Nadezhda E; Dmitrenok, Andrey S; Bilan, Maria I; Shashkov, Alexander S; Gerbst, Alexey G; Usov, Anatolii I; Nifantiev, Nikolay E

    2016-03-24

    The influence of pH variation on chemical shift values in NMR spectra of fucosylated chondroitin sulfates was studied using polysaccharides isolated from three sea cucumber species Apostichopus japonicus, Actinopyga mauritiana and Cucumaria japonica. The signals of glucuronic acid residues were found to be the most sensitive to pH changes in comparison to the chemical shifts of the sulfated galactosamine and fucosyl units, most of which were altered insignificantly. It was shown that in the presence of imidazole-HCl buffer (pH 7.2) NMR spectra of the polysaccharides from A. japonicus and A. mauritiana were sufficiently resolved, whereas under acidic conditions their (1)H NMR spectra were complicated by overlapping of H-1 signals of GlcA and GalNAc. In the case of polysaccharide from C. japonica bearing 3-O-fucosylated and 3-O-sulfated glucuronic acid residues in the backbone, acidification of the medium led to separation of H-1 signals of GlcA3S and GalNAc. Therefore, the combination of data obtained at different pH values may be useful for interpretation of overcrowded spectra of fucosylated chondroitin sulfates.

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

    NASA Astrophysics Data System (ADS)

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

    2016-09-01

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

  1. NMR Spectra Transformed by Electron-Nuclear Coupling as Indicator of Structural Peculiarities of Magnetically Active Molecular Systems.

    PubMed

    Voronov, Vladimir K

    2016-09-01

    The peculiarities of nuclear spin relaxation in the paramagnetic systems have been analyzed taking into account the exchange processes. The analysis is based on the modified Solomon-Bloembergen equations. In this line, the conditions of detecting of the NMR signals of samples are discussed depending on resonance frequency of the NMR spectrometer and characteristic relaxation time. On this basis, (1)H NMR spectra of cobalt semiquinolate complex have been analyzed. It has been shown that the satellite signals observed in the spectrum are caused by hyperfine coupling of the tert-butyl group protons with α and β states (localized on pz orbital of the aromatic carbon) of unpaired electron spin. The relaxation process of the resonance protons is controlled by paramagnetic dipole-dipole coupling. The contact hyperfine coupling does not contribute to the paramagnetic broadening. A mechanism involving paramagnetic molecular structures, which are responsible for intramolecular exchange processes in the cobalt semiquinolate complex, is given. PMID:27513208

  2. A general method for diagonal peak suppression in homonuclear correlated NMR spectra by spatially and frequency selective pulses☆

    PubMed Central

    Glanzer, Simon; Schrank, Evelyne; Zangger, Klaus

    2013-01-01

    Homonuclear two- and multidimensional NMR spectra are standard experiments for the structure determination of small to medium-sized molecules. In the large majority of homonuclear correlated spectra the diagonal contains the most intense peaks. Cross-peaks near the diagonal could overlap with huge tails of diagonal peaks and can therefore be easily overlooked. Here we present a general method for the suppression of peaks along the diagonal in homonuclear correlated spectra. It is based on a spatially selective excitation followed by the suppression of magnetization which has not changed the frequency during the mixing process. In addition to the auto correlation removal, these experiments are also less affected by magnetic field inhomogeneities due to the slice selective excitation, which on the other side leads to a reduced intensity compared to regular homonuclear correlated spectra. PMID:23665403

  3. Resistively detected NMR spectra of the crystal states of the two-dimensional electron gas in a quantizing magnetic field

    NASA Astrophysics Data System (ADS)

    Côté, R.; Simoneau, Alexandre M.

    2016-02-01

    Transport experiments on the two-dimensional electron gas (2DEG) confined into a semiconductor quantum well and subjected to a quantizing magnetic field have uncovered a rich variety of uniform and nonuniform phases such as the Laughlin liquids, the Wigner, bubble, and Skyrme crystals, and the quantum Hall stripe state. Optically pumped nuclear magnetic resonance (OP-NMR) has also been extremely useful in studying the magnetization and dynamics of electron solids with exotic spin textures such as the Skyrme crystal. Recently, it has been demonstrated that a related technique, resistively-detected nuclear magnetic resonance (RD-NMR), could be a good tool to study the topography of the electron solids in the fractional and integer quantum Hall regimes. In this work, we compute theoretically the RD-NMR line shapes of various crystal phases of the 2DEG and study the relation between their spin density and texture and their NMR spectra. This allows us to evaluate the ability of the RD-NMR to discriminate between the various types of crystal states.

  4. Experimental and theoretical studies on compositions, structures, and IR and NMR spectra of functionalized protic ionic liquids.

    PubMed

    Cui, Yingna; Yin, Jingmei; Li, Changping; Li, Shenmin; Wang, Ailing; Yang, Guang; Jia, Yingping

    2016-07-20

    The compositions and structures of amine-based functionalized protic ionic liquids (PILs), namely N,N-dimethyl(cyanoethyl)ammonium propionate (DMCEAP) and N,N-dimethyl(hydroxyethyl)ammonium propionate (DMEOAP) have been investigated systematically by IR and (1)H NMR spectroscopy and density functional theory (DFT) calculations. Analysis of the IR spectra suggests that both DMCEAP and DMEOAP are composed of neutral and ionized species in the liquid phase, the former one mainly existing in the state of precursor molecules, and the latter mainly as ion-pairs. The ratio of precursor molecules to ion-pairs in the liquid phase depends on the types of precursors, especially the functional groups of cations. (1)H NMR spectra indicate that there is a dynamic equilibrium between the neutral and ionized species, probably due to the formation of some intermediates in the PILs. The DFT calculations have been carried out to reveal the conformation, and obtain the corresponding IR and (1)H NMR spectra of the neutral and ionized species, so that the theoretical support to the experimental results can be provided. The present study will help understand the properties of PILs and provide guidance for further applications of PILs. PMID:27385035

  5. Vibrational spectra, monomer, dimer, NBO, HOMO, LUMO and NMR analyses of trans-4-hydroxy-L-proline

    NASA Astrophysics Data System (ADS)

    Xavier, R. John; Dinesh, P.

    2014-07-01

    This work presents the characterization of trans-4-hydroxy-L-proline (abbreviated as THLP) by quantum chemical calculations and spectral techniques. The spectroscopic properties were investigated by FT-IR, FT-Raman and 1H and 13C nuclear magnetic resonance (NMR) techniques. The FT-IR (4000-400 cm-1) and FT-Raman (3500-10 cm-1) spectra in the solid phase were recorded for THLP. The 1H and 13C NMR spectra were recorded in DMSO solution. The energies of THLP are obtained for all the eight conformers form density functional theory (DFT) with 6-311++G(d,p) basis set calculations. From the computational results, C1 conformer is identified as the most stable conformer of THLP. The theoretical wavenumbers were scaled and compared with experimental FT-IR and FT-Raman spectra. The complete assignments were performed on the basis of the experimental results and potential energy distribution (PED) of the vibrational modes, calculated with scaled quantum mechanical (SQM) method in terms of fundamental modes. The values of the total dipole moment (μ) and the first order hyperpolarizability (β) of the investigated compound were computed using B3LYP/6-311++G(d,p) calculations. The calculated HOMO-LUMO energies reveal charges transfer occurs within the molecule. The isotropic chemical shift computed by 1H and 13C NMR chemical shifts of the THLF, calculated using the gauge invariant atomic orbital (GIAO) method also shows good agreement with experimental observations.

  6. 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.

  7. Near-silence of isothiocyanate carbon in (13)C NMR spectra: a case study of allyl isothiocyanate.

    PubMed

    Glaser, Rainer; Hillebrand, Roman; Wycoff, Wei; Camasta, Cory; Gates, Kent S

    2015-05-01

    (1)H and (13)C NMR spectra of allyl isothiocyanate (AITC) were measured, and the exchange dynamics were studied to explain the near-silence of the ITC carbon in (13)C NMR spectra. The dihedral angles α = ∠(C1-C2-C3-N4) and β = ∠(C2-C3-N4-C5) describe the conformational dynamics (conformation change), and the bond angles γ = ∠(C3-N4-C5) and ε = ∠(N4-C5-S6) dominate the molecular dynamics (conformer flexibility). The conformation space of AITC contains three minima, Cs-M1 and enantiomers M2 and M2'; the exchange between conformers is very fast, and conformational effects on (13)C chemical shifts are small (νM1 - νM2 < 3 ppm). Isotropic chemical shifts, ICS(γ), were determined for sp, sp(x), and sp(2) N-hybridization, and the γ dependencies of δ(N4) and δ(C5) are very large (10-33 ppm). Atom-centered density matrix propagation trajectories show that every conformer can access a large region of the potential energy surface AITC(γ,ε,...) with 120° < γ < 180° and 155° < ε < 180°. Because the extreme broadening of the (13)C NMR signal of the ITC carbon is caused by the structural flexibility of every conformer of AITC, the analysis provides a general explanation for the near-silence of the ITC carbon in (13)C NMR spectra of organic isothiocyanates.

  8. Singular spectrum analysis for an automated solvent artifact removal and baseline correction of 1D NMR spectra

    NASA Astrophysics Data System (ADS)

    De Sanctis, Silvia; Malloni, Wilhelm M.; Kremer, Werner; Tomé, Ana M.; Lang, Elmar W.; Neidig, Klaus-Peter.; Kalbitzer, Hans Robert

    2011-06-01

    NMR spectroscopy in biology and medicine is generally performed in aqueous solutions, thus in 1H NMR spectroscopy, the dominant signal often stems from the partly suppressed solvent and can be many orders of magnitude larger than the resonances of interest. Strong solvent signals lead to a disappearance of weak resonances of interest close to the solvent artifact and to base plane variations all over the spectrum. The AUREMOL-SSA/ALS approach for automated solvent artifact removal and baseline correction has been originally developed for multi-dimensional NMR spectroscopy. Here, we describe the necessary adaptations for an automated application to one-dimensional NMR spectra. Its core algorithm is still based on singular spectrum analysis (SSA) applied on time domain signals (FIDs) and it is still combined with an automated baseline correction (ALS) in the frequency domain. However, both steps (SSA and ALS) have been modified in order to achieve optimal results when dealing with one-dimensional spectra. The performance of the method has been tested on one-dimensional synthetic and experimental spectra including the back-calculated spectrum of HPr protein and an experimental spectrum of a human urine sample. The latter has been recorded with the typically used NOESY-type 1D pulse sequence including water pre-saturation. Furthermore, the fully automated AUREMOL-SSA/ALS procedure includes the managing of oversampled, digitally filtered and zero-filled data and the correction of the frequency domain phase shift caused by the group delay time shift from the digital finite response filtering.

  9. Matrix-dependent modulation of anisotropic effects on NMR spectra from 7Li+ and 23Na+ encapsulated in cryptands.

    PubMed

    Naumann, Christoph; Kuchel, Philip W

    2013-01-01

    (7)Li and (23)Na NMR spectra of the respective cations in gelatin and ι-carrageenan gels containing cryptand-[2.1.1] (for Li(+)) or cryptand-[2.2.2] (for Na(+)) displayed two transitions: the one at higher frequency corresponded to the cation surrounded by gel, the other to cation inside its appropriately sized cryptand. While binding to cryptands yielded much broader lines and shorter T (1) relaxation times, anisotropic splitting in first order (7)Li or (23)Na NMR spectra was not detected. Stretching the gels resulted in increasing the anisotropic electric field gradient tensor; thus, the NMR transitions of the cation in the gel were split (removal of degeneracy) to display its characteristic 3:4:3 triplet for spin = 3/2 nuclei. The transitions of the cryptand-bound cations (Li(+)-cryptand-[2.1.1] and Na(+)-cryptand-[2.2.2]) showed different extents of interaction with the electric field gradient tensor depending on the composition of the gel matrix. The NMR signal for (7)Li(+)-cryptand-[2.1.1] in stretched gelatin gel showed a five-fold increased splitting as compared to the (7)Li(+) signal in the reference gel. In stretched ι-carrageenan gels, no anisotropic splitting from the cryptand-bound Li(+) was recorded. Steady-state irradiation envelopes or z-spectra showed evidence of Li(+) exchange between isotropic (cryptand) and anisotropic (gel) sites only at higher temperatures (55 °C). For Na(+) bound to the cryptand-[2.2.2], anisotropic splitting (three-fold smaller compared with the (23)Na signal in the reference gel) was only recorded in stretched ι-carrageenan gels, whereas gelatin gels showed only anisotropic splitting for the (23)Na signal in the reference gel.

  10. Analysis of the electronic, IR, and 1H NMR spectra of conjugated oligomers based on 4,4'-triphenylamine vinylene

    NASA Astrophysics Data System (ADS)

    Baryshnikov, G. V.; Minaeva, V. A.; Minaev, B. F.; Sun, V.-H.; Grigoras, M.

    2016-09-01

    Two types of conjugated oligomers based on 4,4'-triphenylamine vinylene have been synthesized and characterized by the methods of IR, UV-visible, and 1H NMR spectroscopy. The corresponding spectra have also been simulated theoretically at the density functional theory level with application of the B3LYP and BMK hybrid exchange-correlation functionals. A comparative analysis of the experimental and theoretical spectra of polymers and oligomers has revealed regularities of the manifestation of spectral signals depending on the conjugation chain length and the presence of a substituent in the triphenylamine core. It has been established, in particular, that the absolute intensity of IR bands satisfies a linear dependence with increase in the degree of polymerization; however, no frequency shift is observed at the same time. The position of the main peak in electron absorption spectra demonstrates the bathochromic shift with an increase in the oligomeric chain length due to the narrowing of the energy gap between the boundary molecular orbitals. Based on the theoretical estimation of the hydrogen atoms chemical shifts, the signals of various protons types in the strongly broadened experimental 1H NMR spectra of the bis-(4-iodine phenyl)-phenylamine and N,N-bis-(4-iodine phenyl)-4'-(phenylethynyl)-phenylamine polymerization products have also been identified.

  11. Biaxial Q-shearing of 27Al 3QMAS NMR spectra: insight into the structural disorder of framework aluminosilicates.

    PubMed

    Kobera, Libor; Brus, Jiri; Klein, Petr; Dedecek, Jiri; Urbanova, Martina

    2014-01-01

    In this contribution, we present the application potentiality of biaxial Q-shearing of (27)Al 3QMAS NMR spectra in the analysis of structural defects of aluminium units in aluminosilicates. This study demonstrates that the combination of various shearing transformations of the recorded (27)Al 3QMAS NMR spectra enables an understanding of the broadening processes of the correlation signals of disordered framework aluminosilicates, for which a wide distribution of (27)Al MAS NMR chemical shifts and quadrupolar parameters (i.e., second-order quadrupolar splitting and quadrupole-induced chemical shifts) can be expected. By combining the suitably selected shearing transformation procedures, the mechanisms of the formation of local defects in aluminosilicate frameworks, including Al/Si substitution effects in the next-nearest neighbouring T-sites, variations in bond angles, and/or variations in the physicochemical nature of charge-balancing counter-ions, can be identified. The proposed procedure has been extensively tested on a range of model aluminosilicate materials (kyanite, γ-alumina, metakaolin, analcime, chabazite, natrolite, phillipsite, mordenite, zeolite A, and zeolite Y).

  12. Spatially resolved NMR spectra for the Swiss cheese model in heavy fermion PuCoGa5 superconductor

    NASA Astrophysics Data System (ADS)

    Das, Tanmoy; Zhu, Jian-Xin; Balatsky, A. V.; Graf, M. J.

    2011-03-01

    Spatially resolved NMR experiments, which probe the local electronic excitations, play a vital role for studying the pairing symmetry of unconventional superconductors. Here we calculate the spatial modulation of the NMR spin-lattice relaxation rate (1/T1) for the Swiss cheese model as a function of impurity concentration in PuCoGa5 superconductor. The local suppression of the superconducting order parameter due to impurities is related to the number of holes in the Swiss cheese model. Our results indicate that Friedel-like oscillations,as seen in the local-density of states near an impurity, are also present in the behavior of 1/T1 as one moves away from the impurity site. We demonstrate that the gap nodes, which are filled by disorder, can be probed by NMR through the local information encoded in the spectra. The advantage of spatially resolved NMR compared to STM measurements is that the former probe is not sensitive to surface states. Work is supported by US DOE.

  13. (1)H, (13)C, (15)N backbone and side chain NMR resonance assignments for E73 from Sulfolobus spindle-shaped virus ragged hills, a hyperthermophilic crenarchaeal virus from Yellowstone National Park.

    PubMed

    Schlenker, Casey; Menon, Smita; Lawrence, C Martin; Copié, Valérie

    2009-12-01

    Crenarchaeal viruses are commonly found in hyperthermal acidic environments such as those of Yellowstone National Park. These remarkable viruses not only exhibit unusual morphologies, but also display extreme genetic diversity. However, little is known about crenarchaeal viral life cycles, virus-host interactions, and their adaptation to hyperthermophilic environments. In an effort to better understand the functions of crenarchaeal viruses and the proteins encoded by their genomes, we have undertaken detailed structural and functional studies of gene products encoded in the open reading frames of Sulfolobus spindle-shaped virus ragged hills. Herein, we report ((15)N, (13)C, (1)H) resonance assignments of backbone and side chain atoms of a 19.1 kDa homodimeric E73 protein of SSVRH.

  14. Ab initio study of 59Co NMR spectra in Co2FeAl1-xSix Heusler alloys

    NASA Astrophysics Data System (ADS)

    Nishihara, H.; Sato, K.; Akai, H.; Takiguchi, C.; Geshi, M.; Kanomata, T.; Sakon, T.; Wada, T.

    2015-05-01

    Ab initio electronic structure calculation of a series of Co2FeAl1-xSix Heusler alloys has been performed, using the Korringa-Kohn-Rostoker-coherent potential approximation method to explain experimental 59Co NMR spectra. Two prominent features are explained semi-quantitatively-a global shift of the 59Co resonance line due to alloying with Al and Si atoms in Co2FeAl1-xSix, and the effect of local disorder in creating distinct satellite lines of 59Co NMR in Co2FeAl. The importance is stressed of the positive contribution to the 59Co hyperfine field from valence electron polarization, which emerges from the half-metallic band structure inherent in Co-based Heusler alloys.

  15. 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

  16. Vibrational spectra, monomer, dimer, NBO, HOMO, LUMO and NMR analyses of trans-4-hydroxy-L-proline.

    PubMed

    Xavier, R John; Dinesh, P

    2014-07-15

    This work presents the characterization of trans-4-hydroxy-L-proline (abbreviated as THLP) by quantum chemical calculations and spectral techniques. The spectroscopic properties were investigated by FT-IR, FT-Raman and (1)H and (13)C nuclear magnetic resonance (NMR) techniques. The FT-IR (4000-400 cm(-1)) and FT-Raman (3500-10 cm(-1)) spectra in the solid phase were recorded for THLP. The (1)H and (13)C NMR spectra were recorded in DMSO solution. The energies of THLP are obtained for all the eight conformers form density functional theory (DFT) with 6-311++G(d,p) basis set calculations. From the computational results, C1 conformer is identified as the most stable conformer of THLP. The theoretical wavenumbers were scaled and compared with experimental FT-IR and FT-Raman spectra. The complete assignments were performed on the basis of the experimental results and potential energy distribution (PED) of the vibrational modes, calculated with scaled quantum mechanical (SQM) method in terms of fundamental modes. The values of the total dipole moment (μ) and the first order hyperpolarizability (β) of the investigated compound were computed using B3LYP/6-311++G(d,p) calculations. The calculated HOMO-LUMO energies reveal charges transfer occurs within the molecule. The isotropic chemical shift computed by (1)H and (13)C NMR chemical shifts of the THLF, calculated using the gauge invariant atomic orbital (GIAO) method also shows good agreement with experimental observations. PMID:24657468

  17. 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

  18. Fast and simple acquisition of solid-state 14N NMR spectra with signal enhancement via population transfer.

    PubMed

    O'Dell, Luke A; Schurko, Robert W

    2009-05-20

    A new approach for the acquisition of static, wideline (14)N NMR powder patterns is outlined. The method involves the use of frequency-swept pulses which serve two simultaneous functions: (1) broad-band excitation of magnetization and (2) signal enhancement via population transfer. The signal enhancement mechanism is described using numerical simulations and confirmed experimentally. This approach, which we call DEISM (Direct Enhancement of Integer Spin Magnetization), allows high-quality (14)N spectra to be acquired at intermediate field strengths in an uncomplicated way and in a fraction of the time required for previously reported methods.

  19. Automatic phase correction of fourier transform NMR spectra based on the dispersion versus absorption (DISPA) lineshape analysis

    NASA Astrophysics Data System (ADS)

    Sotak, Christopher H.; Dumoulin, Charles L.; Newsham, Mark D.

    A method for automatic phase correction of Fourier transform NMR spectra bused on the dispersion versus absorption (DISPA) lineshape analysis is described. The DISPA display of a single misphased Lorentzian line gives a unit circle which has been rotated about the origin (relative to its "reference circle") by a number of degrees equal to the phase misadjustment. This rotation, Φ, is a combination of the zero- and first-order phase angles at the frequency of the resonance. Calculation of Φ for two or more resonances allows the spectral phasing parameters to be determined and applied to correct the spectrum. This approach has been implemented in both automatic and "semi-automatic" modes.

  20. Constraining 17O and 27Al NMR spectra of high-pressure crystals and glasses: New data for jadeite, pyrope, grossular, and mullite

    USGS Publications Warehouse

    Kelsey, K.E.; Stebbins, J.F.; Du, L.-S.; Hankins, B.

    2007-01-01

    The 17O NMR spectra of glasses quenched from melts at high pressure are often difficult to interpret due to overlapping peaks and lack of crystalline model compounds. High-pressure aluminosilicate glasses often contain significant amounts of [5]Al and [6]Al, thus these high-pressure glasses must contain oxygen bonded to high-coordinated aluminum. The 17O NMR parameters for the minerals jadeite, pyrope, grossular, and mullite are presented to assist interpretation of glass spectra and to help test quantum chemical calculations. The 17O NMR parameters for jadeite and grossular support previous peak assignments of oxygen bonded to Si and high-coordinated Al in high-pressure glasses as well as quantum chemical calculations. The oxygen tricluster in mullite is very similar to the previously observed tricluster in grossite (CaAl4 O7) and suspected triclusters in glasses. We also present 27Al NMR spectra for pyrope, grossular, and mullite.

  1. Tendencies of 31P chemical shifts changes in NMR spectra of nucleotide derivatives.

    PubMed

    Lebedev, A V; Rezvukhin, A I

    1984-07-25

    31P NMR chemical shifts of the selected mono- and oligonucleotide derivatives, including the compounds with P-N, P-C, P-S bonds and phosphite nucleotide analogues have been presented. The influence of substituents upon 31P chemical shifts has been discussed. The concrete examples of 31P chemical shifts data application in the field of nucleotide chemistry have been considered.

  2. HiFSA Fingerprinting Applied to Isomers with Near-Identical NMR Spectra: The Silybin/Isosilybin Case

    PubMed Central

    Napolitano, José G.; Lankin, David C.; Graf, Tyler N.; Friesen, J. Brent; Chen, Shao-Nong; McAlpine, James B.; Oberlies, Nicholas H.; Pauli, Guido F.

    2013-01-01

    This study demonstrates how regio- and diastereo-isomers with near-identical NMR spectra can be distinguished and unambiguously assigned using quantum mechanical driven, 1H iterative Full Spin Analysis (HiFSA). The method is illustrated with four natural products, the flavonolignans silybin A, silybin B, isosilybin A, and isosilybin B, which exhibit extremely similar coupling patterns and chemical shift differences well below the commonly reported level of accuracy of 0.01 ppm. The HiFSA approach generated highly reproducible 1H NMR fingerprints that enable distinction of all four isomers at 1H frequencies from 300 to 900 MHz. Furthermore, it is demonstrated that the underlying numeric 1H NMR profiles, combined with iterative computational analysis, allow parallel quantification of all four isomers, even in difficult to characterize reference materials and mixtures. The results shed new light on the historical challenges to the qualitative and quantitative analysis of these therapeutically relevant flavonolignans and open new opportunities to explore hidden diversity in the chemical space of organic molecules. PMID:23461697

  3. {sup 139}La NMR in lanthanum manganites: Indication of the presence of magnetic polarons from spectra and nuclear relaxations

    SciTech Connect

    Allodi, G.; De Renzi, R.; Guidi, G.

    1998-01-01

    We present {sup 139}La NMR experiments on five powder samples of lanthanum manganites, with a Mn{sup 4+} concentration ranging from the antiferromagnetic-insulator (AFM) to the ferromagnetic-conducting (FM) region of the phase diagram. We measure a positive hyperfine coupling C=0.13 T/{mu}{sub B}. A signal from nuclei in a FM environment is present at all compositions, as evidenced by a hyperfine frequency in zero-field experiments, by a positive hyperfine shift in NMR experiments below T{sub c}, and by a paramagnetic frequency shift following Curie-Weiss law. A signal from nuclei in an AFM environment is identified by a similar negative intercept Curie-Weiss law. The NMR spectra reveal a large temperature dependent fraction of static spin defects below T{sub c} in the FM domains. Nuclear relaxation indicates that the FM regions are influenced by diffusing, AFM-correlated excitations, while the AFM regions probe spin fluctuations from diffusing, FM correlated excitations. These results are interpreted in terms of electronic inhomogeneities due to the presence of a magnetic small polaron. {copyright} {ital 1998} {ital The American Physical Society}

  4. HiFSA fingerprinting applied to isomers with near-identical NMR spectra: the silybin/isosilybin case.

    PubMed

    Napolitano, José G; Lankin, David C; Graf, Tyler N; Friesen, J Brent; Chen, Shao-Nong; McAlpine, James B; Oberlies, Nicholas H; Pauli, Guido F

    2013-04-01

    This study demonstrates how regio- and diastereo-isomers with near-identical NMR spectra can be distinguished and unambiguously assigned using quantum mechanical driven (1)H iterative Full Spin Analysis (HiFSA). The method is illustrated with four natural products, the flavonolignans silybin A, silybin B, isosilybin A, and isosilybin B, which exhibit extremely similar coupling patterns and chemical shift differences well below the commonly reported level of accuracy of 0.01 ppm. The HiFSA approach generated highly reproducible (1)H NMR fingerprints that enable distinction of all four isomers at (1)H frequencies from 300 to 900 MHz. Furthermore, it is demonstrated that the underlying numeric (1)H NMR profiles, combined with iterative computational analysis, allow parallel quantification of all four isomers, even in difficult to characterize reference materials and mixtures. The results shed new light on the historical challenges to the qualitative and quantitative analysis of these therapeutically relevant flavonolignans and open new opportunities to explore hidden diversity in the chemical space of organic molecules. PMID:23461697

  5. The structure elucidation of mequindox and 1,4-bisdesoxymequindox: NMR analyses, FT-IR spectra, DFT calculations and thermochemical studies

    NASA Astrophysics Data System (ADS)

    Zhang, Jiaheng; He, Xin; Gao, Haixiang

    2011-10-01

    In the current work, we report a combined experimental and theoretical study on the molecular conformation, vibrational spectra, and nuclear magnetic resonance (NMR) spectra of mequindox (MEQ) and 1,4-bisdesoxymequindox (1,4-BDM). The geometric structure and vibrational frequencies of MEQ and 1,4-BDM have been calculated by density functional theory employing the B3LYP functional and 6-311++G(d,p) basis set. The 1H and 13C NMR chemical shifts have been calculated by gauge-including atomic orbital method with B3LYP 6-311++G(2df,2pd) approach. The calculation results have been applied to simulate the infrared and NMR spectra of the compounds. The theoretical results agree well with the observed spectra. The bond dissociation enthalpy of MEQ and the heat of formation of MEQ and 1,4-BDM have also been computed.

  6. A Global Approach to Accurate and Automatic Quantitative Analysis of NMR Spectra by Complex Least-Squares Curve Fitting

    NASA Astrophysics Data System (ADS)

    Martin, Y. L.

    The performance of quantitative analysis of 1D NMR spectra depends greatly on the choice of the NMR signal model. Complex least-squares analysis is well suited for optimizing the quantitative determination of spectra containing a limited number of signals (<30) obtained under satisfactory conditions of signal-to-noise ratio (>20). From a general point of view it is concluded, on the basis of mathematical considerations and numerical simulations, that, in the absence of truncation of the free-induction decay, complex least-squares curve fitting either in the time or in the frequency domain and linear-prediction methods are in fact nearly equivalent and give identical results. However, in the situation considered, complex least-squares analysis in the frequency domain is more flexible since it enables the quality of convergence to be appraised at every resonance position. An efficient data-processing strategy has been developed which makes use of an approximate conjugate-gradient algorithm. All spectral parameters (frequency, damping factors, amplitudes, phases, initial delay associated with intensity, and phase parameters of a baseline correction) are simultaneously managed in an integrated approach which is fully automatable. The behavior of the error as a function of the signal-to-noise ratio is theoretically estimated, and the influence of apodization is discussed. The least-squares curve fitting is theoretically proved to be the most accurate approach for quantitative analysis of 1D NMR data acquired with reasonable signal-to-noise ratio. The method enables complex spectral residuals to be sorted out. These residuals, which can be cumulated thanks to the possibility of correcting for frequency shifts and phase errors, extract systematic components, such as isotopic satellite lines, and characterize the shape and the intensity of the spectral distortion with respect to the Lorentzian model. This distortion is shown to be nearly independent of the chemical species

  7. Site-resolved 2H relaxation experiments in solid materials by global line-shape analysis of MAS NMR spectra

    NASA Astrophysics Data System (ADS)

    Lindh, E. L.; Stilbs, P.; Furó, I.

    2016-07-01

    We investigate a way one can achieve good spectral resolution in 2H MAS NMR experiments. The goal is to be able to distinguish between and study sites in various deuterated materials with small chemical shift dispersion. We show that the 2H MAS NMR spectra recorded during a spin-relaxation experiment are amenable to spectral decomposition because of the different evolution of spectral components during the relaxation delay. We verify that the results are robust by global least-square fitting of the spectral series both under the assumption of specific line shapes and without such assumptions (COmponent-REsolved spectroscopy, CORE). In addition, we investigate the reliability of the developed protocol by analyzing spectra simulated with different combinations of spectral parameters. The performance is demonstrated in a model material of deuterated poly(methacrylic acid) that contains two 2H spin populations with similar chemical shifts but different quadrupole splittings. In 2H-exchanged cellulose containing two 2H spin populations with very similar chemical shifts and quadrupole splittings, the method provides new site-selective information about the molecular dynamics.

  8. Pulse Electron Double Resonance Detected Multinuclear NMR Spectra of Distant and Low Sensitivity Nuclei and Its Application to the Structure of Mn(II) Centers in Organisms.

    PubMed

    Bruch, Eduardo M; Warner, Melissa T; Thomine, Sébastien; Tabares, Leandro C; Un, Sun

    2015-10-29

    The ability to characterize the structure of metal centers beyond their primary ligands is important to understanding their chemistry. High-magnetic-field pulsed electron double resonance detected NMR (ELDOR-NMR) is shown to be a very sensitive approach to measuring the multinuclear NMR spectra of the nuclei surrounding Mn(II) ions. Resolved spectra of intact organisms with resonances arising from (55)Mn, (31)P, (1)H, (39)K, (35)Cl, (23)Na, and (14)N nuclei surrounding Mn(2+) centers were obtained. Naturally abundant cellular (13)C could be routinely measured as well. The amplitudes of the (14)N and (2)H ELDOR-NMR spectra were found to be linearly dependent on the number of nuclei in the ligand sphere. The evolution of the Mn(II) ELDOR-NMR spectra as a function of excitation time was found to be best described by a saturation phenomenon rather than a coherently driven process. Mn(II) ELDOR-NMR revealed details about not only the immediate ligands to the Mn(II) ions but also more distant nuclei, providing a view of their extended structures. This will be important for understanding the speciation and chemistry of the manganese complexes as well as other metals found in organisms.

  9. Metabonomics classifies pathways affected by bioactive compounds. Artificial neural network classification of NMR spectra of plant extracts.

    PubMed

    Ott, Karl-Heinz; Araníbar, Nelly; Singh, Bijay; Stockton, Gerald W

    2003-03-01

    The biochemical mode-of-action (MOA) for herbicides and other bioactive compounds can be rapidly and simultaneously classified by automated pattern recognition of the metabonome that is embodied in the 1H NMR spectrum of a crude plant extract. The ca. 300 herbicides that are used in agriculture today affect less than 30 different biochemical pathways. In this report, 19 of the most interesting MOAs were automatically classified. Corn (Zea mays) plants were treated with various herbicides such as imazethapyr, glyphosate, sethoxydim, and diuron, which represent various biochemical modes-of-action such as inhibition of specific enzymes (acetohydroxy acid synthase [AHAS], protoporphyrin IX oxidase [PROTOX], 5-enolpyruvylshikimate-3-phosphate synthase [EPSPS], acetyl CoA carboxylase [ACC-ase], etc.), or protein complexes (photosystems I and II), or major biological process such as oxidative phosphorylation, auxin transport, microtubule growth, and mitosis. Crude isolates from the treated plants were subjected to 1H NMR spectroscopy, and the spectra were classified by artificial neural network analysis to discriminate the herbicide modes-of-action. We demonstrate the use and refinement of the method, and present cross-validated assignments for the metabolite NMR profiles of over 400 plant isolates. The MOA screen also recognizes when a new mode-of-action is present, which is considered extremely important for the herbicide discovery process, and can be used to study deviations in the metabolism of compounds from a chemical synthesis program. The combination of NMR metabolite profiling and neural network classification is expected to be similarly relevant to other metabonomic profiling applications, such as in drug discovery. PMID:12590124

  10. Tendencies of 31P chemical shifts changes in NMR spectra of nucleotide derivatives.

    PubMed

    Lebedev, A V; Rezvukhin, A I

    1984-07-25

    31P NMR chemical shifts of the selected mono- and oligonucleotide derivatives, including the compounds with P-N, P-C, P-S bonds and phosphite nucleotide analogues have been presented. The influence of substituents upon 31P chemical shifts has been discussed. The concrete examples of 31P chemical shifts data application in the field of nucleotide chemistry have been considered. PMID:6087290

  11. Toward hyperpolarized molecular imaging of HIV: synthesis and longitudinal relaxation properties of 15N-Azidothymidine

    PubMed Central

    Shchepin, Roman V.; Chekmenev, Eduard Y.

    2015-01-01

    Previously unreported 15N labeled Azidothymidine (AZT) was prepared as an equimolar mixture of two isotopomers: 1-15N-AZT and 3-15N-AZT. Polarization decay of 15N NMR signal was studied in high (9.4 T) and low (~50 mT) magnetic fields. 15N T1 values were 45 ± 5 s (1-15N-AZT) and 37 ± 2 s (3-15N-AZT) at 9.4 T, and 140 ± 16 s (3-15N-AZT) at 50 mT. 15N-AZT can be potentially 15N hyperpolarized by several methods. These sufficiently long 15N-AZT T1 values potentially enable hyperpolarized in vivo imaging of 15N-AZT, because of the known favorable efficient (i.e., of the time scale shorter than the longest reported here 15N T1) kinetics of uptake of injected AZT. Therefore, 3-15N-AZT can be potentially used for HIV molecular imaging using hyperpolarized magnetic resonance imaging. PMID:25156931

  12. Improving sensitivity and resolution of MQMAS spectra: A 45Sc-NMR case study of scandium sulphate pentahydrate

    NASA Astrophysics Data System (ADS)

    Chandran, C. Vinod; Cuny, Jérôme; Gautier, Régis; Le Pollès, Laurent; Pickard, Chris J.; Bräuniger, Thomas

    2010-04-01

    To efficiently obtain multiple-quantum magic-angle spinning (MQMAS) spectra of the nuclide 45Sc ( I = 7/2), we have combined several previously suggested techniques to enhance the signal-to-noise ratio and to improve spectral resolution for the test sample, scandium sulphate pentahydrate (ScSPH). Whereas the 45Sc-3QMAS spectrum of ScSPH does not offer sufficient resolution to clearly distinguish between the 3 scandium sites present in the crystal structure, these sites are well-resolved in the 5QMAS spectrum. The loss of sensitivity incurred by using MQMAS with 5Q coherence order is partly compensated for by using fast-amplitude modulated (FAM) sequences to improve the efficiency of both 5Q coherence excitation and conversion. Also, heteronuclear decoupling is employed to minimise dephasing of the 45Sc signal during the 5Q evolution period due to dipolar couplings with the water protons in the ScSPH sample. Application of multi-pulse decoupling schemes such as TPPM and SPINAL results in improved sensitivity and resolution in the F1 (isotropic) dimension of the 5QMAS spectrum, the best results being achieved with the recently suggested SW f-TPPM sequence. By numerical fitting of the 45Sc-NMR spectra of ScSPH from 3QMAS, 5QMAS and single-quantum MAS at magnetic fields B0 = 9.4 T and 17.6 T, the isotropic chemical shift δiso, the quadrupolar coupling constant χ, and the asymmetry parameter η were obtained. Averaging over all experiments, the NMR parameters determined for the 3 scandium sites, designated (a), (b) and (c) are: δiso( a) = -15.5 ± 0.5 ppm, χ( a) = 5.60 ± 0.10 MHz, η( a) = 0.06 ± 0.05; δiso( b) = -12.9 ± 0.5 ppm, χ( b) = 4.50 ± 0.10 MHz, η( b) = 1.00 ± 0.00; and δiso( c) = -4.7 ± 0.2 ppm, χ( c) = 4.55 ± 0.05 MHz, η( c) = 0.50 ± 0.02. The NMR scandium species were assigned to the independent crystallographic sites by evaluating their experimental response to proton decoupling, and by density functional theory (DFT) calculations using

  13. Optical detection of NMR J-spectra at zero magnetic field

    NASA Astrophysics Data System (ADS)

    Ledbetter, M. P.; Crawford, C. W.; Pines, A.; Wemmer, D. E.; Knappe, S.; Kitching, J.; Budker, D.

    2009-07-01

    Scalar couplings of the form JI1 · I2 between nuclei impart valuable information about molecular structure to nuclear magnetic-resonance spectra. Here we demonstrate direct detection of J-spectra due to both heteronuclear and homonuclear J-coupling in a zero-field environment where the Zeeman interaction is completely absent. We show that characteristic functional groups exhibit distinct spectra with straightforward interpretation for chemical identification. Detection is performed with a microfabricated optical atomic magnetometer, providing high sensitivity to samples of microliter volumes. We obtain 0.1 Hz linewidths and measure scalar-coupling parameters with 4-mHz statistical uncertainty. We anticipate that the technique described here will provide a new modality for high-precision "J spectroscopy" using small samples on microchip devices for multiplexed screening, assaying, and sample identification in chemistry and biomedicine.

  14. Modified Prony Method to Resolve and Quantify in Vivo31P NMR Spectra of Tumors

    NASA Astrophysics Data System (ADS)

    Barone, P.; Guidoni, L.; Ragona, R.; Viti, V.; Furman, E.; Degani, H.

    Prony's method, successfully used in processing NMR signals, performs poorly at low signal-to-noise ratios. To overcome this problem, a statistical approach has been adopted by using Prony's method as a sampling device from the distribution associated with the true spectrum. Specifically, Prony's method is applied for each regression order p and number of data points n, both considered in a suitable range, and the estimates of frequencies, amplitudes, and decay factors are pooled separately. A histogram of the pooled frequencies is computed and, looking at the histogram, a lower and an upper frequency bound for each line of interest is determined. All frequency estimates in each of the determined intervals as well as associated decay factors and amplitudes are considered to be independent normal variates. A mean value and a corresponding 95% confidence interval are computed for each parameter. 31P NMR signals from MCF7 human breast cancer cells, inoculated into athymic mice and which developed into tumors, have been processed with traditional methods and with this modified Prony's method. The main components of the phosphomonoester peak, namely those deriving from phosphorylcholine and phosphorylethanolamine, are always well resolved with this new approach and their relative amplitudes can be consequently evaluated. Peak intensities of these two signals show different behavior during treatment of tumors with the antiestrogenic drug tamoxifen. The results of this new approach are compared with those obtainable with traditional techniques.

  15. Pulsed field gradients in simulations of one- and two-dimensional NMR spectra.

    PubMed

    Meresi, G H; Cuperlovic, M; Palke, W E; Gerig, J T

    1999-03-01

    A method for the inclusion of the effects of z-axis pulsed field gradients in computer simulations of an arbitrary pulsed NMR experiment with spin (1/2) nuclei is described. Recognizing that the phase acquired by a coherence following the application of a z-axis pulsed field gradient bears a fixed relation to its order and the spatial position of the spins in the sample tube, the sample is regarded as a collection of volume elements, each phase-encoded by a characteristic, spatially dependent precession frequency. The evolution of the sample's density matrix is thus obtained by computing the evolution of the density matrix for each volume element. Following the last gradient pulse, these density matrices are combined to form a composite density matrix which evolves through the rest of the experiment to yield the observable signal. This approach is implemented in a program which includes capabilities for rigorous inclusion of spin relaxation by dipole-dipole, chemical shift anisotropy, and random field mechanisms, plus the effects of arbitrary RF fields. Mathematical procedures for accelerating these calculations are described. The approach is illustrated by simulations of representative one- and two-dimensional NMR experiments.

  16. A novel approach to the rapid assignment of (13)C NMR spectra of major components of vegetable oils such as avocado, mango kernel and macadamia nut oils.

    PubMed

    Retief, Liezel; McKenzie, Jean M; Koch, Klaus R

    2009-09-01

    Assignment of (13)C nuclear magnetic resonance (NMR) spectra of major fatty acid components of South African produced vegetable oils was attempted using a method in which the vegetable oil was spiked with a standard triacylglycerol. This proved to be inadequate and therefore a new rapid and potentially generic graphical linear correlation method is proposed for assignment of the (13)C NMR spectra of major fatty acid components of apricot kernel, avocado pear, grapeseed, macadamia nut, mango kernel and marula vegetable oils. In this graphical correlation method, chemical shifts of fatty acids present in a known standard triacylglycerol is plotted against the corresponding chemical shifts of fatty acids present in the vegetable oils. This new approach (under carefully defined conditions and concentrations) was found especially useful for spectrally crowded regions where significant peak overlap occurs and was validated with the well-known (13)C NMR spectrum of olive oil which has been extensively reported in the literature. In this way, a full assignment of the (13)C{1H} NMR spectra of the vegetable oils, as well as tripalmitolein was readily achieved and the resonances belonging to the palmitoleic acid component of the triacylglycerols in the case of macadamia nut and avocado pear oil resonances were also assigned for the first time in the (13)C NMR spectra of these oils.

  17. A novel approach to the rapid assignment of (13)C NMR spectra of major components of vegetable oils such as avocado, mango kernel and macadamia nut oils.

    PubMed

    Retief, Liezel; McKenzie, Jean M; Koch, Klaus R

    2009-09-01

    Assignment of (13)C nuclear magnetic resonance (NMR) spectra of major fatty acid components of South African produced vegetable oils was attempted using a method in which the vegetable oil was spiked with a standard triacylglycerol. This proved to be inadequate and therefore a new rapid and potentially generic graphical linear correlation method is proposed for assignment of the (13)C NMR spectra of major fatty acid components of apricot kernel, avocado pear, grapeseed, macadamia nut, mango kernel and marula vegetable oils. In this graphical correlation method, chemical shifts of fatty acids present in a known standard triacylglycerol is plotted against the corresponding chemical shifts of fatty acids present in the vegetable oils. This new approach (under carefully defined conditions and concentrations) was found especially useful for spectrally crowded regions where significant peak overlap occurs and was validated with the well-known (13)C NMR spectrum of olive oil which has been extensively reported in the literature. In this way, a full assignment of the (13)C{1H} NMR spectra of the vegetable oils, as well as tripalmitolein was readily achieved and the resonances belonging to the palmitoleic acid component of the triacylglycerols in the case of macadamia nut and avocado pear oil resonances were also assigned for the first time in the (13)C NMR spectra of these oils. PMID:19544589

  18. Analysis of 31P MAS NMR spectra and transversal relaxation of bacteriophage M13 and tobacco mosaic virus.

    PubMed Central

    Magusin, P C; Hemminga, M A

    1994-01-01

    Phosphorus magic angle spinning nuclear magnetic resonance (NMR) spectra and transversal relaxation of M13 and TMV are analyzed by use of a model, which includes both local backbone motions of the encapsulated nucleic acid molecules and overall rotational diffusion of the rod-shaped virions about their length axis. Backbone motions influence the sideband intensities by causing a fast restricted reorientation of the phosphodiesters. To evaluate their influence on the observed sideband patterns, we extend the model that we used previously to analyze nonspinning 31P NMR lineshapes (Magusin, P.C.M.M., and M. A. Hemminga. 1993a. Biophys. J. 64:1861-1868) to magic angle spinning NMR experiments. Backbone motions also influence the conformation of the phosphodiesters, causing conformational averaging of the isotropic chemical shift, which offers a possible explanation for the various linewidths of the centerband and the sidebands observed for M13 gels under various conditions. The change of the experimental lineshape of M13 as a function of temperature and hydration is interpreted in terms of fast restricted fluctuation of the dihedral angles between the POC and the OCH planes on both sides of the 31P nucleus in the nucleic acid backbone. Backbone motions also seem to be the main cause of transversal relaxation measured at spinning rates of 4 kHz or higher. At spinning rates less than 2 kHz, transversal relaxation is significantly faster. This effect is assigned to slow, overall rotation of the rod-shaped M13 phage about its length axis. Equations are derived to simulate the observed dependence of T2e on the spinning rate. PMID:8038391

  19. Structure of dimethylphenyl betaine hydrochloride studied by X-ray diffraction, DFT calculation, NMR and FTIR spectra

    NASA Astrophysics Data System (ADS)

    Szafran, M.; Katrusiak, A.; Dega-Szafran, Z.; Kowalczyk, I.

    2013-01-01

    The structure of dimethylphenyl betaine hydrochloride (1) has been studied by X-ray diffraction, DFT calculations, NMR and FTIR spectra. The crystals are monoclinic, space group P21/c. In the crystal, the Cl- anion is connected with protonated betaine through the O-H⋯Cl- hydrogen bond of 2.943(2) Å. The structures in the gas phase (2) and water solution (3) have been optimized by the B3LYP/6-311++G(d,p) approach and the geometrical results have been compared with the X-ray data of 1. The FTIR spectrum of the solid compound is consistent with the X-ray results. The probable assignments of the anharmonic experimental vibrational frequencies of the investigated chloride (1) based on the calculated harmonic frequencies in water solution (3) are proposed. The correlations between the experimental 1H and 13C NMR chemical shifts (δexp) of 1 in D2O and the magnetic isotropic shielding constants (σcalc) calculated by the GIAO/B3LYP/6-311G++(d,p) approach, using the screening solvation model (COSMO), δexp = a + b σcalc, for optimized molecule 3 in water solution are linear and correctly reproduce the experimental chemical shifts.

  20. The effect of sample hydration on 13C CPMAS NMR spectra of fulvic acids

    USGS Publications Warehouse

    Hatcher, P.G.; Wilson, M.A.

    1991-01-01

    Three fulvic acids, two of which have been well studied by a number of other groups (Armadale and Suwannee river fulvic acids) have been examined by high resolution solid-state 13C-NMR techniques to delineate the effect of absorbed water. Two main effects of absorbed water were observed: (1) changes in spin lattice relaxation times in the rotating frame and cross polarization times and (2) total loss of signal so that some fulvic acid is effectively in solution. These results suggest that discrepancies in the literature concerning observed relative signal intensities from different structural groups are due to absorbed water and emphasize the necessity for proper precautionary drying before spectroscopic analysis. ?? 1991.

  1. Evaluation of standard and advanced preprocessing methods for the univariate analysis of blood serum 1H-NMR spectra.

    PubMed

    De Meyer, Tim; Sinnaeve, Davy; Van Gasse, Bjorn; Rietzschel, Ernst-R; De Buyzere, Marc L; Langlois, Michel R; Bekaert, Sofie; Martins, José C; Van Criekinge, Wim

    2010-10-01

    Proton nuclear magnetic resonance ((1)H-NMR)-based metabolomics enables the high-resolution and high-throughput assessment of a broad spectrum of metabolites in biofluids. Despite the straightforward character of the experimental methodology, the analysis of spectral profiles is rather complex, particularly due to the requirement of numerous data preprocessing steps. Here, we evaluate how several of the most common preprocessing procedures affect the subsequent univariate analyses of blood serum spectra, with a particular focus on how the standard methods perform compared to more advanced examples. Carr-Purcell-Meiboom-Gill 1D (1)H spectra were obtained for 240 serum samples from healthy subjects of the Asklepios study. We studied the impact of different preprocessing steps--integral (standard method) and probabilistic quotient normalization; no, equidistant (standard), and adaptive-intelligent binning; mean (standard) and maximum bin intensity data summation--on the resonance intensities of three different types of metabolites: triglycerides, glucose, and creatinine. The effects were evaluated by correlating the differently preprocessed NMR data with the independently measured metabolite concentrations. The analyses revealed that the standard methods performed inferiorly and that a combination of probabilistic quotient normalization after adaptive-intelligent binning and maximum intensity variable definition yielded the best overall results (triglycerides, R = 0.98; glucose, R = 0.76; creatinine, R = 0.70). Therefore, at least in the case of serum metabolomics, these or equivalent methods should be preferred above the standard preprocessing methods, particularly for univariate analyses. Additional optimization of the normalization procedure might further improve the analyses.

  2. A method based on covariance and pattern recognition for improving resolutions of spatially encoded NMR spectra.

    PubMed

    Qiu, Wenqi; Chen, Youhe; Wei, Zhiliang; Yang, Jian; Lin, Yulan; Chen, Zhong

    2015-11-01

    The spatially encoded technique enables the fast acquisition of two-dimensional (2D) nuclear magnetic resonance spectrum within a single scan, serving as a powerful tool for studying various systems and phenomena in short time scales. In spatially encoded spectroscopy, the resolution in the direct dimension can be enhanced by increasing effective acquisition times. However, spectral widths and resolutions in indirect dimensions are no longer independent of each other with wider spectral widths yielding lower resolution. The covariance method, which has achieved success in enhancing resolutions in the indirect dimensions of conventional 2D spectroscopy, is employed here to improve resolutions in the spatially encoded dimension. Moreover, an algorithm is developed based on pattern recognition to eliminate artifacts arising from the employment of the covariance method and experimental imperfections in recording the spatially encoded spectra. Therefore, high-resolution homonuclear 2D correlated spectra are obtained. Experiments are performed to show the feasibility and effectiveness of this proposed method in providing high-resolution spectra within greatly shortened times.

  3. 1H and 15N nuclear magnetic resonance assignment and secondary structure of the cytotoxic ribonuclease alpha-Sarcin.

    PubMed Central

    Campos-Olivas, R.; Bruix, M.; Santoro, J.; Martínez del Pozo, A.; Lacadena, J.; Gavilanes, J. G.; Rico, M.

    1996-01-01

    The ribosome-inactivating protein alpha-Sarcin (alpha S) is a 150-residue fungal ribonuclease that, after entering sensitive cells, selectively cleaves a single phosphodiester bond in an universally conserved sequence of the major rRNA to inactivate the ribosome and thus exert its cytotoxic action. As a first step toward establishing the structure-dynamics-function relationships in this system, we have carried out the assignment of the 1H and 15N NMR spectrum of alpha S on the basis of homonuclear (1H-1H) and heteronuclear (1H-15N) two-dimensional correlation spectra of a uniformly 15N-labeled sample, and two selectively 15N-labeled (Tyr and Phe) samples, as well as a single three-dimensional experiment. The secondary structure of alpha S, as derived from the characteristic patterns of dipolar connectivities between backbone protons, conformational chemical shifts, and the protection of backbone amide protons against exchange, consists of a long N-terminal beta-hairpin, a short alpha-helical segment, and a C-terminal beta-sheet of five short strands arranged in a + 1, + 1, + 1, + 1 topology, connected by long loops in which the 13 Pro residues are located. PMID:8732769

  4. The “Speedy” Synthesis of Atom-Specific 15N Imino/Amido-Labeled RNA

    PubMed Central

    Kreutz, Christoph; Micura, Ronald

    2016-01-01

    Although numerous reports on the synthesis of atom-specific 15N-labeled nucleosides exist, fast and facile access to the corresponding phosphoramidites for RNA solid-phase synthesis is still lacking. This situation represents a severe bottleneck for NMR spectroscopic investigations on functional RNAs. Here, we present optimized procedures to speed up the synthesis of 15N(1) adenosine and 15N(1) guanosine amidites, which are the much needed counterparts of the more straightforward-to-achieve 15N(3) uridine and 15N(3) cytidine amidites in order to tap full potential of 1H/15N/15N-COSY experiments for directly monitoring individual Watson–Crick base pairs in RNA. Demonstrated for two preQ1 riboswitch systems, we exemplify a versatile concept for individual base-pair labeling in the analysis of conformationally flexible RNAs when competing structures and conformational dynamics are encountered. PMID:26237536

  5. Vibrational spectra, molecular structure, NBO, UV, NMR, first order hyperpolarizability, analysis of 4-Methoxy-4'-Nitrobiphenyl by density functional theory.

    PubMed

    Govindarasu, K; Kavitha, E

    2014-03-25

    In this study, geometrical optimization, spectroscopic analysis, electronic structure and nuclear magnetic resonance studies of 4-Methoxy-4'-Nitrobiphenyl (abbreviated as 4M4'NBPL) were investigated by utilizing HF and DFT/B3LYP with 6-31G(d,p) as basis set. The equilibrium geometry, vibrational wavenumbers and the first order hyperpolarizability of the 4M4'NBPL have been calculated with the help of density functional theory computations. The FT-IR and FT-Raman spectra were recorded in the region 4000-400 cm(-1) and 3500-50 cm(-1) respectively. Natural Bond Orbital (NBO) analysis is also used to explain the molecular stability. The UV-Vis absorption spectra of the title compound dissolved in chloroform were recorded in the range of 200-800 cm(-1). The HOMO-LUMO energy gap explains the charge interaction taking place within the molecule. Good correlation between the experimental (1)H and (13)C NMR chemical shifts in chloroform solution and calculated GIAO shielding tensors were found. The dipole moment, linear polarizability and first order hyperpolarizability values were also computed. The linear polarizability and first order hyperpolarizability of the studied molecule indicate that the compound is a good candidate of nonlinear optical materials. The chemical reactivity and thermodynamic properties of 4M4'NBPL at different temperature are calculated. In addition, molecular electrostatic potential (MEP), frontier molecular orbitals (FMO) analysis were investigated using theoretical calculations.

  6. Relativistic force field: parametric computations of proton-proton coupling constants in (1)H NMR spectra.

    PubMed

    Kutateladze, Andrei G; Mukhina, Olga A

    2014-09-01

    Spin-spin coupling constants in (1)H NMR carry a wealth of structural information and offer a powerful tool for deciphering molecular structures. However, accurate ab initio or DFT calculations of spin-spin coupling constants have been very challenging and expensive. Scaling of (easy) Fermi contacts, fc, especially in the context of recent findings by Bally and Rablen (Bally, T.; Rablen, P. R. J. Org. Chem. 2011, 76, 4818), offers a framework for achieving practical evaluation of spin-spin coupling constants. We report a faster and more precise parametrization approach utilizing a new basis set for hydrogen atoms optimized in conjunction with (i) inexpensive B3LYP/6-31G(d) molecular geometries, (ii) inexpensive 4-31G basis set for carbon atoms in fc calculations, and (iii) individual parametrization for different atom types/hybridizations, not unlike a force field in molecular mechanics, but designed for the fc's. With the training set of 608 experimental constants we achieved rmsd <0.19 Hz. The methodology performs very well as we illustrate with a set of complex organic natural products, including strychnine (rmsd 0.19 Hz), morphine (rmsd 0.24 Hz), etc. This precision is achieved with much shorter computational times: accurate spin-spin coupling constants for the two conformers of strychnine were computed in parallel on two 16-core nodes of a Linux cluster within 10 min.

  7. Relativistic force field: parametric computations of proton-proton coupling constants in (1)H NMR spectra.

    PubMed

    Kutateladze, Andrei G; Mukhina, Olga A

    2014-09-01

    Spin-spin coupling constants in (1)H NMR carry a wealth of structural information and offer a powerful tool for deciphering molecular structures. However, accurate ab initio or DFT calculations of spin-spin coupling constants have been very challenging and expensive. Scaling of (easy) Fermi contacts, fc, especially in the context of recent findings by Bally and Rablen (Bally, T.; Rablen, P. R. J. Org. Chem. 2011, 76, 4818), offers a framework for achieving practical evaluation of spin-spin coupling constants. We report a faster and more precise parametrization approach utilizing a new basis set for hydrogen atoms optimized in conjunction with (i) inexpensive B3LYP/6-31G(d) molecular geometries, (ii) inexpensive 4-31G basis set for carbon atoms in fc calculations, and (iii) individual parametrization for different atom types/hybridizations, not unlike a force field in molecular mechanics, but designed for the fc's. With the training set of 608 experimental constants we achieved rmsd <0.19 Hz. The methodology performs very well as we illustrate with a set of complex organic natural products, including strychnine (rmsd 0.19 Hz), morphine (rmsd 0.24 Hz), etc. This precision is achieved with much shorter computational times: accurate spin-spin coupling constants for the two conformers of strychnine were computed in parallel on two 16-core nodes of a Linux cluster within 10 min. PMID:25158224

  8. Towards high resolution ^1H NMR spectra of tannin colloidal aggregates

    NASA Astrophysics Data System (ADS)

    Mirabel, M.; Glories, Y.; Pianet, I.; Dufourc, E. J.

    1999-10-01

    The time dependent colloidal formation of tannins in hydro-alcoholic medium has been studied by 1H-NMR. Line broadening observed with time can be cancelled by making use of magic angle sample spinning (MASS) thus yielding sharp lines that allow structural studies. We used as an example catechin, a constitutive monomer of Bordeaux young red wine tannins. Chemical shift variations of polyphenol protons allow monitoring the time course of aggregation. La formation de tanins colloïdaux au cours du temps, en milieu hydroalcoolique, a été suivie par RMN-^1H. Un élargissement marqué des résonances est observé et peut être supprimé par la rotation de l'échantillon à l'angle magique ce qui ouvre tout un champ d'études structurales sur ces composés colloïdaux. L'exemple proposé est celui de la catéchine, monomère constitutif de tannins présents en grande quantité dans les vins rouges jeunes de Bordeaux. Des variations du déplacement chimique de certains protons polyphénoliques permettent de suivre l'évolution temporelle de l'agrégation.

  9. A specialized database manager for interpretation of NMR spectra of synthetic glucides: JPD

    NASA Astrophysics Data System (ADS)

    Czaplicki, J.; Ponthus, C.

    1998-02-01

    The current communication presents a program, written specifically to create and handle a specialized database, containing NMR spectral patterns of various monosaccharidic units. The program's database format is compatible with that of the Aurelia/Amix Bruker software package. The software facilitates the search for J patterns included in the database and their comparison with an experimental spectrum, in order to identify the components of the studied system, including the contaminants. Nous présentons ici un logiciel écrit spécifiquement pour créer et gérer une base de données spécialisées, contenant les motifs du couplage J des unités monosaccharidiques différentes. Le format de la base de données est compatible avec le format utilisé par le logiciel Aurelia/Amix de Bruker. Le logiciel facilite la recherche des motifs J inclus dans la base de données de leurs comparaisons avec un spectre expérimental, afin d'identifier les constituants de l'échantillon étudié, et ses éventuelles impuretés.

  10. Macroscopic orientation effects in broadline NMR-spectra of model membranes at high magnetic field strength: A method preventing such effects.

    PubMed

    Brumm, T; Möps, A; Dolainsky, C; Brückner, S; Bayerl, T M

    1992-04-01

    The partial orientation of multilamellar vesicles (MLV) in high magnetic fields has been studied and a method to prevent such effects is herewith proposed. The orientation effect was measured with (2)H-, (31)P-NMR and electron microscopy on MLVs of dipalmitoyl phosphatidylcholine with 30 mol% cholesterol. We present the first freeze-etch electron microscopy data obtained from MLV samples that were frozen directly in the NMR magnet at a field strength of 9.4 Tesla. These experiments clearly show that the MLVs adopt an ellipsoidal (but not a cylindrical) shape in the magnetic field. Best fit (31)P-NMR lineshape calculations assuming an ellipsoidal distribution of molecular director axes to the experimentally obtained spectra provide a quantitative measure of the average semiaxis ratio of the ellipsoidal MLVs and its change with temperature. The application of so-called spherical supported vesicles (SSV) is found to prevent any partial orientation effects so that undistorted NMR powder pattern of the bilayer can be measured independently of magnetic field strength and temperature.The usefulness of SSVs is further demonstrated by a direct comparison of spectral data such as (31)P-and (2)H-NMR lineshapes and relaxation times as well as (2)H-NMR dePaked spectra obtained for both model systems. These experiments show that spectral data obtained from partially oriented MLVs are not unambiguous to interpret, in particular, if an external parameter such as temperature is varied.

  11. 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.

  12. Gas-phase NMR spectra of cyclohexene are consistent with a barrier to ring inversion of less than 30 kJ mol -1

    NASA Astrophysics Data System (ADS)

    Suarez, Cristina; Tafazzoli, Mohsen; True, Nancy S.

    1992-08-01

    1H NMR spectra of gaseous cyclohexene at 7.05 T and 195 K do not show line broadening attributable to axial-equatorial proton exchange, indicating that the Gibbs energy of activation, Δ G‡, is less than 30 kJ mol -1, considerably lower than the 43 kJ mol -1 barrier recently determined from a vibrational analysis.

  13. Quantitative analysis of ³¹P NMR spectra of soil extracts--dealing with overlap of broad and sharp signals.

    PubMed

    Doolette, Ashlea L; Smernik, Ronald J

    2015-09-01

    Solution (31)P NMR analysis following extraction with a mixture of sodium hydroxide and ethylenediaminetetraacetic acid is the most widely used method for detailed characterization of soil organic P. However, quantitative analysis of the (31)P NMR spectra is complicated by severe spectral overlap in the monoester region. Various deconvolution procedures have been developed for the task, yet none of these are widely accepted or implemented. In this mini-review, we first describe and compare these varying approaches. We then review approaches to similar issues of spectral overlap in biomedical science applications including NMR-based metabolic profiling and analyzing (31)P magnetic resonance spectra of ex vivo and in vivo intact tissues. The greater maturity and resourcing of this biomedical research means that a wider variety of approaches has been developed. Of particular relevance are approaches to dealing with overlap of broad and sharp signals. Although the existence of this problem is still debated in the context of soil analyses, not only is it well-recognized in biomedical applications, but multiple approaches have been developed to deal with it, including T2 editing and time-domain fitting. Perhaps the most transferable concept is the incorporation of 'prior knowledge' in the fitting of spectra. This is well established in biomedical applications but barely touched in soil analyses. We argue that shortcuts to dealing with overlap in the monoester region (31)P NMR soil spectra are likely to be found in the biomedical literature, although some degree of adaptation will be necessary. PMID:25854619

  14. Quantitative analysis of ³¹P NMR spectra of soil extracts--dealing with overlap of broad and sharp signals.

    PubMed

    Doolette, Ashlea L; Smernik, Ronald J

    2015-09-01

    Solution (31)P NMR analysis following extraction with a mixture of sodium hydroxide and ethylenediaminetetraacetic acid is the most widely used method for detailed characterization of soil organic P. However, quantitative analysis of the (31)P NMR spectra is complicated by severe spectral overlap in the monoester region. Various deconvolution procedures have been developed for the task, yet none of these are widely accepted or implemented. In this mini-review, we first describe and compare these varying approaches. We then review approaches to similar issues of spectral overlap in biomedical science applications including NMR-based metabolic profiling and analyzing (31)P magnetic resonance spectra of ex vivo and in vivo intact tissues. The greater maturity and resourcing of this biomedical research means that a wider variety of approaches has been developed. Of particular relevance are approaches to dealing with overlap of broad and sharp signals. Although the existence of this problem is still debated in the context of soil analyses, not only is it well-recognized in biomedical applications, but multiple approaches have been developed to deal with it, including T2 editing and time-domain fitting. Perhaps the most transferable concept is the incorporation of 'prior knowledge' in the fitting of spectra. This is well established in biomedical applications but barely touched in soil analyses. We argue that shortcuts to dealing with overlap in the monoester region (31)P NMR soil spectra are likely to be found in the biomedical literature, although some degree of adaptation will be necessary.

  15. A Discovery-Based Hydrochlorination of Carvone Utilizing a Guided-Inquiry Approach to Determine the Product Structure from [superscript 13]C NMR Spectra

    ERIC Educational Resources Information Center

    Pelter, Michael W.; Walker, Natalie M.

    2012-01-01

    This experiment describes a discovery-based method for the regio- and stereoselective hydrochlorination of carvone, appropriate for a 3-h second-semester organic chemistry laboratory. The product is identified through interpretation of the [superscript 13]C NMR and DEPT spectra are obtained on an Anasazi EFT-60 at 15 MHz as neat samples. A…

  16. A General Method for Extracting Individual Coupling Constants from Crowded (1)H NMR Spectra.

    PubMed

    Sinnaeve, Davy; Foroozandeh, Mohammadali; Nilsson, Mathias; Morris, Gareth A

    2016-01-18

    Couplings between protons, whether scalar or dipolar, provide a wealth of structural information. Unfortunately, the high number of (1)H-(1)H couplings gives rise to complex multiplets and severe overlap in crowded spectra, greatly complicating their measurement. Many different methods exist for disentangling couplings, but none approaches optimum resolution. Here, we present a general new 2D J-resolved method, PSYCHEDELIC, in which all homonuclear couplings are suppressed in F2, and only the couplings to chosen spins appear, as simple doublets, in F1. This approaches the theoretical limit for resolving (1)H-(1)H couplings, with close to natural linewidths and with only chemical shifts in F2. With the same high sensitivity and spectral purity as the parent PSYCHE pure shift experiment, PSYCHEDELIC offers a robust method for chemists seeking to exploit couplings for structural, conformational, or stereochemical analyses.

  17. Communication: Permanent dipoles contribute to electric polarization in chiral NMR spectra

    SciTech Connect

    Buckingham, A. David

    2014-01-07

    Nuclear magnetic resonance spectroscopy is blind to chirality because the spectra of a molecule and its mirror image are identical unless the environment is chiral. However, precessing nuclear magnetic moments in chiral molecules in a strong magnetic field induce an electric polarization through the nuclear magnetic shielding polarizability. This effect is equal and opposite for a molecule and its mirror image but is small and has not yet been observed. It is shown that the permanent electric dipole moment of a chiral molecule is partially oriented through the antisymmetric part of the nuclear magnetic shielding tensor, causing the electric dipole to precess with the nuclear magnetic moment and producing a much larger temperature-dependent electric polarization with better prospects of detection.

  18. Communication: Permanent dipoles contribute to electric polarization in chiral NMR spectra

    NASA Astrophysics Data System (ADS)

    Buckingham, A. David

    2014-01-01

    Nuclear magnetic resonance spectroscopy is blind to chirality because the spectra of a molecule and its mirror image are identical unless the environment is chiral. However, precessing nuclear magnetic moments in chiral molecules in a strong magnetic field induce an electric polarization through the nuclear magnetic shielding polarizability. This effect is equal and opposite for a molecule and its mirror image but is small and has not yet been observed. It is shown that the permanent electric dipole moment of a chiral molecule is partially oriented through the antisymmetric part of the nuclear magnetic shielding tensor, causing the electric dipole to precess with the nuclear magnetic moment and producing a much larger temperature-dependent electric polarization with better prospects of detection.

  19. A General Method for Extracting Individual Coupling Constants from Crowded 1H NMR Spectra

    PubMed Central

    Foroozandeh, Mohammadali; Nilsson, Mathias; Morris, Gareth A.

    2015-01-01

    Abstract Couplings between protons, whether scalar or dipolar, provide a wealth of structural information. Unfortunately, the high number of 1H‐1H couplings gives rise to complex multiplets and severe overlap in crowded spectra, greatly complicating their measurement. Many different methods exist for disentangling couplings, but none approaches optimum resolution. Here, we present a general new 2D J‐resolved method, PSYCHEDELIC, in which all homonuclear couplings are suppressed in F 2, and only the couplings to chosen spins appear, as simple doublets, in F 1. This approaches the theoretical limit for resolving 1H‐1H couplings, with close to natural linewidths and with only chemical shifts in F 2. With the same high sensitivity and spectral purity as the parent PSYCHE pure shift experiment, PSYCHEDELIC offers a robust method for chemists seeking to exploit couplings for structural, conformational, or stereochemical analyses. PMID:26636773

  20. Resolution and measurement of heteronuclear dipolar couplings of a noncrystalline protein immobilized in a biological supramolecular assembly by proton-detected MAS solid-state NMR spectroscopy

    NASA Astrophysics Data System (ADS)

    Park, Sang Ho; Yang, Chen; Opella, Stanley J.; Mueller, Leonard J.

    2013-12-01

    Two-dimensional 15N chemical shift/1H chemical shift and three-dimensional 1H-15N dipolar coupling/15N chemical shift/1H chemical shift MAS solid-state NMR correlation spectra of the filamentous bacteriophage Pf1 major coat protein show single-site resolution in noncrystalline, intact-phage preparations. The high sensitivity and resolution result from 1H detection at 600 MHz under 50 kHz magic angle spinning using ∼0.5 mg of perdeuterated and uniformly 15N-labeled protein in which the exchangeable amide sites are partially or completely back-exchanged (reprotonated). Notably, the heteronuclear 1H-15N dipolar coupling frequency dimension is shown to select among 15N resonances, which will be useful in structural studies of larger proteins where the resonances exhibit a high degree of overlap in multidimensional chemical shift correlation spectra.

  1. X-ray and DFT studies of the structure, vibrational and NMR spectra of 2-amino-pyridine betaine hydrochloride

    NASA Astrophysics Data System (ADS)

    Szafran, M.; Kowalczyk, I.; Koput, J.; Katrusiak, A.

    2005-06-01

    The effect of hydrogen bonding, inter- and intramolecular electrostatic interactions on the conformation of 2-amino-pyridine betaine hydrochloride (1-carboxymethyl-2-amino-pyridinium chloride), 2-NH 2PBH⋯Cl(c), in the crystal and its isolated molecules has been studied by X-ray diffraction, FT-IR, Raman, 1H and 13C NMR spectroscopies, and by DFT calculations. In the crystal, the Cl - anion is connected with protonated betaine via hydrogen bond, O-H⋯Cl -= 2.975(2) Å, two N(12)-H⋯Cl - hydrogen bonds and two N(1) H⋯Cl - intermolecular electrostatic interactions. Two minima are located in the potential energy surface at the B3LYP/6-31G(d,p) level, 2-NH 2PBH⋯Cl(t) and 2-NH 2PB⋯HCl(c), with the latter being 20,7 kcal/mol higher in energy. The optimized bond lengths and angles of 2-NH 2PBH⋯Cl(t) at B3LYP level of theory are in good agreement with X-ray data, except for the conformation of the COOH group, which is cis ( syn) in the crystal and trans ( anti) in the single molecule. The probable assignments for the anharmonic experimental solid state vibrational spectra of 2-NH 2PBH⋯Cl(c) and 2-ND 2PBD⋯Cl(c) based on the calculated B3LYP/6-31G(d,p) harmonic frequencies have been made. 1H and 13C NMR screening constants for both single molecules have been calculated in the GIAO/B3LYP/6-31G(d,p) approach. Linear correlation between the calculated and experimental 1H chemical shifts holds only for cis conformer. The lack of such a correlation for trans conformer indicates that it is absent in D 2O solution.

  2. 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.

  3. Automated Quantification of Human Brain Metabolites by Artificial Neural Network Analysis from in VivoSingle-Voxel 1H NMR Spectra

    NASA Astrophysics Data System (ADS)

    Kaartinen, Jouni; Mierisová, Šarka; Oja, Joni M. E.; Usenius, Jukka-Pekka; Kauppinen, Risto A.; Hiltunen, Yrjö

    1998-09-01

    A real-time automated way of quantifying metabolites fromin vivoNMR spectra using an artificial neural network (ANN) analysis is presented. The spectral training and test sets for ANN containing peaks at the chemical shift ranges resembling long echo time proton NMR spectra from human brain were simulated. The performance of the ANN constructed was compared with an established lineshape fitting (LF) analysis using both simulated and experimental spectral data as inputs. The correspondence between the ANN and LF analyses showed correlation coefficients of order of 0.915-0.997 for spectra with large variations in both signal-to-noise and peak areas. Water suppressed1H NMR spectra from 24 healthy subjects were collected and choline-containing compounds (Cho), total creatine (Cr), and N-acetyl aspartate (NAA) were quantified with both methods. The ANN quantified these spectra with an accuracy similar to LF analysis (correlation coefficients of 0.915-0.951). These results show that LF and ANN are equally good quantifiers; however, the ANN analyses are more easily automated than LF analyses.

  4. Unusual effects in variable temperature powder NMR spectra of the methyl group protons in 9,10-dimethyltriptycene-d₁₂.

    PubMed

    Bernatowicz, P; Ratajczyk, T; Kalicki, P; Szymanski, S

    2014-01-01

    Variable temperature (1)H wide line NMR spectra of polycrystalline 9,10-dimethyltriptycene-d12 deuterated in the aromatic positions were studied. The spectra show different patterns in an unrepeatable dependence on the way of preparation of the powdered samples. Simultaneously, no anomalies were seen in the MAS and CPMAS proton-decoupled room-temperature (13)C spectra as well as in powder X-ray diffraction patterns. The effects observed in the (1)H spectra are tentatively explained in terms of a phenomenological model. For one of the examined samples it afforded a consistent interpretation of the entire series of temperature dependent spectra in terms of structural non uniformity of the solid material studied. Quantum character of the stochastic dynamics of the methyl groups in the investigated compound was confirmed, although these dynamics are close to the classical limit where the familiar random jump model applies. PMID:24656571

  5. MetaboID: a graphical user interface package for assignment of 1H NMR spectra of bodyfluids and tissues.

    PubMed

    MacKinnon, Neil; Somashekar, Bagganahalli S; Tripathi, Pratima; Ge, Wencheng; Rajendiran, Thekkelnaycke M; Chinnaiyan, Arul M; Ramamoorthy, Ayyalusamy

    2013-01-01

    Nuclear magnetic resonance based measurements of small molecule mixtures continues to be confronted with the challenge of spectral assignment. While multi-dimensional experiments are capable of addressing this challenge, the imposed time constraint becomes prohibitive, particularly with the large sample sets commonly encountered in metabolomic studies. Thus, one-dimensional spectral assignment is routinely performed, guided by two-dimensional experiments on a selected sample subset; however, a publicly available graphical interface for aiding in this process is currently unavailable. We have collected spectral information for 360 unique compounds from publicly available databases including chemical shift lists and authentic full resolution spectra, supplemented with spectral information for 25 compounds collected in-house at a proton NMR frequency of 900 MHz. This library serves as the basis for MetaboID, a Matlab-based user interface designed to aid in the one-dimensional spectral assignment process. The tools of MetaboID were built to guide resonance assignment in order of increasing confidence, starting from cursory compound searches based on chemical shift positions to analysis of authentic spike experiments. Together, these tools streamline the often repetitive task of spectral assignment. The overarching goal of the integrated toolbox of MetaboID is to centralize the one dimensional spectral assignment process, from providing access to large chemical shift libraries to providing a straightforward, intuitive means of spectral comparison. Such a toolbox is expected to be attractive to both experienced and new metabolomic researchers as well as general complex mixture analysts.

  6. The infrared, Raman, NMR and UV spectra, ab initio calculations and spectral assignments of 2-amino-4-chloro-6-methoxypyrimidine

    NASA Astrophysics Data System (ADS)

    Cinar, Z.; Karabacak, M.; Cinar, M.; Kurt, M.; Chinna babu, P.; Sundaraganesan, N.

    2013-12-01

    The 2-amino-4-chloro-6-methoxypyrimidine abbreviated as ACMP have been investigated by both the experimental and theoretical methods; through this work we provide the essential fact about the structural and vibrational insights. The optimized molecular structure, atomic charges, vibrational frequencies and ultraviolet spectral interpretation of ACMP have been studied by performing DFT/B3LYP/6-311++G(df,pd) level of theory. The FT-IR, FT-Raman spectra were recorded in the region 4000-400 cm-1 and 4000-50 cm-1 respectively. The UV absorption spectrum of the compound that dissolved in ethanol and water solution were recorded in the range of 200-400 nm. The scaled wavenumbers are compared with the experimental values. The difference between the observed and scaled wavenumber values of most of the fundamentals is very small. Based on the UV spectrum and TD-DFT calculations, the electronic structure and the assignments of the absorption bands were carried out. The 1H, 13C and DEPT 135 nuclear magnetic resonance (NMR) chemical shifts of the molecule were calculated using with the Gauge Including Atomic Orbital (GIAO) method and compared with experimental results. Besides, molecular electrostatic potential (MEP), frontier molecular orbitals (FMO) analysis were investigated using theoretical calculations.

  7. Study of molecular structure, vibrational, electronic and NMR spectra of oncocalyxone A using DFT and quantum chemical calculations

    NASA Astrophysics Data System (ADS)

    Joshi, Bhawani Datt; Srivastava, Anubha; Honorato, Sara Braga; Tandon, Poonam; Pessoa, Otília Deusdênia Loiola; Fechine, Pierre Basílio Almeida; Ayala, Alejandro Pedro

    2013-09-01

    Oncocalyxone A (C17H18O5) is the major secondary metabolite isolated from ethanol extract from the heartwood of Auxemma oncocalyx Taub popularly known as “pau branco”. Oncocalyxone A (Onco A) has many pharmaceutical uses such as: antitumor, analgesic, antioxidant and causative of inhibition of platelet activation. We have performed the optimized geometry, total energy, conformational study, molecular electrostatic potential mapping, frontier orbital energy gap and vibrational frequencies of Onco A employing ab initio Hartree-Fock (HF) and density functional theory (DFT/B3LYP) method with 6-311++G(d, p) basis set. Stability of the molecule arising from hyperconjugative interactions and/or charge delocalization has been analyzed using natural bond orbital (NBO) analysis. UV-vis spectrum of the compound was recorded in DMSO and MeOH solvent. The TD-DFT calculations have been performed to explore the influence of electronic absorption spectra in the gas phase, as well as in solution environment using IEF-PCM and 6-31G basis set. The 13C NMR chemical shifts have been calculated with the B3LYP/6-311++G(d, p) basis set and compared with the experimental values. These methods have been used as tools for structural characterization of Onco A.

  8. Direct measurements of protein backbone 15N spin relaxation rates from peak line-width using a fully-relaxed Accordion 3D HNCO experiment.

    PubMed

    Chen, Kang; Tjandra, Nico

    2009-03-01

    Protein backbone (15)N spin relaxation rates measured by solution NMR provide useful dynamic information with a site-specific resolution. The conventional method is to record a series of 2D (1)H-(15)N HSQC spectra with varied relaxation delays, and derive relaxation rate from the following curve fitting on the resonance intensities. Proteins with poorly resolved spectra often require several 3D HNCO spectra to be collected on a (15)N/(13)C double labeled protein sample. In order to reduce the relaxation dimension Carr et al. (P.A. Carr, D.A. Fearing, A.G. Palmer, 3D accordion spectroscopy for measuring N-15 and (CO)-Carbon-13 relaxation rates in poorly resolved NMR spectra, J. Magn. Reson. 132 (1998) 25-33) employed an Accordion type HNCO pulse sequence to obtain (15)N or (13)C T(1) relaxation rates by numerical fitting of the relaxation interfered free induction decay (FID) data. To avoid intensive analysis of the time domain data, we propose a modified protocol to measure (15)N T(1) and T(2) relaxation rates from easily obtained line-widths in an Accordion HNCO spectrum. Both T(1) and T(2) relaxation could be simultaneously convoluted into the constant-time evolution periods of (13)C' and (15)N, respectively. The relaxation delay was allowed to reach at least 3 x T(1) or 3 x T(2) so that the signal was substantially decayed by the end of the FID, and the resulting peak full-width at half height (FWHH) could be directly used to calculate relaxation rate. When applied to the 76-residue Ubiquitin and the 226-residue glutamine-binding protein (GlnBP), this method yielded T(1) and T(2) values deviating on average by 4-6% and 5-7%, respectively, from the measurements based on the conventional 2D method. In comparison, the conventional methods possessed intrinsic error ranges of 2-4% for T(1) and 3-6% for T(2). In addition to comparable accuracy, the fully-relaxed Accordion HNCO method presented here allowed measurements of relaxation rates for resonances unresolved in

  9. An approach to the simultaneous quantitative analysis of metabolites in table wines by (1)H NMR self-constructed three-dimensional spectra.

    PubMed

    Li, Bao Qiong; Xu, Min Li; Wang, Xue; Zhai, Hong Lin; Chen, Jing; Liu, Jin Jin

    2017-02-01

    Wine consists of several hundred components with different concentrations, including water, ethanol, glycerol, organic acids and sugars. Accurate quantification of target compounds in such complex samples is a difficult task based on conventional (1)H NMR spectra due to some challenges. In this paper, the three-dimensional spectrum was constructed firstly by simply repeating (1)H NMR spectrum itself so as to extract the features of target compounds by Tchebichef moment method. A proof-of-concept model system, the determination of five metabolites in wines was utilized to evaluate the performance of the proposed strategy. The results indicate that the proposed approach can provide accurate and reliable concentration predictions, probably the best results ever achieved using PLS and interval-PLS methods. Our novel strategy has not only good performance but also does not require laborious multi-step and subjective pretreatments. Therefore, it is expected that the proposed method could extend the application of conventional (1)H NMR. PMID:27596391

  10. Quantitative (13)C Solid-State NMR Spectra by Multiple-Contact Cross-polarization for Drug Delivery: From Active Principles to Excipients and Drug Carriers.

    PubMed

    Saïdi, Fadila; Taulelle, Francis; Martineau, Charlotte

    2016-08-01

    In this contribution, we present an analysis of the main parameters influencing the efficiency of the (1)H → (13)C multiple-contact cross-polarization nuclear magnetic resonance (NMR) experiment in the context of solid pharmaceutical materials. Using the optimum experimental conditions, quantitative (13)C NMR spectra are then obtained for porous metal-organic frameworks (potential drug carriers) and for components present in drug formulations (active principle ingredient and excipients, amorphous or crystalline). Finally, we show that mixtures of components can also be quantified with this method and, hence, that it represents an ideal tool for quantification of pharmaceutical formulations by (13)C cross-polarization under magic-angle spinning NMR in the industry as it is robust and easy to set up, much faster than direct (13)C polarization and is efficient for samples at natural abundance. PMID:27372550

  11. Evaluation of the reliability of the maximum entropy method for reconstructing 3D and 4D NOESY-type NMR spectra of proteins.

    PubMed

    Shigemitsu, Yoshiki; Ikeya, Teppei; Yamamoto, Akihiro; Tsuchie, Yuusuke; Mishima, Masaki; Smith, Brian O; Güntert, Peter; Ito, Yutaka

    2015-02-01

    Despite their advantages in analysis, 4D NMR experiments are still infrequently used as a routine tool in protein NMR projects due to the long duration of the measurement and limited digital resolution. Recently, new acquisition techniques for speeding up multidimensional NMR experiments, such as nonlinear sampling, in combination with non-Fourier transform data processing methods have been proposed to be beneficial for 4D NMR experiments. Maximum entropy (MaxEnt) methods have been utilised for reconstructing nonlinearly sampled multi-dimensional NMR data. However, the artefacts arising from MaxEnt processing, particularly, in NOESY spectra have not yet been clearly assessed in comparison with other methods, such as quantitative maximum entropy, multidimensional decomposition, and compressed sensing. We compared MaxEnt with other methods in reconstructing 3D NOESY data acquired with variously reduced sparse sampling schedules and found that MaxEnt is robust, quick and competitive with other methods. Next, nonlinear sampling and MaxEnt processing were applied to 4D NOESY experiments, and the effect of the artefacts of MaxEnt was evaluated by calculating 3D structures from the NOE-derived distance restraints. Our results demonstrated that sufficiently converged and accurate structures (RMSD of 0.91Å to the mean and 1.36Å to the reference structures) were obtained even with NOESY spectra reconstructed from 1.6% randomly selected sampling points for indirect dimensions. This suggests that 3D MaxEnt processing in combination with nonlinear sampling schedules is still a useful and advantageous option for rapid acquisition of high-resolution 4D NOESY spectra of proteins.

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

    NASA Astrophysics Data System (ADS)

    Badawi, Hassan M.; Khan, Ibrahim

    2016-08-01

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

  13. Systematic Comparison of Sets of 13C NMR Spectra That Are Potentially Identical. Confirmation of the Configuration of a Cuticular Hydrocarbon from the Cane Beetle Antitrogus parvulus

    PubMed Central

    2015-01-01

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

  14. Cellobiose as a model system to reveal cellulose dissolution mechanism in acetate-based ionic liquids: Density functional theory study substantiated by NMR spectra.

    PubMed

    Cao, Bobo; Du, Jiuyao; Du, Dongmei; Sun, Haitao; Zhu, Xiao; Fu, Hui

    2016-09-20

    Cellulose dissolution mechanism in acetate-based ionic liquids was systematically studied in Nuclear Magnetic Resonance (NMR) spectra and Density Functional Theory (DFT) methods by using cellobiose and 1-butyl-3-methylimidazolium acetate (BmimAc) as a model system. The solubility of cellulose in ionic liquid increased with temperature increase in the range of 90-140°C. NMR spectra suggested OAc(-) preferred to form stronger hydrogen bonds with hydrogen of hydroxyl in cellulose. Electrostatic potential method was employed to predict the most possible reaction sites and locate the most stable configuration. Atoms in molecules (AIM) theory was used to study the features of bonds at bond critical points and the variations of bond types. Simultaneously, noncovalent interactions were characterized and visualized by employing reduced density gradient analysis combined with Visual Molecular Dynamics (VMD) program. Natural bond orbital (NBO) theory was applied to study the noncovalent nature and characterize the orbital interactions between cellobiose and Bmim[OAc]. PMID:27261759

  15. Cellobiose as a model system to reveal cellulose dissolution mechanism in acetate-based ionic liquids: Density functional theory study substantiated by NMR spectra.

    PubMed

    Cao, Bobo; Du, Jiuyao; Du, Dongmei; Sun, Haitao; Zhu, Xiao; Fu, Hui

    2016-09-20

    Cellulose dissolution mechanism in acetate-based ionic liquids was systematically studied in Nuclear Magnetic Resonance (NMR) spectra and Density Functional Theory (DFT) methods by using cellobiose and 1-butyl-3-methylimidazolium acetate (BmimAc) as a model system. The solubility of cellulose in ionic liquid increased with temperature increase in the range of 90-140°C. NMR spectra suggested OAc(-) preferred to form stronger hydrogen bonds with hydrogen of hydroxyl in cellulose. Electrostatic potential method was employed to predict the most possible reaction sites and locate the most stable configuration. Atoms in molecules (AIM) theory was used to study the features of bonds at bond critical points and the variations of bond types. Simultaneously, noncovalent interactions were characterized and visualized by employing reduced density gradient analysis combined with Visual Molecular Dynamics (VMD) program. Natural bond orbital (NBO) theory was applied to study the noncovalent nature and characterize the orbital interactions between cellobiose and Bmim[OAc].

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

    PubMed

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

    2006-12-01

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

  17. A Simple Approach for Obtaining High Resolution, High Sensitivity ¹H NMR Metabolite Spectra of Biofluids with Limited Mass Supply

    SciTech Connect

    Hu, Jian Zhi; Rommereim, Donald N.; Wind, Robert A.; Minard, Kevin R.; Sears, Jesse A.

    2006-11-01

    A simple approach is reported that yields high resolution, high sensitivity ¹H NMR spectra of biofluids with limited mass supply. This is achieved by spinning a capillary sample tube containing a biofluid at the magic angle at a frequency of about 80Hz. A 2D pulse sequence called ¹H PASS is then used to produce a high-resolution ¹H NMR spectrum that is free from magnetic susceptibility induced line broadening. With this new approach a high resolution ¹H NMR spectrum of biofluids with a volume less than 1.0 µl can be easily achieved at a magnetic field strength as low as 7.05T. Furthermore, the methodology facilitates easy sample handling, i.e., the samples can be directly collected into inexpensive and disposable capillary tubes at the site of collection and subsequently used for NMR measurements. In addition, slow magic angle spinning improves magnetic field shimming and is especially suitable for high throughput investigations. In this paper first results are shown obtained in a magnetic field of 7.05T on urine samples collected from mice using a modified commercial NMR probe.

  18. Synthesis and NMR Spectral Analysis of Amine Heterocycles: The Effect of Asymmetry on the [superscript 1]H and [superscript 13]C NMR Spectra of N,O-Acetals

    ERIC Educational Resources Information Center

    Saba, Shahrokh; Ciaccio, James A.; Espinal, Jennifer; Aman, Courtney E.

    2007-01-01

    The stereochemical investigation is conducted to give students the combined experience of chemical synthesis of amines and N-heterocycles and structural stereochemical analysis using NMR spectroscopy. Students are introduced to the concept of topicity-stereochemical relationships between ligands within a molecule by synthesizing N,O-acetals.

  19. Measurement of multiple psi torsion angles in uniformly 13C,15N-labeled alpha-spectrin SH3 domain using 3D 15N-13C-13C-15N MAS dipolar-chemical shift correlation spectroscopy.

    PubMed

    Ladizhansky, Vladimir; Jaroniec, Christopher P; Diehl, Annette; Oschkinat, Hartmut; Griffin, Robert G

    2003-06-01

    We demonstrate the simultaneous measurement of several backbone torsion angles psi in the uniformly (13)C,(15)N-labeled alpha-Spectrin SH3 domain using two different 3D 15N-13C-13C-15N dipolar-chemical shift magic-angle spinning (MAS) NMR experiments. The first NCCN experiment utilizes double quantum (DQ) spectroscopy combined with the INADEQUATE type 13C-13C chemical shift correlation. The decay of the DQ coherences formed between 13C'(i) and 13C(alphai) spin pairs is determined by the "correlated" dipolar field due to 15N(i)-13C(alphai) and 13C'(i)-15N(i+1) dipolar couplings and is particularly sensitive to variations of the torsion angle in the regime |psi| > 140 degrees. However, the ability of this experiment to constrain multiple psi-torsion angles is limited by the resolution of the 13C(alpha)-(13)CO correlation spectrum. This problem is partially addressed in the second approach described here, which is an NCOCA NCCN experiment. In this case the resolution is enhanced by the superior spectral dispersion of the 15N resonances present in the 15N(i+1)-13C(alphai) part of the NCOCA chemical shift correlation spectrum. For the case of the 62-residue alpha-spectrin SH3 domain, we determined 13 psi angle constraints with the INADEQUATE NCCN experiment and 22 psi constraints were measured in the NCOCA NCCN experiment.

  20. Proton-decoupled CPMG: a better experiment for measuring (15)N R2 relaxation in disordered proteins.

    PubMed

    Yuwen, Tairan; Skrynnikov, Nikolai R

    2014-04-01

    (15)N R2 relaxation is one of the most informative experiments for characterization of intrinsically disordered proteins (IDPs). Small changes in nitrogen R2 rates are often used to determine how IDPs respond to various biologically relevant perturbations such as point mutations, posttranslational modifications and weak ligand interactions. However collecting high-quality (15)N relaxation data can be difficult. Of necessity, the samples of IDPs are often prepared with low protein concentration and the measurement time can be limited because of rapid sample degradation. Furthermore, due to hardware limitations standard experiments such as (15)N spin-lock and CPMG can sample the relaxation decay only to ca. 150ms. This is much shorter than (15)N T2 times in disordered proteins at or near physiological temperature. As a result, the sampling of relaxation decay profiles in these experiments is suboptimal, which further lowers the precision of the measurements. Here we report a new implementation of the proton-decoupled (PD) CPMG experiment which allows one to sample (15)N R2 relaxation decay up to ca. 0.5-1s. The new experiment has been validated through comparison with the well-established spin-lock measurement. Using dilute samples of denatured ubiquitin, we have demonstrated that PD-CPMG produces up to 3-fold improvement in the precision of the data. It is expected that for intrinsically disordered proteins the gains may be even more substantial. We have also shown that this sequence has a number of favorable properties: (i) the spectra are recorded with narrow linewidth in nitrogen dimension; (ii) (15)N offset correction is small and easy to calculate; (iii) the experiment is immune to various spurious effects arising from solvent exchange; (iv) the results are stable with respect to pulse miscalibration and rf field inhomogeneity; (v) with minimal change, the pulse sequence can also be used to measure R2 relaxation of (15)N(ε) spins in arginine side chains. We

  1. hnCOcaNH and hncoCANH pulse sequences for rapid and unambiguous backbone assignment in (13C, 15N) labeled proteins.

    PubMed

    Kumar, Dinesh; Reddy, Jithender G; Hosur, Ramakrishna V

    2010-09-01

    Time-saving in data acquisition is a major thrust of NMR pulse sequence development in the context of structural proteomics research. The conventional HNCA and HN(CA)CO pulse sequences, routinely used for sequential backbone assignment, have the limitation that they cannot distinguish inter- and intra-residue correlations. In order to remove this ambiguity, one has to record HNCO and HN(CO)CA or sequential HNCA experiments which provide unambiguous information of sequential correlations. However, this almost doubles the experimental time. Besides, they require repeated scanning through the (15)N planes to search for the matching peaks along the carbon dimension. In this background, we present here two pulse sequences, termed as hncoCANH and hnCOcaNH that lead to spectra equivalent to HNCA and HN(CA)CO spectra, respectively, but with direct distinction of inter- and intra-residue peaks; these occur with opposite signs in the new experiments. The two pulse sequences have been derived by simple modification of the previously described HN(C)N pulse sequence [Panchal et al., J. Biomol. NMR 20 (2001) 135-147] to frequency-label (13)C(alpha) or (13)C' instead of (15)N during the t(1) period. Like HN(C)N, these spectra also exhibit special patterns of self and sequential peaks around glycines and prolines, which enable direct identification of certain triplets of residues and thus provide internal checks during the sequential assignment walk. The spectra enable rapid and unambiguous assignment of H(N), (15)N and (13)C(alpha) (or (13)C') in a single experiment, and thus would be of great value in high-throughput structural proteomics. PMID:20643567

  2. Mammalian production of an isotopically enriched outer domain of the HIV-1 gp120 glycoprotein for NMR spectroscopy.

    PubMed

    Sastry, Mallika; Xu, Ling; Georgiev, Ivelin S; Bewley, Carole A; Nabel, Gary J; Kwong, Peter D

    2011-07-01

    NMR spectroscopic characterization of the structure or the dynamics of proteins generally requires the production of samples isotopically enriched in (15)N, (13)C, or (2)H. The bacterial expression systems currently in use to obtain isotopic enrichment, however, cannot produce a number of eukaryotic proteins, especially those that require post-translational modifications such as N-linked glycosylation for proper folding or activity. Here, we report the use of an adenovirus vector-based mammalian expression system to produce isotopically enriched (15)N or (15)N/(13)C samples of an outer domain variant of the HIV-1 gp120 envelope glycoprotein with 15 sites of N-linked glycosylation. Yields for the (15)N- and (15)N/(13)C-labeled gp120s after affinity chromatography were 45 and 44 mg/l, respectively, with an average of over 80% isotope incorporation. Recognition of the labeled gp120 by cognate antibodies that recognize complex epitopes showed affinities comparable to the unlabeled protein. NMR spectra, including (1)H-(15)N and (1)H-(13)C HSQCs, (15)N-edited NOESY-HSQC, and 3D HNCO, were of high quality, with signal-to-noise consistent with an efficient level of isotope incorporation, and with chemical shift dispersion indicative of a well-folded protein. The exceptional protein yields, good isotope incorporation, and ability to obtain well-folded post-translationally modified proteins make this mammalian system attractive for the production of isotopically enriched eukaryotic proteins for NMR spectroscopy.

  3. 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.

  4. Noninvasive Recognition and Biomarkers of Early Allergic Asthma in Cats Using Multivariate Statistical Analysis of NMR Spectra of Exhaled Breath Condensate

    PubMed Central

    Fulcher, Yan G.; Fotso, Martial; Chang, Chee-Hoon; Rindt, Hans; Reinero, Carol R.

    2016-01-01

    Asthma is prevalent in children and cats, and needs means of noninvasive diagnosis. We sought to distinguish noninvasively the differences in 53 cats before and soon after induction of allergic asthma, using NMR spectra of exhaled breath condensate (EBC). Statistical pattern recognition was improved considerably by preprocessing the spectra with probabilistic quotient normalization and glog transformation. Classification of the 106 preprocessed spectra by principal component analysis and partial least squares with discriminant analysis (PLS-DA) appears to be impaired by variances unrelated to eosinophilic asthma. By filtering out confounding variances, orthogonal signal correction (OSC) PLS-DA greatly improved the separation of the healthy and early asthmatic states, attaining 94% specificity and 94% sensitivity in predictions. OSC enhancement of multi-level PLS-DA boosted the specificity of the prediction to 100%. OSC-PLS-DA of the normalized spectra suggest the most promising biomarkers of allergic asthma in cats to include increased acetone, metabolite(s) with overlapped NMR peaks near 5.8 ppm, and a hydroxyphenyl-containing metabolite, as well as decreased phthalate. Acetone is elevated in the EBC of 74% of the cats with early asthma. The noninvasive detection of early experimental asthma, biomarkers in EBC, and metabolic perturbation invite further investigation of the diagnostic potential in humans. PMID:27764146

  5. Deuterium isotope effects on 13C and 15N chemical shifts of intramolecularly hydrogen-bonded enaminocarbonyl derivatives of Meldrum’s and Tetronic acid

    NASA Astrophysics Data System (ADS)

    Ullah, Saif; Zhang, Wei; Hansen, Poul Erik

    2010-07-01

    Secondary deuterium isotope effects on 13C and 15N nuclear shieldings in a series of cyclic enamino-diesters and enamino-esters and acyclic enaminones and enamino-esters have been examined and analysed using NMR and DFT (B3LYP/6-31G(d,p)) methods. One-dimensional and two-dimensional NMR spectra of enaminocarbonyl and their deuterated analogues were recorded in CDCl 3 and CD 2Cl 2 at variable temperatures and assigned. 1JNH coupling constants for the derivatives of Meldrum's and tetronic acids reveal that they exist at the NH-form. It was demonstrated that deuterium isotope effects, for the hydrogen bonded compounds, due to the deuterium substitution at the nitrogen nucleus lead to large one-bond isotope effects at nitrogen, 1Δ 15N(D), and two-bond isotope effects on carbon nuclei, 2ΔC(ND), respectively. A linear correlations exist between 2ΔC(ND) and 1Δ 15N(D) whereas the correlation with δNH is divided into two. A good agreement between the experimentally observed 2ΔC(ND) and calculated dσ 13C/dR NH was obtained. A very good correlation between calculated NH bond lengths and observed NH chemical shifts is found. The observed isotope effects are shown to depend strongly on Resonance Assisted Hydrogen bonding.

  6. Conformational and isomerizational studies of 3- N, N-dimethylhydrazino-2-methylsulfonyl propenenitrile using NMR and vibrational spectra, X-ray analysis and ab initio calculations

    NASA Astrophysics Data System (ADS)

    Gróf, M.; Gatial, A.; Milata, V.; Prónayová, N.; Kožíšek, J.; Breza, M.; Matějka, P.

    2008-11-01

    The IR, Raman and NMR spectra of 3- N, N-dimethylhydrazino-2-methylsulfonyl propenenitrile (DMHSP) [(H 3C) 2N sbnd NH sbnd CH dbnd C(CN) (SO 2CH 3)] as a solid and in different solvents were measured. The spectra and X-ray analysis revealed that DMHSP was prepared as a pure E-isomer and E- syn conformer with the syn orientation of N, N-dimethylhydrazino group towards the C dbnd C double bond in the solid state. Due to the low barrier practically free isomerization process occurred in solutions at room temperature. DMHSP exists in more polar solvents as pure E-isomer in conformational equilibrium between E- syn and E- anti but in a less polar solvent the presence of Z-isomer was observed as well. From the IR and NMR temperature dependence spectra in polar solvents the energy difference between E- anti and E- syn of Δ H = 2.3 ± 0.9 kJ/mol and Δ H = 3.2 ± 0.4 kJ/mol, respectively, was estimated with the syn one being more stable. The geometries and relative energies of possible conformers of DMHSP were evaluated using ab initio MP2 and B3LYP density functional methods in 6-31G ∗∗ basis set and compared with the X-ray data. The interpretation of NMR spectra was supported by ab initio MP2 calculations. The influence of solvent polarity on the conformational equilibrium is discussed with respect to the SCRF solvent effect calculations using PCM model. In addition, the observed IR and Raman bands were compared also with harmonic vibrational frequencies, calculated on the same levels of theory, and assigned on the base of potential energy distribution.

  7. Separation of small metabolites and lipids in spectra from biopsies by diffusion-weighted HR-MAS NMR: a feasibility study.

    PubMed

    Diserens, G; Vermathen, M; Precht, C; Broskey, N T; Boesch, C; Amati, F; Dufour, J-F; Vermathen, P

    2015-01-01

    High Resolution Magic Angle Spinning (HR-MAS) NMR allows metabolic characterization of biopsies. HR-MAS spectra from tissues of most organs show strong lipid contributions that are overlapping metabolite regions, which hamper metabolite estimation. Metabolite quantification and analysis would benefit from a separation of lipids and small metabolites. Generally, a relaxation filter is used to reduce lipid contributions. However, the strong relaxation filter required to eliminate most of the lipids also reduces the signals for small metabolites. The aim of our study was therefore to investigate different diffusion editing techniques in order to employ diffusion differences for separating lipid and small metabolite contributions in the spectra from different organs for unbiased metabonomic analysis. Thus, 1D and 2D diffusion measurements were performed, and pure lipid spectra that were obtained at strong diffusion weighting (DW) were subtracted from those obtained at low DW, which include both small metabolites and lipids. This subtraction yielded almost lipid free small metabolite spectra from muscle tissue. Further improved separation was obtained by combining a 1D diffusion sequence with a T2-filter, with the subtraction method eliminating residual lipids from the spectra. Similar results obtained for biopsies of different organs suggest that this method is applicable in various tissue types. The elimination of lipids from HR-MAS spectra and the resulting less biased assessment of small metabolites have potential to remove ambiguities in the interpretation of metabonomic results. This is demonstrated in a reproducibility study on biopsies from human muscle.

  8. Molecular structure, vibrational spectra, HOMO, LUMO and NMR studies of 2,3,4,5,6-penta bromo toluene and bromo durene based on density functional calculations.

    PubMed

    Krishna Kumar, V; Suganya, S; Mathammal, R

    2014-05-01

    This work deals with the vibrational spectra of 2,3,4,5,6-Penta Bromo Toluene (PBT) and Bromo Durene (BD) by quantum chemical calculations. The solid phase FTIR and FT-Raman spectra of the title compounds were recorded in the regions 4000-400 cm(-1) and 4000-50 cm(-1), respectively. The spectra were interpreted with the aid of normal coordinate analysis based on density functional theory (DFT) using B3LYP/6-31G* level and basis set combinations and was scaled using various scale factors yielding a good agreement between observed and calculated frequencies. The infrared and Raman spectra were also predicted from the calculated intensities. Comparison of the simulated spectra with the experimental spectra provides important information about the ability of the computational method to describe the vibrational modes. The HOMO and LUMO energies were calculated within the molecule. (13)C and (1)H NMR chemical shifts results were also calculated and compared with the experimental values. Thermodynamical properties like entropy heat capacity, zero point energy have been calculated for the title molecules.

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

    NASA Astrophysics Data System (ADS)

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

    2015-05-01

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

  10. Exploring Chromophore-Binding Pocket: High-Resolution Solid-State H-C Interfacial Correlation NMR Spectra with Windowed PMLG Scheme.

    PubMed

    Song, Chen; Lang, Christina; Mailliet, Jo; Hughes, Jon; Gärtner, Wolfgang; Matysik, Jörg

    2012-02-01

    High-resolution two-dimensional (2D) (1)H-(13)C heteronuclear correlation spectra are recorded for selective observation of interfacial 3-5.5 Å contacts of the uniformly (13)C-labeled phycocyanobilin (PCB) chromophore with its unlabeled binding pocket. The experiment is based on a medium- and long-distance heteronuclear correlation (MELODI-HETCOR) method. For improving (1)H spectral resolution, a windowed phase-modulated Lee-Goldburg (wPMLG) decoupling scheme is applied during the t(1) evolution period. Our approach allows for identification of chromophore-protein interactions, in particular for elucidation of the hydrogen-bonding networks and charge distributions within the chromophore-binding pocket. The resulting pulse sequence is tested on the cyanobacterial (Cph1) phytochrome sensory module (residues 1-514, Cph1Δ2) containing uniformly (13)C- and (15)N-labeled PCB chromophore (u-[(13)C,(15)N]-PCB-Cph1Δ2) at 17.6 T. PMID:22303079

  11. N-15 NMR spectra of naturally abundant nitrogen in soil and aquatic natural organic matter samples of the International Humic Substances Society

    SciTech Connect

    Thorn, Kevin A.; Cox, Larry G.

    2009-02-28

    The naturally abundant nitrogen in soil and aquatic NOM samples from the International Humic Substances Society has been characterized by solid state CP/MAS ¹⁵N NMR. Soil samples include humic and fulvic acids from the Elliot soil, Minnesota Waskish peat and Florida Pahokee peat, as well as the Summit Hill soil humic acid and the Leonardite humic acid. Aquatic samples include Suwannee River humic, fulvic and reverse osmosis isolates, Nordic humic and fulvic acids and Pony Lake fulvic acid. Additionally, Nordic and Suwannee River XAD-4 acids and Suwannee River hydrophobic neutral fractions were analyzed. Similar to literature reports, amide/aminoquinone nitrogens comprised the major peaks in the solid state spectra of the soil humic and fulvic acids, along with heterocyclic and amino sugar/terminal amino acid nitrogens. Spectra of aquatic samples, including the XAD-4 acids, contain resolved heterocyclic nitrogen peaks in addition to the amide nitrogens. The spectrum of the nitrogen enriched, microbially derived Pony Lake, Antarctica fulvic acid, appeared to contain resonances in the region of pyrazine, imine and/or pyridine nitrogens, which have not been observed previously in soil or aquatic humic substances by ¹⁵N NMR. Liquid state ¹⁵N NMR experiments were also recorded on the Elliot soil humic acid and Pony Lake fulvic acid, both to examine the feasibility of the techniques, and to determine whether improvements in resolution over the solid state could be realized. For both samples, polarization transfer (DEPT) and indirect detection (¹H–¹⁵N gHSQC) spectra revealed greater resolution among nitrogens directly bonded to protons. The amide/aminoquinone nitrogens could also be observed by direct detection experiments.

  12. Toward an in Vivo Neurochemical Profile: Quantification of 18 Metabolites in Short-Echo-Time 1H NMR Spectra of the Rat Brain

    NASA Astrophysics Data System (ADS)

    Pfeuffer, Josef; Tkáč , Ivan; Provencher, Stephen W.; Gruetter, Rolf

    1999-11-01

    Localized in vivo1H NMR spectroscopy was performed with 2-ms echo time in the rat brain at 9.4 T. Frequency domain analysis with LCModel showed that the in vivo spectra can be explained by 18 metabolite model solution spectra and a highly structured background, which was attributed to resonances with fivefold shorter in vivo T1 than metabolites. The high spectral resolution (full width at half maximum approximately 0.025 ppm) and sensitivity (signal-to-noise ratio approximately 45 from a 63-μL volume, 512 scans) was used for the simultaneous measurement of the concentrations of metabolites previously difficult to quantify in 1H spectra. The strongly represented signals of N-acetylaspartate, glutamate, taurine, myo-inositol, creatine, phosphocreatine, glutamine, and lactate were quantified with Cramér-Rao lower bounds below 4%. Choline groups, phosphorylethanolamine, glucose, glutathione, γ-aminobutyric acid, N-acetylaspartylglutamate, and alanine were below 13%, whereas aspartate and scyllo-inositol were below 22%. Intra-assay variation was assessed from a time series of 3-min spectra, and the coefficient of variation was similar to the calculated Cramér-Rao lower bounds. Interassay variation was determined from 31 pooled spectra, and the coefficient of variation for total creatine was 7%. Tissue concentrations were found to be in very good agreement with neurochemical data from the literature.

  13. Experimental and theoretical investigation of the molecular structure, conformational stability, hyperpolarizability, electrostatic potential, thermodynamic properties and NMR spectra of pharmaceutical important molecule: 4'-methylpropiophenone.

    PubMed

    Karunakaran, V; Balachandran, V

    2014-07-15

    Combined experimental and theoretical studies have been performed on the structure and vibrational spectra (IR and Raman spectra) of 4'-methylpropiophenone (MPP). The FT-IR and FT-Raman spectra of 4'-methylpropiophenone (MPP) have been recorded in the region 4000-400 cm(-1) and 3500-100 cm(-1), respectively. The harmonic vibrational frequencies were calculated and the scaled values have been compared with experimental FT-IR and FT-Raman spectra. A detailed interpretation of the infrared and Raman spectra of MPP are also reported based on total energy distribution (TED). The observed and the calculated frequencies are found to be in good agreement. The (1)H and (13)C NMR chemical shifts have been calculated by Gauge-Independent Atomic Orbital (GIAO) method with B3LYP/6-311++G(d,p). The natural bond orbital (NBO), natural hybrid orbital (NHO) analysis and electronic properties, such as HOMO and LUMO energies, were performed by DFT approach. The calculated HOMO and LUMO energies show that charge transfer occurs within molecule. The first order hyperpolarizability (β0) of the novel molecular system and related properties (βtot, α0 and Δα) of MPP are calculated using DFT/6-311++G(d,p) method on the finite-field approach. The Mulliken charges, the values of electric dipole moment (μ) of the molecule were computed using DFT calculations. The thermodynamic functions of the title compound were also performed at the above method and basis set.

  14. Ultrafast Magic-Angle Spinning: Benefits for the Acquisition of Ultrawide-Line NMR Spectra of Heavy Spin-1/2 Nuclei.

    PubMed

    Pöppler, Ann-Christin; Demers, Jean-Philippe; Malon, Michal; Singh, Amit Pratap; Roesky, Herbert W; Nishiyama, Yusuke; Lange, Adam

    2016-03-16

    The benefits of the ultrafast magic-angle spinning (MAS) approach for the acquisition of ultrawide-line NMR spectra-spectral simplification, increased mass sensitivity allowing the fast study of small amounts of material, efficient excitation, and application to multiple heavy nuclei-are demonstrated for tin(II) oxide (SnO) and the tin complex [(LB)Sn(II) Cl](+) [Sn(II) Cl3 ](-) [LB=2,6-diacetylpyridinebis(2,6-diisopropylanil)] containing two distinct tin environments. The ultrafast MAS experiments provide optimal conditions for the extraction of the chemical-shift anisotropy tensor parameters, anisotropy, and asymmetry for heavy spin-1/2 nuclei.

  15. Influence of inner-sphere processes on the paramagnetic shifts in the {sup 1}H NMR spectra of some mixed-ligand complexes of rare-earth elements

    SciTech Connect

    Khachatryan, A.S.; Vashchuk, A.V.; Panyushkin, V.T.

    1995-12-20

    Concentration dependences of the observed chemical shifts in the NMR spectra of 1:1:1 and 1:2:1 mixed-ligand complexes of rare-earth elements with acetylacetone and acrylic, methacrylic, maleic, and fumaric acids were analyzed. The complexes undergo inner-sphere structural transformations involving different modes of coordination of the unsaturated acid, which is capable of coordination to the central ion through both the carboxylic group and {pi} electrons of the double bond. The possibility of determining equilibrium constants and limiting chemical shifts of the isomeric forms of the complexes was demonstrated. 9 refs., 4 figs.

  16. Absolute nutrient concentration measurements in cell culture media: (1)H q-NMR spectra and data to compare the efficiency of pH-controlled protein precipitation versus CPMG or post-processing filtering approaches.

    PubMed

    Goldoni, Luca; Beringhelli, Tiziana; Rocchia, Walter; Realini, Natalia; Piomelli, Daniele

    2016-09-01

    The NMR spectra and data reported in this article refer to the research article titled "A simple and accurate protocol for absolute polar metabolite quantification in cell cultures using q-NMR" [1]. We provide the (1)H q-NMR spectra of cell culture media (DMEM) after removal of serum proteins, which show the different efficiency of various precipitating solvents, the solvent/DMEM ratios, and pH of the solution. We compare the data of the absolute nutrient concentrations, measured by PULCON external standard method, before and after precipitation of serum proteins and those obtained using CPMG (Carr-Purcell-Meiboom-Gill) sequence or applying post-processing filtering algorithms to remove, from the (1)H q-NMR spectra, the proteins signal contribution. For each of these approaches, the percent error in the absolute value of every measurement for all the nutrients is also plotted as accuracy assessment. PMID:27331118

  17. Ammonia fixation by humic substances: A nitrogen-15 and carbon-13 NMR study

    USGS Publications Warehouse

    Thorn, K.A.; Mikita, M.A.

    1992-01-01

    The process of ammonia fixation has been studied in three well characterized and structurally diverse fulvic and humic acid samples. The Suwannee River fulvic acid, and the IHSS peat and leonardite humic acids, were reacted with 15N-labelled ammonium hydroxide, and analyzed by liquid phase 15N NMR spectrometry. Elemental analyses and liquid phase 13C NMR spectra also were recorded on the samples before and after reaction with ammonium hydroxide. The largest increase in percent nitrogen occurred with the Suwannee River fulvic acid, which had a nitrogen content of 0.88% before fixation and 3.17% after fixation. The 15N NMR spectra revealed that ammonia reacted similarly with all three samples, indicating that the functional groups which react with ammonia exist in structural configurations common to all three samples. The majority of nitrogcn incorporated into the samples appears to be in the form of indole and pyrrole nitrogen, followed by pyridine, pyrazine, amide and aminohydroquinone nitrogen. Chemical changes in the individual samples upon fixation could not be discerned from the 13C NMR spectra.

  18. Using a Problem Solving-Cooperative Learning Approach to Improve Students' Skills for Interpreting [Superscript 1]H NMR Spectra of Unknown Compounds in an Organic Spectroscopy Course

    ERIC Educational Resources Information Center

    Angawi, Rihab F.

    2014-01-01

    To address third- and fourth-year chemistry students' difficulties with the challenge of interpreting [superscript 1]H NMR spectra, a problem solving-cooperative learning technique was incorporated in a Spectra of Organic Compounds course. Using this approach helped students deepen their understanding of the basics of [superscript 1]H NMR…

  19. Combined experimental (FT-IR, UV-visible spectra, NMR) and theoretical studies on the molecular structure, vibrational spectra, HOMO, LUMO, MESP surfaces, reactivity descriptor and molecular docking of Phomarin

    NASA Astrophysics Data System (ADS)

    Kumar, Abhishek; Srivastava, Ambrish Kumar; Gangwar, Shashi; Misra, Neeraj; Mondal, Avijit; Brahmachari, Goutam

    2015-09-01

    Phomarin is an important natural product belonging to anthraquinone series of compounds. The equilibrium geometry of phomarin has been determined and analyzed at DFT method employing B3LYP/6-311++G(d,p) level of computation. The reactivity of molecule using various descriptors such as Fukui functions, local softness, electrophilicity, electronegativity, Hardness, HOMO-LUMO gap are calculated and discussed. The infrared and UV-vis spectra of phomarin are calculated and compared with the experimentally observed ones. Moreover, 1H and 13C NMR spectra have been calculated by using the gauge independent atomic orbital method. We also notice that phomarin shows remarkable biological activities against malaria parasite. The study suggests further investigation on phomarin for their pharmacological importance.

  20. An economical method for (15)N/(13)C isotopic labeling of proteins expressed in Pichia pastoris.

    PubMed

    Rodriguez, E; Krishna, N R

    2001-07-01

    We report a new and cost-effective approach to prepare (15)N/(13)C labeled proteins for NMR using the Pichia pastoris expression system. Four protocols (P1 to P4) were defined and compared using recombinant Ovine interferon-tau (rOvIFN-tau). Our results demonstrate that in order to get full incorporation of (15)N and (13)C, the isotopes are not totally required during the initial growth phase of P. pastoris culture. The addition of small amounts of (15)N and (13)C compounds 6 h prior to the methanol induction phase is sufficient to obtain 99% incorporation of heavy isotopes into the protein. Our optimized protocol P4 is two-thirds less costly than the classical method using (15)N and (13)C isotopes during the entire growth phase.

  1. Conformational and isomerizational studies of 3- N, N-dimethylhydrazino-2-acetyl propenenitrile using X-ray analysis, NMR and vibrational spectra, and ab initio calculations

    NASA Astrophysics Data System (ADS)

    Gróf, M.; Gatial, A.; Milata, V.; Prónayová, N.; Kožíšek, J.; Breza, M.; Matějka, P.

    2009-12-01

    The IR, Raman and NMR spectra of 3- N, N-dimethylhydrazino-2-acetyl propenenitrile (DMHAP) [(H 3C) 2N sbnd NH sbnd CH dbnd C(CN)(COCH 3)] were measured. X-ray analysis revealed that DMHAP exists in solid state as ZZa conformer. Vibrational and NMR spectra confirmed the existence of only one ZZa conformer with an intramolecular hydrogen bond in less polar solvents and next two EZa and EZs conformers of E-isomer with Z-orientation of acetyl group and anti and syn orientation of dimethylhydrazino group in more polar environments. The observed IR and Raman bands were compared with harmonic vibrational frequencies, calculated using ab initio MP2 and DFT/B3LYP methods in 6-31G∗∗ basis set, and assigned on the basis of potential energy distribution. In addition, the geometries and relative energies of the possible isomers and conformers of DMHAP were also evaluated on the same levels and compared with the X-ray data. The influence of environment polarity on this conformational equilibrium is discussed with respect to the SCRF solvent effect calculations using IEFPCM model.

  2. IR and NMR spectra, intramolecular hydrogen bonding and conformations of para-tert-butyl-aminothiacalix[4]arene in solid state and chloroform solution

    NASA Astrophysics Data System (ADS)

    Zvereva, Elena E.; Katsyuba, Sergey A.; Vandyukov, Alexander E.; Chernova, Alla V.; Kovalenko, Valery I.; Solovieva, Svetlana E.; Antipin, Igor S.; Konovalov, Alexander I.

    2010-02-01

    It is demonstrated that dissolution of aminothiacalix[4]arene in chloroform results in transformation of 1,3-alternate conformation, adopted in single-crystal and bulk polycrystalline solids, to the pinched-cone form. This conformer is stabilised by the intramolecular hydrogen bonds of two distal amino-groups acting as H-donors with another two amino moieties that appear as H-acceptors. The H-bonds cause quite small (ca. 10-20 cm -1) red shift of the IR bands of the NH 2 stretching vibrations, which suggests rather weak NH⋯N hydrogen bonding. This latter is sufficient to stabilize the pinched-cone conformation in the chloroform solution, but the energy gap between the pinched-cone and other conformations is small, and solid-state intermolecular forces easily overcome it, leading to realisation of the 1,3-alternate conformer. The comparison of the DFT computed and experimental vibrational and NMR spectra demonstrates good quality of present quantum-chemical computations, allows complete interpretation of the spectra and reveals simple IR and NMR spectroscopic markers of the conformers of aminothiacalix[4]arenes.

  3. Structure determination in "shiftless" solid state NMR of oriented protein samples

    NASA Astrophysics Data System (ADS)

    Yin, Yuanyuan; Nevzorov, Alexander A.

    2011-09-01

    An efficient formalism for calculating protein structures from oriented-sample NMR data in the torsion-angle space is presented. Angular anisotropies of the NMR observables are treated by utilizing an irreducible spherical basis of rotations. An intermediate rotational transformation is introduced that greatly speeds up structural fitting by rendering the dependence on the torsion angles Φ and Ψ in a purely diagonal form. Back-calculation of the simulated solid-state NMR spectra of protein G involving 15N chemical shift anisotropy (CSA), and 1H- 15N and 1H α- 13C α dipolar couplings was performed by taking into account non-planarity of the peptide linkages and experimental uncertainty. Even a relatively small (to within 1 ppm) random variation in the CSA values arising from uncertainties in the tensor parameters yields the RMSD's of the back-calculated structures of more than 10 Å. Therefore, the 15N CSA has been substituted with heteronuclear dipolar couplings which are derived from the highly conserved bond lengths and bond angles associated with the amino-acid covalent geometry. Using the additional 13C α- 15N and 13C'- 15N dipolar couplings makes it possible to calculate protein structures entirely from "shiftless" solid-state NMR data. With the simulated "experimental" uncertainty of 15 Hz for protein G and 120 Hz for a helical hairpin derived from bacteriorhodopsin, back-calculation of the synthetic dipolar NMR spectra yielded a converged set of solutions. The use of distance restraints dramatically improves structural convergence even if larger experimental uncertainties are assumed.

  4. Multinuclear NMR study of some organoplatinum complexes containing multifunctional azines as chelating ligands.

    PubMed

    Gudat, Dietrich; Dogan, Akbey; Kaim, Wolfgang; Klein, Axel

    2004-09-01

    1H-detected indirect NMR techniques were used to determine 15N and 195Pt NMR parameters for a series of organoplatinum(IV) complexes and one platinum(II) complex containing nitrogen-based azobispyridine, bispyridyltetrazine, and bipyrimidine ligands. The inverse technique permitted the detection of small 4J(Pt,H) and 5J(Pt,H) long-range couplings and the acquisition of 15N NMR data in natural isotopic abundance via nJ(N,H) intra- and inter-ligand couplings, but failed in cases where coherence transfer is quenched by rapid relaxation of the metal atom. In one case, analysis of satellite patterns in a set of 1H,15N, 1H,195Pt and 1H,13C correlation spectra allowed a positive sign to be determined for 1J(Pt,15N). Qualitative arguments are presented to explain the observed 15N coordination shifts in complexes with different azine ligands in terms of azine-M dative bond formation and LnM-azine back-donation. PMID:15307061

  5. Anomalous peaks in NMR spectra of iron-containing silicate minerals: pseudo-contact shifts and the potential for mapping the distributions of transition metal ions

    NASA Astrophysics Data System (ADS)

    Stebbins, J. F.; Kelsey, K. E.

    2009-04-01

    High-resolution nuclear magnetic resonance (NMR) spectroscopy has now been applied to problems of mineral structure for more than 25 years. Early attempts to collect MAS spectra on natural minerals rich in iron (or other cations with unpaired electron spins, e.g. more than a few % FeO) showed serious peak broadening, loss of signal, and thus loss of structural information. Spectroscopists have thus largely avoided such materials and have worked either with low-Fe natural minerals (e.g. zeolites) or with Fe-free synthetic compositions. While this problem remains, it has recently become apparent that in silicates with minor contents of such elements (100's to 1000's of ppm), or, in special cases, with much higher contents (at least 4% FeO), NMR spectra of nuclides such as Si-29 and Al-27 may indeed provide interesting and useful structural information that may eventually reveal new details of cation distribution, ordering, clustering, etc. Here we report on the early stages of this new application. In a recent report (Stebbins, Panero, Smyth and Frost, Am. Min. in press) we noted the presence of a variety of tiny "extra" peaks in Si-29 spectra of forsterite and wadsleyite, both containing 10's to 1000's of ppm of transition metal impurities. Some of these have chemical shifts well outside the known range for diamagnetic silicates, and were hypothesized to result from "pseudo-contact" interactions with unpaired electrons, which depend strongly on local structure. Peak shifts of this type have long been known in Sn-119 and Y-89 spectra for oxides such as rare-earth stannates (Grey et al.), but have apparently not been previously reported for silicates. New data on Si-29 and Al-27 NMR of synthetic pyrope (0.6 % CoO) and natural pyropes from the Dora Maira massif (1.5 to 3.5 wt % FeO) also show "anomalous" resonances, some of which again fall well outside the range of normal chemical shifts (e.g. +140 ppm in a Si-29 spectrum, 70 and 35 ppm in the Al-27 spectrum of a

  6. Improving the efficiency of branch-and-bound complete-search NMR assignment using the symmetry of molecules and spectra.

    PubMed

    Bernal, Andrés; Castillo, Andrés M; González, Fabio; Patiny, Luc; Wist, Julien

    2015-02-21

    Nuclear magnetic resonance (NMR) assignment of small molecules is presented as a typical example of a combinatorial optimization problem in chemical physics. Three strategies that help improve the efficiency of solution search by the branch and bound method are presented: 1. reduction of the size of the solution space by resort to a condensed structure formula, wherein symmetric nuclei are grouped together; 2. partitioning of the solution space based on symmetry, that becomes the basis for an efficient branching procedure; and 3. a criterion of selection of input restrictions that leads to increased gaps between branches and thus faster pruning of non-viable solutions. Although the examples chosen to illustrate this work focus on small-molecule NMR assignment, the results are generic and might help solving other combinatorial optimization problems. PMID:25701998

  7. Rapid measurement of multidimensional 1H solid-state NMR spectra at ultra-fast MAS frequencies

    NASA Astrophysics Data System (ADS)

    Ye, Yue Qi; Malon, Michal; Martineau, Charlotte; Taulelle, Francis; Nishiyama, Yusuke

    2014-02-01

    A novel method to realize rapid repetition of 1H NMR experiments at ultra-fast MAS frequencies is demonstrated. The ultra-fast MAS at 110 kHz slows the 1H-1H spin diffusion, leading to variations of 1H T1 relaxation times from atom to atom within a molecule. The different relaxation behavior is averaged by applying 1H-1H recoupling during relaxation delay even at ultra-fast MAS, reducing the optimal relaxation delay to maximize the signal to noise ratio. The way to determine optimal relaxation delay for arbitrary relaxation curve is shown. The reduction of optimal relaxation delay by radio-frequency driven recoupling (RFDR) was demonstrated on powder samples of glycine and ethenzamide with one and multi-dimensional NMR measurements.

  8. Improving the efficiency of branch-and-bound complete-search NMR assignment using the symmetry of molecules and spectra

    NASA Astrophysics Data System (ADS)

    Bernal, Andrés; Castillo, Andrés M.; González, Fabio; Patiny, Luc; Wist, Julien

    2015-02-01

    Nuclear magnetic resonance (NMR) assignment of small molecules is presented as a typical example of a combinatorial optimization problem in chemical physics. Three strategies that help improve the efficiency of solution search by the branch and bound method are presented: 1. reduction of the size of the solution space by resort to a condensed structure formula, wherein symmetric nuclei are grouped together; 2. partitioning of the solution space based on symmetry, that becomes the basis for an efficient branching procedure; and 3. a criterion of selection of input restrictions that leads to increased gaps between branches and thus faster pruning of non-viable solutions. Although the examples chosen to illustrate this work focus on small-molecule NMR assignment, the results are generic and might help solving other combinatorial optimization problems.

  9. Improving the efficiency of branch-and-bound complete-search NMR assignment using the symmetry of molecules and spectra

    SciTech Connect

    Bernal, Andrés; Patiny, Luc; Castillo, Andrés M.; González, Fabio; Wist, Julien

    2015-02-21

    Nuclear magnetic resonance (NMR) assignment of small molecules is presented as a typical example of a combinatorial optimization problem in chemical physics. Three strategies that help improve the efficiency of solution search by the branch and bound method are presented: 1. reduction of the size of the solution space by resort to a condensed structure formula, wherein symmetric nuclei are grouped together; 2. partitioning of the solution space based on symmetry, that becomes the basis for an efficient branching procedure; and 3. a criterion of selection of input restrictions that leads to increased gaps between branches and thus faster pruning of non-viable solutions. Although the examples chosen to illustrate this work focus on small-molecule NMR assignment, the results are generic and might help solving other combinatorial optimization problems.

  10. Rapid proton-detected NMR assignment for proteins with fast magic angle spinning.

    PubMed

    Barbet-Massin, Emeline; Pell, Andrew J; Retel, Joren S; Andreas, Loren B; Jaudzems, Kristaps; Franks, W Trent; Nieuwkoop, Andrew J; Hiller, Matthias; Higman, Victoria; Guerry, Paul; Bertarello, Andrea; Knight, Michael J; Felletti, Michele; Le Marchand, Tanguy; Kotelovica, Svetlana; Akopjana, Inara; Tars, Kaspars; Stoppini, Monica; Bellotti, Vittorio; Bolognesi, Martino; Ricagno, Stefano; Chou, James J; Griffin, Robert G; Oschkinat, Hartmut; Lesage, Anne; Emsley, Lyndon; Herrmann, Torsten; Pintacuda, Guido

    2014-09-01

    Using a set of six (1)H-detected triple-resonance NMR experiments, we establish a method for sequence-specific backbone resonance assignment of magic angle spinning (MAS) nuclear magnetic resonance (NMR) spectra of 5-30 kDa proteins. The approach relies on perdeuteration, amide (2)H/(1)H exchange, high magnetic fields, and high-spinning frequencies (ωr/2π ≥ 60 kHz) and yields high-quality NMR data, enabling the use of automated analysis. The method is validated with five examples of proteins in different condensed states, including two microcrystalline proteins, a sedimented virus capsid, and two membrane-embedded systems. In comparison to contemporary (13)C/(15)N-based methods, this approach facilitates and accelerates the MAS NMR assignment process, shortening the spectral acquisition times and enabling the use of unsupervised state-of-the-art computational data analysis protocols originally developed for solution NMR.

  11. Effects of T2-relaxation in MAS NMR spectra of the satellite transitions for quadrupolar nuclei: a 27Al MAS and single-crystal NMR study of alum KAl(SO 4) 2 · 12H 2O

    NASA Astrophysics Data System (ADS)

    Andersen, Morten Daugaard; Jakobsen, Hans J.; Skibsted, Jørgen

    2005-04-01

    Asymmetries in the manifold of spinning sidebands (ssbs) from the satellite transitions have been observed in variable-temperature 27Al MAS NMR spectra of alum (KAl(SO 4) 2 · 12H 2O), recorded in the temperature range from -76 to 92 °C. The asymmetries decrease with increasing temperature and reflect the fact that the ssbs exhibit systematically different linewidths for different spectral regions of the manifold. From spin-echo 27Al NMR experiments on a single-crystal of alum, it is demonstrated that these variations in linewidth originate from differences in transverse ( T2) relaxation times for the two inner ( m = 1/2 ↔ m = 3/2 and m = -1/2 ↔ m = -3/2) and correspondingly for the two outer ( m = 3/2 ↔ m = 5/2 and m = -3/2 ↔ m = -5/2) satellite transitions. T2 relaxation times in the range 0.5-3.5 ms are observed for the individual satellite transitions at -50 °C and 7.05 T, whereas the corresponding T1 relaxation times, determined from similar saturation-recovery 27Al NMR experiments, are almost constant ( T1 = 0.07-0.10 s) for the individual satellite transitions. The variation in T2 values for the individual 27Al satellite transitions for alum is justified by a simple theoretical approach which considers the cross-correlation of the local fluctuating fields from the quadrupolar coupling and the heteronuclear ( 27Al- 1H) dipolar interaction on the T2 relaxation times for the individual transitions. This approach and the observed differences in T2 values indicate that a single random motional process modulates both the quadrupolar and heteronuclear dipolar interactions for 27Al in alum at low temperatures.

  12. Reparameterization of RNA chi Torsion Parameters for the AMBER Force Field and Comparison to NMR Spectra for Cytidine and Uridine.

    PubMed

    Yildirim, Ilyas; Stern, Harry A; Kennedy, Scott D; Tubbs, Jason D; Turner, Douglas H

    2010-05-11

    A reparameterization of the torsional parameters for the glycosidic dihedral angle, chi, for the AMBER99 force field in RNA nucleosides is used to provide a modified force field, AMBER99chi. Molecular dynamics simulations of cytidine, uridine, adenosine, and guanosine in aqueous solution using the AMBER99 and AMBER99chi force fields are compared with NMR results. For each nucleoside and force field, 10 individual molecular dynamics simulations of 30 ns each were run. For cytidine with AMBER99chi force field, each molecular dynamics simulation time was extended to 120 ns for convergence purposes. Nuclear magnetic resonance (NMR) spectroscopy, including one-dimensional (1D) (1)H, steady-state 1D (1)H nuclear Overhauser effect (NOE), and transient 1D (1)H NOE, was used to determine the sugar puckering and preferred base orientation with respect to the ribose of cytidine and uridine. The AMBER99 force field overestimates the population of syn conformations of the base orientation and of C2'-endo sugar puckering of the pyrimidines, while the AMBER99chi force field's predictions are more consistent with NMR results. Moreover, the AMBER99 force field prefers high anti conformations with glycosidic dihedral angles around 310 degrees for the base orientation of purines. The AMBER99chi force field prefers anti conformations around 185 degrees , which is more consistent with the quantum mechanical calculations and known 3D structures of folded ribonucleic acids (RNAs). Evidently, the AMBER99chi force field predicts the structural characteristics of ribonucleosides better than the AMBER99 force field and should improve structural and thermodynamic predictions of RNA structures.

  13. A comparative study of the conformational equilibria, vibrational, 1H and 13C NMR spectra of isobutyranilide and its derivative the anticancer drug flutamide

    NASA Astrophysics Data System (ADS)

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

    2014-10-01

    The molecular structure of isobutyranilide and flutamide were investigated by DFT-B3LYP/6-311G** and MP2/6-311G** calculations. Isobutyranilide was predicted to exist predominantly in a planar cis conformation, while flutamide in non-planar structures with the CF3 and the NO2 groups adopting an out of the phenyl-plane configuration. The vibrational frequencies of the low energy structures of the two molecules were computed at the DFT-B3LYP level of theory. From the calculated Gibb's free energies, isobutyranilide is estimated to have an equilibrium mixture of 91% cis and 9% trans structures, while flutamide is calculated to have a mixture of 65% cis-cis and 28% trans-cis structures at 298.15 K. The analysis of the observed vibrational spectra supports the presence of isobutyranilide in only one conformation at room temperature. From a 1:1 acetonitrile solvent experiment flutamide is determined to exist in more than one conformation at ambient temperature. Complete vibrational assignments of the normal modes of isobutyranilide and flutamide were provided on the basis of combined normal coordinate calculations and experimental Infrared and Raman spectra. The 1H and 13C NMR spectra of isobutyranilide were measured and their chemical shifts were compared to the corresponding ones of flutamide.

  14. Site-specific φ- and ψ-torsion angle determination in a uniformly/extensively 13C- and 15N-labeled peptide

    NASA Astrophysics Data System (ADS)

    Wi, Sungsool; Spano, Justin

    2011-10-01

    A solid-state rotational-echo double resonance (REDOR) NMR method was introduced to identify the ϕ- and ψ-torsion angle from a 1H- 15N or 1H- 13C' spin system of alanine-like residues in a selectively, uniformly, or extensively 15N-/ 13C-labeled peptide. When a C α( i) or a 15N peak is site-specifically obtainable in the NMR spectrum of a uniformly 15N/ 13C-labeled sample system, the ψ- or ϕ-torsion angle specified by the conformational structure of peptide geometry involving 15N( i)- 1H αi - 15N( i + 1) or 13C'( i - 1)- 1H Ni- 13C'( i) spin system can be identified based on 13C α- or 15N-detected 1H α- 15N or 1H N- 13C REDOR experiment. This method will conveniently be utilized to identify major secondary motifs, such as α-helix, β-sheet, and β-turn, from a uniformly 15N-/ 13C-labled peptide sample system. When tested on a 13C-/ 15N-labeled model system of a three amino acid peptide Gly-[U- 13C, 15N]Ala-[U- 13C, 15N]Leu, the ψ-angle of alanine obtained experimentally, ψ = -40 ± 30°, agreed reasonably well with the X-ray determined angle, ψ = -39°.

  15. Molecular dynamics and information on possible sites of interaction of intramyocellular metabolites in vivo from resolved dipolar couplings in localized 1H NMR spectra

    NASA Astrophysics Data System (ADS)

    Schröder, Leif; Schmitz, Christian; Bachert, Peter

    2004-12-01

    Proton NMR resonances of the endogenous metabolites creatine and phosphocreatine ((P)Cr), taurine (Tau), and carnosine (Cs, β-alanyl- L-histidine) were studied with regard to residual dipolar couplings and molecular mobility. We present an analysis of the direct 1H- 1H interaction that provides information on motional reorientation of subgroups in these molecules in vivo. For this purpose, localized 1H NMR experiments were performed on m. gastrocnemius of healthy volunteers using a 1.5-T clinical whole-body MR scanner. We evaluated the observable dipolar coupling strength SD0 ( S = order parameter) of the (P)Cr-methyl triplet and the Tau-methylene doublet by means of the apparent line splitting. These were compared to the dipolar coupling strength of the (P)Cr-methylene doublet. In contrast to the aliphatic protons of (P)Cr and Tau, the aromatic H2 ( δ = 8 ppm) and H4 ( δ = 7 ppm) protons of the imidazole ring of Cs exhibit second-order spectra at 1.5 T. This effect is the consequence of incomplete transition from Zeeman to Paschen-Back regime and allows a determination of SD0 from H2 and H4 of Cs as an alternative to evaluating the multiplet splitting which can be measured directly in high-resolution 1H NMR spectra. Experimental data showed striking differences in the mobility of the metabolites when the dipolar coupling constant D0 (calculated with the internuclear distance known from molecular geometry in the case of complete absence of molecular dynamics and motion) is used for comparison. The aliphatic signals involve very small order parameters S ≈ (1.4 - 3) × 10 -4 indicating rapid reorientation of the corresponding subgroups in these metabolites. In contrast, analysis of the Cs resonances yielded S ≈ (113 - 137) × 10 -4. Thus, the immobilization of the Cs imidazole ring owing to an anisotropic cellular substructure in human m. gastrocnemius is much more effective than for (P)Cr and Tau subgroups. Furthermore, 1H NMR experiments on aqueous model

  16. Determination of glucan phosphorylation using heteronuclear 1H, 13C double and 1H, 13C, 31P triple-resonance NMR spectra.

    PubMed

    Schmieder, Peter; Nitschke, Felix; Steup, Martin; Mallow, Keven; Specker, Edgar

    2013-10-01

    Phosphorylation and dephosphorylation of starch and glycogen are important for their physicochemical properties and also their physiological functions. It is therefore desirable to reliably determine the phosphorylation sites. Heteronuclear multidimensional NMR-spectroscopy is in principle a straightforward analytical approach even for complex carbohydrate molecules. With heterogeneous samples from natural sources, however, the task becomes more difficult because a full assignment of the resonances of the carbohydrates is impossible to obtain. Here, we show that the combination of heteronuclear (1) H,(13) C and (1) H,(13) C,(31) P techniques and information derived from spectra of a set of reference compounds can lead to an unambiguous determination of the phosphorylation sites even in heterogeneous samples. PMID:23913630

  17. Determination of glucan phosphorylation using heteronuclear 1H, 13C double and 1H, 13C, 31P triple-resonance NMR spectra.

    PubMed

    Schmieder, Peter; Nitschke, Felix; Steup, Martin; Mallow, Keven; Specker, Edgar

    2013-10-01

    Phosphorylation and dephosphorylation of starch and glycogen are important for their physicochemical properties and also their physiological functions. It is therefore desirable to reliably determine the phosphorylation sites. Heteronuclear multidimensional NMR-spectroscopy is in principle a straightforward analytical approach even for complex carbohydrate molecules. With heterogeneous samples from natural sources, however, the task becomes more difficult because a full assignment of the resonances of the carbohydrates is impossible to obtain. Here, we show that the combination of heteronuclear (1) H,(13) C and (1) H,(13) C,(31) P techniques and information derived from spectra of a set of reference compounds can lead to an unambiguous determination of the phosphorylation sites even in heterogeneous samples.

  18. Indole-containing new types of dyes and their UV-vis and NMR spectra and electronic structures: Experimental and theoretical study

    NASA Astrophysics Data System (ADS)

    Kuzu, Burak; Menges, Nurettin

    2016-06-01

    Indole containing dyes were synthesized via a simple method with high yield. These molecules have different colors and UV-vis spectra of them were recorded. Impact of solvents on absorbances was investigated and it was observed that basic solvent such as DMF and pyridine have blue shift. TD-DFT calculations were done and results were compared with experimental data. NMR data of molecules were analyzed and tautomeric forms of colorants and their ratio were determined. It was find out that two tautomers might be formed in solution, called indole and indolenine form. HOMO-LUMO and energy gaps were calculated and plotted. Furthermore, molecular electrostatic potentials were simulated to find out electrophilic and nucleophilic regions.

  19. Indole-containing new types of dyes and their UV-vis and NMR spectra and electronic structures: Experimental and theoretical study.

    PubMed

    Kuzu, Burak; Menges, Nurettin

    2016-06-01

    Indole containing dyes were synthesized via a simple method with high yield. These molecules have different colors and UV-vis spectra of them were recorded. Impact of solvents on absorbances was investigated and it was observed that basic solvent such as DMF and pyridine have blue shift. TD-DFT calculations were done and results were compared with experimental data. NMR data of molecules were analyzed and tautomeric forms of colorants and their ratio were determined. It was find out that two tautomers might be formed in solution, called indole and indolenine form. HOMO-LUMO and energy gaps were calculated and plotted. Furthermore, molecular electrostatic potentials were simulated to find out electrophilic and nucleophilic regions.

  20. Pure shift NMR.

    PubMed

    Zangger, Klaus

    2015-04-01

    Although scalar-coupling provides important structural information, the resulting signal splittings significantly reduce the resolution of NMR spectra. Limited resolution is a particular problem in proton NMR experiments, resulting in part from the limited proton chemical shift range (∼10 ppm) but even more from the splittings due to scalar coupling to nearby protons. "Pure shift" NMR spectroscopy (also known as broadband homonuclear decoupling) has been developed for disentangling overlapped proton NMR spectra. The resulting spectra are considerably simplified as they consist of single lines, reminiscent of proton-decoupled C-13 spectra at natural abundance, with no multiplet structure. The different approaches to obtaining pure shift spectra are reviewed here and several applications presented. Pure shift spectra are especially useful for highly overlapped proton spectra, as found for example in reaction mixtures, natural products and biomacromolecules.

  1. Demystifying fluorine chemical shifts: electronic structure calculations address origins of seemingly anomalous (19)F-NMR spectra of fluorohistidine isomers and analogues.

    PubMed

    Kasireddy, Chandana; Bann, James G; Mitchell-Koch, Katie R

    2015-11-11

    Fluorine NMR spectroscopy is a powerful tool for studying biomolecular structure, dynamics, and ligand binding, yet the origins of (19)F chemical shifts are not well understood. Herein, we use electronic structure calculations to describe the changes in (19)F chemical shifts of 2F- and 4F-histidine/(5-methyl)-imidazole upon acid titration. While the protonation of the 2F species results in a deshielded chemical shift, protonation of the 4F isomer results in an opposite, shielded chemical shift. The deshielding of 2F-histidine/(5-methyl)-imidazole upon protonation can be rationalized by concomitant decreases in charge density on fluorine and a reduced dipole moment. These correlations do not hold for 4F-histidine/(5-methyl)-imidazole, however. Molecular orbital calculations reveal that for the 4F species, there are no lone pair electrons on the fluorine until protonation. Analysis of a series of 4F-imidazole analogues, all with delocalized fluorine electron density, indicates that the deshielding of (19)F chemical shifts through substituent effects correlates with increased C-F bond polarity. In summary, the delocalization of fluorine electrons in the neutral 4F species, with gain of a lone pair upon protonation may help explain the difficulty in developing a predictive framework for fluorine chemical shifts. Ideas debated by chemists over 40 years ago, regarding fluorine's complex electronic effects, are shown to have relevance for understanding and predicting fluorine NMR spectra.

  2. Facilitating quality control for spectra assignments of small organic molecules: nmrshiftdb2--a free in-house NMR database with integrated LIMS for academic service laboratories.

    PubMed

    Kuhn, Stefan; Schlörer, Nils E

    2015-08-01

    nmrshiftdb2 supports with its laboratory information management system the integration of an electronic lab administration and management into academic NMR facilities. Also, it offers the setup of a local database, while full access to nmrshiftdb2's World Wide Web database is granted. This freely available system allows on the one hand the submission of orders for measurement, transfers recorded data automatically or manually, and enables download of spectra via web interface, as well as the integrated access to prediction, search, and assignment tools of the NMR database for lab users. On the other hand, for the staff and lab administration, flow of all orders can be supervised; administrative tools also include user and hardware management, a statistic functionality for accounting purposes, and a 'QuickCheck' function for assignment control, to facilitate quality control of assignments submitted to the (local) database. Laboratory information management system and database are based on a web interface as front end and are therefore independent of the operating system in use. PMID:25998807

  3. Crystal structure and theoretical study of IR and 1H and 13C NMR spectra of cordatin, a natural product with antiulcerogenic activity

    NASA Astrophysics Data System (ADS)

    Brasil, Davi S. B.; Alves, Cláudio N.; Guilhon, Giselle M. S. P.; Muller, Adolfo H.; Secco, Ricardo De S.; Peris, Gabriel; Llusar, Rosa

    Cordatin is a furan diterpenoid with a clerodane skeleton isolated from Croton palanostigma Klotzsch (Euphorbiaceae). This natural product shows significant antiulcerogenic activity, similar to cimetidine (Tagamet®), a compound used for the treatment of peptic ulcers. The crystal structure of cordatin was obtained by X-ray diffraction and its geometrical parameters were compared with theoretical calculations at the B3LYP theory level. The IR and NMR (1H and 13C chemical shifts and coupling constants) spectra were obtained and compared with the theoretical calculations. The B3LYP theory level, with the 6-31G(d,p) and 6-311G(d,p) basis set, provided IR absorption values close to the experimental data. Moreover, theoretical NMR parameters obtained in both gas phase and chloroform solvent at the B3PW91/DGDZVP, B3LYP/6-311+G(2d,p), and B3PW91/6-311+G(2d,p) levels showed good correlations with the experimental results.

  4. FT-IR, FT-Raman, NMR and UV-Vis spectra and DFT calculations of 5-bromo-2-ethoxyphenylboronic acid (monomer and dimer structures).

    PubMed

    Sas, E B; Kose, E; Kurt, M; Karabacak, M

    2015-02-25

    In this study, the Fourier Transform Infrared (FT-IR) and Fourier Transform Raman (FT-Raman) spectra of 5-bromo-2-ethoxyphenylboronic acid (5Br2EPBA) are recorded in the solid phase in the region 4000-400 cm(-1) and 3500-10 cm(-1), respectively. The (1)H, (13)C and DEPT nuclear magnetic resonance (NMR) spectra are recorded in DMSO solution. The UV-Vis absorption spectrum of 5Br2EPBA is saved in the range of 200-400 nm in ethanol and water. The following theoretical calculations for monomeric and dimeric structures are supported by experimental results. The molecular geometry and vibrational frequencies in the ground state are calculated by using DFT methods with 6-31G(d,p) and 6-311G(d,p) basis sets. There are four conformers for the present molecule. The computational results diagnose the most stable conformer of 5Br2EPBA as Trans-Cis (TC) form. The complete assignments are performed on the basis of the total energy distribution (TED) of vibrational modes, calculated with scaled quantum mechanics (SQM) method in parallel quantum solutions (PQS) program. The (1)H and (13)C NMR chemical shifts of 5Br2EPBA molecule are calculated by using the Gauge Invariant Atomic Orbital (GIAO) method in DMSO and gas phase for monomer and dimer structures of the most stable conformer. Moreover, electronic properties, such as the HOMO and LUMO energies (by TD-DFT and CIS methods) and molecular electrostatic potential surface (MEPs) are investigated. Stability of the molecule arising from hyper-conjugative interactions, charge delocalization is analyzed using natural bond orbital (NBO) analysis. Nonlinear optical (NLO) properties and thermodynamic features are presented. All calculated results are compared with the experimental data of the title molecule. The correlation of theoretical and experimental results provides a detailed description of the structural and physicochemical properties of the title molecule.

  5. FT-IR, FT-Raman, NMR and UV-Vis spectra and DFT calculations of 5-bromo-2-ethoxyphenylboronic acid (monomer and dimer structures).

    PubMed

    Sas, E B; Kose, E; Kurt, M; Karabacak, M

    2015-02-25

    In this study, the Fourier Transform Infrared (FT-IR) and Fourier Transform Raman (FT-Raman) spectra of 5-bromo-2-ethoxyphenylboronic acid (5Br2EPBA) are recorded in the solid phase in the region 4000-400 cm(-1) and 3500-10 cm(-1), respectively. The (1)H, (13)C and DEPT nuclear magnetic resonance (NMR) spectra are recorded in DMSO solution. The UV-Vis absorption spectrum of 5Br2EPBA is saved in the range of 200-400 nm in ethanol and water. The following theoretical calculations for monomeric and dimeric structures are supported by experimental results. The molecular geometry and vibrational frequencies in the ground state are calculated by using DFT methods with 6-31G(d,p) and 6-311G(d,p) basis sets. There are four conformers for the present molecule. The computational results diagnose the most stable conformer of 5Br2EPBA as Trans-Cis (TC) form. The complete assignments are performed on the basis of the total energy distribution (TED) of vibrational modes, calculated with scaled quantum mechanics (SQM) method in parallel quantum solutions (PQS) program. The (1)H and (13)C NMR chemical shifts of 5Br2EPBA molecule are calculated by using the Gauge Invariant Atomic Orbital (GIAO) method in DMSO and gas phase for monomer and dimer structures of the most stable conformer. Moreover, electronic properties, such as the HOMO and LUMO energies (by TD-DFT and CIS methods) and molecular electrostatic potential surface (MEPs) are investigated. Stability of the molecule arising from hyper-conjugative interactions, charge delocalization is analyzed using natural bond orbital (NBO) analysis. Nonlinear optical (NLO) properties and thermodynamic features are presented. All calculated results are compared with the experimental data of the title molecule. The correlation of theoretical and experimental results provides a detailed description of the structural and physicochemical properties of the title molecule. PMID:25305625

  6. FT-IR, FT-Raman, NMR and UV-Vis spectra and DFT calculations of 5-bromo-2-ethoxyphenylboronic acid (monomer and dimer structures)

    NASA Astrophysics Data System (ADS)

    Sas, E. B.; Kose, E.; Kurt, M.; Karabacak, M.

    2015-02-01

    In this study, the Fourier Transform Infrared (FT-IR) and Fourier Transform Raman (FT-Raman) spectra of 5-bromo-2-ethoxyphenylboronic acid (5Br2EPBA) are recorded in the solid phase in the region 4000-400 cm-1 and 3500-10 cm-1, respectively. The 1H, 13C and DEPT nuclear magnetic resonance (NMR) spectra are recorded in DMSO solution. The UV-Vis absorption spectrum of 5Br2EPBA is saved in the range of 200-400 nm in ethanol and water. The following theoretical calculations for monomeric and dimeric structures are supported by experimental results. The molecular geometry and vibrational frequencies in the ground state are calculated by using DFT methods with 6-31G(d,p) and 6-311G(d,p) basis sets. There are four conformers for the present molecule. The computational results diagnose the most stable conformer of 5Br2EPBA as Trans-Cis (TC) form. The complete assignments are performed on the basis of the total energy distribution (TED) of vibrational modes, calculated with scaled quantum mechanics (SQM) method in parallel quantum solutions (PQS) program. The 1H and 13C NMR chemical shifts of 5Br2EPBA molecule are calculated by using the Gauge Invariant Atomic Orbital (GIAO) method in DMSO and gas phase for monomer and dimer structures of the most stable conformer. Moreover, electronic properties, such as the HOMO and LUMO energies (by TD-DFT and CIS methods) and molecular electrostatic potential surface (MEPs) are investigated. Stability of the molecule arising from hyper-conjugative interactions, charge delocalization is analyzed using natural bond orbital (NBO) analysis. Nonlinear optical (NLO) properties and thermodynamic features are presented. All calculated results are compared with the experimental data of the title molecule. The correlation of theoretical and experimental results provides a detailed description of the structural and physicochemical properties of the title molecule.

  7. Hydrogen doppler spectroscopy using 15N ions

    NASA Astrophysics Data System (ADS)

    Borucki, L.; Becker, H. W.; Gorris, F.; Kubsky, S.; Schulte, W. H.; Rolfs, C.

    The energy spread of atomic and molecular ion beams from the 4 MV Dynamitron tandem accelerator at the Ruhr-Universität Bochum has been studied and in part minimized. Using the ER= 6.40 MeV narrow resonance in 1H(15N,αγ)12C with an 15N energy spread of 4.55 keV, the Doppler broadening for several hydrogen-bearing gases was found to be in good agreement with expectation: e.g. for NH3 gas a rotational-vibrational Doppler width of 10.41 +/- 0.25 keV was observed (theory = 10.4 keV). Studies of the vibrational Doppler widths of H-bonds on a Si <100> surface were performed using a 4πγ-ray detection system together with UHV-chambers for sample preparation, transport, and analysis. The results showed that further improvements in the experimental set-ups are needed for such investigations.

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

    NASA Astrophysics Data System (ADS)

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

    2013-09-01

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

  9. Algal autolysate medium to label proteins for NMR in mammalian cells.

    PubMed

    Fuccio, Carmelo; Luchinat, Enrico; Barbieri, Letizia; Neri, Sara; Fragai, Marco

    2016-04-01

    In-cell NMR provides structural and functional information on proteins directly inside living cells. At present, the high costs of the labeled media for mammalian cells represent a limiting factor for the development of this methodology. Here we report a protocol to prepare a homemade growth medium from Spirulina platensis autolysate, suitable to express uniformly labeled proteins inside mammalian cells at a reduced cost-per-sample. The human proteins SOD1 and Mia40 were overexpressed in human cells grown in (15)N-enriched S. platensis algal-derived medium, and high quality in-cell NMR spectra were obtained. PMID:27106902

  10. 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.

  11. NMR of 133Cs+ in stretched hydrogels: One-dimensional, z- and NOESY spectra, and probing the ion's environment in erythrocytes

    NASA Astrophysics Data System (ADS)

    Kuchel, Philip W.; Shishmarev, Dmitry; Puckeridge, Max; Levitt, Malcolm H.; Naumann, Christoph; Chapman, Bogdan E.

    2015-12-01

    133Cs nuclear magnetic resonance (NMR) spectroscopy was conducted on 133Cs+ in gelatin hydrogels that were either relaxed or stretched. Stretching generated a septet from this spin-7/2 nucleus, and its nuclear magnetic relaxation was studied via z-spectra, and two-dimensional nuclear Overhauser (NOESY) spectroscopy. Various spectral features were well simulated by using Mathematica and the software package SpinDynamica. Spectra of CsCl in suspensions of human erythrocytes embedded in gelatin gel showed separation of the resonances from the cation inside and outside the cells. Upon stretching the sample, the extracellular 133Cs+ signal split into a septet, while the intracellular peak was unchanged, revealing different alignment/ordering properties of the environment inside and around the cells. Differential interference contrast light microscopy confirmed that the cells were stretched when the overall sample was elongated. Analysis of the various spectral features of 133Cs+ reported here opens up applications of this K+ congener for studies of cation-handling by metabolically-active cells and tissues in aligned states.

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

    PubMed

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

    2003-06-01

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

  13. Structure of 1-methyl-6-oxyquinolinium betaine dihydrate studied by X-ray diffraction, DFT calculations, vibrational and NMR spectra

    NASA Astrophysics Data System (ADS)

    Barczyński, P.; Ratajczak-Sitarz, M.; Katrusiak, A.; Szafran, M.

    2010-07-01

    The crystals of 1-methyl-6-oxyquinolinium betaine dihydrate, 6QB·2H 2O, are triclinic, space group P1¯. The oxygen atom of 6QB exhibits an extremely rare capability of accepting four hydrogen bonds. It is engaged in four hydrogen bonds to water molecules of the 2.823, 2.825, 2.833 and 2.849 Å; each water molecule interacts with two neighbouring 6QB molecules linking them into infinite sheets. Differences in geometrical parameters between the X-ray and calculated molecules reflect changes in their structures between zwitterion and quinonoid forms. The probable assignments of the experimental FTIR solid spectrum have been made on the basis of B3LYP/6-311G(d,p) calculated frequencies in vacuum. Both 1H and 13C chemical shifts are solvent dependent. Linear correlations between the experimental 1H and 13C NMR chemical shifts of 6QB·2H 2O in solutions and the GIAO/B3LYP/6-311G(d,p) calculated magnetic isotropic shielding tensors ( σcal) using the screening solvation model, δexp = a + bσcal, are reported.

  14. A Comparison of NMR Spectra Obtained for Solid-Phase-Synthesis Resins Using Conventional High-Resolution, Magic-Angle-Spinning, and High-Resolution Magic-Angle-Spinning Probes

    NASA Astrophysics Data System (ADS)

    Keifer, Paul A.; Baltusis, Laima; Rice, David M.; Tymiak, Adrienne A.; Shoolery, James N.

    It has recently been shown that high-resolution 1H NMR spectra can be obtained for samples covalently bound to polystyrene-based (Tentagel) solid-phase-synthesis resins by the use of magic-angle spinning (MAS) combined with high-resolution-probe technology. The attainable spectral resolution in the 1H and 13C NMR spectra of these resins is affected by molecular mobility and magnetic-susceptibility mismatches, both within the sample and in the probe itself. Using new high-resolution MAS probes called Nano·nmr probes, the importance of magnetic-susceptibility matching in the construction of these probes is demonstrated, and the limitations of using MAS alone to generate line narrowing in both 1H and 13C NMR are explored using a solvent-swollen functionalized Wang resin. The effects of presaturation, temperature, spin rate, and different solvents upon spectral quality have also been investigated, and advanced 1D- and 2D-experimental capability is demonstrated. This ability to generate high-resolution NMR spectra of samples still bound to the resins is expected to be of extreme interest in not only solid-phase synthesis, but also in the rapidly growing field of combinatorial chemistry.

  15. Technical aspects of fast magic-angle turning NMR for dilute spin-1/2 nuclei with broad spectra.

    PubMed

    Hu, Y-Y; Schmidt-Rohr, K

    2011-09-01

    For obtaining sideband-free spectra of high-Z spin-1/2 nuclei with large (>1000 ppm) chemical-shift anisotropies and broad isotropic-shift dispersion, we recently identified Gan's modified five-pulse magic-angle turning (MAT) experiment as the best available broadband pulse sequence, and adapted it to fast magic-angle spinning. Here, we discuss technical aspects such as pulse timings that compensate for off-resonance effects and are suitable for large CSAs over a range of 1.8γB(1); methods to minimize the duration of z-periods by cyclic decrementation; shearing without digitization artifacts, by sharing between channels (points); and maximizing the sensitivity by echo-matched full-Gaussian filtering. The method is demonstrated on a model sample of mixed amino acids and its large bandwidth is highlighted by comparison with the multiple-π-pulse PASS technique. Applications to various tellurides are shown; these include GeTe, Sb(2)Te(3) and Ag(0.53)Pb(18)Sb(1.2)Te(20), with spectra spanning up to 190 kHz, at 22 kHz MAS. We have also determined the (125)Te chemical shift anisotropies from the intensities of the spinning sidebands resolved by isotropic-shift separation. PMID:21782396

  16. FTIR, FT-RAMAN, NMR, spectra, normal co-ordinate analysis, NBO, NLO and DFT calculation of N,N-diethyl-4-methylpiperazine-1-carboxamide molecule.

    PubMed

    Muthu, S; Elamurugu Porchelvi, E

    2013-11-01

    The Fourier Transform Infrared (FT-IR) and FT-Raman of N,N-diethyl-4-methylpiperazine-1-carboxamide (NND4MC) have been recorded and analyzed. The structure of the compound was optimized and the structural characteristics were determined by density functional theory (DFT) using B3LYP method with 6-31G(d,p) and 6-311G(d,p) basis sets. 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. The detailed interpretation of the vibrational spectra has been carried out with aid of normal coordinate analysis (NCA) following the scaled quantum mechanical force field methodology. Stability of the molecule arising from hyperconjugative interactions and charge delocalization has been analyzed using natural bond orbital (NBO) analysis. The results show that electron density (ED) in the σ(*) and π(*) antibonding orbitals and second order delocalization energies (E2) confirm the occurrence of intramolecular charge transfer (ICT) within the molecule. The electronic dipole moment (μD) and the first hyperpolarizability (βtot) values of the investigated molecule were computed using Density Functional Theory (DFT/B3LYP) with 6-31G(d,p) and 6-311G(d,p) basis sets. The calculated results also show that the NND4MC molecule may have microscopy nonlinear optical (NLO) behavior with non zero values. Mulliken atomic charges of NND4MC were calculated. 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. The UV-Vis spectrum of the compound was recorded. The theoretical electronic absorption spectra have been calculated by using CIS, TD-DFT methods. A study on the electronic properties, such as HOMO and LUMO energies, molecular electrostatic potential (MEP) were also performed.

  17. Probing the influential factors of NMR T1-T2 spectra in the characterization of the kerogen by numerical simulation

    NASA Astrophysics Data System (ADS)

    Ge, Xinmin; Fan, Yiren; Chen, Hua; Deng, Shaogui; Cao, Yingchang; Zahid, Muhammad Aleem

    2015-11-01

    The low field nuclear magnetic resonance (NMR) spectroscopy has been widely used to characterize the longitudinal and transversal relaxation (T1-T2) spectrum of unconventional resources such as shale gas and tight oil containing significant proportions of kerogen and bitumen. However, it requires exquisite design of the acquisition model and the inversion algorithm due to the fast relaxation nature of the kerogen and bitumen. A new direct two dimensional (2D) inversion algorithm combined the iterative truncated singular value decomposition (TSVD) and the Akaiake Information Criterion (AIC) is presented to perform the data inversion efficiently. The fluid component decomposition (FCD) is applied to construct the forward T1-T2 model of the kerogen, and numerical simulations are conducted to investigate factors which may influence inversion results including echo spacing, recovery time series, signal to noise ratio (SNR), and the maximal iteration time. Results show that the T2 component is heavily impaired by the echo spacing, whereas the T1 component is influenced by the recovery time series but with limited effects. The inversion precision is greatly affected by the quality of the data. The inversed spectrum deviates from the model seriously when the SNR of the artificial noise is lower than 50, and the T2 component is more sensitive to the noise than the T1 component. What's more, the maximal iteration time can also affect the inversion result, especially when the maximal iteration time is smaller than 500. Proper acquisition and inversion parameters for the characterization of the kerogen are obtained considering the precision and the computational cost.

  18. Probing the influential factors of NMR T1-T2 spectra in the characterization of the kerogen by numerical simulation.

    PubMed

    Ge, Xinmin; Fan, Yiren; Chen, Hua; Deng, Shaogui; Cao, Yingchang; Zahid, Muhammad Aleem

    2015-11-01

    The low field nuclear magnetic resonance (NMR) spectroscopy has been widely used to characterize the longitudinal and transversal relaxation (T1-T2) spectrum of unconventional resources such as shale gas and tight oil containing significant proportions of kerogen and bitumen. However, it requires exquisite design of the acquisition model and the inversion algorithm due to the fast relaxation nature of the kerogen and bitumen. A new direct two dimensional (2D) inversion algorithm combined the iterative truncated singular value decomposition (TSVD) and the Akaiake Information Criterion (AIC) is presented to perform the data inversion efficiently. The fluid component decomposition (FCD) is applied to construct the forward T1-T2 model of the kerogen, and numerical simulations are conducted to investigate factors which may influence inversion results including echo spacing, recovery time series, signal to noise ratio (SNR), and the maximal iteration time. Results show that the T2 component is heavily impaired by the echo spacing, whereas the T1 component is influenced by the recovery time series but with limited effects. The inversion precision is greatly affected by the quality of the data. The inversed spectrum deviates from the model seriously when the SNR of the artificial noise is lower than 50, and the T2 component is more sensitive to the noise than the T1 component. What's more, the maximal iteration time can also affect the inversion result, especially when the maximal iteration time is smaller than 500. Proper acquisition and inversion parameters for the characterization of the kerogen are obtained considering the precision and the computational cost. PMID:26397220

  19. Automated feature extraction for the classification of human in vivo 13C NMR spectra using statistical pattern recognition and wavelets.

    PubMed

    Tate, A R; Watson, D; Eglen, S; Arvanitis, T N; Thomas, E L; Bell, J D

    1996-06-01

    If magnetic resonance spectroscopy (MRS) is to become a useful tool in clinical medicine, it will be necessary to find reliable methods for analyzing and classifying MRS data. Automated methods are desirable because they can remove user bias and can deal with large amounts of data, allowing the use of all the available information. In this study, techniques for automatically extracting features for the classification of MRS in vivo data are investigated. Among the techniques used were wavelets, principal component analysis, and linear discriminant function analysis. These techniques were tested on a set of 75 in vivo 13C spectra of human adipose tissue from subjects from three different dietary groups (vegan, vegetarian, and omnivore). It was found that it was possible to assign automatically 94% of the vegans and omnivores to their correct dietary groups, without the need for explicit identification or measurement of peaks.

  20. NMR characterization of membrane protein–detergent micelle solutions using microcoil equipment

    PubMed Central

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

    2010-01-01

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

  1. NMR characterization of membrane protein-detergent micelle solutions by use of microcoil equipment.

    PubMed

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

    2009-12-30

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

  2. Fingerprints of molecular structure and hydrogen bonding effects in the /sup 13/C NMR spectra of monosaccharides with partially deuterated hydroxyls

    SciTech Connect

    Reuben, J.

    1984-10-17

    A new NMR approach to structure elucidation of carbohydrates in solution is presented. Examined in detail are the isotopic multiplets in /sup 13/C NMR spectra that result from partial deuteration of the hydroxyls for a series of monosaccharides and some of their deoxy and methyl glycoside derivatives in Me/sub 2/SO-d/sub 6/ solutions. Chemical shift and isotope effect data are presented for the pyranose and furanose forms of aldopentoses, aldohexoses, and ketohexoses. The results show that the magnitude of the ..gamma.. effect resulting from deuteration of a hydroxyl on a vicinal carbon atoms is sensitive to the relative geometric relationship, cis or trans, of the hydroxyls in vicinal diol arrays. Thus, the multiplet pattern for carbons 3 and 4 of the pyranose ring can serve as a fingerprint of molecular structure at the pentopyranose level. The aldopentoses and ketohexoses are amenable to structural analysis by this simple approach. Ambiguity will arise for pairs of aldohexoses related to each other by epimerization at C5. Intramolecular hydrogen bonding between the hydroxyls at C2 and C4 in ..cap alpha..-D-talopyranose gives rise to some unusual effects. A mechanism involving isotopic perturbation of the equilibrium between the hydrogen-bonded structures O4-H...O2-H and O2-H...O4-H is suggested as the possible source of these effects. Similarly, the extra splitting observed in the /sup 13/C resonance of C3 of ..beta..-D-fucofuranose are rationalized in terms of an equilibrium between the hydrogen-bonded structures C5-O5-H...O3-H and Cl-O1-H...O3-H. The approach of isotopic multiplets appears to be uniquely suited for the study of such structures.

  3. Apparatus for rapid adjustment of the degree of alignment of NMR samples in aqueous media: verification with residual quadrupolar splittings in (23)Na and (133)Cs spectra.

    PubMed

    Kuchel, Philip W; Chapman, Bogdan E; Müller, Norbert; Bubb, William A; Philp, David J; Torres, Allan M

    2006-06-01

    NMR spectra of (23)Na(+) and (133)Cs(+) in gelatine in a silicone rubber tube that was stretched to various extents showed remarkably reproducible resonance multiplicity. The relative intensities of the components of the split peaks had ratios, 3:4:3, and 7:12:15:16:15:12:7, respectively, that conformed with those predicted using a Mathematica program. The silicone-rubber tube was sealed at its lower end by a small rubber stopper and placed inside a thick-walled glass tube. Gelatine was injected in solution into the silicone tube and 'set' by cooling below 30 degrees C. A plastic thumb-screw held the silicone tube at various degrees of extension, up to approximately 2-fold. After constituting the gel in buffers containing NaCl and CsCl, both (23)Na and (133)Cs NMR spectroscopy revealed that after stretching the initial single Lorentzian line was split into a well-resolved triplet and a heptet, respectively. This was interpreted as being due to coupling between the electric quadrupoles of the nuclei and the average electric field gradient tensor of the collagen molecules of gelatine; these molecules became progressively more aligned in the direction of the main magnetic field, B(0), of the vertical bore magnet, as the gel was stretched. This apparatus provides a simple way of demonstrating fundamental physical characteristics of quadrupolar cations, some characteristics of gelatine under stretching, and a way to invoke static distortion of red blood cells. It should be useful with these and other cell types, for studies of metabolic and membrane transport characteristics that may change when the cells are distorted, and possibly for structural studies of macromolecules.

  4. Apparatus for rapid adjustment of the degree of alignment of NMR samples in aqueous media: Verification with residual quadrupolar splittings in 23Na and 133Cs spectra

    NASA Astrophysics Data System (ADS)

    Kuchel, Philip W.; Chapman, Bogdan E.; Müller, Norbert; Bubb, William A.; Philp, David J.; Torres, Allan M.

    2006-06-01

    NMR spectra of 23Na + and 133Cs + in gelatine in a silicone rubber tube that was stretched to various extents showed remarkably reproducible resonance multiplicity. The relative intensities of the components of the split peaks had ratios, 3:4:3, and 7:12:15:16:15:12:7, respectively, that conformed with those predicted using a Mathematica program. The silicone-rubber tube was sealed at its lower end by a small rubber stopper and placed inside a thick-walled glass tube. Gelatine was injected in solution into the silicone tube and 'set' by cooling below 30 °C. A plastic thumb-screw held the silicone tube at various degrees of extension, up to ˜2-fold. After constituting the gel in buffers containing NaCl and CsCl, both 23Na and 133Cs NMR spectroscopy revealed that after stretching the initial single Lorentzian line was split into a well-resolved triplet and a heptet, respectively. This was interpreted as being due to coupling between the electric quadrupoles of the nuclei and the average electric field gradient tensor of the collagen molecules of gelatine; these molecules became progressively more aligned in the direction of the main magnetic field, B0, of the vertical bore magnet, as the gel was stretched. This apparatus provides a simple way of demonstrating fundamental physical characteristics of quadrupolar cations, some characteristics of gelatine under stretching, and a way to invoke static distortion of red blood cells. It should be useful with these and other cell types, for studies of metabolic and membrane transport characteristics that may change when the cells are distorted, and possibly for structural studies of macromolecules.

  5. Apoflavodoxin (un)folding followed at the residue level by NMR.

    PubMed Central

    van Mierlo, C. P.; van den Oever, J. M.; Steensma, E.

    2000-01-01

    The denaturant-induced (un)folding of apoflavodoxin from Azotobacter vinelandii has been followed at the residue level by NMR spectroscopy. NH groups of 21 residues of the protein could be followed in a series of 1H-15N heteronuclear single-quantum coherence spectra recorded at increasing concentrations of guanidinium hydrochloride despite the formation of protein aggregate. These NH groups are distributed throughout the whole apoflavodoxin structure. The midpoints of unfolding determined by NMR coincide with the one obtained by fluorescence emission spectroscopy. Both techniques give rise to unfolding curves with transition zones at significantly lower denaturant concentrations than the one obtained by circular dichroism spectroscopy. The NMR (un)folding data support a mechanism for apoflavodoxin folding in which a relatively stable intermediate is involved. Native apoflavodoxin is shown to cooperatively unfold to a molten globule-like state with extremely broadened NMR resonances. This initial unfolding step is slow on the NMR chemical shift timescale. The subsequent unfolding of the molten globule is faster on the NMR chemical shift timescale and the limited appearance of 1H-15N HSQC cross peaks of unfolded apoflavodoxin in the denaturant range studied indicates that it is noncooperative. PMID:10739257

  6. Bayesian reconstruction of projection reconstruction NMR (PR-NMR).

    PubMed

    Yoon, Ji Won

    2014-11-01

    Projection reconstruction nuclear magnetic resonance (PR-NMR) is a technique for generating multidimensional NMR spectra. A small number of projections from lower-dimensional NMR spectra are used to reconstruct the multidimensional NMR spectra. In our previous work, it was shown that multidimensional NMR spectra are efficiently reconstructed using peak-by-peak based reversible jump Markov chain Monte Carlo (RJMCMC) algorithm. We propose an extended and generalized RJMCMC algorithm replacing a simple linear model with a linear mixed model to reconstruct close NMR spectra into true spectra. This statistical method generates samples in a Bayesian scheme. Our proposed algorithm is tested on a set of six projections derived from the three-dimensional 700 MHz HNCO spectrum of a protein HasA. PMID:25218584

  7. Correcting human heart 31P NMR spectra for partial saturation. Evidence that saturation factors for PCr/ATP are homogeneous in normal and disease states

    NASA Astrophysics Data System (ADS)

    Bottomley, Paul A.; Hardy, Christopher J.; Weiss, Robert G.

    Heart PCr/ATP ratios measured from spatially localized 31P NMR spectra can be corrected for partial saturation effects using saturation factors derived from unlocalized chest surface-coil spectra acquired at the heart rate and approximate Ernst angle for phosphor creatine (PCr) and again under fully relaxed conditions during each 31P exam. To validate this approach in studies of normal and disease states where the possibility of heterogeneity in metabolite T1 values between both chest muscle and heart and normal and disease states exists, the properties of saturation factors for metabolite ratios were investigated theoretically under conditions applicable in typical cardiac spectroscopy exams and empirically using data from 82 cardiac 31P exams in six study groups comprising normal controls ( n = 19) and patients with dilated ( n = 20) and hypertrophic ( n = 5) cardiomyopathy, coronary artery disease ( n = 16), heart transplants ( n = 19), and valvular heart disease ( n = 3). When TR ≪ T1,(PCr), with T1(PCr) ⩾ T1(ATP), the saturation factor for PCr/ATP lies in the range 1.5 ± 0.5, regardless of the T1 values. The precise value depends on the ratio of metabolite T1 values rather than their absolute values and is insensitive to modest changes in TR. Published data suggest that the metabolite T1 ratio is the same in heart and muscle. Our empirical data reveal that the saturation factors do not vary significantly with disease state, nor with the relative fractions of muscle and heart contributing to the chest surface-coil spectra. Also, the corrected myocardial PCr/ATP ratios in each normal or disease state bear no correlation with the corresponding saturation factors nor the fraction of muscle in the unlocalized chest spectra. However, application of the saturation correction (mean value, 1.36 ± 0.03 SE) significantly reduced scatter in myocardial PCr/ATP data by 14 ± 11% (SD) ( p ⩽ 0.05). The findings suggest that the relative T1 values of PCr and ATP are

  8. Mammalian production of an isotopically enriched outer domain of the HIV-1 gp120 glycoprotein for NMR spectroscopy.

    PubMed

    Sastry, Mallika; Xu, Ling; Georgiev, Ivelin S; Bewley, Carole A; Nabel, Gary J; Kwong, Peter D

    2011-07-01

    NMR spectroscopic characterization of the structure or the dynamics of proteins generally requires the production of samples isotopically enriched in (15)N, (13)C, or (2)H. The bacterial expression systems currently in use to obtain isotopic enrichment, however, cannot produce a number of eukaryotic proteins, especially those that require post-translational modifications such as N-linked glycosylation for proper folding or activity. Here, we report the use of an adenovirus vector-based mammalian expression system to produce isotopically enriched (15)N or (15)N/(13)C samples of an outer domain variant of the HIV-1 gp120 envelope glycoprotein with 15 sites of N-linked glycosylation. Yields for the (15)N- and (15)N/(13)C-labeled gp120s after affinity chromatography were 45 and 44 mg/l, respectively, with an average of over 80% isotope incorporation. Recognition of the labeled gp120 by cognate antibodies that recognize complex epitopes showed affinities comparable to the unlabeled protein. NMR spectra, including (1)H-(15)N and (1)H-(13)C HSQCs, (15)N-edited NOESY-HSQC, and 3D HNCO, were of high quality, with signal-to-noise consistent with an efficient level of isotope incorporation, and with chemical shift dispersion indicative of a well-folded protein. The exceptional protein yields, good isotope incorporation, and ability to obtain well-folded post-translationally modified proteins make this mammalian system attractive for the production of isotopically enriched eukaryotic proteins for NMR spectroscopy. PMID:21667299

  9. In vivo uniform (15)N-isotope labelling of plants: using the greenhouse for structural proteomics.

    PubMed

    Ippel, Johannes H; Pouvreau, Laurice; Kroef, Toos; Gruppen, Harry; Versteeg, Geurt; van den Putten, Peter; Struik, Paul C; van Mierlo, Carlo P M

    2004-01-01

    Isotope labelling of proteins is important for progress in the field of structural proteomics. It enables the utilisation of the power of nuclear magnetic resonance spectroscopy (NMR) for the characterisation of the three-dimensional structures and corresponding dynamical features of proteins. The usual approach to obtain isotopically labelled protein molecules is by expressing the corresponding gene in bacterial or yeast host organisms, which grow on isotope-enriched media. This method has several drawbacks. Here, we demonstrate that it is possible to fully label a plant with (15)N-isotopes. The advantage of in vivo labelling of higher organisms is that all constituting proteins are labelled and become available as functional, post-translationally modified, correctly folded proteins. A hydroponics set-up was used to create the first example of a uniformly (15)N-labelled (> 98%) plant species, the potato plant (Solanum tuberosum L., cv. Elkana). Two plants were grown at low costs using potassium-[(15)N]-nitrate as the sole nitrogen source. At harvest time, a total of 3.6 kg of potato tubers and 1.6 kg of foliage, stolons and roots were collected, all of which were fully (15)N-labelled. Gram quantities of soluble (15)N-labelled proteins (composed mainly of the glycoprotein patatin and Kunitz-type protease inhibitors) were isolated from the tubers. NMR results on the complete proteome of potato sap and on an isolated protease inhibitor illustrate the success of the labelling procedure. The presented method of isotope labelling is easily modified to label other plants. Its envisioned impact in the field of structural proteomics of plants is discussed.

  10. Potential probe for examining opiate-receptor interactions: model compound study of dynamic effects on /sup 15/N INEPT enhancements

    SciTech Connect

    Schilling, K.H.; Mikita, M.A.

    1987-10-01

    Model systems were chosen in an attempt to mimic the proton exchange environment of an agonist nitrogen in an opiate-receptor interaction. The two model systems studied were an ammonium: 18-crown-6 ether complex and a quinuclidine-trifluoroacetic acid ion pair. Each system was examined for their effects on /sup 15/N NMR INEPT enhancements. Both models were found to retard proton exchange dynamics, as observed by increased enhancements relative to free ions in neutral aqueous solutions. These results suggest that the confinement of a protonated nitrogen, such as that expected in receptor binding, may alter exchange dynamics to favor INEPT enhancements, while unbound agonists would remain unenhanced. As a result, /sup 15/N NMR INEPT enhancements from a solution of receptor subtypes with an appropriate /sup 15/N-labeled agonist may present a means of exploring the dynamics of direct opiate-receptor interactions.

  11. HOMO-LUMO, UV, NLO, NMR and vibrational analysis of 3-methyl-1-phenylpyrazole using FT-IR, FT-RAMAN FT-NMR spectra and HF-DFT computational methods.

    PubMed

    Carthigayan, K; Xavier, S; Periandy, S

    2015-05-01

    In this paper, the spectral analysis of 3-methyl-1-phenylpyrazole is carried out using the FT-IR, FT Raman, FT NMR and UV-Vis spectra with the help of quantum mechanical computations using HF and density functional theories. The different conformers of the compound and their minimum energies are studied using B3LYP functional with 6-311+G (d,p) basis set and the most stable conformer with minimum energy was identified and the same conformer was used for further computations. The computed wave numbers 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 HF and B3LYP 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 thermodynamic properties (heat capacity, entropy and enthalpy) at different temperatures are also calculated. PMID:25710893

  12. HOMO-LUMO, UV, NLO, NMR and vibrational analysis of 3-methyl-1-phenylpyrazole using FT-IR, FT-RAMAN FT-NMR spectra and HF-DFT computational methods.

    PubMed

    Carthigayan, K; Xavier, S; Periandy, S

    2015-05-01

    In this paper, the spectral analysis of 3-methyl-1-phenylpyrazole is carried out using the FT-IR, FT Raman, FT NMR and UV-Vis spectra with the help of quantum mechanical computations using HF and density functional theories. The different conformers of the compound and their minimum energies are studied using B3LYP functional with 6-311+G (d,p) basis set and the most stable conformer with minimum energy was identified and the same conformer was used for further computations. The computed wave numbers 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 HF and B3LYP 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 thermodynamic properties (heat capacity, entropy and enthalpy) at different temperatures are also calculated.

  13. Effect of organic matter application on CP-MAS-13C-NMR spectra of humic acids from a brown soil

    NASA Astrophysics Data System (ADS)

    Dou, S.

    2009-04-01

    -MAS-13C-NMR spectrum of HA. The CP-MAS- 13C-NMR spectra of the HA were quite similar to each other. These spectra exhibited signals for alkyl (0~50 ppm), O-alkyl (50~110 ppm), aromatic (110~160 ppm) and carbonyl (160~200 ppm) regions. The signals in carbonyl C region concentrated between 172 ppm and 173 ppm, and with a small signal occurred in the region of 190~200 ppm, indicating that there was carbonyl C of carboxylic acid, ester and amide, but a little amount carbonyl C of ketonic compounds. In the region of aromatic C, the most obvious peaks were the absorption at 131~133 ppm and 114~117 ppm. The former was mainly the aromatic C substituted by -COOH or -COOMe and the unsubstituted aromatic meta to carbons bearing an oxygen or nitrogen atom; the latter was mainly the unsubstituted aromatic C ortho and para to carbons bearing an oxygen and nitrogen atom. There was a small peak at 152-154ppm, which was the signal of phenolic OH. The signal at 55~56 ppm was methoxyl C. The signals at 71~73 ppm were due to the -CH(OH)- in carbohydrate. The peak at 102~103 ppm was generally assigned to double oxygen-C in polysaccharide (possibly acetal). The maximum absorption at 30 ppm was the contribution of the polymethylene chain -(CH2)n- in saturated hydrocarbons (Wilson, 1981). After OM application, the contents of alkyl C and O-alkyl C increased and the contents of aromatic C and carbonxyl C except to 1986 decreased. Compared with 1986, the contents of O-alkyl C increased and the contents of alkyl C decreased for the same treatment CKbr and O2. Aromaticity decreased significantly in OM treatments, indicating that the OM decreased the content of aromatic C and was simplified the molecular structure. The relative content of O-alkyl C increased indicating that OM application increased the content of methoxyl C and -CH(OH)- in carbohydrate. Alkyl C was probably derived from compounds of plants with high resistance to degradation, such as cutin and suberin (Baldock et al., 1992; Preston

  14. Cosine Modulated HSQC: A Rapid Determination of 3JHNHα Scalar Couplings in 15N-labeled Proteins

    NASA Astrophysics Data System (ADS)

    Petit, Audrey; Vincent, Sébastien J. F.; Zwahlen, Catherine

    2002-06-01

    A two-dimensional HSQC-based NMR method, 15N-COSMO-HSQC, is presented for the rapid determination of homonuclear 3JHNHα couplings in 15N-labeled proteins in solution. Scalar couplings are extracted by comparing the intensity of two separate datasets recorded with and without decoupling of the 3JHNHα during a preparation period. The scalar couplings are introduced through a cosine modulation of the peak intensities. The experiment relies on a BIRD sandwich to selectively invert all amide protons H N and is very simple to implement. 3JHNHα couplings were determined using both the 15N-COSMO-HSQC and quantitative- J on 15N-labeled chemokine RANTES. The two experiments show well-correlated values.

  15. 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

  16. Crystal versus solution structure of enzymes: NMR spectroscopy of a peptide boronic acid-serine protease complex in the crystalline state.

    PubMed Central

    Farr-Jones, S; Smith, S O; Kettner, C A; Griffin, R G; Bachovchin, W W

    1989-01-01

    The effectiveness of boronic acids as inhibitors of serine proteases has been widely ascribed to the ability of the boronyl group to form a tetrahedral adduct with the active-site serine that closely mimics the putative tetrahedral intermediate or transition state formed with substrates. However, recent 15N NMR studies of alpha-lytic protease (EC 3.4.21.12) in solution have shown that some boronic acids and peptide boronic acids form adducts with the active-site histidine instead of with the serine. Such histidine-boron adducts have not thus far been reported in x-ray diffraction studies of boronic acid-serine protease complexes. Here, we report an 15N NMR study of the MeOSuc-Ala-Ala-Pro-boroPhe complex of alpha-lytic protease in the crystalline state using magic-angle spinning. Previous 15N NMR studies have shown this complex involves the formation of a histidine-boron bond in solution. The 15N NMR spectra of the crystalline complex are essentially identical to those of the complex in solution, thereby showing that the structure of this complex is the same in solution and in the crystal and that both involve formation of a histidine-boron adduct. PMID:2780549

  17. Ferroelastic phase transitions by 14N NMR spectra in [N(CH3)4]2CoCl4 and [N(CH3)4]2ZnCl4 single crystals

    NASA Astrophysics Data System (ADS)

    Lim, Ae Ran

    2016-09-01

    Changes in the structural geometry of [N(CH3)4]2BCl4 (B=Co and Zn) crystals near the phase transition temperatures were studied by analyzing the 14N nuclear magnetic resonance (NMR) spectra. Two physically inequivalent a-N(1)(CH3)4 and b-N(2)(CH3)4 groups were observed in these spectra. Abrupt changes in the resonance frequency and splitting of 14N NMR signals near the phase transition temperatures were attributed to structural phase transitions, and the primary mechanism of these phase transitions exhibited ferroelastic characteristics. In addition, ferroelasticity of [N(CH3)4]2BCl4 was identified at low temperatures using optical polarizing microscopy.

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

  19. Quantum-chemical simulation of 1H NMR spectra. 2. Comparison of DFT-based procedures for computing proton-proton coupling constants in organic molecules.

    PubMed

    Bally, Thomas; Rablen, Paul R

    2011-06-17

    The performance of 250 different computational protocols (combinations of density functionals, basis sets and methods) was assessed on a set of 165 well-established experimental (1)H-(1)H nuclear coupling constants (J(H-H)) from 65 molecules spanning a wide range of "chemical space". Thereby we found that, if one uses core-augmented basis sets and allows for linear scaling of the raw results, calculations of only the Fermi contact term yield more accurate predictions than calculations where all four terms that contribute to J(H-H) are evaluated. It turns out that B3LYP/6-31G(d,p)u+1s is the best (and, in addition, one of the most economical) of all tested methods, yielding predictions of J(H-H) with a root-mean-square deviation from experiment of less than 0.5 Hz for our test set. Another method that does similarly well, without the need for additional 1s basis functions, is B3LYP/cc-pVTZ, which is, however, ca. 8 times more "expensive" in terms of CPU time. A selection of the better methods was tested on a probe set comprising 61 J(H-H) values from 37 molecules. In this set we also included five molecules where conformational averaging is required. The rms deviations were better than or equal to those with the training set, which indicates that the method we recommend is generally applicable for organic molecules. We give instructions on how to carry out calculations of (1)H chemical shifts and J(H-H) most economically and provide scripts to extract the relevant information from the outputs of calculations with the Gaussian program in clearly arranged form, e.g., to feed them into programs for simulating entire (1)H NMR spectra.

  20. Alterations in the natural abundance /sup 13/C NMR spectra of skeletal muscle membranes depending on the extraction medium of muscle

    SciTech Connect

    Barany, M.; Arus, C.; Anderson, J.A.; Marotta, S.F.

    1986-03-01

    Minced rat muscles were extracted with NaCl solution with additions: 1) 10 mM EDTA, or 2) 2 mM MgCl/sub 2/, or 3) None (final ionic strength equivalent to 150 mM NaCl, pH 7.0). The total muscle membranes were pelleted between 1500 and 252,000 x g. All membranes were washed several times by homogenization with 0.05 M NaCl, pH 6.1, and centrifugation at 252,000 x g. The final pellets were suspended in /sup 2/H/sub 2/O to contain 150 mg membrane protein/ml in 30% /sup 2/H/sub 2/O. /sup 13/C NMR spectra were recorded at 50.3 MHz, under fully relaxed conditions. The spectral pattern varied according to the extraction medium of muscle: Relative to None addition, EDTA caused a decrease in the intensity of the polyunsaturated carbon resonance (128.6 ppm), whereas with MgCl/sub 2/ the opposite effect was found. Metal analysis, after combustion of the membranes, showed 1.1-1.6 mol Ca/sup 2 +/ per 10/sup 5/ g protein in None and Mgcl/sub 2/ membranes, and 1000-times less Ca/sup 2 +/ in EDTA membranes. The Mg/sup 2 +/ content of the membranes was not affected by EDTA, however, it was increased 5-fold when MgCl/sub 2/ was present in the extraction medium. Thus, the results indicate that membrane-bound Ca/sup 2 +/ and Mg/sup 2 +/ alter the conformation of membrane-phospholipis.

  1. Effect of organic matter application on CP-MAS-13C-NMR spectra of humic acids from a brown soil

    NASA Astrophysics Data System (ADS)

    Dou, S.

    2009-04-01

    -MAS-13C-NMR spectrum of HA. The CP-MAS- 13C-NMR spectra of the HA were quite similar to each other

  2. LINE LISTS FOR THE A {sup 2}Π-X {sup 2}Σ{sup +} (RED) AND B {sup 2}Σ{sup +}-X {sup 2}Σ{sup +} (VIOLET) SYSTEMS OF CN, {sup 13}C{sup 14}N, AND {sup 12}C{sup 15}N, AND APPLICATION TO ASTRONOMICAL SPECTRA

    SciTech Connect

    Sneden, Christopher; Lucatello, Sara; Ram, Ram S.; Brooke, James S. A.; Bernath, Peter E-mail: sara.lucatello@oapd.inaf.it E-mail: jsabrooke@gmail.com

    2014-10-01

    New red and violet system line lists for the CN isotopologues {sup 13}C{sup 14}N and {sup 12}C{sup 15}N have been generated. These new transition data are combined with those previously derived for {sup 12}C{sup 14}N, and applied to the determination of CNO abundances in the solar photosphere and in four red giant stars: Arcturus, the bright, very low-metallicity star HD 122563, and the carbon-enhanced metal-poor stars HD 196944 and HD 201626. When both red and violet system lines are detectable in a star, their derived N abundances are in good agreement. The mean N abundances determined in this work are also generally in accord with published values.

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

    PubMed

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

    2013-09-17

    Many structures of the proteins and protein assemblies that play central roles in fundamental biological processes and disease pathogenesis are not readily accessible via the conventional techniques of single-crystal X-ray diffraction and solution-state nuclear magnetic resonance (NMR). On the other hand, many of these challenging biological systems are suitable targets for atomic-level structural and dynamic analysis by magic-angle spinning (MAS) solid-state NMR spectroscopy, a technique that has far less stringent limitations on the molecular size and crystalline state. Over the past decade, major advances in instrumentation and methodology have prompted rapid growth in the field of biological solid-state NMR. However, despite this progress, one challenge for the elucidation of three-dimensional (3D) protein structures via conventional MAS NMR methods is the relative lack of long-distance data. Specifically, extracting unambiguous interatomic distance restraints larger than ∼5 Å from through-space magnetic dipole-dipole couplings among the protein (1)H, (13)C, and (15)N nuclei has proven to be a considerable challenge for researchers. It is possible to circumvent this problem by extending the structural studies to include several analogs of the protein of interest, intentionally modified to contain covalently attached paramagnetic tags at selected sites. In these paramagnetic proteins, the hyperfine couplings between the nuclei and unpaired electrons can manifest themselves in NMR spectra in the form of relaxation enhancements of the nuclear spins that depend on the electron-nucleus distance. These effects can be significant for nuclei located up to ∼20 Å away from the paramagnetic center. In this Account, we discuss MAS NMR structural studies of nitroxide and EDTA-Cu(2+) labeled variants of a model 56 amino acid globular protein, B1 immunoglobulin-binding domain of protein G (GB1), in the microcrystalline solid phase. We used a set of six EDTA-Cu(2

  4. Solid-state NMR study and assignments of the KcsA potassium ion channel of S. lividans.

    PubMed

    Varga, Krisztina; Tian, Lin; McDermott, Ann E

    2007-12-01

    The extraordinary efficiency and selectivity of potassium channels have made them ideal systems for biophysical and functional studies of ion conduction. We carried out solid-state NMR studies of the selectivity filter region of the protein. Partial site-specific assignments of the NMR signals were obtained based on high field multidimensional solid-state NMR spectra of uniformly (13)C, (15)N enriched KcsA potassium channel from Streptomyces lividans. Both backbone and sidechain atoms were assigned for residues V76-D80 and P83-L90, in and near the selectivity filter region of the protein; this region exhibits good dispersion and useful chemical shift fingerprints. This study will enable structure, dynamic and mechanistic studies of ion conduction by NMR.

  5. Utilizing the charge field effect on amide (15)N chemical shifts for protein structure validation.

    PubMed

    Bader, Reto

    2009-01-01

    Of all the nuclei in proteins, the nuclear magnetic resonance (NMR) chemical shifts of nitrogen are the theoretically least well understood. In this study, quantum chemical methods are used in combination with polarizable-continuum models in order to show that consideration of the effective electric field, including charge screening due to solvation, improves considerably the consistencies of statistical relationships between experimental and computed amide (15)N shifts between various sets of charged and uncharged oligopeptides and small organic molecules. A single conversion scheme between shielding parameters from first principles using density functional theory (DFT) and experimental shifts is derived that holds for all classes of compounds examined here. This relationship is then used to test the accuracy of such (15)N chemical shift predictions in the cyclic decapeptide antibiotic gramicidin S (GS). GS has previously been studied in great detail, both by NMR and X-ray crystallography. It adopts a well-defined backbone conformation, and hence, only a few discrete side chain conformational states need to be considered. Moreover, a charge-relay effect of the two cationic ornithine side chains to the protein backbone has been described earlier by NMR spectroscopy. Here, DFT-derived backbone amide nitrogen chemical shifts were calculated for multiple conformations of GS. Overall, the structural dynamics of GS is revisited in view of chemical shift behavior along with energetic considerations. Together, the study demonstrates proof of concept that (15)N chemical shift information is particularly useful in the analysis and validation of protein conformational states in a charged environment.

  6. An economic approach to efficient isotope labeling in insect cells using homemade 15N-, 13C- and 2H-labeled yeast extracts.

    PubMed

    Opitz, Christian; Isogai, Shin; Grzesiek, Stephan

    2015-07-01

    Heterologous expression of proteins in insect cells is frequently used for crystallographic structural studies due to the high yields even for challenging proteins requiring the eukaryotic protein processing capabilities of the host. However for NMR studies, the need for isotope labeling poses extreme challenges in eukaryotic hosts. Here, we describe a robust method to achieve uniform protein (15)N and (13)C labeling of up to 90 % in baculovirus-infected insect cells. The approach is based on the production of labeled yeast extract, which is subsequently supplemented to insect cell growth media. The method also allows deuteration at levels of >60 % without decrease in expression yield. The economic implementation of the labeling procedures into a standard structural biology laboratory environment is described in a step-by-step protocol. Applications are demonstrated for a variety of NMR experiments using the Abelson kinase domain, GFP, and the beta-1 adrenergic receptor as examples. Deuterated expression of the latter provides spectra of very high quality of a eukaryotic G-protein coupled receptor.

  7. Limiting Values of the 15N Chemical Shift of the Imidazole Ring of Histidine at High-pH§

    PubMed Central

    Vila, Jorge A.

    2012-01-01

    Tautomeric identification by direct observation of 15N chemical shifts of the imidazole ring of histidine (His) has become a common practice in NMR spectroscopy. However, such applications require knowledge of the “canonical” limiting values of the 15N chemical shift of the imidazole ring of His in which each form of His, namely the protonated (H+) and the tautomeric Nε2-H and Nδ1-H forms, respectively, is present to the extent of 100%. So far, the adopted canonical limiting values of the 15N chemical shift have been those available from model compounds. As to whether these canonical values reflect those of the individual pure forms of His is investigated here by carrying out an analysis of the second-order shielding differences, ΔΔ = |Δε − Δδ, with Δξ(ξ = ε or δ) being the DFT-computed average shielding differences between the two nitrogens of the imidazole ring of His in each pure tautomeric form. In the high-pH limit the results indicate that the (i) ΔΔ values from the DFT-computed shielding, but not from the commonly-used canonical limiting values, are in closer agreement with those obtained with experimental chemical shift data from model compounds in solution and solid-state NMR; and (ii) commonly-used canonical limiting values of the 15N chemical shifts lead to an average tautomeric equilibrium constant that differs by a factor of ~2.6 from the one computed by using DFT-based 15N limiting values, raising concern about the practice of using canonical limiting 15N values; this can be avoided by reporting tautomeric equilibrium constants computed by using only limiting 15N values for the Nε2-H tautomer. PMID:22376024

  8. 1H, 13C, and 15N backbone, side-chain, and heme chemical shift assignments for oxidized and reduced forms of the monoheme c-type cytochrome ApcA isolated from the acidophilic metal-reducing bacterium Acidiphilium cryptum.

    SciTech Connect

    Cort, John R.; Swenson, Michael; Magnuson, Timothy S.

    2011-03-04

    We report the 1H, 13C, and 15N chemical shift assignments of both oxidized and reduced forms of an abundant periplasmic c-type cytochrome, designated ApcA, from the acidophilic gram-negative facultatively anaerobic metal-reducing alpha-proteobacterium Acidiphilium cryptum. These resonance assignments prove that ApcA is a monoheme cytochrome c2 and the product of the Acry_2099 gene. An absence of resonance peaks in the NMR spectra for the 21 N-terminal residues suggests that a predicted N-terminal signal sequence is cleaved. We also describe the preparation and purification of the protein in labeled form from laboratory cultures of A. cryptum growing on 13C- and 15N- labeled substrates.

  9. 19F high magnetic field NMR study of beta-ZrF4 and CeF4: from spectra reconstruction to correlation between fluorine sites and 19F isotropic chemical shifts.

    PubMed

    Legein, C; Fayon, F; Martineau, C; Body, M; Buzaré, J-Y; Massiot, D; Durand, E; Tressaud, A; Demourgues, A; Péron, O; Boulard, B

    2006-12-25

    High magnetic field and high spinning frequency one- and two-dimensional one-pulse MAS 19F NMR spectra of beta-ZrF4 and CeF4 were recorded and reconstructed allowing the accurate determination of the 19F chemical shift tensor parameters for the seven different crystallographic fluorine sites of each compound. The attributions of the NMR resonances are performed using the superposition model for 19F isotropic chemical shift calculation initially proposed by Bureau et al. (Bureau, B.; Silly, G.; Emery, J.; Buzaré, J.-Y. Chem. Phys. 1999, 249, 85-104). A satisfactory reliability is reached with a root-mean-square (rms) deviation between calculated and measured isotropic chemical shift values equal to 1.5 and 3.5 ppm for beta-ZrF4 and CeF4, respectively. PMID:17173418

  10. Environmentally friendly flame retardants. A detailed solid-state NMR study of melamine orthophosphate.

    PubMed

    Brinkmann, Andreas; Litvinov, Victor M; Kentgens, Arno P M

    2007-12-01

    We used solid-state NMR spectroscopy to gain detailed information about the proton positions, proximities and the hydrogen-bonding network in the environmentally friendly flame retardant melamine orthophosphate (MP). High-resolution proton one- and two-dimensional solid-state NMR spectra were obtained at high external magnetic field in combination with fast magic angle spinning of the sample. Furthermore, we recorded homo- and heteronuclear correlation spectra of types (15)N–(15)N, (1)H–(13)C, (1)H–(15)N and (1)H–(31)P. In addition, we determined the geometry of the NH and NH(2) groups in MP by (15)N–(1)H heteronuclear recoupling experiments.We were able to completely assign the different isotropic chemical shifts in MP. Furthermore, we could identify the protonation of the melamine and orthophosphate moieties. The experimental results are discussed in connection with the structural model obtained by powder X-ray diffraction together with a combined molecular modeling-Rietveld refinement approach (De Ridder et al. Helv. Chim. Acta 2004; 87: 1894). We show that the geometry of the NH2 groups can only be successfully estimated by solid-state NMR. PMID:18157843

  11. FT-IR, FT-Raman, UV, NMR spectra and molecular structure investigation of (E)-2-(3-chloropyrazin-2-yl)-1-(3-ethyl-2, 6-diphenyl piperidin-4-ylidene) hydrazine: A combined experimental and theoretical study

    NASA Astrophysics Data System (ADS)

    Therasa Alphonsa, A.; Loganathan, C.; Athavan Alias Anand, S.; Kabilan, S.

    2015-11-01

    This work presents the characterization of (E)-2-(3-chloropyrazin-2-yl)-1-(3-ethyl-2, 6-diphenyl piperidin-4-ylidene) hydrazine (HDE) by quantum chemical calculations and spectral techniques. The structure was investigated by FT-IR, FT-Raman, UV-vis and NMR techniques. The geometrical parameters and energies have been obtained from Density functional theory (DFT) B3LYP (6-31G (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 total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method. 1H and 13C NMR chemical shifts of the molecule were calculated using Gauge-independent atomic orbital method (GIAO). The electronic properties such as excitation energies, wavelength, HOMO, LUMO energies performed by Time dependent density functional theory (TD-DFT) results complements with the experimental findings. NBO analysis has been performed for analyzing charge delocalization throughout the molecule. The calculation results were applied to simulate spectra of the title compound, which show excellent agreement with observed spectra. To provide information about the interactions between human cytochrome protein and the novel compound theoretically, docking studies were carried out using Schrödinger software.

  12. (15)N Heteronuclear Chemical Exchange Saturation Transfer MRI.

    PubMed

    Zeng, Haifeng; Xu, Jiadi; Yadav, Nirbhay N; McMahon, Michael T; Harden, Bradley; Frueh, Dominique; van Zijl, Peter C M

    2016-09-01

    A two-step heteronuclear enhancement approach was combined with chemical exchange saturation transfer (CEST) to magnify (15)N MRI signal of molecules through indirect detection via water protons. Previous CEST studies have been limited to radiofrequency (rf) saturation transfer or excitation transfer employing protons. Here, the signal of (15)N is detected indirectly through the water signal by first inverting selectively protons that are scalar-coupled to (15)N in the urea molecule, followed by chemical exchange of the amide proton to bulk water. In addition to providing a small sensitivity enhancement, this approach can be used to monitor the exchange rates and thus the pH sensitivity of the participating (15)N-bound protons. PMID:27548755

  13. hNCOcanH pulse sequence and a robust protocol for rapid and unambiguous assignment of backbone ((1)H(N), (15)N and (13)C') resonances in (15)N/(13)C-labeled proteins.

    PubMed

    Kumar, Dinesh; Hosur, Ramakrishna V

    2011-09-01

    A three-dimensional nuclear magnetic resonance (NMR) pulse sequence named as hNCOcanH has been described to aid rapid sequential assignment of backbone resonances in (15)N/(13)C-labeled proteins. The experiment has been derived by a simple modification of the previously described HN(C)N pulse sequence [Panchal et al., J. Biomol. NMR 20 (2001) 135-147]; t2 evolution is used to frequency label (13)C' rather than (15)N (similar trick has also been used in the design of hNCAnH pulse sequence from hNcaNH [Frueh et al., JACS, 131 (2009) 12880-12881]). The modification results in a spectrum equivalent to HNCO, but in addition to inter-residue correlation peaks (i.e. Hi , Ci-1), the spectrum also contains additional intra-residue correlation peaks (i.e. Hi-1 , Ci-1) in the direct proton dimension which has maximum resolution. This is the main strength of the experiment and thus, even a small difference in amide (1) H chemical shifts (5-6 Hz) can be used for establishing a sequential connectivity. This experiment in combination with the HNN experiment described previously [Panchal et al., J. Biomol. NMR 20 (2001) 135-147] leads to a more robust assignment protocol for backbone resonances ((1) H(N) , (15)N) than could be derived from the combination of HNN and HN(C)N experiments [Bhavesh et al., Biochemistry, 40 (2001) 14727-14735]. Further, this new protocol enables assignment of (13)C' resonances as well. We believe that the experiment and the protocol presented here will be of immense value for structural-and functional-proteomics research by NMR. Performance of this experiment has been demonstrated using (13)C/(15)N labeled ubiquitin.

  14. hNCOcanH pulse sequence and a robust protocol for rapid and unambiguous assignment of backbone ((1)H(N), (15)N and (13)C') resonances in (15)N/(13)C-labeled proteins.

    PubMed

    Kumar, Dinesh; Hosur, Ramakrishna V

    2011-09-01

    A three-dimensional nuclear magnetic resonance (NMR) pulse sequence named as hNCOcanH has been described to aid rapid sequential assignment of backbone resonances in (15)N/(13)C-labeled proteins. The experiment has been derived by a simple modification of the previously described HN(C)N pulse sequence [Panchal et al., J. Biomol. NMR 20 (2001) 135-147]; t2 evolution is used to frequency label (13)C' rather than (15)N (similar trick has also been used in the design of hNCAnH pulse sequence from hNcaNH [Frueh et al., JACS, 131 (2009) 12880-12881]). The modification results in a spectrum equivalent to HNCO, but in addition to inter-residue correlation peaks (i.e. Hi , Ci-1), the spectrum also contains additional intra-residue correlation peaks (i.e. Hi-1 , Ci-1) in the direct proton dimension which has maximum resolution. This is the main strength of the experiment and thus, even a small difference in amide (1) H chemical shifts (5-6 Hz) can be used for establishing a sequential connectivity. This experiment in combination with the HNN experiment described previously [Panchal et al., J. Biomol. NMR 20 (2001) 135-147] leads to a more robust assignment protocol for backbone resonances ((1) H(N) , (15)N) than could be derived from the combination of HNN and HN(C)N experiments [Bhavesh et al., Biochemistry, 40 (2001) 14727-14735]. Further, this new protocol enables assignment of (13)C' resonances as well. We believe that the experiment and the protocol presented here will be of immense value for structural-and functional-proteomics research by NMR. Performance of this experiment has been demonstrated using (13)C/(15)N labeled ubiquitin. PMID:21818779

  15. PIC microcontroller based external fast analog to digital converter to acquire wide-lined solid NMR spectra by BRUKER DRX and Avance-I spectrometers.

    PubMed

    Koczor, Bálint; Rohonczy, János

    2015-01-01

    Concerning many former liquid or hybrid liquid/solid NMR consoles, the built in Analog-to-Digital Converters (ADCs) are incapable of digitizing the fids at sampling rates in the MHz range. Regarding both strong anisotropic interactions in the solid state and wide chemical shift dispersion nuclei in solution phase such as (195)Pt, (119)Sn, (207)Pb etc., the spectrum range of interest might be in the MHz range. As determining the informative tensor components of anisotropic NMR interactions requires nonlinear fitting over the whole spectrum including the asymptotic baseline, it is prohibited by low sampling rates of the ADCs. Wide spectrum width is also useful in solution NMR, since windowing of wide chemical shift ranges is avoidable. We built an external analog to digital converter with 10 MHz maximal sampling rate, which can work simultaneously with the built in ADC of the spectrometer. The ADC was tested on both Bruker DRX and Avance-I NMR consoles. In addition to the analog channels it only requires three external digital lines of the NMR console. The ADC sends data to PC via USB. The whole process is controlled by software written in JAVA which is implemented under TopSpin.

  16. Affordable uniform isotope labeling with (2)H, (13)C and (15)N in insect cells.

    PubMed

    Sitarska, Agnieszka; Skora, Lukasz; Klopp, Julia; Roest, Susan; Fernández, César; Shrestha, Binesh; Gossert, Alvar D

    2015-06-01

    For a wide range of proteins of high interest, the major obstacle for NMR studies is the lack of an affordable eukaryotic expression system for isotope labeling. Here, a simple and affordable protocol is presented to produce uniform labeled proteins in the most prevalent eukaryotic expression system for structural biology, namely Spodoptera frugiperda insect cells. Incorporation levels of 80% can be achieved for (15)N and (13)C with yields comparable to expression in full media. For (2)H,(15)N and (2)H,(13)C,(15)N labeling, incorporation is only slightly lower with 75 and 73%, respectively, and yields are typically twofold reduced. The media were optimized for isotope incorporation, reproducibility, simplicity and cost. High isotope incorporation levels for all labeling patterns are achieved by using labeled algal amino acid extracts and exploiting well-known biochemical pathways. The final formulation consists of just five commercially available components, at costs 12-fold lower than labeling media from vendors. The approach was applied to several cytosolic and secreted target proteins. PMID:25929326

  17. Sequence-specific {sup 1}H, {sup 13}C, and {sup 15}N resonance assignments for intestinal fatty-acid-binding protein complexed with palmitate (15.4 kDA)

    SciTech Connect

    Hodsdon, M.E.; Toner, J.J.; Cistola, D.P.

    1994-12-01

    Intestinal fatty-acid-binding protein (I-FABP) belongs to a family of soluble, cytoplasmic proteins that are thought to function in the intracellular transport and trafficking of polar lipids. Individual members of this protein family have distinct specificities and affinities for fatty acids, cholesterol, bile salts, and retinoids. We are comparing several retinol- and fatty-acid-binding proteins from intestine in order to define the factors that control molecular recognition in this family of proteins. We have established sequential resonance assignments for uniformly {sup 13}C/{sup 15}N-enriched I-FABP complexed with perdeuterated palmitate at pH7.2 and 37{degrees}C. The assignment strategy was similar to that introduced for calmodulin. We employed seven three-dimensional NMR experiments to establish scalar couplings between backbone and sidechain atoms. Backbone atoms were correlated using triple-resonance HNCO, HNCA, TOCSY-HMQC, HCACO, and HCA(CO)N experiments. Sidechain atoms were correlated using CC-TOCSY, HCCH-TOCSY, and TOCSY-HMQC. The correlations of peaks between three-dimensional spectra were established in a computer-assisted manner using NMR COMPASS (Molecular Simulations, Inc.) Using this approach, {sup 1}H, {sup 13}C, and {sup 15}N resonance assignments have been established for 120 of the 131 residues of I-FABP. For 18 residues, amide {sup 1}H and {sup 15}N resonances were unobservable, apparently because of the rapid exchange of amide protons with bulk water at pH 7.2. The missing amide protons correspond to distinct amino acid patterns in the protein sequence, which will be discussed. During the assignment process, several sources of ambiguity in spin correlations were observed. To overcome this ambiguity, the additional inter-residue correlations often observed in the HNCA experiment were used as cross-checks for the sequential backbone assignments.

  18. 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.

  19. Conformation of alamethicin in oriented phospholipid bilayers determined by (15)N solid-state nuclear magnetic resonance.

    PubMed Central

    Bak, M; Bywater, R P; Hohwy, M; Thomsen, J K; Adelhorst, K; Jakobsen, H J; Sørensen, O W; Nielsen, N C

    2001-01-01

    The conformation of the 20-residue antibiotic ionophore alamethicin in macroscopically oriented phospholipid bilayers has been studied using (15)N solid-state nuclear magnetic resonance (NMR) spectroscopy in combination with molecular modeling and molecular dynamics simulations. Differently (15)N-labeled variants of alamethicin and an analog with three of the alpha-amino-isobutyric acid residues replaced by alanines have been investigated to establish experimental structural constraints and determine the orientation of alamethicin in hydrated phospholipid (dimyristoylphosphatidylcholine) bilayers and to investigate the potential for a major kink in the region of the central Pro(14) residue. From the anisotropic (15)N chemical shifts and (1)H-(15)N dipolar couplings determined for alamethicin with (15)N-labeling on the Ala(6), Val(9), and Val(15) residues and incorporated into phospholipid bilayer with a peptide:lipid molar ratio of 1:8, we deduce that alamethicin has a largely linear alpha-helical structure spanning the membrane with the molecular axis tilted by 10-20 degrees relative to the bilayer normal. In particular, we find compatibility with a straight alpha-helix tilted by 17 degrees and a slightly kinked molecular dynamics structure tilted by 11 degrees relative to the bilayer normal. In contrast, the structural constraints derived by solid-state NMR appear not to be compatible with any of several model structures crossing the membrane with vanishing tilt angle or the earlier reported x-ray diffraction structure (Fox and Richards, Nature. 300:325-330, 1982). The solid-state NMR-compatible structures may support the formation of a left-handed and parallel multimeric ion channel. PMID:11509381

  20. 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.

  1. Automated analysis of protein NMR assignments using methods from artificial intelligence.

    PubMed

    Zimmerman, D E; Kulikowski, C A; Huang, Y; Feng, W; Tashiro, M; Shimotakahara, S; Chien, C; Powers, R; Montelione, G T

    1997-06-20

    An expert system for determining resonance assignments from NMR spectra of proteins is described. Given the amino acid sequence, a two-dimensional 15N-1H heteronuclear correlation spectrum and seven to eight three-dimensional triple-resonance NMR spectra for seven proteins, AUTOASSIGN obtained an average of 98% of sequence-specific spin-system assignments with an error rate of less than 0.5%. Execution times on a Sparc 10 workstation varied from 16 seconds for smaller proteins with simple spectra to one to nine minutes for medium size proteins exhibiting numerous extra spin systems attributed to conformational isomerization. AUTOASSIGN combines symbolic constraint satisfaction methods with a domain-specific knowledge base to exploit the logical structure of the sequential assignment problem, the specific features of the various NMR experiments, and the expected chemical shift frequencies of different amino acids. The current implementation specializes in the analysis of data derived from the most sensitive of the currently available triple-resonance experiments. Potential extensions of the system for analysis of additional types of protein NMR data are also discussed.

  2. Phenylalanine δ15N in Paleo Archives as a New Proxy for δ15N of Exported Primary Production

    NASA Astrophysics Data System (ADS)

    McCarthy, M.; Batista, F. C.; Vokhshoori, N. L.; Brown, J. T.; Guilderson, T. P.; Ravelo, A. C.; Sherwood, O.

    2012-12-01

    Compound-specific isotope analysis of individual amino acids (CSI-AA) is emerging as a powerful new tool for studying the paleo nitrogen cycle. Because most detrital organic nitrogen is composed of amino acids, CSI-AA can reveal the mechanistic basis for organic nitrogen diagenesis, preserve a record of past food web structure, and potentially reconstruct the δ15N values of past nitrate and primary production. Within the commonly measured amino acids, the δ15N value of phenylalanine (Phe) appears uniquely promising as a new proxy that reflects the nitrogen isotopic value of the original source. Phe δ15N values remain almost unchanged with trophic transfer through food webs, and also during at least the initial stages of organic matter degradation. Here we synthesize results from both bio-archives and recent sediments, which together suggest that at least in Holocene archives the Phe δ15N value does in fact record the average inorganic nitrogen δ15N value at the base of planktonic food webs. However, several important unknowns also remain. These include the extent of variation in amino acid isotopic fractionation patterns in phylogenetically distinct algal groups. The stability of Phe δ15N values in older sediments where organic matter has undergone extensive diagenesis is also an important research area, which may ultimately establish the temporal limit for application of this approach to study past geological epochs. Together, however, results to date suggest that of Phe δ15N values in paleo archives represent a novel molecular-level proxy which is not tied to any specific organism or group, but rather can provide an integrated estimate of δ15N value of exported primary production.

  3. NMR conformational properties of an Anthrax Lethal Factor domain studied by multiple amino acid-selective labeling

    SciTech Connect

    Vourtsis, Dionysios J.; Chasapis, Christos T.; Pairas, George; Bentrop, Detlef; Spyroulias, Georgios A.

    2014-07-18

    Highlights: • A polypeptide, N-ALF{sub 233}, was overexpressed in E. coli and successfully isolated. • We produced {sup 2}H/{sup 15}N/{sup 13}C labeled protein samples. • Amino acid selective approaches were applied. • We acquired several heteronuclear NMR spectra, to complete the backbone assignment. • Prediction of the secondary structure was performed. - Abstract: NMR-based structural biology urgently needs cost- and time-effective methods to assist both in the process of acquiring high-resolution NMR spectra and their subsequent analysis. Especially for bigger proteins (>20 kDa) selective labeling is a frequently used means of sequence-specific assignment. In this work we present the successful overexpression of a polypeptide of 233 residues, corresponding to the structured part of the N-terminal domain of Anthrax Lethal Factor, using Escherichia coli expression system. The polypeptide was subsequently isolated in pure, soluble form and analyzed structurally by solution NMR spectroscopy. Due to the non-satisfying quality and resolution of the spectra of this 27 kDa protein, an almost complete backbone assignment became feasible only by the combination of uniform and novel amino acid-selective labeling schemes. Moreover, amino acid-type selective triple-resonance NMR experiments proved to be very helpful.

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

    PubMed Central

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

    2011-01-01

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

  5. NBO, HOMO-LUMO, UV, NLO, NMR and vibrational analysis of veratrole using FT-IR, FT-Raman, FT-NMR spectra and HF-DFT computational methods.

    PubMed

    Suvitha, A; Periandy, S; Gayathri, P

    2015-03-01

    This work deals with FT-IR, FT-Raman and FT-NMR spectral analysis and NBO, NLO, HOMO-LUMO and electronic transitions studies on veratrole. The molecular structure, fundamental vibrational frequencies and intensity of the vibrational bands were interpreted with the aid of structure optimizations and geometrical parameter calculations based on Hartree-Fock (HF) and density functional theory (DFT) method with 6-311++G(d, p) basis set. A study on the electronic properties, such as HOMO and LUMO energies were performed by time independent DFT approach. In addition, molecular electrostatic potential (MEP), Natural Bond-Orbital (NBO) analysis and thermodynamic properties were performed. The (1)H and (13)C nuclear magnetic resonance (NMR) chemical shifts of the molecule were calculated by gauge independent atomic orbital (GIAO) method and compared with experimental chemical shift.

  6. Vibrational (FT-IR and FT-Raman), electronic (UV-Vis), NMR (1H and 13C) spectra and reactivity analyses of 4,5-dimethyl-o-phenylenediamine.

    PubMed

    Atac, Ahmet; Karaca, Caglar; Gunnaz, Salih; Karabacak, Mehmet

    2014-09-15

    The structure of 4,5-dimethyl-o-phenylenediamine (C8H12N2, DMPDA) was investigated on the basis of spectroscopic data and theoretical calculations. The sterochemical structure was determined by FT-IR, FT-Raman, UV, 1H and 13C NMR spectra. An experimental study and a theoretical analysis were associated by using the B3LYP method with Gaussian09 package program. FT-IR and FT-Raman spectra were recorded in the region of 4000-400 cm(-1) and 4000-10 cm(-1), respectively. The vibrational spectra were calculated by DFT method and the fundamental vibrations were assigned on the basis of the total energy distribution (TED), calculated with scaled quantum mechanics (SQM) method with Parallel Quantum Solutions (PQS) program. The UV absorption spectrum of the compound that dissolved in ethanol solution were recorded in the range of 190-400 nm. Total density of state (TDOS) and partial density of state (PDOS) of the DMPDA in terms of HOMOs and LUMOs were calculated and analyzed. Chemical shifts were reported in ppm relative to tetramethylsilane (TMS) for 1H and 13C NMR spectra. The compound was dissolved in dimethyl sulfoxide (DMSO). Also, 1H and 13C chemical shifts calculated using the gauge independent atomic orbital (GIAO) method. Mullikan atomic charges and other thermo-dynamical parameters were investigated with the help of B3LYP (DFT) method using 6-311++G** basis set. On the basis of the thermodynamic properties of the title compound at different temperatures have been carried out, revealing the correlations between heat capacity (C), entropy (S), enthalpy changes (H) and temperatures. The optimized bond lengths, bond angles, chemical shifts and vibrational wavenumbers showed the best agreement with the experimental results.

  7. Vibrational (FT-IR and FT-Raman), electronic (UV-Vis), NMR (1H and 13C) spectra and reactivity analyses of 4,5-dimethyl-o-phenylenediamine.

    PubMed

    Atac, Ahmet; Karaca, Caglar; Gunnaz, Salih; Karabacak, Mehmet

    2014-09-15

    The structure of 4,5-dimethyl-o-phenylenediamine (C8H12N2, DMPDA) was investigated on the basis of spectroscopic data and theoretical calculations. The sterochemical structure was determined by FT-IR, FT-Raman, UV, 1H and 13C NMR spectra. An experimental study and a theoretical analysis were associated by using the B3LYP method with Gaussian09 package program. FT-IR and FT-Raman spectra were recorded in the region of 4000-400 cm(-1) and 4000-10 cm(-1), respectively. The vibrational spectra were calculated by DFT method and the fundamental vibrations were assigned on the basis of the total energy distribution (TED), calculated with scaled quantum mechanics (SQM) method with Parallel Quantum Solutions (PQS) program. The UV absorption spectrum of the compound that dissolved in ethanol solution were recorded in the range of 190-400 nm. Total density of state (TDOS) and partial density of state (PDOS) of the DMPDA in terms of HOMOs and LUMOs were calculated and analyzed. Chemical shifts were reported in ppm relative to tetramethylsilane (TMS) for 1H and 13C NMR spectra. The compound was dissolved in dimethyl sulfoxide (DMSO). Also, 1H and 13C chemical shifts calculated using the gauge independent atomic orbital (GIAO) method. Mullikan atomic charges and other thermo-dynamical parameters were investigated with the help of B3LYP (DFT) method using 6-311++G** basis set. On the basis of the thermodynamic properties of the title compound at different temperatures have been carried out, revealing the correlations between heat capacity (C), entropy (S), enthalpy changes (H) and temperatures. The optimized bond lengths, bond angles, chemical shifts and vibrational wavenumbers showed the best agreement with the experimental results. PMID:24813280

  8. Vibrational (FT-IR and FT-Raman), electronic (UV-Vis), NMR (1H and 13C) spectra and reactivity analyses of 4,5-dimethyl-o-phenylenediamine

    NASA Astrophysics Data System (ADS)

    Atac, Ahmet; Karaca, Caglar; Gunnaz, Salih; Karabacak, Mehmet

    2014-09-01

    The structure of 4,5-dimethyl-o-phenylenediamine (C8H12N2, DMPDA) was investigated on the basis of spectroscopic data and theoretical calculations. The sterochemical structure was determined by FT-IR, FT-Raman, UV, 1H and 13C NMR spectra. An experimental study and a theoretical analysis were associated by using the B3LYP method with Gaussian09 package program. FT-IR and FT-Raman spectra were recorded in the region of 4000-400 cm-1 and 4000-10 cm-1, respectively. The vibrational spectra were calculated by DFT method and the fundamental vibrations were assigned on the basis of the total energy distribution (TED), calculated with scaled quantum mechanics (SQM) method with Parallel Quantum Solutions (PQS) program. The UV absorption spectrum of the compound that dissolved in ethanol solution were recorded in the range of 190-400 nm. Total density of state (TDOS) and partial density of state (PDOS) of the DMPDA in terms of HOMOs and LUMOs were calculated and analyzed. Chemical shifts were reported in ppm relative to tetramethylsilane (TMS) for 1H and 13C NMR spectra. The compound was dissolved in dimethyl sulfoxide (DMSO). Also, 1H and 13C chemical shifts calculated using the gauge independent atomic orbital (GIAO) method. Mullikan atomic charges and other thermo-dynamical parameters were investigated with the help of B3LYP (DFT) method using 6-311++G** basis set. On the basis of the thermodynamic properties of the title compound at different temperatures have been carried out, revealing the correlations between heat capacity (C), entropy (S), enthalpy changes (H) and temperatures. The optimized bond lengths, bond angles, chemical shifts and vibrational wavenumbers showed the best agreement with the experimental results.

  9. Spatially selective heteronuclear multiple-quantum coherence (HMQC) spectroscopy for bio-molecular NMR studies

    PubMed Central

    Sathyamoorthy, Bharathwaj; Parish, David M.; Montelione, Gaetano T.; Xiao, Rong; Szyperski, Thomas

    2014-01-01

    Spatially selective heteronuclear multiple-quantum coherence (SS HMQC) NMR spectroscopy was devised for solution studies of proteins. Due to ‘time-staggered’ acquisition of free induction decays (FIDs) in different slices, SS HMQC allows one to employ long delays for longitudinal nuclear spin relaxation at high repetition rates for the acquisition of the FIDs. To also achieve high intrinsic sensitivity, SS HMQC was implemented by combing a single spatially selective 1H excitation pulse with non-selective 1H 180° pulses. High-quality spectra could be obtained within 66 seconds for a 7.6 kDa uniformly 13C,15N-labeled protein, and within 45 and 90 seconds for, respectively, two uniformly 2H,13C,15N-labeled but isoleucine, leucine and valine methyl group protonated proteins with molecular weights of 7.5 and 43 kDa. PMID:24789578

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

    NASA Astrophysics Data System (ADS)

    Knicker, Heike

    2016-04-01

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

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

    NASA Astrophysics Data System (ADS)

    Wang, Tao; Wang, Xueliang

    2015-01-01

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

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

    PubMed

    Wang, Tao; Wang, Xueliang

    2015-01-25

    The title compounds, rabdosinate and rabdosin B, were isolated from the leaves of Isodon japonica, and characterized by IR-NMR spectroscopy. The molecular geometry, vibrational frequencies and gauge including atomic orbital (GIAO-13C) chemical shift values of the title compounds have been calculated by using DFT/B3LYP method with 6-311++G(d,p) basis set. In addition, obtained results were related to the linear regression of experimental 13C NMR chemical shifts values. The integral equation formalism polarized continuum model (IEFPCM) was used in treating chloroform solvation effects on optimized structural parameters and 13C chemical shifts. Besides, molecular electrostatic potential (MEP), HOMO-LUMO analysis were performed by the B3LYP method. PMID:25123947

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

    PubMed

    Wang, Tao; Wang, Xueliang

    2015-01-25

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

  14. **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.

  15. 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.

  16. 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

  17. Modeling 15N NMR chemical shift changes in protein backbone with pressure

    NASA Astrophysics Data System (ADS)

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

    2016-08-01

    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.

  18. 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

  19. Using NMR to Develop New Allosteric and Allo-Network Drugs.

    PubMed

    Smith, Robert E; Tran, Kevin; Richards, Kristy M; Luo, Rensheng

    2015-01-01

    NMR is becoming an important tool for developing new allosteric and allo-network drugs that bind to allosteric sites on enzymes, partially inhibiting them and causing fewer side effects than drugs already developed that target active sites. This is based on systems thinking, in which active enzymes and other proteins are known to be flexible and interact with each other. In other words, proteins can exist in an ensemble of different conformations whose populations are tunable. NMR is being used to find the pathways through which the effects of binding of an allosteric ligand propagate. There are NMR screening assays for studying ligand binding. This includes determining the changes in the spin lattice relaxation due to changes in the mobility of atoms involved in the binding, measuring magnetization transfer from the protein to the ligand by saturation difference transfer NMR (STD-NMR) and the transfer of bulk magnetization to the ligand by water-Ligand Observed via Gradient Spectroscopy, or waterLOGSY. The chemical shifts of (1)H and (15)N of some of the atoms in amino acids change when an allosteric ligand binds to a protein. So, (1)H-(15)N heteronuclear single quantum coherence (HSQC) spectra can be used to identify key amino acids and ligand binding sites. The NMR chemical shifts of amino acids affected by ligand binding form a network that can be characterized. Allosteric networks can be identified by chemical shift covariance analysis (CHESCA). This approach has been used recently to study the binding of new molecular entities (NMEs) to potentially therapeutic drug targets. PMID:26577663

  20. Stereospecificity of (1) H, (13) C and (15) N shielding constants in the isomers of methylglyoxal bisdimethylhydrazone: problem with configurational assignment based on (1) H chemical shifts.

    PubMed

    Afonin, Andrei V; Pavlov, Dmitry V; Ushakov, Igor A; Keiko, Natalia A

    2012-07-01

    In the (13) C NMR spectra of methylglyoxal bisdimethylhydrazone, the (13) C-5 signal is shifted to higher frequencies, while the (13) C-6 signal is shifted to lower frequencies on going from the EE to ZE isomer following the trend found previously. Surprisingly, the (1) H-6 chemical shift and (1) J(C-6,H-6) coupling constant are noticeably larger in the ZE isomer than in the EE isomer, although the configuration around the -CH═N- bond does not change. This paradox can be rationalized by the C-H⋯N intramolecular hydrogen bond in the ZE isomer, which is found from the quantum-chemical calculations including Bader's quantum theory of atoms in molecules analysis. This hydrogen bond results in the increase of δ((1) H-6) and (1) J(C-6,H-6) parameters. The effect of the C-H⋯N hydrogen bond on the (1) H shielding and one-bond (13) C-(1) H coupling complicates the configurational assignment of the considered compound because of these spectral parameters. The (1) H, (13) C and (15) N chemical shifts of the 2- and 8-(CH(3) )(2) N groups attached to the -C(CH(3) )═N- and -CH═N- moieties, respectively, reveal pronounced difference. The ab initio calculations show that the 8-(CH(3) )(2) N group conjugate effectively with the π-framework, and the 2-(CH(3) )(2) N group twisted out from the plane of the backbone and loses conjugation. As a result, the degree of charge transfer from the N-2- and N-8- nitrogen lone pairs to the π-framework varies, which affects the (1) H, (13) C and (15) N shieldings. PMID:22615146

  1. 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.

  2. jsNMR: an embedded platform-independent NMR spectrum viewer.

    PubMed

    Vosegaard, Thomas

    2015-04-01

    jsNMR is a lightweight NMR spectrum viewer written in JavaScript/HyperText Markup Language (HTML), which provides a cross-platform spectrum visualizer that runs on all computer architectures including mobile devices. Experimental (and simulated) datasets are easily opened in jsNMR by (i) drag and drop on a jsNMR browser window, (ii) by preparing a jsNMR file from the jsNMR web site, or (iii) by mailing the raw data to the jsNMR web portal. jsNMR embeds the original data in the HTML file, so a jsNMR file is a self-transforming dataset that may be exported to various formats, e.g. comma-separated values. The main applications of jsNMR are to provide easy access to NMR data without the need for dedicated software installed and to provide the possibility to visualize NMR spectra on web sites.

  3. Combined experimental and computational NMR study of crystalline and amorphous zeolitic imidazolate frameworks.

    PubMed

    Baxter, Emma F; Bennett, Thomas D; Mellot-Draznieks, Caroline; Gervais, Christel; Blanc, Frédéric; Cheetham, Anthony K

    2015-10-14

    Zeolitic imidazolate frameworks (ZIFs) have attracted great interest in recent years due to their high chemical and thermal stability with promising applications in gas storage and separations. We investigate the structures of three different crystalline ZIFs - ZIF-4, ZIF-8, ZIF-zni - and their amorphous counterparts using high field (13)C and (15)N CP MAS NMR. The high field (20 T) allows for the observation of all crystallographically independent carbon and nitrogen atoms in the crystalline ZIFs. Combining our experimental results with density functional theory calculations enabled the assignment of all chemical shifts. The crystalline spectra reveal the potential of high field NMR to distinguish between two ZIF polymorphs, ZIF-4 and ZIF-zni, with identical [Zn(C3H3N2)2] chemical compositions. (13)C and (15)N CP MAS NMR data obtained for the amorphous ZIFs clearly showed signal broadening upon amorphization, confirming the retention of chemical composition and the structural similarity of amorphous ZIF-4 and ZIF-zni. In the case of amorphous ZIF-8, we present evidence for the partial de-coordination of the 2-methyl imidazole linker.

  4. Combined experimental and computational NMR study of crystalline and amorphous zeolitic imidazolate frameworks.

    PubMed

    Baxter, Emma F; Bennett, Thomas D; Mellot-Draznieks, Caroline; Gervais, Christel; Blanc, Frédéric; Cheetham, Anthony K

    2015-10-14

    Zeolitic imidazolate frameworks (ZIFs) have attracted great interest in recent years due to their high chemical and thermal stability with promising applications in gas storage and separations. We investigate the structures of three different crystalline ZIFs - ZIF-4, ZIF-8, ZIF-zni - and their amorphous counterparts using high field (13)C and (15)N CP MAS NMR. The high field (20 T) allows for the observation of all crystallographically independent carbon and nitrogen atoms in the crystalline ZIFs. Combining our experimental results with density functional theory calculations enabled the assignment of all chemical shifts. The crystalline spectra reveal the potential of high field NMR to distinguish between two ZIF polymorphs, ZIF-4 and ZIF-zni, with identical [Zn(C3H3N2)2] chemical compositions. (13)C and (15)N CP MAS NMR data obtained for the amorphous ZIFs clearly showed signal broadening upon amorphization, confirming the retention of chemical composition and the structural similarity of amorphous ZIF-4 and ZIF-zni. In the case of amorphous ZIF-8, we present evidence for the partial de-coordination of the 2-methyl imidazole linker. PMID:26351979

  5. Theoretical investigation of 5-(2-acetoxyethyl)-6-methylpyrimidin-2,4-dione: conformational study, NBO and NLO analysis, molecular structure and NMR spectra.

    PubMed

    Pir, Hacer; Günay, Nergin; Tamer, Ömer; Avcı, Davut; Atalay, Yusuf

    2013-08-01

    Structural and conformational, natural bond orbital (NBO) and nonlinear optical (NLO) analysis was performed, and (1)H and (13)C NMR chemical shifts values of 5-(2-Acetoxyethyl)-6-methylpyrimidin-2,4-dione [C9H12N2O4] in the ground state were calculated by using Density Functional Theory (DFT-B3LYP/6-311++G(d,p)) and Hartree-Fock (HF/6-311++G(d,p)) methods. The NMR data were calculated by means of the GIAO, CSGT, and IGAIM methods. In addition, the molecular frontier orbital energies, thermodynamic parameters (in the range of 200-700 K), molecular surfaces, Mulliken charges and atomic polar tensor-based charges were investigated. Besides, the analysis of all possible conformational of the title compound, a detailed potential energy curve for τ1(C8O3C10O4), τ2 (C8O3C10C11) and τ3 (C5C7C8O3) dihedral angles were performed in steps of 10° from 0° to 360°, and depicted to find the most stable form. Finally, the calculated HOMO and LUMO energies show that charge transfer occurs within the title compound.

  6. 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.

  7. A Monte Carlo/Simulated Annealing Algorithm for Sequential Resonance Assignment in Solid State NMR of Uniformly Labeled Proteins with Magic-Angle Spinning

    PubMed Central

    Tycko, Robert; Hu, Kan-Nian

    2010-01-01

    We describe a computational approach to sequential resonance assignment in solid state NMR studies of uniformly 15N,13C-labeled proteins with magic-angle spinning. As input, the algorithm uses only the protein sequence and lists of 15N/13Cα crosspeaks from 2D NCACX and NCOCX spectra that include possible residue-type assignments of each crosspeak. Assignment of crosspeaks to specific residues is carried out by a Monte Carlo/simulated annealing algorithm, implemented in the program MC_ASSIGN1. The algorithm tolerates substantial ambiguity in residue-type assignments and coexistence of visible and invisible segments in the protein sequence. We use MC_ASSIGN1 and our own 2D spectra to replicate and extend the sequential assignments for uniformly labeled HET-s(218-289) fibrils previously determined manually by Siemer et al. (J. Biomolec. NMR, vol. 34, pp. 75-87, 2006) from a more extensive set of 2D and 3D spectra. Accurate assignments by MC_ASSIGN1 do not require data that are of exceptionally high quality. Use of MC_ASSIGN1 (and its extensions to other types of 2D and 3D data) is likely to alleviate many of the difficulties and uncertainties associated with manual resonance assignments in solid state NMR studies of uniformly labeled proteins, where spectral resolution and signal-to-noise are often sub-optimal. PMID:20547467

  8. Preparation of uniformly isotope labeled KcsA for solid state NMR: Expression, purification, reconstitution into liposomes and functional assay

    PubMed Central

    Bhate, Manasi P.; Wylie, Benjamin J.; Thompson, Ameer; Tian, Lin; Nimigean, Crina; McDermott, Ann E.

    2013-01-01

    We report the expression, purification, liposome reconstitution and functional validation of uniformly 13C and 15N isotope labeled KcsA, a bacterial potassium channel that has high homology with mammalian channels, for solid-state NMR studies. The expression and purification is optimized for an average yield of ~ 35–40 milligrams per liter of M9 media in a time-efficient way. The protein purity is confirmed by gel electrophoresis and the protein concentration is quantified by UV-Vis absorption spectroscopy. Protocols to efficiently reconstitute KcsA into liposomes are also presented. The presence of liposomes is confirmed by cryo-electron microscopy images and the effect of magic angle spinning on liposome packing is shown. High-resolution solid-state NMR spectra of uniformly isotope labeled KcsA in these liposomes reveal that our protocol yields to a very homogenous KcsA sample with high signal to noise and several well-resolved residues in NMR spectra. Electrophysiology of our samples before and after solid-state NMR show that channel function and selectivity remain intact after the solid-state NMR. PMID:23916531

  9. Implications of scaled δ15N fractionation for community predator-prey body mass ratio estimates in size-structured food webs.

    PubMed

    Reum, Jonathan C P; Jennings, Simon; Hunsicker, Mary E

    2015-11-01

    Nitrogen stable isotope ratios (δ(15) N) may be used to estimate community-level relationships between trophic level (TL) and body size in size-structured food webs and hence the mean predator to prey body mass ratio (PPMR). In turn, PPMR is used to estimate mean food chain length, trophic transfer efficiency and rates of change in abundance with body mass (usually reported as slopes of size spectra) and to calibrate and validate food web models. When estimating TL, researchers had assumed that fractionation of δ(15) N (Δδ(15) N) did not change with TL. However, a recent meta-analysis indicated that this assumption was not as well supported by data as the assumption that Δδ(15) N scales negatively with the δ(15) N of prey. We collated existing fish community δ(15) N-body size data for the Northeast Atlantic and tropical Western Arabian Sea with new data from the Northeast Pacific. These data were used to estimate TL-body mass relationships and PPMR under constant and scaled Δδ(15) N assumptions, and to assess how the scaled Δδ(15) N assumption affects our understanding of the structure of these food webs. Adoption of the scaled Δδ(15) N approach markedly reduces the previously reported differences in TL at body mass among fish communities from different regions. With scaled Δδ(15) N, TL-body mass relationships became more positive and PPMR fell. Results implied that realized prey size in these size-structured fish communities are less variable than previously assumed and food chains potentially longer. The adoption of generic PPMR estimates for calibration and validation of size-based fish community models is better supported than hitherto assumed, but predicted slopes of community size spectra are more sensitive to a given change or error in realized PPMR when PPMR is small. PMID:26046788

  10. Implications of scaled δ15N fractionation for community predator-prey body mass ratio estimates in size-structured food webs.

    PubMed

    Reum, Jonathan C P; Jennings, Simon; Hunsicker, Mary E

    2015-11-01

    Nitrogen stable isotope ratios (δ(15) N) may be used to estimate community-level relationships between trophic level (TL) and body size in size-structured food webs and hence the mean predator to prey body mass ratio (PPMR). In turn, PPMR is used to estimate mean food chain length, trophic transfer efficiency and rates of change in abundance with body mass (usually reported as slopes of size spectra) and to calibrate and validate food web models. When estimating TL, researchers had assumed that fractionation of δ(15) N (Δδ(15) N) did not change with TL. However, a recent meta-analysis indicated that this assumption was not as well supported by data as the assumption that Δδ(15) N scales negatively with the δ(15) N of prey. We collated existing fish community δ(15) N-body size data for the Northeast Atlantic and tropical Western Arabian Sea with new data from the Northeast Pacific. These data were used to estimate TL-body mass relationships and PPMR under constant and scaled Δδ(15) N assumptions, and to assess how the scaled Δδ(15) N assumption affects our understanding of the structure of these food webs. Adoption of the scaled Δδ(15) N approach markedly reduces the previously reported differences in TL at body mass among fish communities from different regions. With scaled Δδ(15) N, TL-body mass relationships became more positive and PPMR fell. Results implied that realized prey size in these size-structured fish communities are less variable than previously assumed and food chains potentially longer. The adoption of generic PPMR estimates for calibration and validation of size-based fish community models is better supported than hitherto assumed, but predicted slopes of community size spectra are more sensitive to a given change or error in realized PPMR when PPMR is small.

  11. Aliphatic (1)H, (13)C and (15)N chemical shift assignments of dihydrofolate reductase from the psychropiezophile Moritella profunda in complex with NADP(+) and folate.

    PubMed

    Loveridge, E Joel; Matthews, Stella M; Williams, Christopher; Whittaker, Sara B-M; Günther, Ulrich L; Evans, Rhiannon M; Dawson, William M; Crump, Matthew P; Allemann, Rudolf K

    2013-04-01

    Dihydrofolate reductase from the deep-sea bacterium Moritella profunda (MpDHFR) has been (13)C/(15)N isotopically labelled and purified. Here, we report the aliphatic (1)H, (13)C and (15)N resonance assignments of MpDHFR in complex with NADP(+) and folate. The spectra of MpDHFR suggest considerably greater conformational heterogeneity than is seen in the closely related DHFR from Escherichia coli.

  12. Efficient design of multituned transmission line NMR probes: the electrical engineering approach.

    PubMed

    Frydel, J A; Krzystyniak, M; Pienkowski, D; Pietrzak, M; de Sousa Amadeu, N; Ratajczyk, T; Idzik, K; Gutmann, T; Tietze, D; Voigt, S; Fenn, A; Limbach, H H; Buntkowsky, G

    2011-01-01

    Transmission line-based multi-channel solid state NMR probes have many advantages regarding the cost of construction, number of RF-channels, and achievable RF-power levels. Nevertheless, these probes are only rarely employed in solid state-NMR-labs, mainly owing to the difficult experimental determination of the necessary RF-parameters. Here, the efficient design of multi-channel solid state MAS-NMR probes employing transmission line theory and modern techniques of electrical engineering is presented. As technical realization a five-channel ((1)H, (31)P, (13)C, (2)H and (15)N) probe for operation at 7 Tesla is described. This very cost efficient design goal is a multi port single coil transmission line probe based on the design developed by Schaefer and McKay. The electrical performance of the probe is determined by measuring of Scattering matrix parameters (S-parameters) in particular input/output ports. These parameters are compared to the calculated parameters of the design employing the S-matrix formalism. It is shown that the S-matrix formalism provides an excellent tool for examination of transmission line probes and thus the tool for a rational design of these probes. On the other hand, the resulting design provides excellent electrical performance. From a point of view of Nuclear Magnetic Resonance (NMR), calibration spectra of particular ports (channels) are of great importance. The estimation of the π/2 pulses length for all five NMR channels is presented.

  13. Synthesis of 15 alpha-hydroxyestrogen 15-N-acetylglucosaminides.

    PubMed

    Suzuki, E; Namba, S; Kurihara, H; Goto, J; Matsuki, Y; Nambara, T

    1995-03-01

    The synthesis of 15-N-acetylglucosaminides of 15 alpha-hydroxyesterone, 15 alpha-hydroxyestradiol, and 15 alpha-hydroxyestriol (estetrol) is described. The latter two were prepared by condensation of 2-acetamido-1 alpha-chloro-1,2-dideoxy-3,4,6-trio-O-acetyl-D-glucopyranose with appropriately protected 15 alpha-hydroxyestrogens by the Koenigs-Knorr reaction employing cadmium carbonate as a catalyst. Subsequent removal of protecting groups with methanolic potassium hydroxide provided the desired conjugates. 15 alpha-Hydroxyestrone 15-N-acetylglucosaminide was synthesized from the corresponding 15 alpha-hydroxyestradiol derivative by Jones oxidation followed by brief alkaline hydrolysis. These conjugates underwent enzymatic hydrolysis with beta-N-acetylglucosaminidase from Jack beans to produce 15 alpha-hydroxyestrogens. PMID:7792832

  14. Elucidation of the CCR1- and CCR5-binding modes of MIP-1α by application of an NMR spectra reconstruction method to the transferred cross-saturation experiments.

    PubMed

    Yoshiura, Chie; Ueda, Takumi; Kofuku, Yutaka; Matsumoto, Masahiko; Okude, Junya; Kondo, Keita; Shiraishi, Yutaro; Shimada, Ichio

    2015-12-01

    C-C chemokine receptor 1 (CCR1) and CCR5 are involved in various inflammation and immune responses, and regulate the progression of the autoimmune diseases differently. However, the number of residues identified at the binding interface was not sufficient to clarify the differences in the CCR1- and CCR5-binding modes to MIP-1α, because the NMR measurement time for CCR1 and CCR5 samples was limited to 24 h, due to their low stability. Here we applied a recently developed NMR spectra reconstruction method, Conservation of experimental data in ANAlysis of FOuRier, to the amide-directed transferred cross-saturation experiments of chemokine receptors, CCR1 and CCR5, embedded in lipid bilayers of the reconstituted high density lipoprotein, and MIP-1α. Our experiments revealed that the residues on the N-loop and β-sheets of MIP-1α are close to both CCR1 and CCR5, and those in the C-terminal helix region are close to CCR5. These results suggest that the genetic influence of the single nucleotide polymorphisms of MIP-1α that accompany substitution of residues in the C-terminal helix region, E57 and V63, would provide clues toward elucidating how the CCR5-MIP-1α interaction affects the progress of autoimmune diseases.

  15. NMR-Based Amide Hydrogen-Deuterium Exchange Measurements for Complex Membrane Proteins: Development and Critical Evaluation

    NASA Astrophysics Data System (ADS)

    Czerski, Lech; Vinogradova, Olga; Sanders, Charles R.

    2000-01-01

    A method for measuring site-specific amide hydrogen-deuterium exchange rates for membrane proteins in bilayers is reported and evaluated. This method represents an adaptation and extension of the approach of Dempsey and co-workers (Biophys. J. 70, 1777-1788 (1996)) and is based on reconstituting 15N-labeled membrane proteins into phospholipid bilayers, followed by lyophilization and rehydration with D2O or H2O (control). Following incubation for a time t under hydrated conditions, samples are again lyophilized and then solubilized in an organic solvent system, where 1H-15N HSQC spectra are recorded. Comparison of spectra from D2O-exposed samples to spectra from control samples yields the extent of the H-D exchange which occurred in the bilayers during time t. Measurements are site specific if specific 15N labeling is used. The first part of this paper deals with the search for a suitable solvent system in which to solubilize complex membrane proteins in an amide "exchange-trapped" form for NMR quantitation of amide peak intensities. The second portion of the paper documents application of the overall procedure to measuring site-specific amide exchange rates in diacylglycerol kinase, a representative integral membrane protein. Both the potential usefulness and the significant limitations of the new method are documented.

  16. 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

  17. 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.

  18. In Vivo Fluxes in the Ammonium-Assimilatory Pathways in Corynebacterium glutamicum Studied by 15N Nuclear Magnetic Resonance

    PubMed Central

    Tesch, M.; de Graaf, A. A.; Sahm, H.

    1999-01-01

    Glutamate dehydrogenase (GDH) and glutamine synthetase (GS)–glutamine 2-oxoglutarate-aminotransferase (GOGAT) represent the two main pathways of ammonium assimilation in Corynebacterium glutamicum. In this study, the ammonium assimilating fluxes in vivo in the wild-type ATCC 13032 strain and its GDH mutant were quantitated in continuous cultures. To do this, the incorporation of 15N label from [15N]ammonium in glutamate and glutamine was monitored with a time resolution of about 10 min with in vivo 15N nuclear magnetic resonance (NMR) used in combination with a recently developed high-cell-density membrane-cyclone NMR bioreactor system. The data were used to tune a standard differential equation model of ammonium assimilation that comprised ammonia transmembrane diffusion, GDH, GS, GOGAT, and glutamine amidotransferases, as well as the anabolic incorporation of glutamate and glutamine into biomass. The results provided a detailed picture of the fluxes involved in ammonium assimilation in the two different C. glutamicum strains in vivo. In both strains, transmembrane equilibration of 100 mM [15N]ammonium took less than 2 min. In the wild type, an unexpectedly high fraction of 28% of the NH4+ was assimilated via the GS reaction in glutamine, while 72% were assimilated by the reversible GDH reaction via glutamate. GOGAT was inactive. The analysis identified glutamine as an important nitrogen donor in amidotransferase reactions. The experimentally determined amount of 28% of nitrogen assimilated via glutamine is close to a theoretical 21% calculated from the high peptidoglycan content of C. glutamicum. In the GDH mutant, glutamate was exclusively synthesized over the GS/GOGAT pathway. Its level was threefold reduced compared to the wild type. PMID:10049869

  19. 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.

  20. 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

  1. 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

  2. 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.

  3. Vibrational analysis using FT-IR, FT-Raman spectra and HF-DFT methods and NBO, NLO, NMR, HOMO-LUMO, UV and electronic transitions studies on 2,2,4-trimethyl pentane.

    PubMed

    Suvitha, A; Periandy, S; Govindarajan, M; Gayathri, P

    2015-03-01

    In this work, the vibrational spectral analysis was carried out by using Raman and infrared spectroscopy in the range 100-4000cm(-1)and 50-4000cm(-1), respectively, for 2,2,4-Trimethyl Pentane, TMP (C8H18) molecule. The molecular structure, fundamental vibrational frequencies and intensity of the vibrational bands are interpreted with the aid of structure optimizations and geometrical parameter calculations based on Hartree Fock (HF) and density functional theory (DFT) method with 6-311++G(d,p) basis set. The scaled B3LYP/6-311++G(d,p) results shows the best agreement with the experimental values over the other method. The calculated HOMO and LUMO energies shows that charge transfer within the molecule. The physical reactions of single bond hydrocarbon TMP were investigated. The results of the calculations were applied to simulate spectra of the title compound, which shows the excellent agreement with observed spectra. Besides, Mulliken atomic charges, UV, frontier molecular orbital (FMO), MEP, NLO activity, Natural Bond-Orbital (NBO) analysis, NMR and thermodynamic properties of title molecule were also performed.

  4. Relaxation times of spin states of all ranks and orders of quadrupolar nuclei estimated from NMR z-spectra: Markov chain Monte Carlo analysis applied to 7Li+ and 23Na+ in stretched hydrogels.

    PubMed

    Kuchel, Philip W; Naumann, Christoph; Puckeridge, Max; Chapman, Bogdan E; Szekely, David

    2011-09-01

    The NMR z-spectra of 7Li+ and 23Na+ in stretched hydrogels contain five minima, or critical values, with a sharp "dagger" on the central dip. The mathematical representation of such z-spectra from spin-3/2 nuclei contains nine distinct (the total is 15 but there is redundancy of the ±order-numbers) relaxation rate constants that are unique for each of the spin states, up to rank 3, order 3. We present an approach to multiple-parameter-value estimation that exploits the high level of separability of the effects of each of the relaxation rate constants on the features of the z-spectrum. The Markov chain Monte Carlo (MCMC) method is computationally demanding but it yielded statistically robust estimates (low coefficients of variation) of the parameter values. We describe the implementation of the MCMC analysis (in the present context) and posit that it can obviate the need for using multiple-quantum filtered RF-pulse sequences to estimate all relaxation rate constants/times under experimentally favorable, but readily achievable, circumstances.

  5. Hydrothermal synthesis, X-ray structure refinement, 31P NMR spectra and vibrational study of NaLa(HPO4)2

    NASA Astrophysics Data System (ADS)

    Ben Hassen, C.; Boujelbene, M.; Mhiri, T.

    2013-10-01

    NaLa(HPO4)2 was obtained by hydrothermal synthesis. The structure of NaLa(HPO4)2 was determined by X-ray powder diffraction methods. The results of Rietveld refinement revealed a space group P21/c (No. 14), with lattice parameters of a = 9.7151(17) Å, b = 8.320(12) Å, c = 9.83(2) Å, beta = 114.65(17)°, V = 722 (8) Å3 and Z = 4. Final refinement led to RF = 4.86% and RB = 12.35%.The existence of bound O-H and bound P-O in the structure has been confirmed by IR and Raman spectroscopy. The existence of two crystallographically independent phosphorus atoms in the structure has been confirmed by NMR spectrum. The structure is characterized by LaO6 octahedra which are solely connected to six adjacent HPO4 tetrahedra via common O-corners. This structure contains twelve- and four-membered rings forming channels along [1 1¯ 1]. The cross sections of the channels are given by twelve-membered rings consisting of four lanthanum coordination octahedral and eight hydrogenphosphate groups as well as four-membered rings consisting of two lanthanum coordination octahedra and two hydrogenphosphate tetrahedra. Sodium ions are located within those channels of the twelve-membered rings.

  6. Minimalist Relativistic Force Field: Prediction of Proton-Proton Coupling Constants in (1)H NMR Spectra Is Perfected with NBO Hybridization Parameters.

    PubMed

    Kutateladze, Andrei G; Mukhina, Olga A

    2015-05-15

    We previously developed a reliable method for multiparametric scaling of Fermi contacts to achieve fast and accurate prediction of proton-proton spin-spin coupling constants (SSCC) in (1)H NMR. We now report that utilization of NBO hybridization coefficients for carbon atoms in the involved C-H bonds allows for a significant simplification of this parametric scheme, requiring only four general types of SSCCs: geminal, vicinal, 1,3-, and long-range constants. The method is optimized for inexpensive B3LYP/6-31G(d) molecular geometries. A new DU8 basis set, based on a training set of 475 experimental spin-spin coupling constants, is developed for hydrogen and common non-hydrogen atoms (Li, B, C, N, O, F, Si, P, S, Cl, Se, Br, I) to calculate Fermi contacts. On a test set of 919 SSCCs from a diverse collection of natural products and complex synthetic molecules the method gave excellent accuracy of 0.29 Hz (rmsd) with the maximum unsigned error not exceeding 1 Hz.

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

    PubMed

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

    2012-01-01

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

  8. Insight into dissolution mechanism of cellulose in [C4mim][CH3COO]/DMSO solvent by 13C NMR spectra

    NASA Astrophysics Data System (ADS)

    Xu, Airong; Zhang, Yibo

    2015-05-01

    Recently, it has been reported that 1-butyl-3-methylimidazolium acetate/dimethyl sulfoxide ([C4mim][CH3COO]/DMSO) can efficiently dissolve cellulose at room temperature. In the present study, 13C NMR measurements of 1-butyl-3-methylimidazolium acetate [C4mim][CH3COO] and cellulose were carried out in [C4mim][CH3COO]/DMSO-d6 (Deuterated dimethyl sulfoxide)/cellulose solution to directly reveal the possible dissolution mechanism of cellulose in true [C4mim][CH3COO]/DMSO solvent. The results indicate that both cation and anion of [C4mim][CH3COO] in [C4mim][CH3COO]/DMSO solvent dominate cellulose dissolution, and DMSO mainly serves to dissociate the ion pairs in [C4mim][CH3COO] into solvated cations and anions. Moreover, the hydrogen bonding interaction of anion of [C4mim][CH3COO] with cellulose hydroxyl proton is much stronger than that of cation of [C4mim][CH3COO] with cellulose hydroxyl oxygen.

  9. Minimalist Relativistic Force Field: Prediction of Proton-Proton Coupling Constants in (1)H NMR Spectra Is Perfected with NBO Hybridization Parameters.

    PubMed

    Kutateladze, Andrei G; Mukhina, Olga A

    2015-05-15

    We previously developed a reliable method for multiparametric scaling of Fermi contacts to achieve fast and accurate prediction of proton-proton spin-spin coupling constants (SSCC) in (1)H NMR. We now report that utilization of NBO hybridization coefficients for carbon atoms in the involved C-H bonds allows for a significant simplification of this parametric scheme, requiring only four general types of SSCCs: geminal, vicinal, 1,3-, and long-range constants. The method is optimized for inexpensive B3LYP/6-31G(d) molecular geometries. A new DU8 basis set, based on a training set of 475 experimental spin-spin coupling constants, is developed for hydrogen and common non-hydrogen atoms (Li, B, C, N, O, F, Si, P, S, Cl, Se, Br, I) to calculate Fermi contacts. On a test set of 919 SSCCs from a diverse collection of natural products and complex synthetic molecules the method gave excellent accuracy of 0.29 Hz (rmsd) with the maximum unsigned error not exceeding 1 Hz. PMID:25885091

  10. 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.

  11. NBO, NMR, UV, FT-IR, FT-Raman spectra and molecular structure (monomeric and dimeric structures) investigation of 4-Chloro-3,5-Xylenol: a combined experimental and theoretical study.

    PubMed

    Arivazhagan, M; Gayathri, R

    2013-12-01

    In this work, a joint experimental (FTIR and FT-Raman) and theoretical (DFT and ab initio) study on the structure and the vibrations of 4-Chloro-3,5-Xylenol (CXL) are compared and analyzed. CXL is a chlorinated phenolic antiseptic which is a bactericide against most gram-positive bacteria. The first hyperpolarizability (β0) of this novel molecular system and related non-linear properties of CXL are calculated using HF/6-311++G(d,p) method on the finite-field approach. The energy and oscillator strength calculated using absorption spectra (UV-Vis spectrum), this spectral analysis confirms the charge transfer of the molecule. The theoretical (13)C nuclear magnetic resonance (NMR) chemical shifts of the molecule were calculated by Gauge Including Atomic Orbital (GIAO) method, to analyze the molecular environment as well as the delocalization activities of electron clouds. The directly calculated ionization potential (IP), electron affinity (EA), electronegativity (χ), chemical hardness (η), first electron excitation energy (τ) and electrophilicity index (ω) as well as local reactivity (S) analyzed using HOMO and LUMO energies; the energy band gap are also determined. NBO analysis shows that charge in electron density(ED) in the σ(*) and π(*) antibonding orbitals and E((2)) energies confirms the occurrence of ICT (Intramolecular Charge Transfer) within the molecule. Inter molecular hydrogen bonds exist between -OH group, give the evidence for the formation of dimer entities in the title molecule. The influences of chlorine atom, hydroxyl group and methyl group on the geometry of benzene and its normal modes of vibrations (monomer and dimer of CXL) have also been discussed. Finally the calculated results were applied to simulate Infrared and Raman spectra of the title molecule which show good agreement with observed spectra.

  12. NBO, NMR, UV, FT-IR, FT-Raman spectra and molecular structure (monomeric and dimeric structures) investigation of 4-Chloro-3,5-Xylenol: A combined experimental and theoretical study

    NASA Astrophysics Data System (ADS)

    Arivazhagan, M.; Gayathri, R.

    2013-12-01

    In this work, a joint experimental (FTIR and FT-Raman) and theoretical (DFT and ab initio) study on the structure and the vibrations of 4-Chloro-3,5-Xylenol (CXL) are compared and analyzed. CXL is a chlorinated phenolic antiseptic which is a bactericide against most gram-positive bacteria. The first hyperpolarizability (β0) of this novel molecular system and related non-linear properties of CXL are calculated using HF/6-311++G(d,p) method on the finite-field approach. The energy and oscillator strength calculated using absorption spectra (UV-Vis spectrum), this spectral analysis confirms the charge transfer of the molecule. The theoretical 13C nuclear magnetic resonance (NMR) chemical shifts of the molecule were calculated by Gauge Including Atomic Orbital (GIAO) method, to analyze the molecular environment as well as the delocalization activities of electron clouds. The directly calculated ionization potential (IP), electron affinity (EA), electronegativity (χ), chemical hardness (η), first electron excitation energy (τ) and electrophilicity index (ω) as well as local reactivity (S) analyzed using HOMO and LUMO energies; the energy band gap are also determined. NBO analysis shows that charge in electron density(ED) in the σ* and π* antibonding orbitals and E(2) energies confirms the occurrence of ICT (Intramolecular Charge Transfer) within the molecule. Inter molecular hydrogen bonds exist between -OH group, give the evidence for the formation of dimer entities in the title molecule. The influences of chlorine atom, hydroxyl group and methyl group on the geometry of benzene and its normal modes of vibrations (monomer and dimer of CXL) have also been discussed. Finally the calculated results were applied to simulate Infrared and Raman spectra of the title molecule which show good agreement with observed spectra.

  13. High Resolution NMR Spectroscopy of Nanocrystalline Proteins at Ultra-High Magnetic Field

    PubMed Central

    Sperling, Lindsay J.; Nieuwkoop, Andrew J.; Lipton, Andrew S.; Berthold, Deborah A.; Rienstra, Chad M.

    2010-01-01

    Magic-angle spinning (MAS) solid-state NMR (SSNMR) spectroscopy of uniformly-13C,15N labeled protein samples provides insight into atomic-resolution chemistry and structure. Data collection efficiency has advanced remarkably in the last decade; however, the study of larger proteins is still challenged by relatively low resolution in comparison to solution NMR. In this study, we present a systematic analysis of SSNMR protein spectra acquired at 11.7, 17.6 and 21.1 Tesla (1H frequencies of 500, 750, and 900 MHz). For two protein systems—GB1, a 6 kDa nanocrystalline protein and DsbA, a 21 kDa nanocrystalline protein—line narrowing is demonstrated in all spectral regions with increasing field. Resolution enhancement is greatest in the aliphatic region, including methine, methylene and methyl sites. The resolution for GB1 increases markedly as a function of field, and for DsbA, resolution in the C-C region increases by 42%, according to the number of peaks that can be uniquely picked and integrated in the 900 MHz spectra when compared to the 500 MHz spectra. Additionally, chemical exchange is uniquely observed in the highest field spectra for at least two isoleucine Cδ1 sites in DsbA. These results further illustrate the benefits of high-field MAS SSNMR spectroscopy for protein structural studies. PMID:19953303

  14. Axial ligand modulation of the electronic structures of binuclear copper sites: analysis of paramagnetic 1H NMR spectra of Met160Gln Cu(A).

    PubMed

    Fernández, C O; Cricco, J A; Slutter, C E; Richards, J H; Gray, H B; Vila, A J

    2001-11-28

    Cu(A) is an electron-transfer copper center present in heme-copper oxidases and N2O reductases. The center is a binuclear unit, with two cysteine ligands bridging the metal ions and two terminal histidine residues. A Met residue and a peptide carbonyl group are located on opposite sides of the Cu2S2 plane; these weaker ligands are fully conserved in all known Cu(A) sites. The Met160Gln mutant of the soluble subunit II of Thermus thermophilus ba3 oxidase has been studied by NMR spectroscopy. In its oxidized form, the binuclear copper is a fully delocalized mixed-valence pair, as are all natural Cu(A) centers. The faster nuclear relaxation in this mutant suggests that a low-lying excited state has shifted to higher energies compared to that of the wild-type protein. The introduction of the Gln residue alters the coordination mode of His114 but does not affect His157, thereby confirming the proposal that the axial ligand-to-copper distances influence the copper-His interactions (Robinson, H.; Ang, M. C.; Gao, Y. G.; Hay, M. T.; Lu, Y.; Wang, A. H. Biochemistry 1999, 38, 5677). Changes in the hyperfine coupling constants of the Cys beta-CH2 groups are attributed to minor geometrical changes that affect the Cu-S-C(beta)-H(beta) dihedral angles. These changes, in addition, shift the thermally accessible excited states, thus influencing the spectral position of the Cys beta-CH2 resonances. The Cu-Cys bonds are not substantially altered by the Cu-Gln160 interaction, in contrast to the situation found in the evolutionarily related blue copper proteins. It is possible that regulatory subunits in the mitochondrial oxidases fix the relative positions of thermally accessible Cu(A) excited states by tuning axial ligand interactions.

  15. Multinuclear NMR study of the structure of the Fv fragment of anti-dansyl mouse IgG2a antibody

    SciTech Connect

    Takahashi, Hideo; Odaka, Asano; Matsunaga, Chigusa; Kato, Koichi; Shimada, Ichio; Arata, Yoji ); Kawaminami, Shunro )

    1991-07-02

    A multinuclear NMR study is reported of Fv, which is a minimum antigen-binding unit of immunoglobulin. Fv has been prepared by clostripain digestion of a mouse anti-dansyl IgG2a monoclonal antibody that lacks the entire C{sub H}1 domain. A variety of Fv analogues labeled with {sup 2}H in the aromatic rings and with {sup 13}C and/or {sup 15}N in the peptide bonds have been prepared and used for multinuclear NMR analyses of Fv spectra of Fv sensitively reflect the antigen binding and can be used along with {sup 1}H and {sup 13}C spectral data for the structural analyses of antigen-antibody interactions. Hydrogen-deuterium exchange of the amide protons has been folowed in the absence and presence of DNS-Lys by using the {sup 1}H-{sup 15}N shift correlation spectra. Use of the {beta}-shift observed for the carbonyl carbon resonances has also been helpful in following the hydrogen-deuterium exchange. On the basis of the NMR data obtained, the static and dynamic structure of the Fv fragment in the absence and presence of DNS-Lys has been discussed.

  16. MUSIC in triple-resonance experiments: amino acid type-selective (1)H-(15)N correlations

    PubMed

    Schubert; Smalla; Schmieder; Oschkinat

    1999-11-01

    Amino acid type-selective triple-resonance experiments can be of great help for the assignment of protein spectra, since they help to remove ambiguities in either manual or automated assignment procedures. Here, modified triple-resonance experiments that yield amino acid type-selective (1)H-(15)N correlations are presented. They are based on novel coherence transfer schemes, the MUSIC pulse sequence elements, that replace the initial INEPT transfer and are selective for XH(2) or XH(3) (X can be (15)N or (13)C). The desired amino acid type is thereby selected based on the topology of the side chain. Experiments for Gly (G-HSQC); Ala (A-HSQC); Thr, Val, Ile, and Ala (TAVI-HSQC); Thr and Ala (TA-HSQC), as well as Asn and Gln (N-HSQC and QN-HSQC), are described. The new experiments are recorded as two-dimensional experiments and therefore need only small amounts of spectrometer time. The performance of the experiments is demonstrated with the application to two protein domains. Copyright 1999 Academic Press. PMID:10527741

  17. MUSIC in Triple-Resonance Experiments: Amino Acid Type-Selective 1H- 15N Correlations

    NASA Astrophysics Data System (ADS)

    Schubert, Mario; Smalla, Maika; Schmieder, Peter; Oschkinat, Hartmut

    1999-11-01

    Amino acid type-selective triple-resonance experiments can be of great help for the assignment of protein spectra, since they help to remove ambiguities in either manual or automated assignment procedures. Here, modified triple-resonance experiments that yield amino acid type-selective 1H-15N correlations are presented. They are based on novel coherence transfer schemes, the MUSIC pulse sequence elements, that replace the initial INEPT transfer and are selective for XH2 or XH3 (X can be 15N or 13C). The desired amino acid type is thereby selected based on the topology of the side chain. Experiments for Gly (G-HSQC); Ala (A-HSQC); Thr, Val, Ile, and Ala (TAVI-HSQC); Thr and Ala (TA-HSQC), as well as Asn and Gln (N-HSQC and QN-HSQC), are described. The new experiments are recorded as two-dimensional experiments and therefore need only small amounts of spectrometer time. The performance of the experiments is demonstrated with the application to two protein domains.

  18. MUSIC in triple-resonance experiments: amino acid type-selective (1)H-(15)N correlations

    PubMed

    Schubert; Smalla; Schmieder; Oschkinat

    1999-11-01

    Amino acid type-selective triple-resonance experiments can be of great help for the assignment of protein spectra, since they help to remove ambiguities in either manual or automated assignment procedures. Here, modified triple-resonance experiments that yield amino acid type-selective (1)H-(15)N correlations are presented. They are based on novel coherence transfer schemes, the MUSIC pulse sequence elements, that replace the initial INEPT transfer and are selective for XH(2) or XH(3) (X can be (15)N or (13)C). The desired amino acid type is thereby selected based on the topology of the side chain. Experiments for Gly (G-HSQC); Ala (A-HSQC); Thr, Val, Ile, and Ala (TAVI-HSQC); Thr and Ala (TA-HSQC), as well as Asn and Gln (N-HSQC and QN-HSQC), are described. The new experiments are recorded as two-dimensional experiments and therefore need only small amounts of spectrometer time. The performance of the experiments is demonstrated with the application to two protein domains. Copyright 1999 Academic Press.

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

    ERIC Educational Resources Information Center

    Mills, Nancy S.; Shanklin, Michael

    2011-01-01

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

  20. Uniform isotope labeling of a eukaryotic seven-transmembrane helical protein in yeast enables high-resolution solid-state NMR studies in the lipid environment.

    PubMed

    Fan, Ying; Shi, Lichi; Ladizhansky, Vladimir; Brown, Leonid S

    2011-02-01

    Overexpression of isotope-labeled multi-spanning eukaryotic membrane proteins for structural NMR studies is often challenging. On the one hand, difficulties with achieving proper folding, membrane insertion, and native-like post-translational modifications frequently disqualify bacterial expression systems. On the other hand, eukaryotic cell cultures can be prohibitively expensive. One of the viable alternatives, successfully used for producing proteins for solution NMR studies, is yeast expression systems, particularly Pichia pastoris. We report on successful implementation and optimization of isotope labeling protocols, previously used for soluble secreted proteins, to produce homogeneous samples of a eukaryotic seven-transmembrane helical protein, rhodopsin from Leptosphaeria maculans. Even in shake-flask cultures, yields exceeded 5 mg of purified uniformly (13)C,(15)N-labeled protein per liter of culture. The protein was stable (at least several weeks at 5°C) and functionally active upon reconstitution into lipid membranes at high protein-to-lipid ratio required for solid-state NMR. The samples gave high-resolution (13)C and (15)N solid-state magic angle spinning NMR spectra, amenable to a detailed structural analysis. We believe that similar protocols can be adopted for challenging mammalian targets, which often resist characterization by other structural methods.

  1. The Titan 14N/ 15N and 12C/ 13C isotopic ratios in HCN from Cassini/CIRS

    NASA Astrophysics Data System (ADS)

    Vinatier, Sandrine; Bézard, Bruno; Nixon, Conor A.

    2007-11-01

    We report the detection of H 13CN and HC 15N in mid-infrared spectra recorded by the Composite Infrared Spectrometer (CIRS) aboard Cassini, along with the determination of the 12C/ 13C and 14N/ 15N isotopic ratios. We analyzed two sets of limb spectra recorded near 13-15° S (Tb flyby) and 83° N (T4 flyby) at 0.5 cm -1 resolution. The spectral range 1210-1310 cm -1 was used to retrieve the temperature profile in the range 145-490 km at 13° S and 165-300 km at 83° N. These two temperature profiles were then incorporated in the atmospheric model to retrieve the abundance profile of H 12C 14N, H 13CN and HC 15N from their bands at 713, 706 and 711 cm -1, respectively. The HCN abundance profile was retrieved in the range 90-460 km at 15° S and 165-305 km at 83° N. There is no evidence for vertical variations of the isotopic ratios. Constraining the isotopic abundance profiles to be proportional to the HCN one, we find C12/C13=89-18+22 at 15° S, and 68-12+16 at 83° N, two values that are statistically consistent. A combination of these results yields a 12C/ 13C value equal to 75±12. This global result, as well as the 15° S one, envelop the value in Titan's methane ( 82.3±1) [Niemann, H.B., and 17 colleagues, 2005. Nature 438, 779-784] measured at 10° S and is slightly lower than the terrestrial inorganic standard value (89). The 14N/ 15N isotopic ratio is found equal to 56-13+16 at 15° S and 56-9+10 at 83° N. Combining the two values yields 14N/ 15N = 56 ± 8, which corresponds to an enrichment in 15N of about 4.9 compared with the terrestrial ratio. These results agree with the values obtained from previous ground-based millimeter observations [Hidayat, T., Marten, A., Bézard, B., Gautier, D., Owen, T., Matthews, H.E., Paubert, G., 1997. Icarus 126, 170-182; Marten, A., Hidayat, T., Biraud, Y., Moreno, R., 2002. Icarus 158, 532-544]. The 15N/ 14N ratio found in HCN is ˜3 times higher than in N 2 [Niemann, H.B., and 17 colleagues, 2005. Nature 438, 779

  2. Simulations of molecular dynamics in solid-state NMR spectra of spin-1 nuclei including effects of CSA- and EFG-terms up to second order.

    PubMed

    Larsen, Flemming H

    2007-04-01

    By numerical simulations MAS and QCPMG methods for acquiring spectra of spin-1 nuclei were compared in order to determine the most sensitive experiment for analysis of molecular dynamics. To comply with the large quadrupolar constants for 14N and the CSA reported for 6Li both of these interactions are included up to second order. For 2H and 6Li both QCPMG and single-pulse MAS experiments were suitable for dynamics studies whereas the single-pulse MAS experiment were the method of choice for investigation of 14N dynamics for C(Q)'s larger than 750kHz at 14.1T. This property prohibits excitation of the 14N lineshape using either single hard or softer composite rf-pulses. Focusing on 14N it was demonstrated that the centerband lineshape is sensitive toward both off-MAS and CSA effects. In addition, excitation by real-time pulses showed that proper lineshapes corresponding to a site with a C(Q) of 3MHz may be excited by a very short pulse. PMID:17418539

  3. Identification of the magnesium-histidine stretching vibration of the bacteriochlorophyll cofactors in photosynthetic reaction centers via {sup 15}N-labeling of the histidines

    SciTech Connect

    Czarnecki, K.; Bocian, D.F.; Chynwat, V.; Erickson, J.P.; Frank, H.A.

    1997-03-12

    In this communication, we report low-frequency, near-infrared-exciation RR spectra of bacterial RCs in which the histidine residues of the protein are selectively labeled with {sup 15}N. For practical reasons, the studies were conducted by comparing the vibrational signatures of RCs in which {sup 15}N was universally incorporated (all cofactors and all protein residues) (designated all-{sup 15}N RCs) with those in which [{sup 14}N]histidine was introduced as a reverse label (disignated {sup 14}N-His RCs) into the all {sup 15}N-labeled RCs. The studies of the histidine-labeled RCs reveal that the vibrational characteristics of the BChl core are far more complicated than originally anticipated. These results have clear implications for the photoexcitation dynamics of the BChls in RCs and may also have significant consequences for the dynamics of exogenous ligand binding to heme-based oxygen carriers. 12 refs., 2 figs.

  4. Solid-state NMR and computational investigation of solvent molecule arrangement and dynamics in isostructural solvates of droperidol.

    PubMed

    Bērziņš, Agris; Hodgkinson, Paul

    2015-02-01

    (13)C, (15)N and (2)H solid-state NMR spectroscopy have been used to rationalize arrangement and dynamics of solvent molecules in a set of isostructural solvates of droperidol. The solvent molecules are determined to be dynamically disordered in the methanol and ethanol solvates, while they are ordered in the acetonitrile and nitromethane solvates. (2)H NMR spectra of deuterium-labelled samples allowed the characterization of the solvent molecule dynamics in the alcohol solvates and the non-stoichiometric hydrate. The likely motion of the alcohol molecules is rapid libration within a site, plus occasional exchange into an equivalent site related by the inversion symmetry, while the water molecules are more strongly disordered. DFT calculations strongly suggest that the differences in dynamics between the solvates are related to differences in the energetic penalty for reversing the orientation of a solvent molecule. PMID:25282618

  5. Solid-State NMR Studies of HIV-1 Capsid Protein Assemblies

    PubMed Central

    Han, Yun; Ahn, Jinwoo; Concel, Jason; Byeon, In-Ja L.; Gronenborn, Angela M.; Yang, Jun; Polenova, Tatyana

    2010-01-01

    In mature HIV-1 virions, a 26.6 kDa CA protein is assembled into a characteristic cone shaped core (capsid) that encloses the RNA viral genome. The assembled capsid structure is best described by a fullerene cone model that is made up from a hexameric lattice containing a variable number of CA pentamers, thus allowing for closure of tubular or conical structures. In this report, we present a solid-state NMR analysis of the wild type HIV-1 CA protein, prepared as conical and spherical assemblies that are stable and are not affected by magic angle spinning of the samples at frequencies between 10 and 25 kHz. Multidimensional homo- and heteronuclear correlation spectra of CA assemblies of uniformly 13C,15N-labelled CA exhibit narrow lines, indicative of conformational homogeneity of the protein in these assemblies. For the conical assemblies, partial residue-specific resonance assignments were obtained. Analysis of the NMR spectra recorded for the conical and spherical assemblies indicates that the CA protein structure is not significantly different in the different morphologies. The present results demonstrate that the assemblies of CA protein are amenable to detailed structural analysis by solid-state NMR spectroscopy. PMID:20092249

  6. Theoretical gas to liquid shift of (15)N isotropic nuclear magnetic shielding in nitromethane using ab initio molecular dynamics and GIAO/GIPAW calculations.

    PubMed

    Gerber, Iann C; Jolibois, Franck

    2015-05-14

    Chemical shift requires the knowledge of both the sample and a reference magnetic shielding. In few cases as nitrogen (15N), the standard experimental reference corresponds to its liquid phase. Theoretical estimate of NMR magnetic shielding parameters of compounds in their liquid phase is then mandatory but usually replaced by an easily-get gas phase value, forbidding direct comparisons with experiments. We propose here to combine ab initio molecular dynamic simulations with the calculations of magnetic shielding using GIAO approach on extracted cluster's structures from MD. Using several computational strategies, we manage to accurately calculate 15N magnetic shielding of nitromethane in its liquid phase. Theoretical comparison between liquid and gas phase allows us to extrapolate an experimental value for the 15N magnetic shielding of nitromethane in gas phase between -121.8 and -120.8 ppm.

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

    NASA Astrophysics Data System (ADS)

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

    2006-08-01

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

  8. An experimental and theoretical investigation of Acenaphthene-5-boronic acid: conformational study, NBO and NLO analysis, molecular structure and FT-IR, FT-Raman, NMR and UV spectra.

    PubMed

    Karabacak, Mehmet; Sinha, Leena; Prasad, Onkar; Asiri, Abdullah M; Cinar, Mehmet

    2013-11-01

    The solid state Fourier transform infrared (FT-IR) and FT-Raman spectra of Acenaphthene-5-boronic acid (AN-5-BA), have been recorded in the range 4000-400cm(-1) and 4000-10cm(-1), respectively. Density functional theory (DFT), with the B3LYP functional was used for the optimization of the ground state geometry and simulation of the infrared and Raman spectra of the molecule. The vibrational wave numbers and their assignments were examined theoretically using the Gaussian 09 set of quantum chemistry codes and the normal modes were assigned by a scaled quantum mechanical (SQM) force field approach. Hydrogen-bonded dimer of AN-5-BA, optimized by counterpoise correction, has also been studied by B3LYP at the 6-311++G(d,p) level and the effects of molecular association through O-H⋯O hydrogen bonding have been discussed. The (1)H and (13)C nuclear magnetic resonance (NMR) chemical shifts of the molecule were calculated by Gauge-Including Atomic Orbital (GIAO) method. Natural bond orbital (NBO) analysis has been applied to study stability of the molecule arising from charge delocalization. UV spectrum of the title compound was also recorded and the electronic properties, such as frontier orbitals, and band gap energies were measured by TD-DFT approach. The first order hyperpolarizability 〈β〉, its components and associated properties such as average polarizability and anisotropy of the polarizability (α and Δα) of AN-5-BA was calculated using the finite-field approach. PMID:23892116

  9. An experimental and theoretical investigation of Acenaphthene-5-boronic acid: Conformational study, NBO and NLO analysis, molecular structure and FT-IR, FT-Raman, NMR and UV spectra

    NASA Astrophysics Data System (ADS)

    Karabacak, Mehmet; Sinha, Leena; Prasad, Onkar; Asiri, Abdullah M.; Cinar, Mehmet

    2013-11-01

    The solid state Fourier transform infrared (FT-IR) and FT-Raman spectra of Acenaphthene-5-boronic acid (AN-5-BA), have been recorded in the range 4000-400 cm-1 and 4000-10 cm-1, respectively. Density functional theory (DFT), with the B3LYP functional was used for the optimization of the ground state geometry and simulation of the infrared and Raman spectra of the molecule. The vibrational wave numbers and their assignments were examined theoretically using the Gaussian 09 set of quantum chemistry codes and the normal modes were assigned by a scaled quantum mechanical (SQM) force field approach. Hydrogen-bonded dimer of AN-5-BA, optimized by counterpoise correction, has also been studied by B3LYP at the 6-311++G(d,p) level and the effects of molecular association through O-H⋯O hydrogen bonding have been discussed. The 1H and 13C nuclear magnetic resonance (NMR) chemical shifts of the molecule were calculated by Gauge-Including Atomic Orbital (GIAO) method. Natural bond orbital (NBO) analysis has been applied to study stability of the molecule arising from charge delocalization. UV spectrum of the title compound was also recorded and the electronic properties, such as frontier orbitals, and band gap energies were measured by TD-DFT approach. The first order hyperpolarizability <β>, its components and associated properties such as average polarizability and anisotropy of the polarizability (α and Δα) of AN-5-BA was calculated using the finite-field approach.

  10. 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.

  11. A Solution NMR Investigation into the Early Events of Amelogenin Nanosphere Self-Assembly Initiated with Sodium Chloride or Calcium Chloride

    SciTech Connect

    Buchko, Garry W.; Tarasevich, Barbara J.; Bekhazi, Jacky G.; Snead, Malcolm L.; Shaw, Wendy J.

    2008-12-08

    Using solution-state NMR spectroscopy, new insights into the early intermolecular interactions stabilizing amelogenin supramolecular assembly and the potential role of calcium ions have been discovered. Two-dimensional 1H-15N spectra were recorded for 15N-labeled amelogenin as a function of increasing Ca2+ concentration starting from monomeric conditions. Evidence for protein-protein interactions were observed between residues E18 and E40 in the N-terminus. At higher Ca2+ concentrations there was concurrent involvement of residues in both the N- (Y12-Q56) and the C-terminus (Q144-T171). Neither specific residues nor their stepwise interaction have previously been identified in the initial stages of nanosphere assembly.

  12. Nuclear magnetic resonance study of the Schiff base in bacteriorhodopsin: Counterion effects on the sup 15 N shift anisotropy

    SciTech Connect

    de Groot, H.J.M.; Harbison, G.S.; Herzfeld, J.; Griffin, R.G. )

    1989-04-18

    High-resolution, solid-state {sup 15}N NMR has been used to study the chemical shift anisotropies of the Schiff bases in bacteriorhodopsin (bR) and in an extensive series of model compounds. Using slow-spinning techniques, the authors are able to obtain sufficient rotational sideband intensity to determine the full {sup 15}N chemical shift anisotropy for the Schiff base nitrogen in bR{sub 548} and bR{sub 568}. Comparisons are made between all-trans-bR{sub 568} and N-all-trans-retinylidene butylimine salts with halide, phenolate, and carboxylate counterions. It is argues that for the model compounds the variation in {sup 15}N chemical shift reflects the variation in (hydrogen) bond strength with the various counterions. The results suggest that carboxylates and tyrosinates may form hydrogen bonds of comparable strength in a hydrophobic environment. Thus, the hydrogen bonding strength of a counterion depends on factors that are not completely reflected in the solution pK{sub a} of its conujugate acid. For the model compounds, the two most downfield principal values of the {sup 15}N chemical shift tensor, {sigma}{sub 22} and {sigma}{sub 33}, vary dramatically with different counterions, whereas {sigma}{sub 11} remains essentially unaffected. In addition, there exists a linear correlation between {sigma}{sub 22} and {sigma}{sub 33}, which suggests that a single mechanism is responsible for the variation in chemical shifts present in all three classes of model compounds. The data for bR{sub 568} follow this trend, but the isotropic shift is 11 ppm further upfield than any of the model compounds. This extreme value suggests an unusually weak hydrogen bond in the protein.

  13. Disentangling scalar coupling patterns by real-time SERF NMR.

    PubMed

    Gubensäk, Nina; Fabian, Walter M F; Zangger, Klaus

    2014-10-21

    Scalar coupling constants and signal splitting patterns in NMR spectra contain a wealth of short-range structural information. The extraction of these parameters from (1)H NMR spectra is often prohibited by simultaneous scalar coupling interactions with several other protons. Here we present a high-resolution NMR experiment where scalar coupling to only one selected signal is visible. All other couplings are removed from the spectrum. This real-time selectively refocused NMR experiment is achieved by spatially selective homonuclear broadband decoupling combined with selective refocusing during acquisition. It allows the unperturbed extraction of scalar coupling constants from the highly resolved acquisition dimension of NMR spectra.

  14. A Guided Inquiry Approach to NMR Spectroscopy

    NASA Astrophysics Data System (ADS)

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

    1998-04-01

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

  15. 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+).

  16. Quantification of ammonia binding sites in Davison (Type 3A) zeolite desiccant : a solid-state Nitrogen-15 MAS NMR spectroscopy investigation.

    SciTech Connect

    Alam, Todd Michael; Holland, Gregory P.; Cherry, Brian Ray

    2004-01-01

    The quantitative analysis of ammonia binding sites in the Davison (Type 3A) zeolite desiccant using solid-state {sup 15}N MAS NMR spectroscopy is reported. By utilizing 15N enriched ammonia ({sup 15}NH{sub 3}) gas, the different adsorption/binding sites within the zeolite were investigated as a function of NH{sub 3} loading. Using {sup 15}N MAS NMR multiple sites were resolved that have distinct cross-polarization dynamics and chemical shift behavior. These differences in the {sup 15}N NMR were used to characterize the adsorption environments in both the pure 3A zeolite and the silicone-molded forms of the desiccant.

  17. Achievement of 1020MHz NMR.

    PubMed

    Hashi, Kenjiro; Ohki, Shinobu; Matsumoto, Shinji; Nishijima, Gen; Goto, Atsushi; Deguchi, Kenzo; Yamada, Kazuhiko; Noguchi, Takashi; Sakai, Shuji; Takahashi, Masato; Yanagisawa, Yoshinori; Iguchi, Seiya; Yamazaki, Toshio; Maeda, Hideaki; Tanaka, Ryoji; Nemoto, Takahiro; Suematsu, Hiroto; Miki, Takashi; Saito, Kazuyoshi; Shimizu, Tadashi

    2015-07-01

    We have successfully developed a 1020MHz (24.0T) NMR magnet, establishing the world's highest magnetic field in high resolution NMR superconducting magnets. The magnet is a series connection of LTS (low-Tc superconductors NbTi and Nb3Sn) outer coils and an HTS (high-Tc superconductor, Bi-2223) innermost coil, being operated at superfluid liquid helium temperature such as around 1.8K and in a driven-mode by an external DC power supply. The drift of the magnetic field was initially ±0.8ppm/10h without the (2)H lock operation; it was then stabilized to be less than 1ppb/10h by using an NMR internal lock operation. The full-width at half maximum of a (1)H spectrum taken for 1% CHCl3 in acetone-d6 was as low as 0.7Hz (0.7ppb), which was sufficient for solution NMR. On the contrary, the temporal field stability under the external lock operation for solid-state NMR was 170ppb/10h, sufficient for NMR measurements for quadrupolar nuclei such as (17)O; a (17)O NMR measurement for labeled tri-peptide clearly demonstrated the effect of high magnetic field on solid-state NMR spectra. PMID:25978708

  18. Magic-angle-spinning NMR of the drug resistant S31N M2 proton transporter from influenza A.

    PubMed

    Andreas, Loren B; Eddy, Matthew T; Chou, James J; Griffin, Robert G

    2012-05-01

    We report chemical shift assignments of the drug-resistant S31N mutant of M2(18-60) determined using 3D magic-angle-spinning (MAS) NMR spectra acquired with a (15)N-(13)C ZF-TEDOR transfer followed by (13)C-(13)C mixing by RFDR. The MAS spectra reveal two sets of resonances, indicating that the tetramer assembles as a dimer of dimers, similar to the wild-type channel. Helicies from the two sets of chemical shifts are shown to be in close proximity at residue H37, and the assignments reveal a difference in the helix torsion angles, as predicted by TALOS+, for the key resistance residue N31. In contrast to wild-type M2(18-60), chemical shift changes are minimal upon addition of the inhibitor rimantadine, suggesting that the drug does not bind to S31N M2.

  19. 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.

  20. (1)H, (13)C, and (15)N chemical shifts assignments for human endothelial monocyte-activating polypeptide EMAP II.

    PubMed

    Lozhko, Dmytro; Stanek, Jan; Kazimierczuk, Krzysztof; Zawadzka-Kazimierczuk, Anna; Kozminski, Wiktor; Zhukov, Igor; Kornelyuk, Alexander

    2013-04-01

    Endothelial and monocyte-activating polypeptide II (EMAP II) is a cytokine that plays an important role in inflammation, apoptosis and angiogenesis processes in tumour tissues. Structurally, the EMAP II is a 169 amino acid residues long C-terminal domain (residues 147-312) of auxiliary tRNA binding protein p43. In spite of existence in pdb databank of two X-ray structures there are some important aspects of EMAP II cytokine function which are still not fully understood in detail. To obtain information about 3D structure and backbone dynamic processes in solution we perform structure evaluation of human EMAP II cytokine by NMR spectroscopy. The standard approach to sequence-specific backbone assignment using 3D NMR data sets was not successful in our studies and was supplemented by recently developed 4D NMR experiments with random sampling of evolution time space. Here we report the backbone and side chain (1)H, (13)C, and (15)N chemical shifts in solution for recombinant EMAP II cytokine together with secondary structure provided by TALOS + software.

  1. Synthesis of 13C and 15N labeled 2,4-dinitroanisole.

    PubMed

    Jagadish, Bhumasamudram; Field, Jim A; Chorover, Jon; Sierra-Alvarez, Reyes; Abrell, Leif; Mash, Eugene A

    2014-05-30

    Syntheses of [(13)C6]-2,4-dinitroanisole (ring-(13)C6) from [(13)C6]-anisole (ring-(13)C6) and [(15)N2]-2,4-dinitroanisole from anisole using in situ generated acetyl nitrate and [(15)N]-acetyl nitrate, respectively, are described. Treatment of [(13)C6]-anisole (ring-(13)C6) with acetyl nitrate generated in 100% HNO3 gave [(13)C6]-2,4-dinitroanisole (ring-(13)C6) in 83% yield. Treatment of anisole with [(15)N]-acetyl nitrate generated in 10 N [(15)N]-HNO3 gave [(15)N2 ]-2,4-dinitroanisole in 44% yield after two cycles of nitration. Byproducts in the latter reaction included [(15)N]-2-nitroanisole and [(15)N]-4-nitroanisole.

  2. Differential 14N/15N-Labeling of Peptides Using N-Terminal Charge Derivatization with a High-Proton Affinity for Straightforward de novo Peptide Sequencing

    PubMed Central

    Nihashi, Yoichiro; Miyashita, Masahiro; Awane, Hiroyuki; Miyagawa, Hisashi

    2013-01-01

    While de novo peptide sequencing is essential in many situations, it remains a difficult task. This is because peptide fragmentation results in complicated and often incomplete product ion spectra. In a previous study, we demonstrated that N-terminal charge derivatization with 4-amidinobenzoic acid (Aba) resulted in improved peptide fragmentation under low-energy CID conditions. However, even with this derivatization, some ambiguity exists, due to difficulties in discriminating between N- and C-terminal fragments. In this study, to specifically identify b-ions from complex product ion spectra, the differential 14N/15N-labeling of peptides was performed using Aba derivatization. 15N-Labeled Aba was synthesized in the form of a succinimide ester. Peptides were derivatized individually with 14N-Aba or 15N-Aba and analyzed by ESI-MS/MS using a linear ion trap-Orbitrap hybrid FTMS system. The N-terminal fragments (i.e., b-ions) were then identified based on m/z differences arising from isotope labeling. By comparing the spectra between 14N- and 15N-Aba derivatized peptides, b-ions could be successfully identified based on the m/z shifts, which provided reliable sequencing results for all of the peptides examined in this study. The method developed in this study allows the easy and reliable de novo sequencing of peptides, which is useful in peptidomics and proteomics studies. PMID:24860714

  3. An Integrated Laboratory Project in NMR Spectroscopy.

    ERIC Educational Resources Information Center

    Hudson, Reggie L.; Pendley, Bradford D.

    1988-01-01

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

  4. 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

  5. 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.

  6. Application of Natural Isotopic Abundance ¹H-¹³C- and ¹H-¹⁵N-Correlated Two-Dimensional NMR for Evaluation of the Structure of Protein Therapeutics.

    PubMed

    Arbogast, Luke W; Brinson, Robert G; Marino, John P

    2016-01-01

    Methods for characterizing the higher-order structure of protein therapeutics are in great demand for establishing consistency in drug manufacturing, for detecting drug product variations resulting from modifications in the manufacturing process, and for comparing a biosimilar to an innovator reference product. In principle, solution NMR can provide a robust approach for characterization of the conformation(s) of protein therapeutics in formulation at atomic resolution. However, molecular weight limitations and the perceived need for stable isotope labeling have to date limited its practical applications in the biopharmaceutical industry. Advances in NMR magnet and console technologies, cryogenically cooled probes, and new rapid acquisition methodologies, particularly selective optimized flip-angle short transient pulse schemes and nonuniform sampling, have greatly ameliorated these limitations. Here, we describe experimental methods for the collection and analysis of 2D (1)H(N)-(15)N-amide- and (1)H-(13)C-methyl-correlated spectra applied to protein drug products at natural isotopic abundance, including representatives from the rapidly growing class of monoclonal antibody (mAb) therapeutics. Practical aspects of experimental setup and data acquisition for both standard and rapid acquisition NMR techniques are described. Furthermore, strategies for the statistical comparison of 2D (1)H(N)-(15)N-amide- and (1)H-(13)C-methyl-correlated spectra are detailed.

  7. Automated protein NMR resonance assignments.

    PubMed

    Wan, Xiang; Xu, Dong; Slupsky, Carolyn M; Lin, Guohui

    2003-01-01

    NMR resonance peak assignment is one of the key steps in solving an NMR protein structure. The assignment process links resonance peaks to individual residues of the target protein sequence, providing the prerequisite for establishing intra- and inter-residue spatial relationships between atoms. The assignment process is tedious and time-consuming, which could take many weeks. Though there exist a number of computer programs to assist the assignment process, many NMR labs are still doing the assignments manually to ensure quality. This paper presents (1) a new scoring system for mapping spin systems to residues, (2) an automated adjacency information extraction procedure from NMR spectra, and (3) a very fast assignment algorithm based on our previous proposed greedy filtering method and a maximum matching algorithm to automate the assignment process. The computational tests on 70 instances of (pseudo) experimental NMR data of 14 proteins demonstrate that the new score scheme has much better discerning power with the aid of adjacency information between spin systems simulated across various NMR spectra. Typically, with automated extraction of adjacency information, our method achieves nearly complete assignments for most of the proteins. The experiment shows very promising perspective that the fast automated assignment algorithm together with the new score scheme and automated adjacency extraction may be ready for practical use. PMID:16452794

  8. 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.

  9. Ultrahigh resolution protein structures using NMR chemical shift tensors

    PubMed Central

    Wylie, Benjamin J.; Sperling, Lindsay J.; Nieuwkoop, Andrew J.; Franks, W. Trent; Oldfield, Eric; Rienstra, Chad M.

    2011-01-01

    NMR chemical shift tensors (CSTs) in proteins, as well as their orientations, represent an important new restraint class for protein structure refinement and determination. Here, we present the first determination of both CST magnitudes and orientations for 13Cα and 15N (peptide backbone) groups in a protein, the β1 IgG binding domain of protein G from Streptococcus spp., GB1. Site-specific 13Cα and 15N CSTs were measured using synchronously evolved recoupling experiments in which 13C and 15N tensors were projected onto the 1H-13C and 1H-15N vectors, respectively, and onto the 15N-13C vector in the case of 13Cα. The orientations of the 13Cα CSTs to the 1H-13C and 13C-15N vectors agreed well with the results of ab initio calculations, with an rmsd of approximately 8°. In addition, the measured 15N tensors exhibited larger reduced anisotropies in α-helical versus β-sheet regions, with very limited variation (18 ± 4°) in the orientation of the z-axis of the 15N CST with respect to the 1H-15N vector. Incorporation of the 13Cα CST restraints into structure calculations, in combination with isotropic chemical shifts, transferred echo double resonance 13C-15N distances and vector angle restraints, improved the backbone rmsd to 0.16 Å (PDB ID code 2LGI) and is consistent with existing X-ray structures (0.51 Å agreement with PDB ID code 2QMT). These results demonstrate that chemical shift tensors have considerable utility in protein structure refinement, with the best structures comparable to 1.0-Å crystal structures, based upon empirical metrics such as Ramachandran geometries and χ1/χ2 distributions, providing solid-state NMR with a powerful tool for de novo structure determination. PMID:21969532

  10. Regulation of [15N]urea synthesis from [5-15N]glutamine. Role of pH, hormones, and pyruvate.

    PubMed

    Nissim, I; Yudkoff, M; Brosnan, J T

    1996-12-01

    We have utilized both [5-15N]glutamine and [3-13C] pyruvate as metabolic tracers in order to: (i) examine the effect of pH, glucagon (GLU), or insulin on the precursor-product relationship between 15NH3, [15N]citrulline, and, thereby, [15N]urea synthesis and (ii) elucidate the mechanism(s) by which pyruvate stimulates [15N] urea synthesis. Hepatocytes isolated from rat were incubated at pH 6.8, 7.4, or 7.6 with 1 mM [5-15N]glutamine and 0.1 mM 14NH4Cl in the presence or the absence of [3-13C] pyruvate (2 mM). A separate series of experiments was performed at pH 7.4 in the presence of insulin or GLU. 15NH3 enrichment exceeded or was equal to that of [15N]citrulline under all conditions except for pH 7.6, when the 15N enrichment in citrulline exceeded that in ammonia. The formation of [15N]citrulline (atom % excess) was increased with higher pH. Flux through phosphate-dependent glutaminase (PDG) and [15N]urea synthesis were stimulated (p < 0.05) at pH 7.6 or with GLU and decreased (p < 0.05) at pH 6.8. Insulin had no significant effect on flux through PDG or on [15N]urea synthesis. Decreased [15N]urea production at pH 6.8 was associated with depleted aspartate and glutamate levels. Pyruvate attenuated this decrease in the aspartate and glutamate pools and stimulated [15N]urea synthesis. Production of Asp from pyruvate was increased with increasing medium pH. Approximately 80% of Asp was derived from [3-13C]pyruvate regardless of incubation pH or addition of hormone. Furthermore, approximately 20, 40, and 50% of the mitochondrial N-acetylglutamate (NAG) pool was derived from [3-13C]pyruvate at pH 6.8, 7.4, and 7.6, respectively. Both the concentration and formation of [13C]NAG from [3-13C]pyruvate were increased (p < 0.05) with glucagon and decreased (p < 0.05) with insulin or at pH 6.8. The data suggest a correlation between changes in [15N]urea synthesis and alterations in the level and synthesis of [13C]NAG from pyruvate. The current observations suggest that the

  11. NMR investigation of the interaction of the inhibitor protein Im9 with its partner DNase.

    PubMed Central

    Boetzel, R.; Czisch, M.; Kaptein, R.; Hemmings, A. M.; James, R.; Kleanthous, C.; Moore, G. R.

    2000-01-01

    The bacterial toxin colicin E9 is secreted by producing Escherichia coli cells with its 9.5 kDa inhibitor protein Im9 bound tightly to its 14.5 kDa C-terminal DNase domain. Double- and triple-resonance NMR spectra of the 24 kDa complex of uniformly 13C and 15N labeled Im9 bound to the unlabeled DNase domain have provided sufficient constraints for the solution structure of the bound Im9 to be determined. For the final ensemble of 20 structures, pairwise RMSDs for residues 3-84 were 0.76 +/- 0.14 A for the backbone atoms and 1.36 +/- 0.15 A for the heavy atoms. Representative solution structures of the free and bound Im9 are highly similar, with backbone and heavy atom RMSDs of 1.63 and 2.44 A, respectively, for residues 4-83, suggesting that binding does not cause a major conformational change in Im9. The NMR studies have also allowed the DNase contact surface on Im9 to be investigated through changes in backbone chemical shifts and NOEs between the two proteins determined from comparisons of 1H-1H-13C NOESY-HSQC spectra with and without 13C decoupling. The NMR-defined interface agrees well with that determined in a recent X-ray structure analysis with the major difference being that a surface loop of Im9, which is at the interface, has a different conformation in the solution and crystal structures. Tyr54, a key residue on the interface, is shown to exhibit NMR characteristics indicative of slow rotational flipping. A mechanistic description of the influence binding of Im9 has on the dynamic behavior of E9 DNase, which is known to exist in two slowly interchanging conformers in solution, is proposed. PMID:11045617

  12. NMR studies of two spliced leader RNAs using isotope labeling

    SciTech Connect

    Lapham, J.; Crothers, D.M.

    1994-12-01

    Spliced leader RNAs are a class of RNA molecules (<200 nts) involved in the trans splicing of messenger RNA found in trypanosomes, nematodes, and other lower eukaryotes. The spliced leader RNA from the trypanosome Leptomonas Collosoma exists in two alternate structural forms with similar thermal stabilities. The 54 nucleotides on the 5{prime} end of the SL molecule is structurally independent from the 3{prime} half of the RNA, and displays the two structural forms. Furthermore, the favored of the two structures was shown to contain anomalous nuclease sensitivity and thermal stability features, which suggests that there may be tertiary interactions between the splice site and other nucleotides in the 5{prime} end. Multidimensional NMR studies are underway to elucidate the structural elements present in the SL RNAs that give rise to their physical properties. Two spliced leader sequences have been studied. The first, the 54 nucleotides on the 5{prime} end of the L. Collosoma sequence, was selected because of earlier studies in our laboratory. The second sequence is the 5{prime} end of the trypanosome Crithidia Fasciculata, which was chosen because of its greater sequence homology to other SL sequences. Given the complexity of the NMR spectra for RNA molecules of this size, we have incorporated {sup 15}N/{sup 13}C-labeled nucleotides into the RNA. One of the techniques we have developed to simplify the spectra of these RNA molecules is isotope labeling of specific regions of the RNA. This has been especially helpful in assigning the secondary structure of molecules that may be able to adopt multiple conformations. Using this technique one can examine a part of the molecule without spectral interference from the unlabeled portion. We hope this approach will promote an avenue for studying the structure of larger RNAs in their native surroundings.

  13. Semiautomatic sequence-specific assignment of proteins based on the tertiary structure--the program st2nmr.

    PubMed

    Pristovsek, Primoz; Rüterjans, Heinz; Jerala, Roman

    2002-02-01

    The sequence-specific assignment of resonances is still the most time-consuming procedure that is necessary as the first step in high-resolution NMR studies of proteins. In many cases a reliable three-dimensional (3D) structure of the protein is available, for example, from X-ray spectroscopy or homology modeling. Here we introduce the st2nmr program that uses the 3D structure and Nuclear Overhauser Effect spectroscopy (NOESY) peak list(s) to evaluate and optimize trial sequence-specific assignments of spin systems derived from correlation spectra to residues of the protein. A distance-dependent target function that scores trial assignments based on the presence of expected NOESY crosspeaks is optimized in a Monte Carlo fashion. The performance of the program st2nmr is tested on real NMR data of an alpha-helical (cytochrome c) and beta-sheet (lipocalin) protein using homology models and/or X-ray structures; it succeeded in completely reproducing the correct sequence-specific assignments in most cases using 2D and/or 15N/13C Nuclear Overhauser Effect (NOE) data. Additionally to amino acid residues the program can also handle ligands that are bound to the protein, such as heme, and can be used as a complementary tool to fully automated assignment procedures. PMID:11908496

  14. NMR detection of slow conformational dynamics in an endonuclease toxin.

    PubMed

    Whittaker, S B; Boetzel, R; MacDonald, C; Lian, L Y; Pommer, A J; Reilly, A; James, R; Kleanthous, C; Moore, G R

    1998-07-01

    The cytotoxic activity of the secreted bacterial toxin colicin E9 is due to a non-specific DNase housed in the C-terminus of the protein. Double-resonance and triple-resonance NMR studies of the 134-amino acid 15N- and 13C/15N-labelled DNase domain are presented. Extensive conformational heterogeneity was evident from the presence of far more resonances than expected based on the amino acid sequence of the DNase, and from the appearance of chemical exchange cross-peaks in TOCSY and NOESY spectra. EXSY spectra were recorded to confirm that slow chemical exchange was occurring. Unambiguous sequence-specific resonance assignments are presented for one region of the protein, Pro65-Asn72, which exists in two slowly exchanging conformers based on the identification of chemical exchange cross-peaks in 3D 1H-1H-15N EXSY-HSQC, NOESY-HSQC and TOCSY-HSQC spectra, together with C alpha and C beta chemical shifts measured in triple-resonance spectra and sequential NH NOEs. The rates of conformational exchange for backbone amide resonances in this stretch of amino acids, and for the indole NH of either Trp22 or Trp58, were determined from the intensity variation of the appropriate diagonal and chemical exchange cross-peaks recorded in 3D 1H-1H-15N NOESY-HSQC spectra. The data fitted a model in which this region of the DNase has two conformers, NA and NB, which interchange at 15 degrees C with a forward rate constant of 1.61 +/- 0.5 s-1 and a backward rate constant of 1.05 +/- 0.5 s-1. Demonstration of this conformational equilibrium has led to a reappraisal of a previously proposed kinetic scheme describing the interaction of E9 DNase with immunity proteins [Wallis et al. (1995) Biochemistry, 34, 13743-13750 and 13751-13759]. The revised scheme is consistent with the specific inhibitor protein for the E9 DNase, Im9, associating with both the NA and NB conformers of the DNase and with binding only to the NB conformer detected because the rate of dissociation of the complex of Im9

  15. Nuclear Magnetic Resonance (NMR) as a tool for the study of the metabolism of Rickettsia slovaca.

    PubMed

    García-Álvarez, Lara; Busto, Jesús H; Peregrina, Jesús M; Santibáñez, Sonia; Portillo, Aránzazu; Avenoza, Alberto; Oteo, José A

    2015-01-01

    Rickettsial infections are caused by intracellular bacteria. They do not grow in standard culture media so there are limitations in routine practice to study their metabolism. Nuclear Magnetic Resonance (NMR) spectroscopy is used for identification of metabolites in biological samples. Vero cells infected with Rickettsia slovaca as well as uninfected cells were monitored by (1)H NMR showing the presence of ethanol and lactic acid. As no differences were observed, labeled compounds were added into cultures. When D-[1-13C]glucose was monitored by (13)C NMR no differences among infected and uninfected cells were observed in metabolic profiles. Glucose was transformed into ethanol in all cultures. Monitored experiments carried out with [2-13C]glycine showed differences between infected and uninfected cell cultures spectra. Glycine was partially transformed into serine, but the amount of the serine formed was larger in those infected. Moreover, L-[2-13C]leucine, L-[1-13C]isoleucine and L-[15N]tyrosine were evaluated. No differences among infected and uninfected cells were observed in the metabolic profiles when tyrosine and leucine were monitored. The amino acid L-[1-13C]isoleucine exhibited different metabolism in presence of the R. slovaca, showing a promising behavior as biomarker. In this work we focused on finding one or more compounds that could be metabolized specifically by R. slovaca and could be used as an indicator of its activity.

  16. Parallel β-Sheet Structure of Alanine Tetrapeptide in the Solid State As Studied by Solid-State NMR Spectroscopy.

    PubMed

    Asakura, Tetsuo; Horiguchi, Kumiko; Aoki, Akihiro; Tasei, Yugo; Naito, Akira

    2016-09-01

    The structural analysis of alanine oligopeptides is important for understanding the crystalline region in silks from spiders and wild silkworms and also the mechanism of cellular toxicity of human diseases arising from expansion in polyalanine sequences. The atomic-level structures of alanine tripeptide and tetrapeptide with antiparallel β-sheet structures (AP-Ala3 and AP-Ala4, respectively) together with alanine tripeptide with parallel β-sheet structures (P-Ala3) have been determined, but alanine tetrapeptide with a parallel β-sheet structure (P-Ala4) has not been reported yet. In this article, first, we established the preparation protocol of P-Ala4 from more stable AP-Ala4. Second, complete assignments of the (13)C, (15)N, and (1)H solid-state NMR spectra were performed with (13)C- and (15)N-labeled Ala4 samples using several solid-state NMR techniques. Then, the structural constraints were obtained, for example, the amide proton peaks of P-Ala4 in the (1)H double-quantum magic-angle spinning NMR spectrum were heavily overlapped and observed at about 7.4 ppm, which was a much higher field than that of 8.7-9.1 ppm observed for AP-Ala4, indicating that the intermolecular hydrogen-bond lengths across strands (N-H···O═C) were considerably longer for P-Ala4, that is, 2.21-2.34 Å, than those reported for AP-Ala4, that is, 1.8-1.9 Å. The structural model was proposed for P-Ala4 by NMR results and MD calculations. PMID:27482868

  17. sup 13 C and sup 15 N nuclear magnetic resonance evidence of the ionization state of substrates bound to bovine dihydrofolate reductase

    SciTech Connect

    Selinsky, B.S.; Perlman, M.E.; London, R.E. ); Unkefer, C.J. ); Mitchell, J. ); Blakley, R.L. Univ. of Tennessee, Memphis )

    1990-02-06

    The state of protonation of substrates bound to mammalian dihydrofolate reductase (DHFR) has significance for the mechanism of catalysis. To investigate this, dihydrofolate and dihydropteroylpentaglutamate have been synthesized with {sup 15}N enrichment at N-5. {sup 15}N NMR studies have been performed on the binary complexes formed by bovine DHFR with these compounds and with (5-{sup 15}N)dihydrobiopterin. The results indicate that there is no protonation at N-5 in the binary complexes, and this was confirmed by {sup 13}C NMR studies with folate and dihydrofolate synthesized with {sup 13}C enrichment at C-6. The chemical shift displacements produced by complex formation are in the same direction as those which result from deprotonation of the N-3/C-4-O amide group and are consistent with at least partial loss of the proton from N-3. This would be possible if, as crystallographic data indicate, there is interaction of N-3 and the 2-amino group of the bound ligands with the carboxylate of the active site glutamate residue (Glu{sup 30}).

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

    SciTech Connect

    Carr, M.D.; Birdsall, B.; Jimenez-Barbero, J.; Polshakov, V.I.; McCormick, J.E.; Feeney, J.; Frenkiel, T.A.; Bauer, C.J. ); Roberts, G.C.K. )

    1991-06-25

    Three-dimensional (3D) heteronuclear NMR techniques have been used to make sequential {sup 1}H and {sup 15}H resonance assignments for most of the residues of Lactobacillus casei dihydrofolate reductase (DHFR), a monomeric protein of molecular mass 18,300 Da. A uniformly {sup 15}N-labeled sample of the protein was prepared and its complex with methotrexate (MTX) studied by 3D {sup 15}N/{sup 1}H nuclear Overhauserheteronuclear multiple quantum coherence (NOESY-HMQC), Harmann-Hahn-heteronuclear multiple quantum coherence (HOHAHA-HMQC), and HMQC-NOESY-HMQC experiments. These experiments overcame most of the spectral overlap problems caused by chemical shift degeneracies in 2D spectra and allowed the {sup 1}H-{sup 1}H through-space and through-bond connectivities to be identified unambiguously, leading to the resonance assignments. The novel HMQC-NOESY-HMQC experiment allows NOE cross peaks to be detected between NH protons even when their {sup 1}H chemical shifts are degenerate as long as the amide {sup 15}N chemical shifts are nondegenerate. The 3D experiments, in combination with conventional 2D NOESY, COSY, and HOHAHA experiments on unlabelled and selectively deuterated DHFR, provide backbone assignments for 146 of the 162 residues and side-chain assignments for 104 residues of the protein. Data from the NOE-based experiments and identification of the slowly exchanging amide protons provide detailed information about the secondary structure of the binary complex of the protein with methotrexate.

  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. Variability of the 15N Chemical Shielding Tensors in the B3 Domain of Protein G from 15N Relaxation Measurements at Several Fields

    PubMed Central

    Hall, Jennifer B.; Fushman, David

    2008-01-01

    We applied a combination of 15N relaxation and CSA/dipolar cross-correlation measurements at five magnetic fields (9.4, 11.7, 14.1, 16.4, and 18.8 Tesla) to determine the 15N chemical shielding tensors for backbone amides in protein G in solution. The data were analyzed using various model-independent approaches and those based on Lipari-Szabo approximation, all of them yielding similar results. The results indicate a range of site-specific values of the anisotropy (CSA) and orientation of the 15N chemical shielding tensor, similar to those in ubiquitin. Assuming a Gaussian distribution of the 15N CSA values, the mean anisotropy is -173.9 to -177.2 ppm (for 1.02-Å NH-bond length) and the site-so-site CSA variability is ±17.6 to ±21.4 ppm, depending on the method used. This CSA variability is significantly larger than derived previously for ribonuclease H or recently, using “meta-analysis” for ubiquitin. Standard interpretation of 15N relaxation studies of backbone dynamics in proteins involves an a priori assumption of a uniform 15N CSA. We show that this assumption leads to a significant discrepancy between the order parameters obtained at different fields. Using the site-specific CSAs obtained from our study removes this discrepancy and allows simultaneous fit of relaxation data at all five fields to Lipari-Szabo spectral densities. These findings emphasize the necessity of taking into account the variability of 15N CSA for accurate analysis of protein dynamics from 15N relaxation measurements. PMID:16771499

  2. Scalar operators in solid-state NMR

    SciTech Connect

    Sun, Boqin

    1991-11-01

    Selectivity and resolution of solid-state NMR spectra are determined by dispersion of local magnetic fields originating from relaxation effects and orientation-dependent resonant frequencies of spin nuclei. Theoretically, the orientation-dependent resonant frequencies can be represented by a set of irreducible tensors. Among these tensors, only zero rank tensors (scalar operators) are capable of providing high resolution NMR spectra. This thesis presents a series of new developments in high resolution solid-state NMR concerning the reconstruction of various scalar operators motion in solid C{sub 60} is analyzed.

  3. Structural Analysis of Nanoscale Self-Assembled Discoidal Lipid Bilayers by Solid-State NMR Spectroscopy

    PubMed Central

    Li, Ying; Kijac, Aleksandra Z.; Sligar, Stephen G.; Rienstra, Chad M.

    2006-01-01

    Nanodiscs are an example of discoidal nanoscale self-assembled lipid/protein particles similar to nascent high-density lipoproteins, which reduce the risk of coronary artery disease. The major protein component of high-density lipoproteins is human apolipoprotein A-I, and the corresponding protein component of Nanodiscs is membrane scaffold protein 1 (MSP1), a 200-residue lipid-binding domain of human apolipoprotein A-I. Here we present magic-angle spinning (MAS) solid-state NMR studies of uniformly 13C,15N-labeled MSP1 in polyethylene glycol precipitated Nanodiscs. Two-dimensional MAS 13C-13C correlation spectra show excellent microscopic order of MSP1 in precipitated Nanodiscs. Secondary isotropic chemical shifts throughout the protein are consistent with a predominantly helical structure. Moreover, the backbone conformations of prolines derived from their 13C chemical shifts are consistent with the molecular belt model but not the picket fence model of lipid-bound MSP1. Overall comparison of experimental spectra and 13C chemical shifts predicted from several structural models also favors the belt model. Our study thus supports the belt model of Nanodisc structure and demonstrates the utility of MAS NMR to study the structure of high molecular weight lipid-protein complexes. PMID:16905610

  4. High-Resolution Solid-State NMR of Anisotropically Mobile Molecules Under Very Low Power 1H Decoupling and Moderate Magic-Angle Spinning

    PubMed Central

    Doherty, Tim; Hong, Mei

    2011-01-01

    We show that for observing high-resolution heteronuclear NMR spectra of anisotropically mobile systems with order parameters less than 0.25, moderate magic-angle spinning (MAS) rates of ∼11 kHz combined with 1H decoupling at 1-2 kHz are sufficient. Broadband decoupling at this low 1H nutation frequency is achieved by composite pulse sequences such as WALTZ-16. We demonstrate this moderate MAS low-power decoupling technique on hydrated POPC lipid membranes, and show that 1 kHz 1H decoupling yields spectra with the same resolution and sensitivity as spectra measured under 50 kHz 1H decoupling when the same acquisition times (∼ 50 ms) are used, but the low-power decoupled spectra give higher resolution and sensitivity when longer acquisition times (> 150 ms) are used, which are not possible with high-power decoupling. The limits of validity of this approach are explored for a range of spinning rates and molecular mobilities using more rigid membrane systems such as POPC/cholesterol mixed bilayers. Finally, we show 15N and 13C spectra of a uniaxially diffusing membrane peptide assembly, the influenza A M2 transmembrane domain, under 11 kHz MAS and 2 kHz 1H decoupling. The peptide 15N and 13C intensities at low power decoupling are 70-80% of the high-power decoupled intensities. Therefore, it is possible to study anisotropically mobile lipids and membrane peptides using liquid-state NMR equipment, relatively large rotors, and moderate MAS frequencies. PMID:19501003

  5. 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 interprete