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Sample records for 15n nmr chemical

  1. 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.

  2. 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

  3. 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

  4. 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.

  5. 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.

  6. 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

  7. 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

  8. 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.

  9. 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

  10. 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.

  11. 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

  12. 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.

  13. 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.

  14. 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).

  15. 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

  16. 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

  17. 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

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

    NASA Astrophysics Data System (ADS)

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

    1999-07-01

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

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

    SciTech Connect

    Jones, R.A.

    1994-12-01

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

  20. 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…

  1. 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…

  2. 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.

  3. 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

  4. (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

  5. 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.

  6. 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

  7. 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.

  8. 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.

  9. 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.

  10. (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.

  11. (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

  12. 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.

  13. 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.

  14. 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.

  15. 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.

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

    PubMed

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

    2008-11-01

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

  17. 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.

  18. 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.

  19. 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.

  20. 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

  1. 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.

  2. 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.

  3. 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

  4. 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

  5. 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

  6. 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

  7. 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.

  8. 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

  9. 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

  10. 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

  11. 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.

  12. 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

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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

  8. 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}).

  9. 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

  10. 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

  11. 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

  12. 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.

  13. 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

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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

  19. 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.

  20. 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

  1. 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.

  2. (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.

  3. 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.

  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. **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.

  6. 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.

  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. 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...

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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

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

    PubMed Central

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

    2012-01-01

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

  17. 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.

  18. 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.

  19. Influence of N-H...O and O-H...O hydrogen bonds on the (17)O, (15)N and (13)C chemical shielding tensors in crystalline acetaminophen: a density functional theory study.

    PubMed

    Esrafili, Mehdi D; Behzadi, Hadi; Hadipour, Nasser L

    2007-06-01

    A computational investigation was carried out to characterize the (17)O, (15)N and (13)C chemical shielding tensors in crystalline acetaminophen. We found that N-H...O and O-H...O hydrogen bonds around the acetaminophen molecule in the crystal lattice have different influences on the calculated (17)O, (15)N and (13)C chemical shielding eigenvalues and their orientations in the molecular frame of axes. The calculations were performed with the B3LYP method and 6-311++G(d, p) and 6-311+G(d) standard basis sets using the Gaussian 98 suite of programs. Calculated chemical shielding tensors were used to evaluate the (17)O, (15)N, and (13)C NMR chemical shift tensors in crystalline acetaminophen, which are in reasonable agreement with available experimental data. The difference between the calculated NMR parameters of the monomer and molecular clusters shows how much hydrogen-bonding interactions affect the chemical shielding tensors of each nucleus. The computed (17)O chemical shielding tensor on O(1), which is involved in two intermolecular hydrogen bonds, shows remarkable sensitivity toward the choice of the cluster model, whereas the (17)O chemical shielding tensor on O(2) involved in one N-H...O hydrogen bond, shows smaller improvement toward the hydrogen-bonding interactions. Also, a reasonably good agreement between the experimentally obtained solid-state (15)N and (13)C NMR chemical shifts and B3LYP/6-311++G(d, p) calculations is achievable only in molecular cluster model where a complete hydrogen-bonding network is considered. Moreover, at the B3LYP/6-311++G(d, p) level of theory, the calculated (17)O, (15)N and (13)C chemical shielding tensor orientations are able to reproduce the experimental values to a reasonably good degree of accuracy.

  20. 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

  1. 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.

  2. 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

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

    SciTech Connect

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

    1990-03-06

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

  4. 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.

  5. 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

  6. 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

  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. 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.

  9. A new approach to NMR chemical shift additivity parameters using simultaneous linear equation method.

    PubMed

    Shahab, Yosif A; Khalil, Rabah A

    2006-10-01

    A new approach to NMR chemical shift additivity parameters using simultaneous linear equation method has been introduced. Three general nitrogen-15 NMR chemical shift additivity parameters with physical significance for aliphatic amines in methanol and cyclohexane and their hydrochlorides in methanol have been derived. A characteristic feature of these additivity parameters is the individual equation can be applied to both open-chain and rigid systems. The factors that influence the (15)N chemical shift of these substances have been determined. A new method for evaluating conformational equilibria at nitrogen in these compounds using the derived additivity parameters has been developed. Conformational analyses of these substances have been worked out. In general, the results indicate that there are four factors affecting the (15)N chemical shift of aliphatic amines; paramagnetic term (p-character), lone pair-proton interactions, proton-proton interactions, symmetry of alkyl substituents and molecular association.

  10. 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.

  11. 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.

  12. 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

  13. 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

  14. Simultaneous CT-13C and VT-15N chemical shift labelling: application to 3D NOESY-CH3NH and 3D 13C,15N HSQC-NOESY-CH3NH.

    PubMed

    Uhrín, D; Bramham, J; Winder, S J; Barlow, P N

    2000-11-01

    Based on the HSQC scheme, we have designed a 2D heterocorrelated experiment which combines constant time (CT) 13C and variable time (VT) 15N chemical shift labelling. Although applicable to all carbons, this mode is particularly suitable for simultaneous recording of methyl-carbon and nitrogen chemical shifts at high digital resolution. The methyl carbon magnetisation is in the transverse plane during the whole CT period (1/J(CC) = 28.6 ms). The magnetisation originating from NH protons is initially stored in the 2HzNz state, then prior to the VT chemical shift labelling period is converted into 2HzNy coherence. The VT -15N mode eliminates the effect of 1J(N,CO) and 1,2J(N,CA) coupling constants without the need for band-selective carbon pulses. An optional editing procedure is incorporated which eliminates signals from CH2 groups, thus removing any potential overlap with the CH3 signals. The CT-13CH3,VT-15N HSQC building block is used to construct two 3D experiments: 3D NOESY-CH3NH and 3D 13C,15N HSQC-NOESY-CH3NH. Combined use of these experiments yields proton and heteronuclear chemical shifts for moieties experiencing NOEs with CH3 and NH protons. These NOE interactions are resolved as a consequence of the high digital resolution in the carbon and nitrogen chemical shifts of CH3 and NH groups, respectively. The techniques are illustrated using a double labelled sample of the CH domain from calponin.

  15. Inhibition of thermolysin by phosphonamidate transition-state analogues: measurement of 31P-15N bond lengths and chemical shifts in two enzyme-inhibitor complexes by solid-state nuclear magnetic resonance.

    PubMed

    Copié, V; Kolbert, A C; Drewry, D H; Bartlett, P A; Oas, T G; Griffin, R G

    1990-10-01

    31P and 15N chemical shifts and 31P-15N bond lengths have been measured with solid-state NMR techniques in two inhibitors of thermolysin, carbobenzoxy-Glyp-L-Leu-L-Ala (ZGpLA) and carbobenzoxy-L-Phep-L-Leu-L-Ala (ZFpLA), both as free lithium salts and when bound to the enzyme. Binding of both inhibitors to thermolysin results in large changes in the 31P chemical shifts. These changes are more dramatic for the tighter binding inhibitor ZFpLA, where a approximately 20 ppm downfield movement of the 31P isotropic chemical shift (sigma iso) is observed. This shift is due to changes in the shift tensor elements sigma 11 and sigma 22, while sigma 33 remains essentially constant. We observed a similar pattern for ZGpLA, but only a approximately 5 ppm change occurs in sigma iso. The changes in the 15N chemical shifts for both inhibitors are small upon binding, amounting to downfield shifts of 2 and 4 ppm for ZGpLA and ZFpLA, respectively. This indicates that there are no changes in the protonation state of the 15N in either the ZFpLA- or the ZGpLA-thermolysin complex. NMR distance measurements yield a P-N bond length rP-N = 1.68 +/- 0.03 A for the tight binding inhibitor ZFpLA both in its free lithium salt form and in its thermolysin-ZFpLA complex, a distance that is much shorter than the 1.90-A distance reported by X-ray crystallography studies [Holden et al. (1987) Biochemistry 26, 8542-8553].(ABSTRACT TRUNCATED AT 250 WORDS) PMID:2271586

  16. Inhibition of thermolysin by phosphonamidate transition-state analogues: measurement of 31P-15N bond lengths and chemical shifts in two enzyme-inhibitor complexes by solid-state nuclear magnetic resonance.

    PubMed

    Copié, V; Kolbert, A C; Drewry, D H; Bartlett, P A; Oas, T G; Griffin, R G

    1990-10-01

    31P and 15N chemical shifts and 31P-15N bond lengths have been measured with solid-state NMR techniques in two inhibitors of thermolysin, carbobenzoxy-Glyp-L-Leu-L-Ala (ZGpLA) and carbobenzoxy-L-Phep-L-Leu-L-Ala (ZFpLA), both as free lithium salts and when bound to the enzyme. Binding of both inhibitors to thermolysin results in large changes in the 31P chemical shifts. These changes are more dramatic for the tighter binding inhibitor ZFpLA, where a approximately 20 ppm downfield movement of the 31P isotropic chemical shift (sigma iso) is observed. This shift is due to changes in the shift tensor elements sigma 11 and sigma 22, while sigma 33 remains essentially constant. We observed a similar pattern for ZGpLA, but only a approximately 5 ppm change occurs in sigma iso. The changes in the 15N chemical shifts for both inhibitors are small upon binding, amounting to downfield shifts of 2 and 4 ppm for ZGpLA and ZFpLA, respectively. This indicates that there are no changes in the protonation state of the 15N in either the ZFpLA- or the ZGpLA-thermolysin complex. NMR distance measurements yield a P-N bond length rP-N = 1.68 +/- 0.03 A for the tight binding inhibitor ZFpLA both in its free lithium salt form and in its thermolysin-ZFpLA complex, a distance that is much shorter than the 1.90-A distance reported by X-ray crystallography studies [Holden et al. (1987) Biochemistry 26, 8542-8553].(ABSTRACT TRUNCATED AT 250 WORDS)

  17. 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

  18. 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.

  19. (1)H, (13)C, and (15)N backbone and side-chain chemical shift assignments for the 36 proline-containing, full length 29 kDa human chimera-type galectin-3.

    PubMed

    Ippel, Hans; Miller, Michelle C; Berbís, Manuel Alvaro; Suylen, Dennis; André, Sabine; Hackeng, Tilman M; Cañada, F Javier; Weber, Christian; Gabius, Hans-Joachim; Jiménez-Barbero, Jesús; Mayo, Kevin H

    2015-04-01

    Galectin-3, an adhesion/growth regulatory lectin, has a unique trimodular design consisting of the canonical carbohydrate recognition domain, a collagen-like tandem-repeat section, and an N-terminal peptide with two sites for Ser phosphorylation. Structural characterization of the full length protein with its non-lectin part (115 of 250 residues total) will help understand the multi functionality of this potent cellular effector. Here, we report (1)H, (13)C, and (15)N chemical shift assignments as determined by heteronuclear NMR spectroscopy .

  20. 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

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. Chemical Equilibrium in Supramolecular Systems as Studied by NMR Spectrometry

    ERIC Educational Resources Information Center

    Gonzalez-Gaitano, Gustavo; Tardajos, Gloria

    2004-01-01

    Undergraduate students are required to study the chemical balance in supramolecular assemblies constituting two or more interacting species, by using proton NMR spectrometry. A good knowledge of physical chemistry, fundamentals of chemical balance, and NMR are pre-requisites for conducting this study.

  6. Protein NMR chemical shift calculations based on the automated fragmentation QM/MM approach.

    PubMed

    He, Xiao; Wang, Bing; Merz, Kenneth M

    2009-07-30

    An automated fragmentation quantum mechanics/molecular mechanics (AF-QM/MM) approach has been developed to routinely calculate ab initio protein NMR chemical shielding constants. The AF-QM/MM method is linear-scaling and trivially parallel. A general fragmentation scheme is employed to generate each residue-centric region which is treated by quantum mechanics, and the environmental electrostatic field is described with molecular mechanics. The AF-QM/MM method shows good agreement with standard self-consistent field (SCF) calculations of the NMR chemical shieldings for the mini-protein Trp cage. The root-mean-square errors (RMSEs) for 1H, 13C, and 15N NMR chemical shieldings are equal to or less than 0.09, 0.32, and 0.78 ppm, respectively, for all Hartree-Fock (HF) and density functional theory (DFT) calculations reported in this work. The environmental electrostatic potential is necessary to accurately reproduce the NMR chemical shieldings using the AF-QM/MM approach. The point-charge models provided by AMBER, AM1/CM2, PM3/CM1, and PM3/CM2 all effectively model the electrostatic field. The latter three point-charge models are generated via semiempirical linear-scaling SCF calculations of the entire protein system. The correlations between experimental 1H NMR chemical shifts and theoretical predictions are >0.95 for AF-QM/MM calculations using B3LYP with the 6-31G**, 6-311G**, and 6-311++G** basis sets. Our study, not unexpectedly, finds that conformational changes within a protein structure play an important role in the accurate prediction of experimental NMR chemical shifts from theory.

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

    PubMed Central

    2016-01-01

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

  8. A suite of sensitive chemical methods to determine the δ15N of ammonium, nitrate and total dissolved N in soil extracts.

    PubMed

    Lachouani, Petra; Frank, Alexander H; Wanek, Wolfgang

    2010-12-30

    Natural (15) N abundances (δ(15) N values) of different soil nitrogen pools deliver crucial information on the soil N cycle for the analysis of biogeochemical processes. Here we report on a complete suite of methods for sensitive δ(15) N analysis in soil extracts. A combined chemical reaction of vanadium(III) chloride (VCl(3) ) and sodium azide under acidic conditions is used to convert nitrate into N(2) O, which is subsequently analyzed by purge-and-trap isotope ratio mass spectrometry (PTIRMS) with a cryo-focusing unit. Coupled with preparation steps (microdiffusion for collection of ammonium, alkaline persulfate oxidation to convert total dissolved N (TDN) or ammonium into nitrate) this allows the determination of the δ(15) N values of nitrate, ammonium and total dissolved N (dissolved organic N, microbial biomass N) in soil extracts with the same basic protocol. The limits of quantification for δ(15) N analysis with a precision of 0.5‰ were 12.4 µM for ammonium, 23.7 µM for TDN, 16.5 µM for nitrate and 22.7 µM for nitrite.

  9. Recoupling of chemical shift anisotropy by R-symmetry sequences in magic angle spinning NMR spectroscopy

    PubMed Central

    Hou, Guangjin; Byeon, In-Ja L.; Ahn, Jinwoo; Gronenborn, Angela M.; Polenova, Tatyana

    2012-01-01

    13C and 15N chemical shift (CS) interaction is a sensitive probe of structure and dynamics in a wide variety of biological and inorganic systems, and in the recent years several magic angle spinning NMR approaches have emerged for residue-specific measurements of chemical shift anisotropy (CSA) tensors in uniformly and sparsely enriched proteins. All of the currently existing methods are applicable to slow and moderate magic angle spinning (MAS) regime, i.e., MAS frequencies below 20 kHz. With the advent of fast and ultrafast MAS probes capable of spinning frequencies of 40–100 kHz, and with the superior resolution and sensitivity attained at such high frequencies, development of CSA recoupling techniques working under such conditions is necessary. In this work, we present a family of R-symmetry based pulse sequences for recoupling of 13C/15N CSA interactions that work well in both natural abundance and isotopically enriched systems. We demonstrate that efficient recoupling of either first-rank (σ1) or second-rank (σ2) spatial components of CSA interaction is attained with appropriately chosen γ-encoded RNnv symmetry sequences. The advantage of these γ-encoded RNnv-symmetry based CSA (RNCSA) recoupling schemes is that they are suitable for CSA recoupling under a wide range of MAS frequencies, including fast MAS regime. Comprehensive analysis of the recoupling properties of these RNnv symmetry sequences reveals that the σ1-CSA recoupling symmetry sequences exhibit large scaling factors; however, the partial homonuclear dipolar Hamiltonian components are symmetry allowed, which makes this family of sequences suitable for CSA measurements in systems with weak homonuclear dipolar interactions. On the other hand, the γ-encoded symmetry sequences for σ2-CSA recoupling have smaller scaling factors but they efficiently suppress the homonuclear dipole-dipole interactions. Therefore, the latter family of sequences is applicable for measurements of CSA parameters in

  10. Recoupling of chemical shift anisotropy by R-symmetry sequences in magic angle spinning NMR spectroscopy

    NASA Astrophysics Data System (ADS)

    Hou, Guangjin; Byeon, In-Ja L.; Ahn, Jinwoo; Gronenborn, Angela M.; Polenova, Tatyana

    2012-10-01

    13C and 15N chemical shift (CS) interaction is a sensitive probe of structure and dynamics in a wide variety of biological and inorganic systems, and in the recent years several magic angle spinning NMR approaches have emerged for residue-specific measurements of chemical shift anisotropy (CSA) tensors in uniformly and sparsely enriched proteins. All of the currently existing methods are applicable to slow and moderate magic angle spinning (MAS) regime, i.e., MAS frequencies below 20 kHz. With the advent of fast and ultrafast MAS probes capable of spinning frequencies of 40-100 kHz, and with the superior resolution and sensitivity attained at such high frequencies, development of CSA recoupling techniques working under such conditions is necessary. In this work, we present a family of R-symmetry based pulse sequences for recoupling of 13C/15N CSA interactions that work well in both natural abundance and isotopically enriched systems. We demonstrate that efficient recoupling of either first-rank (σ1) or second-rank (σ2) spatial components of CSA interaction is attained with appropriately chosen γ-encoded RNnv symmetry sequences. The advantage of these γ-encoded RNnv-symmetry based CSA (RNCSA) recoupling schemes is that they are suitable for CSA recoupling under a wide range of MAS frequencies, including fast MAS regime. Comprehensive analysis of the recoupling properties of these RNnv symmetry sequences reveals that the σ1-CSA recoupling symmetry sequences exhibit large scaling factors; however, the partial homonuclear dipolar Hamiltonian components are symmetry allowed, which makes this family of sequences suitable for CSA measurements in systems with weak homonuclear dipolar interactions. On the other hand, the γ-encoded symmetry sequences for σ2-CSA recoupling have smaller scaling factors but they efficiently suppress the homonuclear dipole-dipole interactions. Therefore, the latter family of sequences is applicable for measurements of CSA parameters in

  11. 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.

  12. 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.

  13. 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+.

  14. (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.

  15. Relative Configuration of Natural Products Using NMR Chemical Shifts

    Technology Transfer Automated Retrieval System (TEKTRAN)

    By comparing calculated with experimental NMR chemical shifts, we were able to determine the relative configurations of three monoterpene diastereomers produced by the walkingstick Anisomorpha buprestoides. The combined RMSDs of both 1H and 13C quantum chemically calculated shifts were able to predi...

  16. Theoretical Modeling of (99)Tc NMR Chemical Shifts.

    PubMed

    Hall, Gabriel B; Andersen, Amity; Washton, Nancy M; Chatterjee, Sayandev; Levitskaia, Tatiana G

    2016-09-01

    Technetium-99 (Tc) displays a rich chemistry due to its wide range of accessible oxidation states (from -I to +VII) and ability to form coordination compounds. Determination of Tc speciation in complex mixtures is a major challenge, and (99)Tc nuclear magnetic resonance (NMR) spectroscopy is widely used to probe chemical environments of Tc in odd oxidation states. However, interpretation of (99)Tc NMR data is hindered by the lack of reference compounds. Density functional theory (DFT) calculations can help to fill this gap, but to date few computational studies have focused on (99)Tc NMR of compounds and complexes. This work evaluates the effectiveness of both pure generalized gradient approximation and their corresponding hybrid functionals, both with and without the inclusion of scalar relativistic effects, to model the (99)Tc NMR spectra of Tc(I) carbonyl compounds. With the exception of BLYP, which performed exceptionally well overall, hybrid functionals with inclusion of scalar relativistic effects are found to be necessary to accurately calculate (99)Tc NMR spectra. The computational method developed was used to tentatively assign an experimentally observed (99)Tc NMR peak at -1204 ppm to fac-Tc(CO)3(OH)3(2-). This study examines the effectiveness of DFT computations for interpretation of the (99)Tc NMR spectra of Tc(I) coordination compounds in high salt alkaline solutions. PMID:27518482

  17. Spin coherence transfer in chemical transformations monitoredNMR

    SciTech Connect

    Anwar, Sabieh M.; Hilty, Christian; Chu, Chester; Bouchard,Louis-S.; Pierce, Kimberly L.; Pines, Alexander

    2006-07-31

    We demonstrate the use of micro-scale nuclear magneticresonance (NMR) for studying the transfer of spin coherence innon-equilibrium chemical processes, using spatially separated NMRencoding and detection coils. As an example, we provide the map ofchemical shift correlations for the amino acid alanine as it transitionsfrom the zwitterionic to the anionic form. Our method is unique in thesense that it allows us to track the chemical migration of encodednuclear spins during the course of chemical transformations.

  18. Effects of structural differences on the NMR chemical shifts in isostructural dipeptides.

    PubMed

    Altheimer, Benjamin D; Mehta, Manish A

    2014-04-10

    Porous crystalline dipeptides have gained recent attention for their potential as gas-storage materials. Within this large class is a group of dipeptides containing alanine, valine, and isoleucine with very similar crystal structures. We report the (13)C (carbonyl and Cα) and (15)N (amine and amide) solid-state NMR isotropic chemical shifts in a series of seven such isostructural porous dipeptides as well as shift tensor data for the carbonyl and amide sites. Using their known crystal structures and aided by ab initio quantum chemical calculations for the resonance assignments, we elucidate trends relating local structure, hydrogen-bonding patterns, and chemical shift. We find good correlation between the backbone dihedral angles and the Cα1 and Cα2 shifts. For the C1 shift tensor, the δ11 value shifts downfield as the hydrogen-bond distance increases, δ22 shifts upfield, and δ33 shows little variation. The C2 shift tensor shows no appreciable correlation with structural parameters. For the N2 tensor, δ11 shows little dependence on the hydrogen-bond length, whereas δ22 and δ33 both show a decrease in shielding as the hydrogen bond shortens. Our analysis teases apart some, but not all, structural contributors to the observed differences the solid-state NMR chemical shifts.

  19. 1H, 15N, and 13C chemical shift assignments of cyanobacteriochrome NpR6012g4 in the red-absorbing dark state.

    PubMed

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

    2016-04-01

    Cyanobacteriochrome (CBCR) photosensory proteins are phytochrome homologs using bilin chromophores for light sensing across the visible spectrum. NpR6012g4 is a CBCR from Nostoc punctiforme that serves as a model for a widespread CBCR subfamily with red/green photocycles. We report NMR chemical shift assignments for both the protein backbone and side-chain resonances of the red-absorbing dark state of NpR6012g4 (BMRB no. 26582).

  20. Low Cost CE-NMR with Microcoils for Chemical Detection

    SciTech Connect

    Adams, K; Klunder, G; Demas, V; Malba, V; Bernhardt, A; Evan, L; Harvey, C; Maxwell, R; Herberg, J L

    2009-01-08

    Understanding speciation in solids and solutions is important for environmental and toxicological purposes. Capillary electrophoresis (CE) is a simple rapid separation technique that can be used to identify species in solution. CE is particularly is well suited for rapid separations of metal containing samples. Direct on-capillary measurement of metal compound speciation can be obtained with nuclear magnetic resonance (NMR). The development of a low-cost microcoil CE-NMR system for in situ characterization of samples of interest is discussed. High precision laser lithography is used to produce copper sputtered microcoils that have comparable resistivity and quality factors to that of hand wound microcoils. A portable NMR system coupled with a CE system has the potential to identify chemical species in aqueous solutions. In addition, transient isotachophoresis can separate and pre-concentrate samples of interest to obtain separate chemical peaks for speciation by online NMR analysis. We are developing separation assays to determine the speciation of chemical complexes in solutions with minimal perturbation to the original sample equilibrium. On-line NMR measurements will be made downstream of the UV detector.

  1. Low Cost CE-NMR with Microcoils for Chemical Detection

    SciTech Connect

    Adams, K L; Klunder, G; Demas, V; Malba, V; Bernhardt, A; Evan, L; Harvey, C; Maxwell, R; Herberg, J

    2008-07-25

    Understanding speciation in solids and solutions is important for environmental and toxicological purposes. Capillary electrophoresis (CE) is a simple rapid separation technique that can be used to identify species in solution. CE is particularly is well suited for rapid separations of metal containing samples. Direct on-capillary measurement of metal compound speciation can be obtained with nuclear magnetic resonance (NMR). The development of a low-cost microcoil CE-NMR system for in situ characterization of samples of interest is discussed. High precision laser lithography is used to produce copper sputtered microcoils that have comparable resistivity and quality factors to that of hand wound microcoils. A portable NMR system coupled with a CE system has the potential to identify chemical species in aqueous solutions. In addition, transient isotachophoresis can separate and pre-concentrate samples of interest to obtain separate chemical peaks for speciation by online NMR analysis. We are developing separation assays to determine the speciation of chemical complexes in solutions with minimal perturbation to the original sample equilibrium. On-line NMR measurements will be made downstream of the UV detector.

  2. 1H, 13C and 15N NMR assignments of the aciniform spidroin (AcSp1) repetitive domain of Argiope trifasciata wrapping silk.

    PubMed

    Xu, Lingling; Tremblay, Marie-Laurence; Meng, Qing; Liu, Xiang-Qin; Rainey, Jan K

    2012-10-01

    Spider silk is one of nature's most remarkable biomaterials due to extraordinary strength and toughness not found in today's synthetic materials. Of the seven types of silk, wrapping silk (AcSp1) is the most extensible of the types of silks and has no sequence similarity to the other types. Here we report the chemical shifts for the AcSp1 199 amino acid protein repeat unit and its anticipated secondary structure based on secondary chemical shifts. PMID:21989955

  3. 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.

  4. TALOS+: a hybrid method for predicting protein backbone torsion angles from NMR chemical shifts.

    PubMed

    Shen, Yang; Delaglio, Frank; Cornilescu, Gabriel; Bax, Ad

    2009-08-01

    NMR chemical shifts in proteins depend strongly on local structure. The program TALOS establishes an empirical relation between 13C, 15N and 1H chemical shifts and backbone torsion angles phi and psi (Cornilescu et al. J Biomol NMR 13 289-302, 1999). Extension of the original 20-protein database to 200 proteins increased the fraction of residues for which backbone angles could be predicted from 65 to 74%, while reducing the error rate from 3 to 2.5%. Addition of a two-layer neural network filter to the database fragment selection process forms the basis for a new program, TALOS+, which further enhances the prediction rate to 88.5%, without increasing the error rate. Excluding the 2.5% of residues for which TALOS+ makes predictions that strongly differ from those observed in the crystalline state, the accuracy of predicted phi and psi angles, equals +/-13 degrees . Large discrepancies between predictions and crystal structures are primarily limited to loop regions, and for the few cases where multiple X-ray structures are available such residues are often found in different states in the different structures. The TALOS+ output includes predictions for individual residues with missing chemical shifts, and the neural network component of the program also predicts secondary structure with good accuracy.

  5. Protein structural information derived from NMR chemical shift with the neural network program TALOS-N.

    PubMed

    Shen, Yang; Bax, Ad

    2015-01-01

    Chemical shifts are obtained at the first stage of any protein structural study by NMR spectroscopy. Chemical shifts are known to be impacted by a wide range of structural factors, and the artificial neural network based TALOS-N program has been trained to extract backbone and side-chain torsion angles from (1)H, (15)N, and (13)C shifts. The program is quite robust and typically yields backbone torsion angles for more than 90 % of the residues and side-chain χ 1 rotamer information for about half of these, in addition to reliably predicting secondary structure. The use of TALOS-N is illustrated for the protein DinI, and torsion angles obtained by TALOS-N analysis from the measured chemical shifts of its backbone and (13)C(β) nuclei are compared to those seen in a prior, experimentally determined structure. The program is also particularly useful for generating torsion angle restraints, which then can be used during standard NMR protein structure calculations.

  6. Handling the influence of chemical shift in amplitude-modulated heteronuclear dipolar recoupling solid-state NMR

    NASA Astrophysics Data System (ADS)

    Basse, Kristoffer; Shankar, Ravi; Bjerring, Morten; Vosegaard, Thomas; Nielsen, Niels Chr.; Nielsen, Anders B.

    2016-09-01

    We present a theoretical analysis of the influence of chemical shifts on amplitude-modulated heteronuclear dipolar recoupling experiments in solid-state NMR spectroscopy. The method is demonstrated using the Rotor Echo Short Pulse IRrAdiaTION mediated Cross-Polarization (RESPIRATIONCP) experiment as an example. By going into the pulse sequence rf interaction frame and employing a quintuple-mode operator-based Floquet approach, we describe how chemical shift offset and anisotropic chemical shift affect the efficiency of heteronuclear polarization transfer. In this description, it becomes transparent that the main attribute leading to non-ideal performance is a fictitious field along the rf field axis, which is generated from second-order cross terms arising mainly between chemical shift tensors and themselves. This insight is useful for the development of improved recoupling experiments. We discuss the validity of this approach and present quaternion calculations to determine the effective resonance conditions in a combined rf field and chemical shift offset interaction frame transformation. Based on this, we derive a broad-banded version of the RESPIRATIONCP experiment. The new sequence is experimentally verified using SNNFGAILSS amyloid fibrils where simultaneous 15N → 13CO and 15N → 13Cα coherence transfer is demonstrated on high-field NMR instrumentation, requiring great offset stability.

  7. 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.

  8. 1H, 13C, and 15N chemical shift assignments of cyanobacteriochrome NpR6012g4 in the green-absorbing photoproduct state.

    PubMed

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

    2016-04-01

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

  9. Photochemical pump and NMR probe: chemically created NMR coherence on a microsecond time scale.

    PubMed

    Torres, Olga; Procacci, Barbara; Halse, Meghan E; Adams, Ralph W; Blazina, Damir; Duckett, Simon B; Eguillor, Beatriz; Green, Richard A; Perutz, Robin N; Williamson, David C

    2014-07-16

    We report pump-probe experiments employing laser-synchronized reactions of para-hydrogen (para-H2) with transition metal dihydride complexes in conjunction with nuclear magnetic resonance (NMR) detection. The pump-probe experiment consists of a single nanosecond laser pump pulse followed, after a precisely defined delay, by a single radio frequency (rf) probe pulse. Laser irradiation eliminates H2 from either Ru(PPh3)3(CO)(H)2 1 or cis-Ru(dppe)2(H)2 2 in C6D6 solution. Reaction with para-H2 then regenerates 1 and 2 in a well-defined nuclear spin state. The rf probe pulse produces a high-resolution, single-scan (1)H NMR spectrum that can be recorded after a pump-probe delay of just 10 μs. The evolution of the spectra can be followed as the pump-probe delay is increased by micro- or millisecond increments. Due to the sensitivity of this para-H2 experiment, the resulting NMR spectra can have hydride signal-to-noise ratios exceeding 750:1. The spectra of 1 oscillate in amplitude with frequency 1101 ± 3 Hz, the chemical shift difference between the chemically inequivalent hydrides. The corresponding hydride signals of 2 oscillate with frequency 83 ± 5 Hz, which matches the difference between couplings of the hydrides to the equatorial (31)P nuclei. We use the product operator formalism to show that this oscillatory behavior arises from a magnetic coherence in the plane orthogonal to the magnetic field that is generated by use of the laser pulse without rf initialization. In addition, we demonstrate how chemical shift imaging can differentiate the region of laser irradiation thereby distinguishing between thermal and photochemical reactivity within the NMR tube.

  10. 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.

  11. Chemical structure and intra-molecular effects on NMR-NQR tensors of harmine and harmaline alkaloids

    NASA Astrophysics Data System (ADS)

    Ahmadinejad, Neda; Tahan, Arezoo; Talebi Tari, Mostafa

    2016-02-01

    Density functional theory (DFT) methods were used to analyze the effects of molecular structure and ring currents on the NMR chemical shielding tensors and NQR frequencies of harmine and harmaline alkaloids in the gas phase. The results demonstrated that NMR tensors and NQR frequencies of 15N nuclei in these compounds depend on chemical environment and resonance interactions. Hence, their values are obviously different in the mentioned structures. The interpretation of natural bond orbital (NBO) data suggests that in harmine structure, the lone pair participation of N9 in π-system electron clouds causes to development of aromaticity nature in pyrrole ring. However, the chemical shielding around N9 atom in harmine structure is higher than in harmaline, while in harmaline structure, lone pair participation of N2 in π-system electron clouds causes to development of aromaticity nature in pyridine ring. Hence, chemical shielding around N2 atom in harmaline structure is higher than in harmine. It can be deduced that by increasing lone pair electrons contribution of nitrogen atoms in ring resonance interactions and aromaticity development, the values of NMR chemical shielding around them increase, while χ and q zz values of these nuclei decrease.

  12. Chemical weathering and the role of sulfuric and nitric acids in carbonate weathering: Isotopes (13C, 15N, 34S, and 18O) and chemical constraints

    NASA Astrophysics Data System (ADS)

    Li, Cai; Ji, Hongbing

    2016-05-01

    Multiple isotopes (13C-DIC, 34S and 18O-SO42-, 15N and 18O-NO3-) and water chemistry were used to evaluate weathering rates and associated CO2 consumption by carbonic acid and strong acids (H2SO4 and HNO3) in a typical karst watershed (Wujiang River, Southwest China). The dual sulfate isotopes indicate that sulfate is mainly derived from sulfide oxidation in coal stratum and sulfide-containing minerals, and dual nitrate isotopes indicate that nitrate is mainly derived from soil N and nitrification. The correlation between isotopic compositions and water chemistry suggests that sulfuric and nitric acids, in addition to carbonic acid, are involved in carbonate weathering. The silicate and carbonate weathering rates are 7.2 t km-2 yr-1 and 76 t km-2 yr-1, respectively. In comparison with carbonate weathering rates (43 t km-2 yr-1) by carbonic acid alone, the subsequent increase in rates indicates significant enhancement of weathering when combined with sulfuric and nitric acids. Therefore, the role of sulfuric and nitric acids in the rock weathering should be considered in the global carbon cycle.

  13. Chemical constituents of the lichen, Candelaria concolor: a complete NMR and chemical degradative investigation.

    PubMed

    Dias, Daniel A; Urban, Sylvia

    2009-01-01

    A detailed chemical and spectroscopic investigation of the terrestrial lichen Candelaria concolor has yielded several lichenic metabolites belonging to the pulvinic acid series, as well as several depside derivatives including pulvinic dilactone (1), vulpinic acid (4) and calycin (5). The chemical transformation of 1 to pulvinic acid (3) is reported for the first time, as is the conversion of atranorin (6) to 5-chloroatranorin (7) and then finally to 5,5'-dichloroatranorin (8) under very mild conditions. Also presented is the complete 1D and 2D NMR assignment for compounds 1, 3, 4, 5 and 8, including partial NMR chemical shift assignments for the unstable depside (7). Previously, these metabolites had only been partially assigned by NMR spectroscopy. PMID:19521906

  14. Solid-State NMR Studies of Chemically Lithiated CFx

    PubMed Central

    Leifer, N. D.; Johnson, V. S.; Ben-Ari, R.; Gan, H.; Lehnes, J. M.; Guo, R.; Lu, W.; Muffoletto, B. C.; Reddy, T.; Stallworth, P. E.; Greenbaum, S. G.

    2010-01-01

    Three types of fluorinated carbon, all in their original form and upon sequential chemical lithiations via n-butyllithium, were investigated by 13C and 19F solid-state NMR methods. The three starting CFx materials [where x = 1 (nominally)] were fiber based, graphite based, and petroleum coke based. The aim of the current study was to identify, at the atomic/molecular structural level, factors that might account for differences in electrochemical performance among the different kinds of CFx. Differences were noted in the covalent F character among the starting compounds and in the details of LiF production among the lithiated samples. PMID:20676233

  15. Solid-State NMR Studies of Chemically Lithiated CF.

    PubMed

    Leifer, N D; Johnson, V S; Ben-Ari, R; Gan, H; Lehnes, J M; Guo, R; Lu, W; Muffoletto, B C; Reddy, T; Stallworth, P E; Greenbaum, S G

    2010-01-01

    Three types of fluorinated carbon, all in their original form and upon sequential chemical lithiations via n-butyllithium, were investigated by (13)C and (19)F solid-state NMR methods. The three starting CF(x) materials [where x = 1 (nominally)] were fiber based, graphite based, and petroleum coke based. The aim of the current study was to identify, at the atomic/molecular structural level, factors that might account for differences in electrochemical performance among the different kinds of CF(x). Differences were noted in the covalent F character among the starting compounds and in the details of LiF production among the lithiated samples.

  16. 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.

  17. NMR chemical shift pattern changed by ammonium sulfate precipitation in cyanobacterial phytochrome Cph1.

    PubMed

    Song, Chen; Lang, Christina; Kopycki, Jakub; Hughes, Jon; Matysik, Jörg

    2015-01-01

    Phytochromes are dimeric biliprotein photoreceptors exhibiting characteristic red/far-red photocycles. Full-length cyanobacterial phytochrome Cph1 from Synechocystis 6803 is soluble initially but tends to aggregate in a concentration-dependent manner, hampering attempts to solve the structure using NMR and crystallization methods. Otherwise, the Cph1 sensory module (Cph1Δ2), photochemically indistinguishable from the native protein and used extensively in structural and other studies, can be purified to homogeneity in >10 mg amounts at mM concentrations quite easily. Bulk precipitation of full-length Cph1 by ammonium sulfate (AmS) was expected to allow us to produce samples for solid-state magic-angle spinning (MAS) NMR from dilute solutions before significant aggregation began. It was not clear, however, what effects the process of partial dehydration might have on the molecular structure. Here we test this by running solid-state MAS NMR experiments on AmS-precipitated Cph1Δ2 in its red-absorbing Pr state carrying uniformly (13)C/(15)N-labeled phycocyanobilin (PCB) chromophore. 2D (13)C-(13)C correlation experiments allowed a complete assignment of (13)C responses of the chromophore. Upon precipitation, (13)C chemical shifts for most of PCB carbons move upfield, in which we found major changes for C4 and C6 atoms associated with the A-ring positioning. Further, the broad spectral lines seen in the AmS (13)C spectrum reflect primarily the extensive inhomogeneous broadening presumably due to an increase in the distribution of conformational states in the protein, in which less free water is available to partake in the hydration shells. Our data suggest that the effect of dehydration process indeed leads to changes of electronic structure of the bilin chromophore and a decrease in its mobility within the binding pocket, but not restricted to the protein surface. The extent of the changes induced differs from the freezing process of the solution samples routinely

  18. NMR chemical shift pattern changed by ammonium sulfate precipitation in cyanobacterial phytochrome Cph1

    PubMed Central

    Song, Chen; Lang, Christina; Kopycki, Jakub; Hughes, Jon; Matysik, Jörg

    2015-01-01

    Phytochromes are dimeric biliprotein photoreceptors exhibiting characteristic red/far-red photocycles. Full-length cyanobacterial phytochrome Cph1 from Synechocystis 6803 is soluble initially but tends to aggregate in a concentration-dependent manner, hampering attempts to solve the structure using NMR and crystallization methods. Otherwise, the Cph1 sensory module (Cph1Δ2), photochemically indistinguishable from the native protein and used extensively in structural and other studies, can be purified to homogeneity in >10 mg amounts at mM concentrations quite easily. Bulk precipitation of full-length Cph1 by ammonium sulfate (AmS) was expected to allow us to produce samples for solid-state magic-angle spinning (MAS) NMR from dilute solutions before significant aggregation began. It was not clear, however, what effects the process of partial dehydration might have on the molecular structure. Here we test this by running solid-state MAS NMR experiments on AmS-precipitated Cph1Δ2 in its red-absorbing Pr state carrying uniformly 13C/15N-labeled phycocyanobilin (PCB) chromophore. 2D 13C–13C correlation experiments allowed a complete assignment of 13C responses of the chromophore. Upon precipitation, 13C chemical shifts for most of PCB carbons move upfield, in which we found major changes for C4 and C6 atoms associated with the A-ring positioning. Further, the broad spectral lines seen in the AmS 13C spectrum reflect primarily the extensive inhomogeneous broadening presumably due to an increase in the distribution of conformational states in the protein, in which less free water is available to partake in the hydration shells. Our data suggest that the effect of dehydration process indeed leads to changes of electronic structure of the bilin chromophore and a decrease in its mobility within the binding pocket, but not restricted to the protein surface. The extent of the changes induced differs from the freezing process of the solution samples routinely used in

  19. 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

  20. Vicinal deuterium perturbations on hydrogen NMR chemical shifts in cyclohexanes.

    PubMed

    O'Leary, Daniel J; Allis, Damian G; Hudson, Bruce S; James, Shelly; Morgera, Katherine B; Baldwin, John E

    2008-10-15

    The substitution of a deuterium for a hydrogen is known to perturb the NMR chemical shift of a neighboring hydrogen atom. The magnitude of such a perturbation may depend on the specifics of bonding and stereochemical relationships within a molecule. For deuterium-labeled cyclohexanes held in a chair conformation at -80 degrees C or lower, all four possible perturbations of H by D as H-C-C-H is changed to D-C-C-H have been determined experimentally, and the variations seen, ranging from 6.9 to 10.4 ppb, have been calculated from theory and computational methods. The predominant physical origins of the NMR chemical shift perturbations in deuterium-labeled cyclohexanes have been identified and quantified. The trends defined by the Delta delta perturbation values obtained through spectroscopic experiments and by theory agree satisfactorily. They do not match the variations typically observed in vicinal J(H-H) coupling constants as a function of dihedral angles.

  1. High-throughput backbone resonance assignment of small 13C, 15N-labeled proteins by a triple-resonance experiment with four sequential connectivity pathways using chemical shift-dependent, apparent 1J ( 1H, 13C): HNCACB codedHAHB

    NASA Astrophysics Data System (ADS)

    Pegan, Scott; Kwiatkowski, Witek; Choe, Senyon; Riek, Roland

    2003-12-01

    The proposed three-dimensional triple-resonance experiment HNCACB codedHAHB correlates sequential 15N, 1H moieties via the chemical shifts of 13C α, 13C β, 1H α, and 1H β. The four sequential correlation pathways are achieved by the incorporation of the concept of chemical shift-coding [J. Biomol. NMR 25 (2003) 281] to the TROSY-HNCACB experiment. The monitored 1H α and 1H β chemical shifts are then coded in the line shape of the cross-peaks of 13C α, 13C β along the 13C dimension through an apparent residual scalar coupling, the size of which depends on the attached hydrogen chemical shift. The information of four sequential correlation pathways enables a rapid backbone assignment. The HNCACB codedHAHB experiment was applied to ˜85% labeled 13C, 15N-labeled amino-terminal fragment of Vaccinia virus DNA topoisomerase I comprising residues 1-77. After one day of measurement on a Bruker Avance 700 MHz spectrometer and 8 h of manual analysis of the spectrum 93% of the backbone assignment was achieved.

  2. Predicting the redox state and secondary structure of cysteine residues using multi-dimensional classification analysis of NMR chemical shifts.

    PubMed

    Wang, Ching-Cheng; Lai, Wen-Chung; Chuang, Woei-Jer

    2016-09-01

    A tool for predicting the redox state and secondary structure of cysteine residues using multi-dimensional analyses of different combinations of nuclear magnetic resonance (NMR) chemical shifts has been developed. A data set of cysteine [Formula: see text], (13)C(α), (13)C(β), (1)H(α), (1)H(N), and (15)N(H) chemical shifts was created, classified according to redox state and secondary structure, using a library of 540 re-referenced BioMagResBank (BMRB) entries. Multi-dimensional analyses of three, four, five, and six chemical shifts were used to derive rules for predicting the structural states of cysteine residues. The results from 60 BMRB entries containing 122 cysteines showed that four-dimensional analysis of the C(α), C(β), H(α), and N(H) chemical shifts had the highest prediction accuracy of 100 and 95.9 % for the redox state and secondary structure, respectively. The prediction of secondary structure using 3D, 5D, and 6D analyses had the accuracy of ~90 %, suggesting that H(N) and [Formula: see text] chemical shifts may be noisy and made the discrimination worse. A web server (6DCSi) was established to enable users to submit NMR chemical shifts, either in BMRB or key-in formats, for prediction. 6DCSi displays predictions using sets of 3, 4, 5, and 6 chemical shifts, which shows their consistency and allows users to draw their own conclusions. This web-based tool can be used to rapidly obtain structural information regarding cysteine residues directly from experimental NMR data.

  3. 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

  4. Protein Dielectric Constants Determined from NMR Chemical Shift Perturbations

    PubMed Central

    Kukic, Predrag; Farrell, Damien; McIntosh, Lawrence P.; E., Bertrand García-Moreno; Jensen, Kristine Steen; Toleikis, Zigmantas; Teilum, Kaare; Nielsen, Jens Erik

    2015-01-01

    Understanding the connection between protein structure and function requires a quantitative understanding of electrostatic effects. Structure-based electrostatics calculations are essential for this purpose, but their use have been limited by a long-standing discussion on which value to use for the dielectric constants (εeff and εp) required in Coulombic models and Poisson-Boltzmann models. The currently used values for εeff and εp are essentially empirical parameters calibrated against thermodynamic properties that are indirect measurements of protein electric fields. We determine optimal values for εeff and εp by measuring protein electric fields in solution using direct detection of NMR chemical shift perturbations (CSPs). We measured CSPs in fourteen proteins to get a broad and general characterization of electric fields. Coulomb's law reproduces the measured CSPs optimally with a protein dielectric constant (εeff) from 3 to 13, with an optimal value across all proteins of 6.5. However, when the water-protein interface is treated with finite difference Poisson-Boltzmann calculations, the optimal protein dielectric constant (εp) rangedsfrom 2-5 with an optimum of 3. It is striking how similar this value is to the dielectric constant of 2-4 measured for protein powders, and how different it is from the εp of 6-20 used in models based on the Poisson-Boltzmann equation when calculating thermodynamic parameters. Because the value of εp = 3 is obtained by analysis of NMR chemical shift perturbations instead of thermodynamic parameters such as pKa values, it is likely to describe only the electric field and thus represent a more general, intrinsic, and transferable εp common to most folded proteins. PMID:24124752

  5. NMR characterization of cellulose acetate: chemical shift assignments, substituent effects, and chemical shift additivity.

    PubMed

    Kono, Hiroyuki; Hashimoto, Hisaho; Shimizu, Yuuichi

    2015-03-15

    A series of cellulose acetates (CA) with degrees of substitution (DS) ranging from 2.92-0.92 dissolved in dimethylsulfoxide (DMSO)-d6 and cellulose dissolved in tetrabutylammonium fluoride (TBAF)/DMSO-d6 were investigated by two-dimensional NMR spectroscopy. The NMR spectroscopic analysis allowed the determination of the (1)H and (13)C NMR chemical shifts of the eight anhydroglucose units (AGUs) that contain CA: 2,3,6-tri-, 2,3-di-, 2,6-di-, 3,6-di-, 2-mono-, 3-mono-, 6-mono-, and unacetylated AGUs. A comparative analysis of the chemical shift data revealed the substituent effect of acetyl groups at the 2-, 3-, and 6-positions on the (1)H and (13)C nuclei in the same AGU. In addition, chemical shift additivity could be applied to the (1)H and (13)C chemical shifts of CA because the chemical shifts of the diacetylated and triacetylated AGUs could be almost completely explained by the acetyl substituent effects at the 2-, 3-, and 6-positions.

  6. Reliable resonance assignments of selected residues of proteins with known structure based on empirical NMR chemical shift prediction

    NASA Astrophysics Data System (ADS)

    Li, Da-Wei; Meng, Dan; Brüschweiler, Rafael

    2015-05-01

    A robust NMR resonance assignment method is introduced for proteins whose 3D structure has previously been determined by X-ray crystallography. The goal of the method is to obtain a subset of correct assignments from a parsimonious set of 3D NMR experiments of 15N, 13C labeled proteins. Chemical shifts of sequential residue pairs are predicted from static protein structures using PPM_One, which are then compared with the corresponding experimental shifts. Globally optimized weighted matching identifies the assignments that are robust with respect to small changes in NMR cross-peak positions. The method, termed PASSPORT, is demonstrated for 4 proteins with 100-250 amino acids using 3D NHCA and a 3D CBCA(CO)NH experiments as input producing correct assignments with high reliability for 22% of the residues. The method, which works best for Gly, Ala, Ser, and Thr residues, provides assignments that serve as anchor points for additional assignments by both manual and semi-automated methods or they can be directly used for further studies, e.g. on ligand binding, protein dynamics, or post-translational modification, such as phosphorylation.

  7. Resolving Nitrogen-15 and Proton Chemical Shifts for Mobile Segments of Elastin with Two-dimensional NMR Spectroscopy*

    PubMed Central

    Ohgo, Kosuke; Niemczura, Walter P.; Seacat, Brian C.; Wise, Steven G.; Weiss, Anthony S.; Kumashiro, Kristin K.

    2012-01-01

    In this study, one- and two-dimensional NMR experiments are applied to uniformly 15N-enriched synthetic elastin, a recombinant human tropoelastin that has been cross-linked to form an elastic hydrogel. Hydrated elastin is characterized by large segments that undergo “liquid-like” motions that limit the efficiency of cross-polarization. The refocused insensitive nuclei enhanced by polarization transfer experiment is used to target these extensive, mobile regions of this protein. Numerous peaks are detected in the backbone amide region of the protein, and their chemical shifts indicate the completely unstructured, “random coil” model for elastin is unlikely. Instead, more evidence is gathered that supports a characteristic ensemble of conformations in this rubber-like protein. PMID:22474297

  8. Ultrafast multidimensional Laplace NMR for a rapid and sensitive chemical analysis.

    PubMed

    Ahola, Susanna; Zhivonitko, Vladimir V; Mankinen, Otto; Zhang, Guannan; Kantola, Anu M; Chen, Hsueh-Ying; Hilty, Christian; Koptyug, Igor V; Telkki, Ville-Veikko

    2015-09-18

    Traditional nuclear magnetic resonance (NMR) spectroscopy relies on the versatile chemical information conveyed by spectra. To complement conventional NMR, Laplace NMR explores diffusion and relaxation phenomena to reveal details on molecular motions. Under a broad concept of ultrafast multidimensional Laplace NMR, here we introduce an ultrafast diffusion-relaxation correlation experiment enhancing the resolution and information content of corresponding 1D experiments as well as reducing the experiment time by one to two orders of magnitude or more as compared with its conventional 2D counterpart. We demonstrate that the method allows one to distinguish identical molecules in different physical environments and provides chemical resolution missing in NMR spectra. Although the sensitivity of the new method is reduced due to spatial encoding, the single-scan approach enables one to use hyperpolarized substances to boost the sensitivity by several orders of magnitude, significantly enhancing the overall sensitivity of multidimensional Laplace NMR.

  9. Ultrafast multidimensional Laplace NMR for a rapid and sensitive chemical analysis

    PubMed Central

    Ahola, Susanna; Zhivonitko, Vladimir V; Mankinen, Otto; Zhang, Guannan; Kantola, Anu M.; Chen, Hsueh-Ying; Hilty, Christian; Koptyug, Igor V.; Telkki, Ville-Veikko

    2015-01-01

    Traditional nuclear magnetic resonance (NMR) spectroscopy relies on the versatile chemical information conveyed by spectra. To complement conventional NMR, Laplace NMR explores diffusion and relaxation phenomena to reveal details on molecular motions. Under a broad concept of ultrafast multidimensional Laplace NMR, here we introduce an ultrafast diffusion-relaxation correlation experiment enhancing the resolution and information content of corresponding 1D experiments as well as reducing the experiment time by one to two orders of magnitude or more as compared with its conventional 2D counterpart. We demonstrate that the method allows one to distinguish identical molecules in different physical environments and provides chemical resolution missing in NMR spectra. Although the sensitivity of the new method is reduced due to spatial encoding, the single-scan approach enables one to use hyperpolarized substances to boost the sensitivity by several orders of magnitude, significantly enhancing the overall sensitivity of multidimensional Laplace NMR. PMID:26381101

  10. Ultrafast multidimensional Laplace NMR for a rapid and sensitive chemical analysis

    NASA Astrophysics Data System (ADS)

    Ahola, Susanna; Zhivonitko, Vladimir V.; Mankinen, Otto; Zhang, Guannan; Kantola, Anu M.; Chen, Hsueh-Ying; Hilty, Christian; Koptyug, Igor V.; Telkki, Ville-Veikko

    2015-09-01

    Traditional nuclear magnetic resonance (NMR) spectroscopy relies on the versatile chemical information conveyed by spectra. To complement conventional NMR, Laplace NMR explores diffusion and relaxation phenomena to reveal details on molecular motions. Under a broad concept of ultrafast multidimensional Laplace NMR, here we introduce an ultrafast diffusion-relaxation correlation experiment enhancing the resolution and information content of corresponding 1D experiments as well as reducing the experiment time by one to two orders of magnitude or more as compared with its conventional 2D counterpart. We demonstrate that the method allows one to distinguish identical molecules in different physical environments and provides chemical resolution missing in NMR spectra. Although the sensitivity of the new method is reduced due to spatial encoding, the single-scan approach enables one to use hyperpolarized substances to boost the sensitivity by several orders of magnitude, significantly enhancing the overall sensitivity of multidimensional Laplace NMR.

  11. 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

  12. 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)

  13. Dissemination of original NMR data enhances reproducibility and integrity in chemical research.

    PubMed

    Bisson, Jonathan; Simmler, Charlotte; Chen, Shao-Nong; Friesen, J Brent; Lankin, David C; McAlpine, James B; Pauli, Guido F

    2016-08-25

    The notion of data transparency is gaining a strong awareness among the scientific community. The availability of raw data is actually regarded as a fundamental way to advance science by promoting both integrity and reproducibility of research outcomes. Particularly, in the field of natural product and chemical research, NMR spectroscopy is a fundamental tool for structural elucidation and quantification (qNMR). As such, the accessibility of original NMR data, i.e., Free Induction Decays (FIDs), fosters transparency in chemical research and optimizes both peer review and reproducibility of reports by offering the fundamental tools to perform efficient structural verification. Although original NMR data are known to contain a wealth of information, they are rarely accessible along with published data. This viewpoint discusses the relevance of the availability of original NMR data as part of good research practices not only to promote structural correctness, but also to enhance traceability and reproducibility of both chemical and biological results. PMID:27197893

  14. Chemical analysis using J-coupling multiplets in zero-field NMR

    NASA Astrophysics Data System (ADS)

    Theis, Thomas; Blanchard, John W.; Butler, Mark C.; Ledbetter, Micah P.; Budker, Dmitry; Pines, Alexander

    2013-08-01

    Zero-field nuclear magnetic resonance (NMR) spectroscopy is emerging as a new, potentially portable, and cost-effective NMR modality with the ability to provide information-rich, high-resolution spectra. We present simple rules for analysis of zero-field NMR spectra based on first-order perturbation theory and the addition of angular momenta. These rules allow for the prediction of observed spectral lines without numerical simulation. Results are presented for a few small organic molecules with characteristic spin topologies, demonstrating unambiguous assignment of peaks, highlighting the potential of zero-field NMR as a tool for chemical identification.

  15. 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.

  16. 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.

  17. Quantum calculation of protein NMR chemical shifts based on the automated fragmentation method.

    PubMed

    Zhu, Tong; Zhang, John Z H; He, Xiao

    2015-01-01

    The performance of quantum mechanical methods on the calculation of protein NMR chemical shifts is reviewed based on the recently developed automatic fragmentation quantum mechanics/molecular mechanics (AF-QM/MM) approach. By using the Poisson-Boltzmann (PB) model and first solvation water molecules, the influence of solvent effect is also discussed. Benefiting from the fragmentation algorithm, the AF-QM/MM approach is computationally efficient, linear-scaling with a low pre-factor, and thus can be applied to routinely calculate the ab initio NMR chemical shifts for proteins of any size. The results calculated using Density Functional Theory (DFT) show that when the solvent effect is included, this method can accurately reproduce the experimental ¹H NMR chemical shifts, while the ¹³C NMR chemical shifts are less affected by the solvent. However, although the inclusion of solvent effect shows significant improvement for ¹⁵N chemical shifts, the calculated values still have large deviations from the experimental observations. Our study further demonstrates that AF-QM/MM calculated results accurately reflect the dependence of ¹³C(α) NMR chemical shifts on the secondary structure of proteins, and the calculated ¹H chemical shift can be utilized to discriminate the native structure of proteins from decoys.

  18. NMR-based analysis of the chemical composition of Japanese persimmon aqueous extracts.

    PubMed

    Ryu, Shoraku; Furihata, Kazuo; Koda, Masanori; Wei, Feifei; Miyakawa, Takuya; Tanokura, Masaru

    2016-03-01

    Japanese persimmon (Diospyros kaki L.) is recognized as an outstanding source of biologically active compounds relating to many health benefits. In the present study, NMR spectroscopy provided a comprehensive metabolic overview of Japanese persimmon juice. Detailed signal assignments of Japanese persimmon juice were carried out using various 2D NMR techniques incorporated with broadband water suppression enhanced through T1 effects (BB-WET) or WET sequences, and 26 components, including minor components, were identified. In addition, most components were quantitatively evaluated by the integration of signals using conventional (1) H NMR and BB-WET NMR. This is the first detailed analysis combined with quantitative characterization of chemical components using NMR for Japanese persimmon. Copyright © 2015 John Wiley & Sons, Ltd. PMID:26482562

  19. NMR-based analysis of the chemical composition of Japanese persimmon aqueous extracts.

    PubMed

    Ryu, Shoraku; Furihata, Kazuo; Koda, Masanori; Wei, Feifei; Miyakawa, Takuya; Tanokura, Masaru

    2016-03-01

    Japanese persimmon (Diospyros kaki L.) is recognized as an outstanding source of biologically active compounds relating to many health benefits. In the present study, NMR spectroscopy provided a comprehensive metabolic overview of Japanese persimmon juice. Detailed signal assignments of Japanese persimmon juice were carried out using various 2D NMR techniques incorporated with broadband water suppression enhanced through T1 effects (BB-WET) or WET sequences, and 26 components, including minor components, were identified. In addition, most components were quantitatively evaluated by the integration of signals using conventional (1) H NMR and BB-WET NMR. This is the first detailed analysis combined with quantitative characterization of chemical components using NMR for Japanese persimmon. Copyright © 2015 John Wiley & Sons, Ltd.

  20. (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.

  1. NMR crystallography of enzyme active sites: probing chemically detailed, three-dimensional structure in tryptophan synthase.

    PubMed

    Mueller, Leonard J; Dunn, Michael F

    2013-09-17

    NMR crystallography--the synergistic combination of X-ray diffraction, solid-state NMR spectroscopy, and computational chemistry--offers unprecedented insight into three-dimensional, chemically detailed structure. Initially, researchers used NMR crystallography to refine diffraction data from organic and inorganic solids. Now we are applying this technique to explore active sites in biomolecules, where it reveals chemically rich detail concerning the interactions between enzyme site residues and the reacting substrate. Researchers cannot achieve this level of detail from X-ray, NMR,or computational methodologies in isolation. For example, typical X-ray crystal structures (1.5-2.5 Å resolution) of enzyme-bound intermediates identify possible hydrogen-bonding interactions between site residues and substrate but do not directly identify the protonation states. Solid-state NMR can provide chemical shifts for selected atoms of enzyme-substrate complexes, but without a larger structural framework in which to interpret them only empirical correlations with local chemical structure are possible. Ab initio calculations and molecular mechanics can build models for enzymatic processes, but they rely on researcher-specified chemical details. Together, however, X-ray diffraction, solid-state NMR spectroscopy, and computational chemistry can provide consistent and testable models for structure and function of enzyme active sites: X-ray crystallography provides a coarse framework upon which scientists can develop models of the active site using computational chemistry; they can then distinguish these models by comparing calculated NMR chemical shifts with the results of solid-state NMR spectroscopy experiments. Conceptually, each technique is a puzzle piece offering a generous view of the big picture. Only when correctly pieced together, however, can they reveal the big picture at the highest possible resolution. In this Account, we detail our first steps in the development of

  2. 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

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

    PubMed

    Berjanskii, Mark; Arndt, David; Liang, Yongjie; Wishart, David S

    2015-11-01

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

  4. Complete 1H NMR spectral analysis of ten chemical markers of Ginkgo biloba

    PubMed Central

    Napolitano, José G.; Lankin, David C.; Chen, Shao-Nong; Pauli, Guido F.

    2013-01-01

    The complete and unambiguous 1H NMR assignments of ten marker constituents of Ginkgo biloba are described. The comprehensive 1H NMR profiles (fingerprints) of ginkgolide A, ginkgolide B, ginkgolide C, ginkgolide J, bilobalide, quercetin, kaempferol, isorhamnetin, isoquercetin, and rutin in DMSO-d6 were obtained through the examination of 1D 1H NMR and 2D 1H,1H-COSY data, in combination with 1H iterative Full Spin Analysis (HiFSA). The computational analysis of discrete spin systems allowed a detailed characterization of all the 1H NMR signals in terms of chemical shifts (δH) and spin-spin coupling constants (JHH), regardless of signal overlap and higher order coupling effects. The capability of the HiFSA-generated 1H fingerprints to reproduce experimental 1H NMR spectra at different field strengths was also evaluated. As a result of this analysis, a revised set of 1H NMR parameters for all ten phytoconstituents was assembled. Furthermore, precise 1H NMR assignments of the sugar moieties of isoquercetin and rutin are reported for the first time. PMID:22730238

  5. 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

  6. 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.

  7. Magnetic couplings in the chemical shift of paramagnetic NMR.

    PubMed

    Vaara, Juha; Rouf, Syed Awais; Mareš, Jiří

    2015-10-13

    We apply the Kurland-McGarvey (J. Magn. Reson. 1970, 2, 286) theory for the NMR shielding of paramagnetic molecules, particularly its special case limited to the ground-state multiplet characterized by zero-field splitting (ZFS) interaction of the form S·D·S. The correct formulation for this problem was recently presented by Soncini and Van den Heuvel (J. Chem. Phys. 2013, 138, 054113). With the effective electron spin quantum number S, the theory involves 2S+1 states, of which all but one are low-lying excited states, between which magnetic couplings take place by Zeeman and hyperfine interactions. We investigate these couplings as a function of temperature, focusing on both the high- and low-temperature behaviors. As has been seen in work by others, the full treatment of magnetic couplings is crucial for a realistic description of the temperature behavior of NMR shielding up to normal measurement temperatures. At high temperatures, depending on the magnitude of ZFS, the effect of magnetic couplings diminishes, and the Zeeman and hyperfine interactions become effectively averaged in the thermally occupied states of the multiplet. At still higher temperatures, the ZFS may be omitted altogether, and the shielding properties may be evaluated using a doublet-like formula, with all the 2S+1 states becoming effectively degenerate at the limit of vanishing magnetic field. We demonstrate these features using first-principles calculations of Ni(II), Co(II), Cr(II), and Cr(III) complexes, which have ZFS of different sizes and signs. A non-monotonic inverse temperature dependence of the hyperfine shift is predicted for axially symmetric integer-spin systems with a positive D parameter of ZFS. This is due to the magnetic coupling terms that are proportional to kT at low temperatures, canceling the Curie-type 1/kT prefactor of the hyperfine shielding in this case. PMID:26574272

  8. Scalar Relativistic Computations and Localized Orbital Analyses of Nuclear Hyperfine Coupling and Paramagnetic NMR Chemical Shifts

    SciTech Connect

    Aquino, Fredy W.; Pritchard, Ben; Autschbach, Jochen

    2012-02-14

    A method is reported by which calculated hyperfine coupling constants (HFCCs) and paramagnetic NMR (pNMR) chemical shifts can be analyzed in a chemically intuitive way by decomposition into contributions from localized molecular orbitals (LMOs). A new module for density functional calculations with nonhybrid functionals, global hybrids, and range-separated hybrids, utilizing the two-component relativistic zeroth-order regular approximation (ZORA), has been implemented in the parallel open-source NWChem quantum chemistry package. Benchmark results are reported for a test set of few-atom molecules with light and heavy elements. Finite nucleus effects on ¹⁹⁹Hg HFCCs are shown to be on the order of -11 to -15%. A proof of concept for the LMO analysis is provided for the metal and fluorine HFCCs of TiF₃ and NpF₆. Calculated pNMR chemical shifts are reported for the 2-methylphenyl-t-butylnitroxide radical and for five cyclopentadienyl (Cp) sandwich complexes with 3d metals. Nickelocene and vanadocene carbon pNMR shifts are analyzed in detail, demonstrating that the large carbon pNMR shifts calculated as +1540 for Ni (exptl.: +1514) and -443 for V (exptl.: -510) are caused by different spin-polarization mechanisms. For Ni, Cp to Ni π back-donation dominates the result, whereas for vanadocene, V to Cp σ donation with relaxation of the carbon 1s shells can be identified as the dominant mechanism.

  9. Predicting (17)O NMR chemical shifts of polyoxometalates using density functional theory.

    PubMed

    Sharma, Rupali; Zhang, Jie; Ohlin, C André

    2016-03-21

    We have investigated the computation of (17)O NMR chemical shifts of a wide range of polyoxometalates using density functional theory. The effects of basis sets and exchange-correlation functionals are explored, and whereas pure DFT functionals generally predict the chemical shifts of terminal oxygen sites quite well, hybrid functionals are required for the prediction of accurate chemical shifts in conjunction with linear regression. By using PBE0/def2-tzvp//PBE0/cc-pvtz(H-Ar), lanl2dz(K-) we have computed the chemical shifts of 37 polyoxometalates, corresponding to 209 (17)O NMR signals. We also show that at this level of theory the protonation-induced pH dependence of the chemical shift of the triprotic hexaniobate Lindqvist anion, [HxNb6O19]((8-x)), can be reproduced, which suggests that hypotheses regarding loci of protonation can be confidently tested. PMID:26925832

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

    SciTech Connect

    Yoon, Young-Gui; Pfrommer, Bernd G.; Louie, Steven G.; Canning, Andrew

    2002-03-03

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

  11. Prediction of (19)F NMR Chemical Shifts in Labeled Proteins: Computational Protocol and Case Study.

    PubMed

    Isley, William C; Urick, Andrew K; Pomerantz, William C K; Cramer, Christopher J

    2016-07-01

    The structural analysis of ligand complexation in biomolecular systems is important in the design of new medicinal therapeutic agents; however, monitoring subtle structural changes in a protein's microenvironment is a challenging and complex problem. In this regard, the use of protein-based (19)F NMR for screening low-molecular-weight molecules (i.e., fragments) can be an especially powerful tool to aid in drug design. Resonance assignment of the protein's (19)F NMR spectrum is necessary for structural analysis. Here, a quantum chemical method has been developed as an initial approach to facilitate the assignment of a fluorinated protein's (19)F NMR spectrum. The epigenetic "reader" domain of protein Brd4 was taken as a case study to assess the strengths and limitations of the method. The overall modeling protocol predicts chemical shifts for residues in rigid proteins with good accuracy; proper accounting for explicit solvation of fluorinated residues by water is critical. PMID:27218275

  12. 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

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

    SciTech Connect

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

    1993-02-01

    New structures, termed ultralaminae, were recently shown to occur in kerogens from numerous oil shales and source rocks. Morphological and chemical studies revealed that ultralaminae originate from the selective preservation of the non-hydrolysable biomacromolecules (algaenans) building up the thin outer walls of several Chlorophyceae (green microalgae) including the cosmopolitan general Scenedesmus and Chlorella. The chemical correlation between such algaenans and fossil ultralaminae was mainly based on the production, on pyrolysis, of nitrogen compounds, n-alkylnitriles, with specific distributions depending on the lacustrine of marine origin of the considered samples. In addition, these bio-and geopolymers were characterized by quite high N levels.

  14. 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

  15. 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.

  16. 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

  17. Predicting Pt-195 NMR chemical shift using new relativistic all-electron basis set.

    PubMed

    Paschoal, D; Guerra, C Fonseca; de Oliveira, M A L; Ramalho, T C; Dos Santos, H F

    2016-10-01

    Predicting NMR properties is a valuable tool to assist the experimentalists in the characterization of molecular structure. For heavy metals, such as Pt-195, only a few computational protocols are available. In the present contribution, all-electron Gaussian basis sets, suitable to calculate the Pt-195 NMR chemical shift, are presented for Pt and all elements commonly found as Pt-ligands. The new basis sets identified as NMR-DKH were partially contracted as a triple-zeta doubly polarized scheme with all coefficients obtained from a Douglas-Kroll-Hess (DKH) second-order scalar relativistic calculation. The Pt-195 chemical shift was predicted through empirical models fitted to reproduce experimental data for a set of 183 Pt(II) complexes which NMR sign ranges from -1000 to -6000 ppm. Furthermore, the models were validated using a new set of 75 Pt(II) complexes, not included in the descriptive set. The models were constructed using non-relativistic Hamiltonian at density functional theory (DFT-PBEPBE) level with NMR-DKH basis set for all atoms. For the best model, the mean absolute deviation (MAD) and the mean relative deviation (MRD) were 150 ppm and 6%, respectively, for the validation set (75 Pt-complexes) and 168 ppm (MAD) and 5% (MRD) for all 258 Pt(II) complexes. These results were comparable with relativistic DFT calculation, 200 ppm (MAD) and 6% (MRD). © 2016 Wiley Periodicals, Inc. PMID:27510431

  18. Predicting Pt-195 NMR chemical shift using new relativistic all-electron basis set.

    PubMed

    Paschoal, D; Guerra, C Fonseca; de Oliveira, M A L; Ramalho, T C; Dos Santos, H F

    2016-10-01

    Predicting NMR properties is a valuable tool to assist the experimentalists in the characterization of molecular structure. For heavy metals, such as Pt-195, only a few computational protocols are available. In the present contribution, all-electron Gaussian basis sets, suitable to calculate the Pt-195 NMR chemical shift, are presented for Pt and all elements commonly found as Pt-ligands. The new basis sets identified as NMR-DKH were partially contracted as a triple-zeta doubly polarized scheme with all coefficients obtained from a Douglas-Kroll-Hess (DKH) second-order scalar relativistic calculation. The Pt-195 chemical shift was predicted through empirical models fitted to reproduce experimental data for a set of 183 Pt(II) complexes which NMR sign ranges from -1000 to -6000 ppm. Furthermore, the models were validated using a new set of 75 Pt(II) complexes, not included in the descriptive set. The models were constructed using non-relativistic Hamiltonian at density functional theory (DFT-PBEPBE) level with NMR-DKH basis set for all atoms. For the best model, the mean absolute deviation (MAD) and the mean relative deviation (MRD) were 150 ppm and 6%, respectively, for the validation set (75 Pt-complexes) and 168 ppm (MAD) and 5% (MRD) for all 258 Pt(II) complexes. These results were comparable with relativistic DFT calculation, 200 ppm (MAD) and 6% (MRD). © 2016 Wiley Periodicals, Inc.

  19. Unified Electrostatic Understanding on the Solvation-Induced Changes in the CN Stretching Frequency and the NMR Chemical Shifts of a Nitrile.

    PubMed

    Torii, Hajime

    2016-09-15

    Understanding on the spectroscopic properties of a functional group is essential to use it to detect changes in the structural and/or dynamical properties through the situations of intermolecular interactions. The present study is devoted to elucidating the factors that control the solvation-induced changes in the C≡N stretching frequency and the (13)C and (15)N NMR chemical shifts of the nitrile group. It is shown that the nonelectrostatic contribution of the hydration-induced changes in the C≡N stretching frequency as previously thought, as well as the specific effect of hydrogen bonding on the (13)C and (15)N chemical shifts, actually originate from the spatially inhomogeneous nature of the electrostatic situation generated by the hydrogen-bond donating water molecule, especially by the OH bond dipole. On this basis, a unified electrostatic interaction model that encompasses the cases of both hydration and dipolar solvation is constructed. The responses of electrons in these two cases are also discussed. PMID:27547990

  20. Automatic NMR-based identification of chemical reaction types in mixtures of co-occurring reactions.

    PubMed

    Latino, Diogo A R S; Aires-de-Sousa, João

    2014-01-01

    The combination of chemoinformatics approaches with NMR techniques and the increasing availability of data allow the resolution of problems far beyond the original application of NMR in structure elucidation/verification. The diversity of applications can range from process monitoring, metabolic profiling, authentication of products, to quality control. An application related to the automatic analysis of complex mixtures concerns mixtures of chemical reactions. We encoded mixtures of chemical reactions with the difference between the (1)H NMR spectra of the products and the reactants. All the signals arising from all the reactants of the co-occurring reactions were taken together (a simulated spectrum of the mixture of reactants) and the same was done for products. The difference spectrum is taken as the representation of the mixture of chemical reactions. A data set of 181 chemical reactions was used, each reaction manually assigned to one of 6 types. From this dataset, we simulated mixtures where two reactions of different types would occur simultaneously. Automatic learning methods were trained to classify the reactions occurring in a mixture from the (1)H NMR-based descriptor of the mixture. Unsupervised learning methods (self-organizing maps) produced a reasonable clustering of the mixtures by reaction type, and allowed the correct classification of 80% and 63% of the mixtures in two independent test sets of different similarity to the training set. With random forests (RF), the percentage of correct classifications was increased to 99% and 80% for the same test sets. The RF probability associated to the predictions yielded a robust indication of their reliability. This study demonstrates the possibility of applying machine learning methods to automatically identify types of co-occurring chemical reactions from NMR data. Using no explicit structural information about the reactions participants, reaction elucidation is performed without structure elucidation of

  1. (77)Se chemical shift tensor of L-selenocystine: experimental NMR measurements and quantum chemical investigations of structural effects.

    PubMed

    Struppe, Jochem; Zhang, Yong; Rozovsky, Sharon

    2015-03-01

    The genetically encoded amino acid selenocysteine and its dimeric form, selenocystine, are both utilized by nature. They are found in active sites of selenoproteins, enzymes that facilitate a diverse range of reactions, including the detoxification of reactive oxygen species and regulation of redox pathways. Due to selenocysteine and selenocystine's specialized biological roles, it is of interest to examine their (77)Se NMR properties and how those can in turn be employed to study biological systems. We report the solid-state (77)Se NMR measurements of the L-selenocystine chemical shift tensor, which provides the first experimental chemical shift tensor information on selenocysteine-containing systems. Quantum chemical calculations of L-selenocystine models were performed to help understand various structural effects on (77)Se L-selenocystine's chemical shift tensor. The effects of protonation state, protein environment, and substituent of selenium-bonded carbon on the isotropic chemical shift were found to be in a range of ca. 10-20 ppm. However, the conformational effect was found to be much larger, spanning ca. 600 ppm for the C-Se-Se-C dihedral angle range of -180° to +180°. Our calculations show that around the minimum energy structure with a C-Se-Se-C dihedral angle of ca. -90°, the energy costs to alter the dihedral angle in the range from -120° to -60° are within only 2.5 kcal/mol. This makes it possible to realize these conformations in a protein or crystal environment. (77)Se NMR was found to be a sensitive probe to such changes and has an isotropic chemical shift range of 272 ± 30 ppm for this energetically favorable conformation range. The energy-minimized structures exhibited calculated isotropic shifts that lay within 3-9% of those reported in previous solution NMR studies. The experimental solid-state NMR isotropic chemical shift is near the lower bound of this calculated range for these readily accessible conformations. These results suggest

  2. 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

  3. Complete (1)H and (13)C NMR chemical shift assignments of mono-, di-, and trisaccharides as basis for NMR chemical shift predictions of polysaccharides using the computer program casper.

    PubMed

    Roslund, Mattias U; Säwén, Elin; Landström, Jens; Rönnols, Jerk; Jonsson, K Hanna M; Lundborg, Magnus; Svensson, Mona V; Widmalm, Göran

    2011-08-16

    The computer program casper uses (1)H and (13)C NMR chemical shift data of mono- to trisaccharides for the prediction of chemical shifts of oligo- and polysaccharides. In order to improve the quality of these predictions the (1)H and (13)C, as well as (31)P when applicable, NMR chemical shifts of 30 mono-, di-, and trisaccharides were assigned. The reducing sugars gave two distinct sets of NMR resonances due to the α- and β-anomeric forms. In total 35 (1)H and (13)C NMR chemical shift data sets were obtained from the oligosaccharides. One- and two-dimensional NMR experiments were used for the chemical shift assignments and special techniques were employed in some cases such as 2D (1)H,(13)C-HSQC Hadamard Transform methodology which was acquired approximately 45 times faster than a regular t(1) incremented (1)H,(13)C-HSQC experiment and a 1D (1)H,(1)H-CSSF-TOCSY experiment which was able to distinguish spin-systems in which the target protons were only 3.3Hz apart. The (1)H NMR chemical shifts were subsequently refined using total line-shape analysis with the PERCH NMR software. The acquired NMR data were then utilized in the casper program (http://www.casper.organ.su.se/casper/) for NMR chemical shift predictions of the O-antigen polysaccharides from Klebsiella O5, Shigella flexneri serotype X, and Salmonella arizonae O62. The data were compared to experimental data of the polysaccharides from the two former strains and the lipopolysaccharide of the latter strain showing excellent agreement between predicted and experimental (1)H and (13)C NMR chemical shifts.

  4. NMR chemical shift perturbation mapping of DNA binding by a zinc-finger domain from the yeast transcription factor ADR1.

    PubMed Central

    Schmiedeskamp, M.; Rajagopal, P.; Klevit, R. E.

    1997-01-01

    Mutagenesis studies have revealed that the minimal DNA-binding domain of the yeast transcription factor ADR1 consists of two Cys2-His2 zinc fingers plus an additional 20 residues proximal and N-terminal to the fingers. We have assigned NMR 1H, 15N, and 13C chemical shifts for the entire minimal DNA-binding domain of ADR1 both free and bound to specific DNA. 1H chemical shift values suggest little structural difference between the zinc fingers in this construct and in single-finger constructs, and 13C alpha chemical shift index analysis indicates little change in finger structure upon DNA binding. 1H chemical shift perturbations upon DNA binding are observed, however, and these are mapped to define the protein-DNA interface. The two zinc fingers appear to bind DNA with different orientations, as the entire helix of finger 1 is perturbed, while only the extreme N-terminus of the finger 2 helix is affected. Furthermore, residues N-terminal to the first finger undergo large chemical shift changes upon DNA binding suggesting a role at the protein-DNA interface. A striking correspondence is observed between the protein-DNA interface mapped by chemical shift changes and that previously mapped by mutagenesis. PMID:9300483

  5. A combined deuterium NMR and quantum chemical investigation of inequivalent hydrogen bonds in organic solids.

    PubMed

    Webber, Renee; Penner, Glenn H

    2012-01-01

    Deuterium magic angle spinning (MAS) NMR spectroscopy and quantum chemical calculations are used to investigate organic solids in which inequivalent hydrogen bonds are present. The use of (2)H MAS allows one to measure the chemical shift, δ, quadrupolar coupling constant, C(Q), and asymmetry in the quadrupolar interaction, η(Q), for each type of hydrogen bond present in the system. Quantum chemical calculations of the magnetic shielding (σ, which can be related to δ) and the electric field gradient (EFG, which can be related to C(Q)) are compared to the experimental results and are discussed with respect to the relative strengths of the hydrogen bonds within each system.

  6. 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

  7. The effect of chemical stability on the NIPAM gel dosimeter using 1H-NMR

    NASA Astrophysics Data System (ADS)

    Huang, You-Ruei; Hsieh, Ling-Ling; Chang, Yuan-Jen; Hsieh, Bor-Tsung

    2013-06-01

    Radiation-induced chemical changes in the N-isopropylacrylamide (NIPAM) gels used in three-dimensional dosimeters were investigated using 1H-NMR in this study. The experimental results show that the signal from C=C bonds of NIPAM and N,N'-Methylenediacrylamide (BIS) are 5.5 and 6.3 ppm, respectively. The double bonds from the NIPAM and BIS disappeared with half-dose (D50) were about 10.90 Gy ± 0.76 Gy and 10.09 Gy ± 0.29 Gy, respectively. This observation demonstrates that the polymerization rate of BIS is faster than that of the NIPAM monomer. The 1H-NMR can indicate the chemical structure changes of the polymer gel dosimeter after irradiation and successfully determine the D50 in the NIPAM gel dosimeter.

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

    NASA Astrophysics Data System (ADS)

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

    2002-08-01

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

  9. Chemical structure and heterogeneity differences of two lignins from loblolly pine as investigated by advanced solid-state NMR spectroscopy

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Advanced solid-state NMR was employed to investigate differences in chemical structure and heterogeneity between milled wood lignin (MWL) and residual enzyme lignin (REL). Wiley and conventional milled woods were also studied. The advanced NMR techniques included 13C quantitative direct polarization...

  10. NMR ANALYSIS OF MALE FATHEAD MINNOW URINARY METABOLITES: A POTENTIAL APPROACH FOR STUDYING IMPACTS OF CHEMICAL EXPOSURES

    EPA Science Inventory

    The potential for profiling endogenous metabolites in urine from male fathead minnows (Pimephales promelas) to assess chemical exposures was explored using nuclear magnetic resonance (NMR) spectroscopy. Both one dimensional (1D) and two dimensional (2D) NMR spectroscopy w...

  11. Stereoregularity of poly (lactic acid) and their model compounds as studied by NMR and quantum chemical calculations

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In order to understand the origin of the tacticity splitting in the NMR spectrum of poly(lactic acid), monomer model compound and dimer model compounds (both isotactic and syndiotactic) were synthesized and their 1H and 13C NMR chemical shifts observed. Two energetically stable conformations were o...

  12. Investigation of 1H NMR chemical shifts of organic dye with hydrogen bonds and ring currents.

    PubMed

    Park, Sung Soo; Won, Yong Sun; Lee, Woojin; Kim, Jae Hong

    2011-04-01

    The (1)H NMR chemical shifts were theoretically computed for the organic dyes 2-(2,6-dimethyl-4H-pyran-4-ylidene)-malononitrile (1), cyano-(2,6-dimethyl-4H-pyran-4-ylidene)-acetic acid methyl ester (2), 2-(2,6-bis(4-(dimethylamino)styryl)-4H-pyran-4-ylidene)-malononitrile (3), and methyl 2-(2,6-bis(4-(dimethylamino)styryl)-4H-pyran-4-ylidene)-2-cyanoacetate (4) at the GIAO/B3LYP/6-311++G(d,p)//B3LYP/6-311++G(d,p) level of theory. Moreover, the intramolecular rotational barriers of the molecules were calculated to evaluate the internal flexibility with respect to the torsional degrees of freedom, and the nuclear-independent chemical shifts (NICS) were employed to analyze the ring currents. The difference was explained in terms of intramolecular hydrogen bonds and ring currents of the molecules. The (1)H NMR spectra were reproduced by experiments for the comparison with computationally constructed data. Our results suggest a good guideline in interpreting (1)H NMR chemical shifts using computational methods and furthermore a reliable perspective for designing molecular structures.

  13. 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.

  14. 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.

  15. Quantitative H-1 NMR Analysis of Chemical Stabilities in Anion-Exchange Membranes

    SciTech Connect

    Nunez, SA; Hickner, MA

    2013-01-01

    We compared the alkaline stability of three classes of anion exchange membranes that are leading candidates for applications in platinum-free fuel cells. A methodology is presented for the study of chemical stability of anion-exchange polymers in alkaline media that provides clear and quantitative H-1 NMR spectroscopic data of dissolved polymers containing benzyltrimethylammonium functionalities. Recent studies have investigated the stabilities of benzimidazolium- and alkylimidazolium-bearing polymers using periodic H-1 NMR sampling. These studies included varying alkaline concentrations, external heating sources, and excessive processing and contained no internal standard for absolute measurements. Key aspects of our time-resolved H-1 NMR method include in situ heating and sampling within the spectrometer, fixed Stoichiometric relationships between the benzyltrimethylammonium functionalities of each polymer and potassium deuteroxide (KOD), and the incorporation of an internal standard for the absolute measurement of the polymer degradation. In addition, our method permits the identification of the degradation products to find the underlying cause of chemical lability. Our results demonstrate that a styrene-based polymer containing benzyltrimethylammonium functional groups is remarkably stable when exposed to 20 equivalents per cation of KOD at 80 degrees C with a half-life (t(1/2)) of 231 h. Under these standard conditions, functionalized poly(phenylene oxide) and poly(arylene ether sulfone) copolymers, both bearing benzyltrimethylammonium functionalities were found to degrade with a half-lives of 57.8 and 2.7 h, respectively.

  16. Calculation of NMR chemical shifts in organic solids: accounting for motional effects.

    PubMed

    Dumez, Jean-Nicolas; Pickard, Chris J

    2009-03-14

    NMR chemical shifts were calculated from first principles for well defined crystalline organic solids. These density functional theory calculations were carried out within the plane-wave pseudopotential framework, in which truly extended systems are implicitly considered. The influence of motional effects was assessed by averaging over vibrational modes or over snapshots taken from ab initio molecular dynamics simulations. It is observed that the zero-point correction to chemical shifts can be significant, and that thermal effects are particularly noticeable for shielding anisotropies and for a temperature-dependent chemical shift. This study provides insight into the development of highly accurate first principles calculations of chemical shifts in solids, highlighting the role of motional effects on well defined systems.

  17. 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.

  18. 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.

  19. Monitoring chemical reactions by low-field benchtop NMR at 45 MHz: pros and cons.

    PubMed

    Silva Elipe, Maria Victoria; Milburn, Robert R

    2016-06-01

    Monitoring chemical reactions is the key to controlling chemical processes where NMR can provide support. High-field NMR gives detailed structural information on chemical compounds and reactions; however, it is expensive and complex to operate. Conversely, low-field NMR instruments are simple and relatively inexpensive alternatives. While low-field NMR does not provide the detailed information as the high-field instruments as a result of their smaller chemical shift dispersion and the complex secondary coupling, it remains of practical value as a process analytical technology (PAT) tool and is complimentary to other established methods, such as ReactIR and Raman spectroscopy. We have tested a picoSpin-45 (currently under ThermoFisher Scientific) benchtop NMR instrument to monitor three types of reactions by 1D (1) H NMR: a Fischer esterification, a Suzuki cross-coupling, and the formation of an oxime. The Fischer esterification is a relatively simple reaction run at high concentration and served as proof of concept. The Suzuki coupling is an example of a more complex, commonly used reaction involving overlapping signals. Finally, the oxime formation involved a reaction in two phases that cannot be monitored by other PAT tools. Here, we discuss the pros and cons of monitoring these reactions at a low-field of 45 MHz by 1D (1) H NMR. Copyright © 2015 John Wiley & Sons, Ltd.

  20. A new approach to quantitative NMR: fluoroquinolones analysis by evaluating the chemical shift displacements.

    PubMed

    Michaleas, S; Antoniadou-Vyza, E

    2006-10-11

    Quantitative NMR spectroscopy is always an attractive goal as the identity and quantity could be simultaneously determined. Although significant advancements have been achieved in this field it is common that all reported quantitative NMR methods perform the analysis by utilizing the average integral intensities of selected signals. During the calculation of the area under NMR peaks several response problems can occur which should always be treated carefully to overcome inaccuracies. In the method proposed in this work the quantitative information is obtained utilizing the measurement of selected protons chemical shift displacements which is a quite straightforward and highly reproducible process. The (1)H NMR spectra of multiple fluoroquinolone (FQ) solutions revealed that the chemical shifts of protons, especially the aromatic ones, were concentration dependent for all tested compounds, as a result of extensive self-association phenomena. In the present work a novel methodology is described for the quantitation of several FQs based on this dependence. The proposed method was applied to Ciprofloxacin solutions over a wide range of concentrations. Evaluation of the obtained data presented acceptable characteristics regarding accuracy, precision, and robustness. The applicability limitations of this method were found to be posed by current instrumentation, mainly by the magnetic field frequency e.g. the slope of the response function achieved with a 400MHz instrument was twice the one achieved at 200MHz. The pH effect was negligible from pD 2.5 to 5.5. The phenomenon appeared in a pattern that can be applied for a plethora of drug categories revealing self-association phenomena in a range of concentration determined by the magnet strength of the instrument.

  1. Chemical Shifts to Metabolic Pathways: Identifying Metabolic Pathways Directly from a Single 2D NMR Spectrum.

    PubMed

    Dubey, Abhinav; Rangarajan, Annapoorni; Pal, Debnath; Atreya, Hanudatta S

    2015-12-15

    Identifying cellular processes in terms of metabolic pathways is one of the avowed goals of metabolomics studies. Currently, this is done after relevant metabolites are identified to allow their mapping onto specific pathways. This task is daunting due to the complex nature of cellular processes and the difficulty in establishing the identity of individual metabolites. We propose here a new method: ChemSMP (Chemical Shifts to Metabolic Pathways), which facilitates rapid analysis by identifying the active metabolic pathways directly from chemical shifts obtained from a single two-dimensional (2D) [(13)C-(1)H] correlation NMR spectrum without the need for identification and assignment of individual metabolites. ChemSMP uses a novel indexing and scoring system comprised of a "uniqueness score" and a "coverage score". Our method is demonstrated on metabolic pathways data from the Small Molecule Pathway Database (SMPDB) and chemical shifts from the Human Metabolome Database (HMDB). Benchmarks show that ChemSMP has a positive prediction rate of >90% in the presence of decluttered data and can sustain the same at 60-70% even in the presence of noise, such as deletions of peaks and chemical shift deviations. The method tested on NMR data acquired for a mixture of 20 amino acids shows a success rate of 93% in correct recovery of pathways. When used on data obtained from the cell lysate of an unexplored oncogenic cell line, it revealed active metabolic pathways responsible for regulating energy homeostasis of cancer cells. Our unique tool is thus expected to significantly enhance analysis of NMR-based metabolomics data by reducing existing impediments.

  2. 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

  3. SENSASS NMR: New NMR techniques for enhancing the sensitivity and the spectral resolution of polymer supported chemicals

    NASA Astrophysics Data System (ADS)

    Prosa, Nicolò; Scherrmann, Marie-Christine; Merlet, Denis; Farjon, Jonathan

    2013-12-01

    The use of polyethylene glycols (PEGs) as organic polymer soluble supports for synthesis has been receiving growing interest. The main advantages of using PEGs as support are related to their non-toxicity, their commercial availability and their solubility properties allowing easy recovery and analysis of compounds linked to the polymer. The NMR characterization of PEG-branched products could however be difficult due to the presence of huge signals of the polymeric support. In order to overcome this problem, we developed new NMR experiments named SENSitivity increAsed and resolution enhanced by Signal Suppression or SENSASS NMR. These experiments implement either semi-selective pulses or Water Gate sequences for reducing signals of the polymer as well as fast pulsing techniques optimizing the recycling delay for enhancing the sensitivity of signals. They have been successfully implemented in classical NMR characterization experiments namely, COSY, HSQC and HMBC experiments.

  4. 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.

  5. 13C and 15N—Chemical Shift Anisotropy of Ampicillin and Penicillin-V Studied by 2D-PASS and CP/MAS NMR

    NASA Astrophysics Data System (ADS)

    Antzutkin, Oleg N.; Lee, Young K.; Levitt, Malcolm H.

    1998-11-01

    The principal values of the chemical shift tensors of all13C and15N sites in two antibiotics, ampicillin and penicillin-V, were determined by 2-dimensionalphaseadjustedspinningsideband (2D-PASS) and conventional CP/MAS experiments. The13C and15N chemical shift anisotropies (CSA), and their confidence limits, were evaluated using a Mathematica program. The CSA values suggest a revised assignment of the 2-methyl13C sites in the case of ampicillin. We speculate on a relationship between the chemical shift principal values of many of the13C and15N sites and the β-lactam ring conformation.

  6. Subtle Chemical Shifts Explain the NMR Fingerprints of Oligomeric Proanthocyanidins with High Dentin Biomodification Potency.

    PubMed

    Nam, Joo-Won; Phansalkar, Rasika S; Lankin, David C; Bisson, Jonathan; McAlpine, James B; Leme, Ariene A; Vidal, Cristina M P; Ramirez, Benjamin; Niemitz, Matthias; Bedran-Russo, Ana; Chen, Shao-Nong; Pauli, Guido F

    2015-08-01

    The ability of certain oligomeric proanthocyanidins (OPACs) to enhance the biomechanical properties of dentin involves collagen cross-linking of the 1.3-4.5 nm wide space via protein-polyphenol interactions. A systematic interdisciplinary search for the bioactive principles of pine bark has yielded the trimeric PAC, ent-epicatechin-(4β→8)-epicatechin-(2β→O→7,4β→8)-catechin (3), representing the hitherto most potent single chemical entity capable of enhancing dentin stiffness. Building the case from two congeneric PAC dimers, a detailed structural analysis decoded the stereochemistry, spatial arrangement, and chemical properties of three dentin biomodifiers. Quantum-mechanics-driven (1)H iterative full spin analysis (QM-HiFSA) of NMR spectra distinguished previously unrecognized details such as higher order J coupling and provided valuable information about 3D structure. Detection and quantification of H/D-exchange effects by QM-HiFSA identified C-8 and C-6 as (re)active sites, explain preferences in biosynthetic linkage, and suggest their involvement in dentin cross-linking activity. Mapping of these molecular properties underscored the significance of high δ precision in both (1)H and (13)C NMR spectroscopy. Occurring at low- to subppb levels, these newly characterized chemical shift differences in ppb are small but diagnostic measures of dynamic processes inherent to the OPAC pharmacophores and can help augment our understanding of nanometer-scale intermolecular interactions in biomodified dentin macromolecules.

  7. Subtle Chemical Shifts Explain the NMR Fingerprints of Oligomeric Proanthocyanidins with High Dentin Biomodification Potency.

    PubMed

    Nam, Joo-Won; Phansalkar, Rasika S; Lankin, David C; Bisson, Jonathan; McAlpine, James B; Leme, Ariene A; Vidal, Cristina M P; Ramirez, Benjamin; Niemitz, Matthias; Bedran-Russo, Ana; Chen, Shao-Nong; Pauli, Guido F

    2015-08-01

    The ability of certain oligomeric proanthocyanidins (OPACs) to enhance the biomechanical properties of dentin involves collagen cross-linking of the 1.3-4.5 nm wide space via protein-polyphenol interactions. A systematic interdisciplinary search for the bioactive principles of pine bark has yielded the trimeric PAC, ent-epicatechin-(4β→8)-epicatechin-(2β→O→7,4β→8)-catechin (3), representing the hitherto most potent single chemical entity capable of enhancing dentin stiffness. Building the case from two congeneric PAC dimers, a detailed structural analysis decoded the stereochemistry, spatial arrangement, and chemical properties of three dentin biomodifiers. Quantum-mechanics-driven (1)H iterative full spin analysis (QM-HiFSA) of NMR spectra distinguished previously unrecognized details such as higher order J coupling and provided valuable information about 3D structure. Detection and quantification of H/D-exchange effects by QM-HiFSA identified C-8 and C-6 as (re)active sites, explain preferences in biosynthetic linkage, and suggest their involvement in dentin cross-linking activity. Mapping of these molecular properties underscored the significance of high δ precision in both (1)H and (13)C NMR spectroscopy. Occurring at low- to subppb levels, these newly characterized chemical shift differences in ppb are small but diagnostic measures of dynamic processes inherent to the OPAC pharmacophores and can help augment our understanding of nanometer-scale intermolecular interactions in biomodified dentin macromolecules. PMID:26214362

  8. DFT calculations of 1H and 13C NMR chemical shifts in transition metal hydrides.

    PubMed

    del Rosal, I; Maron, L; Poteau, R; Jolibois, F

    2008-08-14

    Transition metal hydrides are of great interest in chemistry because of their reactivity and their potential use as catalysts for hydrogenation. Among other available techniques, structural properties in transition metal (TM) complexes are often probed by NMR spectroscopy. In this paper we will show that it is possible to establish a viable methodological strategy in the context of density functional theory, that allows the determination of 1H NMR chemical shifts of hydride ligands attached to transition metal atoms in mononuclear systems and clusters with good accuracy with respect to experiment. 13C chemical shifts have also been considered in some cases. We have studied mononuclear ruthenium complexes such as Ru(L)(H)(dppm)2 with L = H or Cl, cationic complex [Ru(H)(H2O)(dppm)2]+ and Ru(H)2(dppm)(PPh3)2, in which hydride ligands are characterized by a negative 1H NMR chemical shift. For these complexes all calculations are in relatively good agreement compared to experimental data with errors not exceeding 20% except for the hydrogen atom in Ru(H)2(dppm)(PPh3)2. For this last complex, the relative error increases to 30%, probably owing to the necessity to take into account dynamical effects of phenyl groups. Carbonyl ligands are often encountered in coordination chemistry. Specific issues arise when calculating 1H or 13C NMR chemical shifts in TM carbonyl complexes. Indeed, while errors of 10 to 20% with respect to experiment are often considered good in the framework of density functional theory, this difference in the case of mononuclear carbonyl complexes culminates to 80%: results obtained with all-electron calculations are overall in very satisfactory agreement with experiment, the error in this case does not exceed 11% contrary to effective core potentials (ECPs) calculations which yield errors always larger than 20%. We conclude that for carbonyl groups the use of ECPs is not recommended, although their use could save time for very large systems, for

  9. DFT calculations of 1H and 13C NMR chemical shifts in transition metal hydrides.

    PubMed

    del Rosal, I; Maron, L; Poteau, R; Jolibois, F

    2008-08-14

    Transition metal hydrides are of great interest in chemistry because of their reactivity and their potential use as catalysts for hydrogenation. Among other available techniques, structural properties in transition metal (TM) complexes are often probed by NMR spectroscopy. In this paper we will show that it is possible to establish a viable methodological strategy in the context of density functional theory, that allows the determination of 1H NMR chemical shifts of hydride ligands attached to transition metal atoms in mononuclear systems and clusters with good accuracy with respect to experiment. 13C chemical shifts have also been considered in some cases. We have studied mononuclear ruthenium complexes such as Ru(L)(H)(dppm)2 with L = H or Cl, cationic complex [Ru(H)(H2O)(dppm)2]+ and Ru(H)2(dppm)(PPh3)2, in which hydride ligands are characterized by a negative 1H NMR chemical shift. For these complexes all calculations are in relatively good agreement compared to experimental data with errors not exceeding 20% except for the hydrogen atom in Ru(H)2(dppm)(PPh3)2. For this last complex, the relative error increases to 30%, probably owing to the necessity to take into account dynamical effects of phenyl groups. Carbonyl ligands are often encountered in coordination chemistry. Specific issues arise when calculating 1H or 13C NMR chemical shifts in TM carbonyl complexes. Indeed, while errors of 10 to 20% with respect to experiment are often considered good in the framework of density functional theory, this difference in the case of mononuclear carbonyl complexes culminates to 80%: results obtained with all-electron calculations are overall in very satisfactory agreement with experiment, the error in this case does not exceed 11% contrary to effective core potentials (ECPs) calculations which yield errors always larger than 20%. We conclude that for carbonyl groups the use of ECPs is not recommended, although their use could save time for very large systems, for

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

    PubMed

    Görling, Benjamin; Bräse, Stefan; Luy, Burkhard

    2016-01-01

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

  11. Chemical reactivity of graphene oxide towards amines elucidated by solid-state NMR

    NASA Astrophysics Data System (ADS)

    Vacchi, Isabella A.; Spinato, Cinzia; Raya, Jésus; Bianco, Alberto; Ménard-Moyon, Cécilia

    2016-07-01

    Graphene oxide (GO) is an attractive nanomaterial for many applications. Controlling the functionalization of GO is essential for the design of graphene-based conjugates with novel properties. But, the chemical composition of GO has not been fully elucidated yet. Due to the high reactivity of the oxygenated moieties, mainly epoxy, hydroxyl and carboxyl groups, several derivatization reactions may occur concomitantly. The reactivity of GO with amine derivatives has been exploited in the literature to design graphene-based conjugates, mainly through amidation. However, in this study we undoubtedly demonstrate using magic angle spinning (MAS) solid-state NMR that the reaction between GO and amine functions occurs via ring opening of the epoxides, and not by amidation. We also prove that there is a negligible amount of carboxylic acid groups in two GO samples obtained by a different synthesis process, hence eliminating the possibility of amidation reactions with amine derivatives. This work brings additional insights into the chemical reactivity of GO, which is fundamental to control its functionalization, and highlights the major role of MAS NMR spectroscopy for a comprehensive characterization of derivatized GO.Graphene oxide (GO) is an attractive nanomaterial for many applications. Controlling the functionalization of GO is essential for the design of graphene-based conjugates with novel properties. But, the chemical composition of GO has not been fully elucidated yet. Due to the high reactivity of the oxygenated moieties, mainly epoxy, hydroxyl and carboxyl groups, several derivatization reactions may occur concomitantly. The reactivity of GO with amine derivatives has been exploited in the literature to design graphene-based conjugates, mainly through amidation. However, in this study we undoubtedly demonstrate using magic angle spinning (MAS) solid-state NMR that the reaction between GO and amine functions occurs via ring opening of the epoxides, and not by

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

    PubMed

    Görling, Benjamin; Bräse, Stefan; Luy, Burkhard

    2016-09-02

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

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

    PubMed Central

    Görling, Benjamin; Bräse, Stefan; Luy, Burkhard

    2016-01-01

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

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

    PubMed

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

    2015-10-14

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

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

    SciTech Connect

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

    2015-10-14

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

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

    SciTech Connect

    Schaefer, J.

    1994-12-01

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

  17. Chemical reactivity of graphene oxide towards amines elucidated by solid-state NMR.

    PubMed

    Vacchi, Isabella A; Spinato, Cinzia; Raya, Jésus; Bianco, Alberto; Ménard-Moyon, Cécilia

    2016-07-14

    Graphene oxide (GO) is an attractive nanomaterial for many applications. Controlling the functionalization of GO is essential for the design of graphene-based conjugates with novel properties. But, the chemical composition of GO has not been fully elucidated yet. Due to the high reactivity of the oxygenated moieties, mainly epoxy, hydroxyl and carboxyl groups, several derivatization reactions may occur concomitantly. The reactivity of GO with amine derivatives has been exploited in the literature to design graphene-based conjugates, mainly through amidation. However, in this study we undoubtedly demonstrate using magic angle spinning (MAS) solid-state NMR that the reaction between GO and amine functions occurs via ring opening of the epoxides, and not by amidation. We also prove that there is a negligible amount of carboxylic acid groups in two GO samples obtained by a different synthesis process, hence eliminating the possibility of amidation reactions with amine derivatives. This work brings additional insights into the chemical reactivity of GO, which is fundamental to control its functionalization, and highlights the major role of MAS NMR spectroscopy for a comprehensive characterization of derivatized GO. PMID:27411370

  18. Conformational Sampling by Ab Initio Molecular Dynamics Simulations Improves NMR Chemical Shift Predictions.

    PubMed

    Dračínský, Martin; Möller, Heiko M; Exner, Thomas E

    2013-08-13

    Car-Parrinello molecular dynamics simulations were performed for N-methyl acetamide as a small test system for amide groups in protein backbones, and NMR chemical shifts were calculated based on the generated ensemble. If conformational sampling and explicit solvent molecules are taken into account, excellent agreement between the calculated and experimental chemical shifts is obtained. These results represent a landmark improvement over calculations based on classical molecular dynamics (MD) simulations especially for amide protons, which are predicted too high-field shifted based on the latter ensembles. We were able to show that the better results are caused by the solute-solvents interactions forming shorter hydrogen bonds as well as by the internal degrees of freedom of the solute. Inspired by these results, we propose our approach as a new tool for the validation of force fields due to its power of identifying the structural reasons for discrepancies between the experimental and calculated data. PMID:26584127

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

    PubMed

    Shen, Yang; Bax, Ad

    2013-07-01

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

  20. High-sensitivity chemical derivatization NMR analysis for condition monitoring of aged elastomers.

    SciTech Connect

    Assink, Roger Alan; Celina, Mathias Christopher; Skutnik, Julie Michelle

    2004-06-01

    An aged polybutadiene-based elastomer was reacted with trifluoroacetic anhydride (TFAA) and subsequently analyzed via 19F NMR spectroscopy. Derivatization between the TFAA and hydroxyl functionalities produced during thermo-oxidative aging was achieved, resulting in the formation of trifluoroester groups on the polymer. Primary and secondary alcohols were confirmed to be the main oxidation products of this material, and the total percent oxidation correlated with data obtained from oxidation rate measurements. The chemical derivatization appears to be highly sensitive and can be used to establish the presence and identity of oxidation products in aged polymeric materials. This methodology represents a novel condition monitoring approach for the detection of chemical changes that are otherwise difficult to analyze.

  1. Interactions between CusF and CusB identified by NMR spectroscopy and chemical cross-linking coupled to mass spectrometry.

    PubMed

    Mealman, Tiffany D; Bagai, Ireena; Singh, Pragya; Goodlett, David R; Rensing, Christopher; Zhou, Hongjun; Wysocki, Vicki H; McEvoy, Megan M

    2011-04-01

    The Escherichia coli periplasmic proteins CusF and CusB, as part of the CusCFBA efflux system, aid in the resistance of elevated levels of copper and silver by direct metal transfer between the metallochaperone CusF and the membrane fusion protein CusB before metal extrusion from the periplasm to the extracellular space. Although previous in vitro experiments have demonstrated highly specific interactions between CusF and CusB that are crucial for metal transfer to occur, the structural details of the interaction have not been determined. Here, the interactions between CusF and CusB are mapped through nuclear magnetic resonance (NMR) spectroscopy and chemical cross-linking coupled with high-resolution mass spectrometry to better understand how recognition and metal transfer occur between these proteins. The NMR (1)H-(15)N correlation spectra reveal that CusB interacts with the metal-binding face of CusF. In vitro chemical cross-linking with a 7.7 Å homobifunctional amine-reactive cross-linker, BS(2)G, was used to capture the CusF/CusB interaction site, and mass spectral data acquired on an LTQ-Orbitrap confirm the following two cross-links: CusF K31 to CusB K29 and CusF K58 to CusB K32, thus revealing that the N-terminal region of CusB interacts with the metal-binding face of CusF. The proteins transiently interact in a metal-dependent fashion, and contacts between CusF and CusB are localized to regions near their respective metal-binding sites. PMID:21323389

  2. Interactions between CusF and CusB identified by NMR spectroscopy and chemical cross-linking coupled to mass spectrometry

    PubMed Central

    Mealman, Tiffany D.; Bagai, Ireena; Singh, Pragya; Goodlett, David R.; Rensing, Christopher; Zhou, Hongjun; Wysocki, Vicki H.; McEvoy, Megan M.

    2011-01-01

    The E. coli periplasmic proteins CusF and CusB, as part of the CusCFBA efflux system, aid in the resistance of elevated levels of copper and silver by direct metal transfer between the metallochaperone CusF and the membrane fusion protein CusB, before metal extrusion from the periplasm to the extracellular space. Although previous in vitro experiments have demonstrated highly specific interactions between CusF and CusB that are crucial for metal transfer to occur, the structural details of the interaction have not been determined. Here, the interactions between CusF and CusB are mapped through nuclear magnetic resonance (NMR) spectroscopy and chemical cross-linking coupled with high-resolution mass spectrometry to better understand how recognition and metal transfer occur between these proteins. The NMR 1H-15N correlation spectra reveal that CusB interacts with the metal-binding face of CusF. In vitro chemical cross-linking with a 7.7 Å homobifunctional amine-reactive cross-linker, BS2G, was used to capture the CusF/CusB interaction site and mass spectral data acquired on an LTQ-Orbitrap confirm the following two cross-links: CusF K31 to CusB K29 and CusF K58 to CusB K32; thus, revealing that the N-terminal region of CusB interacts with the metal-binding face of CusF. The proteins transiently interact in a metal-dependent fashion and contacts between CusF and CusB are localized to regions near their respective metal binding sites. PMID:21323389

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

    PubMed

    Swails, Jason; Zhu, Tong; He, Xiao; Case, David A

    2015-10-01

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

  4. Equilibrium simulations of proteins using molecular fragment replacement and NMR chemical shifts.

    PubMed

    Boomsma, Wouter; Tian, Pengfei; Frellsen, Jes; Ferkinghoff-Borg, Jesper; Hamelryck, Thomas; Lindorff-Larsen, Kresten; Vendruscolo, Michele

    2014-09-23

    Methods of protein structure determination based on NMR chemical shifts are becoming increasingly common. The most widely used approaches adopt the molecular fragment replacement strategy, in which structural fragments are repeatedly reassembled into different complete conformations in molecular simulations. Although these approaches are effective in generating individual structures consistent with the chemical shift data, they do not enable the sampling of the conformational space of proteins with correct statistical weights. Here, we present a method of molecular fragment replacement that makes it possible to perform equilibrium simulations of proteins, and hence to determine their free energy landscapes. This strategy is based on the encoding of the chemical shift information in a probabilistic model in Markov chain Monte Carlo simulations. First, we demonstrate that with this approach it is possible to fold proteins to their native states starting from extended structures. Second, we show that the method satisfies the detailed balance condition and hence it can be used to carry out an equilibrium sampling from the Boltzmann distribution corresponding to the force field used in the simulations. Third, by comparing the results of simulations carried out with and without chemical shift restraints we describe quantitatively the effects that these restraints have on the free energy landscapes of proteins. Taken together, these results demonstrate that the molecular fragment replacement strategy can be used in combination with chemical shift information to characterize not only the native structures of proteins but also their conformational fluctuations.

  5. Benchmarking quantum mechanical calculations with experimental NMR chemical shifts of 2-HADNT

    NASA Astrophysics Data System (ADS)

    Liu, Yuemin; Junk, Thomas; Liu, Yucheng; Tzeng, Nianfeng; Perkins, Richard

    2015-04-01

    In this study, both GIAO-DFT and GIAO-MP2 calculations of nuclear magnetic resonance (NMR) spectra were benchmarked with experimental chemical shifts. The experimental chemical shifts were determined experimentally for carbon-13 (C-13) of seven carbon atoms for the TNT degradation product 2-hydroxylamino-4,6-dinitrotoluene (2-HADNT). Quantum mechanics GIAO calculations were implemented using Becke-3-Lee-Yang-Parr (B3LYP) and other six hybrid DFT methods (Becke-1-Lee-Yang-Parr (B1LYP), Becke-half-and-half-Lee-Yang-Parr (BH and HLYP), Cohen-Handy-3-Lee-Yang-Parr (O3LYP), Coulomb-attenuating-B3LYP (CAM-B3LYP), modified-Perdew-Wang-91-Lee-Yang-Parr (mPW1LYP), and Xu-3-Lee-Yang-Parr (X3LYP)) which use the same correlation functional LYP. Calculation results showed that the GIAO-MP2 method gives the most accurate chemical shift values, and O3LYP method provides the best prediction of chemical shifts among the B3LYP and other five DFT methods. Three types of atomic partial charges, Mulliken (MK), electrostatic potential (ESP), and natural bond orbital (NBO), were also calculated using MP2/aug-cc-pVDZ method. A reasonable correlation was discovered between NBO partial charges and experimental chemical shifts of carbon-13 (C-13).

  6. Origin of the conformational modulation of the 13C NMR chemical shift of methoxy groups in aromatic natural compounds.

    PubMed

    Toušek, Jaromír; Straka, Michal; Sklenář, Vladimír; Marek, Radek

    2013-01-24

    The interpretation of nuclear magnetic resonance (NMR) parameters is essential to understanding experimental observations at the molecular and supramolecular levels and to designing new and more efficient molecular probes. In many aromatic natural compounds, unusual (13)C NMR chemical shifts have been reported for out-of-plane methoxy groups bonded to the aromatic ring (~62 ppm as compared to the typical value of ~56 ppm for an aromatic methoxy group). Here, we analyzed this phenomenon for a series of aromatic natural compounds using Density Functional Theory (DFT) calculations. First, we checked the methodology used to optimize the structure and calculate the NMR chemical shifts in aromatic compounds. The conformational effects of the methoxy group on the (13)C NMR chemical shift then were interpreted by the Natural Bond Orbital (NBO) and Natural Chemical Shift (NCS) approaches, and by excitation analysis of the chemical shifts, breaking down the total nuclear shielding tensor into the contributions from the different occupied orbitals and their magnetic interactions with virtual orbitals. We discovered that the atypical (13)C NMR chemical shifts observed are not directly related to a different conjugation of the lone pair of electrons of the methoxy oxygen with the aromatic ring, as has been suggested. Our analysis indicates that rotation of the methoxy group induces changes in the virtual molecular orbital space, which, in turn, correlate with the predominant part of the contribution of the paramagnetic deshielding connected with the magnetic interactions of the BD(CMet-H)→BD*(CMet-OMet) orbitals, resulting in the experimentally observed deshielding of the (13)C NMR resonance of the out-of-plane methoxy group.

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

    NASA Astrophysics Data System (ADS)

    Abbas, Ashgar; Gökce, Halil; Bahçeli, Semiha

    2016-01-01

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

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

    PubMed

    Abbas, Ashgar; Gökce, Halil; Bahçeli, Semiha

    2016-01-01

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

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

    PubMed

    Fritzsching, K J; Yang, Y; Schmidt-Rohr, K; Hong, Mei

    2013-06-01

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

  10. Toward Relatively General and Accurate Quantum Chemical Predictions of Solid-State 17O NMR Chemical Shifts in Various Biologically Relevant Oxygen-containing Compounds

    PubMed Central

    Rorick, Amber; Michael, Matthew A.; Yang, Liu; Zhang, Yong

    2015-01-01

    Oxygen is an important element in most biologically significant molecules and experimental solid-state 17O NMR studies have provided numerous useful structural probes to study these systems. However, computational predictions of solid-state 17O NMR chemical shift tensor properties are still challenging in many cases and in particular each of the prior computational work is basically limited to one type of oxygen-containing systems. This work provides the first systematic study of the effects of geometry refinement, method and basis sets for metal and non-metal elements in both geometry optimization and NMR property calculations of some biologically relevant oxygen-containing compounds with a good variety of XO bonding groups, X= H, C, N, P, and metal. The experimental range studied is of 1455 ppm, a major part of the reported 17O NMR chemical shifts in organic and organometallic compounds. A number of computational factors towards relatively general and accurate predictions of 17O NMR chemical shifts were studied to provide helpful and detailed suggestions for future work. For the studied various kinds of oxygen-containing compounds, the best computational approach results in a theory-versus-experiment correlation coefficient R2 of 0.9880 and mean absolute deviation of 13 ppm (1.9% of the experimental range) for isotropic NMR shifts and R2 of 0.9926 for all shift tensor properties. These results shall facilitate future computational studies of 17O NMR chemical shifts in many biologically relevant systems, and the high accuracy may also help refinement and determination of active-site structures of some oxygen-containing substrate bound proteins. PMID:26274812

  11. Toward Relatively General and Accurate Quantum Chemical Predictions of Solid-State (17)O NMR Chemical Shifts in Various Biologically Relevant Oxygen-Containing Compounds.

    PubMed

    Rorick, Amber; Michael, Matthew A; Yang, Liu; Zhang, Yong

    2015-09-01

    Oxygen is an important element in most biologically significant molecules, and experimental solid-state (17)O NMR studies have provided numerous useful structural probes to study these systems. However, computational predictions of solid-state (17)O NMR chemical shift tensor properties are still challenging in many cases, and in particular, each of the prior computational works is basically limited to one type of oxygen-containing system. This work provides the first systematic study of the effects of geometry refinement, method, and basis sets for metal and nonmetal elements in both geometry optimization and NMR property calculations of some biologically relevant oxygen-containing compounds with a good variety of XO bonding groups (X = H, C, N, P, and metal). The experimental range studied is of 1455 ppm, a major part of the reported (17)O NMR chemical shifts in organic and organometallic compounds. A number of computational factors toward relatively general and accurate predictions of (17)O NMR chemical shifts were studied to provide helpful and detailed suggestions for future work. For the studied kinds of oxygen-containing compounds, the best computational approach results in a theory-versus-experiment correlation coefficient (R(2)) value of 0.9880 and a mean absolute deviation of 13 ppm (1.9% of the experimental range) for isotropic NMR shifts and an R(2) value of 0.9926 for all shift-tensor properties. These results shall facilitate future computational studies of (17)O NMR chemical shifts in many biologically relevant systems, and the high accuracy may also help the refinement and determination of active-site structures of some oxygen-containing substrate-bound proteins.

  12. NMR studies on the chemical alteration of soil organic matter precursors during controlled charring

    NASA Astrophysics Data System (ADS)

    Knicker, Heike

    2010-05-01

    Beside the production of volatiles, vegetation fire transforms various amounts of labile organic components into recalcitrant dark colored and highly aromatic structures. They are incorporated into soils and are assumed to represent an important sink within the global carbon cycle. In order to elucidate the real importance of PyOM as a C-sink, a good understanding of its chemistry is crucial. Although several 'Black Carbon' (BC) models are reported, a commonly accepted view of the chemistry involved in its formation is still missing. Its biogeochemical recalcitrance is commonly associated with a highly condensed aromatic structure. However, recent studies indicated that this view may be oversimplified for PyOM derived from vegetation fire. In order to bring some more light on the structural properties of PyOM produced during vegetation fire, charred plant residues and model chars derived from typical plant macromolecules (casein, cellulose, lignin and condensed tannins) were subjected to controlled charring under oxic conditions (350°C and 450°C) and then characterized by nuclear magnetic resonance (NMR) spectroscopy and elemental analysis. Subsequently, the chemical features of the PyOM were related to its chemical recalcitrance as determined by chemical oxidation with acid potassium dichromate. Charring cellulose (350°C, 8 min) yielded in a low C-recovery (11%). Treating casein in the same way resulted in a survival of 62% of its C and 46% of its N. Comparable high C-recoveries are reported for lignin. After charring Lolium perenne, 34% of its N and C were recovered. NMR-spectroscopic studies revealed that for this sample most of the charred N and C occurred in pyrrole-type structures. Our studies further indicate that the aromatic skeleton of char accumulating after a vegetation fire must contain remains of the lignin backbone and considerable contributions of furans and anhydrosugars from thermally altered cellulose. Enhancing the temperature during the

  13. A NMR experiment for simultaneous correlations of valine and leucine/isoleucine methyls with carbonyl chemical shifts in proteins.

    PubMed

    Tugarinov, Vitali; Venditti, Vincenzo; Marius Clore, G

    2014-01-01

    A methyl-detected 'out-and-back' NMR experiment for obtaining simultaneous correlations of methyl resonances of valine and isoleucine/leucine residues with backbone carbonyl chemical shifts, SIM-HMCM(CGCBCA)CO, is described. The developed pulse-scheme serves the purpose of convenience in recording a single data set for all Ile(δ1), Leu(δ) and Val(γ) (ILV) methyl positions instead of acquiring two separate spectra selective for valine or leucine/isoleucine residues. The SIM-HMCM(CGCBCA)CO experiment can be used for ILV methyl assignments in moderately sized protein systems (up to ~100 kDa) where the backbone chemical shifts of (13)C(α), (13)Cβ and (13)CO are known from prior NMR studies and where some losses in sensitivity can be tolerated for the sake of an overall reduction in NMR acquisition time.

  14. Solid-state NMR studies of theophylline co-crystals with dicarboxylic acids.

    PubMed

    Pindelska, Edyta; Sokal, Agnieszka; Szeleszczuk, Lukasz; Pisklak, Dariusz Maciej; Kolodziejski, Waclaw

    2014-11-01

    In this work, three polycrystalline materials containing co-crystals of theophylline with malonic, maleic, and glutaric acids were studied using (13)C, (15)N and (1)H solid-state NMR and FT-IR spectroscopy. The NMR assignments were supported by gauge including projector augmented waves (GIPAW) calculations of chemical shielding, performed using X-ray determined geometry. The experimental (13)C cross polarization/magic angle spinning (CP/MAS) NMR results and the calculated isotropic chemical shifts were in excellent agreement. A rapid and convenient method for theophylline co-crystals crystal structure analysis has been proposed for co-crystals, which are potentially new APIs.

  15. Correction of erroneously packed protein's side chains in the NMR structure based on ab initio chemical shift calculations.

    PubMed

    Zhu, Tong; Zhang, John Z H; He, Xiao

    2014-09-14

    In this work, protein side chain (1)H chemical shifts are used as probes to detect and correct side-chain packing errors in protein's NMR structures through structural refinement. By applying the automated fragmentation quantum mechanics/molecular mechanics (AF-QM/MM) method for ab initio calculation of chemical shifts, incorrect side chain packing was detected in the NMR structures of the Pin1 WW domain. The NMR structure is then refined by using molecular dynamics simulation and the polarized protein-specific charge (PPC) model. The computationally refined structure of the Pin1 WW domain is in excellent agreement with the corresponding X-ray structure. In particular, the use of the PPC model yields a more accurate structure than that using the standard (nonpolarizable) force field. For comparison, some of the widely used empirical models for chemical shift calculations are unable to correctly describe the relationship between the particular proton chemical shift and protein structures. The AF-QM/MM method can be used as a powerful tool for protein NMR structure validation and structural flaw detection.

  16. 13C solid-state NMR chemical shift anisotropy analysis of the anomeric carbon in carbohydrates.

    PubMed

    Chen, Ying-Ying; Luo, Shun-Yuan; Hung, Shang-Cheng; Chan, Sunney I; Tzou, Der-Lii M

    2005-03-21

    (13)C NMR solid-state structural analysis of the anomeric center in carbohydrates was performed on six monosaccharides: glucose (Glc), mannose (Man), galactose (Gal), galactosamine hydrochloride (GalN), glucosamine hydrochloride (GlcN), and N-acetyl-glucosamine (GlcNAc). In the 1D (13)C cross-polarization/magic-angle spinning (CP/MAS) spectrum, the anomeric center C-1 of these carbohydrates revealed two well resolved resonances shifted by 3-5ppm, which were readily assigned to the anomeric alpha and beta forms. From this experiment, we also extracted the (13)C chemical shift anisotropy (CSA) tensor elements of the two forms from their spinning sideband intensities, respectively. It was found out that the chemical shift tensor for the alpha anomer was more axially symmetrical than that of the beta form. A strong linear correlation was obtained when the ratio of the axial asymmetry of the (13)C chemical shift tensors of the two anomeric forms was plotted in a semilogarithmic plot against the relative population of the two anomers. Finally, we applied REDOR spectroscopy to discern whether or not there were any differences in the sugar ring conformation between the anomers. Identical two-bond distances of 2.57A (2.48A) were deduced for both the alpha and beta forms in GlcNAc (GlcN), suggesting that the two anomers have essentially identical sugar ring scaffolds in these sugars. In light of these REDOR distance measurements and the strong correlation observed between the ratio of the axial asymmetry parameters of the (13)C chemical shift tensors and the relative population between the two anomeric forms, we concluded that the anomeric effect arises principally from interaction of the electron charge clouds between the C-1-O-5 and the C-1-O-1 bonds in these monosaccharides.

  17. Noninvasive measurements of glycogen in perfused mouse livers using chemical exchange saturation transfer NMR and comparison to (13)C NMR spectroscopy.

    PubMed

    Miller, Corin O; Cao, Jin; Chekmenev, Eduard Y; Damon, Bruce M; Cherrington, Alan D; Gore, John C

    2015-06-01

    Liver glycogen represents an important physiological form of energy storage. It plays a key role in the regulation of blood glucose concentrations, and dysregulations in hepatic glycogen metabolism are linked to many diseases including diabetes and insulin resistance. In this work, we develop, optimize, and validate a noninvasive protocol to measure glycogen levels in isolated perfused mouse livers using chemical exchange saturation transfer (CEST) NMR spectroscopy. Model glycogen solutions were used to determine optimal saturation pulse parameters which were then applied to intact perfused mouse livers of varying glycogen content. Glycogen measurements from serially acquired CEST Z-spectra of livers were compared with measurements from interleaved natural abundance (13)C NMR spectra. Experimental data revealed that CEST-based glycogen measurements were highly correlated with (13)C NMR glycogen spectra. Monte Carlo simulations were then used to investigate the inherent (i.e., signal-to-noise-based) errors in the quantification of glycogen with each technique. This revealed that CEST was intrinsically more precise than (13)C NMR, although in practice may be prone to other errors induced by variations in experimental conditions. We also observed that the CEST signal from glycogen in liver was significantly less than that observed from identical amounts in solution. Our results demonstrate that CEST provides an accurate, precise, and readily accessible method to noninvasively measure liver glycogen levels and their changes. Furthermore, this technique can be used to map glycogen distributions via conventional proton magnetic resonance imaging, a capability universally available on clinical and preclinical magnetic resonance imaging (MRI) scanners vs (13)C detection, which is limited to a small fraction of clinical-scale MRI scanners. PMID:25946616

  18. Noninvasive measurements of glycogen in perfused mouse livers using chemical exchange saturation transfer NMR and comparison to (13)C NMR spectroscopy.

    PubMed

    Miller, Corin O; Cao, Jin; Chekmenev, Eduard Y; Damon, Bruce M; Cherrington, Alan D; Gore, John C

    2015-06-01

    Liver glycogen represents an important physiological form of energy storage. It plays a key role in the regulation of blood glucose concentrations, and dysregulations in hepatic glycogen metabolism are linked to many diseases including diabetes and insulin resistance. In this work, we develop, optimize, and validate a noninvasive protocol to measure glycogen levels in isolated perfused mouse livers using chemical exchange saturation transfer (CEST) NMR spectroscopy. Model glycogen solutions were used to determine optimal saturation pulse parameters which were then applied to intact perfused mouse livers of varying glycogen content. Glycogen measurements from serially acquired CEST Z-spectra of livers were compared with measurements from interleaved natural abundance (13)C NMR spectra. Experimental data revealed that CEST-based glycogen measurements were highly correlated with (13)C NMR glycogen spectra. Monte Carlo simulations were then used to investigate the inherent (i.e., signal-to-noise-based) errors in the quantification of glycogen with each technique. This revealed that CEST was intrinsically more precise than (13)C NMR, although in practice may be prone to other errors induced by variations in experimental conditions. We also observed that the CEST signal from glycogen in liver was significantly less than that observed from identical amounts in solution. Our results demonstrate that CEST provides an accurate, precise, and readily accessible method to noninvasively measure liver glycogen levels and their changes. Furthermore, this technique can be used to map glycogen distributions via conventional proton magnetic resonance imaging, a capability universally available on clinical and preclinical magnetic resonance imaging (MRI) scanners vs (13)C detection, which is limited to a small fraction of clinical-scale MRI scanners.

  19. Cigarette butt decomposition and associated chemical changes assessed by 13C CPMAS NMR.

    PubMed

    Bonanomi, Giuliano; Incerti, Guido; Cesarano, Gaspare; Gaglione, Salvatore A; Lanzotti, Virginia

    2015-01-01

    Cigarette butts (CBs) are the most common type of litter on earth, with an estimated 4.5 trillion discarded annually. Apart from being unsightly, CBs pose a serious threat to living organisms and ecosystem health when discarded in the environment because they are toxic to microbes, insects, fish and mammals. In spite of the CB toxic hazard, no studies have addressed the effects of environmental conditions on CB decomposition rate. In this study we investigate the interactive effects of substrate fertility and N transfer dynamics on CB decomposition rate and carbon quality changes. We carried out an experiment using smoked CBs and wood sticks, used as a slow decomposing standard organic substrate, incubated in both laboratory and field conditions for two years. CB carbon quality changes during decomposition was assessed by 13C CPMAS NMR. Our experiment confirmed the low degradation rate of CBs which, on average, lost only 37.8% of their initial mass after two years of decomposition. Although a net N transfer occurred from soil to CBs, contrary to our hypothesis, mass loss in the medium-term (two years) was unaffected by N availability in the surrounding substrate. The opposite held for wood sticks, in agreement with the model that N-rich substrates promote the decomposition of other N-poor natural organic materials with a high C/N ratio. As regards CB chemical quality, after two years of decomposition 13C NMR spectroscopy highlighted very small changes in C quality that are likely to reflect a limited microbial attack.

  20. Cigarette Butt Decomposition and Associated Chemical Changes Assessed by 13C CPMAS NMR

    PubMed Central

    Bonanomi, Giuliano; Incerti, Guido; Cesarano, Gaspare; Gaglione, Salvatore A.; Lanzotti, Virginia

    2015-01-01

    Cigarette butts (CBs) are the most common type of litter on earth, with an estimated 4.5 trillion discarded annually. Apart from being unsightly, CBs pose a serious threat to living organisms and ecosystem health when discarded in the environment because they are toxic to microbes, insects, fish and mammals. In spite of the CB toxic hazard, no studies have addressed the effects of environmental conditions on CB decomposition rate. In this study we investigate the interactive effects of substrate fertility and N transfer dynamics on CB decomposition rate and carbon quality changes. We carried out an experiment using smoked CBs and wood sticks, used as a slow decomposing standard organic substrate, incubated in both laboratory and field conditions for two years. CB carbon quality changes during decomposition was assessed by 13C CPMAS NMR. Our experiment confirmed the low degradation rate of CBs which, on average, lost only 37.8% of their initial mass after two years of decomposition. Although a net N transfer occurred from soil to CBs, contrary to our hypothesis, mass loss in the medium-term (two years) was unaffected by N availability in the surrounding substrate. The opposite held for wood sticks, in agreement with the model that N-rich substrates promote the decomposition of other N-poor natural organic materials with a high C/N ratio. As regards CB chemical quality, after two years of decomposition 13C NMR spectroscopy highlighted very small changes in C quality that are likely to reflect a limited microbial attack. PMID:25625643

  1. Nuclei-selected NMR shielding calculations: a sublinear-scaling quantum-chemical method.

    PubMed

    Beer, Matthias; Kussmann, Jörg; Ochsenfeld, Christian

    2011-02-21

    An ab initio method for the direct calculation of NMR shieldings for selected nuclei at the Hartree-Fock and density-functional theory level is presented. Our method shows a computational effort scaling only sublinearly with molecular size, as it is motivated by the physical consideration that the chemical shielding is dominated by its local environment. The key feature of our method is to avoid the conventionally performed calculation of all NMR shieldings but instead to solve directly for specific nuclear shieldings. This has important implications not only for the study of large molecules, but also for the simulation of solvent effects and molecular dynamics, since often just a few shieldings are of interest. Our theory relies on two major aspects both necessary to provide a sublinear scaling behavior: First, an alternative expression for the shielding tensor is derived, which involves the response density matrix with respect to the nuclear magnetic moment instead of the response to the external magnetic field. Second, as unphysical long-range contributions occur within the description of distributed gauge origin methods that do not influence the final expectation value, we present a screening procedure to truncate the B-field dependent basis set, which is crucial in order to ensure an early onset of the sublinear scaling. The screening is in line with the r(-2) distance decay of Biot-Savarts law for induced magnetic fields. Our present truncation relies on the introduced concept of "individual gauge shielding contributions" applied to a reformulated shielding tensor, the latter consisting of gauge-invariant terms. The presented method is generally applicable and shows typical speed-ups of about one order of magnitude; moreover, due to the reduced scaling behavior of O(1) as compared to O(N), the wins become larger with increasing system size. We illustrate the validity of our method for several test systems, including ring-current dominated systems and

  2. Chemical curing in alkyd paints: an evaluation via FT-IR and NMR spectroscopies.

    PubMed

    Bartolozzi, G; Marchiafava, V; Mirabello, V; Peruzzini, M; Picollo, M

    2014-01-24

    A study aimed at determining the time necessary for an alkyd paint to attain chemical curing is presented. In particular, the object of our investigation was an oil paint made by Winsor & Newton, namely French ultramarine (PB29) in the Griffin Alkyd "fast drying oil colour" series. Using this paint, we prepared several mock-ups on glass. These were left in the laboratory at room temperature in a piece of furniture with glass doors for a total of 70 days. Samples were taken at different times, and the changes in their composition were monitored by means of FT-IR and multinuclear NMR spectroscopic analyses. Since the cross-linking reactions involved in the formation of the pictorial film mainly affect the amount of carbon-carbon double bonds, we monitored the decrease in allyl, diallyl and vinyl protons and carbons. The data obtained from the use of both techniques led us to conclude that, in our particular experimental conditions, the chemical curing of the paint layer is reached within the first 70 days, thus establishing the beginning of the ageing phenomena. PMID:24084480

  3. Chemical curing in alkyd paints: An evaluation via FT-IR and NMR spectroscopies

    NASA Astrophysics Data System (ADS)

    Bartolozzi, G.; Marchiafava, V.; Mirabello, V.; Peruzzini, M.; Picollo, M.

    2014-01-01

    A study aimed at determining the time necessary for an alkyd paint to attain chemical curing is presented. In particular, the object of our investigation was an oil paint made by Winsor & Newton, namely French ultramarine (PB29) in the Griffin Alkyd “fast drying oil colour” series. Using this paint, we prepared several mock-ups on glass. These were left in the laboratory at room temperature in a piece of furniture with glass doors for a total of 70 days. Samples were taken at different times, and the changes in their composition were monitored by means of FT-IR and multinuclear NMR spectroscopic analyses. Since the cross-linking reactions involved in the formation of the pictorial film mainly affect the amount of carbon-carbon double bonds, we monitored the decrease in allyl, diallyl and vinyl protons and carbons. The data obtained from the use of both techniques led us to conclude that, in our particular experimental conditions, the chemical curing of the paint layer is reached within the first 70 days, thus establishing the beginning of the ageing phenomena.

  4. 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.

  5. 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.

  6. 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}).

  7. 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.

  8. Bacterial spore detection and analysis using hyperpolarized 129Xe chemical exchange saturation transfer (Hyper-CEST) NMR

    PubMed Central

    Bai, Yubin; Wang, Yanfei; Goulian, Mark; Driks, Adam

    2014-01-01

    Previously, we reported hyperpolarized 129Xe chemical exchange saturation transfer (Hyper-CEST) NMR techniques for the ultrasensitive (i.e., 1 picomolar) detection of xenon host molecules known as cryptophane. Here, we demonstrate a more general role for Hyper-CEST NMR as a spectroscopic method for probing nanoporous structures, without the requirement for cryptophane or engineered xenon-binding sites. Hyper-CEST 129Xe NMR spectroscopy was employed to detect Bacillus anthracis and Bacillus subtilis spores in solution, and interrogate the layers that comprise their structures. 129Xe-spore samples were selectively irradiated with radiofrequency pulses; the depolarized 129Xe returned to aqueous solution and depleted the 129Xe-water signal, providing measurable contrast. Removal of the outermost spore layers in B. anthracis and B. subtilis (the exosporium and coat, respectively) enhanced 129Xe exchange with the spore interior. Notably, the spores were invisible to hyperpolarized 129Xe NMR direct detection methods, highlighting the lack of high-affinity xenon-binding sites, and the potential for extending Hyper-CEST NMR structural analysis to other biological and synthetic nanoporous structures. PMID:25089181

  9. Interactions of ionic liquids and acetone: thermodynamic properties, quantum-chemical calculations, and NMR analysis.

    PubMed

    Ruiz, Elia; Ferro, Victor R; Palomar, Jose; Ortega, Juan; Rodriguez, Juan Jose

    2013-06-20

    The interactions between ionic liquids (ILs) and acetone have been studied to obtain a further understanding of the behavior of their mixtures, which generally give place to an exothermic process, mutual miscibility, and negative deviation of Raoult's law. COSMO-RS was used as a suitable computational method to systematically analyze the excess enthalpy of IL-acetone systems (>300), in terms of the intermolecular interactions contributing to the mixture behavior. Spectroscopic and COSMO-RS results indicated that acetone, as a polar compound with strong hydrogen bond acceptor character, in most cases, establishes favorable hydrogen bonding with ILs. This interaction is strengthened by the presence of an acidic cation and an anion with dispersed charge and non-HB acceptor character in the IL. COSMO-RS predictions indicated that gas-liquid and vapor-liquid equilibrium data for IL-acetone systems can be finely tuned by the IL selection, that is, acting on the intermolecular interactions between the molecular and ionic species in the liquid phase. NMR measurements for IL-acetone mixtures at different concentrations were also carried out. Quantum-chemical calculations by using molecular clusters of acetone and IL species were finally performed. These results provided additional evidence of the main role played by hydrogen bonding in the behavior of systems containing ILs and HB acceptor compounds, such as acetone. PMID:23688030

  10. Temperature dependence of contact and dipolar NMR chemical shifts in paramagnetic molecules

    SciTech Connect

    Martin, Bob; Autschbach, Jochen

    2015-02-07

    Using a recently proposed equation for NMR nuclear magnetic shielding for molecules with unpaired electrons [A. Soncini and W. Van den Heuvel, J. Chem. Phys. 138, 021103 (2013)], equations for the temperature (T) dependent isotropic shielding for multiplets with an effective spin S equal to 1/2, 1, 3/2, 2, and 5/2 in terms of electron paramagnetic resonance spin Hamiltonian parameters are derived and then expanded in powers of 1/T. One simplifying assumption used is that a matrix derived from the zero-field splitting (ZFS) tensor and the Zeeman coupling matrix (g-tensor) share the same principal axis system. The influence of the rhombic ZFS parameter E is only investigated for S = 1. Expressions for paramagnetic contact shielding (from the isotropic part of the hyperfine coupling matrix) and pseudo-contact or dipolar shielding (from the anisotropic part of the hyperfine coupling matrix) are considered separately. The leading order is always 1/T. A temperature dependence of the contact shielding as 1/T and of the dipolar shielding as 1/T{sup 2}, which is sometimes assumed in the assignment of paramagnetic chemical shifts, is shown to arise only if S ≥ 1 and zero-field splitting is appreciable, and only if the Zeeman coupling matrix is nearly isotropic (Δg = 0). In such situations, an assignment of contact versus dipolar shifts may be possible based only on linear and quadratic fits of measured variable-temperature chemical shifts versus 1/T. Numerical data are provided for nickelocene (S = 1). Even under the assumption of Δg = 0, a different leading order of contact and dipolar shifts in powers of 1/T is not obtained for S = 3/2. When Δg is not very small, dipolar and contact shifts both depend in leading order in 1/T in all cases, with sizable contributions in order 1/T{sup n} with n = 2 and higher.

  11. Experimental Determination of pK[subscript a] Values by Use of NMR Chemical Shifts, Revisited

    ERIC Educational Resources Information Center

    Gift, Alan D.; Stewart, Sarah M.; Bokashanga, Patrick Kwete

    2012-01-01

    This laboratory experiment, using proton NMR spectroscopy to determine the dissociation constant for heterocyclic bases, has been modified from a previously described experiment. A solution of a substituted pyridine is prepared using deuterium oxide (D[subscript 2]O) as the solvent. The pH of the solution is adjusted and proton NMR spectra are…

  12. 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°.

  13. Cluster models and ab initio calculations of (19)F NMR isotropic chemical shifts for inorganic fluorides.

    PubMed

    Body, Monique; Silly, Gilles; Legein, Christophe; Buzaré, Jean-Yves

    2005-05-26

    (19)F NMR isotropic chemical shift (delta(iso)) calculations are performed in crystallized compounds using the GIAO method with the B3LYP hybrid functional at DFT level. Clusters centered on the studied fluorine atoms mimic the crystalline structures. The 6-311+G(d) basis set is chosen for the central fluorine atom, and the LanL2DZ basis set for the others. The metal atoms are described by the 3-21G(2d) basis set or, when not available, by the CRENBL basis set with the corresponding ECP, and augmented with 2d polarization functions when existing. First, for high-symmetry systems (MF, MF(2), and MF(3) compounds), a systematization of the cluster building up from coordination spheres is proposed, generalized to fluoroperovskites and fluoroaluminates KAlF(4) and RbAlF(4). When applied to rather low symmetry systems such as barium fluorometalates BaMgF(4), BaZnF(4), and Ba(2)ZnF(6), the definition of the coordination spheres is far from easy. Then, for structures built up from a MF(6) octahedron network, we may define different "starting clusters": [FM(2)F(8)] for the shared fluorine atoms, [FMF(4)] for the unshared ones, and [FBa(4)](7+) for the "free" ones. Analogous "starting clusters" are then tested on compounds from the NaF-AlF(3), BaF(2)-AlF(3), and CaF(2)-AlF(3) binary systems and for alpha-BaCaAlF(7) that are also built up from a MF(6) octahedron network. For each of these corresponding fluorine sites, delta(iso) values are calculated with the "starting clusters" and several larger clusters and compared to the experimental delta(iso) values. For the barium-containing clusters, the RMS deviation is equal to 51 ppm. It is suggested that this result may be related to the poor quality of the barium basis sets for which no polarization functions are available for the moment. In total, chemical shifts were calculated for 122 fluorine sites, in a various range of compounds. For the clusters without barium, the ab initio method leads to a RMS equal to 22 ppm, which is

  14. 6-Aminopenicillanic acid revisited: A combined solid state NMR and in silico refinement

    NASA Astrophysics Data System (ADS)

    Aguiar, Daniel Lima Marques de; San Gil, Rosane Aguiar da Silva; Alencastro, Ricardo Bicca de; Souza, Eugenio Furtado de; Borré, Leandro Bandeira; Vaiss, Viviane da Silva; Leitão, Alexandre Amaral

    2016-09-01

    13C/15N (experimental and ab initio) solid-state NMR was used to achieve an affordable way to improve hydrogen refinement of 6-aminopenicillanic acid (6-APA) structure. The lattice effect on the isotropic chemical shifts was probed by using two different magnetic shielding calculations: isolated molecules and periodic crystal structure. The electron density difference maps of optimized and non-optimized structures were calculated in order to investigate the interactions inside the 6-APA unit cell. The 13C and 15N chemical shifts assignments were unambiguously stablished. In addition, some of the literature 13C resonances ambiguities could be properly solved.

  15. Predicting paramagnetic 1H NMR chemical shifts and state-energy separations in spin-crossover host-guest systems.

    PubMed

    Isley, William C; Zarra, Salvatore; Carlson, Rebecca K; Bilbeisi, Rana A; Ronson, Tanya K; Nitschke, Jonathan R; Gagliardi, Laura; Cramer, Christopher J

    2014-06-14

    The behaviour of metal-organic cages upon guest encapsulation can be difficult to elucidate in solution. Paramagnetic metal centres introduce additional dispersion of signals that is useful for characterisation of host-guest complexes in solution using nuclear magnetic resonance (NMR). However, paramagnetic centres also complicate spectral assignment due to line broadening, signal integration error, and large changes in chemical shifts, which can be difficult to assign even for known compounds. Quantum chemical predictions can provide information that greatly facilitates the assignment of NMR signals and identification of species present. Here we explore how the prediction of paramagnetic NMR spectra may be used to gain insight into the spin crossover (SCO) properties of iron(II)-based metal organic coordination cages, specifically examining how the structure of the local metal coordination environment affects SCO. To represent the tetrahedral metal-organic cage, a model system is generated by considering an isolated metal-ion vertex: fac-ML3(2+) (M = Fe(II), Co(II); L = N-phenyl-2-pyridinaldimine). The sensitivity of the (1)H paramagnetic chemical shifts to local coordination environments is assessed and utilised to shed light on spin crossover behaviour in iron complexes. Our data indicate that expansion of the metal coordination sphere must precede any thermal SCO. An attempt to correlate experimental enthalpies of SCO with static properties of bound guests shows that no simple relationship exists, and that effects are likely due to nuanced dynamic response to encapsulation. PMID:24752730

  16. Structure, chemical bonding, and 45Sc solid state NMR of Sc 2RuSi 2

    NASA Astrophysics Data System (ADS)

    Harmening, Thomas; Al Alam, Adel; Matar, Samir F.; Eckert, Hellmut; Pöttgen, Rainer

    2009-07-01

    The silicide Sc 2RuSi 2 was synthesized from the elements by arc-melting. The structure was refined on the basis of single crystal X-ray diffractometer data: Zr 2CoSi 2 type, C2/ m, a = 1004.7 (2), b = 406.8 (1), c = 946.6 (2) pm, β = 117.95 (2), w R2 = 0.0230, 743 F2 values, and 32 variables. The structure consists of a rigid three-dimensional [RuSi 2] network in which the two crystallographically independent scandium atoms fill larger cages of coordination numbers 16 and 15, respectively. The [RuSi 2] network shows short Ru-Si distances (234-247 pm) and two different Si 2 pairs: Si1-Si1 at 247 and Si2-Si2 at 243 pm. Each silicon atom has trigonal prismatic Sc 6 (for Si2) or Sc 4Ru 2 (for Si1) coordination. These building units are condensed via common edges and faces. The various Sc-Sc distances between the prisms range from 327 to 361 pm. From electronic structure investigation within DFT, chemical bonding shows a major role of Ru-Si bonding and the presence of strong electron localization around Si-Si pairs pointing to a polyanionic silicide network [RuSi 2] δ-. The 45Sc MAS-NMR spectra recorded at 11.7 and 9.4 T clearly resolve the two distinct scandium sites. The large electric field gradients present at both scandium sites result in typical line shapes arising from second-order quadrupole perturbation effects.

  17. Determination of NMR chemical shifts for cholesterol crystals from first-principles

    NASA Astrophysics Data System (ADS)

    Kucukbenli, Emine; de Gironcoli, Stefano

    2011-03-01

    Solid State Nuclear Magnetic Resonance (NMR) is a powerful tool in crystallography when combined with theoretical predictions. So far, empirical calculations of spectra have been employed for an unambiguous identification. However, many complex systems are outside the scope of these methods. Our implementation of ultrasoft and projector augmented wave pseudopotentials within ab initio gauge including projector augmented plane wave (GIPAW) method in Quantum Espresso simulation package allows affordable calculations of NMR spectra for systems of thousands of electrons. We report here the first ab initio determination of NMR spectra for several crystal structures of cholesterol. Cholesterol crystals, the main component of human gallstones, are of interest to medical research as their structural properties can shed light on the pathologies of gallbladder. With our application we show that ab initio calculations can be employed to aid NMR crystallography.

  18. 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.

  19. Isotope-Labeled Amyloids via Synthesis, Expression, and Chemical Ligation for Use in FTIR, 2D IR, and NMR Studies.

    PubMed

    Zhang, Tianqi O; Grechko, Maksim; Moran, Sean D; Zanni, Martin T

    2016-01-01

    This chapter provides protocols for isotope-labeling the human islet amyloid polypeptide (hIAPP or amylin) involved in type II diabetes and γD-crystallin involved in cataract formation. Because isotope labeling improves the structural resolution, these protocols are useful for experiments using Fourier transform infrared (FTIR), two-dimensional infrared (2D IR), and NMR spectroscopies. Our research group specializes in using 2D IR spectroscopy and isotope labeling. 2D IR spectroscopy provides structural information by measuring solvation from 2D diagonal lineshapes and vibrational couplings from cross peaks. Infrared spectroscopy can be used to study kinetics, membrane proteins, and aggregated proteins. Isotope labeling provides greater certainty in the spectral assignment, which enables new structural insights that are difficult to obtain with other methods. For amylin, we provide a protocol for (13)C/(18)O labeling backbone carbonyls at one or more desired amino acids in order to obtain residue-specific structural resolution. We also provide a protocol for expressing and purifying amylin from E. coli, which enables uniform (13)C or (13)C/(15)N labeling. Uniform labeling is useful for measuring the monomer infrared spectrum in an amyloid oligomer or fiber as well as amyloid protein bound to another polypeptide or protein, such as a chaperone or an inhibitor. In addition, our expression protocol results in 2-2.5 mg of amylin peptide per 1 L cell culture, which is a high enough yield to straightforwardly obtain the 2-10 mg needed for high resolution and solid-state NMR experiments. Finally, we provide a protocol to isotope-label either of the two domains of γD-crystallin using expressed protein ligation. Domain labeling makes it possible to resolve the structures of the two halves of the protein in FTIR and 2D IR spectra. With modifications, these strategies and protocols for isotope labeling can be applied to other amyloid polypeptides and proteins.

  20. Handling the influence of chemical shift in amplitude-modulated heteronuclear dipolar recoupling solid-state NMR.

    PubMed

    Basse, Kristoffer; Shankar, Ravi; Bjerring, Morten; Vosegaard, Thomas; Nielsen, Niels Chr; Nielsen, Anders B

    2016-09-01

    We present a theoretical analysis of the influence of chemical shifts on amplitude-modulated heteronuclear dipolar recoupling experiments in solid-state NMR spectroscopy. The method is demonstrated using the Rotor Echo Short Pulse IRrAdiaTION mediated Cross-Polarization ((RESPIRATION)CP) experiment as an example. By going into the pulse sequence rf interaction frame and employing a quintuple-mode operator-based Floquet approach, we describe how chemical shift offset and anisotropic chemical shift affect the efficiency of heteronuclear polarization transfer. In this description, it becomes transparent that the main attribute leading to non-ideal performance is a fictitious field along the rf field axis, which is generated from second-order cross terms arising mainly between chemical shift tensors and themselves. This insight is useful for the development of improved recoupling experiments. We discuss the validity of this approach and present quaternion calculations to determine the effective resonance conditions in a combined rf field and chemical shift offset interaction frame transformation. Based on this, we derive a broad-banded version of the (RESPIRATION)CP experiment. The new sequence is experimentally verified using SNNFGAILSS amyloid fibrils where simultaneous (15)N → (13)CO and (15)N → (13)Cα coherence transfer is demonstrated on high-field NMR instrumentation, requiring great offset stability. PMID:27608995

  1. Weak Intermolecular Hydrogen Bonds with Fluorine: Detection and Implications for Enzymatic/Chemical Reactions, Chemical Properties, and Ligand/Protein Fluorine NMR Screening.

    PubMed

    Dalvit, Claudio; Vulpetti, Anna

    2016-05-23

    It is known that strong hydrogen-bonding interactions play an important role in many chemical and biological systems. However, weak or very weak hydrogen bonds, which are often difficult to detect and characterize, may also be relevant in many recognition and reaction processes. Fluorine serving as a hydrogen-bond acceptor has been the subject of many controversial discussions and there are different opinions about it. It now appears that there is compelling experimental evidence for the involvement of fluorine in weak intramolecular or intermolecular hydrogen bonds. Using established NMR methods, we have previously characterized and measured the strengths of intermolecular hydrogen-bond complexes involving the fluorine moieties CH2 F, CHF2 , and CF3 , and have compared them with the well-known hydrogen-bond complex formed between acetophenone and the strong hydrogen-bond donor p-fluorophenol. We now report evidence for the formation of hydrogen bonds involving fluorine with significantly weaker donors, namely 5-fluoroindole and water. A simple NMR method is proposed for the simultaneous measurement of the strengths of hydrogen bonds between an acceptor and a donor or water. Important implications of these results for enzymatic/chemical reactions involving fluorine, for chemical and physical properties, and for ligand/protein (19) F NMR screening are analyzed through experiments and theoretical simulations.

  2. Characterization of the conformational equilibrium between the two major substates of RNase A using NMR chemical shifts.

    PubMed

    Camilloni, Carlo; Robustelli, Paul; De Simone, Alfonso; Cavalli, Andrea; Vendruscolo, Michele

    2012-03-01

    Following the recognition that NMR chemical shifts can be used for protein structure determination, rapid advances have recently been made in methods for extending this strategy for proteins and protein complexes of increasing size and complexity. A remaining major challenge is to develop approaches to exploit the information contained in the chemical shifts about conformational fluctuations in native states of proteins. In this work we show that it is possible to determine an ensemble of conformations representing the free energy surface of RNase A using chemical shifts as replica-averaged restraints in molecular dynamics simulations. Analysis of this surface indicates that chemical shifts can be used to characterize the conformational equilibrium between the two major substates of this protein.

  3. 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.

  4. The use of IRMS, (1)H NMR and chemical analysis to characterise Italian and imported Tunisian olive oils.

    PubMed

    Camin, Federica; Pavone, Anita; Bontempo, Luana; Wehrens, Ron; Paolini, Mauro; Faberi, Angelo; Marianella, Rosa Maria; Capitani, Donatella; Vista, Silvia; Mannina, Luisa

    2016-04-01

    Isotope Ratio Mass Spectrometry (IRMS), (1)H Nuclear Magnetic Resonance ((1)H NMR), conventional chemical analysis and chemometric elaboration were used to assess quality and to define and confirm the geographical origin of 177 Italian PDO (Protected Denomination of Origin) olive oils and 86 samples imported from Tunisia. Italian olive oils were richer in squalene and unsaturated fatty acids, whereas Tunisian olive oils showed higher δ(18)O, δ(2)H, linoleic acid, saturated fatty acids β-sitosterol, sn-1 and 3 diglyceride values. Furthermore, all the Tunisian samples imported were of poor quality, with a K232 and/or acidity values above the limits established for extra virgin olive oils. By combining isotopic composition with (1)H NMR data using a multivariate statistical approach, a statistical model able to discriminate olive oil from Italy and those imported from Tunisia was obtained, with an optimal differentiation ability arriving at around 98%.

  5. Solid-state NMR heteronuclear coherence transfer using phase and amplitude modulated rf irradiation at the Hartmann Hahn sideband conditions

    NASA Astrophysics Data System (ADS)

    Bjerring, Morten; Nielsen, Niels Chr.

    2003-12-01

    An improved variant of the popular double cross-polarization (DCP) experiment for heteronuclear dipolar recoupling in solid-state NMR spectroscopy under magic-angle-spinning is introduced. By simple phase and amplitude modulation of the rf irradiation at the Hartman-Hahn sideband conditions, the new pulse sequence, dubbed iDCP, enables broadband excitation with the high efficiency of γ-encoded coherence transfer. The efficiency and robustness of iDCP toward isotropic chemical shift variations and chemical shift anisotropies, in the order typically applying for the backbone atoms in uniformly 13C, 15N-labeled proteins, is demonstrated numerically and experimentally by 15N to 13C coherence transfer for 15N-labeled N-Ac- L-valyl- L-leucine and 13C, 15N-labeled- L-threonine.

  6. Carbon-13 chemical-shift tensors in indigo: A two-dimensional NMR-ROCSA and DFT Study.

    PubMed

    Holmes, Sean T; Dybowski, Cecil

    2015-11-01

    The principal components of the (13)C NMR chemical-shift tensors for the eight unique carbon sites of crystalline indigo have been measured using the ROCSA pulse sequence. The chemical shifts have been assigned unambiguously to their respective nuclear sites through comparison of the experimental data to the results of density-functional calculations employing a refined X-ray diffraction structure. These measurements expand the database of measured aromatic (13)C chemical-shift tensors to the indole ring. Magnetic shielding calculations for hypoxanthine and adenosine are also reported. Comparisons of calculations that include the effect of the crystalline lattice with calculations that model indigo as an isolated molecule give an estimate of the intermolecular contribution to the magnetic shielding.

  7. Carbon-13 chemical-shift tensors in indigo: A two-dimensional NMR-ROCSA and DFT Study

    PubMed Central

    Holmes, Sean T.; Dybowski, Cecil

    2016-01-01

    The principal components of the 13C NMR chemical-shift tensors for the eight unique carbon sites of crystalline indigo have been measured using the ROCSA pulse sequence. The chemical shifts have been assigned unambiguously to their respective nuclear sites through comparison of the experimental data to the results of density-functional calculations employing a refined X-ray diffraction structure. These measurements expand the database of measured aromatic 13C chemical-shift tensors to the indole ring. Magnetic shielding calculations for hypoxanthine and adenosine are also reported. Comparisons of calculations that include the effect of the crystalline lattice with calculations that model indigo as an isolated molecule give an estimate of the intermolecular contribution to the magnetic shielding. PMID:26344134

  8. Explaining the effects of T-O-T bond angles on NMR chemical shifts in aluminosilicates: A natural bonding orbital (NBO) and natural chemical shielding (NCS) analysis.

    PubMed

    Liu, Yun; Nekvasil, Hanna; Tossell, John

    2005-04-01

    It has long been recognized that the 29Si and 27Al NMR chemical shifts for aluminosilicate crystals and glasses correlate to some extent with the T-O-T bond angle (where T is the tetrahedral atom Si or Al). With increasing T-O-T bond angle, the 29Si and 27Al NMR shieldings increase and the shifts thus become more negative. This result has been demonstrated both experimentally and through quantum computations. However, no simple qualitative explanation has ever been given for what appears to be a simple qualitative trend. We here provide such an explanation based upon quantum calculations. We have used high level ab initio NMR shielding calculations, natural bonding orbital (NBO) analysis, and natural chemical shielding (NCS) analysis, performed on model clusters with different T-O-T angles, to obtain an explanation for this trend from an electronic structure point of view. On the basis of both NBO populations and the NCS analysis, the following factors account for the correlation of shift with T-O-T angle: (1) a slight increase in population of the Al-O and Si-O bond orbital electrons and a dramatic change in bond orbital shapes and hybridization (with more s character and less bond bending as the T-O-T angle increases), (2) a movement of one of the lone pairs on O toward the vicinity of the Si or Al as the T-O-T angle increases, and (3) a change in the shielding contribution from the core 2p electrons of Al or Si. The changes in the 17O NMR shift with T-O-T angle are more complex, and the shifts are also more strongly influenced by distant atoms, but some systematic changes in O lone pair contributions can be identified.

  9. Chemical structures of manure from conventional and phytase transgenic pigs investigated by advanced solid-state NMR spectroscopy.

    PubMed

    Mao, Jingdong; Ajakaiye, Ayodele; Lan, Yeqing; Olk, Dan C; Ceballos, Michael; Zhang, Tiequan; Fan, Ming Z; Forsberg, Cecil W

    2008-03-26

    Nonpoint phosphorus (P) pollution from animal manure is becoming a serious global problem. The current solution for the swine industry includes the enzyme phytase as a component in oil meal and cereal grain-based swine diets. A long-term approach is the production of transgenic phytase pigs that express phytase in the salivary glands and secrete it in the saliva. This study provides a detailed comparison of chemical structures of manure from conventional pigs and transgenic pigs that express phytase under growing and finishing phases using new solid-state NMR techniques. Spectral editing techniques and quantitative NMR techniques were used to identify and quantify specific functional groups. Two-dimensional (1)H- (13)C heteronuclear correlation NMR was used to detect their connectivity. Manure from conventional and transgenic pigs had similar peptide, carbohydrate, and fatty acid components, while those from transgenic pigs contained more carbohydrates and fewer nonpolar alkyls. There was no consistent effect from diets with or without supplemental phosphate or growth stages. PMID:17973446

  10. Accurate ab initio prediction of NMR chemical shifts of nucleic acids and nucleic acids/protein complexes

    PubMed Central

    Victora, Andrea; Möller, Heiko M.; Exner, Thomas E.

    2014-01-01

    NMR chemical shift predictions based on empirical methods are nowadays indispensable tools during resonance assignment and 3D structure calculation of proteins. However, owing to the very limited statistical data basis, such methods are still in their infancy in the field of nucleic acids, especially when non-canonical structures and nucleic acid complexes are considered. Here, we present an ab initio approach for predicting proton chemical shifts of arbitrary nucleic acid structures based on state-of-the-art fragment-based quantum chemical calculations. We tested our prediction method on a diverse set of nucleic acid structures including double-stranded DNA, hairpins, DNA/protein complexes and chemically-modified DNA. Overall, our quantum chemical calculations yield highly/very accurate predictions with mean absolute deviations of 0.3–0.6 ppm and correlation coefficients (r2) usually above 0.9. This will allow for identifying misassignments and validating 3D structures. Furthermore, our calculations reveal that chemical shifts of protons involved in hydrogen bonding are predicted significantly less accurately. This is in part caused by insufficient inclusion of solvation effects. However, it also points toward shortcomings of current force fields used for structure determination of nucleic acids. Our quantum chemical calculations could therefore provide input for force field optimization. PMID:25404135

  11. 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.

  12. A multiple pulse zero crossing NMR technique, and its application to F-19 chemical shift measurements in solids

    NASA Technical Reports Server (NTRS)

    Burum, D. P.; Elleman, D. D.; Rhim, W.-K.

    1978-01-01

    A simple multiple-pulse 'zero crossing technique' for accurately determining the first moment of a solid-state NMR spectrum is introduced. This technique was applied to obtain the F-19 chemical shift versus pressure curves up to 5 kbar for single crystals of CaF2 (0.29 + or - 0.02 ppm/kbar) and BaF2 (0.62 + or - 0.05 ppm/kbar). Results at ambient temperature and pressure are also reported for a number of other fluorine compounds. Because of its high data rate, this technique is potentially several orders of magnitude more sensitive than similar CW methods.

  13. Pyrolysis temperature affects phosphorus transformation in biochar: Chemical fractionation and (31)P NMR analysis.

    PubMed

    Xu, Gang; Zhang, You; Shao, Hongbo; Sun, Junna

    2016-11-01

    Phosphorus (P) recycling or reuse by pyrolyzing crop residue has recently elicited increased research interest. However, the effects of feedstock and pyrolysis conditions on P species have not been fully understood. Such knowledge is important in identifying the agronomic and environmental uses of biochar. Residues of three main Chinese agricultural crops and the biochars (produced at 300°C-600°C) derived from these crops were used to determine P transformations during pyrolysis. Hedley sequential fractionation and (31)P NMR analyses were used in the investigation. Our results showed that P transformation in biochar was significantly affected by pyrolysis temperature regardless of feedstock (Wheat straw, maize straw and peanut husk). Pyrolysis treatment transformed water soluble P into a labile (NaHCO3-Pi) or semi-labile pool (NaOH-Pi) and into a stable pool (Dil. HCl P and residual-P). At the same time, organic P was transformed into inorganic P fractions which was identified by the rapid decomposition of organic P detected with solution (31)P NMR. The P transformation during pyrolysis process suggested more stable P was formed at a higher pyrolysis temperature. This result was also evidenced by the presence of less soluble or stable P species, such as such as poly-P, crandallite (CaAl3(OH)5(PO4)2) and Wavellite (Al3(OH)3(PO4)2·5H2O), as detected by solid-state (31)P NMR in biochars formed at a higher pyrolysis temperature. Furthermore, a significant proportion of less soluble pyrophosphate was identified by solution (2%-35%) and solid-state (8%-53%) (31)P NMR, which was also responsible for the stable P forms at higher pyrolysis temperature although their solubility or stability requires further investigation. Results suggested that a relatively lower pyrolysis temperature retains P availability regardless of feedstock during pyrolysis process.

  14. Chemical tagging of chlorinated phenols for their facile detection and analysis by NMR spectroscopy

    SciTech Connect

    Valdez, Carlos A.; Leif, Roald N.

    2015-03-22

    A derivatization method that employs diethyl (bromodifluoromethyl) phosphonate (DBDFP) to efficiently tag the endocrine disruptor pentachlorophenol (PCP) and other chlorinated phenols (CPs) along with their reliable detection and analysis by NMR is presented. The method accomplishes the efficient alkylation of the hydroxyl group in CPs with the difluoromethyl (CF2H) moiety in extremely rapid fashion (5 min), at room temperature and in an environmentally benign manner. The approach proved successful in difluoromethylating a panel of 18 chlorinated phenols, yielding derivatives that displayed unique 1H, 19F NMR spectra allowing for the clear discrimination between isomerically related CPs. Due to its biphasic nature, the derivatization can be applied to both aqueous and organic mixtures where the analysis of CPs is required. Furthermore, the methodology demonstrates that PCP along with other CPs can be selectively derivatized in the presence of other various aliphatic alcohols, underscoring the superiority of the approach over other general derivatization methods that indiscriminately modify all analytes in a given sample. The present work demonstrates the first application of NMR on the qualitative analysis of these highly toxic and environmentally persistent species.

  15. Carbon-13 NMR in conformational analysis of nucleic acid fragments. Heteronuclear chemical shift correlation spectroscopy of RNA constituents.

    PubMed Central

    Lankhorst, P P; Erkelens, C; Haasnoot, C A; Altona, C

    1983-01-01

    The assignment of the non-quaternary 13C resonances by means of two-dimensional heteronuclear chemical shift correlation spectroscopy is presented for several oligoribonucleotides: The dimers m6(2)AU, m6(2)Am6(2)A and mpUm6(2)A and the trimers m6(2)AUm6(2)A and m4(2)Cm4(2)Cm6(2)A. The temperature and concentration dependency of the 13C chemical shifts are studied with emphasis on the behaviour of the dimer m6(2)AU. The present study shows that in the 5-50 mM range the concentration-dependent chemical shift changes of the ribose carbons are negligible compared to chemical shift changes due to intramolecular events. All compounds studied show a surprising correlation between the chemical shifts of the carbon atoms of the ribose ring and the sugar conformational equilibrium as expressed by the percentage N or S conformer. Thus the chemical shift data can be used to obtain the thermodynamical parameters of the two-state N/S equilibrium. Parameters deduced for m6(2)AU are Tm = 306 K and delta S = -25 cal mol-1 K-1, which values are in satisfactory agreement with results obtained earlier from 1H NMR and from Circular Dichroism. PMID:6195595

  16. N-15 NMR study of the immobilization of 2,4- and 2,6-dinitrotoluene in aerobic compost

    USGS Publications Warehouse

    Thorn, K.A.; Pennington, J.C.; Kennedy, K.R.; Cox, L.G.; Hayes, C.A.; Porter, B.E.

    2008-01-01

    Large-scale aerobic windrow composting has been used to bioremediate washout lagoon soils contaminated with the explosives TNT (2,4,6- trinitrotoluene) and RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine) at several sites within the United States. We previously used 15N NMR to investigate the reduction and binding of T15NT in aerobic bench -scale reactors simulating the conditions of windrow composting. These studies have been extended to 2,4-dinitrotoluene (2,4DNT) and 2,6-dinitrotoluene (2,6DNT), which, as impurities in TNT, are usually present wherever soils have been contaminated with TNT. Liquid-state 15N NMR analyses of laboratory reactions between 4-methyl-3-nitroaniline-15N, the major monoamine reduction product of 2,4DNT, and the Elliot soil humic acid, both in the presence and absence of horseradish peroxidase, indicated that the amine underwent covalent binding with quinone and other carbonyl groups in the soil humic acid to form both heterocyclic and non-heterocyclic condensation products. Liquid-state 15N NMR analyses of the methanol extracts of 20 day aerobic bench-scale composts of 2,4-di-15N-nitrotoluene and 2,6-di-15N-nitrotoluene revealed the presence of nitrite and monoamine, but not diamine, reduction products, indicating the occurrence of both dioxygenase enzyme and reductive degradation pathways. Solid-state CP/MAS 15N NMR analyses of the whole composts, however, suggested that reduction to monoamines followed by covalent binding of the amines to organic matter was the predominant pathway. ?? 2008 American Chemical Society.

  17. 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

  18. 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.

  19. Fungal Functioning In A Pine Forest: Evidence From A 15N-Labeled Global Change Experiment

    NASA Astrophysics Data System (ADS)

    Hobbie, E. A.; Hofmockel, K.; van Diepen, L.

    2012-12-01

    In this study, we used tracer 15N labeling and a concurrent six-year nitrogen fertilization experiment in a Pinus taeda Free Air CO2 Enrichment (FACE) experiment to investigate the functioning of saprotrophic and ectomycorrhizal fungi in nitrogen cycling. Ectomycorrhizal fungi with hydrophobic ectomycorrhizae acquired nitrogen from deeper in the soil profile than taxa with hydrophilic ectomycorrhizae, whereas saprotrophic fungi acquired nitrogen primarily from relatively recent surface litter. By combining natural abundance and tracer measurements, we estimated the 15N enrichment of fungi relative to source nitrogen at between 4‰ and 9‰, depending on genus, with some genera sampling pools more 15N-enriched in the labeling experiment than could be measured by bulk analyses. Thus, biologically relevant nitrogen fractions may correspond poorly to what can be extracted chemically. The multiple 15N labels in this FACE experiment proved useful for tracking nitrogen into different fungal taxa from potential nitrogen sources.

  20. (31)P Solid-State NMR study of the chemical setting process of a dual-paste injectable brushite cements.

    PubMed

    Legrand, A P; Sfihi, H; Lequeux, N; Lemaître, J

    2009-10-01

    The composition and evolution of a brushite-type calcium phosphate cement was investigated by Solid-State NMR and X-ray during the setting process. The cement is obtained by mixing beta-tricalcium phosphate [Ca(3)(PO(4))(2), beta-TCP] and monocalcium phosphate monohydrate [Ca(H(2)PO(4))(2).H(2)O, MCPM] in presence of water, with formation of dicalcium phosphate dihydrate or brushite [CaHPO(2).2H(2)O, DCPD]. Analysis of the initial beta-TCP paste has shown the presence of beta-calcium pyrophosphate [Ca(2)P(2)O(7), beta-CPy] and that of the initial MCPM a mixture of MCPM and dicalcium phosphate [CaHPO(4), DCP]. Follow-up of the chemical composition by (31)P Solid-State NMR enables to show that the chemical setting process appeared to reach an end after 20 min. The constant composition observed at the end of the process was similarly determined.

  1. 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.

  2. 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.

  3. Intermolecular Interactions in Crystalline Theobromine as Reflected in Electron Deformation Density and (13)C NMR Chemical Shift Tensors.

    PubMed

    Bouzková, Kateřina; Babinský, Martin; Novosadová, Lucie; Marek, Radek

    2013-06-11

    An understanding of the role of intermolecular interactions in crystal formation is essential to control the generation of diverse crystalline forms which is an important concern for pharmaceutical industry. Very recently, we reported a new approach to interpret the relationships between intermolecular hydrogen bonding, redistribution of electron density in the system, and NMR chemical shifts (Babinský et al. J. Phys. Chem. A, 2013, 117, 497). Here, we employ this approach to characterize a full set of crystal interactions in a sample of anhydrous theobromine as reflected in (13)C NMR chemical shift tensors (CSTs). The important intermolecular contacts are identified by comparing the DFT-calculated NMR CSTs for an isolated theobromine molecule and for clusters composed of several molecules as selected from the available X-ray diffraction data. Furthermore, electron deformation density (EDD) and shielding deformation density (SDD) in the proximity of the nuclei involved in the proposed interactions are calculated and visualized. In addition to the recently reported observations for hydrogen bonding, we focus here particularly on the stacking interactions. Although the principal relations between the EDD and CST for hydrogen bonding (HB) and stacking interactions are similar, the real-space consequences are rather different. Whereas the C-H···X hydrogen bonding influences predominantly and significantly the in-plane principal component of the (13)C CST perpendicular to the HB path and the C═O···H hydrogen bonding modulates both in-plane components of the carbonyl (13)C CST, the stacking modulates the out-of-plane electron density resulting in weak deshielding (2-8 ppm) of both in-plane principal components of the CST and weak shielding (∼ 5 ppm) of the out-of-plane component. The hydrogen-bonding and stacking interactions may add to or subtract from one another to produce total values observed experimentally. On the example of theobromine, we demonstrate

  4. Nitrogen cycling in an extreme hyperarid environment inferred from δ(15)N analyses of plants, soils and herbivore diet.

    PubMed

    Díaz, Francisca P; Frugone, Matías; Gutiérrez, Rodrigo A; Latorre, Claudio

    2016-01-01

    Climate controls on the nitrogen cycle are suggested by the negative correlation between precipitation and δ(15)N values across different ecosystems. For arid ecosystems this is unclear, as water limitation among other factors can confound this relationship. We measured herbivore feces, foliar and soil δ(15)N and δ(13)C values and chemically characterized soils (pH and elemental composition) along an elevational/climatic gradient in the Atacama Desert, northern Chile. Although very positive δ(15)N values span the entire gradient, soil δ(15)N values show a positive correlation with aridity as expected. In contrast, foliar δ(15)N values and herbivore feces show a hump-shaped relationship with elevation, suggesting that plants are using a different N source, possibly of biotic origin. Thus at the extreme limits of plant life, biotic interactions may be just as important as abiotic processes, such as climate in explaining ecosystem δ(15)N values. PMID:26956399

  5. Nitrogen cycling in an extreme hyperarid environment inferred from δ15N analyses of plants, soils and herbivore diet

    NASA Astrophysics Data System (ADS)

    Díaz, Francisca P.; Frugone, Matías; Gutiérrez, Rodrigo A.; Latorre, Claudio

    2016-03-01

    Climate controls on the nitrogen cycle are suggested by the negative correlation between precipitation and δ15N values across different ecosystems. For arid ecosystems this is unclear, as water limitation among other factors can confound this relationship. We measured herbivore feces, foliar and soil δ15N and δ13C values and chemically characterized soils (pH and elemental composition) along an elevational/climatic gradient in the Atacama Desert, northern Chile. Although very positive δ15N values span the entire gradient, soil δ15N values show a positive correlation with aridity as expected. In contrast, foliar δ15N values and herbivore feces show a hump-shaped relationship with elevation, suggesting that plants are using a different N source, possibly of biotic origin. Thus at the extreme limits of plant life, biotic interactions may be just as important as abiotic processes, such as climate in explaining ecosystem δ15N values.

  6. Nitrogen cycling in an extreme hyperarid environment inferred from δ15N analyses of plants, soils and herbivore diet

    PubMed Central

    Díaz, Francisca P.; Frugone, Matías; Gutiérrez, Rodrigo A.; Latorre, Claudio

    2016-01-01

    Climate controls on the nitrogen cycle are suggested by the negative correlation between precipitation and δ15N values across different ecosystems. For arid ecosystems this is unclear, as water limitation among other factors can confound this relationship. We measured herbivore feces, foliar and soil δ15N and δ13C values and chemically characterized soils (pH and elemental composition) along an elevational/climatic gradient in the Atacama Desert, northern Chile. Although very positive δ15N values span the entire gradient, soil δ15N values show a positive correlation with aridity as expected. In contrast, foliar δ15N values and herbivore feces show a hump-shaped relationship with elevation, suggesting that plants are using a different N source, possibly of biotic origin. Thus at the extreme limits of plant life, biotic interactions may be just as important as abiotic processes, such as climate in explaining ecosystem δ15N values. PMID:26956399

  7. Chemical Composition and Seasonality of Aromatic Mediterranean Plant Species by NMR-Based Metabolomics

    PubMed Central

    Scognamiglio, Monica; D'Abrosca, Brigida; Esposito, Assunta; Fiorentino, Antonio

    2015-01-01

    An NMR-based metabolomic approach has been applied to analyse seven aromatic Mediterranean plant species used in traditional cuisine. Based on the ethnobotanical use of these plants, the approach has been employed in order to study the metabolic changes during different seasons. Primary and secondary metabolites have been detected and quantified. Flavonoids (apigenin, quercetin, and kaempferol derivatives) and phenylpropanoid derivatives (e.g., chlorogenic and rosmarinic acid) are the main identified polyphenols. The richness in these metabolites could explain the biological properties ascribed to these plant species. PMID:25785229

  8. J-GFT NMR for precise measurement of mutually correlated nuclear spin-spin couplings.

    PubMed

    Atreya, Hanudatta S; Garcia, Erwin; Shen, Yang; Szyperski, Thomas

    2007-01-24

    G-matrix Fourier transform (GFT) NMR spectroscopy is presented for accurate and precise measurement of chemical shifts and nuclear spin-spin couplings correlated according to spin system. The new approach, named "J-GFT NMR", is based on a largely extended GFT NMR formalism and promises to have a broad impact on projection NMR spectroscopy. Specifically, constant-time J-GFT (6,2)D (HA-CA-CO)-N-HN was implemented for simultaneous measurement of five mutually correlated NMR parameters, that is, 15N backbone chemical shifts and the four one-bond spin-spin couplings 13Calpha-1Halpha, 13Calpha-13C', 15N-13C', and 15N-1HNu. The experiment was applied for measuring residual dipolar couplings (RDCs) in an 8 kDa protein Z-domain aligned with Pf1 phages. Comparison with RDC values extracted from conventional NMR experiments reveals that RDCs are measured with high precision and accuracy, which is attributable to the facts that (i) the use of constant time evolution ensures that signals do not broaden whenever multiple RDCs are jointly measured in a single dimension and (ii) RDCs are multiply encoded in the multiplets arising from the joint sampling. This corresponds to measuring the couplings multiple times in a statistically independent manner. A key feature of J-GFT NMR, i.e., the correlation of couplings according to spin systems without reference to sequential resonance assignments, promises to be particularly valuable for rapid identification of backbone conformation and classification of protein fold families on the basis of statistical analysis of dipolar couplings.

  9. 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.

  10. Comparison of the computational NMR chemical shifts of choline with the experimental data

    NASA Astrophysics Data System (ADS)

    Alcorn, C.; Cuperlovic-Culf, M.; Ghandi, K.

    2012-02-01

    One of the main biological markers of the presence of cancer in living patients is an over-expression of total choline (tCho), which is the sum of free choline and its derivatives. 1H Magnetic Resonance Spectroscopy, or H-MRS, enables the quantification of tCho via its proton spectra, and thus has the potential to be a diagnostic tool for the presence of cancer and an accurate early indicator of the response of cancer to treatment. However, it remains difficult to quantify individual choline derivatives, since they share a large structural similarity ((CH3)3-N+-CH2-CH2-O-), of which the strongest signal detectable by MRS is that of the choline "head group": the three methyl groups bonded to the nitrogen. This work used ACENet, a high performance computing system, to attempt to model the NMR parameters of choline derivatives, with the focus of this report being free choline. Optimized structures were determined using Density Functional Theory and the B3LYP electron correlation functional. The Polarizable Continuum Model was used to evaluate solvent effects. The Gauge-Invariant Atomic Orbital method was found to be the superior method for calculating the NMR parameters of cholines.

  11. High-performance liquid chromatographic separation of natural and synthetic desulphoglucosinolates and their chemical validation by UV, NMR and chemical ionisation-MS methods.

    PubMed

    Kiddle, G; Bennett, R N; Botting, N P; Davidson, N E; Robertson, A A; Wallsgrove, R M

    2001-01-01

    Methods are described for the optimised extraction, desulphation and HPLC separation of desulphoglucosinolates. These methods provide rapid separation, identification and quantitative measurements of glucosinolates extracted from Brassica napus L and related crops, of unusual glucosinolates found in crucifer weed species, and also of synthetic alkylglucosinolates. The desulphoglucosinolates used in these studies were either chemically synthesised (at least one example from each major structural class), or purified from various plant sources. Validation of the identities of the desulphoglucosinolates was by comparison of retention times with standards, and by UV, 1H- and 13C-NMR and chemical ionisation MS analysis. A list of useful species, and the specific tissues, from which high concentrations of standards can be extracted is included. PMID:11705329

  12. Aliphatic β-nitroalcohols for therapeutic corneoscleral cross-linking: chemical stability studies using 1H-NMR spectroscopy†

    PubMed Central

    Li, Xia; Li, Yongjun; Kim, MiJung; Trokel, Stephen L.; Turro, Nicholas J.; Paik, David C.

    2013-01-01

    Recent studies suggest that aliphatic β-nitro alcohols (BNAs) may represent a useful class of compounds for use as in vivo therapeutic corneoscleral cross-linking agents with higher order nitroalcohols (HONAs) showing enhanced efficacy over the mono-nitroalcohols. The current study was undertaken in order to evaluate the chemical stability of these compounds during storage conditions. Two mono-nitroalcohols (2-nitroethanol=2ne and 2-nitro-1-propanol=2nprop) and two HONAs, a nitrodiol (2-methyl-2-nitro-1,3-propanediol=MNPD), and a nitrotriol (2-hydroxymethyl-2-nitro-1,3-propanediol=HNPD) were monitored for chemical stability by 1H-NMR for up to 7 months. Each compound was studied at two concentrations (1% and 10%) either in unbuffered H2O or 0.2 M NaH2PO4/Na2HPO4 (pH=5), and at 0°C and room temperature (RT) for a total of 8 conditions for each compound. The 1H-NMR spectra for the starting material were compared to subsequent spectra. Under all 4 of the conditions studied, both the nitrodiol (MNPD) and nitrotriol (HNPD) were stable for the duration of 7 months. 2nprop became unstable under all conditions at 3 months. 2ne was the most unstable of all the compounds tested. HONAs exhibit excellent chemical stability under long-term storage conditions. In contrast, the nitromonols tested are significantly less stable. These findings are relevant to the translation of this technology into clinical use. PMID:23998198

  13. Determination of Relative Tensor Orientations by γ-encoded Chemical Shift Anisotropy/Heteronuclear Dipolar Coupling 3D NMR Spectroscopy in Biological Solids

    PubMed Central

    Hou, Guangjin; Paramasivam, Sivakumar; Byeon, In-Ja L.; Gronenborn, Angela M.

    2011-01-01

    In this paper, we present 3D chemical shift anisotropy (CSA)/dipolar coupling correlation experiments, based on γ-encoded R-type symmetry sequences. The γ-encoded correlation spectra are exquisitely sensitive to the relative orientation of the CSA and dipolar tensors and can provide important structural and dynamic information in peptides and proteins. We show that the first-order (m = ±1) and second-order (m = ±2) Hamiltonians in the R-symmetry recoupling sequences give rise to different correlation patterns due to their different dependencies on the crystallite orientation. The relative orientation between CSA and dipolar tensors can be determined by fitting the corresponding correlation patterns. The orientation of 15N CSA tensor in the quasi-molecular frame is determined by the relative Euler angles, αNH and βNH, when the combined symmetry schemes are applied for orientational studies of 1H-15N dipolar and 15N CSA tensors. The correlation experiments introduced here work at moderate magic angle spinning frequencies (10-20 kHz) and allow for simultaneous measurement of multiple sites of interest. We studied the orientational sensitivity of γ-encoded symmetry-based recoupling techniques numerically and experimentally. The results are demonstrated on [15N]-N-acetyl-valine (NAV) and N-formyl-Met-Leu-Phe (MLF) tripeptide. PMID:20936218

  14. Probing physical and chemical changes in cortical bone due to osteoporosis and type 2 diabetes by solid-state NMR

    NASA Astrophysics Data System (ADS)

    Zhou, Donghua; Taylor, Amanda; Rendina, Beth; Smith, Brenda; Department of Physics Collaboration; Department of Nutritional Sciences Collaboration

    2013-03-01

    Approximately 1.5 million fractures occur each year in the U.S. due to osteoporosis, which is characterized by decreased bone mineral density and deterioration of bone micro-architecture. On the other hand, type 2 diabetes also significantly increases fracture risks, despite having a normal or even higher bone mineral density. Solid-state NMR has been applied to bone tissues from normal and disease-inflicted mouse models to study structural and chemical dynamics as the disease progresses. Proton relaxation experiments were performed to measure water populations in the bone matrix and pores. Collagen-bound water has strong influence on bone resilience, while water content in the pores reveals amount and size of pores from micro- to millimeter range. Other biochemical and atomic-scale structural alterations in the mineral and organic phases and their interface were investigated by proton, phosphorus, and carbon NMR spectroscopy. Experiments were designed to individually detect different types of phosphorus environments: near the mineral surface, similar to hydroxyapatite, and deficient of hydrogens due to substitution of the hydroxyl group by other ions. A new method was also developed for accurate quantification of each phosphorus species. The authors appreciate financial support for this project from the College of Human Sciences and the College of Arts and Sciences, Oklahoma State University.

  15. Emulsion droplet sizing using low-field NMR with chemical shift resolution and the block gradient pulse method

    NASA Astrophysics Data System (ADS)

    Lingwood, I. A.; Chandrasekera, T. C.; Kolz, J.; Fridjonsson, E. O.; Johns, M. L.

    2012-01-01

    Pulsed Field Gradient (PFG) measurements are commonly used to determine emulsion droplet size distributions based on restricted self-diffusion within the emulsion droplets. Such measurement capability is readily available on commercial NMR bench-top apparatus. A significant limitation is the requirement to selectively detect signal from the liquid phase within the emulsion droplets; this is currently achieved using either relaxation or self-diffusion contrast. Here we demonstrate the use of a 1.1 T bench-top NMR magnet, which when coupled with an rf micro-coil, is able to provide sufficient chemical shift resolution such that unambiguous signal selection is achieved from the dispersed droplet phase. We also improve the accuracy of the numerical inversion process required to produce the emulsion droplet size distribution, by employing the Block Gradient Pulse (bgp) method, which partially relaxes the assumptions of a Gaussian phase distribution or infinitely short gradient pulse application inherent in current application. The techniques are successfully applied to size 3 different emulsions.

  16. Indirectly detected chemical shift correlation NMR spectroscopy in solids under fast magic angle spinning

    SciTech Connect

    Mao, Kanmi

    2011-01-01

    The development of fast magic angle spinning (MAS) opened up an opportunity for the indirect detection of insensitive low-γ nuclei (e.g., 13C and 15N) via the sensitive high-{gamma} nuclei (e.g., 1H and 19F) in solid-state NMR, with advanced sensitivity and resolution. In this thesis, new methodology utilizing fast MAS is presented, including through-bond indirectly detected heteronuclear correlation (HETCOR) spectroscopy, which is assisted by multiple RF pulse sequences for 1H-1H homonuclear decoupling. Also presented is a simple new strategy for optimization of 1H-1H homonuclear decoupling. As applications, various classes of materials, such as catalytic nanoscale materials, biomolecules, and organic complexes, are studied by combining indirect detection and other one-dimensional (1D) and two-dimensional (2D) NMR techniques. Indirectly detected through-bond HETCOR spectroscopy utilizing refocused INEPT (INEPTR) mixing was developed under fast MAS (Chapter 2). The time performance of this approach in 1H detected 2D 1H{l_brace}13C{r_brace} spectra was significantly improved, by a factor of almost 10, compared to the traditional 13C detected experiments, as demonstrated by measuring naturally abundant organic-inorganic mesoporous hybrid materials. The through-bond scheme was demonstrated as a new analytical tool, which provides complementary structural information in solid-state systems in addition to through-space correlation. To further benefit the sensitivity of the INEPT transfer in rigid solids, the combined rotation and multiple-pulse spectroscopy (CRAMPS) was implemented for homonuclear 1H decoupling under fast MAS (Chapter 3). Several decoupling schemes (PMLG5m$\\bar{x}$, PMLG5mm$\\bar{x}$x and SAM3) were analyzed to maximize the performance of through-bond transfer based

  17. Hyperpolarized 15N-pyridine Derivatives as pH-Sensitive MRI Agents

    PubMed Central

    Jiang, Weina; Lumata, Lloyd; Chen, Wei; Zhang, Shanrong; Kovacs, Zoltan; Sherry, A. Dean; Khemtong, Chalermchai

    2015-01-01

    Highly sensitive MR imaging agents that can accurately and rapidly monitor changes in pH would have diagnostic and prognostic value for many diseases. Here, we report an investigation of hyperpolarized 15N-pyridine derivatives as ultrasensitive pH-sensitive imaging probes. These molecules are easily polarized to high levels using standard dynamic nuclear polarization (DNP) techniques and their 15N chemical shifts were found to be highly sensitive to pH. These probes displayed sharp 15N resonances and large differences in chemical shifts (Δδ >90 ppm) between their free base and protonated forms. These favorable features make these agents highly suitable candidates for the detection of small changes in tissue pH near physiological values. PMID:25774436

  18. 13C and 1H chemical shift assignments and conformation confirmation of trimedlure-Y via 2-D NMR

    NASA Astrophysics Data System (ADS)

    Warthen, J. D.; Waters, R. M.; McGovern, T. P.

    The conformation of 1,1-dimethylethyl 5-chloro- cis-2-methylcyclohexane-1-carboxylate (trimedlure-Y) was confirmed as 1,2,5 equatorial, axial, equatorial via 13C, 1H, APT, CSCM and COSY NMR analyses. The carbon and proton nuclei in trimedlure-Y and the previously unassigned eight cyclohexyl protons (1.50-2.60 ppm) in 1,1-dimethylethyl 5-chloro- trans-2-methylcyclohexane-1-carboxylate (trimedlure-B 1; 1,2,5 equatorial, equatorial, equatorial) were also characterized by these methods. The effects of the 2-CH 3 in the axial or equatorial conformation upon the chemical shifts of the other nuclei in the molecule are discussed.

  19. Single-Crystalline cooperite (PtS): Crystal-Chemical characterization, ESR spectroscopy, and {sup 195}Pt NMR spectroscopy

    SciTech Connect

    Rozhdestvina, V. I. Ivanov, A. V.; Zaremba, M. A.; Antsutkin, O. N.; Forsling, W.

    2008-05-15

    Single-crystalline cooperite (PtS) with a nearly stoichiometric composition was characterized in detail by X-ray diffraction, electron-probe X-ray microanalysis, and high-resolution scanning electron microscopy. For the first time it was demonstrated that {sup 195}Pt static and MAS NMR spectroscopy can be used for studying natural platinum minerals. The {sup 195}Pt chemical-shift tensor of cooperite was found to be consistent with the axial symmetry and is characterized by the following principal values: {delta}{sub xx} = -5920 ppm, {delta}{sub yy} = -3734 ppm, {delta}{sub zz} = +4023 ppm, and {delta}{sub iso} = -1850 ppm. According to the ESR data, the samples of cooperite contain copper(II), which is adsorbed on the surface during the layer-by-layer crystal growth and is not involved in the crystal lattice.

  20. CSI 3.0: a web server for identifying secondary and super-secondary structure in proteins using NMR chemical shifts.

    PubMed

    Hafsa, Noor E; Arndt, David; Wishart, David S

    2015-07-01

    The Chemical Shift Index or CSI 3.0 (http://csi3.wishartlab.com) is a web server designed to accurately identify the location of secondary and super-secondary structures in protein chains using only nuclear magnetic resonance (NMR) backbone chemical shifts and their corresponding protein sequence data. Unlike earlier versions of CSI, which only identified three types of secondary structure (helix, β-strand and coil), CSI 3.0 now identifies total of 11 types of secondary and super-secondary structures, including helices, β-strands, coil regions, five common β-turns (type I, II, I', II' and VIII), β hairpins as well as interior and edge β-strands. CSI 3.0 accepts experimental NMR chemical shift data in multiple formats (NMR Star 2.1, NMR Star 3.1 and SHIFTY) and generates colorful CSI plots (bar graphs) and secondary/super-secondary structure assignments. The output can be readily used as constraints for structure determination and refinement or the images may be used for presentations and publications. CSI 3.0 uses a pipeline of several well-tested, previously published programs to identify the secondary and super-secondary structures in protein chains. Comparisons with secondary and super-secondary structure assignments made via standard coordinate analysis programs such as DSSP, STRIDE and VADAR on high-resolution protein structures solved by X-ray and NMR show >90% agreement between those made with CSI 3.0. PMID:25979265

  1. CSI 3.0: a web server for identifying secondary and super-secondary structure in proteins using NMR chemical shifts.

    PubMed

    Hafsa, Noor E; Arndt, David; Wishart, David S

    2015-07-01

    The Chemical Shift Index or CSI 3.0 (http://csi3.wishartlab.com) is a web server designed to accurately identify the location of secondary and super-secondary structures in protein chains using only nuclear magnetic resonance (NMR) backbone chemical shifts and their corresponding protein sequence data. Unlike earlier versions of CSI, which only identified three types of secondary structure (helix, β-strand and coil), CSI 3.0 now identifies total of 11 types of secondary and super-secondary structures, including helices, β-strands, coil regions, five common β-turns (type I, II, I', II' and VIII), β hairpins as well as interior and edge β-strands. CSI 3.0 accepts experimental NMR chemical shift data in multiple formats (NMR Star 2.1, NMR Star 3.1 and SHIFTY) and generates colorful CSI plots (bar graphs) and secondary/super-secondary structure assignments. The output can be readily used as constraints for structure determination and refinement or the images may be used for presentations and publications. CSI 3.0 uses a pipeline of several well-tested, previously published programs to identify the secondary and super-secondary structures in protein chains. Comparisons with secondary and super-secondary structure assignments made via standard coordinate analysis programs such as DSSP, STRIDE and VADAR on high-resolution protein structures solved by X-ray and NMR show >90% agreement between those made with CSI 3.0.

  2. Sensitivity and resolution enhancement of oriented solid-state NMR: Application to membrane proteins

    PubMed Central

    Gopinath, T.; Mote, Kaustubh R.; Veglia, Gianluigi

    2013-01-01

    Oriented solid-state NMR (O-ssNMR) spectroscopy is a major technique for the high-resolution analysis of the structure and topology of transmembrane proteins in native-like environments. Unlike magic angle spinning (MAS) techniques, O-ssNMR spectroscopy requires membrane protein preparations that are uniformly oriented (mechanically or magnetically) so that anisotropic NMR parameters, such as dipolar and chemical shift interactions, can be measured to determine structure and orientation of membrane proteins in lipid bilayers. Traditional sample preparations involving mechanically aligned lipids often result in short relaxation times which broaden the 15N resonances and encumber the manipulation of nuclear spin coherences. The introduction of lipid bicelles as membrane mimicking systems has changed this scenario, and the more favorable relaxation properties of membrane protein 15N and 13C resonances make it possible to develop new, more elaborate pulse sequences for higher spectral resolution and sensitivity. Here, we describe our recent progress in the optimization of O-ssNMR pulse sequences. We explain the theory behind these experiments, demonstrate their application to small and medium size proteins, and describe the technical details for setting up these new experiments on the new generation of NMR spectrometers. PMID:24160761

  3. Comprehensive Chemical Profiling of Picrorhiza kurroa Royle ex Benth Using NMR, HPTLC and LC-MS/MS Techniques.

    PubMed

    Kumar, Dinesh; Kumar, Rakesh; Singh, Bikram; Ahuja, Paramvir Singh

    2016-01-01

    Picrorhiza kurroa is an important herb in Indian medicine and contains cucurbitacins, flavonoids, phenolics, iridoid-glucoside and their derivatives as active constituents for the treatment of indigestion, fever, hepatitis, cancer, liver and respiratory diseases. Extensive use of P. kurroa needs detailed analysis and recognition of chemical diversity, is of great importance to evaluate their role as quality control markers. In the present study, comprehensive metabolic profiling of crude extracts of leaves and rhizomes of P. kurroa was carried out using NMR, HPTLC and LC-MS/MS. Primary and secondary metabolites were unambiguously identified along with a new report of monoterpenic glycoside (1-β-D-glucopyranosyl)-8-hydroxy-3,7-dimethyl-oct-2(E),6(E)-dienoate) in P. Kurroa. Significant qualitative differences with respect to the secondary metabolites were noticed between the leaves and rhizomes tissues. Leaves contained more cucurbitacins and flavonoids while iridoids were present more in rhizomes. The comprehensive chemical profiling is expected to give an idea of chemical diversity and quality of P. kurroa, for their ultimate utilisation in various applications.

  4. Comprehensive Chemical Profiling of Picrorhiza kurroa Royle ex Benth Using NMR, HPTLC and LC-MS/MS Techniques.

    PubMed

    Kumar, Dinesh; Kumar, Rakesh; Singh, Bikram; Ahuja, Paramvir Singh

    2016-01-01

    Picrorhiza kurroa is an important herb in Indian medicine and contains cucurbitacins, flavonoids, phenolics, iridoid-glucoside and their derivatives as active constituents for the treatment of indigestion, fever, hepatitis, cancer, liver and respiratory diseases. Extensive use of P. kurroa needs detailed analysis and recognition of chemical diversity, is of great importance to evaluate their role as quality control markers. In the present study, comprehensive metabolic profiling of crude extracts of leaves and rhizomes of P. kurroa was carried out using NMR, HPTLC and LC-MS/MS. Primary and secondary metabolites were unambiguously identified along with a new report of monoterpenic glycoside (1-β-D-glucopyranosyl)-8-hydroxy-3,7-dimethyl-oct-2(E),6(E)-dienoate) in P. Kurroa. Significant qualitative differences with respect to the secondary metabolites were noticed between the leaves and rhizomes tissues. Leaves contained more cucurbitacins and flavonoids while iridoids were present more in rhizomes. The comprehensive chemical profiling is expected to give an idea of chemical diversity and quality of P. kurroa, for their ultimate utilisation in various applications. PMID:26777484

  5. Unraveling the 13C NMR Chemical Shifts in Single-Walled Carbon Nanotubes: Dependence on Diameter and Electronic Structure

    SciTech Connect

    Engtrakul, C.; Irurzun, V. M.; Gjersing, E. L.; Holt, J. M.; Larsen, B. A.; Resasco, D. E.; Blackburn, J. L.

    2012-03-14

    The atomic specificity afforded by nuclear magnetic resonance (NMR) spectroscopy could enable detailed mechanistic information about single-walled carbon nanotube (SWCNT) functionalization as well as the noncovalent molecular interactions that dictate ground-state charge transfer and separation by electronic structure and diameter. However, to date, the polydispersity present in as-synthesized SWCNT populations has obscured the dependence of the SWCNT {sup 13}C chemical shift on intrinsic parameters such as diameter and electronic structure, meaning that no information is gleaned for specific SWCNTs with unique chiral indices. In this article, we utilize a combination of {sup 13}C labeling and density gradient ultracentrifugation (DGU) to produce an array of {sup 13}C-labeled SWCNT populations with varying diameter, electronic structure, and chiral angle. We find that the SWCNT isotropic {sup 13}C chemical shift decreases systematically with increasing diameter for semiconducting SWCNTs, in agreement with recent theoretical predictions that have heretofore gone unaddressed. Furthermore, we find that the {sup 13}C chemical shifts for small diameter metallic and semiconducting SWCNTs differ significantly, and that the full-width of the isotropic peak for metallic SWCNTs is much larger than that of semiconducting nanotubes, irrespective of diameter.

  6. Influence of temperature on 31P NMR chemical shifts of phospholipids and their metabolites I. In chloroform-methanol-water.

    PubMed

    Estrada, Rosendo; Stolowich, Neal; Yappert, M Cecilia

    2008-09-01

    Spectral overlap of (31)P NMR resonances and the lack of reproducibility in chemical shifts corresponding to phospholipids in organic solvents challenge the accuracy of band assignments and quantification. To alleviate these problems, the use of temperature coefficients is proposed. Changes in temperature enable the resolution of overlapped resonances and provide a facile approach for the computation of temperature coefficients. The coefficients were evaluated for various glycero- and sphingo-phospholipids. Their values suggest that differences in H-bonding between the phosphate and the head groups are responsible for the changes of chemical shift with temperature. Among parent phospholipids, and in addition to sphingomyelin, the smallest temperature coefficient values (closest to zero) were observed for phosphatidylcholine, phosphatidylglycerol, dihydrosphingomyelin, and cardiolipin. The highest values were exhibited by phospholipids with protonated head groups, such as phosphatidylserine and phosphatidylethanolamine. The lowest and, in fact, negative values were measured for phospholipids with an exposed phosphate group: phosphatidic acid, ceramide-1-phosphate, and dihydroceramide-1-phosphate. Diacyl, alkyl-acyl, and alkenyl-acyl phospholipids with the same head group exhibited comparable coefficients but differed slightly in chemical shifts. Compared to their parent glycerophospholipids, all lyso analogs had greater temperature coefficients, possibly due to the presence of an extra OH capable of forming a H-bond with the phosphate group. PMID:18534182

  7. 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.

  8. Investigations on the Crystal-Chemical Behavior of Transition-Metal-Bearing Aluminosilicate Garnet Solid Solutions Using 27Al and 29Si NMR Spectroscopy

    NASA Astrophysics Data System (ADS)

    Palke, A. C.; Geiger, C. A.; Stebbins, J. F.

    2015-12-01

    The petrological importance of silicate garnet is derived from the presence of three distinct cation sites of varying size and coordination number. This allows for a wide range of trace, minor, and major element substitutions. However, a full and precise crystal-chemical understanding of the nature of transition metals in garnet is not at hand. Possible mechanisms of various charge-balanced substitutions (e.g. octahedral Ti4+ or tetrahedral Al3+) and the structural state of solid solutions (i.e. short- to long-range ordering) need study. We report on ongoing efforts in these directions using 27Al and 29Si Magic-Angle Spinning Nuclear Magnetic Resonance (MAS-NMR) spectroscopy. Early work on synthetic and natural Fe- and Mn-bearing pyrope- and grossular-rich garnets focused on the effect these paramagnetic transition metals have in measuring and interpreting NMR spectra. These results have been expanded with NMR measurements on synthetic pyrope-rich garnets containing other paramagnetic transition metals including Cr3+, V3+, Co2+, and Ni2+ as well as diamagnetic Ti4+. NMR peaks are severely broadened in the presence of even small concentrations of Cr3+, Mn2+, and Fe3+ leading to a loss of spectral resolution. On the other hand, the spectra of garnet containing V3+, Fe2+, Co2+, and Ni2+ have better resolution and show separate paramagnetically shifted NMR peaks. In some cases, crystal-chemical information can be obtained because of the large frequency separations between the NMR peaks that can be assigned to various local atomic configurations around Al and Si. Furthermore, the 27Al NMR spectrum of a synthetic pyrope garnet with about 2% diamagnetic Ti4+ on the octahedral site showed the absence of any tetrahedral Al3+, which rules out the substitution mechanism VITi + IVAl = VIAl + IVSi in the solid solution. Our NMR investigations on garnet are now being made at the exploratory level. We think that NMR spectra of diamagnetic garnet can provide information on a

  9. 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

  10. 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

  11. Physico-chemical and NMR relaxometric characterization of gadolinium hydroxide and dysprosium oxide nanoparticles

    NASA Astrophysics Data System (ADS)

    Gossuin, Yves; Hocq, Aline; Vuong, Quoc Lam; Disch, Sabrina; Hermann, Raphaël P.; Gillis, Pierre

    2008-11-01

    Gadolinium hydroxide and dysprosium oxide nanoparticles, which constitute a new interesting class of magnetic nanoparticles, are characterized by different methods, using x-ray diffraction, magnetometry and NMR relaxometry at multiple fields. The rod-like particles are first shown to have a simple paramagnetic behavior, like the bulk compound, without any influence of the nanometric size of the particles. Because of their paramagnetic moment, these particles considerably shorten water relaxation times, especially the transverse relaxation time at high fields. The relaxation induced by gadolinium hydroxide particles is due to a proton exchange between the particle surface and bulk water, while the transverse relaxation caused by dysprosium oxide particles is governed by the diffusion of water protons around the magnetized particles. 1/T2 increases linearly with the magnetic field for gadolinium hydroxide particles while a quadratic increase is observed for dysprosium oxide nanoparticles. The relaxation results are compared with those from previous studies and interpreted using different theories for the relaxation induced by magnetic particles.

  12. Probing silicon and aluminium chemical environments in silicate and aluminosilicate glasses by solid state NMR spectroscopy and accurate first-principles calculations

    NASA Astrophysics Data System (ADS)

    Gambuzzi, Elisa; Pedone, Alfonso; Menziani, Maria Cristina; Angeli, Frédéric; Caurant, Daniel; Charpentier, Thibault

    2014-01-01

    Silicon and aluminium chemical environments in silicate and aluminosilicate glasses with compositions 60SiO2·20Na2O·20CaO (CSN), 60SiO2·20Al2O3·20CaO (CAS), 78SiO2·11Al2O3·11Na2O (NAS) and 60SiO2·10Al2O3·10Na2O·20CaO (CASN) have been investigated by 27Al and 29Si solid state magic angle spinning (MAS) and multiple quantum MAS (MQMAS) nuclear magnetic resonance (NMR) experiments. To interpret the NMR data, first-principles calculations using density functional theory were performed on structural models of these glasses. These models were generated by Shell-model molecular dynamics (MD) simulations. The theoretical NMR parameters and spectra were computed using the gauge including projected augmented wave (GIPAW) method and spin-effective Hamiltonians, respectively. This synergetic computational-experimental approach offers a clear structural characterization of these glasses, particularly in terms of network polymerization, chemical disorder (i.e. Si and Al distribution in second coordination sphere) and modifier cation distributions. The relationships between the local structural environments and the 29Si and 27Al NMR parameters are highlighted, and show that: (i) the isotropic chemical shift of both 29Si and 27Al increases of about +5 ppm for each Al added in the second sphere and (ii) both the 27Al and 29Si isotropic chemical shifts linearly decrease with the reduction of the average Si/Al-O-T bond angle. Conversely, 27Al and 29Si NMR parameters are much less sensitive to the connectivity with triple bridging oxygen atoms, precluding their indirect detection from 27Al and 29Si NMR.

  13. 1H, 15N and 13C assignments of the N-terminal domain of the Mediator complex subunit MED26.

    PubMed

    Peruzzini, Riccardo; Lens, Zoé; Verger, Alexis; Dewitte, Frédérique; Ferreira, Elisabeth; Baert, Jean-Luc; Villeret, Vincent; Landrieu, Isabelle; Cantrelle, François-Xavier

    2016-04-01

    MED26 is a subunit of the Mediator, a very large complex involved in regulation of gene transcription by RNA Polymerase II. MED26 regulates the switch between initiation and elongation phases of the transcription. This function requires interaction of its N-terminal domain (NTD) with several protein partners implicated in transcriptional regulation. Molecular details of the structure and interaction mode of MED26 NTD would improve understanding of this complex regulation. As a first step towards structural characterization, sequence specific (1)H, (13)C and (15)N assignments for MED26 NTD was performed based on Nuclear Magnetic Resonance spectroscopy. TALOS+ analysis of the chemical shifts data revealed a domain solely composed of helices. Assignments will be further used to solve NMR structure and dynamics of MED26 NTD and investigate the molecular details of its interaction with protein partners.

  14. 1H, 13C, and 15N resonance assignments for Escherichia coli ytfP, a member of the broadly conserved UPF0131 protein domain family

    SciTech Connect

    Aramini, James M.; Swapna, G.V.T.; Huang, Yuanpeng; Rajan, Paranji K.; Xiao, Rong; Shastry, Ritu; Acton, Thomas; Cort, John R.; Kennedy, Michael A.; Montelione, Gaetano

    2005-11-01

    Protein ytfP from Escherichia coli (Swiss-Prot ID: YTFP-ECOLI; NESG target ID: ER111; Wunderlich et al., 2004) is a 113-residue member of the UPF0131 protein family (Pfam ID: PF03674) of unknown function. This domain family is found in organisms from all three kingdoms, archaea, eubacteria and eukaryotes. Using triple resonance NMR techniques, we have determined 97% of backbone and 91% of side chain 1H, 13C, and 15N resonance assignments. The chemical shift and 3J(HN?Ha) scalar coupling data reveal a mixed a/b topology,????????. BMRB deposit with Accession No. 6448. Reference: Wunderlich et al. (2004) Proteins, 56, 181?187.

  15. 1H, 13C, and 15N resonance assignments for the protein coded by gene locus BB0938 of Bordetella bronchiseptica

    SciTech Connect

    Rossi, Paolo; Ramelot, Theresa A.; Xiao, Rong; Ho, Chi K.; Ma, LiChung; Acton, Thomas; Kennedy, Michael A.; Montelione, Gaetano

    2005-11-01

    The product of gene locus BB0938 from Bordetella bronchiseptica (Swiss-Prot ID: Q7WNU7-BORBR; NESG target ID: BoR11; Wunderlich et al., 2004; Pfam ID: PF03476) is a 128-residue protein of unknown function. This broadly conserved protein family is found in eubacteria and eukaryotes. Using triple resonance NMR techniques, we have determined 98% of backbone and 94% of side chain 1H, 13C, and 15N resonance assignments. The chemical shift and 3J(HN?Ha) scalar coupling data reveal a b topology with a seven-residue helical insert, ??????????. BMRB deposit with accession number 6693. Reference: Wunderlich et al. (2004) Proteins, 56, 181?187.

  16. Water chemical shift in 1H NMR of red cells: effects of pH when transmembrane magnetic susceptibility differences are low.

    PubMed

    Larkin, Timothy J; Bubb, William A; Kuchel, Philip W

    2008-04-01

    The (1)H magic angle spinning (MAS) NMR spectrum of water in erythrocyte suspensions shows peaks from each of the intracellular and extracellular water pools. The splitting is a true chemical shift and is brought about by the elimination of water exchange under MAS conditions due to physical separation of the two water populations. The size of the chemical shift difference is determined by the concentration of intracellular protein affecting the average extent of hydrogen bonding of water. We present here a model of the chemical shift behavior for water in erythrocytes under normal high-resolution NMR conditions based on results from MAS experiments on these cells exposed to different pH and osmotic conditions. The model accurately predicts the chemical shift of water for a static sample, and the results demonstrate that in high-resolution NMR experiments the chemical shift of water will appear to be invariant if differences in magnetic susceptibility across the cell membrane are minimal (<10% of the magnetic susceptibility of water). Thus, changes in the shape and chemical shift of the water resonance are not due to pH changes in the physiological range. The findings are fundamental to an interpretation of the mechanism of chemical shift effects on the water resonance that may occur in functional MRI.

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

    PubMed

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

    2016-04-15

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

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

    PubMed

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

    2016-04-15

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

  19. 15N Fractionation in Star-Forming Regions and Solar System Objects

    NASA Technical Reports Server (NTRS)

    Wirstrom, Eva; Milam, Stefanie; Adande, GIlles; Charnley, Steven; Cordiner, Martin

    2015-01-01

    A central issue for understanding the formation and evolution of matter in the early Solar System is the relationship between the chemical composition of star-forming interstellar clouds and that of primitive Solar System materials. The pristinemolecular content of comets, interplanetary dust particles and carbonaceous chondrites show significant bulk nitrogen isotopic fractionation relative to the solar value, 14N15N 440. In addition, high spatial resolution measurements in primitive materials locally show even more extreme enhancements of 14N15N 100.

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

    PubMed

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

    2016-02-24

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

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

    PubMed

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

    2016-02-24

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

  2. Simulation of Chemical Isomerization Reaction Dynamics on a NMR Quantum Simulator

    NASA Astrophysics Data System (ADS)

    Lu, Dawei; Xu, Nanyang; Xu, Ruixue; Chen, Hongwei; Gong, Jiangbin; Peng, Xinhua; Du, Jiangfeng

    2011-07-01

    Quantum simulation can beat current classical computers with minimally a few tens of qubits. Here we report an experimental demonstration that a small nuclear-magnetic-resonance quantum simulator is already able to simulate the dynamics of a prototype laser-driven isomerization reaction using engineered quantum control pulses. The experimental results agree well with classical simulations. We conclude that the quantum simulation of chemical reaction dynamics not computable on current classical computers is feasible in the near future.

  3. 1H NMR spectra part 31: 1H chemical shifts of amides in DMSO solvent.

    PubMed

    Abraham, Raymond J; Griffiths, Lee; Perez, Manuel

    2014-07-01

    The (1)H chemical shifts of 48 amides in DMSO solvent are assigned and presented. The solvent shifts Δδ (DMSO-CDCl3 ) are large (1-2 ppm) for the NH protons but smaller and negative (-0.1 to -0.2 ppm) for close range protons. A selection of the observed solvent shifts is compared with calculated shifts from the present model and from GIAO calculations. Those for the NH protons agree with both calculations, but other solvent shifts such as Δδ(CHO) are not well reproduced by the GIAO calculations. The (1)H chemical shifts of the amides in DMSO were analysed using a functional approach for near ( ≤ 3 bonds removed) protons and the electric field, magnetic anisotropy and steric effect of the amide group for more distant protons. The chemical shifts of the NH protons of acetanilide and benzamide vary linearly with the π density on the αN and βC atoms, respectively. The C=O anisotropy and steric effect are in general little changed from the values in CDCl3. The effects of substituents F, Cl, Me on the NH proton shifts are reproduced. The electric field coefficient for the protons in DMSO is 90% of that in CDCl3. There is no steric effect of the C=O oxygen on the NH proton in an NH…O=C hydrogen bond. The observed deshielding is due to the electric field effect. The calculated chemical shifts agree well with the observed shifts (RMS error of 0.106 ppm for the data set of 257 entries). PMID:24824670

  4. Energy landscapes of a hairpin peptide including NMR chemical shift restraints.

    PubMed

    Carr, Joanne M; Whittleston, Chris S; Wade, David C; Wales, David J

    2015-08-21

    Methods recently introduced to improve the efficiency of protein structure prediction simulations by adding a restraint potential to a molecular mechanics force field introduce additional input parameters that can affect the performance. Here we investigate the changes in the energy landscape as the relative weight of the two contributions, force field and restraint potential, is systematically altered, for restraint functions constructed from calculated nuclear magnetic resonance chemical shifts. Benchmarking calculations were performed on a 12-residue peptide, tryptophan zipper 1, which features both secondary structure (a β-hairpin) and specific packing of tryptophan sidechains. Basin-hopping global optimization was performed to assess the efficiency with which lowest-energy structures are located, and the discrete path sampling approach was employed to survey the energy landscapes between unfolded and folded structures. We find that inclusion of the chemical shift restraints improves the efficiency of structure prediction because the energy landscape becomes more funnelled and the proportion of local minima classified as native increases. However, the funnelling nature of the landscape is reduced as the relative contribution of the chemical shift restraint potential is increased past an optimal value. PMID:26186565

  5. Substituent effects in the 13C NMR chemical shifts of alpha-mono-substituted acetonitriles.

    PubMed

    Reis, Adriana K C A; Rittner, Roberto

    2007-03-01

    13C chemical shifts empirical calculations, through a very simple additivity relationship, for the alpha-methylene carbon of some alpha-mono-substituted acetonitriles, Y-CH(2)-CN (Y=H, F, Cl, Br, I, OMe, OEt, SMe, SEt, NMe(2), NEt(2), Me and Et), lead to similar, or even better, results in comparison to the reported values obtained through Quantum Mechanics methods. The observed deviations, for some substituents, are very similar for both approaches. This divergence between experimental and calculated, either empirically or theoretically, values are smaller than for the corresponding acetones, amides, acetic acids and methyl esters, which had been named non-additivity effects (or intramolecular interaction chemical shifts, ICS) and attributed to some orbital interactions. Here, these orbital interactions do not seem to be the main reason for the non-additivity effects in the empirical calculations, which must be due solely to the magnetic anisotropy of the heavy atom present in the substituent. These deviations, which were also observed in the theoretical calculations, were attributed in that case to the non-inclusion of relativistic effects and spin-orbit coupling in the Hamiltonian. Some divergence is also observed for the cyano carbon chemical shifts, probably due to the same reasons.

  6. Thermal effects and vibrational corrections to transition metal NMR chemical shifts.

    PubMed

    Grigoleit, Sonja; Bühl, Michael

    2004-10-25

    Both zero-point and classical thermal effects on the chemical shift of transition metals have been calculated at appropriate levels of density functional theory for a number of complexes of titanium, vanadium, manganese and iron. The zero-point effects were computed by applying a perturbational approach, whereas classical thermal effects were probed by Car-Parrinello molecular dynamics simulations. The systematic investigation shows that both procedures lead to a deshielding of the magnetic shielding constants evaluated at the GIAO-B3 LYP level, which in general also leads to a downfield shift in the relative chemical shifts, delta. The effect is small for the titanium and vanadium complexes, where it is typically on the order of a few dozen ppm, and is larger for the manganese and iron complexes, where it can amount to several hundred ppm. Zero-point corrections are usually smaller than the classical thermal effect. The pronounced downfield shift is due to the sensitivity of the shielding of the metal centre with regard to the metal-ligand bond length, which increase upon vibrational averaging. Both applied methods improve the accuracy of the chemical shifts in some cases, but not in general.

  7. 1H, 13C and 15N resonance assignments and secondary structure analysis of CmPI-II, a serine protease inhibitor isolated from marine snail Cenchritis muricatus.

    PubMed

    Cabrera-Muñoz, Aymara; Rojas, Laritza; Alonso-del-Rivero Antigua, Maday; Pires, José Ricardo

    2016-04-01

    A protease inhibitor (CmPI-II) (UNIPROT: IPK2_CENMR) from the marine mollusc Cenchritis muricatus, has been isolated and characterized. It is the first member of a new group (group 3) of non-classical Kazal-type inhibitors. CmPI-II is a tight-binding inhibitor of serine proteases: trypsin, human neutrophil elastase (HNE), subtilisin A and pancreatic elastase. This specificity is exceptional in the members of Kazal-type inhibitor family. Several models of three-dimensional structure of CmPI-II have been constructed by homology with other inhibitors of the family but its structure has not yet been solved experimentally. Here we report the (1)H, (15)N and (13)C chemical shift assignments of CmPI-II as basis for NMR structure determination and interaction studies. Secondary structure analyses deduced from the NMR chemical shift data have identified three β-strands β1: residues 14-19, β2: 23-35 and β3: 43-45 and one helix α1: 28-37 arranged in the sequential order β1-β2-α1-β3. These secondary structure elements suggest that CmPI-II adopts the typical scaffold of a Kazal-type inhibitor. PMID:26547437

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

    NASA Astrophysics Data System (ADS)

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

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

  9. The family of ferrocene-stabilized silylium ions: synthesis, 29Si NMR characterization, Lewis acidity, substituent scrambling, and quantum-chemical analyses.

    PubMed

    Müther, Kristine; Hrobárik, Peter; Hrobáriková, Veronika; Kaupp, Martin; Oestreich, Martin

    2013-12-01

    The purpose of this systematic experimental and theoretical study is to deeply understand the unique bonding situation in ferrocene-stabilized silylium ions as a function of the substituents at the silicon atom and to learn about the structure parameters that determine the (29)Si NMR chemical shift and electrophilicity of these strong Lewis acids. For this, ten new members of the family of ferrocene-stabilized silicon cations were prepared by a hydride abstraction reaction from silanes with the trityl cation and characterized by multinuclear (1)H and (29)Si NMR spectroscopy. A closer look at the NMR spectra revealed that additional minor sets of signals were not impurities but silylium ions with substitution patterns different from that of the initially formed cation. Careful assignment of these signals furnished experimental proof that sterically less hindered silylium ions are capable of exchanging substituents with unreacted silane precursors. Density functional theory calculations provided mechanistic insight into that substituent transfer in which the migrating group is exchanged between two silicon fragments in a concerted process involving a ferrocene-bridged intermediate. Moreover, the quantum-chemical analysis of the (29)Si NMR chemical shifts revealed a linear relationship between δ((29)Si) values and the Fe···Si distance for subsets of silicon cations. An electron localization function and electron localizability indicator analysis shows a three-center two-electron bonding attractor between the iron, silicon, and C'(ipso) atoms, clearly distinguishing the silicon cations from the corresponding carbenium ions and boranes. Correlations between (29)Si NMR chemical shifts and Lewis acidity, evaluated in terms of fluoride ion affinities, are seen only for subsets of silylium ions, sometimes with non-intuitive trends, indicating a complicated interplay of steric and electronic effects on the degree of the Fe···Si interaction.

  10. Structure, solvent, and relativistic effects on the NMR chemical shifts in square-planar transition-metal complexes: assessment of DFT approaches.

    PubMed

    Vícha, Jan; Novotný, Jan; Straka, Michal; Repisky, Michal; Ruud, Kenneth; Komorovsky, Stanislav; Marek, Radek

    2015-10-14

    The role of various factors (structure, solvent, and relativistic treatment) was evaluated for square-planar 4d and 5d transition-metal complexes. The DFT method for calculating the structures was calibrated using a cluster approach and compared to X-ray geometries, with the PBE0 functional (def2-TZVPP basis set) providing the best results, followed closely by the hybrid TPSSH and the MN12SX functionals. Calculations of the NMR chemical shifts using the two-component (2c, Zeroth-Order Regular Approximation as implemented in the ADF package) and four-component (4c, Dirac-Coulomb as implemented in the ReSpect code) relativistic approaches were performed to analyze and demonstrate the importance of solvent corrections (2c) as well as a proper treatment of relativistic effects (4c). The importance of increased exact-exchange admixture in the functional (here PBE0) for reproducing the experimental data using the current implementation of the 2c approach is partly rationalized as a compensation for the missing exchange-correlation response kernel. The kernel contribution was identified to be about 15-20% of the spin-orbit-induced NMR chemical shift, ΔδSO, which roughly corresponds to an increase in ΔδSO introduced by the artificially increased exact-exchange admixture in the functional. Finally, the role of individual effects (geometry, solvent, relativity) in the NMR chemical shift is discussed in selected complexes. Although a fully relativistic DFT approach is still awaiting the implementation of GIAOs for hybrid functionals and an implicit solvent model, it nevertheless provides reliable NMR chemical shift data at an affordable computational cost. It is expected to outperform the 2c approach, in particular for the calculation of NMR parameters in heavy-element compounds. PMID:26344822

  11. NMR analysis and chemical shift calculations of poly(lactic acid) dimer model compounds with different tacticities

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In this work, PLA dimer model compounds with different tacticities were synthesized and studied in detail by 1H and 13C NMR in three solvents, CDCl3/CCl4 (20/80 v/v), CDCl3 and DMSO-d6. All the peaks in the 1H and 13C NMR spectra were assigned with the help of two-dimensional NMR. Although the solve...

  12. NMR fingerprints of the drug-like natural-product space identify iotrochotazine A: a chemical probe to study Parkinson's disease.

    PubMed

    Grkovic, Tanja; Pouwer, Rebecca H; Vial, Marie-Laure; Gambini, Luca; Noël, Alba; Hooper, John N A; Wood, Stephen A; Mellick, George D; Quinn, Ronald J

    2014-06-10

    The NMR spectrum of a mixture of small molecules is a fingerprint of all of its components. Herein, we present an NMR fingerprint method that takes advantage of the fact that fractions contain simplified NMR profiles, with minimal signal overlap, to allow the identification of unique spectral patterns. The approach is exemplified in the identification of a novel natural product, iotrochotazine A (1), sourced from an Australian marine sponge Iotrochota sp. Compound 1 was used as a chemical probe in a phenotypic assay panel based on human olfactory neurosphere-derived cells (hONS) from idiopathic Parkinson's disease patients. Compound 1 at 1 μM was not cytotoxic but specifically affected the morphology and cellular distribution of lysosomes and early endosomes.

  13. Correlations between (51)V solid-state NMR parameters and chemical structure of vanadium (V) complexes as models for related metalloproteins and catalysts.

    PubMed

    Fenn, Annika; Wächtler, Maria; Gutmann, Torsten; Breitzke, Hergen; Buchholz, Axel; Lippold, Ines; Plass, Winfried; Buntkowsky, Gerd

    2009-12-01

    The parameters describing the quadrupolar and CSA interactions of 51V solid-state MAS NMR investigations of model complexes mimicking vanadoenzymes as well as vanadium containing catalysts and enzyme complexes are interpreted with respect to the chemical structure. The interpretation is based on the data of 15 vanadium complexes including two new complexes with previously unpublished data and 13 complexes with data previously published by us. Correlations between the chemical structure and the 51V solid-state NMR data of this class of compounds have been established. Especially for the isotropic chemical shift delta(iso) and the chemical shift anisotropy delta(sigma), correlations with specific structural features like the coordination number of the vanadium atom, the number of coordinating nitrogens, the number of oxygen atoms and the chemical surrounding of the complex could be established for these compounds. Moreover, quantitative correlations between the solid-state NMR parameters and specific bond angles and bond lengths have been obtained. Our results can be of particular interest for future investigations concerning the structure and the mode of action of related vanadoenzymes and vanadate protein assemblies, including the use of vanadate adducts as transition state analogs for phosphate metabolizing systems.

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

    NASA Astrophysics Data System (ADS)

    Albrecht, Remy; Sebag, David; Verrecchia, Eric

    2013-04-01

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

  15. Chemically selective NMR imaging of a 3-component (solid-solid-liquid) sedimenting system.

    PubMed

    Beyea, Steven D; Altobelli, Stephen A; Mondy, Lisa A

    2003-04-01

    A novel magnetic resonance imaging (MRI) technique which resolves the separate components of the evolving vertical concentration profiles of 3-component non-colloidal suspensions is described. This method exploits the sensitivity of MRI to chemical differences between the three phases to directly image the fluid phase and one of the solid phases, with the third phase obtained by subtraction. 19F spin-echo imaging of a polytetrafluoroethylene (PTFE) oil was interlaced with 1H SPRITE imaging of low-density polyethylene (LDPE) particles. The third phase was comprised of borosilicate glass spheres, which were not visible while imaging the PTFE or LDPE phases. The method is demonstrated by performing measurements on 2-phase materials containing only the floating (LDPE) particles, with the results contrasted to the experimental behaviour of the individual phases in the full 3-phase system. All experiments were performed using nearly monodisperse particles, with initial suspension volume fractions, phi(i), of 0.1. PMID:12713970

  16. A palm-size μNMR relaxometer using a digital microfluidic device and a semiconductor transceiver for chemical/biological diagnosis.

    PubMed

    Lei, Ka-Meng; Mak, Pui-In; Law, Man-Kay; Martins, Rui P

    2015-08-01

    Herein, we describe a micro-nuclear magnetic resonance (μNMR) relaxometer miniaturized to palm-size and electronically automated for multi-step and multi-sample chemical/biological diagnosis. The co-integration of microfluidic and microelectronic technologies enables an association between the droplet managements and μNMR assays inside a portable sub-Tesla magnet (1.2 kg, 0.46 Tesla). Targets in unprocessed biological samples, captured by specific probe-decorated magnetic nanoparticles (NPs), can be sequentially quantified by their spin-spin relaxation time (T2) via multiplexed μNMR screening. Distinct droplet samples are operated by a digital microfluidic device that electronically manages the electrowetting-on-dielectric effects over an electrode array. Each electrode (3.5 × 3.5 mm(2)) is scanned with capacitive sensing to locate the distinct droplet samples in real time. A cross-domain-optimized butterfly-coil-input semiconductor transceiver transduces between magnetic and electrical signals to/from a sub-10 μL droplet sample for high-sensitivity μNMR screening. A temperature logger senses the ambient temperature (0 to 40 °C) and a backend processor calibrates the working frequency for the transmitter to precisely excite the protons. In our experiments, the μNMR relaxometer quantifies avidin using biotinylated Iron NPs (Φ: 30 nm, [Fe]: 0.5 mM) with a sensitivity of 0.2 μM. Auto-handling and identification of two targets (avidin and water) are demonstrated and completed within 2.2 min. This μNMR relaxometer holds promise for combinatorial chemical/biological diagnostic protocols using closed-loop electronic automation.

  17. A palm-size μNMR relaxometer using a digital microfluidic device and a semiconductor transceiver for chemical/biological diagnosis.

    PubMed

    Lei, Ka-Meng; Mak, Pui-In; Law, Man-Kay; Martins, Rui P

    2015-08-01

    Herein, we describe a micro-nuclear magnetic resonance (μNMR) relaxometer miniaturized to palm-size and electronically automated for multi-step and multi-sample chemical/biological diagnosis. The co-integration of microfluidic and microelectronic technologies enables an association between the droplet managements and μNMR assays inside a portable sub-Tesla magnet (1.2 kg, 0.46 Tesla). Targets in unprocessed biological samples, captured by specific probe-decorated magnetic nanoparticles (NPs), can be sequentially quantified by their spin-spin relaxation time (T2) via multiplexed μNMR screening. Distinct droplet samples are operated by a digital microfluidic device that electronically manages the electrowetting-on-dielectric effects over an electrode array. Each electrode (3.5 × 3.5 mm(2)) is scanned with capacitive sensing to locate the distinct droplet samples in real time. A cross-domain-optimized butterfly-coil-input semiconductor transceiver transduces between magnetic and electrical signals to/from a sub-10 μL droplet sample for high-sensitivity μNMR screening. A temperature logger senses the ambient temperature (0 to 40 °C) and a backend processor calibrates the working frequency for the transmitter to precisely excite the protons. In our experiments, the μNMR relaxometer quantifies avidin using biotinylated Iron NPs (Φ: 30 nm, [Fe]: 0.5 mM) with a sensitivity of 0.2 μM. Auto-handling and identification of two targets (avidin and water) are demonstrated and completed within 2.2 min. This μNMR relaxometer holds promise for combinatorial chemical/biological diagnostic protocols using closed-loop electronic automation. PMID:26034784

  18. 129Xe NMR chemical shift in Xe@C60 calculated at experimental conditions: essential role of the relativity, dynamics, and explicit solvent.

    PubMed

    Standara, Stanislav; Kulhánek, Petr; Marek, Radek; Straka, Michal

    2013-08-15

    The isotropic (129)Xe nuclear magnetic resonance (NMR) chemical shift (CS) in Xe@C60 dissolved in liquid benzene was calculated by piecewise approximation to faithfully simulate the experimental conditions and to evaluate the role of different physical factors influencing the (129)Xe NMR CS. The (129)Xe shielding constant was obtained by averaging the (129)Xe nuclear magnetic shieldings calculated for snapshots obtained from the molecular dynamics trajectory of the Xe@C60 system embedded in a periodic box of benzene molecules. Relativistic corrections were added at the Breit-Pauli perturbation theory (BPPT) level, included the solvent, and were dynamically averaged. It is demonstrated that the contribution of internal dynamics of the Xe@C60 system represents about 8% of the total nonrelativistic NMR CS, whereas the effects of dynamical solvent add another 8%. The dynamically averaged relativistic effects contribute by 9% to the total calculated (129)Xe NMR CS. The final theoretical value of 172.7 ppm corresponds well to the experimental (129)Xe CS of 179.2 ppm and lies within the estimated errors of the model. The presented computational protocol serves as a prototype for calculations of (129)Xe NMR parameters in different Xe atom guest-host systems.

  19. 129Xe NMR chemical shift in Xe@C60 calculated at experimental conditions: essential role of the relativity, dynamics, and explicit solvent.

    PubMed

    Standara, Stanislav; Kulhánek, Petr; Marek, Radek; Straka, Michal

    2013-08-15

    The isotropic (129)Xe nuclear magnetic resonance (NMR) chemical shift (CS) in Xe@C60 dissolved in liquid benzene was calculated by piecewise approximation to faithfully simulate the experimental conditions and to evaluate the role of different physical factors influencing the (129)Xe NMR CS. The (129)Xe shielding constant was obtained by averaging the (129)Xe nuclear magnetic shieldings calculated for snapshots obtained from the molecular dynamics trajectory of the Xe@C60 system embedded in a periodic box of benzene molecules. Relativistic corrections were added at the Breit-Pauli perturbation theory (BPPT) level, included the solvent, and were dynamically averaged. It is demonstrated that the contribution of internal dynamics of the Xe@C60 system represents about 8% of the total nonrelativistic NMR CS, whereas the effects of dynamical solvent add another 8%. The dynamically averaged relativistic effects contribute by 9% to the total calculated (129)Xe NMR CS. The final theoretical value of 172.7 ppm corresponds well to the experimental (129)Xe CS of 179.2 ppm and lies within the estimated errors of the model. The presented computational protocol serves as a prototype for calculations of (129)Xe NMR parameters in different Xe atom guest-host systems. PMID:23703381

  20. Detailed Chemical Composition of Condensed Tannins via Quantitative (31)P NMR and HSQC Analyses: Acacia catechu, Schinopsis balansae, and Acacia mearnsii.

    PubMed

    Crestini, Claudia; Lange, Heiko; Bianchetti, Giulia

    2016-09-23

    The chemical composition of Acacia catechu, Schinopsis balansae, and Acacia mearnsii proanthocyanidins has been determined using a novel analytical approach that rests on the concerted use of quantitative (31)P NMR and two-dimensional heteronuclear NMR spectroscopy. This approach has offered significant detailed information regarding the structure and purity of these complex and often elusive proanthocyanidins. More specifically, rings A, B, and C of their flavan-3-ol units show well-defined and resolved absorbance regions in both the quantitative (31)P NMR and HSQC spectra. By integrating each of these regions in the (31)P NMR spectra, it is possible to identify the oxygenation patterns of the flavan-3-ol units. At the same time it is possible to acquire a fingerprint of the proanthocyanidin sample and evaluate its purity via the HSQC information. This analytical approach is suitable for both the purified natural product proanthocyanidins and their commercial analogues. Overall, this effort demonstrates the power of the concerted use of these two NMR techniques for the structural elucidation of natural products containing labile hydroxy protons and a carbon framework that can be traced out via HSQC. PMID:27551744

  1. 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

  2. CHEMICAL SHIFTS IN AMINO ACIDS, PEPTIDES, AND PROTEINS: From Quantum Chemistry to Drug Design

    NASA Astrophysics Data System (ADS)

    Oldfield, Eric

    2002-10-01

    This chapter discusses recent progress in the investigation and use of 13C, 15N, and 19F nuclear magnetic resonance (NMR) chemical shifts and chemical shift tensors in proteins and model systems primarily using quantum chemical (ab initio Hartree-Fock and density functional theory) techniques. Correlations between spectra and structure are made and the techniques applied to other spectroscopic and electrostatic properties as well, including hydrogen bonding, ligand binding to heme proteins, J-couplings, electric field gradients, and atoms-in-molecules theory, together with a brief review of the use of NMR chemical shifts in drug design.

  3. 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.

  4. 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.

  5. Thermal unfolding in a GCN4-like leucine zipper: 13C alpha NMR chemical shifts and local unfolding curves.

    PubMed Central

    Holtzer, M E; Lovett, E G; d'Avignon, D A; Holtzer, A

    1997-01-01

    13C alpha chemical shifts and site-specific unfolding curves are reported for 12 sites on a 33-residue, GCN4-like leucine zipper peptide (GCN4-lzK), ranging over most of the chain and sampling most heptad positions. Data were derived from NMR spectra of nine synthetic, isosequential peptides bearing 99% 13C alpha at sites selected to avoid spectral overlap in each peptide. At each site, separate resonances appear for unfolded and folded forms, and most sites show resonances for two folded forms near room temperature. The observed chemical shifts suggest that 1) urea-unfolded GCN4-lzK chains are randomly coiled; 2) thermally unfolded chains include significant transient structure, except at the ends; 3) the coiled-coli structure in the folded chains is atypical near the C-terminus; 4) only those interior sites surrounded by canonical interchain salt bridges fail to show two folded forms. Local unfolding curves, obtained from integrated resonance intensities, show that 1) sites differ in structure content and in melting temperature, so the equilibrium population must comprise more than two molecular conformations; 2) there is significant end-fraying, even at the lowest temperatures, but thermal unfolding is not a progressive unwinding from the ends; 3) residues 9-16 are in the lowest melting region; 4) heptad position does not dictate stability; 5) significant unfolding occurs below room temperature, so the shallow, linear decline in backbone CD seen there has conformational significance. It seems that only a relatively complex array of conformational states could underlie these findings. PMID:9251820

  6. 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.

  7. DFT-GIAO(1)H NMR chemical shifts prediction for the spectral assignment and conformational analysis of the anticholinergic drugs (-)-scopolamine and (-)-hyoscyamine.

    PubMed

    Muñoz, Marcelo A; Joseph-Nathan, Pedro

    2010-06-01

    The relatively large chemical shift differences observed in the (1)H NMR spectra of the anticholinergic drugs (-)-scopolamine 1 and (-)-hyoscyamine 2 measured in CDCl(3) are explained using a combination of systematic/molecular mechanics force field (MMFF) conformational searches and gas-phase density functional theory (DFT) single point calculations, geometry optimizations and chemical shift calculations within the gauge including/invariant atomic orbital (GIAO) approximation. These calculations show that both molecules prefer a compact conformation in which the phenyl ring of the tropic ester is positioned under the tropane bicycle, clearly suggesting that the chemical shift differences are produced by the anisotropic effect of the aromatic ring. As the calculations fairly well predict these experimental differences, diastereotopic NMR signal assignments for the two studied molecules are proposed. In addition, a cursory inspection of the published (1)H and (13)C NMR spectra of different forms of 1 and 2 in solution reveals that most of them show these diastereotopic chemical shift differences, strongly suggesting a preference for the compact conformation quite independent of the organic or aqueous nature of the solvent.

  8. Adducts of nitrogenous ligands with rhodium(II) tetracarboxylates and tetraformamidinate: NMR spectroscopy and density functional theory calculations.

    PubMed

    Cmoch, Piotr; Głaszczka, Rafał; Jaźwiński, Jarosław; Kamieński, Bohdan; Senkara, Elżbieta

    2014-03-01

    Complexation of tetrakis(μ2-N,N'-diphenylformamidinato-N,N')-di-rhodium(II) with ligands containing nitrile, isonitrile, amine, hydroxyl, sulfhydryl, isocyanate, and isothiocyanate functional groups has been studied in liquid and solid phases using (1)H, (13)C and (15)N NMR, (13)C and (15)N cross polarisation-magic angle spinning NMR, and absorption spectroscopy in the visible range. The complexation was monitored using various NMR physicochemical parameters, such as chemical shifts, longitudinal relaxation times T1 , and NOE enhancements. Rhodium(II) tetraformamidinate selectively bonded only unbranched amine (propan-1-amine), pentanenitrile, and (1-isocyanoethyl)benzene. No complexation occurred in the case of ligands having hydroxyl, sulfhydryl, isocyanate, and isothiocyanate functional groups, and more expanded amine molecules such as butan-2-amine and 1-azabicyclo[2.2.2]octane. Such features were opposite to those observed in rhodium(II) tetracarboxylates, forming adducts with all kind of ligands. Special attention was focused on the analysis of Δδ parameters, defined as a chemical shift difference between signal in adduct and corresponding signal in free ligand. In the case of (1)H NMR, Δδ values were either negative in adducts of rhodium(II) tetraformamidinate or positive in adducts of rhodium(II) tetracarboxylates. Experimental findings were supported by density functional theory molecular modelling and gauge independent atomic orbitals chemical shift calculations. The calculation of chemical shifts combined with scaling procedure allowed to reproduce qualitatively Δδ parameters.

  9. 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.

  10. Vibrational, NMR and quantum chemical investigations of acetoacetanilde, 2-chloroacetoacetanilide and 2-methylacetoacetanilide

    NASA Astrophysics Data System (ADS)

    Arjunan, V.; Kalaivani, M.; Senthilkumari, S.; Mohan, S.

    2013-11-01

    The vibrational assignment and analysis of the fundamental modes of the compounds acetoacetanilide (AAA), 2-chloroacetoacetanilide (2CAAA) and 2-methylacetoacetanilide (2MAAA) have been performed. Density functional theory studies have been carried out with B3LYP method utilising 6-311++G** and cc-pVTZ basis sets to determine structural, thermodynamic and vibrational characteristics of the compounds and also to understand the influence of chloro and methyl groups on the characteristic frequencies of amide (sbnd CONHsbnd ) group. Intramolecular hydrogen bond exists in acetoacetanilide and o-substituted acetoacetanilide molecules and the N⋯O distance is found to be around 2.7 Å. The 1H and 13C nuclear magnetic resonance chemical shifts of the molecules were determined and the same have been calculated using the gauge independent atomic orbital (GIAO) method. The energies of the frontier molecular orbitals have been determined. In AAA, 2CAAA and 2MAAA molecules, the nN → πCO∗ interaction between the nitrogen lone pair and the amide Cdbnd O antibonding orbital gives strong stabilization of 64.75, 62.84 and 64.18 kJ mol-1, respectively. The blue shift in amide-II band of 2MAAA is observed by 45-50 cm-1 than that of AAA. The steric effect of ortho methyl group significantly operating on the Nsbnd H bond properties. The amide-III, the Csbnd N stretching mode of methyl and chloro substituted acetoacetanilide compounds are not affected by the substitution while the amide-V band, the Nsbnd H out of plane bending mode of 2-chloroacetoacetanilide compound is shifted to a higher frequency than that of AAA. The substituent chlorine plays significantly and the blue shift in o-substituted compounds than the parent in the amide-V vibration is observed. The amide-VI, Cdbnd O out of plane bending modes of 2MAAA and 2CAAA are significantly raised than that of AAA. A blue shift of amide-VI, Cdbnd O out of plane bending modes of 2MAAA and 2CAAA than AAA is observed.

  11. 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.

  12. 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

  13. Accurate structure and dynamics of the metal-site of paramagnetic metalloproteins from NMR parameters using natural bond orbitals.

    PubMed

    Hansen, D Flemming; Westler, William M; Kunze, Micha B A; Markley, John L; Weinhold, Frank; Led, Jens J

    2012-03-14

    A natural bond orbital (NBO) analysis of unpaired electron spin density in metalloproteins is presented, which allows a fast and robust calculation of paramagnetic NMR parameters. Approximately 90% of the unpaired electron spin density occupies metal-ligand NBOs, allowing the majority of the density to be modeled by only a few NBOs that reflect the chemical bonding environment. We show that the paramagnetic relaxation rate of protons can be calculated accurately using only the metal-ligand NBOs and that these rates are in good agreement with corresponding rates measured experimentally. This holds, in particular, for protons of ligand residues where the point-dipole approximation breaks down. To describe the paramagnetic relaxation of heavy nuclei, also the electron spin density in the local orbitals must be taken into account. Geometric distance restraints for (15)N can be derived from the paramagnetic relaxation enhancement and the Fermi contact shift when local NBOs are included in the analysis. Thus, the NBO approach allows us to include experimental paramagnetic NMR parameters of (15)N nuclei as restraints in a structure optimization protocol. We performed a molecular dynamics simulation and structure determination of oxidized rubredoxin using the experimentally obtained paramagnetic NMR parameters of (15)N. The corresponding structures obtained are in good agreement with the crystal structure of rubredoxin. Thus, the NBO approach allows an accurate description of the geometric structure and the dynamics of metalloproteins, when NMR parameters are available of nuclei in the immediate vicinity of the metal-site.

  14. Accurate Structure and Dynamics of the Metal-Site of Paramagnetic Metalloproteins from NMR Parameters Using Natural Bond Orbitals

    PubMed Central

    2012-01-01

    A natural bond orbital (NBO) analysis of unpaired electron spin density in metalloproteins is presented, which allows a fast and robust calculation of paramagnetic NMR parameters. Approximately 90% of the unpaired electron spin density occupies metal–ligand NBOs, allowing the majority of the density to be modeled by only a few NBOs that reflect the chemical bonding environment. We show that the paramagnetic relaxation rate of protons can be calculated accurately using only the metal–ligand NBOs and that these rates are in good agreement with corresponding rates measured experimentally. This holds, in particular, for protons of ligand residues where the point-dipole approximation breaks down. To describe the paramagnetic relaxation of heavy nuclei, also the electron spin density in the local orbitals must be taken into account. Geometric distance restraints for 15N can be derived from the paramagnetic relaxation enhancement and the Fermi contact shift when local NBOs are included in the analysis. Thus, the NBO approach allows us to include experimental paramagnetic NMR parameters of 15N nuclei as restraints in a structure optimization protocol. We performed a molecular dynamics simulation and structure determination of oxidized rubredoxin using the experimentally obtained paramagnetic NMR parameters of 15N. The corresponding structures obtained are in good agreement with the crystal structure of rubredoxin. Thus, the NBO approach allows an accurate description of the geometric structure and the dynamics of metalloproteins, when NMR parameters are available of nuclei in the immediate vicinity of the metal-site. PMID:22329704

  15. Protein structure by solid-state NMR of oriented systems

    SciTech Connect

    Stewart, P.L.

    1987-01-01

    A method for determining protein backbone structure from angular information obtainable by solid state NMR spectroscopy is presented. Various spin interactions including quadrupole, dipole, and chemical shift interactions and nuclei including /sup 14/N, /sup 15/N, /sup 13/C, and /sup 2/H may be observed. Angularly dependent measurements can be made when the sample has at least one direction of order along the externally applied magnetic field. Several NMR parameters are used to determine the orientation of each peptide plane with respect to the magnetic field vector, B/sub O/, to within a few symmetry related possibilities. The computer program Totlink can then be used to perform the necessary coordinate transformations and to evaluate the possible backbone structures and select for the most chemically reasonable. Experimental /sup 14/N NMR structural studies of the model peptides n-acetyl-d,l-valine, n-acetyl-l-valyl-l-leucine, and l-alanyl-glycyl-glycine and preliminary /sup 14/N NMR results on a large single crystal of orthorhombic lysozyme are presented.

  16. Synthesis of a new 1,2,3,4,5-pentasubstituted cyclohexanol and determining its stereochemistry by NMR spectroscopy and quantum-chemical calculations.

    PubMed

    Mamedov, Ibrahim; Abbasoglu, Rza; Bayramov, Musa; Maharramov, Abel

    2016-04-01

    The presence of substituents in cyclohexane can influence to the ratio of conformers; for some cases, the boat form is preferable. The new six-membered cyclohexanol derivative 2 has been obtained by the synthesis of (E)-1-(bromophenyl)-3-phenylpropen-2-one (1). The NMR and quantum-chemical conformational analysis for the 2 have carried out, and its possible mechanism of formation was given. Copyright © 2015 John Wiley & Sons, Ltd. PMID:26939987

  17. 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.

  18. 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

  19. 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.

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

    NASA Astrophysics Data System (ADS)

    Alver, Özgür; Dikmen, Gökhan

    2016-03-01

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

  1. 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

  2. Sub-cellular localisation of a 15N-labelled peptide vector using NanoSIMS imaging

    NASA Astrophysics Data System (ADS)

    Römer, Winfried; Wu, Ting-Di; Duchambon, Patricia; Amessou, Mohamed; Carrez, Danièle; Johannes, Ludger; Guerquin-Kern, Jean-Luc

    2006-07-01

    Dynamic SIMS imaging is proposed to map sub-cellular distributions of isotopically labelled, exogenous compounds. NanoSIMS imaging allows the characterisation of the intracellular transport pathways of exogenous molecules, including peptide vectors employed in innovative therapies, using stable isotopes as molecular markers to detect the compound of interest. Shiga toxin B-subunit (STxB) was chosen as a representative peptide vector. The recombinant protein ( 15N-STxB) was synthesised in Escherichia coli using 15NH 4Cl as sole nitrogen source resulting in 15N enrichment in the molecule. Using the NanoSIMS 50 ion microprobe (Cameca), different ion species ( 12C 14N -, 12C 15N -, 31P -) originating from the same sputtered micro volume were simultaneously detected. High mass resolving power enabled the discrimination of 12C 15N - from its polyatomic isobars of mass 27. We imaged the membrane binding and internalisation of 15N-STxB in HeLa cells at spatial resolutions of less than 100 nm. Thus, the use of rare stable isotopes like 15N with dynamic SIMS imaging permits sub-cellular detection of isotopically labelled, exogenous molecules and imaging of their transport pathways at high mass and spatial resolution. Application of stable isotopes as markers can replace the large and chemically complex tags used for fluorescence microscopy, without altering the chemical and physical properties of the molecule.

  3. Protein structure determination with paramagnetic solid-state NMR spectroscopy.

    PubMed

    Sengupta, Ishita; Nadaud, Philippe S; Jaroniec, Christopher P

    2013-09-17

    +)-tagged GB1 mutants to rapidly determine the global protein fold in a de novo fashion. Remarkably, these studies required quantitative measurements of only approximately four or five backbone amide (15)N longitudinal paramagnetic relaxation enhancements per residue, in the complete absence of the usual internuclear distance restraints. Importantly, this paramagnetic solid-state NMR methodology is general and can be directly applied to larger proteins and protein complexes for which a significant fraction of the signals can be assigned in standard 2D and 3D MAS NMR chemical shift correlation spectra.

  4. 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.

  5. FTIR and 1H MAS NMR investigations on the correlation between the frequency of stretching vibration and the chemical shift of surface OH groups of solids

    NASA Astrophysics Data System (ADS)

    Brunner, Eike; Karge, H. G.; Pfeifer, H.

    1992-03-01

    The study of surface hydroxyl groups of solids, especially of zeolites, belongs to the 'classical' topics of IR spectroscopy since physico-chemical information may be derived from the wavenumber (nu) OH of the stretching vibration of the different hydroxyls. On the other hand, the last decade has seen the development of high resolution solid-state NMR spectroscopy and through the use of the so-called magic-angle-spinning technique (MAS) the signals of different hydroxyl species can be resolved in the 1H NMR spectra of solids. The chemical shift (delta) H describing the position of these lines may be used as well as (nu) OH to characterize quantitatively the strength of acidity of surface OH groups of solids. In a first comparison of (nu) OH with (delta) H for several types of surface OH groups, a linear correlation between them could be found. The aim of this paper was to prove the validity of this correlation for a wide variety of hydroxyls. The IR measurements were carried out on a Perkin-Elmer FTIR spectrometer 1800 at the Fritz Haber Institute of the Max Planck Society, Berlin, and the 1H MAS NMR spectra were recorded on a Bruker MSL- 300 at the University of Leipzig.

  6. Hydrogen-bonding and the dissolution mechanism of uracil in an acetate ionic liquid: new insights from NMR spectroscopy and quantum chemical calculations.

    PubMed

    Araújo, João M M; Pereiro, Ana B; Canongia Lopes, José N; Rebelo, Luís P N; Marrucho, Isabel M

    2013-04-18

    The dissolution of uracil-a pyrimidine nucleic acid base-in the ionic liquid 1-ethyl-3-methylimidazolium acetate ([C2mim][CH3COO]) has been investigated by methods of (1)H and (13)C NMR spectroscopy, (1)H-(1)H NOESY NMR spectroscopy, and quantum chemical calculations. The uracil-[C2mim][CH3COO] interactions that define the dissolution mechanism comprise the hydrogen bonds between the oxygen atoms of the acetate anion and the hydrogen atoms of the N1-H and N3-H groups of uracil and also the hydrogen bonds between the most acidic aromatic hydrogen atom (H2) of the imidazolium cation and the oxygen atoms of the carbonyl groups of uracil. The bifunctional solvation nature of the ionic liquid can be inferred from the presence of interactions between both ions of the ionic liquid and the uracil molecule. The location of such interaction sites was revealed using NMR data ((1)H and (13)C chemical shifts both in the IL and in the uracil molecule), complemented by DFT calculations. NOESY experiments provided additional evidence concerning the cation-uracil interactions.

  7. Molecular level investigations of phosphate sorption on corundum (α-Al2O3) by 31P solid state NMR, ATR-FTIR and quantum chemical calculation

    NASA Astrophysics Data System (ADS)

    Li, Wei; Pierre-Louis, Andro-Marc; Kwon, Kideok D.; Kubicki, James D.; Strongin, Daniel R.; Phillips, Brian L.

    2013-04-01

    Phosphate sorption at the corundum (α-Al2O3)/water interface was investigated as a function of phosphate concentration (0.1-1 mM) and pH (3-11) by 31P solid state NMR spectroscopy, ATR-FTIR, and quantum chemical calculation. The 31P NMR spectra indicate that under these experimental conditions phosphate adsorbs onto corundum mainly as inner-sphere complexes that yield a peak at δP = -2.8 ppm with full width at half maximum (FWHM) of 9.2 ppm, with a small amount aluminum phosphate surface precipitates as suggested by an NMR signal observed from δP = -12 to -20 ppm. We employed 31P{27Al} rotational echo adiabatic passage double resonance (REAPDOR) to further analyze the phosphate adsorption samples prepared at pH 5 and 9 in order to determine the phosphate/Al coordination. To aid interpretation of the NMR data, a series of bidentate and monodentate structural models of phosphate adsorbed on corundum (0 0 1) and (0 1 2) surfaces were calculated using density function theory (DFT). By comparing the experimental REAPDOR curves and those simulated from these models, we can assign the dominant peaks to bidentate binuclear surface complexes. Formation of bidentate binuclear surface complexes is supported by the ATR/FTIR spectra combined with DFT calculation, which further suggests a mixture of non-protonated bidentate and mono-protonated bidentate surface complexes on the corundum surface at pH 5. At pH 9, both NMR and ATR/FTIR indicate the formation of bidentate surface complexes on corundum surface.

  8. Solid-state NMR and density functional theory studies of ionization states of thiamin.

    PubMed

    Paramasivam, Sivakumar; Balakrishnan, Anand; Dmitrenko, Olga; Godert, Amy; Begley, Tadhg P; Jordan, Frank; Polenova, Tatyana

    2011-02-01

    Thiamin diphosphate (ThDP) is a key coenzyme in sugar metabolism. The 4'-aminopyrimidine ring of ThDP cycles through several ionization and tautomeric states during enzyme catalysis, but it is not fully understood which states are adopted during the individual steps of the catalytic cycle. Thiamin has been synthesized with labels selectively inserted into the C2 and C6' positions, as well as into the amino group, creating [C2, C6'-(13)C(2)] thiamin and [N4'-(15)N] thiamin. Magic-angle spinning (MAS) NMR spectroscopy has been employed to record the (13)C and (15)N chemical shift anisotropy (CSA) tensors for C2, C6', and N4' atoms. Our results indicate that the isotropic chemical shifts as well as the principal components of the (13)C and (15)N CSA tensors are very sensitive to the protonation states in these compounds and, therefore, permit differentiating between the two ionization states, 4-aminopyrimidine and 4-aminopyrimidinium. Using density functional theory (DFT), we have calculated the magnetic shielding anisotropy tensors of C2, C6', and N4' and found excellent agreement between the computed and the experimental tensors. Our findings indicate that MAS NMR spectroscopy in conjunction with DFT calculations is a sensitive probe of ionization states in the thiamin cofactor. The results of this study will serve as a guide for characterization of ionization and tautomeric states of thiamin in complexes with thiamin-dependent enzymes.

  9. Probing NMR parameters, structure and dynamics of 5-nitroimidazole derivatives. Density functional study of prototypical radiosensitizers.

    PubMed

    Ramalho, Teodorico C; Bühl, Michael

    2005-02-01

    The 15N chemical shifts of metronidazole (1), secnidazole (2), nimorazole (3) and tinidazole (4), radiosensitizers based on the 5-nitroimidazole motif, are reported. A detailed computational study of 1 is presented, calling special attention to the performance of various theoretical methods in reproducing the 13C and 15N data observed in solution. The most sophisticated approach involves density functional-based Car-Parrinello molecular dynamics simulations (CPMD) of 1 in aqueous solution (BP86 level) and averaging chemical shifts over snapshots from the trajectory. In the NMR calculations for these snapshots (performed at the B3LYP level), a small number of discrete water molecules are retained, and the remaining bulk solution effects are included via a polarizable continuum model (PCM). A similarly good accord with experiment is obtained from much less involved, static geometry optimization and NMR computation of pristine 1 employing a PCM approach. Solvent effects on delta(15N), which are of the order of up to 20 ppm, are not due to changes in geometric parameters upon solvation, but arise from the direct response of the electronic wavefunction to the presence of the solvent, which can be represented by discrete molecules and/or the dielectric bulk. PMID:15558660

  10. Vertical δ13C and δ15N changes during pedogenesis

    NASA Astrophysics Data System (ADS)

    Brunn, Melanie; Spielvogel, Sandra; Wells, Andrew; Condron, Leo; Oelmann, Yvonne

    2015-04-01

    The natural abundance of soil organic matter (SOM) stable C and N isotope ratios are subjected to vertical changes throughout the soil profile. This vertical distribution is a widely reported phenomenon across varieties of ecosystems and constitutes important insights of soil carbon cycling. In most ecosystems, SOM becomes enriched in heavy isotopes by several per mill in the first few centimeters of the topsoil. The enrichment of 13C in SOM with soil depth is attributed to biological and physical-chemical processes in soil e.g., plant physiological impacts, microbial decomposition, sorption and transport processes. Such vertical trends in 13C and 15N abundance have rarely been related to SOM composition during pedogenesis. The aims of our study were to investigate short and long-term δ13C and δ15N depth changes and their interrelations under progressing pedogenesis and ecosystem development. We sampled soils across the well studied fordune progradation Haast-chronosequence, a dune ridge system under super-humid climate at the West Coast of New Zealand's South Island (43° 53' S, 169° 3' E). Soils from 11 sites with five replicates each covered a time span of around 2870 yr of soil development (from Arenosol to Podzol). Vertical changes of δ13C and δ15N values of SOM were investigated in the organic layers and in 1-cm depth intervals of the upper 10 cm of the mineral soil. With increasing soil depth SOM became enriched in δ13C by 1.9 ± SE 0.1 o and in δ15N by 6.0 ± 0.4 ‰˙Litter δ13C values slightly decreased with increasing soil age (r = -0.61; p = 0.00) likely due to less efficient assimilation linked to nutrient limitations. Fractionation processes during mycorrhizal transfer appeared to affect δ15N values in the litter. We found a strong decrease of δ15N in the early succession stages ≤ 300 yr B.P. (r = -0.95; p = 0.00). Positive relations of vertical 13C and 15N enrichment with soil age might be related to decomposition and appeared to be

  11. Conformational and configurational analysis of an N,N carbonyl dipyrrinone-derived oximate and nitrone by NMR and quantum chemical calculations.

    PubMed

    Walton, Ian; Davis, Marauo; Yang, Liu; Zhang, Yong; Tillman, Destin; Jarrett, William L; Huggins, Michael T; Wallace, Karl J

    2011-05-01

    The geometries and relative energies of new N,N carbonyl dipyrrinone-derived oxime molecules (E/Z-s-cis 4a and E/Z-s-cis 4b) have been investigated. The calculated energies, molecular geometries, and (1) H/(13) C NMR chemical shifts agree with experimental data, and the results are presented herein. The E-s-cis conformations of 4a and 4b and the Z-s-cis conformation of 5b were found to be the thermodynamically most stable isomers with the oxime hydrogen atom or the methyl functional group adopting an anti-orientation with respect to the dipyrrinone group. This conformation was unambiguously supported by a number of 2D NMR experiments.

  12. Synthetic analogues of the histidine-chlorophyll complex: a NMR study to mimic structural features of the photosynthetic reaction center and the light-harvesting complex.

    PubMed

    van Gammeren, Adriaan J; Hulsbergen, Frans B; Erkelens, Cornelis; De Groot, Huub J M

    2004-01-01

    Mg(II)-porphyrin-ligand and (bacterio)chlorophyl-ligand coordination interactions have been studied by solution and solid-state MAS NMR spectroscopy. (1)H, (13)C and (15)N coordination shifts due to ring currents, electronic perturbations and structural effects are resolved for imidazole (Im) and 1-methylimidazole (1-MeIm) coordinated axially to Mg(II)-OEP and (B)Chl a. As a consequence of a single axial coordination of Im or 1-MeIm to the Mg(II) ion, 0.9-5.2 ppm (1)H, 0.2-5.5 ppm (13)C and 2.1-27.2 ppm (15)N coordination shifts were measured for selectively labeled [1,3-(15)N]-Im, [1,3-(15)N,2-(13)C]-Im and [1,3-(15)N,1,2-(13)C]-1-MeIm. The coordination shifts depend on the distance of the nuclei to the porphyrin plane and the perturbation of the electronic structure. The signal intensities in the (1)H NMR spectrum reveal a five-coordinated complex, and the isotropic chemical shift analysis shows a close analogy with the electronic structure of the BChl a-histidine in natural light harvesting 2 complexes. The line broadening of the ligand responses support the complementary IR data and provide evidence for a dynamic coordination bond in the complex. PMID:14663650

  13. Implications of using approximate Bloch-McConnell equations in NMR analyses of chemically exchanging systems: application to the electron self-exchange of plastocyanin

    NASA Astrophysics Data System (ADS)

    Flemming Hansen, D.; Led, Jens J.

    2003-08-01

    The validity of a series of approximate solutions of the Bloch-McConnell equations normally applied in the analyses of chemically exchanging systems is evaluated, using the electron self-exchange (ESE) in the blue copper protein plastocyanin from Anabaena variabilis as an example. The evaluation is based on a comparison with the results of a complete analysis of the NMR signals of chemically exchanging nuclei that allows an independent and accurate determination of all the involved parameters. The complete analysis is based on the general solution of the Bloch-McConnell equations. It includes a simultaneous analysis of the chemical shift, and the transverse and longitudinal relaxation rates of the observed nuclei as well as the variation of these parameters with the molar fractions of the exchanging species and the rate of the chemical exchange process. The linear prediction model method was used in the data analysis to achieve the highest possible precision. Surprisingly, it is found that the fast exchange condition may not be fulfilled even in cases where a single exchange-averaged NMR signal is observed, and the Larmor frequency and relaxation rates depend linearly on the molar fractions of the exchanging species. In such cases the use of approximate solutions in the analysis of the transverse relaxation rates and the pseudo-contact shifts can lead to erroneous results. In limiting cases close to the fast exchange and slow exchange regimes correct values of some of the parameters can be obtained using the second order approximate solution of the Bloch-McConnell equations. In contrast, the complete analysis of the NMR signals results in an accurate determination of the exchange rates and the NMR parameters of the exchanging sites. This, in turn, can provide information about the structure and function of a protein undergoing chemically exchange. For the investigated plastocyanin the complete analysis results in an accurate determination of the paramagnetic

  14. HR-MAS NMR spectroscopy of reconstructed human epidermis: potential for the in situ investigation of the chemical interactions between skin allergens and nucleophilic amino acids.

    PubMed

    Elbayed, Karim; Berl, Valérie; Debeuckelaere, Camille; Moussallieh, François-Marie; Piotto, Martial; Namer, Izzie-Jacques; Lepoittevin, Jean-Pierre

    2013-01-18

    High-resolution magic angle spinning (HR-MAS) is a nuclear magnetic resonance (NMR) technique that enables the characterization of metabolic phenotypes/metabolite profiles of cells, tissues, and organs, under both normal and pathological conditions, without resorting to time-consuming extraction techniques. In this article, we explore a new domain of application of HR-MAS, namely, reconstructed human epidermis (RHE) and the in situ observation of chemical interactions between skin sensitizers and nucleophilic amino acids. First, the preparation, storage, and analysis of RHE were optimized, and this work demonstrated that HR-MAS NMR was well adapted for investigating RHE with spectra of good quality allowing qualitative as well as quantitative studies of metabolites. Second, in order to study the response of RHE to chemical sensitizers, the ((13)C)methyldodecanesulfonate was chosen as an NMR probe, and we compared adducts formed on human serum albumin (HSA) in solution and adducts formed in RHE. Thus, while the modification of proteins or peptides in solution takes several days to lead to a significant amount of modification, in RHE the modifications of nucleophilic amino acids were observable already at 24 h. The chemioselectivity also appeared to be different with major modifications taking place on histidine, methionine, and cysteine residues in RHE, while on HSA, significant modifications were observed on lysine residues with the formation of methylated and dimethylated amino groups. We thus demonstrated that RHE could be used to investigate in situ chemical interactions taking place between skin sensitizers and nucleophilic amino acids. This opens perspectives for the molecular understanding of the skin immune system activation by sensitizing chemicals.

  15. 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.

  16. Predictions of the fluorine NMR chemical shifts of perfluorinated carboxylic acids, CnF(2n+1)COOH (n = 6-8).

    PubMed

    Liu, Zizhong; Goddard, John D

    2009-12-17

    Perfluorinated carboxylic acids (PFCAs) are a class of persistent environmental pollutants. Commercially available PFCAs are mixtures of linear and branched isomers, possibly with impurities. Different isomers have different physical and chemical properties and toxicities. However, little is known about the properties and the finer details of the structures of the individual branched isomers. Full geometry optimizations for the linear n-alkane (C(6)-C(27)) PFCAs indicated that all have helical structures. The helical angle increases slightly with increasing chain length, from 16.3 degrees in C(6)F(13)COOH to 17.0 degrees in C(27)F(55)COOH. This study predicts (19)F NMR parameters for 69 linear and branched isomers of the perfluoro carboxylic acids C(6)F(13)COOH, C(7)F(15)COOH, and C(8)F(17)COOH. B3LYP-GIAO/6-31++G(d,p)//B3LYP/6-31G(d,p) was used for the NMR calculations with analysis of the chemical shifts by the natural bond orbital method. The predictions of the (19)F chemical shifts revealed the differences among the CF(3), CF(2), and CF groups. In general, the absolute values for the chemical shifts for the CF(3) group are smaller than 90 ppm, for the CF larger than 160 ppm, and for the CF(2) between 110 and 130 ppm. The chemical shifts of the branched isomers are smaller in magnitude than the linear ones. The decrease is correlated with the steric hindrance of the CF(3) groups, the more hindered the CF(3), the greater the decrease in the (19)F chemical shifts. The predicted (19)F chemical shifts are similar to those for analogous perfluoro compounds with other terminal functional groups such as -SO(3)H or -SO(3)NH(2)CH(2)CH(3).

  17. Chemical Characterization and Water Content Determination of Bio-Oils Obtained from Various Biomass Species using 31P NMR Spectroscopy

    SciTech Connect

    David, K.; Ben, H.; Muzzy, J.; Feik, C.; Iisa, K.; Ragauskas, A.

    2012-03-01

    Pyrolysis is a promising approach to utilize biomass for biofuels. One of the key challenges for this conversion is how to analyze complicated components in the pyrolysis oils. Water contents of pyrolysis oils are normally analyzed by Karl Fischer titration. The use of 2-chloro-4,4,5,5,-tetramethyl-1,3,2-dioxaphospholane followed by {sup 31}P NMR analysis has been used to quantitatively analyze the structure of hydroxyl groups in lignin and whole biomass. Results: {sup 31}P NMR analysis of pyrolysis oils is a novel technique to simultaneously characterize components and analyze water contents in pyrolysis oils produced from various biomasses. The water contents of various pyrolysis oils range from 16 to 40 wt%. The pyrolysis oils obtained from Loblolly pine had higher guaiacyl content, while that from oak had a higher syringyl content. Conclusion: The comparison with Karl Fischer titration shows that {sup 31}P NMR could also reliably be used to measure the water content of pyrolysis oils. Simultaneously with analysis of water content, quantitative characterization of hydroxyl groups, including aliphatic, C-5 substituted/syringyl, guaiacyl, p-hydroxyl phenyl and carboxylic hydroxyl groups, could also be provided by {sup 31}P NMR analysis.

  18. Chemical Origins of Permanent Set in a Peroxide Cured Filled Silicone Elastomer - Tensile and 1H NMR Analysis

    SciTech Connect

    Chinn, S; Deteresa, S; Shields, A; Sawvel, A; Balazs, B; Maxwell, R S

    2004-10-29

    The aging of a commercial filled siloxane polymeric composite in states of high stress and Co-60 {gamma}-radiation exposure has been studied. DC-745 is a commercially available silicone elastomer consisting of dimethyl, methyl-phenyl, and vinyl-methyl siloxane monomers crosslinked with a peroxide vinyl specific curing agent. It is filled with {approx}30 wt.% mixture of high and low surface area silicas. This filled material is shown to be subject to permanent set if exposed to radiation while under tensile stress. Tensile modulus measurements show that the material gets marginally softer with combined radiation exposure and tensile strain as compared to material exposed to radiation without tensile strain. In addition, the segmental dynamics as measured by both uniaxial NMR relaxometry and Multiple Quantum NMR methods indicate that the material is undergoes radiatively-induced crosslinking in the absence of tensile strain and a combination of crosslinking and strain dependent increase in dynamic order parameter for the network chains. The MQ-NMR also suggests a small change in the number of polymer chains associated with the silica filler surface. Comparison of the prediction of the relative change in crosslink density from the NMR data as well as solvent swelling data and from that predicted from the Tobolsky model suggest that degradation leads to a deviation from Gaussian chain statistics and the formation of increased numbers of elastically ineffective network chains.

  19. Geometries and tautomerism of OHN hydrogen bonds in aprotic solution probed by H/D isotope effects on (13)C NMR chemical shifts.

    PubMed

    Tolstoy, Peter M; Guo, Jing; Koeppe, Benjamin; Golubev, Nikolai S; Denisov, Gleb S; Smirnov, Sergei N; Limbach, Hans-Heinrich

    2010-10-14

    The (1)H and (13)C NMR spectra of 17 OHN hydrogen-bonded complexes formed by CH(3)(13)COOH(D) with 14 substituted pyridines, 2 amines, and N-methylimidazole have been measured in the temperature region between 110 and 150 K using CDF(3)/CDF(2)Cl mixture as solvent. The slow proton and hydrogen bond exchange regime was reached, and the H/D isotope effects on the (13)C chemical shifts of the carboxyl group were measured. In combination with the analysis of the corresponding (1)H chemical shifts, it was possible to distinguish between OHN hydrogen bonds exhibiting a single proton position and those exhibiting a fast proton tautomerism between molecular and zwitterionic forms. Using H-bond correlations, we relate the H/D isotope effects on the (13)C chemical shifts of the carboxyl group with the OHN hydrogen bond geometries.

  20. 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

  1. High accuracy NMR chemical shift corrected for bulk magnetization as a tool for structural elucidation of dilutable microemulsions. Part 1 - Proof of concept.

    PubMed

    Hoffman, Roy E; Darmon, Eliezer; Aserin, Abraham; Garti, Nissim

    2016-02-01

    In microemulsions, changes in droplet size and shape and possible transformations occur under various conditions. They are difficult to characterize by most analytical tools because of their nano-sized structure and dynamic nature. Several methods are usually combined to obtain reliable information, guiding the scientist in understanding their physical behavior. We felt that there is a need for a technique that complements those in use today in order to provide more information on the microemulsion behavior, mainly as a function of dilution with water. The improvement of NMR chemical shift measurements independent of bulk magnetization effects makes it possible to study the very weak intermolecular chemical shift effects. In the present study, we used NMR high resolution magic angle spinning to measure the chemical shift very accurately, free of bulk magnetization effects. The chemical shift of microemulsion components is measured as a function of the water content in order to validate the method in an interesting and promising, U-type dilutable microemulsion, which had been previously studied by a variety of techniques. Phase transition points of the microemulsion (O/W, bicontinuous, W/O) and changes in droplet shape were successfully detected using high-accuracy chemical shift measurements. We analyzed the results and found them to be compatible with the previous studies, paving the way for high-accuracy chemical shifts to be used for the study of other microemulsion systems. We detected two transition points along the water dilution line of the concentrate (reverse micelles) corresponding to the transition from swollen W/O nano-droplets to bicontinuous to the O/W droplets along with the changes in the droplets' sizes and shapes. The method seems to be in excellent agreement with other previously studied techniques and shows the advantage of this easy and valid technique.

  2. 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

  3. Use of solid waste for chemical stabilization: Adsorption isotherms and {sup 13}C solid-state NMR study of hazardous organic compounds sorbed on coal fly ash

    SciTech Connect

    Netzel, D.A.; Lane, D.C.; Rovani, J.F.; Cox, J.D.; Clark, J.A.; Miknis, F.P.

    1993-09-01

    Adsorption of hazardous organic compounds on the Dave Johnston plant fly ash is described. Fly ash from Dave Johnston and Laramie River power plants were characterized using elemental, x-ray, and {sup 29}Si NMR; the Dave Johnston (DJ) fly ash had higher quartz contents, while the Laramie River fly ash had more monomeric silicate anions. Adsorption data for hydroaromatics and chlorobenzenes indicate that the adsorption capacity of DJ coal fly ash is much less than that of activated carbon by a factor of >3000; but it is needed to confirm that solid-gas and solid-liquid equilibrium isotherms can indeed be compared. However, for pyridine, pentachlorophenol, naphthalene, and 1,1,2,2-tetrachloroethane, the DJ fly ash appears to adsorb these compounds nearly as well as activated carbon. {sup 13}C NMR was used to study the adsorption of hazardous org. cpds on coal fly ash; the nuclear spin relaxation times often were very long, resulting in long experimental times to obtain a spectrum. Using a jumbo probe, low concentrations of some hazardous org. cpds could be detected; for pentachlorophenol adsorbed onto fly ash, the chemical shift of the phenolic carbon was changed. Use of NMR to study the adsorption needs further study.

  4. Chemical proteomic tool for ligand mapping of CYP antitargets: an NMR-compatible 3D QSAR descriptor in the Heme-Based Coordinate System.

    PubMed

    Yao, Huili; Costache, Aurora D; Sem, Daniel S

    2004-01-01

    Chemical proteomic strategies strive to probe and understand protein-ligand interactions across gene families. One gene family of particular interest in drug and xenobiotic metabolism are the cytochromes P450 (CYPs), the topic of this article. Although numerous tools exist to probe affinity of CYP-ligand interactions, fewer exist for the rapid experimental characterization of the structural nature of these interactions. As a complement to recent advances in X-ray crystallography, NMR methods are being developed that allow for fairly high throughput characterization of protein-ligand interactions. One especially promising NMR approach involves the use of paramagnetic induced relaxation effects to measure distances of ligand atoms from the heme iron in CYP enzymes. Distances obtained from these T(1) relaxation measurements can be used as a direct source of 1-dimensional structural information or to restrain a ligand docking to generate a 3-dimensional data set. To facilitate such studies, we introduce the concept of the Heme-Based Coordinate System and present how it can be used in combination with NMR T(1) relaxation data to derive 3D QSAR descriptors directly or in combination with in silico docking. These descriptors should have application in defining the binding preferences of CYP binding sites using 3D QSAR models. They are especially well-suited for the biasing of fragment assembly and combinatorial chemistry drug design strategies, to avoid fragment or reagent combinations with enhanced affinity for CYP antitargets.

  5. 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.

  6. Empirical Calculations of {sup 29}Si NMR Chemical Shielding Tensors: A Partial Charge Model Investigation of Hydrolysis in Organically Modified Alkoxy Silanes

    SciTech Connect

    Alam, Todd M.; Henry, Marc

    1999-08-05

    Organically modified alkoxy silanes play an important role in tailoring different properties of silica produced by the sol-gel method. Changes in the size and functionality of the organic group allows control of both physical and chemical properties of the resulting gel, with the kinetics of the polymerization process playing an important role in the design of new siloxane materials. High resolution {sup 29}Si NMR has proven to be valuable tool for monitoring the polymerization reaction, and has been used to investigate a variety of organically modified alkoxy silane systems.

  7. 1H and 13C NMR Chemical Shift Assignments and Conformational Analysis for the Two Diastereomers of the Vitamin K Epoxide Reductase Inhibitor Brodifacoum

    SciTech Connect

    Cort, John R.; Cho, Herman M.

    2009-10-01

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

  8. 1H, 13C and 15N resonance assignments and secondary structure analysis of translation initiation factor 1 from Pseudomonas aeruginosa

    PubMed Central

    Bernal, Alejandra; Hu, Yanmei; Palmer, Stephanie O.; Silva, Aaron; Bullard, James; Zhang, Yonghong

    2016-01-01

    Pseudomonas aeruginosa is a Gram-negative opportunistic pathogen and a primary cause of infection in humans. P. aeruginosa can acquire resistance against multiple groups of antimicrobial agents, including β-lactams, aminoglycosides and fluoroquinolones, and multidrug resistance is increasing in this organism which makes treatment of the infections difficult and expensive. This has led to the unmet need for discovery of new compounds distinctly different from present antimicrobials. Protein synthesis is an essential metabolic process and a validated target for the development of new antibiotics. Translation initiation factor 1 from P. aeruginosa (Pa-IF1) is the smallest of the three initiation factors that acts to establish the 30S initiation complex to initiate translation during protein biosynthesis, and its structure is unknown. Here we report the 1H, 13C and 15N chemical shift assignments of Pa-IF1 as the basis for NMR structure determination and interaction studies. Secondary structure analyses deduced from the NMR chemical shift data have identified five β-strands with an unusually extended β-strand at the C-terminal end of the protein and one short α-helix arranged in the sequential order β1–β2–β3–α1–β4–β5. This is further supported by 15N–{1H} hetero NOEs. These secondary structure elements suggest the Pa-IF1 adopts the typical β-barrel structure and is composed of an oligomer-binding motif. PMID:26983940

  9. Nanoscale studies of cement chemistry with 15N resonance reaction analysis

    NASA Astrophysics Data System (ADS)

    Schweitzer, Jeffrey S.; Livingston, Richard A.; Rolfs, Claus; Becker, Hans-Werner; Kubsky, Stefan; Spillane, Timothy; Castellote, Marta; de Viedma, Paloma G.

    2005-12-01

    Analyses of materials with ion beams have proven to be a valuable technique for describing the spatial distributions of specific elements in host materials. We have applied this technique using the 15N(p, αγ)12C reaction to study the time dependence of the chemical reactions involved in the curing of cement. By using the Dynamitron Tandem accelerator at the Ruhr Universität, Bochum, Germany, we have been able to achieve a few nanometer spatial resolution at the surface of cement grains and to study the hydrogen distributions to a depth of about 2 μm. By applying a technique for stopping the chemical reactions at arbitrary times, the time dependence of the chemical reactions involving specific components of cement can be investigated. In addition, the effects of additives on the chemical reactions have been studied, as have materials that are components of concrete.

  10. New strategy for stable-isotope-aided, multidimensional NMR spectroscopy of DNA oligomers

    SciTech Connect

    Ono, Okira; Tate, Shin-Ichi; Kainosho, Masatsune

    1994-12-01

    Nuclear Magnetic Resonance (NMR) is the most efficient method for determining the solution structures of biomolecules. By applying multidimensional heteronuclear NMR techniques to {sup 13}C/{sup 15}N-labeled proteins, we can determine the solution structures of proteins with molecular mass of 20 to 30kDa at an accuracy similar to that of x-ray crystallography. Improvements in NMR instrumentation and techniques as well as the development of protein engineering methods for labeling proteins have rapidly advanced multidimensional heteronuclear NMR of proteins. In contrast, multidimensional heteronuclear NMR studies of nucleic acids is less advanced because there were no efficient methods for preparing large amounts of labeled DNA/RNA oligomers. In this report, we focused on the chemical synthesis of DNA oligomers labeled at specific residue(s). RNA oligomers with specific labels, which are difficult to synthesize by the enzyme method, can be synthesized by the chemical method. The specific labels are useful for conformational analysis of larger molecules such as protein-nucleic acid complexes.

  11. 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

  12. Effects of structural differences on the NMR chemical shifts in cinnamic acid derivatives: Comparison of GIAO and GIPAW calculations

    NASA Astrophysics Data System (ADS)

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

    2016-06-01

    In this article we report the results of combined theoretical and experimental structural studies on cinnamic acid derivatives (CADs), one of the main groups of secondary metabolites present in various medicinal plant species and food products of plant origin. The effects of structural differences in CADs on their spectroscopic properties were studied in detail by both: solid-state NMR and GIAO/GIPAW calculations. Theoretical computations were used in order to perform signal assignment in 13C CP/MAS NMR spectra of the cinnamic, o-coumaric, m-coumaric, p-coumaric, caffeic, ferulic, sinapic and 3,4-dimethoxycinnamic acids, and to evaluate the accuracy of GIPAW and GIAO methodology.

  13. Asymmetric simultaneous phase-inversion cross-polarization in solid-state MAS NMR: Relaxing selective polarization transfer condition between two dilute spins

    NASA Astrophysics Data System (ADS)

    Zhang, Zhengfeng; Fu, Riqiang; Li, Jianping; Yang, Jun

    2014-05-01

    Double cross polarization (DCP) has been widely used for heteronuclear polarization transfer between 13C and 15N in solid-state magic-angle spinning (MAS) NMR. However, DCP is such sensitive to experimental settings that small variations or deviations in RF fields would deteriorate its efficiency. Here, we report on asymmetric simultaneous phase-inversion cross polarization (referred as aSPICP) for selective polarization transfer between low-γ 13C and 15N spins. We have demonstrated through simulations and experiments using biological solids that the asymmetric duration in the simultaneous phase-inversion cross polarization scheme leads to efficient polarization transfer between 13C and 15N even with large chemical shift anisotropies in the presence of B1 field variations or mismatch of the Hartmann-Hahn conditions. This could be very useful in the aspect of long-duration experiments for membrane protein studies at high fields.

  14. Lab-on-a-chip reactor imaging with unprecedented chemical resolution by Hadamard-encoded remote detection NMR.

    PubMed

    Telkki, Ville-Veikko; Zhivonitko, Vladimir V; Selent, Anne; Scotti, Gianmario; Leppäniemi, Jarmo; Franssila, Sami; Koptyug, Igor V

    2014-10-13

    The development of microfluidic processes requires information-rich detection methods. Here we introduce the concept of remote detection exchange NMR spectroscopy (RD-EXSY), and show that, along with indirect spatial information extracted from time-of-flight data, it provides unique information about the active regions, reaction pathways, and intermediate products in a lab-on-a-chip reactor. Furthermore, we demonstrate that direct spatial resolution can be added to RD-EXSY efficiently by applying the principles of Hadamard spectroscopy.

  15. MILLIMETER-WAVE OBSERVATIONS OF CN AND HNC AND THEIR {sup 15}N ISOTOPOLOGUES: A NEW EVALUATION OF THE {sup 14}N/{sup 15}N RATIO ACROSS THE GALAXY

    SciTech Connect

    Adande, G. R.; Ziurys, L. M.

    2012-01-10

    The N = 1 {yields} 0 transitions of CN and C{sup 15}N (X{sup 2}{Sigma}{sup +}), as well as the J = 1 {yields} 0 lines of HN{sup 13}C and H{sup 15}NC, have been observed toward 11 molecular clouds using the new 3 mm ALMA-type receiver of the 12 m telescope of the Arizona Radio Observatory. These sources span a wide range of distances from the Galactic center and are all regions of star formation. From these observations, {sup 14}N/{sup 15}N ratios have been determined using two independent methods. First, the measurements of C{sup 14}N and C{sup 15}N were directly compared to establish this ratio, correcting for high opacities when needed, as indicated by the nitrogen hyperfine intensities. Second, the ratio was calculated from the quantity [HN{sup 13}C]/[H{sup 15}NC], determined from the HNC data, and then scaled by {sup 12}C/{sup 13}C ratios previously established, i.e., the so-called double isotope method. Values from both methods are in reasonable agreement, and fall in the range {approx}120-400, somewhat lower than previous {sup 14}N/{sup 15}N ratios derived from HCN. The ratios exhibit a distinct positive gradient with distance from the Galactic center, following the relationship{sup 14}N/{sup 15}N = 21.1 (5.2) kpc{sup -1} D{sub GC} + 123.8 (37.1). This gradient is consistent with predictions of Galactic chemical evolution models in which {sup 15}N has a secondary origin in novae, while primary and secondary sources exist for {sup 14}N. The local interstellar medium value was found to be {sup 4}N/{sup 15}N = 290 {+-} 40, in agreement with the ratio found in nearby diffuse clouds and close to the value of 272 found in Earth's atmosphere.

  16. A novel method for trapping and analyzing 15N in NO for tracing NO sources

    NASA Astrophysics Data System (ADS)

    Kang, Ronghua; Mulder, Jan; Dörsch, Peter

    2016-04-01

    15N isotope tracing is an effective and direct approach to investigate the biological and chemical sources of nitric oxide (NO) in soil. However, NO is highly reactive and rapidly converted to nitrogen dioxide (NO2) in the presence of ozone. Various chemical conversions of NO to the more stable solutes nitrite (NO2-) and nitrate (NO3-) have been proposed, which allow analysing the 15N abundance without major fractionation. However, NO emissions from soils are usually small, posing major challenges to conversion efficiency and background contamination. Here we present a novel method in which NO is oxidized to NO2- by chromium trioxide (CrO3) prior to conversion to NO2- and NO3- in an alkaline hydrogen peroxide (H2O2) solution. Immediately following trapping, manganese dioxide (MnO2) and 5M HCl are added to remove excess H2O2, and to adjust the pH to around 6.0-7.0, respectively. The resulting solution can be stored until analysis and is none-toxic, allowing to use a modified denitrifier method (Zhu et al., submitted), where NO2- and NO3- are reduced quantitatively to nitrous oxide (N2O). Optimum NO conversion rates of > 90% even at extremely low initial NO concentration were obtained with 4% H2O2, 0.5 M NaOH, and 0.5 L min-1 gas flow rate. In a laboratory test, using NO gas with different 15N signals produced from unlabelled and labelled NO2-, we found an overall precision of 0.4‰ for unlabelled and 49.7‰ for NO enriched with 1.0 atom% 15N, respectively. This indicates that this method can be used for both natural abundance studies of NO, as well as in labelling studies tracing NO sources. Zhu J, Yu L, Bakken LR, Mørkved PT, Mulder J, Dörsch P. Controlled induction of denitrification in Pseudomonas aureofaciens: a modified denitrifier method for 15N and 18O analysis in NO3- from natural water samples by IRMS. Submitted.

  17. Application of ChemDraw NMR Tool: Correlation of Program-Generated (Super 13)C Chemical Shifts and pK[subscript a] Values of Para-Substituted Benzoic Acids

    ERIC Educational Resources Information Center

    Hongyi Wang

    2005-01-01

    A study uses the ChemDraw nuclear magnetic resonance spectroscopy (NMR) tool to process 15 para-substituted benzoic acids and generate (super 13)C NMR chemical shifts of C1 through C5. The data were plotted against their pK[subscript a] value and a fairly good linear fit was found for pK[subscript a] versus delta[subscript c1].

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

    NASA Astrophysics Data System (ADS)

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

    2016-12-01

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

  19. Chemical characterization (GC/MS and NMR Fingerprinting) and bioactivities of South-African Pelargonium capitatum (L.) L' Her. (Geraniaceae) essential oil.

    PubMed

    Guerrini, Alessandra; Rossi, Damiano; Paganetto, Guglielmo; Tognolini, Massimiliano; Muzzoli, Mariavittoria; Romagnoli, Carlo; Antognoni, Fabiana; Vertuani, Silvia; Medici, Alessandro; Bruni, Alessandro; Useli, Chiara; Tamburini, Elena; Bruni, Renato; Sacchetti, Gianni

    2011-04-01

    Chemical fingerprinting of commercial Pelargonium capitatum (Geraniaceae) essential oil samples of south African origin was performed by GC, GC/MS, and (13) C- and (1) H-NMR. Thirty-seven compounds were identified, among which citronellol (32.71%) and geraniol (19.58%) were the most abundant. NMR Spectra of characteristic chemicals were provided. Broad-spectrum bioactivity properties of the oil were evaluated and compared with those of commercial Thymus vulgaris essential oil with the aim to obtain a functional profile in terms of efficacy and safety. P. capitatum essential oil provides a good performance as antimicrobial, with particular efficacy against Candida albicans strains. Antifungal activity performed against dermatophyte and phytopathogen strains revealed the latter as more sensitive, while antibacterial activity was not remarkable against both Gram-positive and Gram-negative bacteria. P. capitatum oil provided a lower antioxidant activity (IC(50) ) than that expressed by thyme essential oil, both in the 1,1-diphenyl-2-picrylhydrazyl (DPPH) and β-carotene bleaching tests. Results in photochemiluminescence (PCL) assay were negligible. To test the safety aspects of P. capitatum essential oil, mutagenic and toxicity properties were assayed by Ames test, with and without metabolic activation. Possible efficacy of P. capitatum essential oil as mutagenic protective agent against NaN(3) , 2-nitrofluorene, and 2-aminoanthracene was also assayed, providing interesting and significant antigenotoxic properties.

  20. Chemical characterization (GC/MS and NMR Fingerprinting) and bioactivities of South-African Pelargonium capitatum (L.) L' Her. (Geraniaceae) essential oil.

    PubMed

    Guerrini, Alessandra; Rossi, Damiano; Paganetto, Guglielmo; Tognolini, Massimiliano; Muzzoli, Mariavittoria; Romagnoli, Carlo; Antognoni, Fabiana; Vertuani, Silvia; Medici, Alessandro; Bruni, Alessandro; Useli, Chiara; Tamburini, Elena; Bruni, Renato; Sacchetti, Gianni

    2011-04-01

    Chemical fingerprinting of commercial Pelargonium capitatum (Geraniaceae) essential oil samples of south African origin was performed by GC, GC/MS, and (13) C- and (1) H-NMR. Thirty-seven compounds were identified, among which citronellol (32.71%) and geraniol (19.58%) were the most abundant. NMR Spectra of characteristic chemicals were provided. Broad-spectrum bioactivity properties of the oil were evaluated and compared with those of commercial Thymus vulgaris essential oil with the aim to obtain a functional profile in terms of efficacy and safety. P. capitatum essential oil provides a good performance as antimicrobial, with particular efficacy against Candida albicans strains. Antifungal activity performed against dermatophyte and phytopathogen strains revealed the latter as more sensitive, while antibacterial activity was not remarkable against both Gram-positive and Gram-negative bacteria. P. capitatum oil provided a lower antioxidant activity (IC(50) ) than that expressed by thyme essential oil, both in the 1,1-diphenyl-2-picrylhydrazyl (DPPH) and β-carotene bleaching tests. Results in photochemiluminescence (PCL) assay were negligible. To test the safety aspects of P. capitatum essential oil, mutagenic and toxicity properties were assayed by Ames test, with and without metabolic activation. Possible efficacy of P. capitatum essential oil as mutagenic protective agent against NaN(3) , 2-nitrofluorene, and 2-aminoanthracene was also assayed, providing interesting and significant antigenotoxic properties. PMID:21480508

  1. Isotope labeling for NMR studies of macromolecular structure and interactions

    SciTech Connect

    Wright, P.E.

    1994-12-01

    Implementation of biosynthetic methods for uniform or specific isotope labeling of proteins, coupled with the recent development of powerful heteronuclear multidimensional NMR methods, has led to a dramatic increase in the size and complexity of macromolecular systems that are now amenable to NMR structural analysis. In recent years, a new technology has emerged that combines uniform {sup 13}C, {sup 15}N labeling with heteronuclear multidimensional NMR methods to allow NMR structural studies of systems approaching 25 to 30 kDa in molecular weight. In addition, with the introduction of specific {sup 13}C and {sup 15}N labels into ligands, meaningful NMR studies of complexes of even higher molecular weight have become feasible. These advances usher in a new era in which the earlier, rather stringent molecular weight limitations have been greatly surpassed and NMR can begin to address many central biological problems that involve macromolecular structure, dynamics, and interactions.

  2. NbF{sub 5} and TaF{sub 5}: Assignment of {sup 19}F NMR resonances and chemical bond analysis from GIPAW calculations

    SciTech Connect

    Biswal, Mamata; Body, Monique; Legein, Christophe; Sadoc, Aymeric; Boucher, Florent

    2013-11-15

    The {sup 19}F isotropic chemical shifts (δ{sub iso}) of two isomorphic compounds, NbF{sub 5} and TaF{sub 5}, which involve six nonequivalent fluorine sites, have been experimentally determined from the reconstruction of 1D {sup 19}F MAS NMR spectra. In parallel, the corresponding {sup 19}F chemical shielding tensors have been calculated using the GIPAW method for both experimental and DFT-optimized structures. Furthermore, the [M{sub 4}F{sub 20}] units of NbF{sub 5} and TaF{sub 5} being held together by van der Waals interactions, the relevance of Grimme corrections to the DFT optimization processes has been evaluated. However, the semi-empirical dispersion correction term introduced by such a method does not show any significant improvement. Nonetheless, a complete and convincing assignment of the {sup 19}F NMR lines of NbF{sub 5} and TaF{sub 5} is obtained, ensured by the linearity between experimental {sup 19}F δ{sub iso} values and calculated {sup 19}F isotropic chemical shielding σ{sub iso} values. The effects of the geometry optimizations have been carefully analyzed, confirming among other matters, the inaccuracy of the experimental structure of NbF{sub 5}. The relationships between the fluorine chemical shifts, the nature of the fluorine atoms (bridging or terminal), the position of the terminal ones (opposite or perpendicular to the bridging ones), the fluorine charges, the ionicity and the length of the M–F bonds have been established. Additionally, for three of the {sup 19}F NMR lines of NbF{sub 5}, distorted multiplets, arising from {sup 1}J-coupling and residual dipolar coupling between the {sup 19}F and {sup 93}Nb nuclei, were simulated yielding to values of {sup 93}Nb–{sup 19}F {sup 1}J-coupling for the corresponding fluorine sites. - Graphical abstract: The complete assignment of the {sup 19}F NMR lines of NbF{sub 5} and TaF{sub 5} allow establishing relationships between the {sup 19}F δ{sub iso} values, the nature of the fluorine atoms

  3. 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.

  4. 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.

  5. 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

  6. Fischer indolisation of N-(α-ketoacyl)anthranilic acids into 2-(indol-2-carboxamido)benzoic acids and 2-indolyl-3,1-benzoxazin-4-ones and their NMR study.

    PubMed

    Proisl, Karel; Kafka, Stanislav; Urankar, Damijana; Gazvoda, Martin; Kimmel, Roman; Košmrlj, Janez

    2014-12-21

    N-(α-ketoacyl)anthranilic acids reacted with phenylhydrazinium chloride in boiling acetic acid to afford 2-(indol-2-carboxamido)benzoic acids in good to excellent yields and 2-indolyl-3,1-benzoxazin-4-ones as by-products. The formation of the latter products could easily be suppressed by a hydrolytic workup. Alternatively, by increasing the reaction temperature and/or time, 2-indolyl-3,1-benzoxazin-4-ones can be obtained exclusively. Optimisations of the reaction conditions as well as the scope and the course of the transformations were investigated. The products were characterized by (1)H, (13)C and (15)N NMR spectroscopy. The corresponding resonances were assigned on the basis of the standard 1D and gradient selected 2D NMR experiments ((1)H-(1)H gs-COSY, (1)H-(13)C gs-HSQC, (1)H-(13)C gs-HMBC) with (1)H-(15)N gs-HMBC as a practical tool to determine (15)N NMR chemical shifts at the natural abundance level of (15)N isotope.

  7. 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

  8. Ab initio study of {sup 13}C NMR chemical shifts for the chromophores of rhodopsin and bacteriorhodopsin. 2. Comprehensive analysis of the {sup 13}C chemical shifts of protonated all-trans-retinylidene Schiff base

    SciTech Connect

    Sakurai, Minoru; Wada, Mitsuhito; Inoue, Yoshio; Tamura, Yusuke; Watanabe, Yoichi

    1996-02-01

    Theoretical analysis was performed for the {sup 13}C chemical shifts of the retinal chromophore in bacteriorhodopsin (bR) by means of ab initio NMR shielding calculation, based on the localized orbital/ local origin method. In order to comprehensively investigate the correlation between the {sup 13}C chemical shieldings of the unsaturated carbons and physicochemical perturbations relating to the spectral tuning of bacteriorhodopsin, the following three factors are taken into account in the present calculation: (1) change in strength of the hydrogen bonding between protonated retinylidene Schiff base and its counterion, (2) conformational changes about single bonds of the conjugated chain, and (3) electrostatic interactions between the Schiff base and electric dipoles. On the basis of these calculations, we successfully find a molecular model for which the shielding calculation almost completely reproduces the observed chemical shift data for the chromophore of bR. 47 refs., 13 figs.

  9. Structural determination of complex natural products by quantum mechanical calculations of (13)C NMR chemical shifts: development of a parameterized protocol for terpenes.

    PubMed

    de Albuquerque, Ana Carolina Ferreira; Ribeiro, Daniel Joras; de Amorim, Mauro Barbosa

    2016-08-01

    Nuclear magnetic resonance (NMR) spectroscopy is one of the most important tools for determining the structures of organic molecules. Despite the advances made in this technique, revisions of erroneously established structures for natural products are still commonly published in the literature. In this context, the prediction of chemical shifts through ab initio and density functional theory (DFT) calculations has become a very powerful tool for assisting with the structural determination of complex organic molecules. In this work, we present the development of a protocol for (13)C chemical shift calculations of terpenes, a class of natural products that are widely distributed among plant species and are very important due to their biological and pharmacological activities. This protocol consists of GIAO-DFT calculations of chemical shifts and the application of a parameterized scaling factor in order to ensure accurate structural determination of this class of natural products. The application of this protocol to a set of five terpenes yielded accurate calculated chemical shifts, showing that this is a very attractive tool for the calculation of complex organic structures such as terpenes. PMID:27424297

  10. Disorder and the extent of polymerization in calcium silicate and aluminosilicate glasses: O-17 NMR results and quantum chemical molecular orbital calculations

    NASA Astrophysics Data System (ADS)

    Lee, Sung Keun; Stebbins, Jonathan F.

    2006-08-01

    Estimation of the framework connectivity and the atomic structure of depolymerized silicate melts and glasses (NBO/T > 0) remains a difficult question in high-temperature geochemistry relevant to magmatic processes and glass science. Here, we explore the extent of disorder and the nature of polymerization in binary Ca-silicate and ternary Ca-aluminosilicate glasses with varying NBO/T (from 0 to 2.67) using O-17 NMR at two different magnetic fields of 9.4 and 14.1 T in conjunction with quantum chemical calculations. Non-random distributions among framework cations (Si and Al) are demonstrated in the variation of relative populations of oxygen sites with NBO/T. The proportion of non-bridging oxygen (NBO, Ca-O-Si) in the binary and ternary aluminosilicate glasses increases with NBO/T. While the trend is consistent with predictions from composition, the detailed fractions apparently deviate from the predicted values, suggesting further complications in the nature of polymerization. The proportion of each bridging oxygen in the glasses also varies with NBO/T. The fractions of Al-O-Si and Al-O-Al increase with increasing polymerization as CaO is replaced with Al 2O 3, while that of Si-O-Si seems to decrease, implying that activity of silica may decrease from calcium silicate to polymerized aluminosilicates (X=constant). Quantum chemical molecular orbital calculations based on density functional theory show that a silicate chain with Al-NBO (Ca-O-Al) has an energy penalty (calculated cluster energy difference) of about 108 kJ/mol compared with the cluster with Ca-O-Si, consistent with preferential depolymerization of Si-networks, reported in an earlier O-17 NMR study [Allwardt, J., Lee, S.K., Stebbins, J.F., 2003. Bonding preferences of non-bridging oxygens in calcium aluminosilicate glass: Evidence from O-17 MAS and 3QMAS NMR on calcium aluminate glass. Am. Mineral.88, 949-954]. These prominent types of non-randomness in the distributions suggest significant chemical

  11. H2O/OH ratio determination in hydrous aluminosilicate glasses by static proton NMR and the effect of chemical shift anisotropy.

    PubMed

    Riemer, T; Schmidt, B; Behrens, H; Dupree, R

    2000-04-01

    Static 1H NMR spectra of hydrous NaAlSi3O8 glasses have been acquired at low temperature (140 K) in order to quantitatively determine OH and H2O concentrations. Since both components overlap in the spectra, an unambiguous determination of the line shapes is required. The structurally bonded hydroxyl groups are well described by a Gaussian line and the water molecules exhibit a Pake doublet-like line shape due to the strong proton-proton dipolar interaction. However, at proton resonance frequencies used in this study (360 MHz), the Pake doublet has an asymmetric line shape due to chemical shift anisotropy (CSA), which is significant and must be included in any simulation in order to reproduce the experimental line shape successfully. The simulations for rigid water molecules dissolved in our hydrous aluminosilicate glasses result in a CSA of 30+/-5 ppm and a dipolar interaction constant of 63.8+/-2.5 kHz (i.e., dipolar coupling constant (DCC) of 42.6+/-1.7 kHz), corresponding to a proton-proton distance of r(ij) = 154+/-2 pm. In contrast to earlier work, water speciation obtained from the simulations of our 1H NMR spectra are in excellent agreement with those obtained from infrared (IR) spectroscopy.

  12. Error tolerant NMR backbone resonance assignment and automated structure generation.

    PubMed

    Alipanahi, Babak; Gao, Xin; Karakoc, Emre; Li, Shuai Cheng; Balbach, Frank; Feng, Guangyu; Donaldson, Logan; Li, Ming

    2011-02-01

    Error tolerant backbone resonance assignment is the cornerstone of the NMR structure determination process. Although a variety of assignment approaches have been developed, none works sufficiently well on noisy fully automatically picked peaks to enable the subsequent automatic structure determination steps. We have designed an integer linear programming (ILP) based assignment system (IPASS) that has enabled fully automatic protein structure determination for four test proteins. IPASS employs probabilistic spin system typing based on chemical shifts and secondary structure predictions. Furthermore, IPASS extracts connectivity information from the inter-residue information and the (automatically picked) (15)N-edited NOESY peaks which are then used to fix reliable fragments. When applied to automatically picked peaks for real proteins, IPASS achieves an average precision and recall of 82% and 63%, respectively. In contrast, the next best method, MARS, achieves an average precision and recall of 77% and 36%, respectively. The assignments generated by IPASS are then fed into our protein structure calculation system, FALCON-NMR, to determine the 3D structures without human intervention. The final models have backbone RMSDs of 1.25Å, 0.88Å, 1.49Å, and 0.67Å to the reference native structures for proteins TM1112, CASKIN, VRAR, and HACS1, respectively. The web server is publicly available at http://monod.uwaterloo.ca/nmr/ipass.

  13. NMR-based metabolomic investigation of bioactivity of chemical constituents in black raspberry (Rubus occidentalis L.) fruit extracts.

    PubMed

    Paudel, Liladhar; Wyzgoski, Faith J; Giusti, M Monica; Johnson, Jodee L; Rinaldi, Peter L; Scheerens, Joseph C; Chanon, Ann M; Bomser, Joshua A; Miller, A Raymond; Hardy, James K; Reese, R Neil

    2014-02-26

    Black raspberry (Rubus occidentalis L.) (BR) fruit extracts with differing compound profiles have shown variable antiproliferative activities against HT-29 colon cancer cell lines. This study used partial least-squares (PLS) regression analysis to develop a high-resolution (1)H NMR-based multivariate statistical model for discerning the biological activity of BR constituents. This model identified specific bioactive compounds and ascertained their relative contribution against cancer cell proliferation. Cyanidin 3-rutinoside and cyanidin 3-xylosylrutinoside were the predominant contributors to the extract bioactivity, but salicylic acid derivatives (e.g., salicylic acid glucosyl ester), quercetin 3-glucoside, quercetin 3-rutinoside, p-coumaric acid, epicatechin, methyl ellagic acid derivatives (e.g., methyl ellagic acetyl pentose), and citric acid derivatives also contributed significantly to the antiproliferative activity of the berry extracts. This approach enabled the identification of new bioactive components in BR fruits and demonstrates the utility of the method for assessing chemopreventive compounds in foods and food products.

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

    ERIC Educational Resources Information Center

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

    2015-01-01

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

  15. Multiple active site histidine protonation states in Acetobacter aceti N5-carboxyaminoimidazole ribonucleotide mutase detected by REDOR NMR.

    PubMed

    Schaefer, Jacob; Jiang, Hong; Ransome, Aaron E; Kappock, T Joseph

    2007-08-21

    Class I PurE (N5-carboxyaminoimidazole mutase) catalyzes a chemically unique mutase reaction. A working mechanistic hypothesis involves a histidine (His45 in Escherichia coli PurE) functioning as a general acid, but no evidence for multiple protonation states has been obtained. Solution NMR is a peerless tool for this task but has had limited application to enzymes, most of which are larger than its effective molecular size limit. Solid-state NMR is not subject to this limit. REDOR NMR studies of a 151 kDa complex of uniformly 15N-labeled Acetobacter aceti PurE (AaPurE) and the active site ligand [6-13C]citrate probed a single ionization equilibrium associated with the key histidine (AaPurE His59). In the AaPurE complex, the citrate central carboxylate C6 13C peak moves upfield, indicating diminution of negative charge, and broadens, indicating heterogeneity. Histidine 15N chemical shifts indicate His59 exists in approximately equimolar amounts of an Ndelta-unprotonated (pyridine-like) form and an Ndelta-protonated (pyrrole-like) form, each of which is approximately 4 A from citrate C6. The spectroscopic data are consistent with proton transfers involving His59 Ndelta that are invoked in the class I PurE mechanism.

  16. 1H NMR spectroscopic investigations on the conformation of amphiphilic aromatic amino acid derivatives in solution: effect of chemical architecture of amphiphiles and polarity of solvent medium.

    PubMed

    Vijay, R; Mandal, A B; Baskar, Geetha

    2010-11-01

    In this study, the conformation of the amphiphilic lauryl esters of L-tyrosine (LET) and L-phenylalanine (LEP) in water and dimethyl sulfoxide is established. The alkyl chain protons of LEP in D(2)O appear at δ 1.010-1.398 and show an upfield shift and large line width, suggesting the proximity of the phenyl ring to the alkyl chain in contrast to that of LET. Quite interestingly, in DMSO-d(6), the (1)H NMR spectra of LET and LEP show a strong similarity that is suggestive of an orientation that positions the aromatic ring and aliphatic chain away from each other. These results are substantiated with two-dimensional nuclear Overhauser enhancement spectroscopy (2D NOSEY). Theoretical molecular models of the conformation at the interface corroborate the experimental findings. Investigations of the solvent polarity and chemical structure-dependent conformation are discussed.

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

    NASA Astrophysics Data System (ADS)

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

    2013-05-01

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

  18. Spectroscopic (FTIR, FT-Raman, UV and NMR) investigation and NLO, HOMO-LUMO, NBO analysis of 2-Benzylpyridine based on quantum chemical calculations.

    PubMed

    Mathammal, R; Sudha, N; Guru Prasad, L; Ganga, N; Krishnakumar, V

    2015-02-25

    In this work, the vibrational characteristics of 2-Benzylpyridine have been investigated. The structure of the molecule has been optimized and the structural characteristics of the molecule have been determined by density functional theory B3LYP method with 6-31G(d,p) basis set. The infrared and Raman spectra have been simulated from calculated intensities. Both the experimental and theoretical vibrational data confirms the presence of functional groups in the title compound. The (1)H and (13)C NMR spectra were recorded and (1)H and (13)C nuclear magnetic resonance chemical shifts of the molecule were calculated using the gauge independent atomic orbital method. UV-Visible spectrum of the title compound was recorded in the region 190-1100 nm and the electronic properties HOMO and LUMO energies were calculated by CIS approach. Nonlinear optical and thermodynamic properties were interpreted. All the calculated results were compared with the available experimental data of the title molecule.

  19. 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.

  20. High-level ab-initio calculation of gas-phase NMR chemical shifts and secondary isotope effects of methanol

    NASA Astrophysics Data System (ADS)

    Auer, Alexander A.

    2009-01-01

    In this contribution high-level ab-initio calculations of the chemical shifts of methanol including zero-point vibrational and temperature corrections are presented. For the first time, secondary isotope effects have been calculated via second order vibrational perturbation theory. In comparison with recent experimental gas-phase data and in contrast to other quantum-chemical methods the results are consistent and in very good agreement with the experimental 13C, 17O and 1H chemical shifts reported by Makulski [W. Makulski, J. Mol. Struct. 872 (2008) 81]. Secondary isotope effects can be calculated with remarkable accuracy of a few hundredths of a ppm in comparison to experiment.

  1. Modern NMR Spectroscopy.

    ERIC Educational Resources Information Center

    Jelinski, Lynn W.

    1984-01-01

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

  2. Nitrate Reduction in a Groundwater Microcosm Determined by 15N Gas Chromatography-Mass Spectrometry

    PubMed Central

    Bengtsson, Göran; Annadotter, Heléne

    1989-01-01

    Aerobic and anaerobic groundwater continuous-flow microcosms were designed to study nitrate reduction by the indigenous bacteria in intact saturated soil cores from a sandy aquifer with a concentration of 3.8 mg of NO3−-N liter−1. Traces of 15NO3− were added to filter-sterilized groundwater by using a Darcy flux of 4 cm day−1. Both assimilatory and dissimilatory reduction rates were estimated from analyses of 15N2, 15N2O, 15NH4+, and 15N-labeled protein amino acids by capillary gas chromatography-mass spectrometry. N2 and N2O were separated on a megabore fused-silica column and quantified by electron impact-selected ion monitoring. NO3− and NH4+ were analyzed as pentafluorobenzoyl amides by multiple-ion monitoring and protein amino acids as their N-heptafluorobutyryl isobutyl ester derivatives by negative ion-chemical ionization. The numbers of bacteria and their [methyl-3H]thymidine incorporation rates were simultaneously measured. Nitrate was completely reduced in the microcosms at a rate of about 250 ng g−1 day−1. Of this nitrate, 80 to 90% was converted by aerobic denitrification to N2, whereas only 35% was denitrified in the anaerobic microcosm, where more than 50% of NO3− was reduced to NH4+. Assimilatory reduction was recorded only in the aerobic microcosm, where N appeared in alanine in the cells. The nitrate reduction rates estimated for the aquifer material were low in comparison with rates in eutrophic lakes and coastal sediments but sufficiently high to remove nitrate from an uncontaminated aquifer of the kind examined in less than 1 month. PMID:16348048

  3. 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.

  4. Experimental study of resolution of proton chemical shifts in solids: Combined multiple pulse NMR and magic-angle spinning

    SciTech Connect

    Ryan, L.M.; Taylor, R.E.; Paff, A.J.; Gerstein, B.C.

    1980-01-01

    High-resolution nuclear magnetic resonance spectra of protons in rigid, randomly oriented solids have been measured using combined homonuclear dipolar decoupling (via multiple pulse techniques) and attenuation of chemical shift anisotropies (via magic-angle sample spinning). Under those conditions, isotropic proton chemical shifts were recorded for a variety of chemical species, with individual linewidths varying from about 55 to 110 Hz (1--2 ppm). Residual line broadening was due predominately to (i) magnetic-field instability and inhomogeneity, (ii) unresolved proton--proton spin couplings, (iii) chemical shift dispersion, (iv) residual dipolar broadening, and (v) lifetime broadening under the multiple pulse sequences used. The magnitudes of those effects and the current limits of resolution for this experiment in our spectrometer have been investigated. The compounds studied included organic solids (4, 4'-dimethylbenzophenone, 2, 6-dimethylbenzoic acid, and aspirin), polymers (polystyrene and polymethylmethacrylate), and the vitrain portion of a bituminous coal.

  5. Chemical prospection of important ayurvedic plant Tinospora cordifolia by UPLC-DAD-ESI-QTOF-MS/MS and NMR.

    PubMed

    Bala, Manju; Verma, Praveen Kumar; Awasthi, Shiv; Kumar, Neeraj; Lal, Brij; Singh, Bikram

    2015-01-01

    A rapid, sensitive, and accurate ultra-performance liquid chromatography coupled with mass spectrometric method (UPLC-MS) was developed and validated for simultaneous determination of four bioactive compounds, syringin (3), cordifolioside A (4), magnoflorine (6) and tinocordiside (10) in the stem of Tinospora cordifolia. The analysis was performed using an Acquity C18 column and gradient elution of 0.05% formic acid in water and acetonitrile at a detection wavelength of 267 nm in 5 min. A high correlation coefficient (r2 > 0.998) indicated good correlation between investigated compounds concentration and their peak area within the test ranges. The LODs for compounds 3, 4, 6 and 10 were 1.95, 0.97, 3.90 and 0.97 ng/mL, respectively, and LOQs were 6.64, 3.20, 12.87 and 3.20 ng/mL, respectively. The overall intra- and inter-day variations of the four compounds were less than 1%. The variation of these four bioactive compounds in T. cordifolia hosted on fifteen different trees was also determined. The compounds (3, 4, 6 and 10) were found in high amount in the T. cordifolia hosted on Azadirachta indica and Mangifera indica as compared with other plants. Twelve compounds were identified on the basis of their mass and UV-vis spectra. The NMR fingerprinting of the extract revealed the presence of alkaloids, fatty acid methyl esters, polysaccharides and marker components of T. cordifolia. PMID:25920217

  6. 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

  7. Operando NMR and XRD study of chemically synthesized LiCx oxidation in a dry room environment

    DOE PAGES

    Sacci, Robert L.; Gill, Lance W.; Hagaman, Edward W.; Dudney, Nancy J.

    2015-04-07

    We test the stability of pre-lithiated graphite anodes for Li-ion batteries in a dry room battery processing room. The reaction between LiCx and laboratory air was followed using operando NMR and x-ray diffraction as these methods are sensitive to change in Li stoichiometry in graphite. There is minimal reactivity between LiC6 and N2, CO2 or O2; however, LiC6 reacts with moisture to form lithium (hydr)oxide. The reaction rate follows zero-order kinetics with respects to intercalated lithium suggesting that lithium transport through the graphite is fast. The reaction mechanism occurs by sequential formation of higher stages LiC12, then LiC18, and thenmore » LiC24 as the hydrolysis proceeds to the formation of LixOHy and graphite end products. Slowing down the formation rate of the LixOHy passivation layer stabilizes of the higher stages.« less

  8. Operando NMR and XRD study of chemically synthesized LiCx oxidation in a dry room environment

    SciTech Connect

    Sacci, Robert L.; Gill, Lance W.; Hagaman, Edward W.; Dudney, Nancy J.

    2015-04-07

    We test the stability of pre-lithiated graphite anodes for Li-ion batteries in a dry room battery processing room. The reaction between LiCx and laboratory air was followed using operando NMR and x-ray diffraction as these methods are sensitive to change in Li stoichiometry in graphite. There is minimal reactivity between LiC6 and N2, CO2 or O2; however, LiC6 reacts with moisture to form lithium (hydr)oxide. The reaction rate follows zero-order kinetics with respects to intercalated lithium suggesting that lithium transport through the graphite is fast. The reaction mechanism occurs by sequential formation of higher stages LiC12, then LiC18, and then LiC24 as the hydrolysis proceeds to the formation of LixOHy and graphite end products. Slowing down the formation rate of the LixOHy passivation layer stabilizes of the higher stages.

  9. 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.

  10. 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

  11. Prediction of physical-chemical properties of crude oils by 1H NMR analysis of neat samples and chemometrics.

    PubMed

    Masili, Alice; Puligheddu, Sonia; Sassu, Lorenzo; Scano, Paola; Lai, Adolfo

    2012-11-01

    In this work, we report the feasibility study to predict the properties of neat crude oil samples from 300-MHz NMR spectral data and partial least squares (PLS) regression models. The study was carried out on 64 crude oil samples obtained from 28 different extraction fields and aims at developing a rapid and reliable method for characterizing the crude oil in a fast and cost-effective way. The main properties generally employed for evaluating crudes' quality and behavior during refining were measured and used for calibration and testing of the PLS models. Among these, the UOP characterization factor K (K(UOP)) used to classify crude oils in terms of composition, density (D), total acidity number (TAN), sulfur content (S), and true boiling point (TBP) distillation yields were investigated. Test set validation with an independent set of data was used to evaluate model performance on the basis of standard error of prediction (SEP) statistics. Model performances are particularly good for K(UOP) factor, TAN, and TPB distillation yields, whose standard error of calibration and SEP values match the analytical method precision, while the results obtained for D and S are less accurate but still useful for predictions. Furthermore, a strategy that reduces spectral data preprocessing and sample preparation procedures has been adopted. The models developed with such an ample crude oil set demonstrate that this methodology can be applied with success to modern refining process requirements.

  12. 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+).

  13. Precursor discrimination of designer drug benzylpiperazine using δ13C and δ15N stable isotopes.

    PubMed

    Beckett, Nicola M; Grice, Darren I; Carter, James F; Cresswell, Sarah L

    2015-01-01

    Advances in analytical technology and emerging techniques have resulted in the increased exploitation of chemical and isotopic profiling for source linkage/discrimination of illicit drugs for forensic purposes. Although not routinely used for illicit drug investigations, such information has been obtained and its application demonstrated through the use of isotope ratio mass spectrometry (IRMS). There is a solid platform of research available relating to the isotopic analysis of methylenedioxymethamphetamine (MDMA) and methamphetamine (MA), however with the recently flourishing designer drug market it was of interest to examine the isotopic profiles of the popular 'party drug' benzylpiperazine hydrochloride (BZP·HCl). A preliminary analysis of δ13C and δ15N isotopic ratios in BZP·HCl products and corresponding synthetic intermediates (piperazine·HCl) synthesized in-house from three different precursor suppliers was conducted using IRMS. Analysis of the δ13C and δ15N isotopic data indicated that discrimination and correct grouping of all the intermediates and some of the product samples examined in this study were achievable.

  14. Selective observation of biologically important 15N-labeled metabolites in isolated rat brain and liver by 1H-detected multiple-quantum-coherence spectroscopy

    NASA Astrophysics Data System (ADS)

    Kanamori, Keiko; Ross, Brian D.; Parivar, Farhad

    Four cerebral metabolites of importance in neurotransmission, serotonin, L-tryptophan, L-glutamine, and N-acetyl- L-aspartate, and two hepatic urea-cycle intermediates, citrulline and urea, were found to be observable by 1H- 15N heteronuclear multiple-quantum-coherence (HMQC) spectroscopy in aqueous solution at physiological pH and temperature, through the protons spin-coupled to their indole, amide, or ureido nitrogen. Their 1H chemical shifts were well dispersed over a 5-10 ppm region while the 1J 15N- 1H values were 87-99 Hz. For [γ- 15N]glutamine, a 50- to 100-fold increase in sensitivity over direct 15N detection was achieved, in contrast to a 2-fold increase by the polarization-transfer method. In the isolated brain of portacaval-shunted rats, the amide protons of biologically 15N-enriched [γ- 15N]glutamine were observed in 2 min of acquisition, with suppression of proton signals from all other cerebral metabolites. In isolated liver of 15N-enriched control rats, [ 15NIurea protons were observed in 16 min. The HMQC method is likely to be effective for the in vivo study of cerebral and hepatic nitrogen metabolism.

  15. 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.

  16. 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.

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

    SciTech Connect

    Sevelsted, Tine F.; Herfort, Duncan

    2013-10-15

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

  18. 15N isotope fractionation in an aquatic food chain: Bellamya aeruginosa (Reeve) as an algal control agent.

    PubMed

    Han, Shiqun; Yan, Shaohua; Chen, Kaining; Zhang, Zhenhua; Zed, Rengel; Zhang, Jianqiu; Song, Wei; Liu, Haiqin

    2010-01-01

    15N isotope tracer techniques and ecological modeling were adopted to investigate the fractionation of nitrogen, its uptake and transformation in algae and snail (Bellamya aeruginosa Reeve). Different algal species were found to differ in their uptake of nitrogen isotopes. Microcystis aeruginisa Kütz. demonstrated the greatest 15N accumulation capacity, with the natural variation in isotopic ratio (delta 15N) and the isotope fractionation factor (epsilon, % per hundred) being the highest among the species investigated. The transformation and utilization of 15N by snails differed depending on the specific algae consumed (highest for Chlorella pyrenoidosa Chick., lowest for M. aeruginisa). When snails was seeded in the experimental pond, the algae population structure changed significantly, and total algal biomass as well as the concentration of all nitrogen species decreased, causing an increase in water transparency. A model, incorporating several chemical and biological parameters, was developed to predict algal biomass in an aquatic system when snails was present. The data collected during this investigation indicated that the gastropods such as snails could significantly impact biological community and water quality of small water bodies, suggesting a role for biological control of noxious algal blooms associated with eutrophication.

  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. The conformational analysis of push-pull enaminoketones using Fourier transform IR and NMR spectroscopy, and quantum chemical calculations: II. Beta-dimethylaminoacrolein.

    PubMed

    Vdovenko, Sergey I; Gerus, Igor I; Fedorenko, Elena A

    2009-12-01

    IR Fourier and (1)H NMR spectra of beta-dimethylaminoacrolein (DMAA) were investigated in various pure solvents. Quantum chemical calculations by the method AM1 also was carried out to evaluate relative energy and dipole moment of each conformer. On the basis of NMR and IR-spectra we showed that the (DMAA) presented in solutions as equilibrium of two conformers, (E-s-Z) <==> (E-s-E). Constant of this equilibrium, K(eq) = C(E-s-E)/C(E-s-Z), depended strongly on the total (DMAA) concentration: ln K(eq) = ln K(eq0) + a(1 - e(-bC) total). Besides, (E-s-Z) conformer of the (DMAA) was more polar and more stable than the (E-s-E) conformer. Correlation of the out-of-phase nu(C=O) and in-phase nu(C=C) vibrations with solvatochromic parameters of Kamlet, Abbot, and Taft (KAT) revealed that the main contribution to the shift of the out-of-phase nu(C=O) vibrations of the both conformers made solvent's hydrogen bond acceptor (HBA) (beta) term, whereas hydrogen bond donor (HBD) acidity (alpha) term influenced predominantly on the shift of the in-phase nu(C=C) vibrations of the conformers. Moreover, influence of these dominated terms was more pronounced for the (E-s-Z) conformer in comparison with the (E-s-E) conformer, hence the first conformer was more polarized than the last. Investigations of the enthalpies of the (E-s-Z) <==> (E-s-E) equilibrium in carbon tetrachloride, 1,4-dioxane and their mixtures showed that these enthalpies depended predominantly on the solvent's atomic and electronic polarization and dispersive interactions.

  1. Effect of solvent on an NMR chemical shift difference between glycyl geminal α-protons as a probe of β-turn formation of short peptides

    NASA Astrophysics Data System (ADS)

    Tonan, Kenji; Ikawa, Shun-ichi

    2003-01-01

    Proton NMR spectra of short peptides with a glycyl (Gly) or N-methylglycyl (sarcosyl, Sar) residue were measured in various mixed solvents with a wide range of dielectric constants: 78.3-2.3. From analyses of the octet and quartet signals of the geminal α-protons of Gly and Sar residues, respectively, we have estimated chemical shift differences between the two α-protons, Δ δα/α'. It is found that the Δ δα/α' values increase with decreasing solvent polarity and the increasing rates depend significantly on amino acid sequences. By referring to infrared spectra and chemical shift of the terminal NH protons, δNH, of the peptides, the Δ δα/α' values were found to be a good probe of β-turn formation. From solvent-dependent change of Δ δα/α', we estimated the free energies for the β-turn formation and compared the results with those estimated from δNH. Using the resulting free energies, we have discussed effects of solvent on the β-turn formation.

  2. Precision and sensitivity of the measurement of 15N enrichment in D-alanine from bacterial cell walls using positive/negative ion mass spectrometry

    NASA Technical Reports Server (NTRS)

    Tunlid, A.; Odham, G.; Findlay, R. H.; White, D. C.

    1985-01-01

    Sensitive detection of cellular components from specific groups of microbes can be utilized as 'signatures' in the examination of microbial consortia from soils, sediments or biofilms. Utilizing capillary gas chromatography/mass spectrometry and stereospecific derivatizing agents, D-alanine, a component localized in the prokaryotic (bacterial) cell wall, can be detected reproducibly. Enrichments of D-[15N]alanine determined in E. coli grown with [15N]ammonia can be determined with precision at 1.0 atom%. Chemical ionization with methane gas and the detection of negative ions (M - HF)- and (M - F or M + H - HF)- formed from the heptafluorobutyryl D-2 butanol ester of D-alanine allowed as little as 8 pg (90 fmol) to be detected reproducibly. This method can be utilized to define the metabolic activity in terms of 15N incorporation at the level of 10(3)-10(4) cells, as a function of the 15N-14N ratio.

  3. NMR imaging microscopy

    SciTech Connect

    Not Available

    1986-10-01

    In the past several years, proton nuclear magnetic resonance (NMR) imaging has become an established technique in diagnostic medicine and biomedical research. Although much of the work in this field has been directed toward development of whole-body imagers, James Aguayo, Stephen Blackband, and Joseph Schoeninger of the Johns Hopkins University School of Medicine working with Markus Hintermann and Mark Mattingly of Bruker Medical Instruments, recently developed a small-bore NMR microscope with sufficient resolution to image a single African clawed toad cell (Nature 1986, 322, 190-91). This improved resolution should lead to increased use of NMR imaging for chemical, as well as biological or physiological, applications. The future of NMR microscopy, like that of many other newly emerging techniques, is ripe with possibilities. Because of its high cost, however, it is likely to remain primarily a research tool for some time. ''It's like having a camera,'' says Smith. ''You've got a way to look at things at very fine levels, and people are going to find lots of uses for it. But it is a very expensive technique - it costs $100,000 to add imaging capability once you have a high-resolution NMR, which itself is at least a $300,000 instrument. If it can answer even a few questions that can't be answered any other way, though, it may be well worth the cost.''

  4. 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.

  5. 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

  6. Fermentation and Cost-Effective 13C/15N Labeling of the Nonribosomal Peptide Gramicidin S for Nuclear Magnetic Resonance Structure Analysis.

    PubMed

    Berditsch, Marina; Afonin, Sergii; Steineker, Anna; Orel, Nataliia; Jakovkin, Igor; Weber, Christian; Ulrich, Anne S

    2015-06-01

    Gramicidin S (GS) is a nonribosomally synthesized decapeptide from Aneurinibacillus migulanus. Its pronounced antibiotic activity is attributed to amphiphilic structure and enables GS interaction with bacterial membranes. Despite its medical use for over 70 years, the peptide-lipid interactions of GS and its molecular mechanism of action are still not fully understood. Therefore, a comprehensive structural analysis of isotope-labeled GS needs to be performed in its biologically relevant membrane-bound state, using advanced solid-state nuclear magnetic resonance (NMR) spectroscopy. Here, we describe an efficient method for producing the uniformly (13)C/(15)N-labeled peptide in a minimal medium supplemented by selected amino acids. As GS is an intracellular product of A. migulanus, we characterized the producer strain DSM 5759 (rough-convex phenotype) and examined its biosynthetic activity in terms of absolute and biomass-dependent peptide accumulation. We found that the addition of either arginine or ornithine increases the yield only at very high supplementing concentrations (1% and 0.4%, respectively) of these expensive (13)C/(15)N-labeled amino acids. The most cost-effective production of (13)C/(15)N-GS, giving up to 90 mg per gram of dry cell weight, was achieved in a minimal medium containing 1% (13)C-glycerol and 0.5% (15)N-ammonium sulfate, supplemented with only 0.025% of (13)C/(15)N-phenylalanine. The 100% efficiency of labeling is corroborated by mass spectrometry and preliminary solid-state NMR structure analysis of the labeled peptide in the membrane-bound state.

  7. A Series of Diamagnetic Pyridine Monoimine Rhenium Complexes with Different Degrees of Metal-to-Ligand Charge Transfer: Correlating (13) C NMR Chemical Shifts with Bond Lengths in Redox-Active Ligands.

    PubMed

    Sieh, Daniel; Kubiak, Clifford P

    2016-07-18

    A set of pyridine monoimine (PMI) rhenium(I) tricarbonyl chlorido complexes with substituents of different steric and electronic properties was synthesized and fully characterized. Spectroscopic (NMR and IR) and single-crystal X-ray diffraction analyses of these complexes showed that the redox-active PMI ligands are neutral and that the overall electronic structure is little affected by the choices of the substituent at the ligand backbone. One- and two-electron reduction products were prepared from selected starting compounds and could also be characterized by multiple spectroscopic methods and X-ray diffraction. The final product of a one-electron reduction in THF is a diamagnetic metal-metal-bonded dimer after loss of the chlorido ligand. Bond lengths in and NMR chemical shifts of the PMI ligand backbone indicate partial electron transfer to the ligand. Two-electron reduction in THF also leads to the loss of the chlorido ligand and a pentacoordinate complex is obtained. The comparison with reported bond lengths and (13) C NMR chemical shifts of doubly reduced free pyridine monoaldimine ligands indicates that both redox equivalents in the doubly reduced rhenium complex investigated here are located in the PMI ligand. With diamagnetic complexes varying over three formal reduction stages at the PMI ligand we were, for the first time, able to establish correlations of the (13) C NMR chemical shifts with the relevant bond lengths in redox-active ligands over a full redox series. PMID:27319753

  8. A Series of Diamagnetic Pyridine Monoimine Rhenium Complexes with Different Degrees of Metal-to-Ligand Charge Transfer: Correlating (13) C NMR Chemical Shifts with Bond Lengths in Redox-Active Ligands.

    PubMed

    Sieh, Daniel; Kubiak, Clifford P

    2016-07-18

    A set of pyridine monoimine (PMI) rhenium(I) tricarbonyl chlorido complexes with substituents of different steric and electronic properties was synthesized and fully characterized. Spectroscopic (NMR and IR) and single-crystal X-ray diffraction analyses of these complexes showed that the redox-active PMI ligands are neutral and that the overall electronic structure is little affected by the choices of the substituent at the ligand backbone. One- and two-electron reduction products were prepared from selected starting compounds and could also be characterized by multiple spectroscopic methods and X-ray diffraction. The final product of a one-electron reduction in THF is a diamagnetic metal-metal-bonded dimer after loss of the chlorido ligand. Bond lengths in and NMR chemical shifts of the PMI ligand backbone indicate partial electron transfer to the ligand. Two-electron reduction in THF also leads to the loss of the chlorido ligand and a pentacoordinate complex is obtained. The comparison with reported bond lengths and (13) C NMR chemical shifts of doubly reduced free pyridine monoaldimine ligands indicates that both redox equivalents in the doubly reduced rhenium complex investigated here are located in the PMI ligand. With diamagnetic complexes varying over three formal reduction stages at the PMI ligand we were, for the first time, able to establish correlations of the (13) C NMR chemical shifts with the relevant bond lengths in redox-active ligands over a full redox series.

  9. 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.

  10. Composite-180° pulse-based symmetry sequences to recouple proton chemical shift anisotropy tensors under ultrafast MAS solid-state NMR spectroscopy.

    PubMed

    Pandey, Manoj Kumar; Malon, Michal; Ramamoorthy, Ayyalusamy; Nishiyama, Yusuke

    2015-01-01

    There is considerable interest in the measurement of proton ((1)H) chemical shift anisotropy (CSA) tensors to obtain deeper insights into H-bonding interactions which find numerous applications in chemical and biological systems. However, the presence of strong (1)H/(1)H dipolar interaction makes it difficult to determine small size (1)H CSAs from the homogeneously broadened NMR spectra. Previously reported pulse sequences for (1)H CSA recoupling are prone to the effects of radio frequency field (B1) inhomogeneity. In the present work we have carried out a systematic study using both numerical and experimental approaches to evaluate γ-encoded radio frequency (RF) pulse sequences based on R-symmetries that recouple (1)H CSA in the indirect dimension of a 2D (1)H/(1)H anisotropic/isotropic chemical shift correlation experiment under ultrafast magic angle spinning (MAS) frequencies. The spectral resolution and sensitivity can be significantly improved in both frequency dimensions of the 2D (1)H/(1)H correlation spectrum without decoupling (1)H/(1)H dipolar couplings but by using ultrafast MAS rates up to 70 kHz. We successfully demonstrate that with a reasonable RF field requirement (<200 kHz) a set of symmetry-based recoupling sequences, with a series of phase-alternating 270°0-90°180 composite-180° pulses, are more robust in combating B1 inhomogeneity effects. In addition, our results show that the new pulse sequences render remarkable (1)H CSA recoupling efficiency and undistorted CSA lineshapes. Experimental results on citric acid and malonic acid comparing the efficiencies of these newly developed pulse sequences with that of previously reported CSA recoupling pulse sequences are also reported under ultrafast MAS conditions. PMID:25497846

  11. Trace level detection of compounds related to the chemical weapons convention by 1H-detected 13C NMR spectroscopy executed with a sensitivity-enhanced, cryogenic probehead.

    PubMed

    Cullinan, David B; Hondrogiannis, George; Henderson, Terry J

    2008-04-15

    Two-dimensional 1H-13C HSQC (heteronuclear single quantum correlation) and fast-HMQC (heteronuclear multiple quantum correlation) pulse sequences were implemented using a sensitivity-enhanced, cryogenic probehead for detecting compounds relevant to the Chemical Weapons Convention present in complex mixtures. The resulting methods demonstrated exceptional sensitivity for detecting the analytes at trace level concentrations. 1H-13C correlations of target analytes at < or = 25 microg/mL were easily detected in a sample where the 1H solvent signal was approximately 58,000-fold more intense than the analyte 1H signals. The problem of overlapping signals typically observed in conventional 1H spectroscopy was essentially eliminated, while 1H and 13C chemical shift information could be derived quickly and simultaneously from the resulting spectra. The fast-HMQC pulse sequences generated magnitude mode spectra suitable for detailed analysis in approximately 4.5 h and can be used in experiments to efficiently screen a large number of samples. The HSQC pulse sequences, on the other hand, required roughly twice the data acquisition time to produce suitable spectra. These spectra, however, were phase-sensitive, contained considerably more resolution in both dimensions, and proved to be superior for detecting analyte 1H-13C correlations. Furthermore, a HSQC spectrum collected with a multiplicity-edited pulse sequence provided additional structural information valuable for identifying target analytes. The HSQC pulse sequences are ideal for collecting high-quality data sets with overnight acquisitions and logically follow the use of fast-HMQC pulse sequences to rapidly screen samples for potential target analytes. Use of the pulse sequences considerably improves the performance of NMR spectroscopy as a complimentary technique for the screening, identification, and validation of chemical warfare agents and other small-molecule analytes present in complex mixtures and environmental

  12. 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.

  13. The topology of lysine-containing amphipathic peptides in bilayers by circular dichroism, solid-state NMR, and molecular modeling.

    PubMed Central

    Vogt, B; Ducarme, P; Schinzel, S; Brasseur, R; Bechinger, B

    2000-01-01

    In order to better understand the driving forces that determine the alignment of amphipathic helical polypeptides with respect to the surface of phospholipid bilayers, lysine-containing peptide sequences were designed, prepared by solid-phase chemical synthesis, and reconstituted into membranes. CD spectroscopy indicates that all peptides exhibit a high degree of helicity in the presence of SDS micelles or POPC small unilamellar vesicles. Proton-decoupled (31)P-NMR solid-state NMR spectroscopy demonstrates that in the presence of peptides liquid crystalline phosphatidylcholine membranes orient well along glass surfaces. The orientational distribution and dynamics of peptides labeled with (15)N at selected sites were investigated by proton-decoupled (15)N solid-state NMR spectroscopy. Polypeptides with a single lysine residue adopt a transmembrane orientation, thereby locating this polar amino acid within the core region of the bilayer. In contrast, peptides with > or = 3 lysines reside along the surface of the membrane. With 2 lysines in the center of an otherwise hydrophobic amino acid sequence the peptides assume a broad orientational distribution. The energy of lysine discharge, hydrophobic, polar, and all other interactions are estimated to quantitatively describe the polypeptide topologies observed. Furthermore, a molecular modeling algorithm based on the hydrophobicities of atoms in a continuous hydrophilic-hydrophobic-hydrophilic potential describes the experimentally observed peptide topologies well. PMID:11053137

  14. 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

  15. Chemical shift and electric field gradient tensors for the amide and carboxyl hydrogens in the model peptide N-acetyl-D,L-valine. Single-crystal deuterium NMR study.

    SciTech Connect

    Gerald, R. E., II; Bernhard, T.; Haeberlen, U.; Rendell, J.; Opella, S.; Chemical Engineering

    1993-01-01

    Solid-state NMR spectroscopy is well established as a method for describing molecular structure with resolution on the atomic scale. Many of the NMR observables result from anisotropic interactions between the nuclear spin and its environment. These observables can be described by second-rank tensors. For example, the eigenvalues of the traceless symmetric part of the hydrogen chemical shift (CS) tensor provide information about the strength of inter- or intramolecular hydrogen bonding. On the other hand, the eigenvectors of the deuterium electric field gradient (EFG) tensor give deuteron/proton bond directions with an accuracy rivalled only by neutron diffraction. In this paper the authors report structural information of this type for the amide and carboxyl hydrogen sites in a single crystal of the model peptide N-acetyl-D,L-valine (NAV). They use deuterium NMR to infer both the EFG and CS tensors at the amide and carboxyl hydrogen sites in NAV. Advantages of this technique over multiple-pulse proton